beautify

501 files changed, 21014 insertions, 20127 deletions

diff --git a/OnDiskPt/Main.cpp b/OnDiskPt/Main.cpp
index 5d4e0be8d..c3cda2a75 100644
--- a/OnDiskPt/Main.cpp
+++ b/OnDiskPt/Main.cpp
@@ -50,14 +50,14 @@ int main (int argc, char * const argv[])
   }
 
   int numSourceFactors	= Moses::Scan<int>(argv[1])
-     , numTargetFactors	= Moses::Scan<int>(argv[2])
-     , numScores				= Moses::Scan<int>(argv[3])
-     , tableLimit				= Moses::Scan<int>(argv[4]);
+                          , numTargetFactors	= Moses::Scan<int>(argv[2])
+                              , numScores				= Moses::Scan<int>(argv[3])
+                                  , tableLimit				= Moses::Scan<int>(argv[4]);
   TargetPhraseCollection::s_sortScoreInd			= Moses::Scan<int>(argv[5]);
   assert(TargetPhraseCollection::s_sortScoreInd < numScores);
-  
+
   const string filePath 	= argv[6]
-               ,destPath	= argv[7];
+                            ,destPath	= argv[7];
 
   Moses::InputFileStream inStream(filePath);
 
@@ -128,10 +128,10 @@ OnDiskPt::PhrasePtr Tokenize(SourcePhrase &sourcePhrase, TargetPhrase &targetPhr
     } else {
       switch (stage) {
       case 0: {
-    	WordPtr w = Tokenize(sourcePhrase, tok, true, true, onDiskWrapper);
-    	if (w != NULL)
-    	  out->AddWord(w);
-    	
+        WordPtr w = Tokenize(sourcePhrase, tok, true, true, onDiskWrapper);
+        if (w != NULL)
+          out->AddWord(w);
+
         break;
       }
       case 1: {
@@ -146,19 +146,19 @@ OnDiskPt::PhrasePtr Tokenize(SourcePhrase &sourcePhrase, TargetPhrase &targetPhr
       }
       case 3: {
         //targetPhrase.Create1AlignFromString(tok);
-    	targetPhrase.CreateAlignFromString(tok);	
+        targetPhrase.CreateAlignFromString(tok);
         break;
       }
       case 4:
         ++stage;
         break;
-	/*      case 5: {
-        // count info. Only store the 2nd one
-        float val = Moses::Scan<float>(tok);
-        misc[0] = val;
-        ++stage;
-        break;
-	}*/
+        /*      case 5: {
+              // count info. Only store the 2nd one
+              float val = Moses::Scan<float>(tok);
+              misc[0] = val;
+              ++stage;
+              break;
+        }*/
       case 5: {
         // count info. Only store the 2nd one
         //float val = Moses::Scan<float>(tok);
@@ -167,12 +167,12 @@ OnDiskPt::PhrasePtr Tokenize(SourcePhrase &sourcePhrase, TargetPhrase &targetPhr
         break;
       }
       case 6: {
-	// store only the 3rd one (rule count)
+        // store only the 3rd one (rule count)
         float val = Moses::Scan<float>(tok);
         misc[0] = val;
         ++stage;
         break;
-	}
+      }
       default:
         cerr << "ERROR in line " << line << endl;
         assert(false);
@@ -189,8 +189,8 @@ OnDiskPt::PhrasePtr Tokenize(SourcePhrase &sourcePhrase, TargetPhrase &targetPhr
 } // Tokenize()
 
 OnDiskPt::WordPtr Tokenize(OnDiskPt::Phrase &phrase
-              , const std::string &token, bool addSourceNonTerm, bool addTargetNonTerm
-              , OnDiskPt::OnDiskWrapper &onDiskWrapper)
+                           , const std::string &token, bool addSourceNonTerm, bool addTargetNonTerm
+                           , OnDiskPt::OnDiskWrapper &onDiskWrapper)
 {
 
   bool nonTerm = false;
@@ -218,7 +218,7 @@ OnDiskPt::WordPtr Tokenize(OnDiskPt::Phrase &phrase
       if (addSourceNonTerm) {
         WordPtr word(new Word());
         word->CreateFromString(wordStr, onDiskWrapper.GetVocab());
-        phrase.AddWord(word);        
+        phrase.AddWord(word);
       }
 
       wordStr = token.substr(splitPos, tokSize - splitPos);
@@ -237,7 +237,7 @@ OnDiskPt::WordPtr Tokenize(OnDiskPt::Phrase &phrase
     phrase.AddWord(word);
     out = word;
   }
-  
+
   return out;
 }
 
diff --git a/OnDiskPt/Main.h b/OnDiskPt/Main.h
index b79827589..5c7efa43c 100644
--- a/OnDiskPt/Main.h
+++ b/OnDiskPt/Main.h
@@ -26,12 +26,12 @@ typedef std::pair<size_t, size_t>  AlignPair;
 typedef std::vector<AlignPair> AlignType;
 
 OnDiskPt::WordPtr Tokenize(OnDiskPt::Phrase &phrase
-              , const std::string &token, bool addSourceNonTerm, bool addTargetNonTerm
-              , OnDiskPt::OnDiskWrapper &onDiskWrapper);
+                           , const std::string &token, bool addSourceNonTerm, bool addTargetNonTerm
+                           , OnDiskPt::OnDiskWrapper &onDiskWrapper);
 OnDiskPt::PhrasePtr Tokenize(OnDiskPt::SourcePhrase &sourcePhrase, OnDiskPt::TargetPhrase &targetPhrase
-              , char *line, OnDiskPt::OnDiskWrapper &onDiskWrapper
-              , int numScores
-              , std::vector<float> &misc);
+                             , char *line, OnDiskPt::OnDiskWrapper &onDiskWrapper
+                             , int numScores
+                             , std::vector<float> &misc);
 
 void InsertTargetNonTerminals(std::vector<std::string> &sourceToks, const std::vector<std::string> &targetToks, const AlignType &alignments);
 void SortAlign(AlignType &alignments);
diff --git a/OnDiskPt/OnDiskQuery.cpp b/OnDiskPt/OnDiskQuery.cpp
index c39697d04..2cc7380db 100644
--- a/OnDiskPt/OnDiskQuery.cpp
+++ b/OnDiskPt/OnDiskQuery.cpp
@@ -3,10 +3,10 @@
 namespace OnDiskPt
 {
 
-void OnDiskQuery::Tokenize(Phrase &phrase, 
-    const std::string &token,
-    bool addSourceNonTerm,
-    bool addTargetNonTerm)
+void OnDiskQuery::Tokenize(Phrase &phrase,
+                           const std::string &token,
+                           bool addSourceNonTerm,
+                           bool addTargetNonTerm)
 {
   bool nonTerm = false;
   size_t tokSize = token.size();
@@ -50,13 +50,13 @@ void OnDiskQuery::Tokenize(Phrase &phrase,
     phrase.AddWord(word);
   }
 }
-  
+
 SourcePhrase OnDiskQuery::Tokenize(const std::vector<std::string>& tokens)
 {
   SourcePhrase sourcePhrase;
-  if (tokens.size() > 0){
+  if (tokens.size() > 0) {
     std::vector<std::string>::const_iterator token = tokens.begin();
-    for (; token + 1 != tokens.end(); ++token){
+    for (; token + 1 != tokens.end(); ++token) {
       Tokenize(sourcePhrase, *token, true, true);
     }
     // last position. LHS non-term
@@ -64,22 +64,20 @@ SourcePhrase OnDiskQuery::Tokenize(const std::vector<std::string>& tokens)
   }
   return sourcePhrase;
 }
-  
+
 const PhraseNode* OnDiskQuery::Query(const SourcePhrase& sourcePhrase)
 {
-    const PhraseNode *node = &m_wrapper.GetRootSourceNode();
-    assert(node);
-    
-    for (size_t pos = 0; pos < sourcePhrase.GetSize(); ++pos)
-    {
-      const Word &word = sourcePhrase.GetWord(pos);
-      node = node->GetChild(word, m_wrapper);
-      if (node == NULL)
-      {
-        break;
-      }
+  const PhraseNode *node = &m_wrapper.GetRootSourceNode();
+  assert(node);
+
+  for (size_t pos = 0; pos < sourcePhrase.GetSize(); ++pos) {
+    const Word &word = sourcePhrase.GetWord(pos);
+    node = node->GetChild(word, m_wrapper);
+    if (node == NULL) {
+      break;
     }
-    return node;
+  }
+  return node;
 }
 
 }
diff --git a/OnDiskPt/OnDiskQuery.h b/OnDiskPt/OnDiskQuery.h
index 679f545fa..233603c6c 100644
--- a/OnDiskPt/OnDiskQuery.h
+++ b/OnDiskPt/OnDiskQuery.h
@@ -18,22 +18,21 @@ private:
 
 public:
 
-  OnDiskQuery(OnDiskWrapper &wrapper):m_wrapper(wrapper){}
+  OnDiskQuery(OnDiskWrapper &wrapper):m_wrapper(wrapper) {}
+
+  void Tokenize(Phrase &phrase,
+                const std::string &token,
+                bool addSourceNonTerm,
+                bool addTargetNonTerm);
 
-  void Tokenize(Phrase &phrase, 
-      const std::string &token,
-      bool addSourceNonTerm, 
-      bool addTargetNonTerm);
-  
   SourcePhrase Tokenize(const std::vector<std::string>& tokens);
 
   const PhraseNode *Query(const SourcePhrase& sourcePhrase);
 
-  inline const PhraseNode *Query(const std::vector<std::string>& tokens)
-  {
+  inline const PhraseNode *Query(const std::vector<std::string>& tokens) {
     return Query(Tokenize(tokens));
   }
-  
+
 };
 
 
diff --git a/OnDiskPt/OnDiskWrapper.cpp b/OnDiskPt/OnDiskWrapper.cpp
index 3a1773c0a..8f90862be 100644
--- a/OnDiskPt/OnDiskWrapper.cpp
+++ b/OnDiskPt/OnDiskWrapper.cpp
@@ -204,16 +204,16 @@ Word *OnDiskWrapper::ConvertFromMoses(Moses::FactorDirection /* direction */
   Word *newWord = new Word(isNonTerminal);
   stringstream strme;
 
-  size_t factorType = factorsVec[0];  
+  size_t factorType = factorsVec[0];
   const Moses::Factor *factor = origWord.GetFactor(factorType);
-  CHECK(factor);  
+  CHECK(factor);
   strme << factor->GetString();
 
   for (size_t ind = 1 ; ind < factorsVec.size() ; ++ind) {
     size_t factorType = factorsVec[ind];
     const Moses::Factor *factor = origWord.GetFactor(factorType);
-    if (factor == NULL)
-    { // can have less factors than factorType.size()
+    if (factor == NULL) {
+      // can have less factors than factorType.size()
       break;
     }
     CHECK(factor);
diff --git a/OnDiskPt/OnDiskWrapper.h b/OnDiskPt/OnDiskWrapper.h
index f763194c1..8b786d346 100644
--- a/OnDiskPt/OnDiskWrapper.h
+++ b/OnDiskPt/OnDiskWrapper.h
@@ -28,7 +28,7 @@ namespace OnDiskPt
 {
 const float DEFAULT_COUNT = 66666;
 
-/** Global class with misc information need to create and use the on-disk rule table. 
+/** Global class with misc information need to create and use the on-disk rule table.
  * 1 object of this class should be instantiated per rule table.
  * Currently only hierarchical/syntax models use this, but can & should be used with pb models too
  */
diff --git a/OnDiskPt/PhraseNode.cpp b/OnDiskPt/PhraseNode.cpp
index c3f2ebdc4..c259aa077 100644
--- a/OnDiskPt/PhraseNode.cpp
+++ b/OnDiskPt/PhraseNode.cpp
@@ -38,7 +38,7 @@ size_t PhraseNode::GetNodeSize(size_t numChildren, size_t wordSize, size_t count
 }
 
 PhraseNode::PhraseNode()
-  : m_value(0) 
+  : m_value(0)
   ,m_currChild(NULL)
   ,m_saved(false)
   ,m_memLoad(NULL)
@@ -58,7 +58,7 @@ PhraseNode::PhraseNode(UINT64 filePos, OnDiskWrapper &onDiskWrapper)
   CHECK(filePos == (UINT64)file.tellg());
 
   file.read((char*) &m_numChildrenLoad, sizeof(UINT64));
-  
+
   size_t memAlloc = GetNodeSize(m_numChildrenLoad, onDiskWrapper.GetSourceWordSize(), countSize);
   m_memLoad = (char*) malloc(memAlloc);
 
@@ -168,7 +168,7 @@ void PhraseNode::AddTargetPhrase(const SourcePhrase &sourcePhrase, TargetPhrase
 void PhraseNode::AddTargetPhrase(size_t pos, const SourcePhrase &sourcePhrase
                                  , TargetPhrase *targetPhrase, OnDiskWrapper &onDiskWrapper
                                  , size_t tableLimit, const std::vector<float> &counts, OnDiskPt::PhrasePtr spShort)
-{	
+{
   size_t phraseSize = sourcePhrase.GetSize();
   if (pos < phraseSize) {
     const Word &word = sourcePhrase.GetWord(pos);
@@ -185,7 +185,7 @@ void PhraseNode::AddTargetPhrase(size_t pos, const SourcePhrase &sourcePhrase
       m_currChild = &node;
     }
 
-    // keep searching for target phrase node.. 
+    // keep searching for target phrase node..
     node.AddTargetPhrase(pos + 1, sourcePhrase, targetPhrase, onDiskWrapper, tableLimit, counts, spShort);
   } else {
     // drilled down to the right node
diff --git a/OnDiskPt/PhraseNode.h b/OnDiskPt/PhraseNode.h
index fbd20ce36..6b629a401 100644
--- a/OnDiskPt/PhraseNode.h
+++ b/OnDiskPt/PhraseNode.h
@@ -53,7 +53,7 @@ protected:
   void AddTargetPhrase(size_t pos, const SourcePhrase &sourcePhrase
                        , TargetPhrase *targetPhrase, OnDiskWrapper &onDiskWrapper
                        , size_t tableLimit, const std::vector<float> &counts, OnDiskPt::PhrasePtr spShort);
-  size_t ReadChild(Word &wordFound, UINT64 &childFilePos, const char *mem) const; 
+  size_t ReadChild(Word &wordFound, UINT64 &childFilePos, const char *mem) const;
   void GetChild(Word &wordFound, UINT64 &childFilePos, size_t ind, OnDiskWrapper &onDiskWrapper) const;
 
 public:
diff --git a/OnDiskPt/TargetPhrase.cpp b/OnDiskPt/TargetPhrase.cpp
index 6ca2ef5f9..2e3e3511b 100644
--- a/OnDiskPt/TargetPhrase.cpp
+++ b/OnDiskPt/TargetPhrase.cpp
@@ -64,13 +64,13 @@ void TargetPhrase::Create1AlignFromString(const std::string &align1Str)
 
 void TargetPhrase::CreateAlignFromString(const std::string &alignStr)
 {
-	vector<std::string> alignPairs;
-	boost::split(alignPairs, alignStr, boost::is_any_of("\t "));
-	for (size_t i = 0; i < alignPairs.size(); ++i) {
-		vector<size_t> alignPoints;
-		Moses::Tokenize<size_t>(alignPoints, alignPairs[i], "-");
-		m_align.push_back(pair<size_t, size_t>(alignPoints[0], alignPoints[1]) );
-	}
+  vector<std::string> alignPairs;
+  boost::split(alignPairs, alignStr, boost::is_any_of("\t "));
+  for (size_t i = 0; i < alignPairs.size(); ++i) {
+    vector<size_t> alignPoints;
+    Moses::Tokenize<size_t>(alignPoints, alignPairs[i], "-");
+    m_align.push_back(pair<size_t, size_t>(alignPoints[0], alignPoints[1]) );
+  }
 }
 
 
@@ -97,16 +97,16 @@ char *TargetPhrase::WriteToMemory(OnDiskWrapper &onDiskWrapper, size_t &memUsed)
 {
   size_t phraseSize = GetSize();
   size_t targetWordSize = onDiskWrapper.GetTargetWordSize();
-  
+
   const PhrasePtr sp = GetSourcePhrase();
   size_t spSize = sp->GetSize();
   size_t sourceWordSize = onDiskWrapper.GetSourceWordSize();
-  
+
   size_t memNeeded = sizeof(UINT64)						// num of words
                      + targetWordSize * phraseSize	// actual words. lhs as last words
-                     + sizeof(UINT64)					// num source words         
-  	  	  	  	  	 + sourceWordSize * spSize;   // actual source words              
- 
+                     + sizeof(UINT64)					// num source words
+                     + sourceWordSize * spSize;   // actual source words
+
   memUsed = 0;
   UINT64 *mem = (UINT64*) malloc(memNeeded);
 
@@ -125,13 +125,13 @@ char *TargetPhrase::WriteToMemory(OnDiskWrapper &onDiskWrapper, size_t &memUsed)
   char *currPtr = (char*)mem + memUsed;
   UINT64 *memTmp = (UINT64*) currPtr;
   memTmp[0] = spSize;
-  memUsed += sizeof(UINT64);                                  
+  memUsed += sizeof(UINT64);
   for (size_t pos = 0; pos < spSize; ++pos) {
     const Word &word = sp->GetWord(pos);
     char *currPtr = (char*)mem + memUsed;
     memUsed += word.WriteToMemory((char*) currPtr);
   }
-  
+
   CHECK(memUsed == memNeeded);
   return (char *) mem;
 }
@@ -174,7 +174,7 @@ char *TargetPhrase::WriteOtherInfoToMemory(OnDiskWrapper &onDiskWrapper, size_t
   // phrase id
   memcpy(mem, &m_filePos, sizeof(UINT64));
   memUsed += sizeof(UINT64);
-  
+
   // align
   size_t tmp = WriteAlignToMemory(mem + memUsed);
   memUsed += tmp;
@@ -223,7 +223,7 @@ size_t TargetPhrase::WriteScoresToMemory(char *mem) const
 }
 
 
-Moses::TargetPhrase *TargetPhrase::ConvertToMoses(const std::vector<Moses::FactorType> & inputFactors 
+Moses::TargetPhrase *TargetPhrase::ConvertToMoses(const std::vector<Moses::FactorType> & inputFactors
     , const std::vector<Moses::FactorType> &outputFactors
     , const Vocab &vocab
     , const Moses::PhraseDictionary &phraseDict
@@ -244,7 +244,7 @@ Moses::TargetPhrase *TargetPhrase::ConvertToMoses(const std::vector<Moses::Facto
   int index = 0;
   Moses::AlignmentInfo::CollType alignTerm, alignNonTerm;
   std::set<std::pair<size_t, size_t> > alignmentInfo;
-  const PhrasePtr sp = GetSourcePhrase(); 
+  const PhrasePtr sp = GetSourcePhrase();
   for (size_t ind = 0; ind < m_align.size(); ++ind) {
     const std::pair<size_t, size_t> &entry = m_align[ind];
     alignmentInfo.insert(entry);
@@ -252,11 +252,10 @@ Moses::TargetPhrase *TargetPhrase::ConvertToMoses(const std::vector<Moses::Facto
     size_t targetPos = entry.second;
 
     if (GetWord(targetPos).IsNonTerminal()) {
-    	alignNonTerm.insert(std::pair<size_t,size_t>(sourcePos, targetPos));
+      alignNonTerm.insert(std::pair<size_t,size_t>(sourcePos, targetPos));
+    } else {
+      alignTerm.insert(std::pair<size_t,size_t>(sourcePos, targetPos));
     }
-  	else {
-  		alignTerm.insert(std::pair<size_t,size_t>(sourcePos, targetPos));
-  	}
 
   }
   ret->SetAlignTerm(alignTerm);
@@ -313,7 +312,7 @@ UINT64 TargetPhrase::ReadFromFile(std::fstream &fileTP)
     bytesRead += word->ReadFromFile(fileTP);
     AddWord(word);
   }
-  
+
   // read source words
   UINT64 numSourceWords;
   fileTP.read((char*) &numSourceWords, sizeof(UINT64));
@@ -371,7 +370,7 @@ UINT64 TargetPhrase::ReadScoresFromFile(std::fstream &fileTPColl)
 void TargetPhrase::DebugPrint(ostream &out, const Vocab &vocab) const
 {
   Phrase::DebugPrint(out, vocab);
-  
+
   for (size_t ind = 0; ind < m_align.size(); ++ind) {
     const AlignPair &alignPair = m_align[ind];
     out << alignPair.first << "-" << alignPair.second << " ";
diff --git a/OnDiskPt/TargetPhrase.h b/OnDiskPt/TargetPhrase.h
index 5510ddd11..c4bb40454 100644
--- a/OnDiskPt/TargetPhrase.h
+++ b/OnDiskPt/TargetPhrase.h
@@ -49,7 +49,7 @@ class TargetPhrase: public Phrase
   friend std::ostream& operator<<(std::ostream&, const TargetPhrase&);
 protected:
   AlignType m_align;
-  PhrasePtr m_sourcePhrase; 
+  PhrasePtr m_sourcePhrase;
 
   std::vector<float> m_scores;
   UINT64 m_filePos;
@@ -73,10 +73,10 @@ public:
   const PhrasePtr GetSourcePhrase() const {
     return m_sourcePhrase;
   }
-  const std::vector<float> &GetScores() const{
+  const std::vector<float> &GetScores() const {
     return m_scores;
   }
-  
+
   void SetLHS(WordPtr lhs);
 
   void Create1AlignFromString(const std::string &align1Str);
@@ -107,7 +107,7 @@ public:
   UINT64 ReadOtherInfoFromFile(UINT64 filePos, std::fstream &fileTPColl);
   UINT64 ReadFromFile(std::fstream &fileTP);
 
-	virtual void DebugPrint(std::ostream &out, const Vocab &vocab) const;
+  virtual void DebugPrint(std::ostream &out, const Vocab &vocab) const;
 
 };
 
diff --git a/OnDiskPt/TargetPhraseCollection.cpp b/OnDiskPt/TargetPhraseCollection.cpp
index f29bea9cf..c865c2df7 100644
--- a/OnDiskPt/TargetPhraseCollection.cpp
+++ b/OnDiskPt/TargetPhraseCollection.cpp
@@ -82,7 +82,7 @@ void TargetPhraseCollection::Save(OnDiskWrapper &onDiskWrapper)
   CollType::iterator iter;
   for (iter = m_coll.begin(); iter != m_coll.end(); ++iter) {
     // save phrase
-	TargetPhrase &targetPhrase = **iter;
+    TargetPhrase &targetPhrase = **iter;
     targetPhrase.Save(onDiskWrapper);
 
     // save coll
@@ -150,9 +150,9 @@ void TargetPhraseCollection::ReadFromFile(size_t tableLimit, UINT64 filePos, OnD
 {
   fstream &fileTPColl = onDiskWrapper.GetFileTargetColl();
   fstream &fileTP = onDiskWrapper.GetFileTargetInd();
-    
+
   size_t numScores = onDiskWrapper.GetNumScores();
-    
+
 
   UINT64 numPhrases;
 
@@ -164,9 +164,9 @@ void TargetPhraseCollection::ReadFromFile(size_t tableLimit, UINT64 filePos, OnD
   numPhrases = std::min(numPhrases, (UINT64) tableLimit);
 
   currFilePos += sizeof(UINT64);
- 
+
   for (size_t ind = 0; ind < numPhrases; ++ind) {
-    TargetPhrase *tp = new TargetPhrase(numScores);    
+    TargetPhrase *tp = new TargetPhrase(numScores);
 
     UINT64 sizeOtherInfo = tp->ReadOtherInfoFromFile(currFilePos, fileTPColl);
     tp->ReadFromFile(fileTP);
@@ -197,7 +197,7 @@ const TargetPhrase &TargetPhraseCollection::GetTargetPhrase(size_t ind) const
   assert(ind < GetSize());
   return *m_coll[ind];
 }
-  
+
 }
 
 
diff --git a/OnDiskPt/TargetPhraseCollection.h b/OnDiskPt/TargetPhraseCollection.h
index e0d5d1599..d6086850f 100644
--- a/OnDiskPt/TargetPhraseCollection.h
+++ b/OnDiskPt/TargetPhraseCollection.h
@@ -64,9 +64,9 @@ public:
   size_t GetSize() const {
     return m_coll.size();
   }
-  
+
   const TargetPhrase &GetTargetPhrase(size_t ind) const;
-  
+
   UINT64 GetFilePos() const;
 
   Moses::TargetPhraseCollection *ConvertToMoses(const std::vector<Moses::FactorType> &inputFactors
diff --git a/OnDiskPt/Vocab.cpp b/OnDiskPt/Vocab.cpp
index 5de620b75..03af2d886 100644
--- a/OnDiskPt/Vocab.cpp
+++ b/OnDiskPt/Vocab.cpp
@@ -44,7 +44,7 @@ bool Vocab::Load(OnDiskWrapper &onDiskWrapper)
   // assume contiguous vocab id
   m_lookup.resize(m_vocabColl.size() + 1);
   m_nextId = m_lookup.size();
-  
+
   CollType::const_iterator iter;
   for (iter = m_vocabColl.begin(); iter != m_vocabColl.end(); ++iter) {
     UINT32 vocabId = iter->second;
diff --git a/OnDiskPt/Word.cpp b/OnDiskPt/Word.cpp
index 13c77f739..1664571c5 100644
--- a/OnDiskPt/Word.cpp
+++ b/OnDiskPt/Word.cpp
@@ -97,13 +97,14 @@ size_t Word::ReadFromFile(std::fstream &file)
 }
 
 void Word::ConvertToMoses(
-    const std::vector<Moses::FactorType> &outputFactorsVec, 
-    const Vocab &vocab,
-    Moses::Word &overwrite) const {
+  const std::vector<Moses::FactorType> &outputFactorsVec,
+  const Vocab &vocab,
+  Moses::Word &overwrite) const
+{
   Moses::FactorCollection &factorColl = Moses::FactorCollection::Instance();
   overwrite = Moses::Word(m_isNonTerminal);
 
-  // TODO: this conversion should have been done at load time.  
+  // TODO: this conversion should have been done at load time.
   util::TokenIter<util::SingleCharacter> tok(vocab.GetString(m_vocabId), '|');
 
   for (std::vector<Moses::FactorType>::const_iterator t = outputFactorsVec.begin(); t != outputFactorsVec.end(); ++t, ++tok) {
@@ -144,14 +145,14 @@ bool Word::operator==(const Word &compare) const
 
 void Word::DebugPrint(ostream &out, const Vocab &vocab) const
 {
- 	const string &str = vocab.GetString(m_vocabId);
+  const string &str = vocab.GetString(m_vocabId);
   out << str;
 }
 
 std::ostream& operator<<(std::ostream &out, const Word &word)
 {
   out << "(";
- 	out << word.m_vocabId;
+  out << word.m_vocabId;
 
   out << (word.m_isNonTerminal ? "n" : "t");
   out << ")";
diff --git a/OnDiskPt/Word.h b/OnDiskPt/Word.h
index 64be6f148..254959737 100644
--- a/OnDiskPt/Word.h
+++ b/OnDiskPt/Word.h
@@ -50,8 +50,8 @@ public:
   {}
 
   explicit Word(bool isNonTerminal)
-  :m_isNonTerminal(isNonTerminal)
-  ,m_vocabId(0)
+    :m_isNonTerminal(isNonTerminal)
+    ,m_vocabId(0)
   {}
 
   Word(const Word &copy);
@@ -77,8 +77,7 @@ public:
     Moses::Word &overwrite) const;
 
   void DebugPrint(std::ostream &out, const Vocab &vocab) const;
-  inline const std::string &GetString(const Vocab &vocab) const
-  {
+  inline const std::string &GetString(const Vocab &vocab) const {
     return vocab.GetString(m_vocabId);
   }
 
diff --git a/OnDiskPt/queryOnDiskPt.cpp b/OnDiskPt/queryOnDiskPt.cpp
index 8126a2b75..776dd8a2c 100644
--- a/OnDiskPt/queryOnDiskPt.cpp
+++ b/OnDiskPt/queryOnDiskPt.cpp
@@ -33,8 +33,7 @@ int main(int argc, char **argv)
       if(i + 1 == argc)
         usage();
       ttable = argv[++i];
-    }
-    else
+    } else
       usage();
   }
 
@@ -55,30 +54,27 @@ int main(int argc, char **argv)
 
     cerr << "line: " << line << endl;
     const PhraseNode* node = onDiskQuery.Query(tokens);
-    
-    if (node)
-    { // source phrase points to a bunch of rules
+
+    if (node) {
+      // source phrase points to a bunch of rules
       const TargetPhraseCollection *coll = node->GetTargetPhraseCollection(tableLimit, onDiskWrapper);
       string str = coll->GetDebugStr();
       cout << "Found " << coll->GetSize() << endl;
-      
-      for (size_t ind = 0; ind < coll->GetSize(); ++ind)
-      {
+
+      for (size_t ind = 0; ind < coll->GetSize(); ++ind) {
         const TargetPhrase &targetPhrase = coll->GetTargetPhrase(ind);
         cerr << "  ";
         targetPhrase.DebugPrint(cerr, onDiskWrapper.GetVocab());
         cerr << endl;
       }
-    }
-    else
-    {
+    } else {
       cout << "Not found" << endl;
     }
-    
+
     std::cout << '\n';
     std::cout.flush();
   }
-  
+
   cerr << "Finished." << endl;
 }
 
diff --git a/biconcor/Alignment.cpp b/biconcor/Alignment.cpp
index e73e18840..814802531 100644
--- a/biconcor/Alignment.cpp
+++ b/biconcor/Alignment.cpp
@@ -5,7 +5,8 @@
 #include <stdlib.h>
 #include <cstring>
 
-namespace {
+namespace
+{
 
 const int LINE_MAX_LENGTH = 10000;
 
@@ -84,10 +85,10 @@ void Alignment::Create(const string& fileName)
 }
 
 Alignment::Alignment()
-    : m_array(NULL),
-      m_sentenceEnd(NULL),
-      m_size(0),
-      m_sentenceCount(0) {}
+  : m_array(NULL),
+    m_sentenceEnd(NULL),
+    m_size(0),
+    m_sentenceCount(0) {}
 
 Alignment::~Alignment()
 {
diff --git a/biconcor/Mismatch.cpp b/biconcor/Mismatch.cpp
index 31140b200..c3afec781 100644
--- a/biconcor/Mismatch.cpp
+++ b/biconcor/Mismatch.cpp
@@ -23,16 +23,16 @@ enum {
 };
 
 Mismatch::Mismatch( SuffixArray *sa, TargetCorpus *tc, Alignment *a, INDEX sentence_id, INDEX position, int source_length, int target_length, int source_start, int source_end )
-    :m_suffixArray(sa)
-    ,m_targetCorpus(tc)
-    ,m_alignment(a)
-    ,m_sentence_id(sentence_id)
-    ,m_source_length(source_length)
-    ,m_target_length(target_length)
-    ,m_source_position(position)
-    ,m_source_start(source_start)
-    ,m_source_end(source_end)
-    ,m_unaligned(true)
+  :m_suffixArray(sa)
+  ,m_targetCorpus(tc)
+  ,m_alignment(a)
+  ,m_sentence_id(sentence_id)
+  ,m_source_length(source_length)
+  ,m_target_length(target_length)
+  ,m_source_position(position)
+  ,m_source_start(source_start)
+  ,m_source_end(source_end)
+  ,m_unaligned(true)
 {
   // initialize unaligned indexes
   for (int i = 0; i < m_source_length; i++) {
@@ -42,7 +42,7 @@ Mismatch::Mismatch( SuffixArray *sa, TargetCorpus *tc, Alignment *a, INDEX sente
     m_target_unaligned[i] = true;
   }
   m_num_alignment_points =
-      m_alignment->GetNumberOfAlignmentPoints( sentence_id );
+    m_alignment->GetNumberOfAlignmentPoints( sentence_id );
   for(INDEX ap=0; ap<m_num_alignment_points; ap++) {
     m_source_unaligned[ (int)m_alignment->GetSourceWord( sentence_id, ap ) ] = false;
     m_target_unaligned[ (int)m_alignment->GetTargetWord( sentence_id, ap ) ] = false;
@@ -58,234 +58,235 @@ Mismatch::~Mismatch () {}
 
 void Mismatch::PrintClippedHTML( ostream* out, int width )
 {
-    int source_annotation[256], target_annotation[256];
-    vector< string > label_class;
-	label_class.push_back( "" );
-	label_class.push_back( "mismatch_pre_aligned" );
-	label_class.push_back( "mismatch_post_aligned" );
-	label_class.push_back( "null_aligned" );
-	label_class.push_back( "mismatch_misaligned" );
-	label_class.push_back( "mismatch_aligned" );
+  int source_annotation[256], target_annotation[256];
+  vector< string > label_class;
+  label_class.push_back( "" );
+  label_class.push_back( "mismatch_pre_aligned" );
+  label_class.push_back( "mismatch_post_aligned" );
+  label_class.push_back( "null_aligned" );
+  label_class.push_back( "mismatch_misaligned" );
+  label_class.push_back( "mismatch_aligned" );
 
-	for(int i=0; i<m_source_length;i++) source_annotation[i] = UNANNOTATED;
-	for(int i=0; i<m_target_length;i++) target_annotation[i] = UNANNOTATED;
-	
-	if (m_unaligned) {
-		// find alignment points for prior and next word(s) and
-		// center target phrase around those.
-		bool found_aligned = false;
-		for(int i=1; i<m_source_length && !found_aligned; i++) {
-			if (m_source_start-i >= 0) {
-				int word_id =  m_source_start-i;
-				source_annotation[ word_id ] = UNALIGNED;
-				if (!m_source_unaligned[ word_id ]) {
-					found_aligned = true;
-					LabelSourceMatches( source_annotation, target_annotation, word_id, PRE_ALIGNED );
-				}
-			}
+  for(int i=0; i<m_source_length; i++) source_annotation[i] = UNANNOTATED;
+  for(int i=0; i<m_target_length; i++) target_annotation[i] = UNANNOTATED;
 
-			if (m_source_end+i < m_source_length) {
-				int word_id = m_source_end+i;
-				source_annotation[ word_id ] = UNALIGNED;
-				if (!m_source_unaligned[ word_id ]) {
-					found_aligned = true;
-					LabelSourceMatches( source_annotation, target_annotation, word_id, POST_ALIGNED );
-				}
-			}
-		}
-		
-	}
-	// misalignment
-	else {
-		// label aligned output words
-		for(int i=m_source_start; i<=m_source_end; i++)
-			LabelSourceMatches( source_annotation, target_annotation, i, ALIGNED );
+  if (m_unaligned) {
+    // find alignment points for prior and next word(s) and
+    // center target phrase around those.
+    bool found_aligned = false;
+    for(int i=1; i<m_source_length && !found_aligned; i++) {
+      if (m_source_start-i >= 0) {
+        int word_id =  m_source_start-i;
+        source_annotation[ word_id ] = UNALIGNED;
+        if (!m_source_unaligned[ word_id ]) {
+          found_aligned = true;
+          LabelSourceMatches( source_annotation, target_annotation, word_id, PRE_ALIGNED );
+        }
+      }
 
-		// find first and last
-		int target_start = -1;
-		int target_end;
-		for(int i=0; i<m_target_length; i++)
-			if (target_annotation[i] == ALIGNED) {
-				if (target_start == -1)
-					target_start = i;
-				target_end = i;
-			}
-		// go over all enclosed target words
-		for(int i=target_start; i<=target_end; i++) {
-			// label other target words as unaligned or misaligned
-			if (m_target_unaligned[ i ])
-				target_annotation[ i ] = UNALIGNED;
-			else {
-				if (target_annotation[ i ] != ALIGNED)
-					target_annotation[ i ] = MISALIGNED;
-				// loop over aligned source words
-				for(INDEX ap=0; ap<m_num_alignment_points; ap++) {
-					if (m_alignment->GetTargetWord( m_sentence_id, ap ) == i) {
-						int source_word = m_alignment->GetSourceWord( m_sentence_id, ap );
-						// if not part of the source phrase -> also misaligned
-						if (source_word < m_source_start || source_word > m_source_end)
-							source_annotation[ source_word ] = MISALIGNED;
-					}
-				}
-			}						
-		}
-		// closure
-		bool change = true;
-		while(change) {
-			change = false;
-			for(INDEX ap=0; ap<m_num_alignment_points; ap++) {
-				int source_word = m_alignment->GetSourceWord( m_sentence_id, ap );
-				int target_word = m_alignment->GetTargetWord( m_sentence_id, ap );
-				if (source_annotation[source_word] != UNANNOTATED &&
-						target_annotation[target_word] == UNANNOTATED) {
-					target_annotation[target_word] = MISALIGNED;
-					change = true;
-				}
-				if (source_annotation[source_word] == UNANNOTATED &&
-						target_annotation[target_word] != UNANNOTATED) {
-					source_annotation[source_word] = MISALIGNED;
-					change = true;
-				}
-			}
-		}
-	}
-	
-	// print source
-	// shorten source context if too long
+      if (m_source_end+i < m_source_length) {
+        int word_id = m_source_end+i;
+        source_annotation[ word_id ] = UNALIGNED;
+        if (!m_source_unaligned[ word_id ]) {
+          found_aligned = true;
+          LabelSourceMatches( source_annotation, target_annotation, word_id, POST_ALIGNED );
+        }
+      }
+    }
+
+  }
+  // misalignment
+  else {
+    // label aligned output words
+    for(int i=m_source_start; i<=m_source_end; i++)
+      LabelSourceMatches( source_annotation, target_annotation, i, ALIGNED );
+
+    // find first and last
+    int target_start = -1;
+    int target_end;
+    for(int i=0; i<m_target_length; i++)
+      if (target_annotation[i] == ALIGNED) {
+        if (target_start == -1)
+          target_start = i;
+        target_end = i;
+      }
+    // go over all enclosed target words
+    for(int i=target_start; i<=target_end; i++) {
+      // label other target words as unaligned or misaligned
+      if (m_target_unaligned[ i ])
+        target_annotation[ i ] = UNALIGNED;
+      else {
+        if (target_annotation[ i ] != ALIGNED)
+          target_annotation[ i ] = MISALIGNED;
+        // loop over aligned source words
+        for(INDEX ap=0; ap<m_num_alignment_points; ap++) {
+          if (m_alignment->GetTargetWord( m_sentence_id, ap ) == i) {
+            int source_word = m_alignment->GetSourceWord( m_sentence_id, ap );
+            // if not part of the source phrase -> also misaligned
+            if (source_word < m_source_start || source_word > m_source_end)
+              source_annotation[ source_word ] = MISALIGNED;
+          }
+        }
+      }
+    }
+    // closure
+    bool change = true;
+    while(change) {
+      change = false;
+      for(INDEX ap=0; ap<m_num_alignment_points; ap++) {
+        int source_word = m_alignment->GetSourceWord( m_sentence_id, ap );
+        int target_word = m_alignment->GetTargetWord( m_sentence_id, ap );
+        if (source_annotation[source_word] != UNANNOTATED &&
+            target_annotation[target_word] == UNANNOTATED) {
+          target_annotation[target_word] = MISALIGNED;
+          change = true;
+        }
+        if (source_annotation[source_word] == UNANNOTATED &&
+            target_annotation[target_word] != UNANNOTATED) {
+          source_annotation[source_word] = MISALIGNED;
+          change = true;
+        }
+      }
+    }
+  }
+
+  // print source
+  // shorten source context if too long
   int sentence_start = m_source_position - m_source_start;
-	int context_space = width/2;
-	for(int i=m_source_start;i<=m_source_end;i++)
-		context_space -= m_suffixArray->GetWord( sentence_start + i ).size() + 1;
-	context_space /= 2;
+  int context_space = width/2;
+  for(int i=m_source_start; i<=m_source_end; i++)
+    context_space -= m_suffixArray->GetWord( sentence_start + i ).size() + 1;
+  context_space /= 2;
 
-	int remaining = context_space;
-	int start_word = m_source_start;
-	for(;start_word>0 && remaining>0; start_word--)
-		remaining -= m_suffixArray->GetWord( sentence_start + start_word-1 ).size() + 1;
-	if (remaining<0 || start_word == -1) start_word++;
+  int remaining = context_space;
+  int start_word = m_source_start;
+  for(; start_word>0 && remaining>0; start_word--)
+    remaining -= m_suffixArray->GetWord( sentence_start + start_word-1 ).size() + 1;
+  if (remaining<0 || start_word == -1) start_word++;
 
-	remaining = context_space;
-	int end_word = m_source_end;
-	for(;end_word<m_source_length && remaining>0; end_word++)
-		remaining -= m_suffixArray->GetWord( sentence_start + end_word ).size() + 1;
-	end_word--;
+  remaining = context_space;
+  int end_word = m_source_end;
+  for(; end_word<m_source_length && remaining>0; end_word++)
+    remaining -= m_suffixArray->GetWord( sentence_start + end_word ).size() + 1;
+  end_word--;
 
-	// output with markup
-	*out << "<tr><td class=\"pp_source_left\">";
-	char current_label = UNANNOTATED;
-	if (start_word>0) {
-		current_label = source_annotation[start_word-1];
-		*out << "... ";
-	}
-	for(int i=start_word; i<=end_word; i++) {
-		// change to phrase block
-		if (i == m_source_start) {
-			if (current_label != UNANNOTATED && i!=start_word) 
-				*out << "</span>";				
-			*out << "</td><td class=\"pp_source\">";
-			current_label = UNANNOTATED;
-		}
+  // output with markup
+  *out << "<tr><td class=\"pp_source_left\">";
+  char current_label = UNANNOTATED;
+  if (start_word>0) {
+    current_label = source_annotation[start_word-1];
+    *out << "... ";
+  }
+  for(int i=start_word; i<=end_word; i++) {
+    // change to phrase block
+    if (i == m_source_start) {
+      if (current_label != UNANNOTATED && i!=start_word)
+        *out << "</span>";
+      *out << "</td><td class=\"pp_source\">";
+      current_label = UNANNOTATED;
+    }
 
-		// change to labeled word 
-		else if (source_annotation[i] != current_label &&
-						 source_annotation[i] != ALIGNED) {
-			if (current_label != UNANNOTATED && i!=start_word) 
-				*out << "</span>";
-			if (source_annotation[i] != UNANNOTATED)
-				*out << "<span class=\""
-						 << label_class[ source_annotation[i] ]
-						 << "\">";
-			current_label = source_annotation[i];
-		}
+    // change to labeled word
+    else if (source_annotation[i] != current_label &&
+             source_annotation[i] != ALIGNED) {
+      if (current_label != UNANNOTATED && i!=start_word)
+        *out << "</span>";
+      if (source_annotation[i] != UNANNOTATED)
+        *out << "<span class=\""
+             << label_class[ source_annotation[i] ]
+             << "\">";
+      current_label = source_annotation[i];
+    }
 
-		// output word
-		*out << m_suffixArray->GetWord( sentence_start + i ) << " ";
+    // output word
+    *out << m_suffixArray->GetWord( sentence_start + i ) << " ";
 
-		// change to right context block
-		if (i == m_source_end) {
-			*out << "</td><td class=\"pp_source_right\">";
-			current_label = UNANNOTATED;
-		}
-	}
+    // change to right context block
+    if (i == m_source_end) {
+      *out << "</td><td class=\"pp_source_right\">";
+      current_label = UNANNOTATED;
+    }
+  }
 
-	if (current_label != UNANNOTATED && end_word>m_source_end)
-		*out << "</span>";
-	if (end_word<m_source_length-1)
-		*out << "... ";
+  if (current_label != UNANNOTATED && end_word>m_source_end)
+    *out << "</span>";
+  if (end_word<m_source_length-1)
+    *out << "... ";
 
-	// print target
-	// shorten target context if too long
-	int target_start = -1;
-	int target_end;
-	for(int i=0; i<m_target_length; i++)
-		if (target_annotation[i] != UNANNOTATED) {
-			if (target_start == -1) 
-				target_start = i;
-			target_end = i;
-		}
+  // print target
+  // shorten target context if too long
+  int target_start = -1;
+  int target_end;
+  for(int i=0; i<m_target_length; i++)
+    if (target_annotation[i] != UNANNOTATED) {
+      if (target_start == -1)
+        target_start = i;
+      target_end = i;
+    }
 
-	context_space = width/2;
-	for(int i=target_start;i<=target_end;i++)
-		context_space -= m_targetCorpus->GetWord( m_sentence_id, i ).size() + 1;
-	while (context_space < 0) { // shorten matched part, if too long
-		context_space += 
-			m_targetCorpus->GetWord( m_sentence_id, target_start ).size() +
-			m_targetCorpus->GetWord( m_sentence_id, target_end ).size() + 2;
-		target_start++;
-		target_end--;
-	}
-	context_space /= 2;
+  context_space = width/2;
+  for(int i=target_start; i<=target_end; i++)
+    context_space -= m_targetCorpus->GetWord( m_sentence_id, i ).size() + 1;
+  while (context_space < 0) { // shorten matched part, if too long
+    context_space +=
+      m_targetCorpus->GetWord( m_sentence_id, target_start ).size() +
+      m_targetCorpus->GetWord( m_sentence_id, target_end ).size() + 2;
+    target_start++;
+    target_end--;
+  }
+  context_space /= 2;
 
-	remaining = context_space;
-	start_word = target_start;
-	for(;start_word>0 && remaining>0; start_word--) {
-		//cerr << "remaining: " << remaining << ", start_word: " << start_word << endl;
-		remaining -= m_targetCorpus->GetWord( m_sentence_id, start_word-1 ).size() + 1;
-	}
-	if (remaining<0 || start_word == -1) start_word++;
+  remaining = context_space;
+  start_word = target_start;
+  for(; start_word>0 && remaining>0; start_word--) {
+    //cerr << "remaining: " << remaining << ", start_word: " << start_word << endl;
+    remaining -= m_targetCorpus->GetWord( m_sentence_id, start_word-1 ).size() + 1;
+  }
+  if (remaining<0 || start_word == -1) start_word++;
 
-	remaining = context_space;
-	end_word = target_end;
-	for(;end_word<m_target_length && remaining>0; end_word++) {
-		//cerr << "remaining: " << remaining << ", end_word: " << end_word << endl;
-		remaining -= m_targetCorpus->GetWord( m_sentence_id, end_word ).size() + 1;
-	}
-	end_word--;
+  remaining = context_space;
+  end_word = target_end;
+  for(; end_word<m_target_length && remaining>0; end_word++) {
+    //cerr << "remaining: " << remaining << ", end_word: " << end_word << endl;
+    remaining -= m_targetCorpus->GetWord( m_sentence_id, end_word ).size() + 1;
+  }
+  end_word--;
 
-	// output with markup
-	*out << "</td><td class=\"mismatch_target\">";
-	current_label = UNANNOTATED;
-	if (start_word>0) {
-		current_label = target_annotation[start_word-1];
-		*out << "... ";
-	}
-	for(int i=start_word; i<=end_word; i++) {
-		if (target_annotation[i] != current_label) {
-			if (current_label != UNANNOTATED && i!=start_word) 
-				*out << "</span>";
-			if (target_annotation[i] != UNANNOTATED)
-				*out << "<span class=\""
-						 << label_class[ target_annotation[i] ]
-						 << "\">";
-			current_label = target_annotation[i];
-		}
+  // output with markup
+  *out << "</td><td class=\"mismatch_target\">";
+  current_label = UNANNOTATED;
+  if (start_word>0) {
+    current_label = target_annotation[start_word-1];
+    *out << "... ";
+  }
+  for(int i=start_word; i<=end_word; i++) {
+    if (target_annotation[i] != current_label) {
+      if (current_label != UNANNOTATED && i!=start_word)
+        *out << "</span>";
+      if (target_annotation[i] != UNANNOTATED)
+        *out << "<span class=\""
+             << label_class[ target_annotation[i] ]
+             << "\">";
+      current_label = target_annotation[i];
+    }
 
-		// output word
-		*out << m_targetCorpus->GetWord( m_sentence_id, i ) << " ";
-	}
+    // output word
+    *out << m_targetCorpus->GetWord( m_sentence_id, i ) << " ";
+  }
 
-	if (current_label != UNANNOTATED && end_word>target_end)
-		*out << "</span>";
-	if (end_word<m_target_length-1)
-		*out << "... ";
-	*out << "</td></tr>";
+  if (current_label != UNANNOTATED && end_word>target_end)
+    *out << "</span>";
+  if (end_word<m_target_length-1)
+    *out << "... ";
+  *out << "</td></tr>";
 }
 
-void Mismatch::LabelSourceMatches(int *source_annotation, int *target_annotation, int source_id, int label ) {
-	for(INDEX ap=0; ap<m_num_alignment_points; ap++) {
-		if (m_alignment->GetSourceWord( m_sentence_id, ap ) == source_id) {
-			source_annotation[ source_id ] = label;
-			target_annotation[ m_alignment->GetTargetWord( m_sentence_id, ap ) ] = label;
-		}
-	}
+void Mismatch::LabelSourceMatches(int *source_annotation, int *target_annotation, int source_id, int label )
+{
+  for(INDEX ap=0; ap<m_num_alignment_points; ap++) {
+    if (m_alignment->GetSourceWord( m_sentence_id, ap ) == source_id) {
+      source_annotation[ source_id ] = label;
+      target_annotation[ m_alignment->GetTargetWord( m_sentence_id, ap ) ] = label;
+    }
+  }
 }
diff --git a/biconcor/Mismatch.h b/biconcor/Mismatch.h
index c0063d049..1277ed95a 100644
--- a/biconcor/Mismatch.h
+++ b/biconcor/Mismatch.h
@@ -34,7 +34,9 @@ public:
   Mismatch( SuffixArray *sa, TargetCorpus *tc, Alignment *a, INDEX sentence_id, INDEX position, int source_length, int target_length, int source_start, int source_end );
   ~Mismatch();
 
-  bool Unaligned() const { return m_unaligned; }
+  bool Unaligned() const {
+    return m_unaligned;
+  }
   void PrintClippedHTML(std::ostream* out, int width );
   void LabelSourceMatches(int *source_annotation, int *target_annotation, int source_id, int label );
 };
diff --git a/biconcor/PhrasePair.cpp b/biconcor/PhrasePair.cpp
index 038fa3a31..b6409258b 100644
--- a/biconcor/PhrasePair.cpp
+++ b/biconcor/PhrasePair.cpp
@@ -37,7 +37,7 @@ void PhrasePair::Print( ostream* out ) const
   INDEX ap_points = m_alignment->GetNumberOfAlignmentPoints( m_sentence_id );
   for( INDEX i=0; i<ap_points; i++) {
     *out << " " << m_alignment->GetSourceWord( m_sentence_id, i )
-	 << "-" << m_alignment->GetTargetWord( m_sentence_id, i );
+         << "-" << m_alignment->GetTargetWord( m_sentence_id, i );
   }
 
   *out << endl;
@@ -185,27 +185,27 @@ void PhrasePair::PrintClippedHTML( ostream* out, int width ) const
   size_t source_pre_width = (source_width-source.size())/2;
   size_t source_post_width = (source_width-source.size()+1)/2;
 
-	// if phrase is too long, don't show any context
+  // if phrase is too long, don't show any context
   if (source.size() > (size_t)width) {
     source_pre_width = 0;
     source_post_width = 0;
   }
-	// too long -> truncate and add "..."
+  // too long -> truncate and add "..."
   if (source_pre.size() > source_pre_width) {
-		// first skip up to a space
-		while(source_pre_width>0 &&
-					source_pre.substr(source_pre.size()-source_pre_width,1) != " ") {
-			source_pre_width--;
-		}
+    // first skip up to a space
+    while(source_pre_width>0 &&
+          source_pre.substr(source_pre.size()-source_pre_width,1) != " ") {
+      source_pre_width--;
+    }
     source_pre = "..." + source_pre.substr( source_pre.size()-source_pre_width, source_pre_width );
-	}
+  }
   if (source_post.size() > source_post_width) {
-		while(source_post_width>0 &&
-					source_post.substr(source_post_width-1,1) != " ") {
-			source_post_width--;
-		}
+    while(source_post_width>0 &&
+          source_post.substr(source_post_width-1,1) != " ") {
+      source_post_width--;
+    }
     source_post = source_post.substr( 0, source_post_width ) + "...";
-	}
+  }
 
   *out << "<tr><td class=\"pp_source_left\">"
        << source_pre
@@ -220,13 +220,13 @@ void PhrasePair::PrintClippedHTML( ostream* out, int width ) const
   string target_pre = "";
   string target = "";
   string target_post = "";
-	size_t target_pre_null_width = 0;
-	size_t target_post_null_width = 0;
+  size_t target_pre_null_width = 0;
+  size_t target_post_null_width = 0;
   for( char i=0; i<m_target_start; i++ ) {
-		WORD word = m_targetCorpus->GetWord( m_sentence_id, i);
+    WORD word = m_targetCorpus->GetWord( m_sentence_id, i);
     target_pre += " " + word;
-		if (i >= m_target_start-m_pre_null)
-			target_pre_null_width += word.size() + 1;
+    if (i >= m_target_start-m_pre_null)
+      target_pre_null_width += word.size() + 1;
   }
   for( char i=m_target_start; i<=m_target_end; i++ ) {
     if (i>m_target_start) target += " ";
@@ -234,11 +234,11 @@ void PhrasePair::PrintClippedHTML( ostream* out, int width ) const
   }
   for( char i=m_target_end+1; i<m_target_length; i++ ) {
     if (i>m_target_end+1) target_post += " ";
-		WORD word = m_targetCorpus->GetWord( m_sentence_id, i);
+    WORD word = m_targetCorpus->GetWord( m_sentence_id, i);
     target_post += word;
-		if (i-(m_target_end+1) < m_post_null) {
-			target_post_null_width += word.size() + 1;
-		}
+    if (i-(m_target_end+1) < m_post_null) {
+      target_post_null_width += word.size() + 1;
+    }
   }
 
   size_t target_pre_width = (target_width-target.size())/2;
@@ -249,46 +249,45 @@ void PhrasePair::PrintClippedHTML( ostream* out, int width ) const
     target_post_width = 0;
   }
 
-  if (target_pre.size() < target_pre_width) 
-		target_pre_width = target_pre.size();
-	else {
-		while(target_pre_width>0 &&
-					target_pre.substr(target_pre.size()-target_pre_width,1) != " ") {
-			target_pre_width--;
-		}
+  if (target_pre.size() < target_pre_width)
+    target_pre_width = target_pre.size();
+  else {
+    while(target_pre_width>0 &&
+          target_pre.substr(target_pre.size()-target_pre_width,1) != " ") {
+      target_pre_width--;
+    }
     target_pre = "..." + target_pre.substr( target_pre.size()-target_pre_width, target_pre_width );
-	}
-
-	if (target_post.size() < target_post_width) {
-		target_post_width = target_post.size();
-	}
-	else {
-		while(target_post_width>0 &&
-					target_post.substr(target_post_width-1,1) != " ") {
-			target_post_width--;
-		}
-		target_post = target_post.substr( 0, target_post_width ) + "...";
-	}
-
-	if (m_pre_null) {
-		//cerr << endl << "target_pre_width=" << target_pre_width << ", target_pre_null_width=" << target_pre_null_width << ", target_pre.size()=" << target_pre.size() << endl;
-		if (target_pre_width < target_pre.size())
-			target_pre_null_width -= target_pre.size()-target_pre_width;
-		target_pre = target_pre.substr(0,target_pre_width-target_pre_null_width) 
-			+ "<span class=\"null_aligned\">"
-			+ target_pre.substr(target_pre_width-target_pre_null_width)
-			+ "</span>";
-	}
-	if (m_post_null) {
-		//cerr << endl << "target_post_width=" << target_post_width << ", target_post_null_width=" << target_post_null_width << ", target_post.size()=" << target_post.size() << endl;
-		if (target_post_null_width > target_post.size()) {
-			target_post_null_width = target_post.size();
-		}
-		target_post = "<span class=\"null_aligned\">"
-			+ target_post.substr(0,target_post_null_width) 
-			+ "</span>"
-			+ target_post.substr(target_post_null_width);
-	}
+  }
+
+  if (target_post.size() < target_post_width) {
+    target_post_width = target_post.size();
+  } else {
+    while(target_post_width>0 &&
+          target_post.substr(target_post_width-1,1) != " ") {
+      target_post_width--;
+    }
+    target_post = target_post.substr( 0, target_post_width ) + "...";
+  }
+
+  if (m_pre_null) {
+    //cerr << endl << "target_pre_width=" << target_pre_width << ", target_pre_null_width=" << target_pre_null_width << ", target_pre.size()=" << target_pre.size() << endl;
+    if (target_pre_width < target_pre.size())
+      target_pre_null_width -= target_pre.size()-target_pre_width;
+    target_pre = target_pre.substr(0,target_pre_width-target_pre_null_width)
+                 + "<span class=\"null_aligned\">"
+                 + target_pre.substr(target_pre_width-target_pre_null_width)
+                 + "</span>";
+  }
+  if (m_post_null) {
+    //cerr << endl << "target_post_width=" << target_post_width << ", target_post_null_width=" << target_post_null_width << ", target_post.size()=" << target_post.size() << endl;
+    if (target_post_null_width > target_post.size()) {
+      target_post_null_width = target_post.size();
+    }
+    target_post = "<span class=\"null_aligned\">"
+                  + target_post.substr(0,target_post_null_width)
+                  + "</span>"
+                  + target_post.substr(target_post_null_width);
+  }
 
   *out << "<td class=\"pp_target_left\">"
        << target_pre
diff --git a/biconcor/PhrasePairCollection.cpp b/biconcor/PhrasePairCollection.cpp
index 7497b2af8..dd21faad3 100644
--- a/biconcor/PhrasePairCollection.cpp
+++ b/biconcor/PhrasePairCollection.cpp
@@ -47,15 +47,15 @@ int PhrasePairCollection::GetCollection( const vector< string >& sourceString )
     int sentence_length = m_suffixArray->GetSentenceLength( sentence_id );
     int target_length = m_targetCorpus->GetSentenceLength( sentence_id );
     //cerr << "match " << (i-first_match)
-         //<< " in sentence " << sentence_id
-         //<< ", starting at word " << source_start
-         //<< " of " << sentence_length
-         //<< ". target sentence has " << target_length << " words.";
+    //<< " in sentence " << sentence_id
+    //<< ", starting at word " << source_start
+    //<< " of " << sentence_length
+    //<< ". target sentence has " << target_length << " words.";
     int target_start, target_end, pre_null, post_null;
     if (m_alignment->PhraseAlignment( sentence_id, target_length, source_start, source_end, target_start, target_end, pre_null, post_null)) {
       //cerr << " aligned to [" << (int)target_start << "," << (int)target_end << "]";
       //cerr << " +(" << (int)pre_null << "," << (int)post_null << ")";
-			bool null_boundary_words = false;
+      bool null_boundary_words = false;
       for (int pre = 0; pre <= pre_null && (pre == 0 || null_boundary_words); pre++ ) {
         for (int post = 0; post <= post_null && (post == 0 || null_boundary_words); post++ ) {
           vector< WORD_ID > targetString;
@@ -75,19 +75,18 @@ int PhrasePairCollection::GetCollection( const vector< string >& sourceString )
           m_size++;
         }
       }
+    } else {
+      //cerr << "mismatch " << (i-first_match)
+      //		 << " in sentence " << sentence_id
+      //		 << ", starting at word " << source_start
+      //		 << " of " << sentence_length
+      //		 << ". target sentence has " << target_length << " words.";
+      Mismatch *mismatch = new Mismatch( m_suffixArray, m_targetCorpus, m_alignment, sentence_id, position, sentence_length, target_length, source_start, source_end );
+      if (mismatch->Unaligned())
+        m_unaligned.push_back( mismatch );
+      else
+        m_mismatch.push_back( mismatch );
     }
-		else {
-			//cerr << "mismatch " << (i-first_match)
-			//		 << " in sentence " << sentence_id
-			//		 << ", starting at word " << source_start
-			//		 << " of " << sentence_length
-			//		 << ". target sentence has " << target_length << " words.";
-			Mismatch *mismatch = new Mismatch( m_suffixArray, m_targetCorpus, m_alignment, sentence_id, position, sentence_length, target_length, source_start, source_end );
-			if (mismatch->Unaligned())
-				m_unaligned.push_back( mismatch );
-			else
-				m_mismatch.push_back( mismatch );
-		}
     //cerr << endl;
 
     if (found > (INDEX)m_max_lookup) {
@@ -111,8 +110,7 @@ void PhrasePairCollection::Print(bool pretty) const
     for(int j=0; j<ppWithSameTarget->size() && j<m_max_example; j++, p++ ) {
       if (pretty) {
         (*p)->PrintPretty( &cout, 100 );
-      }
-      else {
+      } else {
         (*p)->Print( &cout );
       }
       if (ppWithSameTarget->size() > m_max_example) {
@@ -125,33 +123,32 @@ void PhrasePairCollection::Print(bool pretty) const
 void PhrasePairCollection::PrintHTML() const
 {
   int pp_target = 0;
-	bool singleton = false;
-	// loop over all translations
+  bool singleton = false;
+  // loop over all translations
   vector< vector<PhrasePair*> >::const_iterator ppWithSameTarget;
   for( ppWithSameTarget = m_collection.begin(); ppWithSameTarget != m_collection.end() && pp_target<m_max_translation; ppWithSameTarget++, pp_target++ ) {
 
-		int count = ppWithSameTarget->size();
-		if (!singleton) {
-			if (count == 1) {
-				singleton = true;
-				cout << "<p class=\"pp_singleton_header\">singleton"
-						 << (m_collection.end() - ppWithSameTarget==1?"":"s") << " ("
-						 << (m_collection.end() - ppWithSameTarget)
-						 << "/" << m_size << ")</p>";
-			}
-			else {
-				cout << "<p class=\"pp_target_header\">";
-				(*(ppWithSameTarget->begin()))->PrintTarget( &cout );
-				cout << " (" << count << "/" << m_size << ")" << endl;
-				cout << "<p><div id=\"pp_" << pp_target << "\">";
-			}
-			cout << "<table align=\"center\">";
-		}
+    int count = ppWithSameTarget->size();
+    if (!singleton) {
+      if (count == 1) {
+        singleton = true;
+        cout << "<p class=\"pp_singleton_header\">singleton"
+             << (m_collection.end() - ppWithSameTarget==1?"":"s") << " ("
+             << (m_collection.end() - ppWithSameTarget)
+             << "/" << m_size << ")</p>";
+      } else {
+        cout << "<p class=\"pp_target_header\">";
+        (*(ppWithSameTarget->begin()))->PrintTarget( &cout );
+        cout << " (" << count << "/" << m_size << ")" << endl;
+        cout << "<p><div id=\"pp_" << pp_target << "\">";
+      }
+      cout << "<table align=\"center\">";
+    }
 
     vector< PhrasePair* >::const_iterator p;
-		// loop over all sentences where translation occurs
+    // loop over all sentences where translation occurs
     int pp=0;
-		int i=0;
+    int i=0;
     for(p = ppWithSameTarget->begin(); i<10 && pp<count && p != ppWithSameTarget->end(); p++, pp++, i++ ) {
       (*p)->PrintClippedHTML( &cout, 160 );
       if (count > m_max_example) {
@@ -159,54 +156,54 @@ void PhrasePairCollection::PrintHTML() const
         pp += count/m_max_example-1;
       }
     }
-		if (i == 10 && pp < count) {			
-			// extended table
-			cout << "<tr><td colspan=7 align=center class=\"pp_more\" onclick=\"javascript:document.getElementById('pp_" << pp_target << "').style.display = 'none'; document.getElementById('pp_ext_" << pp_target << "').style.display = 'block';\">(more)</td></tr></table></div>";
-			cout << "<div id=\"pp_ext_" << pp_target << "\" style=\"display:none;\";\">";
-			cout << "<table align=\"center\">";
-			for(i=0, pp=0, p = ppWithSameTarget->begin(); i<m_max_example && pp<count && p != ppWithSameTarget->end(); p++, pp++, i++ ) {
-				(*p)->PrintClippedHTML( &cout, 160 );
-				if (count > m_max_example) {
-					p += count/m_max_example-1;
-					pp += count/m_max_example-1;
-				}
-			}
-		}
-		if (!singleton) cout << "</table></div>\n";
-		
-		if (!singleton && pp_target == 9) {
-			cout << "<div id=\"pp_toggle\" onclick=\"javascript:document.getElementById('pp_toggle').style.display = 'none'; document.getElementById('pp_additional').style.display = 'block';\">";
-			cout << "<p class=\"pp_target_header\">(more)</p></div>";
-			cout << "<div id=\"pp_additional\" style=\"display:none;\";\">";
-		}
+    if (i == 10 && pp < count) {
+      // extended table
+      cout << "<tr><td colspan=7 align=center class=\"pp_more\" onclick=\"javascript:document.getElementById('pp_" << pp_target << "').style.display = 'none'; document.getElementById('pp_ext_" << pp_target << "').style.display = 'block';\">(more)</td></tr></table></div>";
+      cout << "<div id=\"pp_ext_" << pp_target << "\" style=\"display:none;\";\">";
+      cout << "<table align=\"center\">";
+      for(i=0, pp=0, p = ppWithSameTarget->begin(); i<m_max_example && pp<count && p != ppWithSameTarget->end(); p++, pp++, i++ ) {
+        (*p)->PrintClippedHTML( &cout, 160 );
+        if (count > m_max_example) {
+          p += count/m_max_example-1;
+          pp += count/m_max_example-1;
+        }
+      }
+    }
+    if (!singleton) cout << "</table></div>\n";
+
+    if (!singleton && pp_target == 9) {
+      cout << "<div id=\"pp_toggle\" onclick=\"javascript:document.getElementById('pp_toggle').style.display = 'none'; document.getElementById('pp_additional').style.display = 'block';\">";
+      cout << "<p class=\"pp_target_header\">(more)</p></div>";
+      cout << "<div id=\"pp_additional\" style=\"display:none;\";\">";
+    }
+  }
+  if (singleton) cout << "</table></div>\n";
+  else if (pp_target > 9)	cout << "</div>";
+
+  size_t max_mismatch = m_max_example/3;
+  // unaligned phrases
+  if (m_unaligned.size() > 0) {
+    cout << "<p class=\"pp_singleton_header\">unaligned"
+         << " (" << (m_unaligned.size()) << ")</p>";
+    cout << "<table align=\"center\">";
+    int step_size = 1;
+    if (m_unaligned.size() > max_mismatch)
+      step_size = (m_unaligned.size()+max_mismatch-1) / max_mismatch;
+    for(size_t i=0; i<m_unaligned.size(); i+=step_size)
+      m_unaligned[i]->PrintClippedHTML( &cout, 160 );
+    cout << "</table>";
+  }
+
+  // mismatched phrases
+  if (m_mismatch.size() > 0) {
+    cout << "<p class=\"pp_singleton_header\">mismatched"
+         << " (" << (m_mismatch.size()) << ")</p>";
+    cout << "<table align=\"center\">";
+    int step_size = 1;
+    if (m_mismatch.size() > max_mismatch)
+      step_size = (m_mismatch.size()+max_mismatch-1) / max_mismatch;
+    for(size_t i=0; i<m_mismatch.size(); i+=step_size)
+      m_mismatch[i]->PrintClippedHTML( &cout, 160 );
+    cout << "</table>";
   }
-	if (singleton) cout << "</table></div>\n";
-	else if (pp_target > 9)	cout << "</div>";
-
-	size_t max_mismatch = m_max_example/3;
-	// unaligned phrases
-	if (m_unaligned.size() > 0) {
-		cout << "<p class=\"pp_singleton_header\">unaligned" 
-				 << " (" << (m_unaligned.size()) << ")</p>";
-		cout << "<table align=\"center\">";
-		int step_size = 1;
-		if (m_unaligned.size() > max_mismatch)
-			step_size = (m_unaligned.size()+max_mismatch-1) / max_mismatch;
-		for(size_t i=0;i<m_unaligned.size();i+=step_size)
-			m_unaligned[i]->PrintClippedHTML( &cout, 160 );
-		cout << "</table>";
-	}
-
-	// mismatched phrases
-	if (m_mismatch.size() > 0) {
-		cout << "<p class=\"pp_singleton_header\">mismatched" 
-				 << " (" << (m_mismatch.size()) << ")</p>";
-		cout << "<table align=\"center\">";
-		int step_size = 1;
-		if (m_mismatch.size() > max_mismatch)
-			step_size = (m_mismatch.size()+max_mismatch-1) / max_mismatch;
-		for(size_t i=0;i<m_mismatch.size();i+=step_size)
-			m_mismatch[i]->PrintClippedHTML( &cout, 160 );
-		cout << "</table>";
-	}	
 }
diff --git a/biconcor/SuffixArray.cpp b/biconcor/SuffixArray.cpp
index 15e6b47b0..f4122a2d8 100644
--- a/biconcor/SuffixArray.cpp
+++ b/biconcor/SuffixArray.cpp
@@ -5,7 +5,8 @@
 #include <stdlib.h>
 #include <cstring>
 
-namespace {
+namespace
+{
 
 const int LINE_MAX_LENGTH = 10000;
 
@@ -14,15 +15,15 @@ const int LINE_MAX_LENGTH = 10000;
 using namespace std;
 
 SuffixArray::SuffixArray()
-    : m_array(NULL),
-      m_index(NULL),
-      m_buffer(NULL),
-      m_wordInSentence(NULL),
-      m_sentence(NULL),
-      m_sentenceLength(NULL),
-      m_vcb(),
-      m_size(0),
-      m_sentenceCount(0) { }
+  : m_array(NULL),
+    m_index(NULL),
+    m_buffer(NULL),
+    m_wordInSentence(NULL),
+    m_sentence(NULL),
+    m_sentenceLength(NULL),
+    m_vcb(),
+    m_size(0),
+    m_sentenceCount(0) { }
 
 SuffixArray::~SuffixArray()
 {
diff --git a/biconcor/TargetCorpus.cpp b/biconcor/TargetCorpus.cpp
index d331a548a..06468007f 100644
--- a/biconcor/TargetCorpus.cpp
+++ b/biconcor/TargetCorpus.cpp
@@ -5,7 +5,8 @@
 #include <stdlib.h>
 #include <cstring>
 
-namespace {
+namespace
+{
 
 const int LINE_MAX_LENGTH = 10000;
 
@@ -14,11 +15,11 @@ const int LINE_MAX_LENGTH = 10000;
 using namespace std;
 
 TargetCorpus::TargetCorpus()
-    : m_array(NULL),
-      m_sentenceEnd(NULL),
-      m_vcb(),
-      m_size(0),
-      m_sentenceCount(0) {}
+  : m_array(NULL),
+    m_sentenceEnd(NULL),
+    m_vcb(),
+    m_size(0),
+    m_sentenceCount(0) {}
 
 TargetCorpus::~TargetCorpus()
 {
diff --git a/biconcor/Vocabulary.cpp b/biconcor/Vocabulary.cpp
index 9c35b3feb..9d52ee44e 100644
--- a/biconcor/Vocabulary.cpp
+++ b/biconcor/Vocabulary.cpp
@@ -2,7 +2,8 @@
 #include "Vocabulary.h"

 #include <fstream>

 

-namespace {

+namespace

+{

 

 const int MAX_LENGTH = 10000;

 

diff --git a/biconcor/base64.cpp b/biconcor/base64.cpp
index 2a863d161..8032399b5 100644
--- a/biconcor/base64.cpp
+++ b/biconcor/base64.cpp
@@ -1,4 +1,4 @@
-/* 
+/*
    base64.cpp and base64.h
 
    Copyright (C) 2004-2008 René Nyffenegger
@@ -28,17 +28,19 @@
 #include "base64.h"
 #include <iostream>
 
-static const std::string base64_chars = 
-             "ABCDEFGHIJKLMNOPQRSTUVWXYZ"
-             "abcdefghijklmnopqrstuvwxyz"
-             "0123456789+/";
+static const std::string base64_chars =
+  "ABCDEFGHIJKLMNOPQRSTUVWXYZ"
+  "abcdefghijklmnopqrstuvwxyz"
+  "0123456789+/";
 
 
-static inline bool is_base64(unsigned char c) {
+static inline bool is_base64(unsigned char c)
+{
   return (isalnum(c) || (c == '+') || (c == '/'));
 }
 
-std::string base64_encode(unsigned char const* bytes_to_encode, unsigned int in_len) {
+std::string base64_encode(unsigned char const* bytes_to_encode, unsigned int in_len)
+{
   std::string ret;
   int i = 0;
   int j = 0;
@@ -59,8 +61,7 @@ std::string base64_encode(unsigned char const* bytes_to_encode, unsigned int in_
     }
   }
 
-  if (i)
-  {
+  if (i) {
     for(j = i; j < 3; j++)
       char_array_3[j] = '\0';
 
@@ -81,7 +82,8 @@ std::string base64_encode(unsigned char const* bytes_to_encode, unsigned int in_
 
 }
 
-std::string base64_decode(std::string const& encoded_string) {
+std::string base64_decode(std::string const& encoded_string)
+{
   int in_len = encoded_string.size();
   int i = 0;
   int j = 0;
@@ -90,7 +92,8 @@ std::string base64_decode(std::string const& encoded_string) {
   std::string ret;
 
   while (in_len-- && ( encoded_string[in_] != '=') && is_base64(encoded_string[in_])) {
-    char_array_4[i++] = encoded_string[in_]; in_++;
+    char_array_4[i++] = encoded_string[in_];
+    in_++;
     if (i ==4) {
       for (i = 0; i <4; i++)
         char_array_4[i] = base64_chars.find(char_array_4[i]);
diff --git a/biconcor/biconcor.cpp b/biconcor/biconcor.cpp
index f4e7c03fb..cb63e855d 100644
--- a/biconcor/biconcor.cpp
+++ b/biconcor/biconcor.cpp
@@ -150,22 +150,19 @@ int main(int argc, char* argv[])
       cout << "TOTAL: " << total << endl;
       if (htmlFlag) {
         ppCollection.PrintHTML();
-      }
-      else {
-	ppCollection.Print(prettyFlag);
+      } else {
+        ppCollection.Print(prettyFlag);
       }
       cout << "-|||- BICONCOR END -|||-" << endl << flush;
     }
-  }
-  else if (queryFlag) {
+  } else if (queryFlag) {
     cerr << "query is " << query << endl;
     vector< string > queryString = alignment.Tokenize( query.c_str() );
     PhrasePairCollection ppCollection( &suffixArray, &targetCorpus, &alignment, max_translation, max_example );
     ppCollection.GetCollection( queryString );
     if (htmlFlag) {
       ppCollection.PrintHTML();
-    }
-    else {
+    } else {
       ppCollection.Print(prettyFlag);
     }
   }
diff --git a/defer/PhraseDictionaryInterpolated.cpp b/defer/PhraseDictionaryInterpolated.cpp
index 764927081..93c74d956 100644
--- a/defer/PhraseDictionaryInterpolated.cpp
+++ b/defer/PhraseDictionaryInterpolated.cpp
@@ -29,155 +29,158 @@ using namespace std;
 namespace Moses
 {
 
-  PhraseDictionaryInterpolated::PhraseDictionaryInterpolated
-    (size_t numScoreComponent,size_t numInputScores,const PhraseDictionaryFeature* feature):
-    PhraseDictionary(numScoreComponent,feature),
-    m_targetPhrases(NULL),
-    m_languageModels(NULL) {}
-
-  bool PhraseDictionaryInterpolated::Load(
-              const std::vector<FactorType> &input
-            , const std::vector<FactorType> &output
-            , const std::vector<std::string>& config
-            , const std::vector<float> &weightT
-            , size_t tableLimit
-            , const LMList &languageModels
-            , float weightWP) {
-
-    m_languageModels = &languageModels;
-    m_weightT = weightT;
-    m_tableLimit = tableLimit;
-    m_weightWP = weightWP;
-
-    //The config should be as follows:
-    //0-3: type factor factor num-components (as usual)
-    //4: combination mode (e.g. naive)
-    //5-(length-2): List of phrase-table files
-    //length-1: Weight string, in the same format as used for tmcombine
-
-    UTIL_THROW_IF(config.size() < 7, util::Exception, "Missing fields from phrase table configuration: expected at least 7");
-    UTIL_THROW_IF(config[4] != "naive", util::Exception, "Unsupported combination mode: '" << config[4] << "'");
-    
-    // Create the dictionaries
-    for (size_t i = 5; i < config.size()-1; ++i) {
-      m_dictionaries.push_back(DictionaryHandle(new PhraseDictionaryTreeAdaptor(
-        GetFeature()->GetNumScoreComponents(),
-        GetFeature()->GetNumInputScores(),
-        GetFeature())));
-      bool ret = m_dictionaries.back()->Load(
-        input,
-        output,
-        config[i],
-        weightT,
-        0,
-        languageModels,
-        weightWP);
-      if (!ret) return ret;
-    }
-
-    //Parse the weight strings
-    for (util::TokenIter<util::SingleCharacter, false> featureWeights(config.back(), util::SingleCharacter(';')); featureWeights; ++featureWeights) {
-      m_weights.push_back(vector<float>());
-      float sum = 0;
-      for (util::TokenIter<util::SingleCharacter, false> tableWeights(*featureWeights, util::SingleCharacter(',')); tableWeights; ++tableWeights) {
-        const float weight = boost::lexical_cast<float>(*tableWeights);
-        m_weights.back().push_back(weight);
-        sum += weight;
-      }
-      UTIL_THROW_IF(m_weights.back().size() != m_dictionaries.size(), util::Exception,
-        "Number of weights (" << m_weights.back().size() << 
-        ") does not match number of dictionaries to combine (" << m_dictionaries.size() << ")");
-      UTIL_THROW_IF(abs(sum - 1) > 0.01, util::Exception, "Weights not normalised");
+PhraseDictionaryInterpolated::PhraseDictionaryInterpolated
+(size_t numScoreComponent,size_t numInputScores,const PhraseDictionaryFeature* feature):
+  PhraseDictionary(numScoreComponent,feature),
+  m_targetPhrases(NULL),
+  m_languageModels(NULL) {}
+
+bool PhraseDictionaryInterpolated::Load(
+  const std::vector<FactorType> &input
+  , const std::vector<FactorType> &output
+  , const std::vector<std::string>& config
+  , const std::vector<float> &weightT
+  , size_t tableLimit
+  , const LMList &languageModels
+  , float weightWP)
+{
 
-    }
+  m_languageModels = &languageModels;
+  m_weightT = weightT;
+  m_tableLimit = tableLimit;
+  m_weightWP = weightWP;
+
+  //The config should be as follows:
+  //0-3: type factor factor num-components (as usual)
+  //4: combination mode (e.g. naive)
+  //5-(length-2): List of phrase-table files
+  //length-1: Weight string, in the same format as used for tmcombine
+
+  UTIL_THROW_IF(config.size() < 7, util::Exception, "Missing fields from phrase table configuration: expected at least 7");
+  UTIL_THROW_IF(config[4] != "naive", util::Exception, "Unsupported combination mode: '" << config[4] << "'");
+
+  // Create the dictionaries
+  for (size_t i = 5; i < config.size()-1; ++i) {
+    m_dictionaries.push_back(DictionaryHandle(new PhraseDictionaryTreeAdaptor(
+                               GetFeature()->GetNumScoreComponents(),
+                               GetFeature()->GetNumInputScores(),
+                               GetFeature())));
+    bool ret = m_dictionaries.back()->Load(
+                 input,
+                 output,
+                 config[i],
+                 weightT,
+                 0,
+                 languageModels,
+                 weightWP);
+    if (!ret) return ret;
+  }
 
-    //check number of weight sets. Make sure there is a weight for every score component
-    //except for the last - which is assumed to be the phrase penalty.
-    UTIL_THROW_IF(m_weights.size() != 1 && m_weights.size() != GetFeature()->GetNumScoreComponents()-1, util::Exception, "Unexpected number of weight sets");
-    //if 1 weight set, then repeat
-    if (m_weights.size() == 1) {
-      while(m_weights.size() < GetFeature()->GetNumScoreComponents()-1) {
-        m_weights.push_back(m_weights[0]);
-      }
+  //Parse the weight strings
+  for (util::TokenIter<util::SingleCharacter, false> featureWeights(config.back(), util::SingleCharacter(';')); featureWeights; ++featureWeights) {
+    m_weights.push_back(vector<float>());
+    float sum = 0;
+    for (util::TokenIter<util::SingleCharacter, false> tableWeights(*featureWeights, util::SingleCharacter(',')); tableWeights; ++tableWeights) {
+      const float weight = boost::lexical_cast<float>(*tableWeights);
+      m_weights.back().push_back(weight);
+      sum += weight;
     }
+    UTIL_THROW_IF(m_weights.back().size() != m_dictionaries.size(), util::Exception,
+                  "Number of weights (" << m_weights.back().size() <<
+                  ") does not match number of dictionaries to combine (" << m_dictionaries.size() << ")");
+    UTIL_THROW_IF(abs(sum - 1) > 0.01, util::Exception, "Weights not normalised");
 
-    return true;
   }
 
-  void PhraseDictionaryInterpolated::InitializeForInput(InputType const& source) {
-    for (size_t i = 0; i < m_dictionaries.size(); ++i) {
-      m_dictionaries[i]->InitializeForInput(source);
+  //check number of weight sets. Make sure there is a weight for every score component
+  //except for the last - which is assumed to be the phrase penalty.
+  UTIL_THROW_IF(m_weights.size() != 1 && m_weights.size() != GetFeature()->GetNumScoreComponents()-1, util::Exception, "Unexpected number of weight sets");
+  //if 1 weight set, then repeat
+  if (m_weights.size() == 1) {
+    while(m_weights.size() < GetFeature()->GetNumScoreComponents()-1) {
+      m_weights.push_back(m_weights[0]);
     }
   }
 
-  typedef 
-    boost::unordered_set<TargetPhrase*,PhrasePtrHasher,PhrasePtrComparator> PhraseSet;
-    
-
-  const TargetPhraseCollection*
-     PhraseDictionaryInterpolated::GetTargetPhraseCollection(const Phrase& src) const {
-
-    delete m_targetPhrases;
-    m_targetPhrases = new TargetPhraseCollection();
-    PhraseSet allPhrases;
-    vector<PhraseSet> phrasesByTable(m_dictionaries.size());
-    for (size_t i = 0; i < m_dictionaries.size(); ++i) {
-      const TargetPhraseCollection* phrases = m_dictionaries[i]->GetTargetPhraseCollection(src);
-      if (phrases) {
-        for (TargetPhraseCollection::const_iterator j = phrases->begin(); 
-          j != phrases->end(); ++j) {
-          allPhrases.insert(*j);
-          phrasesByTable[i].insert(*j);
-        }
+  return true;
+}
+
+void PhraseDictionaryInterpolated::InitializeForInput(InputType const& source)
+{
+  for (size_t i = 0; i < m_dictionaries.size(); ++i) {
+    m_dictionaries[i]->InitializeForInput(source);
+  }
+}
+
+typedef
+boost::unordered_set<TargetPhrase*,PhrasePtrHasher,PhrasePtrComparator> PhraseSet;
+
+
+const TargetPhraseCollection*
+PhraseDictionaryInterpolated::GetTargetPhraseCollection(const Phrase& src) const
+{
+
+  delete m_targetPhrases;
+  m_targetPhrases = new TargetPhraseCollection();
+  PhraseSet allPhrases;
+  vector<PhraseSet> phrasesByTable(m_dictionaries.size());
+  for (size_t i = 0; i < m_dictionaries.size(); ++i) {
+    const TargetPhraseCollection* phrases = m_dictionaries[i]->GetTargetPhraseCollection(src);
+    if (phrases) {
+      for (TargetPhraseCollection::const_iterator j = phrases->begin();
+           j != phrases->end(); ++j) {
+        allPhrases.insert(*j);
+        phrasesByTable[i].insert(*j);
       }
     }
-    ScoreComponentCollection sparseVector;
-    for (PhraseSet::const_iterator i = allPhrases.begin(); i != allPhrases.end(); ++i) {
-      TargetPhrase* combinedPhrase = new TargetPhrase((Phrase)**i);
-      //combinedPhrase->ResetScore();
-      //cerr << *combinedPhrase << " " << combinedPhrase->GetScoreBreakdown() << endl;
-      combinedPhrase->SetSourcePhrase((*i)->GetSourcePhrase());
-      combinedPhrase->SetAlignTerm(&((*i)->GetAlignTerm()));
-      combinedPhrase->SetAlignNonTerm(&((*i)->GetAlignTerm()));
-      Scores combinedScores(GetFeature()->GetNumScoreComponents());
-      for (size_t j = 0; j < phrasesByTable.size(); ++j) {
-        PhraseSet::const_iterator tablePhrase = phrasesByTable[j].find(combinedPhrase);
-        if (tablePhrase != phrasesByTable[j].end()) {
-          Scores tableScores = (*tablePhrase)->GetScoreBreakdown()
-            .GetScoresForProducer(GetFeature());
-          //cerr << "Scores from " << j << " table: ";
-          for (size_t k = 0; k < tableScores.size()-1; ++k) {
-            //cerr << tableScores[k] << "(" << exp(tableScores[k]) << ") ";
-            combinedScores[k] += m_weights[k][j] * exp(tableScores[k]);
-            //cerr << m_weights[k][j] * exp(tableScores[k]) << " ";
-          }
-          //cerr << endl;
+  }
+  ScoreComponentCollection sparseVector;
+  for (PhraseSet::const_iterator i = allPhrases.begin(); i != allPhrases.end(); ++i) {
+    TargetPhrase* combinedPhrase = new TargetPhrase((Phrase)**i);
+    //combinedPhrase->ResetScore();
+    //cerr << *combinedPhrase << " " << combinedPhrase->GetScoreBreakdown() << endl;
+    combinedPhrase->SetSourcePhrase((*i)->GetSourcePhrase());
+    combinedPhrase->SetAlignTerm(&((*i)->GetAlignTerm()));
+    combinedPhrase->SetAlignNonTerm(&((*i)->GetAlignTerm()));
+    Scores combinedScores(GetFeature()->GetNumScoreComponents());
+    for (size_t j = 0; j < phrasesByTable.size(); ++j) {
+      PhraseSet::const_iterator tablePhrase = phrasesByTable[j].find(combinedPhrase);
+      if (tablePhrase != phrasesByTable[j].end()) {
+        Scores tableScores = (*tablePhrase)->GetScoreBreakdown()
+                             .GetScoresForProducer(GetFeature());
+        //cerr << "Scores from " << j << " table: ";
+        for (size_t k = 0; k < tableScores.size()-1; ++k) {
+          //cerr << tableScores[k] << "(" << exp(tableScores[k]) << ") ";
+          combinedScores[k] += m_weights[k][j] * exp(tableScores[k]);
+          //cerr << m_weights[k][j] * exp(tableScores[k]) << " ";
         }
+        //cerr << endl;
       }
-      //map back to log space
-      //cerr << "Combined ";
-      for (size_t k = 0; k < combinedScores.size()-1; ++k) {
-        //cerr << combinedScores[k] << " ";
-        combinedScores[k] = log(combinedScores[k]);
-        //cerr << combinedScores[k] << " ";
-      }
-      //cerr << endl;
-      combinedScores.back() = 1; //assume last is penalty
-      combinedPhrase->SetScore(
-        GetFeature(),
-        combinedScores,
-        sparseVector,
-        m_weightT,
-        m_weightWP,
-        *m_languageModels);
-      //cerr << *combinedPhrase << " " << combinedPhrase->GetScoreBreakdown() <<  endl;
-      m_targetPhrases->Add(combinedPhrase);
     }
+    //map back to log space
+    //cerr << "Combined ";
+    for (size_t k = 0; k < combinedScores.size()-1; ++k) {
+      //cerr << combinedScores[k] << " ";
+      combinedScores[k] = log(combinedScores[k]);
+      //cerr << combinedScores[k] << " ";
+    }
+    //cerr << endl;
+    combinedScores.back() = 1; //assume last is penalty
+    combinedPhrase->SetScore(
+      GetFeature(),
+      combinedScores,
+      sparseVector,
+      m_weightT,
+      m_weightWP,
+      *m_languageModels);
+    //cerr << *combinedPhrase << " " << combinedPhrase->GetScoreBreakdown() <<  endl;
+    m_targetPhrases->Add(combinedPhrase);
+  }
 
-    m_targetPhrases->Prune(true,m_tableLimit);
+  m_targetPhrases->Prune(true,m_tableLimit);
 
 
-    return m_targetPhrases;
-  }
+  return m_targetPhrases;
+}
 
 }
diff --git a/defer/PhraseDictionaryInterpolated.h b/defer/PhraseDictionaryInterpolated.h
index 74add1833..9bb4dcc3c 100644
--- a/defer/PhraseDictionaryInterpolated.h
+++ b/defer/PhraseDictionaryInterpolated.h
@@ -34,12 +34,14 @@ namespace Moses
   **/
 class PhraseDictionaryInterpolated : public PhraseDictionary
 {
-  public:
+public:
 
   PhraseDictionaryInterpolated
-    (size_t numScoreComponent,size_t numInputScores,const PhraseDictionaryFeature* feature);
+  (size_t numScoreComponent,size_t numInputScores,const PhraseDictionaryFeature* feature);
 
-  virtual ~PhraseDictionaryInterpolated() {delete m_targetPhrases;}
+  virtual ~PhraseDictionaryInterpolated() {
+    delete m_targetPhrases;
+  }
 
   // initialize ...
   bool Load(const std::vector<FactorType> &input
@@ -58,7 +60,7 @@ class PhraseDictionaryInterpolated : public PhraseDictionary
     throw std::logic_error("PhraseDictionaryInterpolated.CreateRuleLookupManager() Not implemented");
   }
 
-  private:
+private:
 
   typedef boost::shared_ptr<PhraseDictionaryTreeAdaptor> DictionaryHandle;
   std::vector<DictionaryHandle> m_dictionaries;
diff --git a/defer/PhraseLengthFeatureTest.cpp b/defer/PhraseLengthFeatureTest.cpp
index 42026e805..6fb15e71e 100644
--- a/defer/PhraseLengthFeatureTest.cpp
+++ b/defer/PhraseLengthFeatureTest.cpp
@@ -31,7 +31,8 @@ BOOST_AUTO_TEST_SUITE(phrase_length_feature)
 
 //TODO: Factor out setup code so that it can be reused
 
-static Word MakeWord(string text) {
+static Word MakeWord(string text)
+{
   FactorCollection &factorCollection = FactorCollection::Instance();
   const Factor* f = factorCollection.AddFactor(Input,0,text);
   Word w;
@@ -40,7 +41,8 @@ static Word MakeWord(string text) {
 }
 
 
-BOOST_AUTO_TEST_CASE(evaluate) {
+BOOST_AUTO_TEST_CASE(evaluate)
+{
   Word w1 = MakeWord("w1");
   Word w2 = MakeWord("y2");
   Word w3 = MakeWord("x3");
@@ -78,7 +80,7 @@ BOOST_AUTO_TEST_CASE(evaluate) {
   PhraseBasedFeatureContext context1(topt1,sentence);
   PhraseBasedFeatureContext context2(topt2,sentence);
   PhraseBasedFeatureContext context3(topt3,sentence);
-     
+
   PhraseLengthFeature plf;
 
   ScoreComponentCollection acc1,acc2,acc3;
diff --git a/defer/TargetBigramFeatureTest.cpp b/defer/TargetBigramFeatureTest.cpp
index 4b8d00800..c651c8ed9 100644
--- a/defer/TargetBigramFeatureTest.cpp
+++ b/defer/TargetBigramFeatureTest.cpp
@@ -34,12 +34,13 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 using namespace std;
 using namespace Moses;
 
-namespace MosesTest 
+namespace MosesTest
 {
 
 BOOST_AUTO_TEST_SUITE(target_bigram)
 
-static Word MakeWord(string text) {
+static Word MakeWord(string text)
+{
   FactorCollection &factorCollection = FactorCollection::Instance();
   const Factor* f = factorCollection.AddFactor(Input,0,text);
   Word w;
@@ -47,34 +48,32 @@ static Word MakeWord(string text) {
   return w;
 }
 
-class VocabFileFixture {
-  public:
-    template<class I>
-    VocabFileFixture(I begin, I end) 
-    {
-      char name[] = "TargetBigramXXXXXX";
-      int fd = mkstemp(name);
-      BOOST_CHECK(fd != -1);
-      BOOST_CHECK(!close(fd));
-      filename = name;
-      ofstream out(name);
-      for (I i = begin; i != end; ++i) 
-      {
-        out << *i << endl;
-      }
-      out.close();
+class VocabFileFixture
+{
+public:
+  template<class I>
+  VocabFileFixture(I begin, I end) {
+    char name[] = "TargetBigramXXXXXX";
+    int fd = mkstemp(name);
+    BOOST_CHECK(fd != -1);
+    BOOST_CHECK(!close(fd));
+    filename = name;
+    ofstream out(name);
+    for (I i = begin; i != end; ++i) {
+      out << *i << endl;
     }
+    out.close();
+  }
 
-    ~VocabFileFixture() 
-    {
-      BOOST_CHECK(!remove(filename.c_str()));
-    }
+  ~VocabFileFixture() {
+    BOOST_CHECK(!remove(filename.c_str()));
+  }
 
-    string filename;
+  string filename;
 };
 
 /*
-BOOST_AUTO_TEST_CASE(Test2) 
+BOOST_AUTO_TEST_CASE(Test2)
 {
   HypothesisFixture hypos;
   cerr << hypos.empty() << ", " << *hypos.empty() << endl;
@@ -113,7 +112,7 @@ BOOST_AUTO_TEST_CASE(score_components)
     ScoreProducer::unlimited);
 }
 
-BOOST_AUTO_TEST_CASE(empty_hypo) 
+BOOST_AUTO_TEST_CASE(empty_hypo)
 {
   Sentence s;
   TargetBigramFeature tbf;
@@ -124,7 +123,7 @@ BOOST_AUTO_TEST_CASE(empty_hypo)
 }
 
 //Test of evaluate() where a vocab is specified
-BOOST_AUTO_TEST_CASE(evaluate_vocab) 
+BOOST_AUTO_TEST_CASE(evaluate_vocab)
 {
   string vocab[] = {"i", "do"};
   VocabFileFixture vocabFile(vocab,vocab+2);
@@ -156,7 +155,7 @@ BOOST_AUTO_TEST_CASE(evaluate_all)
   BOOST_CHECK_EQUAL(scc.GetScoreForProducer(&tbf, "do:not"),1);
   BOOST_CHECK_EQUAL(scc.GetScoreForProducer(&tbf, "not:</s>"),0);
   BOOST_CHECK(! currState->Compare(TargetBigramState(MakeWord("not"))));
-  
+
 }
 
 BOOST_AUTO_TEST_CASE(evaluate_empty)
@@ -171,7 +170,7 @@ BOOST_AUTO_TEST_CASE(evaluate_empty)
   BOOST_CHECK(! currState->Compare(*prevState));
 }
 
-BOOST_AUTO_TEST_CASE(evaluate_eos) 
+BOOST_AUTO_TEST_CASE(evaluate_eos)
 {
   HypothesisFixture hypos;
   TargetBigramFeature tbf;
diff --git a/mert/BleuScorer.cpp b/mert/BleuScorer.cpp
index 26723d36b..1d5caa394 100644
--- a/mert/BleuScorer.cpp
+++ b/mert/BleuScorer.cpp
@@ -18,7 +18,8 @@
 
 using namespace std;
 
-namespace {
+namespace
+{
 
 // configure regularisation
 const char KEY_REFLEN[] = "reflen";
@@ -33,8 +34,9 @@ namespace MosesTuning
 
 
 BleuScorer::BleuScorer(const string& config)
-    : StatisticsBasedScorer("BLEU", config),
-      m_ref_length_type(CLOSEST) {
+  : StatisticsBasedScorer("BLEU", config),
+    m_ref_length_type(CLOSEST)
+{
   const string reflen = getConfig(KEY_REFLEN, REFLEN_CLOSEST);
   if (reflen == REFLEN_AVERAGE) {
     m_ref_length_type = AVERAGE;
@@ -101,7 +103,8 @@ void BleuScorer::setReferenceFiles(const vector<string>& referenceFiles)
   }
 }
 
-bool BleuScorer::OpenReference(const char* filename, size_t file_id) {
+bool BleuScorer::OpenReference(const char* filename, size_t file_id)
+{
   ifstream ifs(filename);
   if (!ifs) {
     cerr << "Cannot open " << filename << endl;
@@ -110,7 +113,8 @@ bool BleuScorer::OpenReference(const char* filename, size_t file_id) {
   return OpenReferenceStream(&ifs, file_id);
 }
 
-bool BleuScorer::OpenReferenceStream(istream* is, size_t file_id) {
+bool BleuScorer::OpenReferenceStream(istream* is, size_t file_id)
+{
   if (is == NULL) return false;
 
   string line;
@@ -203,25 +207,27 @@ statscore_t BleuScorer::calculateScore(const vector<int>& comps) const
   return exp(logbleu);
 }
 
-int BleuScorer::CalcReferenceLength(size_t sentence_id, size_t length) {
+int BleuScorer::CalcReferenceLength(size_t sentence_id, size_t length)
+{
   switch (m_ref_length_type) {
-    case AVERAGE:
-      return m_references[sentence_id]->CalcAverage();
-      break;
-    case CLOSEST:
-      return m_references[sentence_id]->CalcClosest(length);
-      break;
-    case SHORTEST:
-      return m_references[sentence_id]->CalcShortest();
-      break;
-    default:
-      cerr << "unknown reference types." << endl;
-      exit(1);
+  case AVERAGE:
+    return m_references[sentence_id]->CalcAverage();
+    break;
+  case CLOSEST:
+    return m_references[sentence_id]->CalcClosest(length);
+    break;
+  case SHORTEST:
+    return m_references[sentence_id]->CalcShortest();
+    break;
+  default:
+    cerr << "unknown reference types." << endl;
+    exit(1);
   }
 }
 
 void BleuScorer::DumpCounts(ostream* os,
-                            const NgramCounts& counts) const {
+                            const NgramCounts& counts) const
+{
   for (NgramCounts::const_iterator it = counts.begin();
        it != counts.end(); ++it) {
     *os << "(";
@@ -238,7 +244,8 @@ void BleuScorer::DumpCounts(ostream* os,
 }
 
 float smoothedSentenceBleu
-  (const std::vector<float>& stats, float smoothing, bool smoothBP) {
+(const std::vector<float>& stats, float smoothing, bool smoothBP)
+{
 
   CHECK(stats.size() == kBleuNgramOrder * 2 + 1);
 
@@ -247,8 +254,8 @@ float smoothedSentenceBleu
     logbleu += log(stats[2 * j] + smoothing) - log(stats[2 * j + 1] + smoothing);
   }
   logbleu /= kBleuNgramOrder;
-  const float reflength = stats[(kBleuNgramOrder * 2)]  + 
-    (smoothBP ? smoothing : 0.0f);
+  const float reflength = stats[(kBleuNgramOrder * 2)]  +
+                          (smoothBP ? smoothing : 0.0f);
   const float brevity = 1.0 - reflength / stats[1];
 
   if (brevity < 0.0) {
@@ -263,7 +270,7 @@ float sentenceLevelBackgroundBleu(const std::vector<float>& sent, const std::vec
   std::vector<float> stats;
   CHECK(sent.size()==bg.size());
   CHECK(sent.size()==kBleuNgramOrder*2+1);
-  for(size_t i=0;i<sent.size();i++)
+  for(size_t i=0; i<sent.size(); i++)
     stats.push_back(sent[i]+bg[i]);
 
   // Calculate BLEU
@@ -282,7 +289,8 @@ float sentenceLevelBackgroundBleu(const std::vector<float>& sent, const std::vec
   return exp(logbleu) * stats[kBleuNgramOrder*2];
 }
 
-float unsmoothedBleu(const std::vector<float>& stats) {
+float unsmoothedBleu(const std::vector<float>& stats)
+{
   CHECK(stats.size() == kBleuNgramOrder * 2 + 1);
 
   float logbleu = 0.0;
@@ -298,50 +306,51 @@ float unsmoothedBleu(const std::vector<float>& stats) {
   return exp(logbleu);
 }
 
-vector<float> BleuScorer::ScoreNbestList(const string& scoreFile, const string& featureFile) {
-	vector<string> scoreFiles;
-	vector<string> featureFiles;
-	scoreFiles.push_back(scoreFile);
-	featureFiles.push_back(featureFile);
-
-	vector<FeatureDataIterator> featureDataIters;
-	vector<ScoreDataIterator> scoreDataIters;
-	for (size_t i = 0; i < featureFiles.size(); ++i) {
-		featureDataIters.push_back(FeatureDataIterator(featureFiles[i]));
-	    scoreDataIters.push_back(ScoreDataIterator(scoreFiles[i]));
-	}
-
-	vector<pair<size_t,size_t> > hypotheses;
-	if (featureDataIters[0] == FeatureDataIterator::end()) {
-		cerr << "Error: at the end of feature data iterator" << endl;
-		exit(1);
-	}
-	for (size_t i = 0; i < featureFiles.size(); ++i) {
-		if (featureDataIters[i] == FeatureDataIterator::end()) {
-			cerr << "Error: Feature file " << i << " ended prematurely" << endl;
-	        exit(1);
-		}
-		if (scoreDataIters[i] == ScoreDataIterator::end()) {
-			cerr << "Error: Score file " << i << " ended prematurely" << endl;
-	        exit(1);
-	    }
-		if (featureDataIters[i]->size() != scoreDataIters[i]->size()) {
-			cerr << "Error: features and scores have different size" << endl;
-	        exit(1);
-		}
-		for (size_t j = 0; j < featureDataIters[i]->size(); ++j) {
-			hypotheses.push_back(pair<size_t,size_t>(i,j));
-	    }
-	}
-
-	// score the nbest list
-	vector<float> bleuScores;
-	for (size_t i=0; i < hypotheses.size(); ++i) {
-		pair<size_t,size_t> translation = hypotheses[i];
-		float bleu = smoothedSentenceBleu(scoreDataIters[translation.first]->operator[](translation.second));
-		bleuScores.push_back(bleu);
-	}
-	return bleuScores;
+vector<float> BleuScorer::ScoreNbestList(const string& scoreFile, const string& featureFile)
+{
+  vector<string> scoreFiles;
+  vector<string> featureFiles;
+  scoreFiles.push_back(scoreFile);
+  featureFiles.push_back(featureFile);
+
+  vector<FeatureDataIterator> featureDataIters;
+  vector<ScoreDataIterator> scoreDataIters;
+  for (size_t i = 0; i < featureFiles.size(); ++i) {
+    featureDataIters.push_back(FeatureDataIterator(featureFiles[i]));
+    scoreDataIters.push_back(ScoreDataIterator(scoreFiles[i]));
+  }
+
+  vector<pair<size_t,size_t> > hypotheses;
+  if (featureDataIters[0] == FeatureDataIterator::end()) {
+    cerr << "Error: at the end of feature data iterator" << endl;
+    exit(1);
+  }
+  for (size_t i = 0; i < featureFiles.size(); ++i) {
+    if (featureDataIters[i] == FeatureDataIterator::end()) {
+      cerr << "Error: Feature file " << i << " ended prematurely" << endl;
+      exit(1);
+    }
+    if (scoreDataIters[i] == ScoreDataIterator::end()) {
+      cerr << "Error: Score file " << i << " ended prematurely" << endl;
+      exit(1);
+    }
+    if (featureDataIters[i]->size() != scoreDataIters[i]->size()) {
+      cerr << "Error: features and scores have different size" << endl;
+      exit(1);
+    }
+    for (size_t j = 0; j < featureDataIters[i]->size(); ++j) {
+      hypotheses.push_back(pair<size_t,size_t>(i,j));
+    }
+  }
+
+  // score the nbest list
+  vector<float> bleuScores;
+  for (size_t i=0; i < hypotheses.size(); ++i) {
+    pair<size_t,size_t> translation = hypotheses[i];
+    float bleu = smoothedSentenceBleu(scoreDataIters[translation.first]->operator[](translation.second));
+    bleuScores.push_back(bleu);
+  }
+  return bleuScores;
 }
 
 
diff --git a/mert/BleuScorer.h b/mert/BleuScorer.h
index af889b13e..248b3e1d1 100644
--- a/mert/BleuScorer.h
+++ b/mert/BleuScorer.h
@@ -38,14 +38,22 @@ public:
   virtual void setReferenceFiles(const std::vector<std::string>& referenceFiles);
   virtual void prepareStats(std::size_t sid, const std::string& text, ScoreStats& entry);
   virtual statscore_t calculateScore(const std::vector<int>& comps) const;
-  virtual std::size_t NumberOfScores() const { return 2 * kBleuNgramOrder + 1; }
+  virtual std::size_t NumberOfScores() const {
+    return 2 * kBleuNgramOrder + 1;
+  }
 
   int CalcReferenceLength(std::size_t sentence_id, std::size_t length);
 
-  ReferenceLengthType GetReferenceLengthType() const { return m_ref_length_type; }
-  void SetReferenceLengthType(ReferenceLengthType type) { m_ref_length_type = type; }
+  ReferenceLengthType GetReferenceLengthType() const {
+    return m_ref_length_type;
+  }
+  void SetReferenceLengthType(ReferenceLengthType type) {
+    m_ref_length_type = type;
+  }
 
-  const std::vector<Reference*>& GetReferences() const { return m_references.get(); }
+  const std::vector<Reference*>& GetReferences() const {
+    return m_references.get();
+  }
 
   /**
    * Count the ngrams of each type, up to the given length in the input line.
@@ -74,7 +82,7 @@ private:
  * This function is used in PRO.
  */
 float smoothedSentenceBleu
-  (const std::vector<float>& stats, float smoothing=1.0, bool smoothBP=false);
+(const std::vector<float>& stats, float smoothing=1.0, bool smoothBP=false);
 
 /** Computes sentence-level BLEU score given a background corpus.
  * This function is used in batch MIRA.
diff --git a/mert/BleuScorerTest.cpp b/mert/BleuScorerTest.cpp
index 136f134eb..a63196a3b 100644
--- a/mert/BleuScorerTest.cpp
+++ b/mert/BleuScorerTest.cpp
@@ -10,16 +10,19 @@
 
 using namespace MosesTuning;
 
-namespace {
+namespace
+{
 
 NgramCounts* g_counts = NULL;
 
-NgramCounts* GetNgramCounts() {
+NgramCounts* GetNgramCounts()
+{
   assert(g_counts);
   return g_counts;
 }
 
-void SetNgramCounts(NgramCounts* counts) {
+void SetNgramCounts(NgramCounts* counts)
+{
   g_counts = counts;
 }
 
@@ -58,33 +61,38 @@ struct Fourgram {
   NgramCounts::Key instance;
 };
 
-bool CheckUnigram(const std::string& str) {
+bool CheckUnigram(const std::string& str)
+{
   Unigram unigram(str);
   NgramCounts::Value v;
   return GetNgramCounts()->Lookup(unigram.instance, &v);
 }
 
-bool CheckBigram(const std::string& a, const std::string& b) {
+bool CheckBigram(const std::string& a, const std::string& b)
+{
   Bigram bigram(a, b);
   NgramCounts::Value v;
   return GetNgramCounts()->Lookup(bigram.instance, &v);
 }
 
 bool CheckTrigram(const std::string& a, const std::string& b,
-                  const std::string& c) {
+                  const std::string& c)
+{
   Trigram trigram(a, b, c);
   NgramCounts::Value v;
   return GetNgramCounts()->Lookup(trigram.instance, &v);
 }
 
 bool CheckFourgram(const std::string& a, const std::string& b,
-                   const std::string& c, const std::string& d) {
+                   const std::string& c, const std::string& d)
+{
   Fourgram fourgram(a, b, c, d);
   NgramCounts::Value v;
   return GetNgramCounts()->Lookup(fourgram.instance, &v);
 }
 
-void SetUpReferences(BleuScorer& scorer) {
+void SetUpReferences(BleuScorer& scorer)
+{
   // The following examples are taken from Koehn, "Statistical Machine Translation",
   // Cambridge University Press, 2010.
   {
@@ -115,7 +123,8 @@ void SetUpReferences(BleuScorer& scorer) {
 
 } // namespace
 
-BOOST_AUTO_TEST_CASE(bleu_reference_type) {
+BOOST_AUTO_TEST_CASE(bleu_reference_type)
+{
   BleuScorer scorer;
   // BleuScorer will use "closest" by default.
   BOOST_CHECK_EQUAL(scorer.GetReferenceLengthType(), BleuScorer::CLOSEST);
@@ -127,7 +136,8 @@ BOOST_AUTO_TEST_CASE(bleu_reference_type) {
   BOOST_CHECK_EQUAL(scorer.GetReferenceLengthType(), BleuScorer::SHORTEST);
 }
 
-BOOST_AUTO_TEST_CASE(bleu_reference_type_with_config) {
+BOOST_AUTO_TEST_CASE(bleu_reference_type_with_config)
+{
   {
     BleuScorer scorer("reflen:average");
     BOOST_CHECK_EQUAL(scorer.GetReferenceLengthType(), BleuScorer::AVERAGE);
@@ -139,7 +149,8 @@ BOOST_AUTO_TEST_CASE(bleu_reference_type_with_config) {
   }
 }
 
-BOOST_AUTO_TEST_CASE(bleu_count_ngrams) {
+BOOST_AUTO_TEST_CASE(bleu_count_ngrams)
+{
   BleuScorer scorer;
 
   std::string line = "I saw a girl with a telescope .";
@@ -198,7 +209,8 @@ BOOST_AUTO_TEST_CASE(bleu_count_ngrams) {
   BOOST_CHECK(CheckFourgram("with", "a", "telescope", "."));
 }
 
-BOOST_AUTO_TEST_CASE(bleu_clipped_counts) {
+BOOST_AUTO_TEST_CASE(bleu_clipped_counts)
+{
   BleuScorer scorer;
   SetUpReferences(scorer);
   std::string line("israeli officials responsibility of airport safety");
@@ -220,7 +232,8 @@ BOOST_AUTO_TEST_CASE(bleu_clipped_counts) {
   BOOST_CHECK_EQUAL(entry.get(7), 3);  // fourgram
 }
 
-BOOST_AUTO_TEST_CASE(calculate_actual_score) {
+BOOST_AUTO_TEST_CASE(calculate_actual_score)
+{
   BOOST_REQUIRE(4 == kBleuNgramOrder);
   std::vector<int> stats(2 * kBleuNgramOrder + 1);
   BleuScorer scorer;
@@ -247,7 +260,8 @@ BOOST_AUTO_TEST_CASE(calculate_actual_score) {
   BOOST_CHECK_CLOSE(0.5115f, scorer.calculateScore(stats), 0.01);
 }
 
-BOOST_AUTO_TEST_CASE(sentence_level_bleu) {
+BOOST_AUTO_TEST_CASE(sentence_level_bleu)
+{
   BOOST_REQUIRE(4 == kBleuNgramOrder);
   std::vector<float> stats(2 * kBleuNgramOrder + 1);
 
diff --git a/mert/CderScorer.cpp b/mert/CderScorer.cpp
index cece29034..21a80ad52 100644
--- a/mert/CderScorer.cpp
+++ b/mert/CderScorer.cpp
@@ -6,9 +6,11 @@
 
 using namespace std;
 
-namespace {
+namespace
+{
 
-inline int CalcDistance(int word1, int word2) {
+inline int CalcDistance(int word1, int word2)
+{
   return word1 == word2 ? 0 : 1;
 }
 
@@ -16,11 +18,11 @@ inline int CalcDistance(int word1, int word2) {
 
 namespace MosesTuning
 {
-  
+
 
 CderScorer::CderScorer(const string& config, bool allowed_long_jumps)
-    : StatisticsBasedScorer(allowed_long_jumps ? "CDER" : "WER", config),
-      m_allowed_long_jumps(allowed_long_jumps) {}
+  : StatisticsBasedScorer(allowed_long_jumps ? "CDER" : "WER", config),
+    m_allowed_long_jumps(allowed_long_jumps) {}
 
 CderScorer::~CderScorer() {}
 
@@ -82,7 +84,8 @@ float CderScorer::calculateScore(const vector<int>& comps) const
 }
 
 void CderScorer::computeCD(const sent_t& cand, const sent_t& ref,
-                           vector<int>& stats) const {
+                           vector<int>& stats) const
+{
   int I = cand.size() + 1; // Number of inter-words positions in candidate sentence
   int L = ref.size() + 1; // Number of inter-words positions in reference sentence
 
@@ -95,11 +98,9 @@ void CderScorer::computeCD(const sent_t& cand, const sent_t& ref,
   for (int i = 1; i < I; ++i) (*row)[i] = 1;
 
   // Calculating costs for next row using costs from the previous row.
-  while (++l < L)
-  {
+  while (++l < L) {
     vector<int>* nextRow = new vector<int>(I);
-    for (int i = 0; i < I; ++i)
-    {
+    for (int i = 0; i < I; ++i) {
       vector<int> possibleCosts;
       if (i > 0) {
         possibleCosts.push_back((*nextRow)[i-1] + 1); // Deletion
diff --git a/mert/CderScorer.h b/mert/CderScorer.h
index 60b6ad125..bd43ec0d8 100644
--- a/mert/CderScorer.h
+++ b/mert/CderScorer.h
@@ -8,13 +8,14 @@
 
 namespace MosesTuning
 {
-  
+
 
 /**
  * CderScorer class can compute both CDER and WER metric.
  */
-class CderScorer: public StatisticsBasedScorer {
- public:
+class CderScorer: public StatisticsBasedScorer
+{
+public:
   explicit CderScorer(const std::string& config, bool allowed_long_jumps = true);
   ~CderScorer();
 
@@ -24,11 +25,13 @@ class CderScorer: public StatisticsBasedScorer {
 
   virtual void prepareStatsVector(std::size_t sid, const std::string& text, std::vector<int>& stats);
 
-  virtual std::size_t NumberOfScores() const { return 2; }
+  virtual std::size_t NumberOfScores() const {
+    return 2;
+  }
 
   virtual float calculateScore(const std::vector<int>& comps) const;
 
- private:
+private:
   bool m_allowed_long_jumps;
 
   typedef std::vector<int> sent_t;
diff --git a/mert/Data.cpp b/mert/Data.cpp
index 1efa080a2..613ce419b 100644
--- a/mert/Data.cpp
+++ b/mert/Data.cpp
@@ -27,11 +27,11 @@ namespace MosesTuning
 {
 
 Data::Data(Scorer* scorer, const string& sparse_weights_file)
-    : m_scorer(scorer),
-      m_score_type(m_scorer->getName()),
-      m_num_scores(0),
-      m_score_data(new ScoreData(m_scorer)),
-      m_feature_data(new FeatureData)
+  : m_scorer(scorer),
+    m_score_type(m_scorer->getName()),
+    m_num_scores(0),
+    m_score_data(new ScoreData(m_scorer)),
+    m_feature_data(new FeatureData)
 {
   TRACE_ERR("Data::m_score_type " << m_score_type << endl);
   TRACE_ERR("Data::Scorer type from Scorer: " << m_scorer->getName() << endl);
@@ -48,7 +48,8 @@ Data::Data(Scorer* scorer, const string& sparse_weights_file)
 //ADDED BY TS
 // TODO: This is too long; consider creating additional functions to
 // reduce the lines of this function.
-void Data::removeDuplicates() {
+void Data::removeDuplicates()
+{
   size_t nSentences = m_feature_data->size();
   assert(m_score_data->size() == nSentences);
 
@@ -128,7 +129,8 @@ void Data::removeDuplicates() {
 }
 //END_ADDED
 
-void Data::load(const std::string &featfile, const std::string &scorefile) {
+void Data::load(const std::string &featfile, const std::string &scorefile)
+{
   m_feature_data->load(featfile, m_sparse_weights);
   m_score_data->load(scorefile);
 }
@@ -192,7 +194,8 @@ void Data::loadNBest(const string &file)
   }
 }
 
-void Data::save(const std::string &featfile, const std::string &scorefile, bool bin) {
+void Data::save(const std::string &featfile, const std::string &scorefile, bool bin)
+{
   if (bin)
     cerr << "Binary write mode is selected" << endl;
   else
@@ -202,7 +205,8 @@ void Data::save(const std::string &featfile, const std::string &scorefile, bool
   m_score_data->save(scorefile, bin);
 }
 
-void Data::InitFeatureMap(const string& str) {
+void Data::InitFeatureMap(const string& str)
+{
   string buf = str;
   string substr;
   string features = "";
@@ -231,7 +235,8 @@ void Data::InitFeatureMap(const string& str) {
 }
 
 void Data::AddFeatures(const string& str,
-                       int sentence_index) {
+                       int sentence_index)
+{
   string buf = str;
   string substr;
   FeatureStats feature_entry;
diff --git a/mert/Data.h b/mert/Data.h
index e17ac0239..cd090bad3 100644
--- a/mert/Data.h
+++ b/mert/Data.h
@@ -44,18 +44,28 @@ public:
     m_feature_data->clear();
   }
 
-  ScoreDataHandle getScoreData() { return m_score_data; }
+  ScoreDataHandle getScoreData() {
+    return m_score_data;
+  }
 
-  FeatureDataHandle getFeatureData() { return m_feature_data; }
+  FeatureDataHandle getFeatureData() {
+    return m_feature_data;
+  }
 
-  Scorer* getScorer() { return m_scorer; }
+  Scorer* getScorer() {
+    return m_scorer;
+  }
 
   std::size_t NumberOfFeatures() const {
     return m_feature_data->NumberOfFeatures();
   }
 
-  std::string Features() const { return m_feature_data->Features(); }
-  void Features(const std::string &f) { m_feature_data->Features(f); }
+  std::string Features() const {
+    return m_feature_data->Features();
+  }
+  void Features(const std::string &f) {
+    m_feature_data->Features(f);
+  }
 
   void loadNBest(const std::string &file);
 
diff --git a/mert/DataTest.cpp b/mert/DataTest.cpp
index 189d8ccda..911171e0b 100644
--- a/mert/DataTest.cpp
+++ b/mert/DataTest.cpp
@@ -10,7 +10,8 @@
 using namespace MosesTuning;
 
 //very basic test of sharding
-BOOST_AUTO_TEST_CASE(shard_basic) {
+BOOST_AUTO_TEST_CASE(shard_basic)
+{
   boost::scoped_ptr<Scorer> scorer(ScorerFactory::getScorer("BLEU", ""));
   Data data(scorer.get());
   FeatureArray fa1, fa2, fa3, fa4;
@@ -39,7 +40,8 @@ BOOST_AUTO_TEST_CASE(shard_basic) {
   BOOST_CHECK_EQUAL(shards[1].getFeatureData()->size(),(std::size_t)2);
 }
 
-BOOST_AUTO_TEST_CASE(init_feature_map_test) {
+BOOST_AUTO_TEST_CASE(init_feature_map_test)
+{
   boost::scoped_ptr<Scorer> scorer(ScorerFactory::getScorer("BLEU", ""));
   Data data(scorer.get());
 
@@ -49,7 +51,8 @@ BOOST_AUTO_TEST_CASE(init_feature_map_test) {
   BOOST_CHECK_EQUAL(expected, data.Features());
 }
 
-BOOST_AUTO_TEST_CASE(add_features_test) {
+BOOST_AUTO_TEST_CASE(add_features_test)
+{
   boost::scoped_ptr<Scorer> scorer(ScorerFactory::getScorer("BLEU", ""));
   Data data(scorer.get());
 
diff --git a/mert/Fdstream.h b/mert/Fdstream.h
index 6dbdb40a6..c59052f02 100644
--- a/mert/Fdstream.h
+++ b/mert/Fdstream.h
@@ -13,27 +13,27 @@
 
 #define BUFFER_SIZE (32768)
 
-namespace MosesTuning 
+namespace MosesTuning
 {
 
 class _fdstream
 {
 protected:
   _fdstream() :
-      _file_descriptor(-1), _filebuf(NULL)
+    _file_descriptor(-1), _filebuf(NULL)
   { }
 
   _fdstream(int file_descriptor, std::ios_base::openmode openmode) :
-      _file_descriptor(file_descriptor), _openmode(openmode)
-  {
+    _file_descriptor(file_descriptor), _openmode(openmode) {
     _filebuf = NULL;
     open(file_descriptor, openmode);
   }
 
-  std::ios_base::openmode openmode() const { return _openmode; }
+  std::ios_base::openmode openmode() const {
+    return _openmode;
+  }
 
-  void open(int file_descriptor, std::ios_base::openmode openmode)
-  {
+  void open(int file_descriptor, std::ios_base::openmode openmode) {
     if (!_filebuf)
       // We create a C++ stream from a file descriptor
       // stdio_filebuf is not synced with stdio.
@@ -41,11 +41,10 @@ protected:
       // You can also create the filebuf from a FILE* with
       // FILE* f = fdopen(file_descriptor, mode);
       _filebuf = new __gnu_cxx::stdio_filebuf<char> (file_descriptor,
-                                                     openmode);
+          openmode);
   }
 
-  virtual ~_fdstream()
-  {
+  virtual ~_fdstream() {
     close(_file_descriptor);
     delete _filebuf;
     _filebuf = NULL;
@@ -60,59 +59,51 @@ class ifdstream : public _fdstream
 {
 public:
   ifdstream() :
-      _fdstream(), _stream(NULL)
+    _fdstream(), _stream(NULL)
   { }
 
   ifdstream(int file_descriptor) :
-      _fdstream(file_descriptor, std::ios_base::in)
-  {
+    _fdstream(file_descriptor, std::ios_base::in) {
     _stream = new std::istream(_filebuf);
   }
 
-  void open(int file_descriptor)
-  {
-    if (!_stream)
-      {
-        _fdstream::open(file_descriptor, std::ios_base::in);
-        _stream = new std::istream(_filebuf);
-      }
+  void open(int file_descriptor) {
+    if (!_stream) {
+      _fdstream::open(file_descriptor, std::ios_base::in);
+      _stream = new std::istream(_filebuf);
+    }
   }
 
-  ifdstream& operator>> (std::string& str)
-  {
+  ifdstream& operator>> (std::string& str) {
     (*_stream) >> str;
 
     return *this;
   }
 
-  std::size_t getline(std::string& str)
-  {
+  std::size_t getline(std::string& str) {
     char tmp[BUFFER_SIZE];
     std::size_t ret = getline(tmp, BUFFER_SIZE);
     str = tmp;
     return ret;
   }
 
-  std::size_t getline(char* s, std::streamsize n)
-  {
+  std::size_t getline(char* s, std::streamsize n) {
     return (getline(s, n, '\n'));
   }
 
-  std::size_t getline(char* s, std::streamsize n, char delim)
-  {
+  std::size_t getline(char* s, std::streamsize n, char delim) {
     int i = 0;
-    do{
+    do {
       s[i] = _stream->get();
       i++;
-    }while(i < n-1 && s[i-1] != delim && s[i-1] != '\0');
+    } while(i < n-1 && s[i-1] != delim && s[i-1] != '\0');
 
     s[i-1] = '\0'; // overwrite the delimiter given with string end
 
     return i-1;
   }
 
-  ~ifdstream()
-  {
+  ~ifdstream() {
     //this->~_fdstream();
     delete _stream;
   }
@@ -125,27 +116,23 @@ class ofdstream : public _fdstream
 {
 public:
   ofdstream() :
-      _fdstream(), _stream(NULL)
+    _fdstream(), _stream(NULL)
   { }
 
   ofdstream(int file_descriptor) :
-      _fdstream(file_descriptor, std::ios_base::out)
-  {
+    _fdstream(file_descriptor, std::ios_base::out) {
     _stream = new std::ostream(_filebuf);
   }
 
-  void open(int file_descriptor)
-  {
-    if (!_stream)
-    {
+  void open(int file_descriptor) {
+    if (!_stream) {
       _fdstream::open(file_descriptor, std::ios_base::out);
       _stream = new std::ostream(_filebuf);
     }
   }
 
 
-  ofdstream& operator<< (const std::string& str)
-  {
+  ofdstream& operator<< (const std::string& str) {
     if (_stream->good())
       (*_stream) << str;
 
@@ -153,8 +140,7 @@ public:
     return *this;
   }
 
-  ~ofdstream()
-  {
+  ~ofdstream() {
     //this->~_fdstream();
     delete _stream;
   }
diff --git a/mert/FeatureArray.cpp b/mert/FeatureArray.cpp
index fd5fea200..d49b53b96 100644
--- a/mert/FeatureArray.cpp
+++ b/mert/FeatureArray.cpp
@@ -19,14 +19,14 @@ namespace MosesTuning
 
 
 FeatureArray::FeatureArray()
-    : m_index(0), m_num_features(0){}
+  : m_index(0), m_num_features(0) {}
 
 FeatureArray::~FeatureArray() {}
 
 void FeatureArray::savetxt(ostream* os)
 {
   *os << FEATURES_TXT_BEGIN << " " << m_index << " " << m_array.size()
-          << " " << m_num_features << " " << m_features << endl;
+      << " " << m_num_features << " " << m_features << endl;
   for (featarray_t::iterator i = m_array.begin(); i != m_array.end(); ++i) {
     i->savetxt(os);
     *os << endl;
@@ -37,7 +37,7 @@ void FeatureArray::savetxt(ostream* os)
 void FeatureArray::savebin(ostream* os)
 {
   *os << FEATURES_BIN_BEGIN << " " << m_index << " " << m_array.size()
-          << " " << m_num_features << " " << m_features << endl;
+      << " " << m_num_features << " " << m_features << endl;
   for (featarray_t::iterator i = m_array.begin(); i != m_array.end(); ++i)
     i->savebin(os);
 
diff --git a/mert/FeatureArray.h b/mert/FeatureArray.h
index 03fe6b40c..f5fc489a2 100644
--- a/mert/FeatureArray.h
+++ b/mert/FeatureArray.h
@@ -36,16 +36,28 @@ public:
   FeatureArray();
   ~FeatureArray();
 
-  void clear() { m_array.clear(); }
+  void clear() {
+    m_array.clear();
+  }
 
 
-  int getIndex() const { return m_index; }
-  void setIndex(const int value) { m_index = value; }
+  int getIndex() const {
+    return m_index;
+  }
+  void setIndex(const int value) {
+    m_index = value;
+  }
 
-  FeatureStats& get(std::size_t i) { return m_array.at(i); }
-  const FeatureStats& get(std::size_t i) const { return m_array.at(i); }
+  FeatureStats& get(std::size_t i) {
+    return m_array.at(i);
+  }
+  const FeatureStats& get(std::size_t i) const {
+    return m_array.at(i);
+  }
 
-  void add(FeatureStats& e) { m_array.push_back(e); }
+  void add(FeatureStats& e) {
+    m_array.push_back(e);
+  }
 
   //ADDED BY TS
   void swap(std::size_t i, std::size_t j) {
@@ -59,13 +71,23 @@ public:
 
   void merge(FeatureArray& e);
 
-  std::size_t size() const { return m_array.size(); }
+  std::size_t size() const {
+    return m_array.size();
+  }
 
-  std::size_t NumberOfFeatures() const { return m_num_features; }
-  void NumberOfFeatures(std::size_t v) { m_num_features = v; }
+  std::size_t NumberOfFeatures() const {
+    return m_num_features;
+  }
+  void NumberOfFeatures(std::size_t v) {
+    m_num_features = v;
+  }
 
-  std::string Features() const { return m_features; }
-  void Features(const std::string& f) { m_features = f; }
+  std::string Features() const {
+    return m_features;
+  }
+  void Features(const std::string& f) {
+    m_features = f;
+  }
 
   void savetxt(std::ostream* os);
   void savebin(std::ostream* os);
diff --git a/mert/FeatureData.cpp b/mert/FeatureData.cpp
index 75888ef6d..13b9b3a96 100644
--- a/mert/FeatureData.cpp
+++ b/mert/FeatureData.cpp
@@ -20,7 +20,7 @@ namespace MosesTuning
 
 
 FeatureData::FeatureData()
-    : m_num_features(0) {}
+  : m_num_features(0) {}
 
 void FeatureData::save(ostream* os, bool bin)
 {
@@ -38,7 +38,8 @@ void FeatureData::save(const string &file, bool bin)
   ofs.close();
 }
 
-void FeatureData::save(bool bin) {
+void FeatureData::save(bool bin)
+{
   save(&cout, bin);
 }
 
@@ -145,7 +146,8 @@ void FeatureData::setFeatureMap(const string& feat)
   }
 }
 
-string FeatureData::ToString() const {
+string FeatureData::ToString() const
+{
   string res;
 
   {
diff --git a/mert/FeatureData.h b/mert/FeatureData.h
index 79e52b330..2510b3aee 100644
--- a/mert/FeatureData.h
+++ b/mert/FeatureData.h
@@ -33,7 +33,9 @@ public:
   FeatureData();
   ~FeatureData() {}
 
-  void clear() { m_array.clear(); }
+  void clear() {
+    m_array.clear();
+  }
 
   FeatureArray& get(size_t idx) {
     return m_array.at(idx);
@@ -61,13 +63,23 @@ public:
   void add(FeatureArray& e);
   void add(FeatureStats& e, int sent_idx);
 
-  std::size_t size() const { return m_array.size(); }
+  std::size_t size() const {
+    return m_array.size();
+  }
 
-  std::size_t NumberOfFeatures() const { return m_num_features; }
-  void NumberOfFeatures(std::size_t v) { m_num_features = v; }
+  std::size_t NumberOfFeatures() const {
+    return m_num_features;
+  }
+  void NumberOfFeatures(std::size_t v) {
+    m_num_features = v;
+  }
 
-  std::string Features() const { return m_features; }
-  void Features(const std::string& f) { m_features = f; }
+  std::string Features() const {
+    return m_features;
+  }
+  void Features(const std::string& f) {
+    m_features = f;
+  }
 
   void save(const std::string &file, bool bin=false);
   void save(std::ostream* os, bool bin=false);
diff --git a/mert/FeatureDataIterator.cpp b/mert/FeatureDataIterator.cpp
index 471da07ee..9deb0ac50 100644
--- a/mert/FeatureDataIterator.cpp
+++ b/mert/FeatureDataIterator.cpp
@@ -32,9 +32,10 @@ using namespace util;
 
 namespace MosesTuning
 {
-  
 
-int ParseInt(const StringPiece& str ) {
+
+int ParseInt(const StringPiece& str )
+{
   char* errIndex;
   //could wrap?
   int value = static_cast<int>(strtol(str.data(), &errIndex,10));
@@ -44,7 +45,8 @@ int ParseInt(const StringPiece& str ) {
   return value;
 }
 
-float ParseFloat(const StringPiece& str) {
+float ParseFloat(const StringPiece& str)
+{
   char* errIndex;
   float value = static_cast<float>(strtod(str.data(), &errIndex));
   if (errIndex == str.data()) {
@@ -53,11 +55,13 @@ float ParseFloat(const StringPiece& str) {
   return value;
 }
 
-bool operator==(FeatureDataItem const& item1, FeatureDataItem const& item2) {
+bool operator==(FeatureDataItem const& item1, FeatureDataItem const& item2)
+{
   return item1.dense==item1.dense && item1.sparse==item1.sparse;
 }
 
-size_t hash_value(FeatureDataItem const& item) {
+size_t hash_value(FeatureDataItem const& item)
+{
   size_t seed = 0;
   boost::hash_combine(seed,item.dense);
   boost::hash_combine(seed,item.sparse);
@@ -67,14 +71,16 @@ size_t hash_value(FeatureDataItem const& item) {
 
 FeatureDataIterator::FeatureDataIterator() {}
 
-FeatureDataIterator::FeatureDataIterator(const string& filename) {
+FeatureDataIterator::FeatureDataIterator(const string& filename)
+{
   m_in.reset(new FilePiece(filename.c_str()));
   readNext();
 }
 
 FeatureDataIterator::~FeatureDataIterator() {}
 
-void FeatureDataIterator::readNext() {
+void FeatureDataIterator::readNext()
+{
   m_next.clear();
   try {
     StringPiece marker = m_in->ReadDelimited();
@@ -101,7 +107,7 @@ void FeatureDataIterator::readNext() {
           //sparse feature
           StringPiece second = *value;
           float floatValue = ParseFloat(second);
-          m_next.back().sparse.set(first.as_string(),floatValue); 
+          m_next.back().sparse.set(first.as_string(),floatValue);
         }
       }
       if (length != m_next.back().dense.size()) {
@@ -117,11 +123,13 @@ void FeatureDataIterator::readNext() {
   }
 }
 
-void FeatureDataIterator::increment() {
+void FeatureDataIterator::increment()
+{
   readNext();
 }
 
-bool FeatureDataIterator::equal(const FeatureDataIterator& rhs) const {
+bool FeatureDataIterator::equal(const FeatureDataIterator& rhs) const
+{
   if (!m_in && !rhs.m_in) {
     return true;
   } else if (!m_in) {
@@ -129,12 +137,13 @@ bool FeatureDataIterator::equal(const FeatureDataIterator& rhs) const {
   } else if (!rhs.m_in) {
     return false;
   } else {
-    return m_in->FileName() == rhs.m_in->FileName() && 
-      m_in->Offset() == rhs.m_in->Offset();
+    return m_in->FileName() == rhs.m_in->FileName() &&
+           m_in->Offset() == rhs.m_in->Offset();
   }
 }
 
-const vector<FeatureDataItem>& FeatureDataIterator::dereference() const {
+const vector<FeatureDataItem>& FeatureDataIterator::dereference() const
+{
   return m_next;
 }
 
diff --git a/mert/FeatureDataIterator.h b/mert/FeatureDataIterator.h
index 8bbb8d497..15a654182 100644
--- a/mert/FeatureDataIterator.h
+++ b/mert/FeatureDataIterator.h
@@ -37,18 +37,21 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 
 #include "FeatureStats.h"
 
-namespace util { class FilePiece; }
+namespace util
+{
+class FilePiece;
+}
 
 namespace MosesTuning
 {
-  
 
-class FileFormatException : public util::Exception 
+
+class FileFormatException : public util::Exception
 {
-  public:
-    explicit FileFormatException(const std::string& filename, const std::string& line) {
-      *this << "Error in line \"" << line << "\" of " << filename;
-    }
+public:
+  explicit FileFormatException(const std::string& filename, const std::string& line) {
+    *this << "Error in line \"" << line << "\" of " << filename;
+  }
 };
 
 
@@ -56,45 +59,45 @@ class FileFormatException : public util::Exception
 int ParseInt(const StringPiece& str );
 
 /** Assumes a delimiter, so only apply to tokens */
-float ParseFloat(const StringPiece& str); 
+float ParseFloat(const StringPiece& str);
 
 
-class FeatureDataItem 
+class FeatureDataItem
 {
-  public:
-    std::vector<float> dense;
-    SparseVector sparse;
+public:
+  std::vector<float> dense;
+  SparseVector sparse;
 };
 
 bool operator==(FeatureDataItem const& item1, FeatureDataItem const& item2);
 std::size_t hash_value(FeatureDataItem const& item);
 
-class FeatureDataIterator : 
+class FeatureDataIterator :
   public boost::iterator_facade<FeatureDataIterator,
-                                const std::vector<FeatureDataItem>,
-                                boost::forward_traversal_tag> 
+  const std::vector<FeatureDataItem>,
+  boost::forward_traversal_tag>
 {
-  public:
-    FeatureDataIterator();
-    explicit FeatureDataIterator(const std::string& filename);
-    ~FeatureDataIterator();
+public:
+  FeatureDataIterator();
+  explicit FeatureDataIterator(const std::string& filename);
+  ~FeatureDataIterator();
 
-    static FeatureDataIterator end() {
-      return FeatureDataIterator();
-    }
+  static FeatureDataIterator end() {
+    return FeatureDataIterator();
+  }
 
 
-  private:
-    friend class boost::iterator_core_access;
+private:
+  friend class boost::iterator_core_access;
 
-    void increment();
-    bool equal(const FeatureDataIterator& rhs) const;
-    const std::vector<FeatureDataItem>& dereference() const;
+  void increment();
+  bool equal(const FeatureDataIterator& rhs) const;
+  const std::vector<FeatureDataItem>& dereference() const;
 
-    void readNext();
+  void readNext();
 
-    boost::shared_ptr<util::FilePiece> m_in;
-    std::vector<FeatureDataItem> m_next;
+  boost::shared_ptr<util::FilePiece> m_in;
+  std::vector<FeatureDataItem> m_next;
 };
 
 }
diff --git a/mert/FeatureDataTest.cpp b/mert/FeatureDataTest.cpp
index 0f3d6a596..916203592 100644
--- a/mert/FeatureDataTest.cpp
+++ b/mert/FeatureDataTest.cpp
@@ -7,10 +7,12 @@
 
 using namespace MosesTuning;
 
-namespace {
+namespace
+{
 
 void CheckFeatureMap(const FeatureData* feature_data,
-                     const char* str, int num_feature, int* cnt) {
+                     const char* str, int num_feature, int* cnt)
+{
   for (int i = 0; i < num_feature; ++i) {
     std::stringstream ss;
     ss << str << "_" << i;
@@ -23,7 +25,8 @@ void CheckFeatureMap(const FeatureData* feature_data,
 
 } // namespace
 
-BOOST_AUTO_TEST_CASE(set_feature_map) {
+BOOST_AUTO_TEST_CASE(set_feature_map)
+{
   std::string str("d_0 d_1 d_2 d_3 d_4 d_5 d_6 lm_0 lm_1 tm_0 tm_1 tm_2 tm_3 tm_4 w_0 ");
   FeatureData feature_data;
 
diff --git a/mert/FeatureStats.cpp b/mert/FeatureStats.cpp
index 242d3fbd0..aa32e1fef 100644
--- a/mert/FeatureStats.cpp
+++ b/mert/FeatureStats.cpp
@@ -18,31 +18,35 @@
 
 using namespace std;
 
-namespace {
+namespace
+{
 const int kAvailableSize = 8;
 } // namespace
 
 namespace MosesTuning
 {
-  
+
 
 SparseVector::name2id_t SparseVector::m_name_to_id;
 SparseVector::id2name_t SparseVector::m_id_to_name;
 
-FeatureStatsType SparseVector::get(const string& name) const {
+FeatureStatsType SparseVector::get(const string& name) const
+{
   name2id_t::const_iterator name2id_iter = m_name_to_id.find(name);
   if (name2id_iter == m_name_to_id.end()) return 0;
   size_t id = name2id_iter->second;
   return get(id);
 }
 
-FeatureStatsType SparseVector::get(size_t id) const {
+FeatureStatsType SparseVector::get(size_t id) const
+{
   fvector_t::const_iterator fvector_iter = m_fvector.find(id);
   if (fvector_iter == m_fvector.end()) return 0;
   return fvector_iter->second;
 }
 
-void SparseVector::set(const string& name, FeatureStatsType value) {
+void SparseVector::set(const string& name, FeatureStatsType value)
+{
   name2id_t::const_iterator name2id_iter = m_name_to_id.find(name);
   size_t id = 0;
   if (name2id_iter == m_name_to_id.end()) {
@@ -55,7 +59,8 @@ void SparseVector::set(const string& name, FeatureStatsType value) {
   m_fvector[id] = value;
 }
 
-void SparseVector::write(ostream& out, const string& sep) const {
+void SparseVector::write(ostream& out, const string& sep) const
+{
   for (fvector_t::const_iterator i = m_fvector.begin(); i != m_fvector.end(); ++i) {
     if (abs(i->second) < 0.00001) continue;
     string name = m_id_to_name[i->first];
@@ -63,11 +68,13 @@ void SparseVector::write(ostream& out, const string& sep) const {
   }
 }
 
-void SparseVector::clear() {
+void SparseVector::clear()
+{
   m_fvector.clear();
 }
 
-void SparseVector::load(const string& file) {
+void SparseVector::load(const string& file)
+{
   ifstream in(file.c_str());
   if (!in) {
     throw runtime_error("Failed to open sparse weights file: " + file);
@@ -84,39 +91,44 @@ void SparseVector::load(const string& file) {
   }
 }
 
-SparseVector& SparseVector::operator-=(const SparseVector& rhs) {
+SparseVector& SparseVector::operator-=(const SparseVector& rhs)
+{
 
   for (fvector_t::const_iterator i = rhs.m_fvector.begin();
-      i != rhs.m_fvector.end(); ++i) {
+       i != rhs.m_fvector.end(); ++i) {
     m_fvector[i->first] =  get(i->first) - (i->second);
   }
   return *this;
 }
 
-FeatureStatsType SparseVector::inner_product(const SparseVector& rhs) const {
+FeatureStatsType SparseVector::inner_product(const SparseVector& rhs) const
+{
   FeatureStatsType product = 0.0;
   for (fvector_t::const_iterator i = m_fvector.begin();
-    i != m_fvector.end(); ++i) {
+       i != m_fvector.end(); ++i) {
     product += ((i->second) * (rhs.get(i->first)));
   }
   return product;
 }
 
-SparseVector operator-(const SparseVector& lhs, const SparseVector& rhs) {
+SparseVector operator-(const SparseVector& lhs, const SparseVector& rhs)
+{
   SparseVector res(lhs);
   res -= rhs;
   return res;
 }
 
-FeatureStatsType inner_product(const SparseVector& lhs, const SparseVector& rhs) {
-    if (lhs.size() >= rhs.size()) {
-      return rhs.inner_product(lhs);
-    } else {
-      return lhs.inner_product(rhs);
-    }
+FeatureStatsType inner_product(const SparseVector& lhs, const SparseVector& rhs)
+{
+  if (lhs.size() >= rhs.size()) {
+    return rhs.inner_product(lhs);
+  } else {
+    return lhs.inner_product(rhs);
+  }
 }
 
-std::vector<std::size_t> SparseVector::feats() const {
+std::vector<std::size_t> SparseVector::feats() const
+{
   std::vector<std::size_t> toRet;
   for(fvector_t::const_iterator iter = m_fvector.begin();
       iter!=m_fvector.end();
@@ -126,7 +138,8 @@ std::vector<std::size_t> SparseVector::feats() const {
   return toRet;
 }
 
-std::size_t SparseVector::encode(const std::string& name) {
+std::size_t SparseVector::encode(const std::string& name)
+{
   name2id_t::const_iterator name2id_iter = m_name_to_id.find(name);
   size_t id = 0;
   if (name2id_iter == m_name_to_id.end()) {
@@ -139,26 +152,29 @@ std::size_t SparseVector::encode(const std::string& name) {
   return id;
 }
 
-std::string SparseVector::decode(std::size_t id) {
+std::string SparseVector::decode(std::size_t id)
+{
   return m_id_to_name[id];
 }
 
-bool operator==(SparseVector const& item1, SparseVector const& item2) {
+bool operator==(SparseVector const& item1, SparseVector const& item2)
+{
   return item1.m_fvector==item2.m_fvector;
 }
 
-std::size_t hash_value(SparseVector const& item) {
+std::size_t hash_value(SparseVector const& item)
+{
   boost::hash<SparseVector::fvector_t> hasher;
   return hasher(item.m_fvector);
 }
 
 FeatureStats::FeatureStats()
-    : m_available_size(kAvailableSize), m_entries(0),
-      m_array(new FeatureStatsType[m_available_size]) {}
+  : m_available_size(kAvailableSize), m_entries(0),
+    m_array(new FeatureStatsType[m_available_size]) {}
 
 FeatureStats::FeatureStats(const size_t size)
-    : m_available_size(size), m_entries(size),
-      m_array(new FeatureStatsType[m_available_size])
+  : m_available_size(size), m_entries(size),
+    m_array(new FeatureStatsType[m_available_size])
 {
   memset(m_array, 0, GetArraySizeWithBytes());
 }
@@ -276,7 +292,8 @@ void FeatureStats::savetxt(ostream* os)
   *os << *this;
 }
 
-void FeatureStats::savetxt() {
+void FeatureStats::savetxt()
+{
   savetxt(&cout);
 }
 
@@ -298,7 +315,8 @@ ostream& operator<<(ostream& o, const FeatureStats& e)
   return o;
 }
 
-bool operator==(const FeatureStats& f1, const FeatureStats& f2) {
+bool operator==(const FeatureStats& f1, const FeatureStats& f2)
+{
   size_t size = f1.size();
 
   if (size != f2.size())
diff --git a/mert/FeatureStats.h b/mert/FeatureStats.h
index 883a89b97..a882e7358 100644
--- a/mert/FeatureStats.h
+++ b/mert/FeatureStats.h
@@ -18,10 +18,11 @@
 
 namespace MosesTuning
 {
-  
+
 
 // Minimal sparse vector
-class SparseVector {
+class SparseVector
+{
 public:
   typedef std::map<std::size_t,FeatureStatsType> fvector_t;
   typedef std::map<std::string, std::size_t> name2id_t;
@@ -32,8 +33,10 @@ public:
   void set(const std::string& name, FeatureStatsType value);
   void clear();
   void load(const std::string& file);
-  std::size_t size() const { return m_fvector.size(); }
-   
+  std::size_t size() const {
+    return m_fvector.size();
+  }
+
   void write(std::ostream& out, const std::string& sep = " ") const;
 
   SparseVector& operator-=(const SparseVector& rhs);
@@ -78,7 +81,9 @@ public:
 
   void Copy(const FeatureStats &stats);
 
-  bool isfull() const { return (m_entries < m_available_size) ? 0 : 1; }
+  bool isfull() const {
+    return (m_entries < m_available_size) ? 0 : 1;
+  }
   void expand();
   void add(FeatureStatsType v);
   void addSparse(const std::string& name, FeatureStatsType v);
@@ -93,23 +98,37 @@ public:
     clear();
   }
 
-  FeatureStatsType get(std::size_t i) { return m_array[i]; }
-  FeatureStatsType get(std::size_t i)const { return m_array[i]; }
-  featstats_t getArray() const { return m_array; }
+  FeatureStatsType get(std::size_t i) {
+    return m_array[i];
+  }
+  FeatureStatsType get(std::size_t i)const {
+    return m_array[i];
+  }
+  featstats_t getArray() const {
+    return m_array;
+  }
 
-  const SparseVector& getSparse() const { return m_map; }
+  const SparseVector& getSparse() const {
+    return m_map;
+  }
 
   void set(std::string &theString, const SparseVector& sparseWeights);
 
-  inline std::size_t bytes() const { return GetArraySizeWithBytes(); }
+  inline std::size_t bytes() const {
+    return GetArraySizeWithBytes();
+  }
 
   std::size_t GetArraySizeWithBytes() const {
     return m_entries * sizeof(FeatureStatsType);
   }
 
-  std::size_t size() const { return m_entries; }
+  std::size_t size() const {
+    return m_entries;
+  }
 
-  std::size_t available() const { return m_available_size; }
+  std::size_t available() const {
+    return m_available_size;
+  }
 
   void savetxt(const std::string &file);
   void savetxt(std::ostream* os);
diff --git a/mert/FileStream.cpp b/mert/FileStream.cpp
index 1a52e53fa..800ce1bfe 100644
--- a/mert/FileStream.cpp
+++ b/mert/FileStream.cpp
@@ -5,15 +5,17 @@
 
 using namespace std;
 
-namespace {
-bool IsGzipFile(const std::string &filename) {
+namespace
+{
+bool IsGzipFile(const std::string &filename)
+{
   return filename.size() > 3 &&
-      filename.substr(filename.size() - 3, 3) == ".gz";
+         filename.substr(filename.size() - 3, 3) == ".gz";
 }
 } // namespace
 
 inputfilestream::inputfilestream(const std::string &filePath)
-    : std::istream(0), m_streambuf(0), m_is_good(false)
+  : std::istream(0), m_streambuf(0), m_is_good(false)
 {
   // check if file is readable
   std::filebuf* fb = new std::filebuf();
@@ -40,7 +42,7 @@ void inputfilestream::close()
 }
 
 outputfilestream::outputfilestream(const std::string &filePath)
-    : std::ostream(0), m_streambuf(0), m_is_good(false)
+  : std::ostream(0), m_streambuf(0), m_is_good(false)
 {
   // check if file is readable
   std::filebuf* fb = new std::filebuf();
diff --git a/mert/FileStream.h b/mert/FileStream.h
index 3fd489cd7..582cbcb59 100644
--- a/mert/FileStream.h
+++ b/mert/FileStream.h
@@ -16,7 +16,9 @@ public:
   explicit inputfilestream(const std::string &filePath);
   virtual ~inputfilestream();
 
-  bool good() const { return m_is_good; }
+  bool good() const {
+    return m_is_good;
+  }
   void close();
 };
 
@@ -30,7 +32,9 @@ public:
   explicit outputfilestream(const std::string &filePath);
   virtual ~outputfilestream();
 
-  bool good() const { return m_is_good; }
+  bool good() const {
+    return m_is_good;
+  }
   void close();
 };
 
diff --git a/mert/GzFileBuf.cpp b/mert/GzFileBuf.cpp
index 9d3ccb588..d61a22525 100644
--- a/mert/GzFileBuf.cpp
+++ b/mert/GzFileBuf.cpp
@@ -5,7 +5,8 @@
 #include <cstdio>
 #include <iostream>
 
-GzFileBuf::GzFileBuf(const char* filename) {
+GzFileBuf::GzFileBuf(const char* filename)
+{
   m_gz_file = gzopen(filename, "rb");
   if (m_gz_file == NULL) {
     std::cerr << "ERROR: Failed to open " << filename << std::endl;
@@ -16,16 +17,19 @@ GzFileBuf::GzFileBuf(const char* filename) {
        m_buf + sizeof(int));    // end position
 }
 
-GzFileBuf::~GzFileBuf() {
+GzFileBuf::~GzFileBuf()
+{
   gzclose(m_gz_file);
 }
 
-int GzFileBuf::overflow(int_type c) {
+int GzFileBuf::overflow(int_type c)
+{
   throw;
 }
 
 // read one character
-int GzFileBuf::underflow() {
+int GzFileBuf::underflow()
+{
   // is read position before end of m_buf?
   if (gptr() < egptr()) {
     return traits_type::to_int_type(*gptr());
@@ -64,17 +68,20 @@ int GzFileBuf::underflow() {
 }
 
 std::streampos GzFileBuf::seekpos(
-    std::streampos sp,
-    std::ios_base::openmode which) {
+  std::streampos sp,
+  std::ios_base::openmode which)
+{
   throw;
 }
 
 std::streamsize GzFileBuf::xsgetn(char* s,
-                                  std::streamsize num) {
+                                  std::streamsize num)
+{
   return static_cast<std::streamsize>(gzread(m_gz_file,s,num));
 }
 
 std::streamsize GzFileBuf::xsputn(const char* s,
-                                  std::streamsize num) {
+                                  std::streamsize num)
+{
   throw;
 }
diff --git a/mert/GzFileBuf.h b/mert/GzFileBuf.h
index 729523e0e..fb57fcfe7 100644
--- a/mert/GzFileBuf.h
+++ b/mert/GzFileBuf.h
@@ -17,8 +17,8 @@ protected:
   virtual int_type underflow();
 
   virtual std::streampos seekpos(
-      std::streampos sp,
-      std::ios_base::openmode which = std::ios_base::in | std::ios_base::out);
+    std::streampos sp,
+    std::ios_base::openmode which = std::ios_base::in | std::ios_base::out);
 
   virtual std::streamsize xsgetn(char* s, std::streamsize num);
 
diff --git a/mert/HypPackEnumerator.cpp b/mert/HypPackEnumerator.cpp
index 776c02857..1cdd1cb7d 100644
--- a/mert/HypPackEnumerator.cpp
+++ b/mert/HypPackEnumerator.cpp
@@ -8,13 +8,13 @@ using namespace std;
 
 namespace MosesTuning
 {
-  
+
 
 StreamingHypPackEnumerator::StreamingHypPackEnumerator
 (
- vector<std::string> const& featureFiles,
- vector<std::string> const& scoreFiles
- )
+  vector<std::string> const& featureFiles,
+  vector<std::string> const& scoreFiles
+)
   : m_featureFiles(featureFiles),
     m_scoreFiles(scoreFiles)
 {
@@ -22,19 +22,20 @@ StreamingHypPackEnumerator::StreamingHypPackEnumerator
     cerr << "No data to process" << endl;
     exit(0);
   }
-  
+
   if (featureFiles.size() != scoreFiles.size()) {
     cerr << "Error: Number of feature files (" << featureFiles.size() <<
-      ") does not match number of score files (" << scoreFiles.size() << ")" << endl;
+         ") does not match number of score files (" << scoreFiles.size() << ")" << endl;
     exit(1);
   }
-  
+
   m_num_lists = scoreFiles.size();
   m_primed = false;
   m_iNumDense = -1;
 }
 
-size_t StreamingHypPackEnumerator::num_dense() const {
+size_t StreamingHypPackEnumerator::num_dense() const
+{
   if(m_iNumDense<0) {
     cerr << "Error: Requested num_dense() for an unprimed StreamingHypPackEnumerator" << endl;
     exit(1);
@@ -42,12 +43,13 @@ size_t StreamingHypPackEnumerator::num_dense() const {
   return (size_t) m_iNumDense;
 }
 
-void StreamingHypPackEnumerator::prime(){
+void StreamingHypPackEnumerator::prime()
+{
   m_current_indexes.clear();
   m_current_featureVectors.clear();
   boost::unordered_set<FeatureDataItem> seen;
   m_primed = true;
-  
+
   for (size_t i = 0; i < m_num_lists; ++i) {
     if (m_featureDataIters[i] == FeatureDataIterator::end()) {
       cerr << "Error: Feature file " << i << " ended prematurely" << endl;
@@ -78,13 +80,14 @@ void StreamingHypPackEnumerator::prime(){
         }
         // Store item for retrieval
         m_current_indexes.push_back(pair<size_t,size_t>(i,j));
-	m_current_featureVectors.push_back(MiraFeatureVector(item));
+        m_current_featureVectors.push_back(MiraFeatureVector(item));
       }
     }
   }
 }
 
-void StreamingHypPackEnumerator::reset(){
+void StreamingHypPackEnumerator::reset()
+{
   m_featureDataIters.clear();
   m_scoreDataIters.clear();
   for (size_t i = 0; i < m_num_lists; ++i) {
@@ -95,11 +98,13 @@ void StreamingHypPackEnumerator::reset(){
   prime();
 }
 
-bool StreamingHypPackEnumerator::finished(){
+bool StreamingHypPackEnumerator::finished()
+{
   return m_featureDataIters[0]==FeatureDataIterator::end();
 }
 
-void StreamingHypPackEnumerator::next(){
+void StreamingHypPackEnumerator::next()
+{
   if(!m_primed) {
     cerr << "Enumerating an unprimed HypPackEnumerator" << endl;
     exit(1);
@@ -113,7 +118,8 @@ void StreamingHypPackEnumerator::next(){
   if(!finished()) prime();
 }
 
-size_t StreamingHypPackEnumerator::cur_size(){
+size_t StreamingHypPackEnumerator::cur_size()
+{
   if(!m_primed) {
     cerr << "Querying size from an unprimed HypPackEnumerator" << endl;
     exit(1);
@@ -121,7 +127,8 @@ size_t StreamingHypPackEnumerator::cur_size(){
   return m_current_indexes.size();
 }
 
-const MiraFeatureVector& StreamingHypPackEnumerator::featuresAt(size_t index){
+const MiraFeatureVector& StreamingHypPackEnumerator::featuresAt(size_t index)
+{
   if(!m_primed) {
     cerr << "Querying features from an unprimed HypPackEnumerator" << endl;
     exit(1);
@@ -129,7 +136,8 @@ const MiraFeatureVector& StreamingHypPackEnumerator::featuresAt(size_t index){
   return m_current_featureVectors[index];
 }
 
-const ScoreDataItem& StreamingHypPackEnumerator::scoresAt(size_t index) {
+const ScoreDataItem& StreamingHypPackEnumerator::scoresAt(size_t index)
+{
   if(!m_primed) {
     cerr << "Querying scores from an unprimed HypPackEnumerator" << endl;
     exit(1);
@@ -138,22 +146,23 @@ const ScoreDataItem& StreamingHypPackEnumerator::scoresAt(size_t index) {
   return m_scoreDataIters[pij.first]->operator[](pij.second);
 }
 
-size_t StreamingHypPackEnumerator::cur_id() {
+size_t StreamingHypPackEnumerator::cur_id()
+{
   return m_sentenceId;
 }
 
 /* --------- RandomAccessHypPackEnumerator ------------- */
 
 RandomAccessHypPackEnumerator::RandomAccessHypPackEnumerator(vector<string> const& featureFiles,
-                                                             vector<string> const& scoreFiles,
-                                                             bool no_shuffle)
+    vector<string> const& scoreFiles,
+    bool no_shuffle)
 {
   StreamingHypPackEnumerator train(featureFiles,scoreFiles);
   size_t index=0;
   for(train.reset(); !train.finished(); train.next()) {
     m_features.push_back(vector<MiraFeatureVector>());
     m_scores.push_back(vector<ScoreDataItem>());
-    for(size_t j=0;j<train.cur_size();j++) {
+    for(size_t j=0; j<train.cur_size(); j++) {
       m_features.back().push_back(train.featuresAt(j));
       m_scores.back().push_back(train.scoresAt(j));
     }
@@ -165,35 +174,43 @@ RandomAccessHypPackEnumerator::RandomAccessHypPackEnumerator(vector<string> cons
   m_num_dense = train.num_dense();
 }
 
-size_t RandomAccessHypPackEnumerator::num_dense() const {
+size_t RandomAccessHypPackEnumerator::num_dense() const
+{
   return m_num_dense;
 }
-  
-void RandomAccessHypPackEnumerator::reset() {
+
+void RandomAccessHypPackEnumerator::reset()
+{
   m_cur_index = 0;
   if(!m_no_shuffle) random_shuffle(m_indexes.begin(),m_indexes.end());
 }
-bool RandomAccessHypPackEnumerator::finished() {
+bool RandomAccessHypPackEnumerator::finished()
+{
   return m_cur_index >= m_indexes.size();
 }
-void RandomAccessHypPackEnumerator::next() {
+void RandomAccessHypPackEnumerator::next()
+{
   m_cur_index++;
 }
 
-size_t RandomAccessHypPackEnumerator::cur_size() {
+size_t RandomAccessHypPackEnumerator::cur_size()
+{
   assert(m_features[m_indexes[m_cur_index]].size()==m_scores[m_indexes[m_cur_index]].size());
   return m_features[m_indexes[m_cur_index]].size();
 }
-const MiraFeatureVector& RandomAccessHypPackEnumerator::featuresAt(size_t i) {
+const MiraFeatureVector& RandomAccessHypPackEnumerator::featuresAt(size_t i)
+{
   return m_features[m_indexes[m_cur_index]][i];
 }
-const ScoreDataItem& RandomAccessHypPackEnumerator::scoresAt(size_t i) {
+const ScoreDataItem& RandomAccessHypPackEnumerator::scoresAt(size_t i)
+{
   return m_scores[m_indexes[m_cur_index]][i];
 }
 
-size_t RandomAccessHypPackEnumerator::cur_id() {
+size_t RandomAccessHypPackEnumerator::cur_id()
+{
   return m_indexes[m_cur_index];
-}  
+}
 // --Emacs trickery--
 // Local Variables:
 // mode:c++
diff --git a/mert/HypPackEnumerator.h b/mert/HypPackEnumerator.h
index 690e53103..957c6d408 100644
--- a/mert/HypPackEnumerator.h
+++ b/mert/HypPackEnumerator.h
@@ -20,11 +20,12 @@
 
 namespace MosesTuning
 {
-  
+
 
 // Start with these abstract classes
 
-class HypPackEnumerator {
+class HypPackEnumerator
+{
 public:
   virtual ~HypPackEnumerator() {}
 
@@ -41,7 +42,8 @@ public:
 
 // Instantiation that streams from disk
 // Low-memory, low-speed, sequential access
-class StreamingHypPackEnumerator : public HypPackEnumerator {
+class StreamingHypPackEnumerator : public HypPackEnumerator
+{
 public:
   StreamingHypPackEnumerator(std::vector<std::string> const& featureFiles,
                              std::vector<std::string> const& scoreFiles);
@@ -75,7 +77,8 @@ private:
 // Instantiation that reads into memory
 // High-memory, high-speed, random access
 // (Actually randomizes with each call to reset)
-class RandomAccessHypPackEnumerator : public HypPackEnumerator {
+class RandomAccessHypPackEnumerator : public HypPackEnumerator
+{
 public:
   RandomAccessHypPackEnumerator(std::vector<std::string> const& featureFiles,
                                 std::vector<std::string> const& scoreFiles,
diff --git a/mert/InterpolatedScorer.cpp b/mert/InterpolatedScorer.cpp
index af3f26bf2..87cec9211 100644
--- a/mert/InterpolatedScorer.cpp
+++ b/mert/InterpolatedScorer.cpp
@@ -11,7 +11,7 @@ namespace MosesTuning
 // TODO: This is too long. Consider creating a function for
 // initialization such as Init().
 InterpolatedScorer::InterpolatedScorer(const string& name, const string& config)
-    : Scorer(name,config)
+  : Scorer(name,config)
 {
   // name would be: HAMMING,BLEU or similar
   string scorers = name;
@@ -66,7 +66,8 @@ InterpolatedScorer::InterpolatedScorer(const string& name, const string& config)
   cerr <<endl;
 }
 
-bool InterpolatedScorer::useAlignment() const {
+bool InterpolatedScorer::useAlignment() const
+{
   //cout << "InterpolatedScorer::useAlignment" << endl;
   for (vector<Scorer*>::const_iterator itsc =  m_scorers.begin(); itsc < m_scorers.end(); itsc++) {
     if ((*itsc)->useAlignment()) {
@@ -176,8 +177,7 @@ void InterpolatedScorer::prepareStats(size_t sid, const string& text, ScoreStats
     ScoreStats tempEntry;
     if ((*itsc)->useAlignment()) {
       (*itsc)->prepareStats(sid, text, tempEntry);
-    }
-    else {
+    } else {
       (*itsc)->prepareStats(sid, sentence, tempEntry);
     }
     if (i > 0) buff <<  " ";
@@ -206,17 +206,17 @@ void InterpolatedScorer::setFactors(const string& factors)
 
 void InterpolatedScorer::setFilter(const string& filterCommand)
 {
-    if (filterCommand.empty()) return;
+  if (filterCommand.empty()) return;
 
-    vector<string> csplit;
-    split(filterCommand, ',', csplit);
+  vector<string> csplit;
+  split(filterCommand, ',', csplit);
 
-    if (csplit.size() != m_scorers.size())
-      throw runtime_error("Number of command specifications does not equal number of interpolated scorers.");
+  if (csplit.size() != m_scorers.size())
+    throw runtime_error("Number of command specifications does not equal number of interpolated scorers.");
 
-    for (size_t i = 0; i < m_scorers.size(); ++i) {
-      m_scorers[i]->setFilter(csplit[i]);
-    }
+  for (size_t i = 0; i < m_scorers.size(); ++i) {
+    m_scorers[i]->setFilter(csplit[i]);
+  }
 }
 
 }
diff --git a/mert/InterpolatedScorer.h b/mert/InterpolatedScorer.h
index 49c065d27..d1078e9e1 100644
--- a/mert/InterpolatedScorer.h
+++ b/mert/InterpolatedScorer.h
@@ -10,7 +10,7 @@
 
 namespace MosesTuning
 {
-  
+
 
 /**
   * Class that includes other scorers eg.
diff --git a/mert/MiraFeatureVector.cpp b/mert/MiraFeatureVector.cpp
index 95805c295..dea9b9b83 100644
--- a/mert/MiraFeatureVector.cpp
+++ b/mert/MiraFeatureVector.cpp
@@ -7,7 +7,7 @@ using namespace std;
 
 namespace MosesTuning
 {
-  
+
 
 MiraFeatureVector::MiraFeatureVector(const FeatureDataItem& vec)
   : m_dense(vec.dense)
@@ -17,8 +17,7 @@ MiraFeatureVector::MiraFeatureVector(const FeatureDataItem& vec)
   size_t lastFeat = 0;
   m_sparseFeats.reserve(sparseFeats.size());
   m_sparseVals.reserve(sparseFeats.size());
-  for(size_t i=0;i<sparseFeats.size();i++)
-  {
+  for(size_t i=0; i<sparseFeats.size(); i++) {
     size_t feat = m_dense.size() + sparseFeats[i];
     m_sparseFeats.push_back(feat);
     m_sparseVals.push_back(vec.sparse.get(sparseFeats[i]));
@@ -26,8 +25,7 @@ MiraFeatureVector::MiraFeatureVector(const FeatureDataItem& vec)
     // Check ordered property
     if(bFirst) {
       bFirst = false;
-    }
-    else {
+    } else {
       if(lastFeat>=feat) {
         cerr << "Error: Feature indeces must be strictly ascending coming out of SparseVector" << endl;
         exit(1);
@@ -61,29 +59,33 @@ MiraFeatureVector::MiraFeatureVector(const vector<ValType>& dense,
   }
 }
 
-ValType MiraFeatureVector::val(size_t index) const {
+ValType MiraFeatureVector::val(size_t index) const
+{
   if(index < m_dense.size())
     return m_dense[index];
   else
     return m_sparseVals[index-m_dense.size()];
 }
 
-size_t MiraFeatureVector::feat(size_t index) const {
+size_t MiraFeatureVector::feat(size_t index) const
+{
   if(index < m_dense.size())
     return index;
   else
     return m_sparseFeats[index-m_dense.size()];
 }
 
-size_t MiraFeatureVector::size() const {
+size_t MiraFeatureVector::size() const
+{
   return m_dense.size() + m_sparseVals.size();
 }
 
-ValType MiraFeatureVector::sqrNorm() const {
+ValType MiraFeatureVector::sqrNorm() const
+{
   ValType toRet = 0.0;
-  for(size_t i=0;i<m_dense.size();i++)
+  for(size_t i=0; i<m_dense.size(); i++)
     toRet += m_dense[i]*m_dense[i];
-  for(size_t i=0;i<m_sparseVals.size();i++)
+  for(size_t i=0; i<m_sparseVals.size(); i++)
     toRet += m_sparseVals[i] * m_sparseVals[i];
   return toRet;
 }
@@ -96,7 +98,7 @@ MiraFeatureVector operator-(const MiraFeatureVector& a, const MiraFeatureVector&
     cerr << "Mismatching dense vectors passed to MiraFeatureVector subtraction" << endl;
     exit(1);
   }
-  for(size_t i=0;i<a.m_dense.size();i++) {
+  for(size_t i=0; i<a.m_dense.size(); i++) {
     dense.push_back(a.m_dense[i] - b.m_dense[i]);
   }
 
@@ -148,7 +150,7 @@ MiraFeatureVector operator-(const MiraFeatureVector& a, const MiraFeatureVector&
 
 ostream& operator<<(ostream& o, const MiraFeatureVector& e)
 {
-  for(size_t i=0;i<e.size();i++) {
+  for(size_t i=0; i<e.size(); i++) {
     if(i>0) o << " ";
     o << e.feat(i) << ":" << e.val(i);
   }
diff --git a/mert/MiraFeatureVector.h b/mert/MiraFeatureVector.h
index 60e765605..cb2b1c87d 100644
--- a/mert/MiraFeatureVector.h
+++ b/mert/MiraFeatureVector.h
@@ -19,11 +19,12 @@
 
 namespace MosesTuning
 {
-  
+
 
 typedef FeatureStatsType ValType;
 
-class MiraFeatureVector {
+class MiraFeatureVector
+{
 public:
   MiraFeatureVector(const FeatureDataItem& vec);
   MiraFeatureVector(const MiraFeatureVector& other);
diff --git a/mert/MiraWeightVector.cpp b/mert/MiraWeightVector.cpp
index c6f0261dc..e23804cbf 100644
--- a/mert/MiraWeightVector.cpp
+++ b/mert/MiraWeightVector.cpp
@@ -6,7 +6,7 @@ using namespace std;
 
 namespace MosesTuning
 {
-  
+
 
 /**
  * Constructor, initializes to the zero vector
@@ -36,9 +36,10 @@ MiraWeightVector::MiraWeightVector(const vector<ValType>& init)
  * \param fv  Feature vector to be added to the weights
  * \param tau FV will be scaled by this value before update
  */
-void MiraWeightVector::update(const MiraFeatureVector& fv, float tau) {
+void MiraWeightVector::update(const MiraFeatureVector& fv, float tau)
+{
   m_numUpdates++;
-  for(size_t i=0;i<fv.size();i++) {
+  for(size_t i=0; i<fv.size(); i++) {
     update(fv.feat(i), fv.val(i)*tau);
   }
 }
@@ -46,7 +47,8 @@ void MiraWeightVector::update(const MiraFeatureVector& fv, float tau) {
 /**
  * Perform an empty update (affects averaging)
  */
-void MiraWeightVector::tick() {
+void MiraWeightVector::tick()
+{
   m_numUpdates++;
 }
 
@@ -54,7 +56,8 @@ void MiraWeightVector::tick() {
  * Score a feature vector according to the model
  * \param fv Feature vector to be scored
  */
-ValType MiraWeightVector::score(const MiraFeatureVector& fv) const {
+ValType MiraWeightVector::score(const MiraFeatureVector& fv) const
+{
   ValType toRet = 0.0;
   for(size_t i=0; i<fv.size(); i++) {
     toRet += weight(fv.feat(i)) * fv.val(i);
@@ -65,7 +68,8 @@ ValType MiraWeightVector::score(const MiraFeatureVector& fv) const {
 /**
  * Return an averaged view of this weight vector
  */
-AvgWeightVector MiraWeightVector::avg() {
+AvgWeightVector MiraWeightVector::avg()
+{
   this->fixTotals();
   return AvgWeightVector(*this);
 }
@@ -73,7 +77,8 @@ AvgWeightVector MiraWeightVector::avg() {
 /**
  * Updates a weight and lazily updates its total
  */
-void MiraWeightVector::update(size_t index, ValType delta) {
+void MiraWeightVector::update(size_t index, ValType delta)
+{
 
   // Handle previously unseen weights
   while(index>=m_weights.size()) {
@@ -91,25 +96,27 @@ void MiraWeightVector::update(size_t index, ValType delta) {
 /**
  * Make sure everyone's total is up-to-date
  */
-void MiraWeightVector::fixTotals() {
+void MiraWeightVector::fixTotals()
+{
   for(size_t i=0; i<m_weights.size(); i++) update(i,0);
 }
 
 /**
  * Helper to handle out of range weights
  */
-ValType MiraWeightVector::weight(size_t index) const {
+ValType MiraWeightVector::weight(size_t index) const
+{
   if(index < m_weights.size()) {
     return m_weights[index];
-  }
-  else {
+  } else {
     return 0;
   }
 }
 
-ValType MiraWeightVector::sqrNorm() const {
+ValType MiraWeightVector::sqrNorm() const
+{
   ValType toRet = 0;
-  for(size_t i=0;i<m_weights.size();i++) {
+  for(size_t i=0; i<m_weights.size(); i++) {
     toRet += weight(i) * weight(i);
   }
   return toRet;
@@ -119,9 +126,9 @@ AvgWeightVector::AvgWeightVector(const MiraWeightVector& wv)
   :m_wv(wv)
 {}
 
-ostream& operator<<(ostream& o, const MiraWeightVector& e) 
+ostream& operator<<(ostream& o, const MiraWeightVector& e)
 {
-  for(size_t i=0;i<e.m_weights.size();i++) {
+  for(size_t i=0; i<e.m_weights.size(); i++) {
     if(abs(e.m_weights[i])>1e-8) {
       if(i>0) o << " ";
       cerr << i << ":" << e.m_weights[i];
@@ -136,14 +143,14 @@ ValType AvgWeightVector::weight(size_t index) const
   else {
     if(index < m_wv.m_totals.size()) {
       return m_wv.m_totals[index] / m_wv.m_numUpdates;
-    }
-    else {
+    } else {
       return 0;
     }
   }
 }
 
-ValType AvgWeightVector::score(const MiraFeatureVector& fv) const {
+ValType AvgWeightVector::score(const MiraFeatureVector& fv) const
+{
   ValType toRet = 0.0;
   for(size_t i=0; i<fv.size(); i++) {
     toRet += weight(fv.feat(i)) * fv.val(i);
@@ -151,7 +158,8 @@ ValType AvgWeightVector::score(const MiraFeatureVector& fv) const {
   return toRet;
 }
 
-size_t AvgWeightVector::size() const {
+size_t AvgWeightVector::size() const
+{
   return m_wv.m_weights.size();
 }
 
diff --git a/mert/MiraWeightVector.h b/mert/MiraWeightVector.h
index 30f8adfa4..eb27e8a6d 100644
--- a/mert/MiraWeightVector.h
+++ b/mert/MiraWeightVector.h
@@ -17,11 +17,12 @@
 
 namespace MosesTuning
 {
-  
+
 
 class AvgWeightVector;
 
-class MiraWeightVector {
+class MiraWeightVector
+{
 public:
   /**
    * Constructor, initializes to the zero vector
@@ -91,7 +92,8 @@ private:
 /**
  * Averaged view of a weight vector
  */
-class AvgWeightVector {
+class AvgWeightVector
+{
 public:
   AvgWeightVector(const MiraWeightVector& wv);
   ValType score(const MiraFeatureVector& fv) const;
diff --git a/mert/Ngram.h b/mert/Ngram.h
index 6363c847c..521dc4928 100644
--- a/mert/Ngram.h
+++ b/mert/Ngram.h
@@ -13,8 +13,9 @@ namespace MosesTuning
  * typical accessors and mutaors, but we intentionally does not allow
  * erasing elements.
  */
-class NgramCounts {
- public:
+class NgramCounts
+{
+public:
   // Used to construct the ngram map
   struct NgramComparator {
     bool operator()(const std::vector<int>& a, const std::vector<int>& b) const {
@@ -45,7 +46,9 @@ class NgramCounts {
   /**
    * If the specified "ngram" is found, we add counts.
    * If not, we insert the default count in the container. */
-  inline void Add(const Key& ngram) { m_counts[ngram]++; }
+  inline void Add(const Key& ngram) {
+    m_counts[ngram]++;
+  }
 
   /**
    * Return true iff the specified "ngram" is found in the container.
@@ -60,34 +63,58 @@ class NgramCounts {
   /**
    * Clear all elments in the container.
    */
-  void clear() { m_counts.clear(); }
+  void clear() {
+    m_counts.clear();
+  }
 
   /**
    * Return true iff the container is empty.
    */
-  bool empty() const { return m_counts.empty(); }
+  bool empty() const {
+    return m_counts.empty();
+  }
 
   /**
    * Return the the number of elements in the container.
    */
-  std::size_t size() const { return m_counts.size(); }
+  std::size_t size() const {
+    return m_counts.size();
+  }
 
-  std::size_t max_size() const { return m_counts.max_size(); }
+  std::size_t max_size() const {
+    return m_counts.max_size();
+  }
 
   // Note: This is mainly used by unit tests.
-  int get_default_count() const { return kDefaultCount; }
+  int get_default_count() const {
+    return kDefaultCount;
+  }
 
-  iterator find(const Key& ngram) { return m_counts.find(ngram); }
-  const_iterator find(const Key& ngram) const { return m_counts.find(ngram); }
+  iterator find(const Key& ngram) {
+    return m_counts.find(ngram);
+  }
+  const_iterator find(const Key& ngram) const {
+    return m_counts.find(ngram);
+  }
 
-  Value& operator[](const Key& ngram) { return m_counts[ngram]; }
+  Value& operator[](const Key& ngram) {
+    return m_counts[ngram];
+  }
 
-  iterator begin() { return m_counts.begin(); }
-  const_iterator begin() const { return m_counts.begin(); }
-  iterator end() { return m_counts.end(); }
-  const_iterator end() const { return m_counts.end(); }
+  iterator begin() {
+    return m_counts.begin();
+  }
+  const_iterator begin() const {
+    return m_counts.begin();
+  }
+  iterator end() {
+    return m_counts.end();
+  }
+  const_iterator end() const {
+    return m_counts.end();
+  }
 
- private:
+private:
   const int kDefaultCount;
   boost::unordered_map<Key, Value> m_counts;
 };
diff --git a/mert/NgramTest.cpp b/mert/NgramTest.cpp
index e6218206f..87f36860b 100644
--- a/mert/NgramTest.cpp
+++ b/mert/NgramTest.cpp
@@ -5,7 +5,8 @@
 
 using namespace MosesTuning;
 
-BOOST_AUTO_TEST_CASE(ngram_basic) {
+BOOST_AUTO_TEST_CASE(ngram_basic)
+{
   NgramCounts counts;
   NgramCounts::Key key;
   key.push_back(1);
@@ -25,7 +26,8 @@ BOOST_AUTO_TEST_CASE(ngram_basic) {
   BOOST_CHECK_EQUAL(it->second, 1);
 }
 
-BOOST_AUTO_TEST_CASE(ngram_Add) {
+BOOST_AUTO_TEST_CASE(ngram_Add)
+{
   NgramCounts counts;
   NgramCounts::Key key;
   key.push_back(1);
@@ -49,7 +51,8 @@ BOOST_AUTO_TEST_CASE(ngram_Add) {
   BOOST_CHECK_EQUAL(counts[key3], counts.get_default_count());
 }
 
-BOOST_AUTO_TEST_CASE(ngram_lookup) {
+BOOST_AUTO_TEST_CASE(ngram_lookup)
+{
   NgramCounts counts;
   NgramCounts::Key key;
   key.push_back(1);
diff --git a/mert/Optimizer.cpp b/mert/Optimizer.cpp
index e5f5854b2..6afbd6241 100644
--- a/mert/Optimizer.cpp
+++ b/mert/Optimizer.cpp
@@ -17,7 +17,8 @@ using namespace std;
 static const float MIN_FLOAT = -1.0 * numeric_limits<float>::max();
 static const float MAX_FLOAT = numeric_limits<float>::max();
 
-namespace {
+namespace
+{
 
 /**
  * Compute the intersection of 2 lines.
@@ -35,7 +36,7 @@ inline float intersect(float m1, float b1, float m2, float b2)
 
 namespace MosesTuning
 {
-  
+
 
 Optimizer::Optimizer(unsigned Pd, const vector<unsigned>& i2O, const vector<bool>& pos, const vector<parameter_t>& start, unsigned int nrandom)
   : m_scorer(NULL), m_feature_data(), m_num_random_directions(nrandom), m_positive(pos)
@@ -198,7 +199,7 @@ statscore_t Optimizer::LineOptimize(const Point& origin, const Point& direction,
             thresholdmap.erase(previnserted); // erase old previnsert
             previnserted = thresholdmap.find(leftmostx); // point previnsert to the new threshold
             previnserted->second.back()=newd; // We update the diff for sentence S
-          // Threshold already exists but is not the previous one.
+            // Threshold already exists but is not the previous one.
           } else {
             // We append the diffs in previnsert to tit before destroying previnsert.
             tit->second.insert(tit->second.end(),previnserted->second.begin(),previnserted->second.end());
@@ -405,8 +406,7 @@ statscore_t SimpleOptimizer::TrueRun(Point& P) const
         for (unsigned int i = 0; i < Point::getdim(); i++)
           direction[i]=0.0;
         direction[d]=1.0;
-      }
-      else { // random direction update
+      } else { // random direction update
         direction.Randomize();
       }
       statscore_t curscore = LineOptimize(P, direction, linebest);//find the minimum on the line
@@ -443,8 +443,7 @@ statscore_t RandomDirectionOptimizer::TrueRun(Point& P) const
   // do specified number of random direction optimizations
   unsigned int nrun = 0;
   unsigned int nrun_no_change = 0;
-  for (; nrun_no_change < m_num_random_directions; nrun++, nrun_no_change++)
-  {
+  for (; nrun_no_change < m_num_random_directions; nrun++, nrun_no_change++) {
     // choose a random direction in which to optimize
     Point direction;
     direction.Randomize();
diff --git a/mert/Optimizer.h b/mert/Optimizer.h
index f81d59d96..80d6d10cc 100644
--- a/mert/Optimizer.h
+++ b/mert/Optimizer.h
@@ -12,7 +12,7 @@ static const float kMaxFloat = std::numeric_limits<float>::max();
 
 namespace MosesTuning
 {
-  
+
 
 class Point;
 
@@ -31,8 +31,12 @@ protected:
 public:
   Optimizer(unsigned Pd, const std::vector<unsigned>& i2O, const std::vector<bool>& positive, const std::vector<parameter_t>& start, unsigned int nrandom);
 
-  void SetScorer(Scorer *scorer) { m_scorer = scorer; }
-  void SetFeatureData(FeatureDataHandle feature_data) { m_feature_data = feature_data; }
+  void SetScorer(Scorer *scorer) {
+    m_scorer = scorer;
+  }
+  void SetFeatureData(FeatureDataHandle feature_data) {
+    m_feature_data = feature_data;
+  }
   virtual ~Optimizer();
 
   unsigned size() const {
@@ -97,7 +101,7 @@ private:
 public:
   RandomDirectionOptimizer(unsigned dim, const std::vector<unsigned>& i2O, const std::vector<bool>& positive,
                            const std::vector<parameter_t>& start, unsigned int nrandom)
-      : Optimizer(dim, i2O, positive, start, nrandom), kEPS(0.0001f) {}
+    : Optimizer(dim, i2O, positive, start, nrandom), kEPS(0.0001f) {}
   virtual statscore_t TrueRun(Point&) const;
 };
 
@@ -109,7 +113,7 @@ class RandomOptimizer : public Optimizer
 public:
   RandomOptimizer(unsigned dim, const std::vector<unsigned>& i2O, const std::vector<bool>& positive,
                   const std::vector<parameter_t>& start, unsigned int nrandom)
-      : Optimizer(dim, i2O, positive, start, nrandom) {}
+    : Optimizer(dim, i2O, positive, start, nrandom) {}
   virtual statscore_t TrueRun(Point&) const;
 };
 
diff --git a/mert/OptimizerFactory.cpp b/mert/OptimizerFactory.cpp
index b33194f33..97288f9a8 100644
--- a/mert/OptimizerFactory.cpp
+++ b/mert/OptimizerFactory.cpp
@@ -5,7 +5,7 @@ using namespace std;
 
 namespace MosesTuning
 {
-  
+
 
 vector<string> OptimizerFactory::m_type_names;
 
@@ -38,11 +38,11 @@ OptimizerFactory::OptimizerType OptimizerFactory::GetOptimizerType(const string&
 }
 
 Optimizer* OptimizerFactory::BuildOptimizer(unsigned dim,
-                                            const vector<unsigned>& i2o,
-                                            const std::vector<bool>& positive,
-                                            const vector<parameter_t>& start,
-                                            const string& type,
-                                            unsigned int nrandom)
+    const vector<unsigned>& i2o,
+    const std::vector<bool>& positive,
+    const vector<parameter_t>& start,
+    const string& type,
+    unsigned int nrandom)
 {
   OptimizerType opt_type = GetOptimizerType(type);
   if (opt_type == NOPTIMIZER) {
@@ -55,18 +55,18 @@ Optimizer* OptimizerFactory::BuildOptimizer(unsigned dim,
   }
 
   switch (opt_type) {
-    case POWELL:
-      return new SimpleOptimizer(dim, i2o, positive, start, nrandom);
-      break;
-    case RANDOM_DIRECTION:
-      return new RandomDirectionOptimizer(dim, i2o, positive, start, nrandom);
-      break;
-    case RANDOM:
-      return new RandomOptimizer(dim, i2o, positive, start, nrandom);
-      break;
-    default:
-      cerr << "Error: unknown optimizer" << type << endl;
-      return NULL;
+  case POWELL:
+    return new SimpleOptimizer(dim, i2o, positive, start, nrandom);
+    break;
+  case RANDOM_DIRECTION:
+    return new RandomDirectionOptimizer(dim, i2o, positive, start, nrandom);
+    break;
+  case RANDOM:
+    return new RandomOptimizer(dim, i2o, positive, start, nrandom);
+    break;
+  default:
+    cerr << "Error: unknown optimizer" << type << endl;
+    return NULL;
   }
 }
 
diff --git a/mert/OptimizerFactory.h b/mert/OptimizerFactory.h
index ae34bcb00..fc0fea65a 100644
--- a/mert/OptimizerFactory.h
+++ b/mert/OptimizerFactory.h
@@ -6,13 +6,13 @@
 
 namespace MosesTuning
 {
-  
+
 
 class Optimizer;
 
 class OptimizerFactory
 {
- public:
+public:
   // NOTE: Add new optimizer here BEFORE NOPTIMZER
   enum OptimizerType {
     POWELL = 0,
@@ -36,7 +36,7 @@ class OptimizerFactory
                                    const std::string& type,
                                    unsigned int nrandom);
 
- private:
+private:
   OptimizerFactory() {}
   ~OptimizerFactory() {}
 
diff --git a/mert/OptimizerFactoryTest.cpp b/mert/OptimizerFactoryTest.cpp
index 4d259c68d..56f894904 100644
--- a/mert/OptimizerFactoryTest.cpp
+++ b/mert/OptimizerFactoryTest.cpp
@@ -7,21 +7,24 @@
 
 using namespace MosesTuning;
 
-namespace {
+namespace
+{
 
 inline bool CheckBuildOptimizer(unsigned dim,
                                 const std::vector<unsigned>& to_optimize,
                                 const std::vector<bool>& positive,
                                 const std::vector<parameter_t>& start,
                                 const std::string& type,
-                                unsigned int num_random) {
+                                unsigned int num_random)
+{
   boost::scoped_ptr<Optimizer> optimizer(OptimizerFactory::BuildOptimizer(dim, to_optimize, positive, start, type, num_random));
   return optimizer.get() != NULL;
 }
 
 } // namespace
 
-BOOST_AUTO_TEST_CASE(optimizer_type) {
+BOOST_AUTO_TEST_CASE(optimizer_type)
+{
   BOOST_CHECK_EQUAL(OptimizerFactory::GetOptimizerType("powell"),
                     OptimizerFactory::POWELL);
   BOOST_CHECK_EQUAL(OptimizerFactory::GetOptimizerType("random"),
@@ -30,7 +33,8 @@ BOOST_AUTO_TEST_CASE(optimizer_type) {
                     OptimizerFactory::RANDOM_DIRECTION);
 }
 
-BOOST_AUTO_TEST_CASE(optimizer_build) {
+BOOST_AUTO_TEST_CASE(optimizer_build)
+{
   const unsigned dim = 3;
   std::vector<unsigned> to_optimize;
   to_optimize.push_back(1);
diff --git a/mert/PerScorer.cpp b/mert/PerScorer.cpp
index 06b53436f..3e157a55e 100644
--- a/mert/PerScorer.cpp
+++ b/mert/PerScorer.cpp
@@ -10,7 +10,7 @@ using namespace std;
 
 namespace MosesTuning
 {
-  
+
 
 PerScorer::PerScorer(const string& config)
   : StatisticsBasedScorer("PER",config) {}
diff --git a/mert/PerScorer.h b/mert/PerScorer.h
index 76ea9bfd7..ffb869942 100644
--- a/mert/PerScorer.h
+++ b/mert/PerScorer.h
@@ -9,7 +9,7 @@
 
 namespace MosesTuning
 {
-  
+
 
 class ScoreStats;
 
@@ -27,7 +27,9 @@ public:
 
   virtual void setReferenceFiles(const std::vector<std::string>& referenceFiles);
   virtual void prepareStats(std::size_t sid, const std::string& text, ScoreStats& entry);
-  virtual std::size_t NumberOfScores() const { return 3; }
+  virtual std::size_t NumberOfScores() const {
+    return 3;
+  }
   virtual float calculateScore(const std::vector<int>& comps) const;
 
 private:
diff --git a/mert/Permutation.cpp b/mert/Permutation.cpp
index 5f3102f26..a4c74b0d2 100644
--- a/mert/Permutation.cpp
+++ b/mert/Permutation.cpp
@@ -16,7 +16,7 @@ using namespace std;
 
 namespace MosesTuning
 {
-  
+
 
 Permutation::Permutation(const string &alignment, const int sourceLength, const int targetLength )
 {
@@ -86,7 +86,7 @@ void Permutation::set(const string & alignment,const int sourceLength)
     //cout << "SP:" << sourcePos << " TP:" << targetPos << endl;
     if (sourcePos > sourceLength) {
       cerr << "Source sentence length:" << sourceLength << " is smaller than alignment source position:" << sourcePos << endl;
-      cerr << "******** Permutation::set :" << alignment << ": len : " << sourceLength <<endl; 
+      cerr << "******** Permutation::set :" << alignment << ": len : " << sourceLength <<endl;
       exit(1);
     }
     //If have multiple target pos aligned to one source,
@@ -187,7 +187,7 @@ float Permutation::distance(const Permutation &permCompare, const distanceMetric
   float score=0;
 
   //bool debug= (verboselevel()>3); // TODO: fix verboselevel()
-  bool debug=false; 
+  bool debug=false;
   if (debug) {
     cout << "*****Permutation::distance" <<endl;
     cout << "Hypo:" << endl;
diff --git a/mert/Permutation.h b/mert/Permutation.h
index 2c47487b6..b8be86a1b 100644
--- a/mert/Permutation.h
+++ b/mert/Permutation.h
@@ -19,7 +19,7 @@
 
 namespace MosesTuning
 {
-  
+
 
 class Permutation
 {
diff --git a/mert/PermutationScorer.cpp b/mert/PermutationScorer.cpp
index 12025a77e..aec389c27 100644
--- a/mert/PermutationScorer.cpp
+++ b/mert/PermutationScorer.cpp
@@ -5,7 +5,7 @@ using namespace std;
 
 namespace MosesTuning
 {
-  
+
 
 const int PermutationScorer::SCORE_PRECISION = 5;
 const int PermutationScorer::SCORE_MULTFACT = 100000; // 100000=10^SCORE_PRECISION
@@ -147,7 +147,7 @@ int PermutationScorer::getNumberWords (const string& text) const
 void PermutationScorer::prepareStats(size_t sid, const string& text, ScoreStats& entry)
 {
   //bool debug= (verboselevel()>3); // TODO: fix verboselevel()
-  bool debug=false; 
+  bool debug=false;
   if (debug) {
     cout << "*******prepareStats" ;
     cout << text << endl;
diff --git a/mert/PermutationScorer.h b/mert/PermutationScorer.h
index 4d5c144ce..c3d0cc960 100644
--- a/mert/PermutationScorer.h
+++ b/mert/PermutationScorer.h
@@ -19,7 +19,7 @@
 
 namespace MosesTuning
 {
-  
+
 /**
   * Permutation
  **/
diff --git a/mert/Point.cpp b/mert/Point.cpp
index 5c446aa8b..2219749bd 100644
--- a/mert/Point.cpp
+++ b/mert/Point.cpp
@@ -29,7 +29,7 @@ Point::Point() : vector<parameter_t>(m_dim), m_score(0.0) {}
 Point::Point(const vector<parameter_t>& init,
              const vector<parameter_t>& min,
              const vector<parameter_t>& max)
-    : vector<parameter_t>(Point::m_dim), m_score(0.0)
+  : vector<parameter_t>(Point::m_dim), m_score(0.0)
 {
   m_min.resize(Point::m_dim);
   m_max.resize(Point::m_dim);
diff --git a/mert/Point.h b/mert/Point.h
index 92cb832dd..f53f5f982 100644
--- a/mert/Point.h
+++ b/mert/Point.h
@@ -8,7 +8,7 @@
 
 namespace MosesTuning
 {
-  
+
 
 class FeatureStats;
 class Optimizer;
@@ -53,11 +53,19 @@ private:
   statscore_t m_score;
 
 public:
-  static unsigned int getdim() { return m_dim; }
-  static void setdim(std::size_t d) { m_dim = d; }
+  static unsigned int getdim() {
+    return m_dim;
+  }
+  static void setdim(std::size_t d) {
+    m_dim = d;
+  }
 
-  static unsigned int getpdim() { return m_pdim; }
-  static void setpdim(std::size_t pd) { m_pdim = pd; }
+  static unsigned int getpdim() {
+    return m_pdim;
+  }
+  static void setpdim(std::size_t pd) {
+    m_pdim = pd;
+  }
 
   static void set_optindices(const std::vector<unsigned int>& indices) {
     m_opt_indices = indices;
@@ -90,7 +98,9 @@ public:
    */
   friend std::ostream& operator<<(std::ostream& o,const Point& P);
 
-  void Normalize() { NormalizeL2(); }
+  void Normalize() {
+    NormalizeL2();
+  }
   void NormalizeL2();
   void NormalizeL1();
 
@@ -100,8 +110,12 @@ public:
    */
   void GetAllWeights(std::vector<parameter_t>& w) const;
 
-  statscore_t GetScore() const { return m_score; }
-  void SetScore(statscore_t score) { m_score = score; }
+  statscore_t GetScore() const {
+    return m_score;
+  }
+  void SetScore(statscore_t score) {
+    m_score = score;
+  }
 };
 
 }
diff --git a/mert/PointTest.cpp b/mert/PointTest.cpp
index df270dec9..f9e8e8bb2 100644
--- a/mert/PointTest.cpp
+++ b/mert/PointTest.cpp
@@ -9,7 +9,8 @@
 using namespace std;
 using namespace MosesTuning;
 
-BOOST_AUTO_TEST_CASE(point_operators) {
+BOOST_AUTO_TEST_CASE(point_operators)
+{
   const unsigned int dim = 5;
   vector<float> init(dim);
   init[0] = 1.0f;
diff --git a/mert/PreProcessFilter.cpp b/mert/PreProcessFilter.cpp
index da26177f7..4fbcc0c89 100644
--- a/mert/PreProcessFilter.cpp
+++ b/mert/PreProcessFilter.cpp
@@ -18,7 +18,7 @@ using namespace std;
 
 namespace MosesTuning
 {
-  
+
 
 // Child exec error signal
 void exec_failed (int sig)
@@ -28,116 +28,108 @@ void exec_failed (int sig)
 }
 
 PreProcessFilter::PreProcessFilter(const string& filterCommand)
-    : m_toFilter(NULL),
-      m_fromFilter(NULL)
+  : m_toFilter(NULL),
+    m_fromFilter(NULL)
 {
-    // Child error signal install
-    // sigaction is the replacement for the traditional signal() method
-    struct sigaction action;
-    action.sa_handler = exec_failed;
-    sigemptyset(&action.sa_mask);
-    action.sa_flags = 0;
-    if (sigaction(SIGUSR1, &action, NULL) < 0)
-    {
-        perror("SIGUSR1 install error");
-        exit(EXIT_FAILURE);
-    }
-
-    int pipe_status;
-    int pipefds_input[2];
-    int pipefds_output[2];
-    // int pipefds_error[2];
-
-    // Create the pipes
-    // We do this before the fork so both processes will know about
-    // the same pipe and they can communicate.
-
-    pipe_status = pipe(pipefds_input);
-    if (pipe_status == -1)
-    {
-        perror("Error creating the pipe");
-        exit(EXIT_FAILURE);
-    }
-
-    pipe_status = pipe(pipefds_output);
-    if (pipe_status == -1)
-    {
-        perror("Error creating the pipe");
-        exit(EXIT_FAILURE);
-    }
-
-    /*
-    pipe_status = pipe(pipefds_error);
-    if (pipe_status == -1)
-    {
-        perror("Error creating the pipe");
-        exit(EXIT_FAILURE);
-    }
-    */
-
-    pid_t pid;
-    // Create child process; both processes continue from here
-    pid = fork();
-
-    if (pid == pid_t(0))
-    {
-        // Child process
-
-        // When the child process finishes sends a SIGCHLD signal
-        // to the parent
-
-        // Tie the standard input, output and error streams to the
-        // appropiate pipe ends
-        // The file descriptor 0 is the standard input
-        // We tie it to the read end of the pipe as we will use
-        // this end of the pipe to read from it
-        dup2 (CHILD_STDIN_READ,0);
-        dup2 (CHILD_STDOUT_WRITE,1);
-        // dup2 (CHILD_STDERR_WRITE,2);
-        // Close in the child the unused ends of the pipes
-        close(CHILD_STDIN_WRITE);
-        close(CHILD_STDOUT_READ);
-        //close(CHILD_STDERR_READ);
-
-        // Execute the program
-        execl("/bin/bash", "bash", "-c", filterCommand.c_str() , (char*)NULL);
-
-        // We should never reach this point
-        // Tell the parent the exec failed
-        kill(getppid(), SIGUSR1);
-        exit(EXIT_FAILURE);
-    }
-    else if (pid > pid_t(0))
-    {
-        // Parent
-
-        // Close in the parent the unused ends of the pipes
-        close(CHILD_STDIN_READ);
-        close(CHILD_STDOUT_WRITE);
-        // close(CHILD_STDERR_WRITE);
-
-        m_toFilter = new ofdstream(CHILD_STDIN_WRITE);
-        m_fromFilter = new ifdstream(CHILD_STDOUT_READ);
-    }
-    else
-    {
-        perror("Error: fork failed");
-        exit(EXIT_FAILURE);
-    }
+  // Child error signal install
+  // sigaction is the replacement for the traditional signal() method
+  struct sigaction action;
+  action.sa_handler = exec_failed;
+  sigemptyset(&action.sa_mask);
+  action.sa_flags = 0;
+  if (sigaction(SIGUSR1, &action, NULL) < 0) {
+    perror("SIGUSR1 install error");
+    exit(EXIT_FAILURE);
+  }
+
+  int pipe_status;
+  int pipefds_input[2];
+  int pipefds_output[2];
+  // int pipefds_error[2];
+
+  // Create the pipes
+  // We do this before the fork so both processes will know about
+  // the same pipe and they can communicate.
+
+  pipe_status = pipe(pipefds_input);
+  if (pipe_status == -1) {
+    perror("Error creating the pipe");
+    exit(EXIT_FAILURE);
+  }
+
+  pipe_status = pipe(pipefds_output);
+  if (pipe_status == -1) {
+    perror("Error creating the pipe");
+    exit(EXIT_FAILURE);
+  }
+
+  /*
+  pipe_status = pipe(pipefds_error);
+  if (pipe_status == -1)
+  {
+      perror("Error creating the pipe");
+      exit(EXIT_FAILURE);
+  }
+  */
+
+  pid_t pid;
+  // Create child process; both processes continue from here
+  pid = fork();
+
+  if (pid == pid_t(0)) {
+    // Child process
+
+    // When the child process finishes sends a SIGCHLD signal
+    // to the parent
+
+    // Tie the standard input, output and error streams to the
+    // appropiate pipe ends
+    // The file descriptor 0 is the standard input
+    // We tie it to the read end of the pipe as we will use
+    // this end of the pipe to read from it
+    dup2 (CHILD_STDIN_READ,0);
+    dup2 (CHILD_STDOUT_WRITE,1);
+    // dup2 (CHILD_STDERR_WRITE,2);
+    // Close in the child the unused ends of the pipes
+    close(CHILD_STDIN_WRITE);
+    close(CHILD_STDOUT_READ);
+    //close(CHILD_STDERR_READ);
+
+    // Execute the program
+    execl("/bin/bash", "bash", "-c", filterCommand.c_str() , (char*)NULL);
+
+    // We should never reach this point
+    // Tell the parent the exec failed
+    kill(getppid(), SIGUSR1);
+    exit(EXIT_FAILURE);
+  } else if (pid > pid_t(0)) {
+    // Parent
+
+    // Close in the parent the unused ends of the pipes
+    close(CHILD_STDIN_READ);
+    close(CHILD_STDOUT_WRITE);
+    // close(CHILD_STDERR_WRITE);
+
+    m_toFilter = new ofdstream(CHILD_STDIN_WRITE);
+    m_fromFilter = new ifdstream(CHILD_STDOUT_READ);
+  } else {
+    perror("Error: fork failed");
+    exit(EXIT_FAILURE);
+  }
 }
 
 string PreProcessFilter::ProcessSentence(const string& sentence)
 {
-    *m_toFilter << sentence << "\n";
-    string processedSentence;
-    m_fromFilter->getline(processedSentence);
-    return processedSentence;
+  *m_toFilter << sentence << "\n";
+  string processedSentence;
+  m_fromFilter->getline(processedSentence);
+  return processedSentence;
 }
 
 PreProcessFilter::~PreProcessFilter()
 {
-    delete m_toFilter;
-    delete m_fromFilter;
+  delete m_toFilter;
+  delete m_fromFilter;
 }
 
 }
diff --git a/mert/PreProcessFilter.h b/mert/PreProcessFilter.h
index 25e627f6d..9946ddccb 100644
--- a/mert/PreProcessFilter.h
+++ b/mert/PreProcessFilter.h
@@ -5,7 +5,7 @@
 
 namespace MosesTuning
 {
-  
+
 
 class ofdstream;
 class ifdstream;
@@ -22,8 +22,8 @@ public:
   ~PreProcessFilter();
 
 private:
-    ofdstream* m_toFilter;
-    ifdstream* m_fromFilter;
+  ofdstream* m_toFilter;
+  ifdstream* m_fromFilter;
 };
 
 }
diff --git a/mert/Reference.h b/mert/Reference.h
index 1d6869a12..2c12f2ed7 100644
--- a/mert/Reference.h
+++ b/mert/Reference.h
@@ -9,38 +9,57 @@
 
 namespace MosesTuning
 {
-  
+
 
 /**
  * Reference class represents reference translations for an output
  * translation used in calculating BLEU score.
  */
-class Reference {
- public:
+class Reference
+{
+public:
   // for m_length
   typedef std::vector<std::size_t>::iterator iterator;
   typedef std::vector<std::size_t>::const_iterator const_iterator;
 
   Reference() : m_counts(new NgramCounts) { }
-  ~Reference() { delete m_counts; }
+  ~Reference() {
+    delete m_counts;
+  }
 
-  NgramCounts* get_counts() { return m_counts; }
-  const NgramCounts* get_counts() const { return m_counts; }
+  NgramCounts* get_counts() {
+    return m_counts;
+  }
+  const NgramCounts* get_counts() const {
+    return m_counts;
+  }
 
-  iterator begin() { return m_length.begin(); }
-  const_iterator begin() const { return m_length.begin(); }
-  iterator end() { return m_length.end(); }
-  const_iterator end() const { return m_length.end(); }
+  iterator begin() {
+    return m_length.begin();
+  }
+  const_iterator begin() const {
+    return m_length.begin();
+  }
+  iterator end() {
+    return m_length.end();
+  }
+  const_iterator end() const {
+    return m_length.end();
+  }
 
-  void push_back(std::size_t len) { m_length.push_back(len); }
+  void push_back(std::size_t len) {
+    m_length.push_back(len);
+  }
 
-  std::size_t num_references() const { return m_length.size(); }
+  std::size_t num_references() const {
+    return m_length.size();
+  }
 
   int CalcAverage() const;
   int CalcClosest(std::size_t length) const;
   int CalcShortest() const;
 
- private:
+private:
   NgramCounts* m_counts;
 
   // multiple reference lengths
@@ -49,16 +68,18 @@ class Reference {
 
 // TODO(tetsuok): fix this function and related stuff.
 // "average" reference length should not be calculated at sentence-level unlike "closest".
-inline int Reference::CalcAverage() const {
+inline int Reference::CalcAverage() const
+{
   int total = 0;
   for (std::size_t i = 0; i < m_length.size(); ++i) {
     total += m_length[i];
   }
   return static_cast<int>(
-      static_cast<float>(total) / m_length.size());
+           static_cast<float>(total) / m_length.size());
 }
 
-inline int Reference::CalcClosest(std::size_t length) const {
+inline int Reference::CalcClosest(std::size_t length) const
+{
   int min_diff = INT_MAX;
   int closest_ref_id = 0; // an index of the closest reference translation
   for (std::size_t i = 0; i < m_length.size(); ++i) {
@@ -79,7 +100,8 @@ inline int Reference::CalcClosest(std::size_t length) const {
   return static_cast<int>(m_length[closest_ref_id]);
 }
 
-inline int Reference::CalcShortest() const {
+inline int Reference::CalcShortest() const
+{
   return *std::min_element(m_length.begin(), m_length.end());
 }
 
diff --git a/mert/ReferenceTest.cpp b/mert/ReferenceTest.cpp
index ad76de1f7..c33321227 100644
--- a/mert/ReferenceTest.cpp
+++ b/mert/ReferenceTest.cpp
@@ -5,12 +5,14 @@
 
 using namespace MosesTuning;
 
-BOOST_AUTO_TEST_CASE(refernece_count) {
+BOOST_AUTO_TEST_CASE(refernece_count)
+{
   Reference ref;
   BOOST_CHECK(ref.get_counts() != NULL);
 }
 
-BOOST_AUTO_TEST_CASE(refernece_length_iterator) {
+BOOST_AUTO_TEST_CASE(refernece_length_iterator)
+{
   Reference ref;
   ref.push_back(4);
   ref.push_back(2);
@@ -24,7 +26,8 @@ BOOST_AUTO_TEST_CASE(refernece_length_iterator) {
   BOOST_CHECK(it == ref.end());
 }
 
-BOOST_AUTO_TEST_CASE(refernece_length_average) {
+BOOST_AUTO_TEST_CASE(refernece_length_average)
+{
   {
     Reference ref;
     ref.push_back(4);
@@ -49,7 +52,8 @@ BOOST_AUTO_TEST_CASE(refernece_length_average) {
   }
 }
 
-BOOST_AUTO_TEST_CASE(refernece_length_closest) {
+BOOST_AUTO_TEST_CASE(refernece_length_closest)
+{
   {
     Reference ref;
     ref.push_back(4);
@@ -92,7 +96,8 @@ BOOST_AUTO_TEST_CASE(refernece_length_closest) {
   }
 }
 
-BOOST_AUTO_TEST_CASE(refernece_length_shortest) {
+BOOST_AUTO_TEST_CASE(refernece_length_shortest)
+{
   {
     Reference ref;
     ref.push_back(4);
diff --git a/mert/ScopedVector.h b/mert/ScopedVector.h
index c87f07071..bd9251a7c 100644
--- a/mert/ScopedVector.h
+++ b/mert/ScopedVector.h
@@ -5,19 +5,26 @@
 
 namespace MosesTuning
 {
-  
+
 template <class T>
-class ScopedVector {
- public:
+class ScopedVector
+{
+public:
   typedef typename std::vector<T*>::iterator iterator;
   typedef typename std::vector<T*>::const_iterator const_iterator;
 
   ScopedVector() {}
-  virtual ~ScopedVector() { reset(); }
+  virtual ~ScopedVector() {
+    reset();
+  }
 
-  bool empty() const { return m_vec.empty(); }
+  bool empty() const {
+    return m_vec.empty();
+  }
 
-  void push_back(T *e) { m_vec.push_back(e); }
+  void push_back(T *e) {
+    m_vec.push_back(e);
+  }
 
   void reset() {
     for (iterator it = m_vec.begin(); it != m_vec.end(); ++it) {
@@ -26,27 +33,53 @@ class ScopedVector {
     m_vec.clear();
   }
 
-  void reserve(std::size_t capacity) { m_vec.reserve(capacity); }
-  void resize(std::size_t size) { m_vec.resize(size); }
+  void reserve(std::size_t capacity) {
+    m_vec.reserve(capacity);
+  }
+  void resize(std::size_t size) {
+    m_vec.resize(size);
+  }
 
-  std::size_t size() const {return m_vec.size(); }
+  std::size_t size() const {
+    return m_vec.size();
+  }
 
-  iterator begin() { return m_vec.begin(); }
-  const_iterator begin() const { return m_vec.begin(); }
+  iterator begin() {
+    return m_vec.begin();
+  }
+  const_iterator begin() const {
+    return m_vec.begin();
+  }
 
-  iterator end() { return m_vec.end(); }
-  const_iterator end() const { return m_vec.end(); }
+  iterator end() {
+    return m_vec.end();
+  }
+  const_iterator end() const {
+    return m_vec.end();
+  }
 
-  std::vector<T*>& get() { return m_vec; }
-  const std::vector<T*>& get() const { return m_vec; }
+  std::vector<T*>& get() {
+    return m_vec;
+  }
+  const std::vector<T*>& get() const {
+    return m_vec;
+  }
 
-  std::vector<T*>* operator->() { return &m_vec; }
-  const std::vector<T*>* operator->() const { return &m_vec; }
+  std::vector<T*>* operator->() {
+    return &m_vec;
+  }
+  const std::vector<T*>* operator->() const {
+    return &m_vec;
+  }
 
-  T*& operator[](std::size_t i) { return m_vec[i]; }
-  const T* operator[](std::size_t i) const { return m_vec[i]; }
+  T*& operator[](std::size_t i) {
+    return m_vec[i];
+  }
+  const T* operator[](std::size_t i) const {
+    return m_vec[i];
+  }
 
- private:
+private:
   std::vector<T*> m_vec;
 
   // no copying allowed.
diff --git a/mert/ScoreArray.cpp b/mert/ScoreArray.cpp
index dcd0f7680..dd9aa5b07 100644
--- a/mert/ScoreArray.cpp
+++ b/mert/ScoreArray.cpp
@@ -17,12 +17,12 @@ namespace MosesTuning
 
 
 ScoreArray::ScoreArray()
-    : m_num_scores(0), m_index(0) {}
+  : m_num_scores(0), m_index(0) {}
 
 void ScoreArray::savetxt(ostream* os, const string& sctype)
 {
   *os << SCORES_TXT_BEGIN << " " << m_index << " " << m_array.size()
-          << " " << m_num_scores << " " << sctype << endl;
+      << " " << m_num_scores << " " << sctype << endl;
   for (scorearray_t::iterator i = m_array.begin(); i !=m_array.end(); i++) {
     i->savetxt(os);
     *os << endl;
@@ -33,7 +33,7 @@ void ScoreArray::savetxt(ostream* os, const string& sctype)
 void ScoreArray::savebin(ostream* os, const string& score_type)
 {
   *os << SCORES_BIN_BEGIN << " " << m_index << " " << m_array.size()
-          << " " << m_num_scores << " " << score_type << endl;
+      << " " << m_num_scores << " " << score_type << endl;
   for (scorearray_t::iterator i = m_array.begin();
        i != m_array.end(); i++) {
     i->savebin(os);
@@ -63,7 +63,8 @@ void ScoreArray::save(const string &file, const string& score_type, bool bin)
   ofs.close();
 }
 
-void ScoreArray::save(const string& score_type, bool bin) {
+void ScoreArray::save(const string& score_type, bool bin)
+{
   save(&cout, score_type, bin);
 }
 
diff --git a/mert/ScoreArray.h b/mert/ScoreArray.h
index 5b6c748cb..438b57e3f 100644
--- a/mert/ScoreArray.h
+++ b/mert/ScoreArray.h
@@ -25,7 +25,7 @@ const char SCORES_BIN_END[] = "SCORES_BIN_END_0";
 
 class ScoreArray
 {
- private:
+private:
   scorearray_t m_array;
   std::string m_score_type;
   std::size_t m_num_scores;
@@ -38,17 +38,29 @@ public:
   ScoreArray();
   ~ScoreArray() {}
 
-  void clear() { m_array.clear(); }
+  void clear() {
+    m_array.clear();
+  }
 
-  int getIndex() const { return m_index; }
+  int getIndex() const {
+    return m_index;
+  }
 
-  void setIndex(int value) { m_index = value; }
+  void setIndex(int value) {
+    m_index = value;
+  }
 
-  ScoreStats& get(std::size_t i) { return m_array.at(i); }
+  ScoreStats& get(std::size_t i) {
+    return m_array.at(i);
+  }
 
-  const ScoreStats& get(std::size_t i) const { return m_array.at(i); }
+  const ScoreStats& get(std::size_t i) const {
+    return m_array.at(i);
+  }
 
-  void add(const ScoreStats& e) { m_array.push_back(e); }
+  void add(const ScoreStats& e) {
+    m_array.push_back(e);
+  }
 
   //ADDED BY TS
   void swap(std::size_t i, std::size_t j) {
@@ -62,15 +74,25 @@ public:
 
   void merge(ScoreArray& e);
 
-  std::string name() const { return m_score_type; }
+  std::string name() const {
+    return m_score_type;
+  }
 
-  void name(std::string &score_type) { m_score_type = score_type; }
+  void name(std::string &score_type) {
+    m_score_type = score_type;
+  }
 
-  std::size_t size() const { return m_array.size(); }
+  std::size_t size() const {
+    return m_array.size();
+  }
 
-  std::size_t NumberOfScores() const { return m_num_scores; }
+  std::size_t NumberOfScores() const {
+    return m_num_scores;
+  }
 
-  void NumberOfScores(std::size_t v) { m_num_scores = v; }
+  void NumberOfScores(std::size_t v) {
+    m_num_scores = v;
+  }
 
   void savetxt(std::ostream* os, const std::string& score_type);
   void savebin(std::ostream* os, const std::string& score_type);
diff --git a/mert/ScoreData.cpp b/mert/ScoreData.cpp
index d02a4d700..0906b3459 100644
--- a/mert/ScoreData.cpp
+++ b/mert/ScoreData.cpp
@@ -50,7 +50,8 @@ void ScoreData::save(const string &file, bool bin)
   ofs.close();
 }
 
-void ScoreData::save(bool bin) {
+void ScoreData::save(bool bin)
+{
   save(&cout, bin);
 }
 
diff --git a/mert/ScoreData.h b/mert/ScoreData.h
index ac3a6faa6..9159e029f 100644
--- a/mert/ScoreData.h
+++ b/mert/ScoreData.h
@@ -40,7 +40,9 @@ public:
   ScoreData(Scorer* scorer);
   ~ScoreData() {}
 
-  void clear() { m_array.clear(); }
+  void clear() {
+    m_array.clear();
+  }
 
   inline ScoreArray& get(std::size_t idx) {
     return m_array.at(idx);
@@ -66,7 +68,9 @@ public:
     return m_array.at(i).get(j);
   }
 
-  std::string name() const { return m_score_type; }
+  std::string name() const {
+    return m_score_type;
+  }
 
   std::string name(const std::string &score_type) {
     return m_score_type = score_type;
@@ -75,8 +79,12 @@ public:
   void add(ScoreArray& e);
   void add(const ScoreStats& e, int sent_idx);
 
-  std::size_t NumberOfScores() const { return m_num_scores; }
-  std::size_t size() const { return m_array.size(); }
+  std::size_t NumberOfScores() const {
+    return m_num_scores;
+  }
+  std::size_t size() const {
+    return m_array.size();
+  }
 
   void save(const std::string &file, bool bin=false);
   void save(std::ostream* os, bool bin=false);
diff --git a/mert/ScoreDataIterator.cpp b/mert/ScoreDataIterator.cpp
index 80568b810..71e05ab0b 100644
--- a/mert/ScoreDataIterator.cpp
+++ b/mert/ScoreDataIterator.cpp
@@ -29,18 +29,20 @@ using namespace util;
 
 namespace MosesTuning
 {
-  
+
 
 ScoreDataIterator::ScoreDataIterator() {}
 
-ScoreDataIterator::ScoreDataIterator(const string& filename) {
+ScoreDataIterator::ScoreDataIterator(const string& filename)
+{
   m_in.reset(new FilePiece(filename.c_str()));
   readNext();
 }
 
 ScoreDataIterator::~ScoreDataIterator() {}
 
-void ScoreDataIterator::readNext() {
+void ScoreDataIterator::readNext()
+{
   m_next.clear();
   try {
     StringPiece marker = m_in->ReadDelimited();
@@ -71,12 +73,14 @@ void ScoreDataIterator::readNext() {
   }
 }
 
-void ScoreDataIterator::increment() {
+void ScoreDataIterator::increment()
+{
   readNext();
 }
 
 
-bool ScoreDataIterator::equal(const ScoreDataIterator& rhs) const {
+bool ScoreDataIterator::equal(const ScoreDataIterator& rhs) const
+{
   if (!m_in && !rhs.m_in) {
     return true;
   } else if (!m_in) {
@@ -84,13 +88,14 @@ bool ScoreDataIterator::equal(const ScoreDataIterator& rhs) const {
   } else if (!rhs.m_in) {
     return false;
   } else {
-    return m_in->FileName() == rhs.m_in->FileName() && 
-      m_in->Offset() == rhs.m_in->Offset();
+    return m_in->FileName() == rhs.m_in->FileName() &&
+           m_in->Offset() == rhs.m_in->Offset();
   }
 }
 
 
-const vector<ScoreDataItem>& ScoreDataIterator::dereference() const {
+const vector<ScoreDataItem>& ScoreDataIterator::dereference() const
+{
   return m_next;
 }
 
diff --git a/mert/ScoreDataIterator.h b/mert/ScoreDataIterator.h
index 50640c158..e5968a8f7 100644
--- a/mert/ScoreDataIterator.h
+++ b/mert/ScoreDataIterator.h
@@ -33,40 +33,43 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 
 #include "FeatureDataIterator.h"
 
-namespace util { class FilePiece; }
+namespace util
+{
+class FilePiece;
+}
 
 namespace MosesTuning
 {
-  
+
 
 typedef std::vector<float> ScoreDataItem;
 
 class ScoreDataIterator :
   public boost::iterator_facade<ScoreDataIterator,
-                                const std::vector<ScoreDataItem>,
-                                boost::forward_traversal_tag>
+  const std::vector<ScoreDataItem>,
+  boost::forward_traversal_tag>
 {
-  public:
-    ScoreDataIterator();
-    explicit ScoreDataIterator(const std::string& filename);
+public:
+  ScoreDataIterator();
+  explicit ScoreDataIterator(const std::string& filename);
 
-    ~ScoreDataIterator();
+  ~ScoreDataIterator();
 
-    static ScoreDataIterator end() {
-      return ScoreDataIterator();
-    }
+  static ScoreDataIterator end() {
+    return ScoreDataIterator();
+  }
 
-  private:
-    friend class boost::iterator_core_access;
+private:
+  friend class boost::iterator_core_access;
 
-    void increment();
-    bool equal(const ScoreDataIterator& rhs) const;
-    const std::vector<ScoreDataItem>& dereference() const;
+  void increment();
+  bool equal(const ScoreDataIterator& rhs) const;
+  const std::vector<ScoreDataItem>& dereference() const;
 
-    void readNext();
+  void readNext();
 
-    boost::shared_ptr<util::FilePiece> m_in;
-    std::vector<ScoreDataItem> m_next;
+  boost::shared_ptr<util::FilePiece> m_in;
+  std::vector<ScoreDataItem> m_next;
 };
 
 }
diff --git a/mert/ScoreStats.cpp b/mert/ScoreStats.cpp
index 20e707005..1c66cdb5f 100644
--- a/mert/ScoreStats.cpp
+++ b/mert/ScoreStats.cpp
@@ -13,21 +13,22 @@
 
 using namespace std;
 
-namespace {
+namespace
+{
 const int kAvailableSize = 8;
 } // namespace
 
 namespace MosesTuning
 {
-  
+
 
 ScoreStats::ScoreStats()
-    : m_available_size(kAvailableSize), m_entries(0),
-      m_array(new ScoreStatsType[m_available_size]) {}
+  : m_available_size(kAvailableSize), m_entries(0),
+    m_array(new ScoreStatsType[m_available_size]) {}
 
 ScoreStats::ScoreStats(const size_t size)
-    : m_available_size(size), m_entries(size),
-      m_array(new ScoreStatsType[m_available_size])
+  : m_available_size(size), m_entries(size),
+    m_array(new ScoreStatsType[m_available_size])
 {
   memset(m_array, 0, GetArraySizeWithBytes());
 }
@@ -123,7 +124,8 @@ void ScoreStats::savetxt(ostream* os)
   *os << *this;
 }
 
-void ScoreStats::savetxt() {
+void ScoreStats::savetxt()
+{
   savetxt(&cout);
 }
 
@@ -140,7 +142,8 @@ ostream& operator<<(ostream& o, const ScoreStats& e)
   return o;
 }
 
-bool operator==(const ScoreStats& s1, const ScoreStats& s2) {
+bool operator==(const ScoreStats& s1, const ScoreStats& s2)
+{
   size_t size = s1.size();
 
   if (size != s2.size())
diff --git a/mert/ScoreStats.h b/mert/ScoreStats.h
index 4088b655e..930b03cea 100644
--- a/mert/ScoreStats.h
+++ b/mert/ScoreStats.h
@@ -18,7 +18,7 @@
 
 namespace MosesTuning
 {
-  
+
 
 class ScoreStats
 {
@@ -41,7 +41,9 @@ public:
 
   void Copy(const ScoreStats &stats);
 
-  bool isfull() const { return (m_entries < m_available_size) ? 0 : 1; }
+  bool isfull() const {
+    return (m_entries < m_available_size) ? 0 : 1;
+  }
 
   void expand();
   void add(ScoreStatsType v);
@@ -55,9 +57,15 @@ public:
     clear();
   }
 
-  ScoreStatsType get(std::size_t i) { return m_array[i]; }
-  ScoreStatsType get(std::size_t i) const { return m_array[i]; }
-  scorestats_t getArray() const { return m_array; }
+  ScoreStatsType get(std::size_t i) {
+    return m_array[i];
+  }
+  ScoreStatsType get(std::size_t i) const {
+    return m_array[i];
+  }
+  scorestats_t getArray() const {
+    return m_array;
+  }
 
   void set(const std::string& str);
 
@@ -69,15 +77,21 @@ public:
     }
   }
 
-  std::size_t bytes() const { return GetArraySizeWithBytes(); }
+  std::size_t bytes() const {
+    return GetArraySizeWithBytes();
+  }
 
   std::size_t GetArraySizeWithBytes() const {
     return m_entries * sizeof(ScoreStatsType);
   }
 
-  std::size_t size() const { return m_entries; }
+  std::size_t size() const {
+    return m_entries;
+  }
 
-  std::size_t available() const { return m_available_size; }
+  std::size_t available() const {
+    return m_available_size;
+  }
 
   void savetxt(const std::string &file);
   void savetxt(std::ostream* os);
diff --git a/mert/Scorer.cpp b/mert/Scorer.cpp
index 1a7136dc0..e3cc3d7e6 100644
--- a/mert/Scorer.cpp
+++ b/mert/Scorer.cpp
@@ -12,27 +12,31 @@ using namespace std;
 namespace MosesTuning
 {
 
-namespace {
+namespace
+{
 // For tokenizing a hypothesis translation, we may encounter unknown tokens which
 // do not exist in the corresponding reference translations.
 const int kUnknownToken = -1;
 } // namespace
 
 Scorer::Scorer(const string& name, const string& config)
-    : m_name(name),
-      m_vocab(mert::VocabularyFactory::GetVocabulary()),
-      m_filter(NULL),
-      m_score_data(NULL),
-      m_enable_preserve_case(true) {
+  : m_name(name),
+    m_vocab(mert::VocabularyFactory::GetVocabulary()),
+    m_filter(NULL),
+    m_score_data(NULL),
+    m_enable_preserve_case(true)
+{
   InitConfig(config);
 }
 
-Scorer::~Scorer() {
+Scorer::~Scorer()
+{
   Singleton<mert::Vocabulary>::Delete();
   delete m_filter;
 }
 
-void Scorer::InitConfig(const string& config) {
+void Scorer::InitConfig(const string& config)
+{
 //    cerr << "Scorer config string: " << config << endl;
   size_t start = 0;
   while (start < config.size()) {
@@ -53,7 +57,8 @@ void Scorer::InitConfig(const string& config) {
   }
 }
 
-void Scorer::TokenizeAndEncode(const string& line, vector<int>& encoded) {
+void Scorer::TokenizeAndEncode(const string& line, vector<int>& encoded)
+{
   for (util::TokenIter<util::AnyCharacter, true> it(line, util::AnyCharacter(" "));
        it; ++it) {
     if (!m_enable_preserve_case) {
@@ -69,7 +74,8 @@ void Scorer::TokenizeAndEncode(const string& line, vector<int>& encoded) {
   }
 }
 
-void Scorer::TokenizeAndEncodeTesting(const string& line, vector<int>& encoded) {
+void Scorer::TokenizeAndEncodeTesting(const string& line, vector<int>& encoded)
+{
   for (util::TokenIter<util::AnyCharacter, true> it(line, util::AnyCharacter(" "));
        it; ++it) {
     if (!m_enable_preserve_case) {
@@ -103,8 +109,7 @@ void Scorer::setFactors(const string& factors)
   if (factors.empty()) return;
   vector<string> factors_vec;
   split(factors, '|', factors_vec);
-  for(vector<string>::iterator it = factors_vec.begin(); it != factors_vec.end(); ++it)
-  {
+  for(vector<string>::iterator it = factors_vec.begin(); it != factors_vec.end(); ++it) {
     int factor = atoi(it->c_str());
     m_factors.push_back(factor);
   }
@@ -115,8 +120,8 @@ void Scorer::setFactors(const string& factors)
  */
 void Scorer::setFilter(const string& filterCommand)
 {
-    if (filterCommand.empty()) return;
-    m_filter = new PreProcessFilter(filterCommand);
+  if (filterCommand.empty()) return;
+  m_filter = new PreProcessFilter(filterCommand);
 }
 
 /**
@@ -130,8 +135,7 @@ string Scorer::applyFactors(const string& sentence) const
   split(sentence, ' ', tokens);
 
   stringstream sstream;
-  for (size_t i = 0; i < tokens.size(); ++i)
-  {
+  for (size_t i = 0; i < tokens.size(); ++i) {
     if (tokens[i] == "") continue;
 
     vector<string> factors;
@@ -141,8 +145,7 @@ string Scorer::applyFactors(const string& sentence) const
 
     if (i > 0) sstream << " ";
 
-    for (size_t j = 0; j < m_factors.size(); ++j)
-    {
+    for (size_t j = 0; j < m_factors.size(); ++j) {
       int findex = m_factors[j];
       if (findex < 0 || findex >= fsize) throw runtime_error("Factor index is out of range.");
 
@@ -158,17 +161,15 @@ string Scorer::applyFactors(const string& sentence) const
  */
 string Scorer::applyFilter(const string& sentence) const
 {
-  if (m_filter)
-  {
+  if (m_filter) {
     return m_filter->ProcessSentence(sentence);
-  }
-  else
-  {
+  } else {
     return sentence;
   }
 }
 
-float Scorer::score(const candidates_t& candidates) const {
+float Scorer::score(const candidates_t& candidates) const
+{
   diffs_t diffs;
   statscores_t scores;
   score(candidates, diffs, scores);
diff --git a/mert/Scorer.h b/mert/Scorer.h
index 0a090d1c4..4a1f4476a 100644
--- a/mert/Scorer.h
+++ b/mert/Scorer.h
@@ -10,7 +10,8 @@
 #include "Types.h"
 #include "ScoreData.h"
 
-namespace mert {
+namespace mert
+{
 
 class Vocabulary;
 
@@ -32,7 +33,7 @@ enum ScorerRegularisationStrategy {REG_NONE, REG_AVERAGE, REG_MINIMUM};
  */
 class Scorer
 {
- public:
+public:
   Scorer(const std::string& name, const std::string& config);
   virtual ~Scorer();
 
@@ -117,14 +118,16 @@ class Scorer
    */
   virtual void setFactors(const std::string& factors);
 
-  mert::Vocabulary* GetVocab() const { return m_vocab; }
+  mert::Vocabulary* GetVocab() const {
+    return m_vocab;
+  }
 
   /**
    * Set unix filter, which will be used to preprocess the sentences
    */
   virtual void setFilter(const std::string& filterCommand);
 
- private:
+private:
   void InitConfig(const std::string& config);
 
   /**
@@ -143,7 +146,7 @@ class Scorer
   std::vector<int> m_factors;
   PreProcessFilter* m_filter;
 
- protected:
+protected:
   ScoreData* m_score_data;
   bool m_enable_preserve_case;
 
@@ -173,41 +176,41 @@ class Scorer
   /**
    * Every inherited scorer should call this function for each sentence
    */
-  std::string preprocessSentence(const std::string& sentence) const
-  {
+  std::string preprocessSentence(const std::string& sentence) const {
     return applyFactors(applyFilter(sentence));
   }
 
 };
 
-namespace {
+namespace
+{
 
-  //regularisation strategies
-  inline float score_min(const statscores_t& scores, size_t start, size_t end)
-  {
-    float min = std::numeric_limits<float>::max();
-    for (size_t i = start; i < end; ++i) {
-      if (scores[i] < min) {
-        min = scores[i];
-      }
+//regularisation strategies
+inline float score_min(const statscores_t& scores, size_t start, size_t end)
+{
+  float min = std::numeric_limits<float>::max();
+  for (size_t i = start; i < end; ++i) {
+    if (scores[i] < min) {
+      min = scores[i];
     }
-    return min;
   }
+  return min;
+}
 
-  inline float score_average(const statscores_t& scores, size_t start, size_t end)
-  {
-    if ((end - start) < 1) {
-      // this shouldn't happen
-      return 0;
-    }
-    float total = 0;
-    for (size_t j = start; j < end; ++j) {
-      total += scores[j];
-    }
-
-    return total / (end - start);
+inline float score_average(const statscores_t& scores, size_t start, size_t end)
+{
+  if ((end - start) < 1) {
+    // this shouldn't happen
+    return 0;
+  }
+  float total = 0;
+  for (size_t j = start; j < end; ++j) {
+    total += scores[j];
   }
 
+  return total / (end - start);
+}
+
 } // namespace
 
 }
diff --git a/mert/ScorerFactory.cpp b/mert/ScorerFactory.cpp
index 126218b65..02000c1bc 100644
--- a/mert/ScorerFactory.cpp
+++ b/mert/ScorerFactory.cpp
@@ -14,9 +14,10 @@ using namespace std;
 
 namespace MosesTuning
 {
-  
 
-vector<string> ScorerFactory::getTypes() {
+
+vector<string> ScorerFactory::getTypes()
+{
   vector<string> types;
   types.push_back(string("BLEU"));
   types.push_back(string("PER"));
@@ -29,7 +30,8 @@ vector<string> ScorerFactory::getTypes() {
   return types;
 }
 
-Scorer* ScorerFactory::getScorer(const string& type, const string& config) {
+Scorer* ScorerFactory::getScorer(const string& type, const string& config)
+{
   if (type == "BLEU") {
     return new BleuScorer(config);
   } else if (type == "PER") {
@@ -48,8 +50,7 @@ Scorer* ScorerFactory::getScorer(const string& type, const string& config) {
   } else {
     if (type.find(',') != string::npos) {
       return new InterpolatedScorer(type, config);
-    }
-    else {
+    } else {
       throw runtime_error("Unknown scorer type: " + type);
     }
   }
diff --git a/mert/ScorerFactory.h b/mert/ScorerFactory.h
index e8b33d87c..b93db3024 100644
--- a/mert/ScorerFactory.h
+++ b/mert/ScorerFactory.h
@@ -6,7 +6,7 @@
 
 namespace MosesTuning
 {
-  
+
 
 class Scorer;
 
diff --git a/mert/SemposOverlapping.cpp b/mert/SemposOverlapping.cpp
index ffcabaab2..718bc7f26 100644
--- a/mert/SemposOverlapping.cpp
+++ b/mert/SemposOverlapping.cpp
@@ -6,7 +6,8 @@
 
 using namespace std;
 
-namespace {
+namespace
+{
 
 MosesTuning::SemposOverlapping* g_overlapping = NULL;
 
@@ -14,9 +15,10 @@ MosesTuning::SemposOverlapping* g_overlapping = NULL;
 
 namespace MosesTuning
 {
-  
 
-SemposOverlapping* SemposOverlappingFactory::GetOverlapping(const string& str, const SemposScorer* sempos) {
+
+SemposOverlapping* SemposOverlappingFactory::GetOverlapping(const string& str, const SemposScorer* sempos)
+{
   if (str == "cap-micro") {
     return new CapMicroOverlapping(sempos);
   } else if (str == "cap-macro") {
@@ -26,7 +28,8 @@ SemposOverlapping* SemposOverlappingFactory::GetOverlapping(const string& str, c
   }
 }
 
-void SemposOverlappingFactory::SetOverlapping(SemposOverlapping* ovr) {
+void SemposOverlappingFactory::SetOverlapping(SemposOverlapping* ovr)
+{
   g_overlapping = ovr;
 }
 
@@ -41,15 +44,13 @@ vector<int> CapMicroOverlapping::prepareStats(const sentence_t& cand, const sent
   int multCoeff = 1000;
 
   float interSum = 0;
-  for (sentence_t::iterator it = intersection.begin(); it != intersection.end(); it++)
-  {
+  for (sentence_t::iterator it = intersection.begin(); it != intersection.end(); it++) {
     interSum += semposScorer->weight(it->first);
   }
 
   float refSum = 0;
-  for (sentence_t::iterator it = ref.begin(); it != ref.end(); it++)
-  {
-    refSum += semposScorer->weight(it->first);    
+  for (sentence_t::iterator it = ref.begin(); it != ref.end(); it++) {
+    refSum += semposScorer->weight(it->first);
   }
 
   stats[0] = (int)(multCoeff * interSum);
diff --git a/mert/SemposOverlapping.h b/mert/SemposOverlapping.h
index 3b5a99f7f..5eddbaef3 100644
--- a/mert/SemposOverlapping.h
+++ b/mert/SemposOverlapping.h
@@ -9,7 +9,7 @@
 
 namespace MosesTuning
 {
-  
+
 
 class SemposScorer;
 
@@ -36,14 +36,15 @@ public:
   virtual std::size_t NumberOfScores() const = 0;
 };
 
-class SemposOverlappingFactory {
- public:
+class SemposOverlappingFactory
+{
+public:
   static SemposOverlapping* GetOverlapping(const std::string& str, const SemposScorer* sempos);
 
   // dependency injection for unit testing.
   static void SetOverlapping(SemposOverlapping* ovr);
 
- private:
+private:
   SemposOverlappingFactory() {}
   ~SemposOverlappingFactory() {}
 };
@@ -62,9 +63,11 @@ public:
 
   virtual std::vector<int> prepareStats(const sentence_t& cand, const sentence_t& ref);
   virtual float calculateScore(const std::vector<int>& stats) const;
-  virtual std::size_t NumberOfScores() const { return 2; }
+  virtual std::size_t NumberOfScores() const {
+    return 2;
+  }
 
- private:
+private:
   // no copying allowed.
   CapMicroOverlapping(const CapMicroOverlapping&);
   CapMicroOverlapping& operator=(const CapMicroOverlapping&);
@@ -82,9 +85,11 @@ public:
 
   virtual std::vector<int> prepareStats(const sentence_t& cand, const sentence_t& ref);
   virtual float calculateScore(const std::vector<int>& stats) const;
-  virtual std::size_t NumberOfScores() const { return kMaxNOC * 2; }
+  virtual std::size_t NumberOfScores() const {
+    return kMaxNOC * 2;
+  }
 
- private:
+private:
   // no copying allowed.
   CapMacroOverlapping(const CapMacroOverlapping&);
   CapMacroOverlapping& operator=(const CapMacroOverlapping&);
diff --git a/mert/SemposScorer.cpp b/mert/SemposScorer.cpp
index 8dd1fc8ee..235f73fbf 100644
--- a/mert/SemposScorer.cpp
+++ b/mert/SemposScorer.cpp
@@ -12,7 +12,7 @@ using namespace std;
 
 namespace MosesTuning
 {
-  
+
 
 SemposScorer::SemposScorer(const string& config)
   : StatisticsBasedScorer("SEMPOS", config),
@@ -25,8 +25,7 @@ SemposScorer::SemposScorer(const string& config)
   m_semposMap.clear();
 
   string weightsfile = getConfig("weightsfile", "");
-  if (weightsfile != "")
-  {
+  if (weightsfile != "") {
     loadWeights(weightsfile);
   }
 }
@@ -144,42 +143,35 @@ int SemposScorer::encodeSempos(const string& sempos)
 
 float SemposScorer::weight(int item) const
 {
-    std::map<int,float>::const_iterator it = weightsMap.find(item);
-    if (it == weightsMap.end())
-    {
-        return 1.0f;
-    }
-    else
-    {
-        return it->second;
-    }
+  std::map<int,float>::const_iterator it = weightsMap.find(item);
+  if (it == weightsMap.end()) {
+    return 1.0f;
+  } else {
+    return it->second;
+  }
 }
 
 void SemposScorer::loadWeights(const string& weightsfile)
 {
-    string line;
-    ifstream myfile;
-    myfile.open(weightsfile.c_str(), ifstream::in);
-    if (myfile.is_open())
-    {
-        while ( myfile.good() )
-        {
-            getline (myfile,line);
-            vector<string> fields;
-            if (line == "") continue;
-            split(line, '\t', fields);
-            if (fields.size() != 2) throw std::runtime_error("Bad format of a row in weights file.");
-            int encoded = encodeString(fields[0]);
-            float weight = atof(fields[1].c_str());
-            weightsMap[encoded] = weight;
-        }
-        myfile.close();
-    }
-    else
-    {
-        cerr << "Unable to open file "<< weightsfile << endl;
-        exit(1);
+  string line;
+  ifstream myfile;
+  myfile.open(weightsfile.c_str(), ifstream::in);
+  if (myfile.is_open()) {
+    while ( myfile.good() ) {
+      getline (myfile,line);
+      vector<string> fields;
+      if (line == "") continue;
+      split(line, '\t', fields);
+      if (fields.size() != 2) throw std::runtime_error("Bad format of a row in weights file.");
+      int encoded = encodeString(fields[0]);
+      float weight = atof(fields[1].c_str());
+      weightsMap[encoded] = weight;
     }
+    myfile.close();
+  } else {
+    cerr << "Unable to open file "<< weightsfile << endl;
+    exit(1);
+  }
 
 }
 
diff --git a/mert/SemposScorer.h b/mert/SemposScorer.h
index bde064349..b6c735bbe 100644
--- a/mert/SemposScorer.h
+++ b/mert/SemposScorer.h
@@ -19,7 +19,7 @@
 
 namespace MosesTuning
 {
-  
+
 
 /**
  * This class represents sempos based metrics.
@@ -32,12 +32,16 @@ public:
 
   virtual void setReferenceFiles(const std::vector<std::string>& referenceFiles);
   virtual void prepareStats(std::size_t sindex, const std::string& text, ScoreStats& entry);
-  virtual std::size_t NumberOfScores() const { return m_ovr->NumberOfScores(); }
+  virtual std::size_t NumberOfScores() const {
+    return m_ovr->NumberOfScores();
+  }
   virtual float calculateScore(const std::vector<int>& comps) const {
     return m_ovr->calculateScore(comps);
   }
 
-  bool EnableDebug() const { return m_enable_debug; }
+  bool EnableDebug() const {
+    return m_enable_debug;
+  }
 
   float weight(int item) const;
 
diff --git a/mert/SentenceLevelScorer.cpp b/mert/SentenceLevelScorer.cpp
index 0b159f0b7..0d1c15140 100644
--- a/mert/SentenceLevelScorer.cpp
+++ b/mert/SentenceLevelScorer.cpp
@@ -17,48 +17,50 @@ namespace MosesTuning
 {
 
 SentenceLevelScorer::SentenceLevelScorer(const string& name, const string& config)
-    : Scorer(name, config),
-      m_regularisationStrategy(REG_NONE),
-      m_regularisationWindow(0) {
+  : Scorer(name, config),
+    m_regularisationStrategy(REG_NONE),
+    m_regularisationWindow(0)
+{
   Init();
 }
 
 SentenceLevelScorer::~SentenceLevelScorer() {}
 
-void SentenceLevelScorer::Init() {
-    // Configure regularisation.
-    static string KEY_TYPE = "regtype";
-    static string KEY_WINDOW = "regwin";
-    static string KEY_CASE = "case";
-    static string TYPE_NONE = "none";
-    static string TYPE_AVERAGE = "average";
-    static string TYPE_MINIMUM = "min";
-    static string TRUE = "true";
-    static string FALSE = "false";
-
-    const string type = getConfig(KEY_TYPE, TYPE_NONE);
-    if (type == TYPE_NONE) {
-      m_regularisationStrategy = REG_NONE;
-    } else if (type == TYPE_AVERAGE) {
-      m_regularisationStrategy = REG_AVERAGE;
-    } else if (type == TYPE_MINIMUM) {
-      m_regularisationStrategy = REG_MINIMUM;
-    } else {
-      throw boost::lexer::runtime_error("Unknown scorer regularisation strategy: " + type);
-    }
-    cerr << "Using scorer regularisation strategy: " << type << endl;
+void SentenceLevelScorer::Init()
+{
+  // Configure regularisation.
+  static string KEY_TYPE = "regtype";
+  static string KEY_WINDOW = "regwin";
+  static string KEY_CASE = "case";
+  static string TYPE_NONE = "none";
+  static string TYPE_AVERAGE = "average";
+  static string TYPE_MINIMUM = "min";
+  static string TRUE = "true";
+  static string FALSE = "false";
+
+  const string type = getConfig(KEY_TYPE, TYPE_NONE);
+  if (type == TYPE_NONE) {
+    m_regularisationStrategy = REG_NONE;
+  } else if (type == TYPE_AVERAGE) {
+    m_regularisationStrategy = REG_AVERAGE;
+  } else if (type == TYPE_MINIMUM) {
+    m_regularisationStrategy = REG_MINIMUM;
+  } else {
+    throw boost::lexer::runtime_error("Unknown scorer regularisation strategy: " + type);
+  }
+  cerr << "Using scorer regularisation strategy: " << type << endl;
 
-    const string window = getConfig(KEY_WINDOW, "0");
-    m_regularisationWindow = atoi(window.c_str());
-    cerr << "Using scorer regularisation window: " << m_regularisationWindow << endl;
+  const string window = getConfig(KEY_WINDOW, "0");
+  m_regularisationWindow = atoi(window.c_str());
+  cerr << "Using scorer regularisation window: " << m_regularisationWindow << endl;
 
-    const string preservecase = getConfig(KEY_CASE, TRUE);
-    if (preservecase == TRUE) {
-      m_enable_preserve_case = true;
-    } else if (preservecase == FALSE) {
-      m_enable_preserve_case = false;
-    }
-    cerr << "Using case preservation: " << m_enable_preserve_case << endl;
+  const string preservecase = getConfig(KEY_CASE, TRUE);
+  if (preservecase == TRUE) {
+    m_enable_preserve_case = true;
+  } else if (preservecase == FALSE) {
+    m_enable_preserve_case = false;
+  }
+  cerr << "Using case preservation: " << m_enable_preserve_case << endl;
 }
 
 void  SentenceLevelScorer::score(const candidates_t& candidates, const diffs_t& diffs,
@@ -83,8 +85,8 @@ void  SentenceLevelScorer::score(const candidates_t& candidates, const diffs_t&
     if (stats.size() != totals.size()) {
       stringstream msg;
       msg << "Statistics for (" << "," << candidates[i] << ") have incorrect "
-      << "number of fields. Found: " << stats.size() << " Expected: "
-      << totals.size();
+          << "number of fields. Found: " << stats.size() << " Expected: "
+          << totals.size();
       throw runtime_error(msg.str());
     }
     //Add up scores for all sentences, would normally be just one score
diff --git a/mert/Singleton.h b/mert/Singleton.h
index 473517170..f50925fa4 100644
--- a/mert/Singleton.h
+++ b/mert/Singleton.h
@@ -5,13 +5,14 @@
 
 namespace MosesTuning
 {
-  
+
 
 // thread *un*safe singleton.
 // TODO: replace this with thread-safe singleton.
 template <typename T>
-class Singleton {
- public:
+class Singleton
+{
+public:
   static T* GetInstance() {
     if (m_instance == NULL) {
       m_instance = new T;
@@ -26,7 +27,7 @@ class Singleton {
     }
   }
 
- private:
+private:
   Singleton();
   static T* m_instance;
 };
diff --git a/mert/SingletonTest.cpp b/mert/SingletonTest.cpp
index a74ce7c6b..36acbeec2 100644
--- a/mert/SingletonTest.cpp
+++ b/mert/SingletonTest.cpp
@@ -5,19 +5,24 @@
 
 using namespace MosesTuning;
 
-namespace {
+namespace
+{
 
 static int g_count = 0;
 
-class Instance {
- public:
-  Instance() { ++g_count; }
+class Instance
+{
+public:
+  Instance() {
+    ++g_count;
+  }
   ~Instance() {}
 };
 
 } // namespace
 
-BOOST_AUTO_TEST_CASE(singleton_basic) {
+BOOST_AUTO_TEST_CASE(singleton_basic)
+{
   Instance* instance1 = Singleton<Instance>::GetInstance();
   Instance* instance2 = Singleton<Instance>::GetInstance();
   Instance* instance3 = Singleton<Instance>::GetInstance();
diff --git a/mert/StatisticsBasedScorer.cpp b/mert/StatisticsBasedScorer.cpp
index 05dd95939..869e2f55a 100644
--- a/mert/StatisticsBasedScorer.cpp
+++ b/mert/StatisticsBasedScorer.cpp
@@ -13,10 +13,11 @@ using namespace std;
 
 namespace MosesTuning
 {
-  
+
 
 StatisticsBasedScorer::StatisticsBasedScorer(const string& name, const string& config)
-: Scorer(name,config) {
+  : Scorer(name,config)
+{
   //configure regularisation
   static string KEY_TYPE = "regtype";
   static string KEY_WINDOW = "regwin";
@@ -26,7 +27,7 @@ StatisticsBasedScorer::StatisticsBasedScorer(const string& name, const string& c
   static string TYPE_MINIMUM = "min";
   static string TRUE = "true";
   static string FALSE = "false";
-  
+
   string type = getConfig(KEY_TYPE,TYPE_NONE);
   if (type == TYPE_NONE) {
     m_regularization_type = NONE;
@@ -38,11 +39,11 @@ StatisticsBasedScorer::StatisticsBasedScorer(const string& name, const string& c
     throw runtime_error("Unknown scorer regularisation strategy: " + type);
   }
   //    cerr << "Using scorer regularisation strategy: " << type << endl;
-  
+
   const string& window = getConfig(KEY_WINDOW, "0");
   m_regularization_window = atoi(window.c_str());
   //    cerr << "Using scorer regularisation window: " << m_regularization_window << endl;
-  
+
   const string& preserve_case = getConfig(KEY_CASE,TRUE);
   if (preserve_case == TRUE) {
     m_enable_preserve_case = true;
@@ -72,8 +73,8 @@ void  StatisticsBasedScorer::score(const candidates_t& candidates, const diffs_t
     if (stats.size() != totals.size()) {
       stringstream msg;
       msg << "Statistics for (" << "," << candidates[i] << ") have incorrect "
-      << "number of fields. Found: " << stats.size() << " Expected: "
-      << totals.size();
+          << "number of fields. Found: " << stats.size() << " Expected: "
+          << totals.size();
       throw runtime_error(msg.str());
     }
     for (size_t k = 0; k < totals.size(); ++k) {
@@ -81,7 +82,7 @@ void  StatisticsBasedScorer::score(const candidates_t& candidates, const diffs_t
     }
   }
   scores.push_back(calculateScore(totals));
-  
+
   candidates_t last_candidates(candidates);
   // apply each of the diffs, and get new scores
   for (size_t i = 0; i < diffs.size(); ++i) {
@@ -91,21 +92,21 @@ void  StatisticsBasedScorer::score(const candidates_t& candidates, const diffs_t
       size_t last_nid = last_candidates[sid];
       for (size_t k  = 0; k < totals.size(); ++k) {
         int diff = m_score_data->get(sid,nid).get(k)
-        - m_score_data->get(sid,last_nid).get(k);
+                   - m_score_data->get(sid,last_nid).get(k);
         totals[k] += diff;
       }
       last_candidates[sid] = nid;
     }
     scores.push_back(calculateScore(totals));
   }
-  
+
   // Regularisation. This can either be none, or the min or average as described in
   // Cer, Jurafsky and Manning at WMT08.
   if (m_regularization_type == NONE || m_regularization_window <= 0) {
     // no regularisation
     return;
   }
-  
+
   // window size specifies the +/- in each direction
   statscores_t raw_scores(scores);      // copy scores
   for (size_t i = 0; i < scores.size(); ++i) {
diff --git a/mert/StatisticsBasedScorer.h b/mert/StatisticsBasedScorer.h
index ca32535ad..644873b60 100644
--- a/mert/StatisticsBasedScorer.h
+++ b/mert/StatisticsBasedScorer.h
@@ -13,7 +13,7 @@
 
 namespace MosesTuning
 {
-  
+
 
 /**
  * Abstract base class for Scorers that work by adding statistics across all
@@ -26,20 +26,20 @@ public:
   virtual ~StatisticsBasedScorer() {}
   virtual void score(const candidates_t& candidates, const diffs_t& diffs,
                      statscores_t& scores) const;
-  
+
 protected:
-  
+
   enum RegularisationType {
     NONE,
     AVERAGE,
     MINIMUM
   };
-  
+
   /**
    * Calculate the actual score.
    */
   virtual statscore_t calculateScore(const std::vector<int>& totals) const = 0;
-  
+
   // regularisation
   RegularisationType m_regularization_type;
   std::size_t  m_regularization_window;
diff --git a/mert/TerScorer.cpp b/mert/TerScorer.cpp
index cc7cf1630..7c11ea66b 100644
--- a/mert/TerScorer.cpp
+++ b/mert/TerScorer.cpp
@@ -14,10 +14,10 @@ using namespace TERCpp;
 
 namespace MosesTuning
 {
-  
+
 
 TerScorer::TerScorer(const string& config)
-    : StatisticsBasedScorer("TER",config), kLENGTH(2) {}
+  : StatisticsBasedScorer("TER",config), kLENGTH(2) {}
 
 TerScorer::~TerScorer() {}
 
diff --git a/mert/TerScorer.h b/mert/TerScorer.h
index 0229f5e8c..5e9fed46f 100644
--- a/mert/TerScorer.h
+++ b/mert/TerScorer.h
@@ -10,7 +10,7 @@
 
 namespace MosesTuning
 {
-  
+
 
 class ScoreStats;
 
diff --git a/mert/Timer.cpp b/mert/Timer.cpp
index 088be93a5..47fa5c750 100644
--- a/mert/Timer.cpp
+++ b/mert/Timer.cpp
@@ -6,14 +6,17 @@
 #include <sys/time.h>
 #endif
 
-namespace {
+namespace
+{
 
 #if !defined(_WIN32) && !defined(_WIN64)
-uint64_t GetMicroSeconds(const struct timeval& tv) {
+uint64_t GetMicroSeconds(const struct timeval& tv)
+{
   return static_cast<uint64_t>(tv.tv_sec) * 1000000 + tv.tv_usec;
 }
 
-uint64_t GetTimeOfDayMicroSeconds() {
+uint64_t GetTimeOfDayMicroSeconds()
+{
   struct timeval tv;
   gettimeofday(&tv, NULL);
   return static_cast<uint64_t>(tv.tv_sec) * 1000000 + tv.tv_usec;
@@ -24,9 +27,10 @@ uint64_t GetTimeOfDayMicroSeconds() {
 
 namespace MosesTuning
 {
-  
 
-void Timer::GetCPUTimeMicroSeconds(Timer::CPUTime* cpu_time) const {
+
+void Timer::GetCPUTimeMicroSeconds(Timer::CPUTime* cpu_time) const
+{
 #if !defined(_WIN32) && !defined(_WIN64)
   struct rusage usage;
   if (getrusage(RUSAGE_SELF, &usage)) {
@@ -41,22 +45,26 @@ void Timer::GetCPUTimeMicroSeconds(Timer::CPUTime* cpu_time) const {
 #endif
 }
 
-double Timer::get_elapsed_cpu_time() const {
+double Timer::get_elapsed_cpu_time() const
+{
   return static_cast<double>(get_elapsed_cpu_time_microseconds()) * 1e-6;
 }
 
-uint64_t Timer::get_elapsed_cpu_time_microseconds() const {
+uint64_t Timer::get_elapsed_cpu_time_microseconds() const
+{
   CPUTime e;
   GetCPUTimeMicroSeconds(&e);
   return (e.user_time - m_start_time.user_time) +
-      (e.sys_time - m_start_time.sys_time);
+         (e.sys_time - m_start_time.sys_time);
 }
 
-double Timer::get_elapsed_wall_time() const {
+double Timer::get_elapsed_wall_time() const
+{
   return static_cast<double>(get_elapsed_wall_time_microseconds()) * 1e-6;
 }
 
-uint64_t Timer::get_elapsed_wall_time_microseconds() const {
+uint64_t Timer::get_elapsed_wall_time_microseconds() const
+{
   return GetTimeOfDayMicroSeconds() - m_wall;
 }
 
@@ -92,7 +100,8 @@ void Timer::check(const char* msg)
   }
 }
 
-std::string Timer::ToString() const {
+std::string Timer::ToString() const
+{
   std::string res;
   const double wall = get_elapsed_wall_time();
   CPUTime e;
diff --git a/mert/Timer.h b/mert/Timer.h
index bae4ab6b3..2adb86412 100644
--- a/mert/Timer.h
+++ b/mert/Timer.h
@@ -7,11 +7,11 @@
 
 namespace MosesTuning
 {
-  
+
 
 class Timer
 {
- private:
+private:
   // Time values are stored in microseconds.
   struct CPUTime {
     uint64_t user_time;                 // user CPU time
@@ -30,15 +30,15 @@ class Timer
   Timer(const Timer&);
   void operator=(const Timer&);
 
- public:
+public:
   /**
    * 'm_is_running' is initially false. A timer needs to be explicitly started
    * using 'start'.
    */
   Timer()
-      : m_is_running(false),
-        m_wall(0),
-        m_start_time() {}
+    : m_is_running(false),
+      m_wall(0),
+      m_start_time() {}
 
   ~Timer() {}
 
@@ -61,7 +61,9 @@ class Timer
 
   /**
    */
-  bool is_running() const { return m_is_running; }
+  bool is_running() const {
+    return m_is_running;
+  }
 
   /**
    * Return the total time in seconds that the timer has been in the
@@ -97,7 +99,8 @@ class Timer
  * for an ostream 'os' and a timer 't'.  For example, "cout << t" will
  * print out the total amount of time 't' has been "running".
  */
-inline std::ostream& operator<<(std::ostream& os, const Timer& t) {
+inline std::ostream& operator<<(std::ostream& os, const Timer& t)
+{
   if (t.is_running()) {
     os << t.ToString();
   } else {
diff --git a/mert/TimerTest.cpp b/mert/TimerTest.cpp
index 3bf0e5573..d72b1c312 100644
--- a/mert/TimerTest.cpp
+++ b/mert/TimerTest.cpp
@@ -8,7 +8,8 @@
 
 using namespace MosesTuning;
 
-BOOST_AUTO_TEST_CASE(timer_basic_test) {
+BOOST_AUTO_TEST_CASE(timer_basic_test)
+{
   Timer timer;
   const int sleep_time_microsec = 40; // ad-hoc microseconds to pass unit tests.
 
diff --git a/mert/Util.cpp b/mert/Util.cpp
index ac7d1803b..67448292f 100644
--- a/mert/Util.cpp
+++ b/mert/Util.cpp
@@ -11,7 +11,8 @@
 
 using namespace std;
 
-namespace {
+namespace
+{
 
 MosesTuning::Timer g_timer;
 int g_verbose = 0;
@@ -56,7 +57,8 @@ size_t getNextPound(std::string &str, std::string &substr,
   return pos;
 }
 
-void split(const std::string &s, char delim, std::vector<std::string> &elems) {
+void split(const std::string &s, char delim, std::vector<std::string> &elems)
+{
   std::stringstream ss(s);
   std::string item;
   while(std::getline(ss, item, delim)) {
@@ -65,7 +67,8 @@ void split(const std::string &s, char delim, std::vector<std::string> &elems) {
 }
 
 void Tokenize(const char *str, const char delim,
-              std::vector<std::string> *res) {
+              std::vector<std::string> *res)
+{
   while (1) {
     const char *begin = str;
     while (*str != delim && *str) str++;
diff --git a/mert/Util.h b/mert/Util.h
index e2071bf1f..5c9c635ab 100644
--- a/mert/Util.h
+++ b/mert/Util.h
@@ -40,7 +40,8 @@ int setverboselevel(int v);
 const float kEPS = 0.0001f;
 
 template <typename T>
-bool IsAlmostEqual(T expected, T actual, float round=kEPS) {
+bool IsAlmostEqual(T expected, T actual, float round=kEPS)
+{
   if (std::abs(expected - actual) < round) {
     return true;
   } else {
@@ -86,7 +87,8 @@ inline T Scan(const std::string &input)
  * Returns true iff "str" ends with "suffix".
  * e.g., Given str = "abc:" and suffix = ":", this function returns true.
  */
-inline bool EndsWith(const std::string& str, const char* suffix) {
+inline bool EndsWith(const std::string& str, const char* suffix)
+{
   return str.find_last_of(suffix) == str.size() - 1;
 }
 
diff --git a/mert/UtilTest.cpp b/mert/UtilTest.cpp
index f3ca6ca80..6f86d5144 100644
--- a/mert/UtilTest.cpp
+++ b/mert/UtilTest.cpp
@@ -5,7 +5,8 @@
 
 using namespace MosesTuning;
 
-BOOST_AUTO_TEST_CASE(util_get_next_pound_test) {
+BOOST_AUTO_TEST_CASE(util_get_next_pound_test)
+{
   {
     std::string str("9 9 7 ");
     std::string substr;
@@ -38,7 +39,8 @@ BOOST_AUTO_TEST_CASE(util_get_next_pound_test) {
   }
 }
 
-BOOST_AUTO_TEST_CASE(util_tokenize_test) {
+BOOST_AUTO_TEST_CASE(util_tokenize_test)
+{
   {
     std::vector<std::string> res;
     Tokenize("9 9 7", ' ', &res);
@@ -66,7 +68,8 @@ BOOST_AUTO_TEST_CASE(util_tokenize_test) {
   }
 }
 
-BOOST_AUTO_TEST_CASE(util_ends_with_test) {
+BOOST_AUTO_TEST_CASE(util_ends_with_test)
+{
   BOOST_CHECK(EndsWith("abc:", ":"));
   BOOST_CHECK(EndsWith("a b c:", ":"));
   BOOST_CHECK(!EndsWith("a", ":"));
diff --git a/mert/Vocabulary.cpp b/mert/Vocabulary.cpp
index 458024ce1..5a17c2c6e 100644
--- a/mert/Vocabulary.cpp
+++ b/mert/Vocabulary.cpp
@@ -1,34 +1,39 @@
 #include "Vocabulary.h"
 #include "Singleton.h"
 
-namespace mert {
-namespace {
+namespace mert
+{
+namespace
+{
 Vocabulary* g_vocab = NULL;
 } // namespace
 
-int Vocabulary::Encode(const std::string& token) {
-	iterator it = m_vocab.find(token);
-	int encoded_token;
-	if (it == m_vocab.end()) {
-		// Add an new entry to the vocaburary.
-		encoded_token = static_cast<int>(m_vocab.size());
-
-		m_vocab[token] = encoded_token;
-	} else {
-		encoded_token = it->second;
-	}
-	return encoded_token;
+int Vocabulary::Encode(const std::string& token)
+{
+  iterator it = m_vocab.find(token);
+  int encoded_token;
+  if (it == m_vocab.end()) {
+    // Add an new entry to the vocaburary.
+    encoded_token = static_cast<int>(m_vocab.size());
+
+    m_vocab[token] = encoded_token;
+  } else {
+    encoded_token = it->second;
+  }
+  return encoded_token;
 }
 
-bool Vocabulary::Lookup(const std::string&str , int* v) const {
+bool Vocabulary::Lookup(const std::string&str , int* v) const
+{
 
-	const_iterator it = m_vocab.find(str);
-	if (it == m_vocab.end()) return false;
-	*v = it->second;
-	return true;
+  const_iterator it = m_vocab.find(str);
+  if (it == m_vocab.end()) return false;
+  *v = it->second;
+  return true;
 }
 
-Vocabulary* VocabularyFactory::GetVocabulary() {
+Vocabulary* VocabularyFactory::GetVocabulary()
+{
   if (g_vocab == NULL) {
     return MosesTuning::Singleton<Vocabulary>::GetInstance();
   } else {
@@ -36,7 +41,8 @@ Vocabulary* VocabularyFactory::GetVocabulary() {
   }
 }
 
-void VocabularyFactory::SetVocabulary(Vocabulary* vocab) {
+void VocabularyFactory::SetVocabulary(Vocabulary* vocab)
+{
   g_vocab = vocab;
 }
 
diff --git a/mert/Vocabulary.h b/mert/Vocabulary.h
index 3ad42f46f..16c8698c6 100644
--- a/mert/Vocabulary.h
+++ b/mert/Vocabulary.h
@@ -4,7 +4,8 @@
 #include <boost/unordered_map.hpp>
 #include <string>
 
-namespace mert {
+namespace mert
+{
 
 /**
  * A map to handle vocabularies to calculate
@@ -12,8 +13,9 @@ namespace mert {
  *
  * TODO: replace this with more efficient data structure.
  */
-class Vocabulary {
- public:
+class Vocabulary
+{
+public:
   typedef boost::unordered_map<std::string, int>::iterator iterator;
   typedef boost::unordered_map<std::string, int>::const_iterator const_iterator;
 
@@ -28,32 +30,53 @@ class Vocabulary {
    */
   bool Lookup(const std::string&str , int* v) const;
 
-  void clear() { m_vocab.clear(); }
-
-  bool empty() const { return m_vocab.empty(); }
-
-  std::size_t size() const { return m_vocab.size(); }
-
-  iterator find(const std::string& str) { return m_vocab.find(str); }
-  const_iterator find(const std::string& str) const { return m_vocab.find(str); }
-
-  int& operator[](const std::string& str) { return m_vocab[str]; }
-
-  iterator begin() { return m_vocab.begin(); }
-  const_iterator begin() const { return m_vocab.begin(); }
-  iterator end() { return m_vocab.end(); }
-  const_iterator end() const { return m_vocab.end(); }
-
- private:
+  void clear() {
+    m_vocab.clear();
+  }
+
+  bool empty() const {
+    return m_vocab.empty();
+  }
+
+  std::size_t size() const {
+    return m_vocab.size();
+  }
+
+  iterator find(const std::string& str) {
+    return m_vocab.find(str);
+  }
+  const_iterator find(const std::string& str) const {
+    return m_vocab.find(str);
+  }
+
+  int& operator[](const std::string& str) {
+    return m_vocab[str];
+  }
+
+  iterator begin() {
+    return m_vocab.begin();
+  }
+  const_iterator begin() const {
+    return m_vocab.begin();
+  }
+  iterator end() {
+    return m_vocab.end();
+  }
+  const_iterator end() const {
+    return m_vocab.end();
+  }
+
+private:
   boost::unordered_map<std::string, int> m_vocab;
 };
 
-class VocabularyFactory {
- public:
+class VocabularyFactory
+{
+public:
   static Vocabulary* GetVocabulary();
   static void SetVocabulary(Vocabulary* vocab);
 
- private:
+private:
   VocabularyFactory() {}
   virtual ~VocabularyFactory() {}
 };
diff --git a/mert/VocabularyTest.cpp b/mert/VocabularyTest.cpp
index 5b453fcda..002b6a64f 100644
--- a/mert/VocabularyTest.cpp
+++ b/mert/VocabularyTest.cpp
@@ -6,16 +6,20 @@
 
 using namespace MosesTuning;
 
-namespace mert {
-namespace {
+namespace mert
+{
+namespace
+{
 
-void TearDown() {
+void TearDown()
+{
   Singleton<Vocabulary>::Delete();
 }
 
 } // namespace
 
-BOOST_AUTO_TEST_CASE(vocab_basic) {
+BOOST_AUTO_TEST_CASE(vocab_basic)
+{
   Vocabulary vocab;
   BOOST_REQUIRE(vocab.empty());
   vocab.clear();
@@ -39,7 +43,8 @@ BOOST_AUTO_TEST_CASE(vocab_basic) {
   BOOST_CHECK(!vocab.Lookup("world", &v));
 }
 
-BOOST_AUTO_TEST_CASE(vocab_factory_test) {
+BOOST_AUTO_TEST_CASE(vocab_factory_test)
+{
   Vocabulary* vocab1 = VocabularyFactory::GetVocabulary();
   Vocabulary* vocab2 = VocabularyFactory::GetVocabulary();
   Vocabulary* vocab3 = VocabularyFactory::GetVocabulary();
diff --git a/mert/evaluator.cpp b/mert/evaluator.cpp
index 58a66b12d..f976f39b3 100644
--- a/mert/evaluator.cpp
+++ b/mert/evaluator.cpp
@@ -14,7 +14,8 @@
 using namespace std;
 using namespace MosesTuning;
 
-namespace {
+namespace
+{
 
 Scorer* g_scorer = NULL;
 bool g_has_more_files = false;
@@ -22,13 +23,14 @@ bool g_has_more_scorers = false;
 const float g_alpha = 0.05;
 
 
-class EvaluatorUtil {
- public:
+class EvaluatorUtil
+{
+public:
   static void evaluate(const string& candFile, int bootstrap);
   static float average(const vector<float>& list);
   static string int2string(int n);
 
- private:
+private:
   EvaluatorUtil() {}
   ~EvaluatorUtil() {}
 };
@@ -43,22 +45,18 @@ void EvaluatorUtil::evaluate(const string& candFile, int bootstrap)
   // Loading sentences and preparing statistics
   ScoreStats scoreentry;
   string line;
-  while (getline(cand, line))
-  {
+  while (getline(cand, line)) {
     g_scorer->prepareStats(entries.size(), line, scoreentry);
     entries.push_back(scoreentry);
   }
 
   int n = entries.size();
-  if (bootstrap)
-  {
+  if (bootstrap) {
     vector<float> scores;
-    for (int i = 0; i < bootstrap; ++i)
-    {
+    for (int i = 0; i < bootstrap; ++i) {
       // TODO: Use smart pointer for exceptional-safety.
       ScoreData* scoredata = new ScoreData(g_scorer);
-      for (int j = 0; j < n; ++j)
-      {
+      for (int j = 0; j < n; ++j) {
         int randomIndex = random() % n;
         scoredata->add(entries[randomIndex], j);
       }
@@ -85,13 +83,10 @@ void EvaluatorUtil::evaluate(const string& candFile, int bootstrap)
     cout.setf(ios::fixed, ios::floatfield);
     cout.precision(4);
     cout << avg << "\t[" << lb << "," << rb << "]" << endl;
-  }
-  else
-  {
+  } else {
     // TODO: Use smart pointer for exceptional-safety.
     ScoreData* scoredata = new ScoreData(g_scorer);
-    for (int sid = 0; sid < n; ++sid)
-    {
+    for (int sid = 0; sid < n; ++sid) {
       scoredata->add(entries[sid], sid);
     }
     g_scorer->setScoreData(scoredata);
@@ -184,56 +179,56 @@ struct ProgramOption {
   bool has_seed;
 
   ProgramOption()
-      : reference(""),
-        candidate(""),
-        bootstrap(0),
-        seed(0),
-        has_seed(false) { }
+    : reference(""),
+      candidate(""),
+      bootstrap(0),
+      seed(0),
+      has_seed(false) { }
 };
 
-void ParseCommandOptions(int argc, char** argv, ProgramOption* opt) {
+void ParseCommandOptions(int argc, char** argv, ProgramOption* opt)
+{
   int c;
   int option_index;
   int last_scorer_index = -1;
   while ((c = getopt_long(argc, argv, "s:c:R:C:b:r:f:l:h", long_options, &option_index)) != -1) {
     switch(c) {
-      case 's':
-        opt->scorer_types.push_back(string(optarg));
-        opt->scorer_configs.push_back(string(""));
-        opt->scorer_factors.push_back(string(""));
-        opt->scorer_filter.push_back(string(""));
-        last_scorer_index++;
-        break;
-      case 'c':
-        opt->scorer_configs[last_scorer_index] = string(optarg);
-        break;
-      case 'R':
-        opt->reference = string(optarg);
-        break;
-      case 'C':
-        opt->candidate = string(optarg);
-        break;
-      case 'b':
-        opt->bootstrap = atoi(optarg);
-        break;
-      case 'r':
-        opt->seed = strtol(optarg, NULL, 10);
-        opt->has_seed = true;
-        break;
-      case 'f':
-        opt->scorer_factors[last_scorer_index] = string(optarg);
-        break;
-      case 'l':
-        opt->scorer_filter[last_scorer_index] = string(optarg);
-        break;
-      default:
-        usage();
+    case 's':
+      opt->scorer_types.push_back(string(optarg));
+      opt->scorer_configs.push_back(string(""));
+      opt->scorer_factors.push_back(string(""));
+      opt->scorer_filter.push_back(string(""));
+      last_scorer_index++;
+      break;
+    case 'c':
+      opt->scorer_configs[last_scorer_index] = string(optarg);
+      break;
+    case 'R':
+      opt->reference = string(optarg);
+      break;
+    case 'C':
+      opt->candidate = string(optarg);
+      break;
+    case 'b':
+      opt->bootstrap = atoi(optarg);
+      break;
+    case 'r':
+      opt->seed = strtol(optarg, NULL, 10);
+      opt->has_seed = true;
+      break;
+    case 'f':
+      opt->scorer_factors[last_scorer_index] = string(optarg);
+      break;
+    case 'l':
+      opt->scorer_filter[last_scorer_index] = string(optarg);
+      break;
+    default:
+      usage();
     }
   }
 
   // Add default scorer if no scorer provided
-  if (opt->scorer_types.size() == 0)
-  {
+  if (opt->scorer_types.size() == 0) {
     opt->scorer_types.push_back(string("BLEU"));
     opt->scorer_configs.push_back(string(""));
     opt->scorer_factors.push_back(string(""));
@@ -241,7 +236,8 @@ void ParseCommandOptions(int argc, char** argv, ProgramOption* opt) {
   }
 }
 
-void InitSeed(const ProgramOption *opt) {
+void InitSeed(const ProgramOption *opt)
+{
   if (opt->has_seed) {
     cerr << "Seeding random numbers with " << opt->seed << endl;
     srandom(opt->seed);
@@ -260,8 +256,7 @@ int main(int argc, char** argv)
   ProgramOption option;
   ParseCommandOptions(argc, argv, &option);
 
-  if (option.bootstrap)
-  {
+  if (option.bootstrap) {
     InitSeed(&option);
   }
 
@@ -278,17 +273,15 @@ int main(int argc, char** argv)
     if (candFiles.size() > 1) g_has_more_files = true;
     if (option.scorer_types.size() > 1) g_has_more_scorers = true;
 
-    for (vector<string>::const_iterator fileIt = candFiles.begin(); fileIt != candFiles.end(); ++fileIt)
-    {
-        for (size_t i = 0; i < option.scorer_types.size(); i++)
-        {
-            g_scorer = ScorerFactory::getScorer(option.scorer_types[i], option.scorer_configs[i]);
-            g_scorer->setFactors(option.scorer_factors[i]);
-            g_scorer->setFilter(option.scorer_filter[i]);
-            g_scorer->setReferenceFiles(refFiles);
-            EvaluatorUtil::evaluate(*fileIt, option.bootstrap);
-            delete g_scorer;
-        }
+    for (vector<string>::const_iterator fileIt = candFiles.begin(); fileIt != candFiles.end(); ++fileIt) {
+      for (size_t i = 0; i < option.scorer_types.size(); i++) {
+        g_scorer = ScorerFactory::getScorer(option.scorer_types[i], option.scorer_configs[i]);
+        g_scorer->setFactors(option.scorer_factors[i]);
+        g_scorer->setFilter(option.scorer_filter[i]);
+        g_scorer->setReferenceFiles(refFiles);
+        EvaluatorUtil::evaluate(*fileIt, option.bootstrap);
+        delete g_scorer;
+      }
     }
     return EXIT_SUCCESS;
   } catch (const exception& e) {
diff --git a/mert/extractor.cpp b/mert/extractor.cpp
index 077d9b94c..38652296e 100644
--- a/mert/extractor.cpp
+++ b/mert/extractor.cpp
@@ -20,7 +20,8 @@
 using namespace std;
 using namespace MosesTuning;
 
-namespace {
+namespace
+{
 
 void usage()
 {
@@ -78,68 +79,69 @@ struct ProgramOption {
   int verbosity;
 
   ProgramOption()
-      : scorerType("BLEU"),
-        scorerConfig(""),
-        scorerFactors(""),
-        scorerFilter(""),
-        referenceFile(""),
-        nbestFile(""),
-        scoreDataFile("statscore.data"),
-        featureDataFile("features.data"),
-        prevScoreDataFile(""),
-        prevFeatureDataFile(""),
-        binmode(false),
-        allowDuplicates(false),
-        verbosity(0) { }
+    : scorerType("BLEU"),
+      scorerConfig(""),
+      scorerFactors(""),
+      scorerFilter(""),
+      referenceFile(""),
+      nbestFile(""),
+      scoreDataFile("statscore.data"),
+      featureDataFile("features.data"),
+      prevScoreDataFile(""),
+      prevFeatureDataFile(""),
+      binmode(false),
+      allowDuplicates(false),
+      verbosity(0) { }
 };
 
-void ParseCommandOptions(int argc, char** argv, ProgramOption* opt) {
+void ParseCommandOptions(int argc, char** argv, ProgramOption* opt)
+{
   int c;
   int option_index;
 
   while ((c = getopt_long(argc, argv, "s:r:f:l:n:S:F:R:E:v:hbd", long_options, &option_index)) != -1) {
     switch (c) {
-      case 's':
-        opt->scorerType = string(optarg);
-        break;
-      case 'c':
-        opt->scorerConfig = string(optarg);
-        break;
-      case 'f':
-        opt->scorerFactors = string(optarg);
-        break;
-      case 'l':
-        opt->scorerFilter = string(optarg);
-        break;
-      case 'r':
-        opt->referenceFile = string(optarg);
-        break;
-      case 'b':
-        opt->binmode = true;
-        break;
-      case 'n':
-        opt->nbestFile = string(optarg);
-        break;
-      case 'S':
-        opt->scoreDataFile = string(optarg);
-        break;
-      case 'F':
-        opt->featureDataFile = string(optarg);
-        break;
-      case 'E':
-        opt->prevFeatureDataFile = string(optarg);
-        break;
-      case 'R':
-        opt->prevScoreDataFile = string(optarg);
-        break;
-      case 'v':
-        opt->verbosity = atoi(optarg);
-        break;
-      case 'd':
-        opt->allowDuplicates = true;
-        break;
-      default:
-        usage();
+    case 's':
+      opt->scorerType = string(optarg);
+      break;
+    case 'c':
+      opt->scorerConfig = string(optarg);
+      break;
+    case 'f':
+      opt->scorerFactors = string(optarg);
+      break;
+    case 'l':
+      opt->scorerFilter = string(optarg);
+      break;
+    case 'r':
+      opt->referenceFile = string(optarg);
+      break;
+    case 'b':
+      opt->binmode = true;
+      break;
+    case 'n':
+      opt->nbestFile = string(optarg);
+      break;
+    case 'S':
+      opt->scoreDataFile = string(optarg);
+      break;
+    case 'F':
+      opt->featureDataFile = string(optarg);
+      break;
+    case 'E':
+      opt->prevFeatureDataFile = string(optarg);
+      break;
+    case 'R':
+      opt->prevScoreDataFile = string(optarg);
+      break;
+    case 'v':
+      opt->verbosity = atoi(optarg);
+      break;
+    case 'd':
+      opt->allowDuplicates = true;
+      break;
+    default:
+      usage();
     }
   }
 }
@@ -202,7 +204,7 @@ int main(int argc, char** argv)
     TRACE_ERR("Scorer type: " << option.scorerType << endl);
 
     boost::scoped_ptr<Scorer> scorer(
-        ScorerFactory::getScorer(option.scorerType, option.scorerConfig));
+      ScorerFactory::getScorer(option.scorerType, option.scorerConfig));
 
     // set Factors and Filter used to preprocess the sentences
     scorer->setFactors(option.scorerFactors);
diff --git a/mert/kbmira.cpp b/mert/kbmira.cpp
index f0d1624e6..a2665ac13 100644
--- a/mert/kbmira.cpp
+++ b/mert/kbmira.cpp
@@ -2,7 +2,7 @@
 // vim:tabstop=2
 /***********************************************************************
 K-best Batch MIRA for Moses
-Copyright (C) 2012, National Research Council Canada / Conseil national 
+Copyright (C) 2012, National Research Council Canada / Conseil national
 de recherches du Canada
 ***********************************************************************/
 
@@ -49,13 +49,14 @@ using namespace MosesTuning;
 
 namespace po = boost::program_options;
 
-ValType evaluate(HypPackEnumerator* train, const AvgWeightVector& wv) {
+ValType evaluate(HypPackEnumerator* train, const AvgWeightVector& wv)
+{
   vector<ValType> stats(kBleuNgramOrder*2+1,0);
   for(train->reset(); !train->finished(); train->next()) {
     // Find max model
     size_t max_index=0;
     ValType max_score=0;
-    for(size_t i=0;i<train->cur_size();i++) {
+    for(size_t i=0; i<train->cur_size(); i++) {
       MiraFeatureVector vec(train->featuresAt(i));
       ValType score = wv.score(vec);
       if(i==0 || score > max_score) {
@@ -64,8 +65,8 @@ ValType evaluate(HypPackEnumerator* train, const AvgWeightVector& wv) {
       }
     }
     // Update stats
-    const vector<float>& sent = train->scoresAt(max_index);    
-    for(size_t i=0;i<sent.size();i++) {
+    const vector<float>& sent = train->scoresAt(max_index);
+    for(size_t i=0; i<sent.size(); i++) {
       stats[i]+=sent[i];
     }
   }
@@ -90,26 +91,26 @@ int main(int argc, char** argv)
   bool model_bg = false; // Use model for background corpus
   bool verbose = false; // Verbose updates
   bool safe_hope = false; // Model score cannot have more than BLEU_RATIO times more influence than BLEU
-  
+
   // Command-line processing follows pro.cpp
   po::options_description desc("Allowed options");
   desc.add_options()
-      ("help,h", po::value(&help)->zero_tokens()->default_value(false), "Print this help message and exit")
-      ("scfile,S", po::value<vector<string> >(&scoreFiles), "Scorer data files")
-      ("ffile,F", po::value<vector<string> > (&featureFiles), "Feature data files")
-      ("random-seed,r", po::value<int>(&seed), "Seed for random number generation")
-      ("output-file,o", po::value<string>(&outputFile), "Output file")
-      ("cparam,C", po::value<float>(&c), "MIRA C-parameter, lower for more regularization (default 0.01)")
-      ("decay,D", po::value<float>(&decay), "BLEU background corpus decay rate (default 0.999)")
-      ("iters,J", po::value<int>(&n_iters), "Number of MIRA iterations to run (default 60)")
-      ("dense-init,d", po::value<string>(&denseInitFile), "Weight file for dense features")
-      ("sparse-init,s", po::value<string>(&sparseInitFile), "Weight file for sparse features")
-      ("streaming", po::value(&streaming)->zero_tokens()->default_value(false), "Stream n-best lists to save memory, implies --no-shuffle")
-      ("no-shuffle", po::value(&no_shuffle)->zero_tokens()->default_value(false), "Don't shuffle hypotheses before each epoch")
-      ("model-bg", po::value(&model_bg)->zero_tokens()->default_value(false), "Use model instead of hope for BLEU background")
-      ("verbose", po::value(&verbose)->zero_tokens()->default_value(false), "Verbose updates")
-      ("safe-hope", po::value(&safe_hope)->zero_tokens()->default_value(false), "Mode score's influence on hope decoding is limited")
-      ;
+  ("help,h", po::value(&help)->zero_tokens()->default_value(false), "Print this help message and exit")
+  ("scfile,S", po::value<vector<string> >(&scoreFiles), "Scorer data files")
+  ("ffile,F", po::value<vector<string> > (&featureFiles), "Feature data files")
+  ("random-seed,r", po::value<int>(&seed), "Seed for random number generation")
+  ("output-file,o", po::value<string>(&outputFile), "Output file")
+  ("cparam,C", po::value<float>(&c), "MIRA C-parameter, lower for more regularization (default 0.01)")
+  ("decay,D", po::value<float>(&decay), "BLEU background corpus decay rate (default 0.999)")
+  ("iters,J", po::value<int>(&n_iters), "Number of MIRA iterations to run (default 60)")
+  ("dense-init,d", po::value<string>(&denseInitFile), "Weight file for dense features")
+  ("sparse-init,s", po::value<string>(&sparseInitFile), "Weight file for sparse features")
+  ("streaming", po::value(&streaming)->zero_tokens()->default_value(false), "Stream n-best lists to save memory, implies --no-shuffle")
+  ("no-shuffle", po::value(&no_shuffle)->zero_tokens()->default_value(false), "Don't shuffle hypotheses before each epoch")
+  ("model-bg", po::value(&model_bg)->zero_tokens()->default_value(false), "Use model instead of hope for BLEU background")
+  ("verbose", po::value(&verbose)->zero_tokens()->default_value(false), "Verbose updates")
+  ("safe-hope", po::value(&safe_hope)->zero_tokens()->default_value(false), "Mode score's influence on hope decoding is limited")
+  ;
 
   po::options_description cmdline_options;
   cmdline_options.add(desc);
@@ -118,9 +119,9 @@ int main(int argc, char** argv)
             options(cmdline_options).run(), vm);
   po::notify(vm);
   if (help) {
-      cout << "Usage: " + string(argv[0]) +  " [options]" << endl;
-      cout << desc << endl;
-      exit(0);
+    cout << "Usage: " + string(argv[0]) +  " [options]" << endl;
+    cout << desc << endl;
+    exit(0);
   }
 
   cerr << "kbmira with c=" << c << " decay=" << decay << " no_shuffle=" << no_shuffle << endl;
@@ -165,7 +166,8 @@ int main(int argc, char** argv)
       exit(3);
     }
     int sparseCount=0;
-    parameter_t val; std::string name;
+    parameter_t val;
+    std::string name;
     while(opt >> name >> val) {
       size_t id = SparseVector::encode(name) + initDenseSize;
       while(initParams.size()<=id) initParams.push_back(0.0);
@@ -175,17 +177,17 @@ int main(int argc, char** argv)
     cerr << "Found " << sparseCount << " initial sparse features" << endl;
     opt.close();
   }
-  
+
   MiraWeightVector wv(initParams);
 
   // Initialize background corpus
   vector<ValType> bg;
-  for(int j=0;j<kBleuNgramOrder;j++){
+  for(int j=0; j<kBleuNgramOrder; j++) {
     bg.push_back(kBleuNgramOrder-j);
     bg.push_back(kBleuNgramOrder-j);
   }
   bg.push_back(kBleuNgramOrder);
-  
+
   // Training loop
   boost::scoped_ptr<HypPackEnumerator> train;
   if(streaming)
@@ -194,8 +196,7 @@ int main(int argc, char** argv)
     train.reset(new RandomAccessHypPackEnumerator(featureFiles, scoreFiles, no_shuffle));
   cerr << "Initial BLEU = " << evaluate(train.get(), wv.avg()) << endl;
   ValType bestBleu = 0;
-  for(int j=0;j<n_iters;j++)
-  {
+  for(int j=0; j<n_iters; j++) {
     // MIRA train for one epoch
     int iNumHyps = 0;
     int iNumExamples = 0;
@@ -273,7 +274,7 @@ int main(int argc, char** argv)
         }
         // Update BLEU statistics
         const vector<float>& model_stats = train->scoresAt(model_index);
-        for(size_t k=0;k<bg.size();k++) {
+        for(size_t k=0; k<bg.size(); k++) {
           bg[k]*=decay;
           if(model_bg)
             bg[k]+=model_stats[k];
@@ -286,7 +287,7 @@ int main(int argc, char** argv)
     // Training Epoch summary
     cerr << iNumUpdates << "/" << iNumExamples << " updates"
          << ", avg loss = " << (totalLoss / iNumExamples);
-         
+
 
     // Evaluate current average weights
     AvgWeightVector avg = wv.avg();
@@ -312,11 +313,11 @@ int main(int argc, char** argv)
       } else {
         out = &cout;
       }
-      for(size_t i=0;i<avg.size();i++) {
+      for(size_t i=0; i<avg.size(); i++) {
         if(i<num_dense)
           *out << "F" << i << " " << avg.weight(i) << endl;
         else {
-          if(abs(avg.weight(i))>1e-8) 
+          if(abs(avg.weight(i))>1e-8)
             *out << SparseVector::decode(i-num_dense) << " " << avg.weight(i) << endl;
         }
       }
diff --git a/mert/mert.cpp b/mert/mert.cpp
index e53c86be2..b73c536d1 100644
--- a/mert/mert.cpp
+++ b/mert/mert.cpp
@@ -30,7 +30,8 @@
 using namespace std;
 using namespace MosesTuning;
 
-namespace {
+namespace
+{
 
 const char kDefaultOptimizer[] = "powell";
 const char kDefaultScorer[] = "BLEU";
@@ -46,10 +47,11 @@ const char kOutputFile[] = "weights.txt";
 /**
  * Runs an optimisation, or a random restart.
  */
-class OptimizationTask : public Moses::Task {
- public:
+class OptimizationTask : public Moses::Task
+{
+public:
   OptimizationTask(Optimizer* optimizer, const Point& point)
-      : m_optimizer(optimizer), m_point(point) {}
+    : m_optimizer(optimizer), m_point(point) {}
 
   ~OptimizationTask() {}
 
@@ -76,7 +78,7 @@ class OptimizationTask : public Moses::Task {
     return m_point;
   }
 
- private:
+private:
   // Do not allow the user to instanciate without arguments.
   OptimizationTask() {}
 
@@ -85,7 +87,8 @@ class OptimizationTask : public Moses::Task {
   statscore_t m_score;
 };
 
-bool WriteFinalWeights(const char* filename, const Point& point) {
+bool WriteFinalWeights(const char* filename, const Point& point)
+{
   ofstream ofs(filename);
   if (!ofs) {
     cerr << "Cannot open " << filename << endl;
@@ -165,91 +168,92 @@ struct ProgramOption {
   size_t shard_count;
 
   ProgramOption()
-      : to_optimize_str(""),
-        pdim(-1),
-        ntry(1),
-        nrandom(0),
-        seed(0),
-        has_seed(false),
-        optimize_type(kDefaultOptimizer),
-        scorer_type(kDefaultScorer),
-        scorer_config(""),
-        scorer_file(kDefaultScorerFile),
-        feature_file(kDefaultFeatureFile),
-        init_file(kDefaultInitFile),
-        positive_string(kDefaultPositiveString),
-        sparse_weights_file(kDefaultSparseWeightsFile),
-        num_threads(1),
-        shard_size(0),
-        shard_count(0) { }
+    : to_optimize_str(""),
+      pdim(-1),
+      ntry(1),
+      nrandom(0),
+      seed(0),
+      has_seed(false),
+      optimize_type(kDefaultOptimizer),
+      scorer_type(kDefaultScorer),
+      scorer_config(""),
+      scorer_file(kDefaultScorerFile),
+      feature_file(kDefaultFeatureFile),
+      init_file(kDefaultInitFile),
+      positive_string(kDefaultPositiveString),
+      sparse_weights_file(kDefaultSparseWeightsFile),
+      num_threads(1),
+      shard_size(0),
+      shard_count(0) { }
 };
 
-void ParseCommandOptions(int argc, char** argv, ProgramOption* opt) {
+void ParseCommandOptions(int argc, char** argv, ProgramOption* opt)
+{
   int c;
   int option_index;
 
   while ((c = getopt_long(argc, argv, "o:r:d:n:m:t:s:S:F:v:p:P:", long_options, &option_index)) != -1) {
     switch (c) {
-      case 'o':
-        opt->to_optimize_str = string(optarg);
-        break;
-      case 'd':
-        opt->pdim = strtol(optarg, NULL, 10);
-        break;
-      case 'n':
-        opt->ntry = strtol(optarg, NULL, 10);
-        break;
-      case 'm':
-        opt->nrandom = strtol(optarg, NULL, 10);
-        break;
-      case 'r':
-        opt->seed = strtol(optarg, NULL, 10);
-        opt->has_seed = true;
-        break;
-      case 't':
-        opt->optimize_type = string(optarg);
-        break;
-      case's':
-        opt->scorer_type = string(optarg);
-        break;
-      case 'c':
-        opt->scorer_config = string(optarg);
-        break;
-      case 'S':
-        opt->scorer_file = string(optarg);
-        break;
-      case 'F':
-        opt->feature_file = string(optarg);
-        break;
-      case 'i':
-        opt->init_file = string(optarg);
-        break;
-      case 'p':
-        opt->sparse_weights_file=string(optarg);
-        break;
-      case 'v':
-        setverboselevel(strtol(optarg, NULL, 10));
-        break;
+    case 'o':
+      opt->to_optimize_str = string(optarg);
+      break;
+    case 'd':
+      opt->pdim = strtol(optarg, NULL, 10);
+      break;
+    case 'n':
+      opt->ntry = strtol(optarg, NULL, 10);
+      break;
+    case 'm':
+      opt->nrandom = strtol(optarg, NULL, 10);
+      break;
+    case 'r':
+      opt->seed = strtol(optarg, NULL, 10);
+      opt->has_seed = true;
+      break;
+    case 't':
+      opt->optimize_type = string(optarg);
+      break;
+    case's':
+      opt->scorer_type = string(optarg);
+      break;
+    case 'c':
+      opt->scorer_config = string(optarg);
+      break;
+    case 'S':
+      opt->scorer_file = string(optarg);
+      break;
+    case 'F':
+      opt->feature_file = string(optarg);
+      break;
+    case 'i':
+      opt->init_file = string(optarg);
+      break;
+    case 'p':
+      opt->sparse_weights_file=string(optarg);
+      break;
+    case 'v':
+      setverboselevel(strtol(optarg, NULL, 10));
+      break;
 #ifdef WITH_THREADS
-      case 'T':
-        opt->num_threads = strtol(optarg, NULL, 10);
-        if (opt->num_threads < 1) opt->num_threads = 1;
-        break;
+    case 'T':
+      opt->num_threads = strtol(optarg, NULL, 10);
+      if (opt->num_threads < 1) opt->num_threads = 1;
+      break;
 #endif
-      case 'a':
-        opt->shard_count = strtof(optarg, NULL);
-        break;
-      case 'b':
-        opt->shard_size = strtof(optarg, NULL);
-        break;
-      case 'h':
-        usage(0);
-        break;
-      case 'P':
-        opt->positive_string = string(optarg);
-        break;
-      default:
-        usage(1);
+    case 'a':
+      opt->shard_count = strtof(optarg, NULL);
+      break;
+    case 'b':
+      opt->shard_size = strtof(optarg, NULL);
+      break;
+    case 'h':
+      usage(0);
+      break;
+    case 'P':
+      opt->positive_string = string(optarg);
+      break;
+    default:
+      usage(1);
     }
   }
 }
@@ -353,7 +357,7 @@ int main(int argc, char **argv)
 
   // it make sense to know what parameter set were used to generate the nbest
   boost::scoped_ptr<Scorer> scorer(
-      ScorerFactory::getScorer(option.scorer_type, option.scorer_config));
+    ScorerFactory::getScorer(option.scorer_type, option.scorer_config));
 
   //load data
   Data data(scorer.get(), option.sparse_weights_file);
diff --git a/mert/pro.cpp b/mert/pro.cpp
index 3777d0470..b8cf81ca3 100644
--- a/mert/pro.cpp
+++ b/mert/pro.cpp
@@ -51,7 +51,8 @@ namespace po = boost::program_options;
 namespace MosesTuning
 {
 
-class SampledPair {
+class SampledPair
+{
 private:
   pair<size_t,size_t> m_translation1;
   pair<size_t,size_t> m_translation2;
@@ -70,12 +71,19 @@ public:
     }
   }
 
-  float getDiff() const { return m_score_diff; }
-  const pair<size_t,size_t>& getTranslation1() const { return m_translation1; }
-  const pair<size_t,size_t>& getTranslation2() const { return m_translation2; }
+  float getDiff() const {
+    return m_score_diff;
+  }
+  const pair<size_t,size_t>& getTranslation1() const {
+    return m_translation1;
+  }
+  const pair<size_t,size_t>& getTranslation2() const {
+    return m_translation2;
+  }
 };
 
-static void outputSample(ostream& out, const FeatureDataItem& f1, const FeatureDataItem& f2) {
+static void outputSample(ostream& out, const FeatureDataItem& f1, const FeatureDataItem& f2)
+{
   // difference in score in regular features
   for(unsigned int j=0; j<f1.dense.size(); j++)
     if (abs(f1.dense[j]-f2.dense[j]) > 0.00001)
@@ -110,13 +118,13 @@ int main(int argc, char** argv)
 
   po::options_description desc("Allowed options");
   desc.add_options()
-      ("help,h", po::value(&help)->zero_tokens()->default_value(false), "Print this help message and exit")
-      ("scfile,S", po::value<vector<string> >(&scoreFiles), "Scorer data files")
-      ("ffile,F", po::value<vector<string> > (&featureFiles), "Feature data files")
-      ("random-seed,r", po::value<int>(&seed), "Seed for random number generation")
-      ("output-file,o", po::value<string>(&outputFile), "Output file")
-      ("smooth-brevity-penalty,b", po::value(&smoothBP)->zero_tokens()->default_value(false), "Smooth the brevity penalty, as in Nakov et al. (Coling 2012)")
-      ;
+  ("help,h", po::value(&help)->zero_tokens()->default_value(false), "Print this help message and exit")
+  ("scfile,S", po::value<vector<string> >(&scoreFiles), "Scorer data files")
+  ("ffile,F", po::value<vector<string> > (&featureFiles), "Feature data files")
+  ("random-seed,r", po::value<int>(&seed), "Seed for random number generation")
+  ("output-file,o", po::value<string>(&outputFile), "Output file")
+  ("smooth-brevity-penalty,b", po::value(&smoothBP)->zero_tokens()->default_value(false), "Smooth the brevity penalty, as in Nakov et al. (Coling 2012)")
+  ;
 
   po::options_description cmdline_options;
   cmdline_options.add(desc);
@@ -125,9 +133,9 @@ int main(int argc, char** argv)
             options(cmdline_options).run(), vm);
   po::notify(vm);
   if (help) {
-      cout << "Usage: " + string(argv[0]) +  " [options]" << endl;
-      cout << desc << endl;
-      exit(0);
+    cout << "Usage: " + string(argv[0]) +  " [options]" << endl;
+    cout << desc << endl;
+    exit(0);
   }
 
   if (vm.count("random-seed")) {
@@ -145,7 +153,7 @@ int main(int argc, char** argv)
 
   if (featureFiles.size() != scoreFiles.size()) {
     cerr << "Error: Number of feature files (" << featureFiles.size() <<
-      ") does not match number of score files (" << scoreFiles.size() << ")" << endl;
+         ") does not match number of score files (" << scoreFiles.size() << ")" << endl;
     exit(1);
   }
 
@@ -238,11 +246,11 @@ int main(int argc, char** argv)
       size_t hypo_id2 = samples[i].getTranslation2().second;
       *out << "1";
       outputSample(*out, featureDataIters[file_id1]->operator[](hypo_id1),
-                        featureDataIters[file_id2]->operator[](hypo_id2));
+                   featureDataIters[file_id2]->operator[](hypo_id2));
       *out << endl;
       *out << "0";
       outputSample(*out, featureDataIters[file_id2]->operator[](hypo_id2),
-                        featureDataIters[file_id1]->operator[](hypo_id1));
+                   featureDataIters[file_id1]->operator[](hypo_id1));
       *out << endl;
     }
     //advance all iterators
diff --git a/mert/sentence-bleu.cpp b/mert/sentence-bleu.cpp
index 17a9737f2..5269d37cd 100644
--- a/mert/sentence-bleu.cpp
+++ b/mert/sentence-bleu.cpp
@@ -18,7 +18,7 @@ int main(int argc, char **argv)
   // TODO all of these are empty for now
   string config;
   string factors;
-  string filter; 
+  string filter;
 
   BleuScorer scorer(config);
   scorer.setFactors(factors);
diff --git a/mira/Decoder.cpp b/mira/Decoder.cpp
index dea6699f6..3dea97f24 100644
--- a/mira/Decoder.cpp
+++ b/mira/Decoder.cpp
@@ -31,357 +31,371 @@ using namespace std;
 using namespace Moses;
 
 
-namespace Mira {
-
-  /**
-    * Allocates a char* and copies string into it.
-  **/
-  static char* strToChar(const string& s) {
-    char* c = new char[s.size()+1];
-    strcpy(c,s.c_str());
-    return c;
+namespace Mira
+{
+
+/**
+  * Allocates a char* and copies string into it.
+**/
+static char* strToChar(const string& s)
+{
+  char* c = new char[s.size()+1];
+  strcpy(c,s.c_str());
+  return c;
+}
+
+MosesDecoder::MosesDecoder(const string& inifile, int debuglevel, int argc, vector<string> decoder_params)
+  : m_manager(NULL)
+{
+  static int BASE_ARGC = 8;
+  Parameter* params = new Parameter();
+  char ** mosesargv = new char*[BASE_ARGC + argc];
+  mosesargv[0] = strToChar("-f");
+  mosesargv[1] = strToChar(inifile);
+  mosesargv[2] = strToChar("-v");
+  stringstream dbgin;
+  dbgin << debuglevel;
+  mosesargv[3] = strToChar(dbgin.str());
+  mosesargv[4] = strToChar("-use-persistent-cache");
+  mosesargv[5] = strToChar("0");
+  mosesargv[6] = strToChar("-persistent-cache-size");
+  mosesargv[7] = strToChar("0");
+
+  for (int i = 0; i < argc; ++i) {
+    char *cstr = &(decoder_params[i])[0];
+    mosesargv[BASE_ARGC + i] = cstr;
   }
 
-  MosesDecoder::MosesDecoder(const string& inifile, int debuglevel, int argc, vector<string> decoder_params)
-	: m_manager(NULL) {
-  	static int BASE_ARGC = 8;
-	  Parameter* params = new Parameter();
-	  char ** mosesargv = new char*[BASE_ARGC + argc];
-	  mosesargv[0] = strToChar("-f");
-	  mosesargv[1] = strToChar(inifile);
-	  mosesargv[2] = strToChar("-v");
-	  stringstream dbgin;
-	  dbgin << debuglevel;
-	  mosesargv[3] = strToChar(dbgin.str());
-	  mosesargv[4] = strToChar("-use-persistent-cache"); 
-	  mosesargv[5] = strToChar("0"); 
-	  mosesargv[6] = strToChar("-persistent-cache-size");
-          mosesargv[7] = strToChar("0");
-
-	  for (int i = 0; i < argc; ++i) {
-		  char *cstr = &(decoder_params[i])[0];
-		  mosesargv[BASE_ARGC + i] = cstr;
-	  }
-
-	  if (!params->LoadParam(BASE_ARGC + argc,mosesargv)) {
-		  cerr << "Loading static data failed, exit." << endl;
-		  exit(1);
-	  }
-	  StaticData::LoadDataStatic(params, "mira");
-	  for (int i = 0; i < BASE_ARGC; ++i) {
-		  delete[] mosesargv[i];
-	  }
-	  delete[] mosesargv;
-
-	  //m_bleuScoreFeature = staticData.GetBleuScoreFeature(); TODO
-	  assert(false);
+  if (!params->LoadParam(BASE_ARGC + argc,mosesargv)) {
+    cerr << "Loading static data failed, exit." << endl;
+    exit(1);
   }
-  
-  void MosesDecoder::cleanup(bool chartDecoding) {
-	  delete m_manager;
-	  if (chartDecoding)
-	  	delete m_chartManager;
-	  else
-	  	delete m_sentence;
+  StaticData::LoadDataStatic(params, "mira");
+  for (int i = 0; i < BASE_ARGC; ++i) {
+    delete[] mosesargv[i];
+  }
+  delete[] mosesargv;
+
+  //m_bleuScoreFeature = staticData.GetBleuScoreFeature(); TODO
+  assert(false);
+}
+
+void MosesDecoder::cleanup(bool chartDecoding)
+{
+  delete m_manager;
+  if (chartDecoding)
+    delete m_chartManager;
+  else
+    delete m_sentence;
+}
+
+vector< vector<const Word*> > MosesDecoder::getNBest(const std::string& source,
+    size_t sentenceid,
+    size_t nBestSize,
+    float bleuObjectiveWeight,
+    float bleuScoreWeight,
+    vector< ScoreComponentCollection>& featureValues,
+    vector< float>& bleuScores,
+    vector< float>& modelScores,
+    size_t numReturnedTranslations,
+    bool realBleu,
+    bool distinct,
+    bool avgRefLength,
+    size_t rank,
+    size_t epoch,
+    string filename)
+{
+  StaticData &staticData = StaticData::InstanceNonConst();
+  bool chartDecoding = (staticData.GetSearchAlgorithm() == ChartDecoding);
+  initialize(staticData, source, sentenceid, bleuObjectiveWeight, bleuScoreWeight, avgRefLength, chartDecoding);
+
+  // run the decoder
+  if (chartDecoding) {
+    return runChartDecoder(source, sentenceid, nBestSize, bleuObjectiveWeight, bleuScoreWeight,
+                           featureValues, bleuScores, modelScores, numReturnedTranslations, realBleu, distinct, rank, epoch);
+  } else {
+    SearchAlgorithm search = staticData.GetSearchAlgorithm();
+    return runDecoder(source, sentenceid, nBestSize, bleuObjectiveWeight, bleuScoreWeight,
+                      featureValues, bleuScores, modelScores, numReturnedTranslations, realBleu, distinct, rank, epoch,
+                      search, filename);
+  }
+}
+
+vector< vector<const Word*> > MosesDecoder::runDecoder(const std::string& source,
+    size_t sentenceid,
+    size_t nBestSize,
+    float bleuObjectiveWeight,
+    float bleuScoreWeight,
+    vector< ScoreComponentCollection>& featureValues,
+    vector< float>& bleuScores,
+    vector< float>& modelScores,
+    size_t numReturnedTranslations,
+    bool realBleu,
+    bool distinct,
+    size_t rank,
+    size_t epoch,
+    SearchAlgorithm& search,
+    string filename)
+{
+  // run the decoder
+  m_manager = new Moses::Manager(0,*m_sentence, search);
+  m_manager->ProcessSentence();
+  TrellisPathList nBestList;
+  m_manager->CalcNBest(nBestSize, nBestList, distinct);
+
+  // optionally print nbest to file (to extract scores and features.. currently just for sentence bleu scoring)
+  if (filename != "") {
+    ofstream out(filename.c_str());
+    if (!out) {
+      ostringstream msg;
+      msg << "Unable to open " << filename;
+      throw runtime_error(msg.str());
+    }
+    // TODO: handle sentence id (for now always 0)
+    //OutputNBest(out, nBestList, StaticData::Instance().GetOutputFactorOrder(), 0, false);
+    out.close();
   }
 
-  vector< vector<const Word*> > MosesDecoder::getNBest(const std::string& source,
-                              size_t sentenceid,
-                              size_t nBestSize,
-                              float bleuObjectiveWeight, 
-                              float bleuScoreWeight,
-                              vector< ScoreComponentCollection>& featureValues,
-                              vector< float>& bleuScores,
-                              vector< float>& modelScores,
-                              size_t numReturnedTranslations,
-                              bool realBleu,
-                              bool distinct,
-                              bool avgRefLength,
-                              size_t rank,
-                              size_t epoch,
-                              string filename)
-  {
-  	StaticData &staticData = StaticData::InstanceNonConst();
-  	bool chartDecoding = (staticData.GetSearchAlgorithm() == ChartDecoding);
-  	initialize(staticData, source, sentenceid, bleuObjectiveWeight, bleuScoreWeight, avgRefLength, chartDecoding);
+  // read off the feature values and bleu scores for each sentence in the nbest list
+  Moses::TrellisPathList::const_iterator iter;
+  for (iter = nBestList.begin() ; iter != nBestList.end() ; ++iter) {
+    const Moses::TrellisPath &path = **iter;
+    featureValues.push_back(path.GetScoreBreakdown());
+    float bleuScore, dynBleuScore, realBleuScore;
+    if (realBleu) realBleuScore = m_bleuScoreFeature->CalculateBleu(path.GetTargetPhrase());
+    else dynBleuScore = getBleuScore(featureValues.back());
+    bleuScore = realBleu ? realBleuScore : dynBleuScore;
+    bleuScores.push_back(bleuScore);
+
+    //std::cout << "Score breakdown: " << path.GetScoreBreakdown() << endl;
+    float scoreWithoutBleu = path.GetTotalScore() - (bleuObjectiveWeight * bleuScoreWeight * bleuScore);
+    modelScores.push_back(scoreWithoutBleu);
+
+    if (iter != nBestList.begin())
+      cerr << endl;
+    cerr << "Rank " << rank << ", epoch " << epoch << ", \"" << path.GetTargetPhrase() << "\", score: "
+         << scoreWithoutBleu << ", Bleu: " << bleuScore << ", total: " << path.GetTotalScore();
+    if (m_bleuScoreFeature->Enabled() && realBleu)
+      cerr << " (d-bleu: " << dynBleuScore << ", r-bleu: " << realBleuScore << ") ";
+
+    // set bleu score to zero in the feature vector since we do not want to optimise its weight
+    setBleuScore(featureValues.back(), 0);
+  }
 
-    // run the decoder
-    if (chartDecoding) {
-    	return runChartDecoder(source, sentenceid, nBestSize, bleuObjectiveWeight, bleuScoreWeight,
-    			featureValues, bleuScores, modelScores, numReturnedTranslations, realBleu, distinct, rank, epoch);
-    }
-    else {
-    	SearchAlgorithm search = staticData.GetSearchAlgorithm();
-    	return runDecoder(source, sentenceid, nBestSize, bleuObjectiveWeight, bleuScoreWeight,
-    			featureValues, bleuScores, modelScores, numReturnedTranslations, realBleu, distinct, rank, epoch,
-    			search, filename);
+  // prepare translations to return
+  vector< vector<const Word*> > translations;
+  for (size_t i=0; i < numReturnedTranslations && i < nBestList.GetSize(); ++i) {
+    const TrellisPath &path = nBestList.at(i);
+    Phrase phrase = path.GetTargetPhrase();
+
+    vector<const Word*> translation;
+    for (size_t pos = 0; pos < phrase.GetSize(); ++pos) {
+      const Word &word = phrase.GetWord(pos);
+      Word *newWord = new Word(word);
+      translation.push_back(newWord);
     }
+    translations.push_back(translation);
   }
 
-  vector< vector<const Word*> > MosesDecoder::runDecoder(const std::string& source,
-  														size_t sentenceid,
-  														size_t nBestSize,
-  														float bleuObjectiveWeight,
-  														float bleuScoreWeight,
-  														vector< ScoreComponentCollection>& featureValues,
-  														vector< float>& bleuScores,
-  														vector< float>& modelScores,
-  														size_t numReturnedTranslations,
-  														bool realBleu,
-  														bool distinct,
-  														size_t rank,
-  														size_t epoch,
-  														SearchAlgorithm& search,
-  														string filename) {
-  	// run the decoder
-    m_manager = new Moses::Manager(0,*m_sentence, search);
-    m_manager->ProcessSentence();
-    TrellisPathList nBestList;
-    m_manager->CalcNBest(nBestSize, nBestList, distinct);
-    
-    // optionally print nbest to file (to extract scores and features.. currently just for sentence bleu scoring)
-    if (filename != "") {
-    	ofstream out(filename.c_str());
-    	if (!out) {
-    		ostringstream msg;
-    		msg << "Unable to open " << filename;
-    		throw runtime_error(msg.str());
-    	}
-    	// TODO: handle sentence id (for now always 0)
-    	//OutputNBest(out, nBestList, StaticData::Instance().GetOutputFactorOrder(), 0, false);
-    	out.close();
-    }
+  return translations;
+}
+
+vector< vector<const Word*> > MosesDecoder::runChartDecoder(const std::string& source,
+    size_t sentenceid,
+    size_t nBestSize,
+    float bleuObjectiveWeight,
+    float bleuScoreWeight,
+    vector< ScoreComponentCollection>& featureValues,
+    vector< float>& bleuScores,
+    vector< float>& modelScores,
+    size_t numReturnedTranslations,
+    bool realBleu,
+    bool distinct,
+    size_t rank,
+    size_t epoch)
+{
+  // run the decoder
+  m_chartManager = new ChartManager(*m_sentence);
+  m_chartManager->ProcessSentence();
+  ChartTrellisPathList nBestList;
+  m_chartManager->CalcNBest(nBestSize, nBestList, distinct);
+
+  // read off the feature values and bleu scores for each sentence in the nbest list
+  ChartTrellisPathList::const_iterator iter;
+  for (iter = nBestList.begin() ; iter != nBestList.end() ; ++iter) {
+    const Moses::ChartTrellisPath &path = **iter;
+    featureValues.push_back(path.GetScoreBreakdown());
+    float bleuScore, dynBleuScore, realBleuScore;
+    dynBleuScore = getBleuScore(featureValues.back());
+    realBleuScore = m_bleuScoreFeature->CalculateBleu(path.GetOutputPhrase());
+    bleuScore = realBleu ? realBleuScore : dynBleuScore;
+    bleuScores.push_back(bleuScore);
+
+    //std::cout << "Score breakdown: " << path.GetScoreBreakdown() << endl;
+    float scoreWithoutBleu = path.GetTotalScore() - (bleuObjectiveWeight * bleuScoreWeight * bleuScore);
+    modelScores.push_back(scoreWithoutBleu);
+
+    if (iter != nBestList.begin())
+      cerr << endl;
+    cerr << "Rank " << rank << ", epoch " << epoch << ", \"" << path.GetOutputPhrase() << "\", score: "
+         << scoreWithoutBleu << ", Bleu: " << bleuScore << ", total: " << path.GetTotalScore();
+    if (m_bleuScoreFeature->Enabled() && realBleu)
+      cerr << " (d-bleu: " << dynBleuScore << ", r-bleu: " << realBleuScore << ") ";
+
+    // set bleu score to zero in the feature vector since we do not want to optimise its weight
+    setBleuScore(featureValues.back(), 0);
+  }
 
-    // read off the feature values and bleu scores for each sentence in the nbest list
-    Moses::TrellisPathList::const_iterator iter;
-    for (iter = nBestList.begin() ; iter != nBestList.end() ; ++iter) {
-    	const Moses::TrellisPath &path = **iter;
-    	featureValues.push_back(path.GetScoreBreakdown());
-    	float bleuScore, dynBleuScore, realBleuScore;
-	if (realBleu) realBleuScore = m_bleuScoreFeature->CalculateBleu(path.GetTargetPhrase());
-	else dynBleuScore = getBleuScore(featureValues.back());  
-    	bleuScore = realBleu ? realBleuScore : dynBleuScore; 
-    	bleuScores.push_back(bleuScore);	
-
-    	//std::cout << "Score breakdown: " << path.GetScoreBreakdown() << endl;
-    	float scoreWithoutBleu = path.GetTotalScore() - (bleuObjectiveWeight * bleuScoreWeight * bleuScore);
-    	modelScores.push_back(scoreWithoutBleu);
-    	
-    	if (iter != nBestList.begin())
-    		cerr << endl;  	
-    	cerr << "Rank " << rank << ", epoch " << epoch << ", \"" << path.GetTargetPhrase() << "\", score: " 
-    		 << scoreWithoutBleu << ", Bleu: " << bleuScore << ", total: " << path.GetTotalScore();
-	if (m_bleuScoreFeature->Enabled() && realBleu)
-	  cerr << " (d-bleu: " << dynBleuScore << ", r-bleu: " << realBleuScore << ") ";
-
-    	// set bleu score to zero in the feature vector since we do not want to optimise its weight
-    	setBleuScore(featureValues.back(), 0);
+  // prepare translations to return
+  vector< vector<const Word*> > translations;
+  for (iter = nBestList.begin() ; iter != nBestList.end() ; ++iter) {
+    const ChartTrellisPath &path = **iter;
+    Phrase phrase = path.GetOutputPhrase();
+
+    vector<const Word*> translation;
+    for (size_t pos = 0; pos < phrase.GetSize(); ++pos) {
+      const Word &word = phrase.GetWord(pos);
+      Word *newWord = new Word(word);
+      translation.push_back(newWord);
     }
+    translations.push_back(translation);
+  }
 
-    // prepare translations to return
-    vector< vector<const Word*> > translations;
-    for (size_t i=0; i < numReturnedTranslations && i < nBestList.GetSize(); ++i) {
-        const TrellisPath &path = nBestList.at(i);
-        Phrase phrase = path.GetTargetPhrase();
-
-        vector<const Word*> translation;
-        for (size_t pos = 0; pos < phrase.GetSize(); ++pos) {
-        	const Word &word = phrase.GetWord(pos);
-        	Word *newWord = new Word(word);
-        	translation.push_back(newWord);
-        }
-        translations.push_back(translation);
-    }
+  return translations;
+}
 
-    return translations;
-  }
+void MosesDecoder::outputNBestList(const std::string& source, size_t sentenceid,
+                                   size_t nBestSize, float bleuObjectiveWeight, float bleuScoreWeight,
+                                   bool distinctNbest, bool avgRefLength, string filename, ofstream& streamOut)
+{
+  StaticData &staticData = StaticData::InstanceNonConst();
+  bool chartDecoding = (staticData.GetSearchAlgorithm() == ChartDecoding);
+  initialize(staticData, source, sentenceid, bleuObjectiveWeight, bleuScoreWeight, avgRefLength, chartDecoding);
 
-  vector< vector<const Word*> > MosesDecoder::runChartDecoder(const std::string& source,
-                              size_t sentenceid,
-                              size_t nBestSize,
-                              float bleuObjectiveWeight,
-                              float bleuScoreWeight,
-                              vector< ScoreComponentCollection>& featureValues,
-                              vector< float>& bleuScores,
-                              vector< float>& modelScores,
-                              size_t numReturnedTranslations,
-                              bool realBleu,
-                              bool distinct,
-                              size_t rank,
-                              size_t epoch) {
-  	// run the decoder
+  if (chartDecoding) {
     m_chartManager = new ChartManager(*m_sentence);
     m_chartManager->ProcessSentence();
     ChartTrellisPathList nBestList;
-    m_chartManager->CalcNBest(nBestSize, nBestList, distinct);
-
-    // read off the feature values and bleu scores for each sentence in the nbest list
-    ChartTrellisPathList::const_iterator iter;
-    for (iter = nBestList.begin() ; iter != nBestList.end() ; ++iter) {
-    	const Moses::ChartTrellisPath &path = **iter;
-    	featureValues.push_back(path.GetScoreBreakdown());
-    	float bleuScore, dynBleuScore, realBleuScore;
-    	dynBleuScore = getBleuScore(featureValues.back());  
-    	realBleuScore = m_bleuScoreFeature->CalculateBleu(path.GetOutputPhrase());
-    	bleuScore = realBleu ? realBleuScore : dynBleuScore; 
-    	bleuScores.push_back(bleuScore);
-
-    	//std::cout << "Score breakdown: " << path.GetScoreBreakdown() << endl;
-    	float scoreWithoutBleu = path.GetTotalScore() - (bleuObjectiveWeight * bleuScoreWeight * bleuScore);
-    	modelScores.push_back(scoreWithoutBleu);
-
-    	if (iter != nBestList.begin())
-    	  cerr << endl;
-    	cerr << "Rank " << rank << ", epoch " << epoch << ", \"" << path.GetOutputPhrase() << "\", score: " 
-    		 << scoreWithoutBleu << ", Bleu: " << bleuScore << ", total: " << path.GetTotalScore();
-	if (m_bleuScoreFeature->Enabled() && realBleu)
-	  cerr << " (d-bleu: " << dynBleuScore << ", r-bleu: " << realBleuScore << ") ";
-
-    	// set bleu score to zero in the feature vector since we do not want to optimise its weight
-    	setBleuScore(featureValues.back(), 0);
-    }
-
-    // prepare translations to return
-    vector< vector<const Word*> > translations;
-    for (iter = nBestList.begin() ; iter != nBestList.end() ; ++iter) {
-        const ChartTrellisPath &path = **iter;
-        Phrase phrase = path.GetOutputPhrase();
-
-        vector<const Word*> translation;
-        for (size_t pos = 0; pos < phrase.GetSize(); ++pos) {
-        	const Word &word = phrase.GetWord(pos);
-        	Word *newWord = new Word(word);
-        	translation.push_back(newWord);
-        }
-        translations.push_back(translation);
-    }
-
-    return translations;
-  }
+    m_chartManager->CalcNBest(nBestSize, nBestList, distinctNbest);
 
-  void MosesDecoder::outputNBestList(const std::string& source, size_t sentenceid,
-  														size_t nBestSize, float bleuObjectiveWeight, float bleuScoreWeight,
-  														bool distinctNbest, bool avgRefLength, string filename, ofstream& streamOut) {
-  	StaticData &staticData = StaticData::InstanceNonConst();
-  	bool chartDecoding = (staticData.GetSearchAlgorithm() == ChartDecoding);
-  	initialize(staticData, source, sentenceid, bleuObjectiveWeight, bleuScoreWeight, avgRefLength, chartDecoding);
-
-    if (chartDecoding) {
-      m_chartManager = new ChartManager(*m_sentence);
-      m_chartManager->ProcessSentence();
-      ChartTrellisPathList nBestList;
-      m_chartManager->CalcNBest(nBestSize, nBestList, distinctNbest);
-
-      cerr << "generate nbest list " << filename << endl;
-      cerr << "not implemented.." << endl;
-      exit(1);
-    	if (filename != "") {
-    		ofstream out(filename.c_str());
-    		if (!out) {
-    			ostringstream msg;
-    			msg << "Unable to open " << filename;
-    			throw runtime_error(msg.str());
-    		}
-    		// TODO: handle sentence id (for now always 0)
+    cerr << "generate nbest list " << filename << endl;
+    cerr << "not implemented.." << endl;
+    exit(1);
+    if (filename != "") {
+      ofstream out(filename.c_str());
+      if (!out) {
+        ostringstream msg;
+        msg << "Unable to open " << filename;
+        throw runtime_error(msg.str());
+      }
+      // TODO: handle sentence id (for now always 0)
 //    		OutputNBestList(const ChartTrellisPathList &nBestList, const ChartHypothesis *bestHypo, const TranslationSystem* system, long translationId, false)
 //    		OutputNBest(out, nBestList, StaticData::Instance().GetOutputFactorOrder(),m_manager->GetTranslationSystem(), 0, false);
-    		out.close();
-    	}
-    	else {
+      out.close();
+    } else {
 //    		OutputNBest(streamOut, nBestList, StaticData::Instance().GetOutputFactorOrder(),m_manager->GetTranslationSystem(), sentenceid, false);
-    	}
     }
-    else {
-    	// run the decoder
-      m_manager = new Moses::Manager(0,*m_sentence, staticData.GetSearchAlgorithm());
-      m_manager->ProcessSentence();
-      TrellisPathList nBestList;
-      m_manager->CalcNBest(nBestSize, nBestList, distinctNbest);
-
-      if (filename != "") {
-    		ofstream out(filename.c_str());
-    		if (!out) {
-    			ostringstream msg;
-    			msg << "Unable to open " << filename;
-    			throw runtime_error(msg.str());
-    		}
-    		// TODO: handle sentence id (for now always 0)
-    		//OutputNBest(out, nBestList, StaticData::Instance().GetOutputFactorOrder(),m_manager->GetTranslationSystem(), 0, false);
-    		out.close();
-      }
-      else {
-	//OutputNBest(streamOut, nBestList, StaticData::Instance().GetOutputFactorOrder(),m_manager->GetTranslationSystem(), sentenceid, false);
-    	  streamOut.flush();
+  } else {
+    // run the decoder
+    m_manager = new Moses::Manager(0,*m_sentence, staticData.GetSearchAlgorithm());
+    m_manager->ProcessSentence();
+    TrellisPathList nBestList;
+    m_manager->CalcNBest(nBestSize, nBestList, distinctNbest);
+
+    if (filename != "") {
+      ofstream out(filename.c_str());
+      if (!out) {
+        ostringstream msg;
+        msg << "Unable to open " << filename;
+        throw runtime_error(msg.str());
       }
+      // TODO: handle sentence id (for now always 0)
+      //OutputNBest(out, nBestList, StaticData::Instance().GetOutputFactorOrder(),m_manager->GetTranslationSystem(), 0, false);
+      out.close();
+    } else {
+      //OutputNBest(streamOut, nBestList, StaticData::Instance().GetOutputFactorOrder(),m_manager->GetTranslationSystem(), sentenceid, false);
+      streamOut.flush();
     }
   }
-
-  void MosesDecoder::initialize(StaticData& staticData, const std::string& source, size_t sentenceid,
-      							float bleuObjectiveWeight, float bleuScoreWeight, bool avgRefLength, bool chartDecoding) {
-  	m_sentence = new Sentence();
-    stringstream in(source + "\n");
-    const std::vector<FactorType> &inputFactorOrder = staticData.GetInputFactorOrder();
-    m_sentence->Read(in,inputFactorOrder);
-
-    // set weight of BleuScoreFeature
-    //cerr << "Reload Bleu feature weight: " << bleuObjectiveWeight*bleuScoreWeight << " (" << bleuObjectiveWeight << "*" << bleuScoreWeight << ")" << endl;
-    staticData.ReLoadBleuScoreFeatureParameter(bleuObjectiveWeight*bleuScoreWeight);
-
-    m_bleuScoreFeature->SetCurrSourceLength((*m_sentence).GetSize());
-    if (chartDecoding)
-      m_bleuScoreFeature->SetCurrNormSourceLength((*m_sentence).GetSize()-2);
-    else
-      m_bleuScoreFeature->SetCurrNormSourceLength((*m_sentence).GetSize());
-    	
-    if (avgRefLength)
-    	m_bleuScoreFeature->SetCurrAvgRefLength(sentenceid);
-    else
-    	m_bleuScoreFeature->SetCurrShortestRefLength(sentenceid);
-    m_bleuScoreFeature->SetCurrReferenceNgrams(sentenceid);
-  }
-
-  float MosesDecoder::getBleuScore(const ScoreComponentCollection& scores) {
-    return scores.GetScoreForProducer(m_bleuScoreFeature);
-  }
-
-  void MosesDecoder::setBleuScore(ScoreComponentCollection& scores, float bleu) {
-    scores.Assign(m_bleuScoreFeature, bleu);
-  }
-
-  ScoreComponentCollection MosesDecoder::getWeights() {
-    return StaticData::Instance().GetAllWeights();
-  }
-
-  void MosesDecoder::setWeights(const ScoreComponentCollection& weights) {
-    StaticData::InstanceNonConst().SetAllWeights(weights);
-  }
-
-  void MosesDecoder::updateHistory(const vector<const Word*>& words) {
-    m_bleuScoreFeature->UpdateHistory(words);
-  }
-
-  void MosesDecoder::updateHistory(const vector< vector< const Word*> >& words, vector<size_t>& sourceLengths, vector<size_t>& ref_ids, size_t rank, size_t epoch) {
-	  m_bleuScoreFeature->UpdateHistory(words, sourceLengths, ref_ids, rank, epoch);
-  }
-
-  void MosesDecoder::printBleuFeatureHistory(std::ostream& out) {
-  	m_bleuScoreFeature->PrintHistory(out);
-  }
-
-  size_t MosesDecoder::getClosestReferenceLength(size_t ref_id, int hypoLength) {
-  	return m_bleuScoreFeature->GetClosestRefLength(ref_id, hypoLength);
-  }
-
-  size_t MosesDecoder::getShortestReferenceIndex(size_t ref_id) {
-  	return m_bleuScoreFeature->GetShortestRefIndex(ref_id);
-  }
-
-  void MosesDecoder::setBleuParameters(bool disable, bool sentenceBleu, bool scaleByInputLength, bool scaleByAvgInputLength,
-		  bool scaleByInverseLength, bool scaleByAvgInverseLength,
-				       float scaleByX, float historySmoothing, size_t scheme, bool simpleHistoryBleu) {
-	  m_bleuScoreFeature->SetBleuParameters(disable, sentenceBleu, scaleByInputLength, scaleByAvgInputLength,
-			  scaleByInverseLength, scaleByAvgInverseLength,
-			  scaleByX, historySmoothing, scheme, simpleHistoryBleu);
-  }
-} 
+}
+
+void MosesDecoder::initialize(StaticData& staticData, const std::string& source, size_t sentenceid,
+                              float bleuObjectiveWeight, float bleuScoreWeight, bool avgRefLength, bool chartDecoding)
+{
+  m_sentence = new Sentence();
+  stringstream in(source + "\n");
+  const std::vector<FactorType> &inputFactorOrder = staticData.GetInputFactorOrder();
+  m_sentence->Read(in,inputFactorOrder);
+
+  // set weight of BleuScoreFeature
+  //cerr << "Reload Bleu feature weight: " << bleuObjectiveWeight*bleuScoreWeight << " (" << bleuObjectiveWeight << "*" << bleuScoreWeight << ")" << endl;
+  staticData.ReLoadBleuScoreFeatureParameter(bleuObjectiveWeight*bleuScoreWeight);
+
+  m_bleuScoreFeature->SetCurrSourceLength((*m_sentence).GetSize());
+  if (chartDecoding)
+    m_bleuScoreFeature->SetCurrNormSourceLength((*m_sentence).GetSize()-2);
+  else
+    m_bleuScoreFeature->SetCurrNormSourceLength((*m_sentence).GetSize());
+
+  if (avgRefLength)
+    m_bleuScoreFeature->SetCurrAvgRefLength(sentenceid);
+  else
+    m_bleuScoreFeature->SetCurrShortestRefLength(sentenceid);
+  m_bleuScoreFeature->SetCurrReferenceNgrams(sentenceid);
+}
+
+float MosesDecoder::getBleuScore(const ScoreComponentCollection& scores)
+{
+  return scores.GetScoreForProducer(m_bleuScoreFeature);
+}
+
+void MosesDecoder::setBleuScore(ScoreComponentCollection& scores, float bleu)
+{
+  scores.Assign(m_bleuScoreFeature, bleu);
+}
+
+ScoreComponentCollection MosesDecoder::getWeights()
+{
+  return StaticData::Instance().GetAllWeights();
+}
+
+void MosesDecoder::setWeights(const ScoreComponentCollection& weights)
+{
+  StaticData::InstanceNonConst().SetAllWeights(weights);
+}
+
+void MosesDecoder::updateHistory(const vector<const Word*>& words)
+{
+  m_bleuScoreFeature->UpdateHistory(words);
+}
+
+void MosesDecoder::updateHistory(const vector< vector< const Word*> >& words, vector<size_t>& sourceLengths, vector<size_t>& ref_ids, size_t rank, size_t epoch)
+{
+  m_bleuScoreFeature->UpdateHistory(words, sourceLengths, ref_ids, rank, epoch);
+}
+
+void MosesDecoder::printBleuFeatureHistory(std::ostream& out)
+{
+  m_bleuScoreFeature->PrintHistory(out);
+}
+
+size_t MosesDecoder::getClosestReferenceLength(size_t ref_id, int hypoLength)
+{
+  return m_bleuScoreFeature->GetClosestRefLength(ref_id, hypoLength);
+}
+
+size_t MosesDecoder::getShortestReferenceIndex(size_t ref_id)
+{
+  return m_bleuScoreFeature->GetShortestRefIndex(ref_id);
+}
+
+void MosesDecoder::setBleuParameters(bool disable, bool sentenceBleu, bool scaleByInputLength, bool scaleByAvgInputLength,
+                                     bool scaleByInverseLength, bool scaleByAvgInverseLength,
+                                     float scaleByX, float historySmoothing, size_t scheme, bool simpleHistoryBleu)
+{
+  m_bleuScoreFeature->SetBleuParameters(disable, sentenceBleu, scaleByInputLength, scaleByAvgInputLength,
+                                        scaleByInverseLength, scaleByAvgInverseLength,
+                                        scaleByX, historySmoothing, scheme, simpleHistoryBleu);
+}
+}
 
diff --git a/mira/Decoder.h b/mira/Decoder.h
index 49a33d4d0..ac8acc26b 100644
--- a/mira/Decoder.h
+++ b/mira/Decoder.h
@@ -36,100 +36,110 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 // Wrapper functions and objects for the decoder.
 //
 
-namespace Mira {
-  
+namespace Mira
+{
+
 /**
   * Wraps moses decoder.
  **/
-class MosesDecoder {
-  public:
-	/**
-	 * Initialise moses (including StaticData) using the given ini file and debuglevel, passing through any
-	 * other command line arguments.
-	 **/
-    MosesDecoder(const std::string& inifile, int debuglevel,  int argc, std::vector<std::string> decoder_params);
-	
-    //returns the best sentence
-    std::vector< std::vector<const Moses::Word*> > getNBest(const std::string& source,
-                          size_t sentenceid,
-                          size_t nbestSize,
-                          float bleuObjectiveweight, //weight of bleu in objective
-                          float bleuScoreWeight, //weight of bleu in score
-                          std::vector< Moses::ScoreComponentCollection>& featureValues,
-                          std::vector< float>& bleuScores,
-                          std::vector< float>& modelScores,
-                          size_t numReturnedTranslations,
-                          bool realBleu,
-                          bool distinct,
-                          bool avgRefLength,
-                          size_t rank,
-                          size_t epoch,
-                          std::string filename);
-    std::vector< std::vector<const Moses::Word*> > runDecoder(const std::string& source,
-                          size_t sentenceid,
-                          size_t nbestSize,
-                          float bleuObjectiveweight, //weight of bleu in objective
-                          float bleuScoreWeight, //weight of bleu in score
-                          std::vector< Moses::ScoreComponentCollection>& featureValues,
-                          std::vector< float>& bleuScores,
-                          std::vector< float>& modelScores,
-                          size_t numReturnedTranslations,
-                          bool realBleu,
-                          bool distinct,
-                          size_t rank,
-                          size_t epoch,
-                          Moses::SearchAlgorithm& seach,
-                          std::string filename);
-    std::vector< std::vector<const Moses::Word*> > runChartDecoder(const std::string& source,
-                          size_t sentenceid,
-                          size_t nbestSize,
-                          float bleuObjectiveweight, //weight of bleu in objective
-                          float bleuScoreWeight, //weight of bleu in score
-                          std::vector< Moses::ScoreComponentCollection>& featureValues,
-                          std::vector< float>& bleuScores,
-                          std::vector< float>& modelScores,
-                          size_t numReturnedTranslations,
-                          bool realBleu,
-                          bool distinct,
-                          size_t rank,
-                          size_t epoch);
-    void outputNBestList(const std::string& source,
-    											size_t sentenceid,
-    											size_t nBestSize,
-    											float bleuObjectiveWeight,
-    											float bleuScoreWeight,
-    											bool distinctNbest,
-    											bool avgRefLength,
-    											std::string filename,
-    											std::ofstream& streamOut);
-    void initialize(Moses::StaticData& staticData, const std::string& source, size_t sentenceid,
-    		 	 	float bleuObjectiveWeight, float bleuScoreWeight, bool avgRefLength, bool chartDecoding);
-    void updateHistory(const std::vector<const Moses::Word*>& words);
-    void updateHistory(const std::vector< std::vector< const Moses::Word*> >& words, std::vector<size_t>& sourceLengths, std::vector<size_t>& ref_ids, size_t rank, size_t epoch);
-    void printBleuFeatureHistory(std::ostream& out);
-    void printReferenceLength(const std::vector<size_t>& ref_ids);
-    size_t getReferenceLength(size_t ref_id);
-    size_t getClosestReferenceLength(size_t ref_id, int hypoLength);
-    size_t getShortestReferenceIndex(size_t ref_id);
-    void setBleuParameters(bool disable, bool sentenceBleu, bool scaleByInputLength, bool scaleByAvgInputLength,
-    		bool scaleByInverseLength, bool scaleByAvgInverseLength,
-		float scaleByX, float historySmoothing, size_t scheme, bool simpleHistoryBleu);
-    void setAvgInputLength (float l) { m_bleuScoreFeature->SetAvgInputLength(l); }
-    Moses::ScoreComponentCollection getWeights();
-    void setWeights(const Moses::ScoreComponentCollection& weights);
-    void cleanup(bool chartDecoding);
-		
-    float getSourceLengthHistory() { return m_bleuScoreFeature->GetSourceLengthHistory(); }
-    float getTargetLengthHistory() { return m_bleuScoreFeature->GetTargetLengthHistory(); }
-    float getAverageInputLength() { return m_bleuScoreFeature->GetAverageInputLength(); }
+class MosesDecoder
+{
+public:
+  /**
+   * Initialise moses (including StaticData) using the given ini file and debuglevel, passing through any
+   * other command line arguments.
+   **/
+  MosesDecoder(const std::string& inifile, int debuglevel,  int argc, std::vector<std::string> decoder_params);
+
+  //returns the best sentence
+  std::vector< std::vector<const Moses::Word*> > getNBest(const std::string& source,
+      size_t sentenceid,
+      size_t nbestSize,
+      float bleuObjectiveweight, //weight of bleu in objective
+      float bleuScoreWeight, //weight of bleu in score
+      std::vector< Moses::ScoreComponentCollection>& featureValues,
+      std::vector< float>& bleuScores,
+      std::vector< float>& modelScores,
+      size_t numReturnedTranslations,
+      bool realBleu,
+      bool distinct,
+      bool avgRefLength,
+      size_t rank,
+      size_t epoch,
+      std::string filename);
+  std::vector< std::vector<const Moses::Word*> > runDecoder(const std::string& source,
+      size_t sentenceid,
+      size_t nbestSize,
+      float bleuObjectiveweight, //weight of bleu in objective
+      float bleuScoreWeight, //weight of bleu in score
+      std::vector< Moses::ScoreComponentCollection>& featureValues,
+      std::vector< float>& bleuScores,
+      std::vector< float>& modelScores,
+      size_t numReturnedTranslations,
+      bool realBleu,
+      bool distinct,
+      size_t rank,
+      size_t epoch,
+      Moses::SearchAlgorithm& seach,
+      std::string filename);
+  std::vector< std::vector<const Moses::Word*> > runChartDecoder(const std::string& source,
+      size_t sentenceid,
+      size_t nbestSize,
+      float bleuObjectiveweight, //weight of bleu in objective
+      float bleuScoreWeight, //weight of bleu in score
+      std::vector< Moses::ScoreComponentCollection>& featureValues,
+      std::vector< float>& bleuScores,
+      std::vector< float>& modelScores,
+      size_t numReturnedTranslations,
+      bool realBleu,
+      bool distinct,
+      size_t rank,
+      size_t epoch);
+  void outputNBestList(const std::string& source,
+                       size_t sentenceid,
+                       size_t nBestSize,
+                       float bleuObjectiveWeight,
+                       float bleuScoreWeight,
+                       bool distinctNbest,
+                       bool avgRefLength,
+                       std::string filename,
+                       std::ofstream& streamOut);
+  void initialize(Moses::StaticData& staticData, const std::string& source, size_t sentenceid,
+                  float bleuObjectiveWeight, float bleuScoreWeight, bool avgRefLength, bool chartDecoding);
+  void updateHistory(const std::vector<const Moses::Word*>& words);
+  void updateHistory(const std::vector< std::vector< const Moses::Word*> >& words, std::vector<size_t>& sourceLengths, std::vector<size_t>& ref_ids, size_t rank, size_t epoch);
+  void printBleuFeatureHistory(std::ostream& out);
+  void printReferenceLength(const std::vector<size_t>& ref_ids);
+  size_t getReferenceLength(size_t ref_id);
+  size_t getClosestReferenceLength(size_t ref_id, int hypoLength);
+  size_t getShortestReferenceIndex(size_t ref_id);
+  void setBleuParameters(bool disable, bool sentenceBleu, bool scaleByInputLength, bool scaleByAvgInputLength,
+                         bool scaleByInverseLength, bool scaleByAvgInverseLength,
+                         float scaleByX, float historySmoothing, size_t scheme, bool simpleHistoryBleu);
+  void setAvgInputLength (float l) {
+    m_bleuScoreFeature->SetAvgInputLength(l);
+  }
+  Moses::ScoreComponentCollection getWeights();
+  void setWeights(const Moses::ScoreComponentCollection& weights);
+  void cleanup(bool chartDecoding);
+
+  float getSourceLengthHistory() {
+    return m_bleuScoreFeature->GetSourceLengthHistory();
+  }
+  float getTargetLengthHistory() {
+    return m_bleuScoreFeature->GetTargetLengthHistory();
+  }
+  float getAverageInputLength() {
+    return m_bleuScoreFeature->GetAverageInputLength();
+  }
 
-	private:
-    float getBleuScore(const Moses::ScoreComponentCollection& scores);
-    void setBleuScore(Moses::ScoreComponentCollection& scores, float bleu);
-    Moses::Manager *m_manager;
-    Moses::ChartManager *m_chartManager;
-    Moses::Sentence *m_sentence;
-    Moses::BleuScoreFeature *m_bleuScoreFeature;
+private:
+  float getBleuScore(const Moses::ScoreComponentCollection& scores);
+  void setBleuScore(Moses::ScoreComponentCollection& scores, float bleu);
+  Moses::Manager *m_manager;
+  Moses::ChartManager *m_chartManager;
+  Moses::Sentence *m_sentence;
+  Moses::BleuScoreFeature *m_bleuScoreFeature;
 };
 
 
diff --git a/mira/Hildreth.cpp b/mira/Hildreth.cpp
index 53d1e0881..03076e767 100644
--- a/mira/Hildreth.cpp
+++ b/mira/Hildreth.cpp
@@ -3,186 +3,173 @@
 using namespace Moses;
 using namespace std;
 
-namespace Mira {
+namespace Mira
+{
 
-  vector<float> Hildreth::optimise (const vector<ScoreComponentCollection>& a, const vector<float>& b) {
+vector<float> Hildreth::optimise (const vector<ScoreComponentCollection>& a, const vector<float>& b)
+{
 
-    size_t i;
-    int max_iter = 10000;
-    float eps = 0.00000001;
-    float zero = 0.000000000001;
+  size_t i;
+  int max_iter = 10000;
+  float eps = 0.00000001;
+  float zero = 0.000000000001;
 
-    vector<float> alpha ( b.size() );
-    vector<float> F ( b.size() );
-    vector<float> kkt ( b.size() );
+  vector<float> alpha ( b.size() );
+  vector<float> F ( b.size() );
+  vector<float> kkt ( b.size() );
 
-    float max_kkt = -1e100;
+  float max_kkt = -1e100;
 
-    size_t K = b.size();
+  size_t K = b.size();
 
-    float A[K][K];
-    bool is_computed[K];
-    for ( i = 0; i < K; i++ )
-    {
-      A[i][i] = a[i].InnerProduct(a[i]);
-      is_computed[i] = false;
+  float A[K][K];
+  bool is_computed[K];
+  for ( i = 0; i < K; i++ ) {
+    A[i][i] = a[i].InnerProduct(a[i]);
+    is_computed[i] = false;
+  }
+
+  int max_kkt_i = -1;
+
+
+  for ( i = 0; i < b.size(); i++ ) {
+    F[i] = b[i];
+    kkt[i] = F[i];
+    if ( kkt[i] > max_kkt ) {
+      max_kkt = kkt[i];
+      max_kkt_i = i;
     }
+  }
 
-    int max_kkt_i = -1;
+  int iter = 0;
+  float diff_alpha;
+  float try_alpha;
+  float add_alpha;
 
+  while ( max_kkt >= eps && iter < max_iter ) {
 
-    for ( i = 0; i < b.size(); i++ )
-    {
-      F[i] = b[i];
+    diff_alpha = A[max_kkt_i][max_kkt_i] <= zero ? 0.0 : F[max_kkt_i]/A[max_kkt_i][max_kkt_i];
+    try_alpha = alpha[max_kkt_i] + diff_alpha;
+    add_alpha = 0.0;
+
+    if ( try_alpha < 0.0 )
+      add_alpha = -1.0 * alpha[max_kkt_i];
+    else
+      add_alpha = diff_alpha;
+
+    alpha[max_kkt_i] = alpha[max_kkt_i] + add_alpha;
+
+    if ( !is_computed[max_kkt_i] ) {
+      for ( i = 0; i < K; i++ ) {
+        A[i][max_kkt_i] = a[i].InnerProduct(a[max_kkt_i] ); // for version 1
+        //A[i][max_kkt_i] = 0; // for version 1
+        is_computed[max_kkt_i] = true;
+      }
+    }
+
+    for ( i = 0; i < F.size(); i++ ) {
+      F[i] -= add_alpha * A[i][max_kkt_i];
       kkt[i] = F[i];
-      if ( kkt[i] > max_kkt )
-      {
+      if ( alpha[i] > zero )
+        kkt[i] = abs ( F[i] );
+    }
+    max_kkt = -1e100;
+    max_kkt_i = -1;
+    for ( i = 0; i < F.size(); i++ )
+      if ( kkt[i] > max_kkt ) {
         max_kkt = kkt[i];
         max_kkt_i = i;
       }
-    }
 
-    int iter = 0;
-    float diff_alpha;
-    float try_alpha;
-    float add_alpha;
-
-    while ( max_kkt >= eps && iter < max_iter )
-    {
-
-      diff_alpha = A[max_kkt_i][max_kkt_i] <= zero ? 0.0 : F[max_kkt_i]/A[max_kkt_i][max_kkt_i];
-      try_alpha = alpha[max_kkt_i] + diff_alpha;
-      add_alpha = 0.0;
-
-      if ( try_alpha < 0.0 )
-        add_alpha = -1.0 * alpha[max_kkt_i];
-      else
-        add_alpha = diff_alpha;
-
-      alpha[max_kkt_i] = alpha[max_kkt_i] + add_alpha;
-
-      if ( !is_computed[max_kkt_i] )
-      {
-        for ( i = 0; i < K; i++ )
-        {
-          A[i][max_kkt_i] = a[i].InnerProduct(a[max_kkt_i] ); // for version 1
-          //A[i][max_kkt_i] = 0; // for version 1
-          is_computed[max_kkt_i] = true;
-        }
-      }
+    iter++;
+  }
 
-      for ( i = 0; i < F.size(); i++ )
-      {
-        F[i] -= add_alpha * A[i][max_kkt_i];
-        kkt[i] = F[i];
-        if ( alpha[i] > zero )
-          kkt[i] = abs ( F[i] );
-      }
-      max_kkt = -1e100;
-      max_kkt_i = -1;
-      for ( i = 0; i < F.size(); i++ )
-        if ( kkt[i] > max_kkt )
-        {
-          max_kkt = kkt[i];
-          max_kkt_i = i;
-        }
-
-      iter++;
-    }
+  return alpha;
+}
 
-    return alpha;
-  }
+vector<float> Hildreth::optimise (const vector<ScoreComponentCollection>& a, const vector<float>& b, float C)
+{
 
-  vector<float> Hildreth::optimise (const vector<ScoreComponentCollection>& a, const vector<float>& b, float C) {
+  size_t i;
+  int max_iter = 10000;
+  float eps = 0.00000001;
+  float zero = 0.000000000001;
 
-    size_t i;
-    int max_iter = 10000;
-    float eps = 0.00000001;
-    float zero = 0.000000000001;
+  vector<float> alpha ( b.size() );
+  vector<float> F ( b.size() );
+  vector<float> kkt ( b.size() );
 
-    vector<float> alpha ( b.size() );
-    vector<float> F ( b.size() );
-    vector<float> kkt ( b.size() );
+  float max_kkt = -1e100;
 
-    float max_kkt = -1e100;
+  size_t K = b.size();
+
+  float A[K][K];
+  bool is_computed[K];
+  for ( i = 0; i < K; i++ ) {
+    A[i][i] = a[i].InnerProduct(a[i]);
+    is_computed[i] = false;
+  }
+
+  int max_kkt_i = -1;
 
-    size_t K = b.size();
 
-    float A[K][K];
-    bool is_computed[K];
-    for ( i = 0; i < K; i++ )
-    {
-      A[i][i] = a[i].InnerProduct(a[i]);
-      is_computed[i] = false;
+  for ( i = 0; i < b.size(); i++ ) {
+    F[i] = b[i];
+    kkt[i] = F[i];
+    if ( kkt[i] > max_kkt ) {
+      max_kkt = kkt[i];
+      max_kkt_i = i;
     }
+  }
 
-    int max_kkt_i = -1;
+  int iter = 0;
+  float diff_alpha;
+  float try_alpha;
+  float add_alpha;
 
+  while ( max_kkt >= eps && iter < max_iter ) {
 
-    for ( i = 0; i < b.size(); i++ )
-    {
-      F[i] = b[i];
-      kkt[i] = F[i];
-      if ( kkt[i] > max_kkt )
-      {
-        max_kkt = kkt[i];
-        max_kkt_i = i;
-      }
-    }
+    diff_alpha = A[max_kkt_i][max_kkt_i] <= zero ? 0.0 : F[max_kkt_i]/A[max_kkt_i][max_kkt_i];
+    try_alpha = alpha[max_kkt_i] + diff_alpha;
+    add_alpha = 0.0;
 
-    int iter = 0;
-    float diff_alpha;
-    float try_alpha;
-    float add_alpha;
-
-    while ( max_kkt >= eps && iter < max_iter )
-    {
-
-      diff_alpha = A[max_kkt_i][max_kkt_i] <= zero ? 0.0 : F[max_kkt_i]/A[max_kkt_i][max_kkt_i];
-      try_alpha = alpha[max_kkt_i] + diff_alpha;
-      add_alpha = 0.0;
-
-      if ( try_alpha < 0.0 )
-        add_alpha = -1.0 * alpha[max_kkt_i];
-      else if (try_alpha > C)
-				add_alpha = C - alpha[max_kkt_i];
-      else
-        add_alpha = diff_alpha;
-
-      alpha[max_kkt_i] = alpha[max_kkt_i] + add_alpha;
-
-      if ( !is_computed[max_kkt_i] )
-      {
-        for ( i = 0; i < K; i++ )
-        {
-          A[i][max_kkt_i] = a[i].InnerProduct(a[max_kkt_i] ); // for version 1
-          //A[i][max_kkt_i] = 0; // for version 1
-          is_computed[max_kkt_i] = true;
-        }
-      }
+    if ( try_alpha < 0.0 )
+      add_alpha = -1.0 * alpha[max_kkt_i];
+    else if (try_alpha > C)
+      add_alpha = C - alpha[max_kkt_i];
+    else
+      add_alpha = diff_alpha;
 
-      for ( i = 0; i < F.size(); i++ )
-      {
-        F[i] -= add_alpha * A[i][max_kkt_i];
-        kkt[i] = F[i];
-        if (alpha[i] > C - zero)
-					kkt[i]=-kkt[i];
-				else if (alpha[i] > zero)
-					kkt[i] = abs(F[i]);
+    alpha[max_kkt_i] = alpha[max_kkt_i] + add_alpha;
 
+    if ( !is_computed[max_kkt_i] ) {
+      for ( i = 0; i < K; i++ ) {
+        A[i][max_kkt_i] = a[i].InnerProduct(a[max_kkt_i] ); // for version 1
+        //A[i][max_kkt_i] = 0; // for version 1
+        is_computed[max_kkt_i] = true;
       }
-      max_kkt = -1e100;
-      max_kkt_i = -1;
-      for ( i = 0; i < F.size(); i++ )
-        if ( kkt[i] > max_kkt )
-        {
-          max_kkt = kkt[i];
-          max_kkt_i = i;
-        }
-
-      iter++;
     }
 
-    return alpha;
+    for ( i = 0; i < F.size(); i++ ) {
+      F[i] -= add_alpha * A[i][max_kkt_i];
+      kkt[i] = F[i];
+      if (alpha[i] > C - zero)
+        kkt[i]=-kkt[i];
+      else if (alpha[i] > zero)
+        kkt[i] = abs(F[i]);
+
+    }
+    max_kkt = -1e100;
+    max_kkt_i = -1;
+    for ( i = 0; i < F.size(); i++ )
+      if ( kkt[i] > max_kkt ) {
+        max_kkt = kkt[i];
+        max_kkt_i = i;
+      }
+
+    iter++;
   }
+
+  return alpha;
+}
 }
diff --git a/mira/Hildreth.h b/mira/Hildreth.h
index da52995aa..373f2ac43 100644
--- a/mira/Hildreth.h
+++ b/mira/Hildreth.h
@@ -1,11 +1,13 @@
 #include "moses/FeatureVector.h"
 #include "moses/ScoreComponentCollection.h"
 
-namespace Mira {
+namespace Mira
+{
 
-  class Hildreth {
-    public :
-      static std::vector<float> optimise (const std::vector<Moses::ScoreComponentCollection>& a, const std::vector<float>& b );
-      static std::vector<float> optimise (const std::vector<Moses::ScoreComponentCollection>& a, const std::vector<float>& b, float C);
-  };
+class Hildreth
+{
+public :
+  static std::vector<float> optimise (const std::vector<Moses::ScoreComponentCollection>& a, const std::vector<float>& b );
+  static std::vector<float> optimise (const std::vector<Moses::ScoreComponentCollection>& a, const std::vector<float>& b, float C);
+};
 }
diff --git a/mira/HildrethTest.cpp b/mira/HildrethTest.cpp
index a32dcd1d3..43e4403e4 100644
--- a/mira/HildrethTest.cpp
+++ b/mira/HildrethTest.cpp
@@ -34,22 +34,31 @@ using namespace Mira;
 namespace MosesTest
 {
 
-class MockSingleFeature : public StatelessFeatureFunction {
-  public:
-    MockSingleFeature(): StatelessFeatureFunction("MockSingle",1) {}
-    std::string GetScoreProducerWeightShortName(unsigned) const {return "sf";}
+class MockSingleFeature : public StatelessFeatureFunction
+{
+public:
+  MockSingleFeature(): StatelessFeatureFunction("MockSingle",1) {}
+  std::string GetScoreProducerWeightShortName(unsigned) const {
+    return "sf";
+  }
 };
 
-class MockMultiFeature : public StatelessFeatureFunction {
-  public:
-    MockMultiFeature(): StatelessFeatureFunction("MockMulti",5) {}
-    std::string GetScoreProducerWeightShortName(unsigned) const {return "mf";}
+class MockMultiFeature : public StatelessFeatureFunction
+{
+public:
+  MockMultiFeature(): StatelessFeatureFunction("MockMulti",5) {}
+  std::string GetScoreProducerWeightShortName(unsigned) const {
+    return "mf";
+  }
 };
 
-class MockSparseFeature : public StatelessFeatureFunction {
-  public:
-    MockSparseFeature(): StatelessFeatureFunction("MockSparse", ScoreProducer::unlimited) {}
-    std::string GetScoreProducerWeightShortName(unsigned) const {return "sf";}
+class MockSparseFeature : public StatelessFeatureFunction
+{
+public:
+  MockSparseFeature(): StatelessFeatureFunction("MockSparse", ScoreProducer::unlimited) {}
+  std::string GetScoreProducerWeightShortName(unsigned) const {
+    return "sf";
+  }
 };
 
 struct MockProducers {
@@ -66,716 +75,716 @@ BOOST_AUTO_TEST_SUITE(hildreth_test)
 
 BOOST_FIXTURE_TEST_CASE(test_hildreth_1, MockProducers)
 {
-	// Feasible example with 2 constraints
-	cerr << "\n>>>>>Hildreth test, without slack and with 0.01 slack" << endl << endl;
-	vector< ScoreComponentCollection> featureValueDiffs;
-	vector< float> lossMinusModelScoreDiff;
-
-	// initial weights
-	float w[] = { 1, 1, 1, 1, 0 };
-	vector<float> vec(w,w+5);
-	ScoreComponentCollection weights;
-	weights.PlusEquals(&multi, vec);
-
-	// feature values (second is oracle)
-	//float arr1[] = {0, -5, -27.0908, -1.83258, 0 };
-	//float arr2[] = {0, -5, -29.158, -1.83258, 0 };
-	//float arr3[] = {0, -5, -27.0908, -1.83258, 0 };
-
-	// feature value differences (to oracle)
-	ScoreComponentCollection s1, s2, s3;
-	float arr1[] = { 0, 0, -2.0672, 0, 0 };
-	float arr2[] = { 0, 0, 0, 0, 0 };
-	float arr3[] = { 0, 0, -2.0672, 0, 0 };
-
-	float loss1 = 2.34085;
-	float loss2 = 0;
-	float loss3 = 2.34085;
-
-	vector<float> vec1(arr1,arr1+5);
-	vector<float> vec2(arr2,arr2+5);
-	vector<float> vec3(arr3,arr3+5);
-
-	s1.PlusEquals(&multi,vec1);
-	s2.PlusEquals(&multi,vec2);
-	s3.PlusEquals(&multi,vec3);
-
-	featureValueDiffs.push_back(s1);
-	featureValueDiffs.push_back(s2);
-	featureValueDiffs.push_back(s3);
-
-	cerr << "feature value diff: " << featureValueDiffs[0] << endl;
-	cerr << "feature value diff: " << featureValueDiffs[1] << endl;
-	cerr << "feature value diff: " << featureValueDiffs[2] << endl << endl;
-
-	float oldModelScoreDiff1 = featureValueDiffs[0].InnerProduct(weights);
-	float oldModelScoreDiff2 = featureValueDiffs[1].InnerProduct(weights);
-	float oldModelScoreDiff3 = featureValueDiffs[2].InnerProduct(weights);
-
-	cerr << "model score diff: " << oldModelScoreDiff1 << ", loss: " << loss1 << endl;
-	cerr << "model score diff: " << oldModelScoreDiff2 << ", loss: " << loss2 << endl;
-	cerr << "model score diff: " << oldModelScoreDiff3 << ", loss: " << loss3 << endl << endl;
-
-	lossMinusModelScoreDiff.push_back(loss1 - oldModelScoreDiff1);
-	lossMinusModelScoreDiff.push_back(loss2 - oldModelScoreDiff2);
-	lossMinusModelScoreDiff.push_back(loss3 - oldModelScoreDiff3);
-
-	vector< float> alphas1 = Hildreth::optimise(featureValueDiffs, lossMinusModelScoreDiff);
-	vector< float> alphas2 = Hildreth::optimise(featureValueDiffs, lossMinusModelScoreDiff, 0.01);
-
-	cerr << "\nalphas without slack:" << endl;
-	for (size_t i = 0; i < alphas1.size(); ++i) {
-		cerr << "alpha " << i << ": " << alphas1[i] << endl;
-	}
-	cerr << endl;
-
-	cerr << "partial updates:" << endl;
-	vector< ScoreComponentCollection> featureValueDiffs1(featureValueDiffs);
-	FVector totalUpdate1 = ScoreComponentCollection::CreateFVector();
-	for (size_t k = 0; k < featureValueDiffs1.size(); ++k) {
-		featureValueDiffs1[k].MultiplyEquals(alphas1[k]);
-		cerr << k << ": " << featureValueDiffs1[k].GetScoresVector() << endl;
-		FVector update = featureValueDiffs1[k].GetScoresVector();
-		totalUpdate1 += update;
-	}
-	cerr << endl;
-	cerr << "total update: " << totalUpdate1 << endl << endl;
-
-	ScoreComponentCollection weightsUpdate1(weights);
-	weightsUpdate1.PlusEquals(totalUpdate1);
-	cerr << "new weights: " << weightsUpdate1 << endl << endl;
-
-	float newModelScoreDiff1 = featureValueDiffs[0].InnerProduct(weightsUpdate1);
-	float newModelScoreDiff2 = featureValueDiffs[1].InnerProduct(weightsUpdate1);
-	float newModelScoreDiff3 = featureValueDiffs[2].InnerProduct(weightsUpdate1);
-
-	cerr << "new model score diff: " << newModelScoreDiff1 << ", loss: " << loss1 << endl;
-	cerr << "new model score diff: " << newModelScoreDiff2 << ", loss: " << loss2 << endl;
-	cerr << "new model score diff: " << newModelScoreDiff3 << ", loss: " << loss3 << endl;
-
-	cerr << "\n\nalphas with slack 0.01:" << endl;
-	for (size_t i = 0; i < alphas2.size(); ++i) {
-		cerr << "alpha " << i << ": " << alphas2[i] << endl;
-	}
-	cerr << endl;
-
-	cerr << "partial updates:" << endl;
-	vector< ScoreComponentCollection> featureValueDiffs2(featureValueDiffs);
-	FVector totalUpdate2 = ScoreComponentCollection::CreateFVector();
-	for (size_t k = 0; k < featureValueDiffs2.size(); ++k) {
-		featureValueDiffs2[k].MultiplyEquals(alphas2[k]);
-		cerr << k << ": " << featureValueDiffs2[k].GetScoresVector() << endl;
-		FVector update = featureValueDiffs2[k].GetScoresVector();
-		totalUpdate2 += update;
-	}
-	cerr << endl;
-	cerr << "total update: " << totalUpdate2 << endl << endl;
-
-	ScoreComponentCollection weightsUpdate2(weights);
-	weightsUpdate2.PlusEquals(totalUpdate2);
-	cerr << "new weights: " << weightsUpdate2 << endl << endl;
-
-	float newModelScoreDiff4 = featureValueDiffs[0].InnerProduct(weightsUpdate2);
-	float newModelScoreDiff5 = featureValueDiffs[1].InnerProduct(weightsUpdate2);
-	float newModelScoreDiff6 = featureValueDiffs[2].InnerProduct(weightsUpdate2);
-
-	cerr << "new model score diff: " << newModelScoreDiff4 << ", loss: " << loss1 << endl;
-	cerr << "new model score diff: " << newModelScoreDiff5 << ", loss: " << loss2 << endl;
-	cerr << "new model score diff: " << newModelScoreDiff6 << ", loss: " << loss3 << endl;
+  // Feasible example with 2 constraints
+  cerr << "\n>>>>>Hildreth test, without slack and with 0.01 slack" << endl << endl;
+  vector< ScoreComponentCollection> featureValueDiffs;
+  vector< float> lossMinusModelScoreDiff;
+
+  // initial weights
+  float w[] = { 1, 1, 1, 1, 0 };
+  vector<float> vec(w,w+5);
+  ScoreComponentCollection weights;
+  weights.PlusEquals(&multi, vec);
+
+  // feature values (second is oracle)
+  //float arr1[] = {0, -5, -27.0908, -1.83258, 0 };
+  //float arr2[] = {0, -5, -29.158, -1.83258, 0 };
+  //float arr3[] = {0, -5, -27.0908, -1.83258, 0 };
+
+  // feature value differences (to oracle)
+  ScoreComponentCollection s1, s2, s3;
+  float arr1[] = { 0, 0, -2.0672, 0, 0 };
+  float arr2[] = { 0, 0, 0, 0, 0 };
+  float arr3[] = { 0, 0, -2.0672, 0, 0 };
+
+  float loss1 = 2.34085;
+  float loss2 = 0;
+  float loss3 = 2.34085;
+
+  vector<float> vec1(arr1,arr1+5);
+  vector<float> vec2(arr2,arr2+5);
+  vector<float> vec3(arr3,arr3+5);
+
+  s1.PlusEquals(&multi,vec1);
+  s2.PlusEquals(&multi,vec2);
+  s3.PlusEquals(&multi,vec3);
+
+  featureValueDiffs.push_back(s1);
+  featureValueDiffs.push_back(s2);
+  featureValueDiffs.push_back(s3);
+
+  cerr << "feature value diff: " << featureValueDiffs[0] << endl;
+  cerr << "feature value diff: " << featureValueDiffs[1] << endl;
+  cerr << "feature value diff: " << featureValueDiffs[2] << endl << endl;
+
+  float oldModelScoreDiff1 = featureValueDiffs[0].InnerProduct(weights);
+  float oldModelScoreDiff2 = featureValueDiffs[1].InnerProduct(weights);
+  float oldModelScoreDiff3 = featureValueDiffs[2].InnerProduct(weights);
+
+  cerr << "model score diff: " << oldModelScoreDiff1 << ", loss: " << loss1 << endl;
+  cerr << "model score diff: " << oldModelScoreDiff2 << ", loss: " << loss2 << endl;
+  cerr << "model score diff: " << oldModelScoreDiff3 << ", loss: " << loss3 << endl << endl;
+
+  lossMinusModelScoreDiff.push_back(loss1 - oldModelScoreDiff1);
+  lossMinusModelScoreDiff.push_back(loss2 - oldModelScoreDiff2);
+  lossMinusModelScoreDiff.push_back(loss3 - oldModelScoreDiff3);
+
+  vector< float> alphas1 = Hildreth::optimise(featureValueDiffs, lossMinusModelScoreDiff);
+  vector< float> alphas2 = Hildreth::optimise(featureValueDiffs, lossMinusModelScoreDiff, 0.01);
+
+  cerr << "\nalphas without slack:" << endl;
+  for (size_t i = 0; i < alphas1.size(); ++i) {
+    cerr << "alpha " << i << ": " << alphas1[i] << endl;
+  }
+  cerr << endl;
+
+  cerr << "partial updates:" << endl;
+  vector< ScoreComponentCollection> featureValueDiffs1(featureValueDiffs);
+  FVector totalUpdate1 = ScoreComponentCollection::CreateFVector();
+  for (size_t k = 0; k < featureValueDiffs1.size(); ++k) {
+    featureValueDiffs1[k].MultiplyEquals(alphas1[k]);
+    cerr << k << ": " << featureValueDiffs1[k].GetScoresVector() << endl;
+    FVector update = featureValueDiffs1[k].GetScoresVector();
+    totalUpdate1 += update;
+  }
+  cerr << endl;
+  cerr << "total update: " << totalUpdate1 << endl << endl;
+
+  ScoreComponentCollection weightsUpdate1(weights);
+  weightsUpdate1.PlusEquals(totalUpdate1);
+  cerr << "new weights: " << weightsUpdate1 << endl << endl;
+
+  float newModelScoreDiff1 = featureValueDiffs[0].InnerProduct(weightsUpdate1);
+  float newModelScoreDiff2 = featureValueDiffs[1].InnerProduct(weightsUpdate1);
+  float newModelScoreDiff3 = featureValueDiffs[2].InnerProduct(weightsUpdate1);
+
+  cerr << "new model score diff: " << newModelScoreDiff1 << ", loss: " << loss1 << endl;
+  cerr << "new model score diff: " << newModelScoreDiff2 << ", loss: " << loss2 << endl;
+  cerr << "new model score diff: " << newModelScoreDiff3 << ", loss: " << loss3 << endl;
+
+  cerr << "\n\nalphas with slack 0.01:" << endl;
+  for (size_t i = 0; i < alphas2.size(); ++i) {
+    cerr << "alpha " << i << ": " << alphas2[i] << endl;
+  }
+  cerr << endl;
+
+  cerr << "partial updates:" << endl;
+  vector< ScoreComponentCollection> featureValueDiffs2(featureValueDiffs);
+  FVector totalUpdate2 = ScoreComponentCollection::CreateFVector();
+  for (size_t k = 0; k < featureValueDiffs2.size(); ++k) {
+    featureValueDiffs2[k].MultiplyEquals(alphas2[k]);
+    cerr << k << ": " << featureValueDiffs2[k].GetScoresVector() << endl;
+    FVector update = featureValueDiffs2[k].GetScoresVector();
+    totalUpdate2 += update;
+  }
+  cerr << endl;
+  cerr << "total update: " << totalUpdate2 << endl << endl;
+
+  ScoreComponentCollection weightsUpdate2(weights);
+  weightsUpdate2.PlusEquals(totalUpdate2);
+  cerr << "new weights: " << weightsUpdate2 << endl << endl;
+
+  float newModelScoreDiff4 = featureValueDiffs[0].InnerProduct(weightsUpdate2);
+  float newModelScoreDiff5 = featureValueDiffs[1].InnerProduct(weightsUpdate2);
+  float newModelScoreDiff6 = featureValueDiffs[2].InnerProduct(weightsUpdate2);
+
+  cerr << "new model score diff: " << newModelScoreDiff4 << ", loss: " << loss1 << endl;
+  cerr << "new model score diff: " << newModelScoreDiff5 << ", loss: " << loss2 << endl;
+  cerr << "new model score diff: " << newModelScoreDiff6 << ", loss: " << loss3 << endl;
 }
 
 
 BOOST_FIXTURE_TEST_CASE(test_hildreth_3, MockProducers)
 {
-	// Unfeasible example with 21 constraints
-	cerr << "\n>>>>>Hildreth test, without slack and with 0.01 slack" << endl << endl;
-	vector< ScoreComponentCollection> featureValueDiffs;
-	vector< float> lossMinusModelScoreDiff;
-
-	// initial weights
-	float w[] = { 1, 1, 0.638672, 1, 0 };
-	vector<float> vec(w,w+5);
-	ScoreComponentCollection weights;
-	weights.PlusEquals(&multi, vec);
-
-	int numberOfConstraints = 21;
-
-	// feature value differences (to oracle)
-	// NOTE: these feature values are only approximations
-	ScoreComponentCollection s1, s2, s3, s4, s5, s6, s7, s8, s9, s10, s11, s12, s13, s14, s15, s16, s17, s18, s19, s20, s21;
-	float arr1[] = { 0, 0, -2.0672, 0, 0 };
-	float arr2[] = { 0, 0, 0, 0, 0 };
-	float arr3[] = { 0, 0, -2.08436, 1.38629, 0 };
-	float arr4[] = { 0, 0, -0.0171661, 1.38629, 0 };
-	float arr5[] = { 0, 0, 4.4283, 0, 0 };
-	float arr6[] = { 0, 0, 3.84829, 1.38629, 0 };
-	float arr7[] = { 0, 0, 6.83689, 0, 0 };
-	float arr8[] = { 0, 0, 0, 0, 0 };
-	float arr9[] = { 0, 0, -2.0672, 0, 0 };
-	float arr10[] = { 0, 0, -0.0171661, 1.38629, 0 };
-	float arr11[] = { 0, 0, -2.08436, 1.38629, 0 };
-	float arr12[] = { 0, 0, 4.4283, 0, 0 };
-	float arr13[] = { 3, 0, 2.41089, 0, 0 };
-	float arr14[] = { 3, 0, 2.32709, 0, 0 };
-	float arr15[] = { 0, 0, -2.0672, 0, 0 };
-	float arr16[] = { 0, 0, -2.08436, 1.38629, 0 };
-	float arr17[] = { 0, 0, 4.4283, 0, 0 };
-	float arr18[] = { 0, 0, 3.84829, 1.38629, 0 };
-	float arr19[] = { 0, 0, -0.0171661, 1.38629, 0 };
-	float arr20[] = { 0, 0, 0, 0, 0 };
-	float arr21[] = { 0, 0, 6.83689, 0, 0 };
-
-	vector<float> losses;
-	losses.push_back(2.73485);
-	losses.push_back(0);
-	losses.push_back(3.64118);
-	losses.push_back(1.47347);
-	losses.push_back(3.64118);
-	losses.push_back(4.16278);
-	losses.push_back(3.13952);
-	losses.push_back(0);
-	losses.push_back(2.73485);
-	losses.push_back(1.47347);
-	losses.push_back(3.64118);
-	losses.push_back(3.64118);
-	losses.push_back(2.51662);
-	losses.push_back(2.73485);
-	losses.push_back(2.73485);
-	losses.push_back(3.64118);
-	losses.push_back(3.64118);
-	losses.push_back(4.16278);
-	losses.push_back(1.47347);
-	losses.push_back(0);
-	losses.push_back(3.13952);
-
-	vector<float> vec1(arr1,arr1+5);
-	vector<float> vec2(arr2,arr2+5);
-	vector<float> vec3(arr3,arr3+5);
-	vector<float> vec4(arr4,arr4+5);
-	vector<float> vec5(arr5,arr5+5);
-	vector<float> vec6(arr6,arr6+5);
-	vector<float> vec7(arr7,arr7+5);
-	vector<float> vec8(arr8,arr8+5);
-	vector<float> vec9(arr9,arr9+5);
-	vector<float> vec10(arr10,arr10+5);
-	vector<float> vec11(arr11,arr11+5);
-	vector<float> vec12(arr12,arr12+5);
-	vector<float> vec13(arr13,arr13+5);
-	vector<float> vec14(arr14,arr14+5);
-	vector<float> vec15(arr15,arr15+5);
-	vector<float> vec16(arr16,arr16+5);
-	vector<float> vec17(arr17,arr17+5);
-	vector<float> vec18(arr18,arr18+5);
-	vector<float> vec19(arr19,arr19+5);
-	vector<float> vec20(arr20,arr20+5);
-	vector<float> vec21(arr21,arr21+5);
-
-	s1.PlusEquals(&multi,vec1);
-	s2.PlusEquals(&multi,vec2);
-	s3.PlusEquals(&multi,vec3);
-	s4.PlusEquals(&multi,vec4);
-	s5.PlusEquals(&multi,vec5);
-	s6.PlusEquals(&multi,vec6);
-	s7.PlusEquals(&multi,vec7);
-	s8.PlusEquals(&multi,vec8);
-	s9.PlusEquals(&multi,vec9);
-	s10.PlusEquals(&multi,vec10);
-	s11.PlusEquals(&multi,vec11);
-	s12.PlusEquals(&multi,vec12);
-	s13.PlusEquals(&multi,vec13);
-	s14.PlusEquals(&multi,vec14);
-	s15.PlusEquals(&multi,vec15);
-	s16.PlusEquals(&multi,vec16);
-	s17.PlusEquals(&multi,vec17);
-	s18.PlusEquals(&multi,vec18);
-	s19.PlusEquals(&multi,vec19);
-	s20.PlusEquals(&multi,vec20);
-	s21.PlusEquals(&multi,vec21);
-
-	featureValueDiffs.push_back(s1);
-	featureValueDiffs.push_back(s2);
-	featureValueDiffs.push_back(s3);
-	featureValueDiffs.push_back(s4);
-	featureValueDiffs.push_back(s5);
-	featureValueDiffs.push_back(s6);
-	featureValueDiffs.push_back(s7);
-	featureValueDiffs.push_back(s8);
-	featureValueDiffs.push_back(s9);
-	featureValueDiffs.push_back(s10);
-	featureValueDiffs.push_back(s11);
-	featureValueDiffs.push_back(s12);
-	featureValueDiffs.push_back(s13);
-	featureValueDiffs.push_back(s14);
-	featureValueDiffs.push_back(s15);
-	featureValueDiffs.push_back(s16);
-	featureValueDiffs.push_back(s17);
-	featureValueDiffs.push_back(s18);
-	featureValueDiffs.push_back(s19);
-	featureValueDiffs.push_back(s20);
-	featureValueDiffs.push_back(s21);
-
-	vector<float> oldModelScoreDiff;
-	for (int i = 0; i < numberOfConstraints; ++i) {
-		oldModelScoreDiff.push_back(featureValueDiffs[i].InnerProduct(weights));
-	}
-
-	for (int i = 0; i < numberOfConstraints; ++i) {
-		cerr << "old model score diff: " << oldModelScoreDiff[i] << ", loss: " << losses[i] << "\t" << (oldModelScoreDiff[i] >= losses[i] ? 1 : 0) << endl;
-	}
-
-	for (int i = 0; i < numberOfConstraints; ++i) {
-		lossMinusModelScoreDiff.push_back(losses[i] - oldModelScoreDiff[i]);
-	}
-
-	for (int i = 0; i < numberOfConstraints; ++i) {
-		cerr << "A: " << featureValueDiffs[i] << ", b: " << lossMinusModelScoreDiff[i] << endl;
-	}
-
-	vector< float> alphas1 = Hildreth::optimise(featureValueDiffs, lossMinusModelScoreDiff);
-	vector< float> alphas2 = Hildreth::optimise(featureValueDiffs, lossMinusModelScoreDiff, 0.01);
-
-	cerr << "\nalphas without slack:" << endl;
-	for (size_t i = 0; i < alphas1.size(); ++i) {
-		cerr << "alpha " << i << ": " << alphas1[i] << endl;
-	}
-	cerr << endl;
-
-	cerr << "partial updates:" << endl;
-	vector< ScoreComponentCollection> featureValueDiffs1(featureValueDiffs);
-	FVector totalUpdate1 = ScoreComponentCollection::CreateFVector();
-	for (size_t k = 0; k < featureValueDiffs1.size(); ++k) {
-		featureValueDiffs1[k].MultiplyEquals(alphas1[k]);
-		cerr << k << ": " << featureValueDiffs1[k].GetScoresVector() << endl;
-		FVector update = featureValueDiffs1[k].GetScoresVector();
-		totalUpdate1 += update;
-	}
-	cerr << endl;
-	cerr << "total update: " << totalUpdate1 << endl << endl;
-
-	ScoreComponentCollection weightsUpdate1(weights);
-	weightsUpdate1.PlusEquals(totalUpdate1);
-	cerr << "old weights: " << weights << endl;
-	cerr << "new weights: " << weightsUpdate1 << endl << endl;
-
-	vector<float> newModelScoreDiff;
-	for (int i = 0; i < numberOfConstraints; ++i) {
-		newModelScoreDiff.push_back(featureValueDiffs[i].InnerProduct(weightsUpdate1));
-	}
-
-	for (int i = 0; i < numberOfConstraints; ++i) {
-		cerr << "new model score diff: " << newModelScoreDiff[i] << ", loss: " << losses[i] << "\t" << (newModelScoreDiff[i] >= losses[i] ? 1 : 0) << endl;
-	}
-
-	cerr << "\n\nalphas with slack 0.01:" << endl;
-	for (size_t i = 0; i < alphas2.size(); ++i) {
-		cerr << "alpha " << i << ": " << alphas2[i] << endl;
-	}
-	cerr << endl;
-
-	cerr << "partial updates:" << endl;
-	vector< ScoreComponentCollection> featureValueDiffs2(featureValueDiffs);
-	FVector totalUpdate2 = ScoreComponentCollection::CreateFVector();
-	for (size_t k = 0; k < featureValueDiffs2.size(); ++k) {
-		featureValueDiffs2[k].MultiplyEquals(alphas2[k]);
-		cerr << k << ": " << featureValueDiffs2[k].GetScoresVector() << endl;
-		FVector update = featureValueDiffs2[k].GetScoresVector();
-		totalUpdate2 += update;
-	}
-	cerr << endl;
-	cerr << "total update: " << totalUpdate2 << endl << endl;
-
-	ScoreComponentCollection weightsUpdate2(weights);
-	weightsUpdate2.PlusEquals(totalUpdate2);
-	cerr << "old weights: " << weights << endl;
-	cerr << "new weights: " << weightsUpdate2 << endl << endl;
-
-	newModelScoreDiff.clear();
-	for (int i = 0; i < numberOfConstraints; ++i) {
-		newModelScoreDiff.push_back(featureValueDiffs[i].InnerProduct(weightsUpdate2));
-	}
-
-	for (int i = 0; i < numberOfConstraints; ++i) {
-		cerr << "new model score diff: " << newModelScoreDiff[i] << ", loss: " << losses[i] << endl;
-	}
+  // Unfeasible example with 21 constraints
+  cerr << "\n>>>>>Hildreth test, without slack and with 0.01 slack" << endl << endl;
+  vector< ScoreComponentCollection> featureValueDiffs;
+  vector< float> lossMinusModelScoreDiff;
+
+  // initial weights
+  float w[] = { 1, 1, 0.638672, 1, 0 };
+  vector<float> vec(w,w+5);
+  ScoreComponentCollection weights;
+  weights.PlusEquals(&multi, vec);
+
+  int numberOfConstraints = 21;
+
+  // feature value differences (to oracle)
+  // NOTE: these feature values are only approximations
+  ScoreComponentCollection s1, s2, s3, s4, s5, s6, s7, s8, s9, s10, s11, s12, s13, s14, s15, s16, s17, s18, s19, s20, s21;
+  float arr1[] = { 0, 0, -2.0672, 0, 0 };
+  float arr2[] = { 0, 0, 0, 0, 0 };
+  float arr3[] = { 0, 0, -2.08436, 1.38629, 0 };
+  float arr4[] = { 0, 0, -0.0171661, 1.38629, 0 };
+  float arr5[] = { 0, 0, 4.4283, 0, 0 };
+  float arr6[] = { 0, 0, 3.84829, 1.38629, 0 };
+  float arr7[] = { 0, 0, 6.83689, 0, 0 };
+  float arr8[] = { 0, 0, 0, 0, 0 };
+  float arr9[] = { 0, 0, -2.0672, 0, 0 };
+  float arr10[] = { 0, 0, -0.0171661, 1.38629, 0 };
+  float arr11[] = { 0, 0, -2.08436, 1.38629, 0 };
+  float arr12[] = { 0, 0, 4.4283, 0, 0 };
+  float arr13[] = { 3, 0, 2.41089, 0, 0 };
+  float arr14[] = { 3, 0, 2.32709, 0, 0 };
+  float arr15[] = { 0, 0, -2.0672, 0, 0 };
+  float arr16[] = { 0, 0, -2.08436, 1.38629, 0 };
+  float arr17[] = { 0, 0, 4.4283, 0, 0 };
+  float arr18[] = { 0, 0, 3.84829, 1.38629, 0 };
+  float arr19[] = { 0, 0, -0.0171661, 1.38629, 0 };
+  float arr20[] = { 0, 0, 0, 0, 0 };
+  float arr21[] = { 0, 0, 6.83689, 0, 0 };
+
+  vector<float> losses;
+  losses.push_back(2.73485);
+  losses.push_back(0);
+  losses.push_back(3.64118);
+  losses.push_back(1.47347);
+  losses.push_back(3.64118);
+  losses.push_back(4.16278);
+  losses.push_back(3.13952);
+  losses.push_back(0);
+  losses.push_back(2.73485);
+  losses.push_back(1.47347);
+  losses.push_back(3.64118);
+  losses.push_back(3.64118);
+  losses.push_back(2.51662);
+  losses.push_back(2.73485);
+  losses.push_back(2.73485);
+  losses.push_back(3.64118);
+  losses.push_back(3.64118);
+  losses.push_back(4.16278);
+  losses.push_back(1.47347);
+  losses.push_back(0);
+  losses.push_back(3.13952);
+
+  vector<float> vec1(arr1,arr1+5);
+  vector<float> vec2(arr2,arr2+5);
+  vector<float> vec3(arr3,arr3+5);
+  vector<float> vec4(arr4,arr4+5);
+  vector<float> vec5(arr5,arr5+5);
+  vector<float> vec6(arr6,arr6+5);
+  vector<float> vec7(arr7,arr7+5);
+  vector<float> vec8(arr8,arr8+5);
+  vector<float> vec9(arr9,arr9+5);
+  vector<float> vec10(arr10,arr10+5);
+  vector<float> vec11(arr11,arr11+5);
+  vector<float> vec12(arr12,arr12+5);
+  vector<float> vec13(arr13,arr13+5);
+  vector<float> vec14(arr14,arr14+5);
+  vector<float> vec15(arr15,arr15+5);
+  vector<float> vec16(arr16,arr16+5);
+  vector<float> vec17(arr17,arr17+5);
+  vector<float> vec18(arr18,arr18+5);
+  vector<float> vec19(arr19,arr19+5);
+  vector<float> vec20(arr20,arr20+5);
+  vector<float> vec21(arr21,arr21+5);
+
+  s1.PlusEquals(&multi,vec1);
+  s2.PlusEquals(&multi,vec2);
+  s3.PlusEquals(&multi,vec3);
+  s4.PlusEquals(&multi,vec4);
+  s5.PlusEquals(&multi,vec5);
+  s6.PlusEquals(&multi,vec6);
+  s7.PlusEquals(&multi,vec7);
+  s8.PlusEquals(&multi,vec8);
+  s9.PlusEquals(&multi,vec9);
+  s10.PlusEquals(&multi,vec10);
+  s11.PlusEquals(&multi,vec11);
+  s12.PlusEquals(&multi,vec12);
+  s13.PlusEquals(&multi,vec13);
+  s14.PlusEquals(&multi,vec14);
+  s15.PlusEquals(&multi,vec15);
+  s16.PlusEquals(&multi,vec16);
+  s17.PlusEquals(&multi,vec17);
+  s18.PlusEquals(&multi,vec18);
+  s19.PlusEquals(&multi,vec19);
+  s20.PlusEquals(&multi,vec20);
+  s21.PlusEquals(&multi,vec21);
+
+  featureValueDiffs.push_back(s1);
+  featureValueDiffs.push_back(s2);
+  featureValueDiffs.push_back(s3);
+  featureValueDiffs.push_back(s4);
+  featureValueDiffs.push_back(s5);
+  featureValueDiffs.push_back(s6);
+  featureValueDiffs.push_back(s7);
+  featureValueDiffs.push_back(s8);
+  featureValueDiffs.push_back(s9);
+  featureValueDiffs.push_back(s10);
+  featureValueDiffs.push_back(s11);
+  featureValueDiffs.push_back(s12);
+  featureValueDiffs.push_back(s13);
+  featureValueDiffs.push_back(s14);
+  featureValueDiffs.push_back(s15);
+  featureValueDiffs.push_back(s16);
+  featureValueDiffs.push_back(s17);
+  featureValueDiffs.push_back(s18);
+  featureValueDiffs.push_back(s19);
+  featureValueDiffs.push_back(s20);
+  featureValueDiffs.push_back(s21);
+
+  vector<float> oldModelScoreDiff;
+  for (int i = 0; i < numberOfConstraints; ++i) {
+    oldModelScoreDiff.push_back(featureValueDiffs[i].InnerProduct(weights));
+  }
+
+  for (int i = 0; i < numberOfConstraints; ++i) {
+    cerr << "old model score diff: " << oldModelScoreDiff[i] << ", loss: " << losses[i] << "\t" << (oldModelScoreDiff[i] >= losses[i] ? 1 : 0) << endl;
+  }
+
+  for (int i = 0; i < numberOfConstraints; ++i) {
+    lossMinusModelScoreDiff.push_back(losses[i] - oldModelScoreDiff[i]);
+  }
+
+  for (int i = 0; i < numberOfConstraints; ++i) {
+    cerr << "A: " << featureValueDiffs[i] << ", b: " << lossMinusModelScoreDiff[i] << endl;
+  }
+
+  vector< float> alphas1 = Hildreth::optimise(featureValueDiffs, lossMinusModelScoreDiff);
+  vector< float> alphas2 = Hildreth::optimise(featureValueDiffs, lossMinusModelScoreDiff, 0.01);
+
+  cerr << "\nalphas without slack:" << endl;
+  for (size_t i = 0; i < alphas1.size(); ++i) {
+    cerr << "alpha " << i << ": " << alphas1[i] << endl;
+  }
+  cerr << endl;
+
+  cerr << "partial updates:" << endl;
+  vector< ScoreComponentCollection> featureValueDiffs1(featureValueDiffs);
+  FVector totalUpdate1 = ScoreComponentCollection::CreateFVector();
+  for (size_t k = 0; k < featureValueDiffs1.size(); ++k) {
+    featureValueDiffs1[k].MultiplyEquals(alphas1[k]);
+    cerr << k << ": " << featureValueDiffs1[k].GetScoresVector() << endl;
+    FVector update = featureValueDiffs1[k].GetScoresVector();
+    totalUpdate1 += update;
+  }
+  cerr << endl;
+  cerr << "total update: " << totalUpdate1 << endl << endl;
+
+  ScoreComponentCollection weightsUpdate1(weights);
+  weightsUpdate1.PlusEquals(totalUpdate1);
+  cerr << "old weights: " << weights << endl;
+  cerr << "new weights: " << weightsUpdate1 << endl << endl;
+
+  vector<float> newModelScoreDiff;
+  for (int i = 0; i < numberOfConstraints; ++i) {
+    newModelScoreDiff.push_back(featureValueDiffs[i].InnerProduct(weightsUpdate1));
+  }
+
+  for (int i = 0; i < numberOfConstraints; ++i) {
+    cerr << "new model score diff: " << newModelScoreDiff[i] << ", loss: " << losses[i] << "\t" << (newModelScoreDiff[i] >= losses[i] ? 1 : 0) << endl;
+  }
+
+  cerr << "\n\nalphas with slack 0.01:" << endl;
+  for (size_t i = 0; i < alphas2.size(); ++i) {
+    cerr << "alpha " << i << ": " << alphas2[i] << endl;
+  }
+  cerr << endl;
+
+  cerr << "partial updates:" << endl;
+  vector< ScoreComponentCollection> featureValueDiffs2(featureValueDiffs);
+  FVector totalUpdate2 = ScoreComponentCollection::CreateFVector();
+  for (size_t k = 0; k < featureValueDiffs2.size(); ++k) {
+    featureValueDiffs2[k].MultiplyEquals(alphas2[k]);
+    cerr << k << ": " << featureValueDiffs2[k].GetScoresVector() << endl;
+    FVector update = featureValueDiffs2[k].GetScoresVector();
+    totalUpdate2 += update;
+  }
+  cerr << endl;
+  cerr << "total update: " << totalUpdate2 << endl << endl;
+
+  ScoreComponentCollection weightsUpdate2(weights);
+  weightsUpdate2.PlusEquals(totalUpdate2);
+  cerr << "old weights: " << weights << endl;
+  cerr << "new weights: " << weightsUpdate2 << endl << endl;
+
+  newModelScoreDiff.clear();
+  for (int i = 0; i < numberOfConstraints; ++i) {
+    newModelScoreDiff.push_back(featureValueDiffs[i].InnerProduct(weightsUpdate2));
+  }
+
+  for (int i = 0; i < numberOfConstraints; ++i) {
+    cerr << "new model score diff: " << newModelScoreDiff[i] << ", loss: " << losses[i] << endl;
+  }
 }
 
 BOOST_FIXTURE_TEST_CASE(test_hildreth_4, MockProducers)
 {
-	// Feasible example with 8 constraints
-	cerr << "\n>>>>>Hildreth test, without slack and with 0.01 slack" << endl << endl;
-	vector< ScoreComponentCollection> featureValueDiffs;
-	vector< float> lossMinusModelScoreDiff;
-
-	// initial weights
-	float w[] = { 1, 1, 0.638672, 1, 0 };
-	vector<float> vec(w,w+5);
-	ScoreComponentCollection weights;
-	weights.PlusEquals(&multi, vec);
-
-	int numberOfConstraints = 8;
-
-	// feature value differences (to oracle)
-	// NOTE: these feature values are only approximations
-	ScoreComponentCollection s1, s2, s3, s4, s5, s6, s7, s8, s9, s10, s11, s12, s13, s14, s15, s16, s17, s18, s19, s20, s21;
-	float arr1[] = { 0, 0, -2.0672, 0, 0 };
-	float arr2[] = { 0, 0, 0, 0, 0 };
-	float arr3[] = { 0, 0, -2.08436, 1.38629, 0 };
-	float arr4[] = { 0, 0, -0.0171661, 1.38629, 0 };
+  // Feasible example with 8 constraints
+  cerr << "\n>>>>>Hildreth test, without slack and with 0.01 slack" << endl << endl;
+  vector< ScoreComponentCollection> featureValueDiffs;
+  vector< float> lossMinusModelScoreDiff;
+
+  // initial weights
+  float w[] = { 1, 1, 0.638672, 1, 0 };
+  vector<float> vec(w,w+5);
+  ScoreComponentCollection weights;
+  weights.PlusEquals(&multi, vec);
+
+  int numberOfConstraints = 8;
+
+  // feature value differences (to oracle)
+  // NOTE: these feature values are only approximations
+  ScoreComponentCollection s1, s2, s3, s4, s5, s6, s7, s8, s9, s10, s11, s12, s13, s14, s15, s16, s17, s18, s19, s20, s21;
+  float arr1[] = { 0, 0, -2.0672, 0, 0 };
+  float arr2[] = { 0, 0, 0, 0, 0 };
+  float arr3[] = { 0, 0, -2.08436, 1.38629, 0 };
+  float arr4[] = { 0, 0, -0.0171661, 1.38629, 0 };
 //	float arr5[] = { 0, 0, 4.4283, 0, 0 };
 //	float arr6[] = { 0, 0, 3.84829, 1.38629, 0 };
 //	float arr7[] = { 0, 0, 6.83689, 0, 0 };
 
-	float arr8[] = { 0, 0, 0, 0, 0 };
-	float arr9[] = { 0, 0, -2.0672, 0, 0 };
+  float arr8[] = { 0, 0, 0, 0, 0 };
+  float arr9[] = { 0, 0, -2.0672, 0, 0 };
 //	float arr10[] = { 0, 0, -0.0171661, 1.38629, 0 };
 //	float arr11[] = { 0, 0, -2.08436, 1.38629, 0 };
 //	float arr12[] = { 0, 0, 4.4283, 0, 0 };
 //	float arr13[] = { 3, 0, 2.41089, 0, 0 };
 //	float arr14[] = { 3, 0, 2.32709, 0, 0 };
 
-	float arr15[] = { 0, 0, -2.0672, 0, 0 };
-	float arr16[] = { 0, 0, -2.08436, 1.38629, 0 };
+  float arr15[] = { 0, 0, -2.0672, 0, 0 };
+  float arr16[] = { 0, 0, -2.08436, 1.38629, 0 };
 //	float arr17[] = { 0, 0, 4.4283, 0, 0 };
 //	float arr18[] = { 0, 0, 3.84829, 1.38629, 0 };
 //	float arr19[] = { 0, 0, -0.0171661, 1.38629, 0 };
 //	float arr20[] = { 0, 0, 0, 0, 0 };
 //	float arr21[] = { 0, 0, 6.83689, 0, 0 };
 
-	vector<float> losses;
-	losses.push_back(2.73485);
-	losses.push_back(0);
-	losses.push_back(3.64118);
-	losses.push_back(1.47347);
+  vector<float> losses;
+  losses.push_back(2.73485);
+  losses.push_back(0);
+  losses.push_back(3.64118);
+  losses.push_back(1.47347);
 //	losses.push_back(3.64118);
 //	losses.push_back(4.16278);
 //	losses.push_back(3.13952);
-	losses.push_back(0);
-	losses.push_back(2.73485);
+  losses.push_back(0);
+  losses.push_back(2.73485);
 //	losses.push_back(1.47347);
 //	losses.push_back(3.64118);
 //	losses.push_back(3.64118);
 //	losses.push_back(2.51662);
 //	losses.push_back(2.73485);
-	losses.push_back(2.73485);
-	losses.push_back(3.64118);
+  losses.push_back(2.73485);
+  losses.push_back(3.64118);
 //	losses.push_back(3.64118);
 //	losses.push_back(4.16278);
 //	losses.push_back(1.47347);
 //	losses.push_back(0);
 //	losses.push_back(3.13952);
 
-	vector<float> vec1(arr1,arr1+5);
-	vector<float> vec2(arr2,arr2+5);
-	vector<float> vec3(arr3,arr3+5);
-	vector<float> vec4(arr4,arr4+5);
+  vector<float> vec1(arr1,arr1+5);
+  vector<float> vec2(arr2,arr2+5);
+  vector<float> vec3(arr3,arr3+5);
+  vector<float> vec4(arr4,arr4+5);
 //	vector<float> vec5(arr5,arr5+5);
 //	vector<float> vec6(arr6,arr6+5);
 //	vector<float> vec7(arr7,arr7+5);
-	vector<float> vec8(arr8,arr8+5);
-	vector<float> vec9(arr9,arr9+5);
+  vector<float> vec8(arr8,arr8+5);
+  vector<float> vec9(arr9,arr9+5);
 //	vector<float> vec10(arr10,arr10+5);
 //	vector<float> vec11(arr11,arr11+5);
 //	vector<float> vec12(arr12,arr12+5);
 //	vector<float> vec13(arr13,arr13+5);
 //	vector<float> vec14(arr14,arr14+5);
-	vector<float> vec15(arr15,arr15+5);
-	vector<float> vec16(arr16,arr16+5);
+  vector<float> vec15(arr15,arr15+5);
+  vector<float> vec16(arr16,arr16+5);
 //	vector<float> vec17(arr17,arr17+5);
 //	vector<float> vec18(arr18,arr18+5);
 //	vector<float> vec19(arr19,arr19+5);
 //	vector<float> vec20(arr20,arr20+5);
 //	vector<float> vec21(arr21,arr21+5);
 
-	s1.PlusEquals(&multi,vec1);
-	s2.PlusEquals(&multi,vec2);
-	s3.PlusEquals(&multi,vec3);
-	s4.PlusEquals(&multi,vec4);
+  s1.PlusEquals(&multi,vec1);
+  s2.PlusEquals(&multi,vec2);
+  s3.PlusEquals(&multi,vec3);
+  s4.PlusEquals(&multi,vec4);
 //	s5.PlusEquals(&multi,vec5);
 //	s6.PlusEquals(&multi,vec6);
 //	s7.PlusEquals(&multi,vec7);
-	s8.PlusEquals(&multi,vec8);
-	s9.PlusEquals(&multi,vec9);
+  s8.PlusEquals(&multi,vec8);
+  s9.PlusEquals(&multi,vec9);
 //	s10.PlusEquals(&multi,vec10);
 //	s11.PlusEquals(&multi,vec11);
 //	s12.PlusEquals(&multi,vec12);
 //	s13.PlusEquals(&multi,vec13);
 //	s14.PlusEquals(&multi,vec14);
-	s15.PlusEquals(&multi,vec15);
-	s16.PlusEquals(&multi,vec16);
+  s15.PlusEquals(&multi,vec15);
+  s16.PlusEquals(&multi,vec16);
 //	s17.PlusEquals(&multi,vec17);
 //	s18.PlusEquals(&multi,vec18);
 //	s19.PlusEquals(&multi,vec19);
 //	s20.PlusEquals(&multi,vec20);
 //	s21.PlusEquals(&multi,vec21);
 
-	featureValueDiffs.push_back(s1);
-	featureValueDiffs.push_back(s2);
-	featureValueDiffs.push_back(s3);
-	featureValueDiffs.push_back(s4);
+  featureValueDiffs.push_back(s1);
+  featureValueDiffs.push_back(s2);
+  featureValueDiffs.push_back(s3);
+  featureValueDiffs.push_back(s4);
 //	featureValueDiffs.push_back(s5);
 //	featureValueDiffs.push_back(s6);
 //	featureValueDiffs.push_back(s7);
-	featureValueDiffs.push_back(s8);
-	featureValueDiffs.push_back(s9);
+  featureValueDiffs.push_back(s8);
+  featureValueDiffs.push_back(s9);
 //	featureValueDiffs.push_back(s10);
 //	featureValueDiffs.push_back(s11);
 //	featureValueDiffs.push_back(s12);
 //	featureValueDiffs.push_back(s13);
 //	featureValueDiffs.push_back(s14);
-	featureValueDiffs.push_back(s15);
-	featureValueDiffs.push_back(s16);
+  featureValueDiffs.push_back(s15);
+  featureValueDiffs.push_back(s16);
 //	featureValueDiffs.push_back(s17);
 //	featureValueDiffs.push_back(s18);
 //	featureValueDiffs.push_back(s19);
 //	featureValueDiffs.push_back(s20);
 //	featureValueDiffs.push_back(s21);
 
-	vector<float> oldModelScoreDiff;
-	for (int i = 0; i < numberOfConstraints; ++i) {
-		oldModelScoreDiff.push_back(featureValueDiffs[i].InnerProduct(weights));
-	}
-
-	for (int i = 0; i < numberOfConstraints; ++i) {
-		cerr << "old model score diff: " << oldModelScoreDiff[i] << ", loss: " << losses[i] << "\t" << (oldModelScoreDiff[i] >= losses[i] ? 1 : 0) << endl;
-	}
-
-	for (int i = 0; i < numberOfConstraints; ++i) {
-		lossMinusModelScoreDiff.push_back(losses[i] - oldModelScoreDiff[i]);
-	}
-
-	for (int i = 0; i < numberOfConstraints; ++i) {
-		cerr << "A: " << featureValueDiffs[i] << ", b: " << lossMinusModelScoreDiff[i] << endl;
-	}
-
-	vector< float> alphas1 = Hildreth::optimise(featureValueDiffs, lossMinusModelScoreDiff);
-	vector< float> alphas2 = Hildreth::optimise(featureValueDiffs, lossMinusModelScoreDiff, 0.01);
-
-	cerr << "\nalphas without slack:" << endl;
-	for (size_t i = 0; i < alphas1.size(); ++i) {
-		cerr << "alpha " << i << ": " << alphas1[i] << endl;
-	}
-	cerr << endl;
-
-	cerr << "partial updates:" << endl;
-	vector< ScoreComponentCollection> featureValueDiffs1(featureValueDiffs);
-	FVector totalUpdate1 = ScoreComponentCollection::CreateFVector();
-	for (size_t k = 0; k < featureValueDiffs1.size(); ++k) {
-		featureValueDiffs1[k].MultiplyEquals(alphas1[k]);
-		cerr << k << ": " << featureValueDiffs1[k].GetScoresVector() << endl;
-		FVector update = featureValueDiffs1[k].GetScoresVector();
-		totalUpdate1 += update;
-	}
-	cerr << endl;
-	cerr << "total update: " << totalUpdate1 << endl << endl;
-
-	ScoreComponentCollection weightsUpdate1(weights);
-	weightsUpdate1.PlusEquals(totalUpdate1);
-	cerr << "old weights: " << weights << endl;
-	cerr << "new weights: " << weightsUpdate1 << endl << endl;
-
-	vector<float> newModelScoreDiff;
-	for (int i = 0; i < numberOfConstraints; ++i) {
-		newModelScoreDiff.push_back(featureValueDiffs[i].InnerProduct(weightsUpdate1));
-	}
-
-	for (int i = 0; i < numberOfConstraints; ++i) {
-		cerr << "new model score diff: " << newModelScoreDiff[i] << ", loss: " << losses[i] << "\t" << (newModelScoreDiff[i] >= losses[i] ? 1 : 0) << endl;
-	}
-
-	cerr << "\n\nalphas with slack 0.01:" << endl;
-	for (size_t i = 0; i < alphas2.size(); ++i) {
-		cerr << "alpha " << i << ": " << alphas2[i] << endl;
-	}
-	cerr << endl;
-
-	cerr << "partial updates:" << endl;
-	vector< ScoreComponentCollection> featureValueDiffs2(featureValueDiffs);
-	FVector totalUpdate2 = ScoreComponentCollection::CreateFVector();
-	for (size_t k = 0; k < featureValueDiffs2.size(); ++k) {
-		featureValueDiffs2[k].MultiplyEquals(alphas2[k]);
-		cerr << k << ": " << featureValueDiffs2[k].GetScoresVector() << endl;
-		FVector update = featureValueDiffs2[k].GetScoresVector();
-		totalUpdate2 += update;
-	}
-	cerr << endl;
-	cerr << "total update: " << totalUpdate2 << endl << endl;
-
-	ScoreComponentCollection weightsUpdate2(weights);
-	weightsUpdate2.PlusEquals(totalUpdate2);
-	cerr << "old weights: " << weights << endl;
-	cerr << "new weights: " << weightsUpdate2 << endl << endl;
-
-	newModelScoreDiff.clear();
-	for (int i = 0; i < numberOfConstraints; ++i) {
-		newModelScoreDiff.push_back(featureValueDiffs[i].InnerProduct(weightsUpdate2));
-	}
-
-	for (int i = 0; i < numberOfConstraints; ++i) {
-		cerr << "new model score diff: " << newModelScoreDiff[i] << ", loss: " << losses[i] << endl;
-	}
+  vector<float> oldModelScoreDiff;
+  for (int i = 0; i < numberOfConstraints; ++i) {
+    oldModelScoreDiff.push_back(featureValueDiffs[i].InnerProduct(weights));
+  }
+
+  for (int i = 0; i < numberOfConstraints; ++i) {
+    cerr << "old model score diff: " << oldModelScoreDiff[i] << ", loss: " << losses[i] << "\t" << (oldModelScoreDiff[i] >= losses[i] ? 1 : 0) << endl;
+  }
+
+  for (int i = 0; i < numberOfConstraints; ++i) {
+    lossMinusModelScoreDiff.push_back(losses[i] - oldModelScoreDiff[i]);
+  }
+
+  for (int i = 0; i < numberOfConstraints; ++i) {
+    cerr << "A: " << featureValueDiffs[i] << ", b: " << lossMinusModelScoreDiff[i] << endl;
+  }
+
+  vector< float> alphas1 = Hildreth::optimise(featureValueDiffs, lossMinusModelScoreDiff);
+  vector< float> alphas2 = Hildreth::optimise(featureValueDiffs, lossMinusModelScoreDiff, 0.01);
+
+  cerr << "\nalphas without slack:" << endl;
+  for (size_t i = 0; i < alphas1.size(); ++i) {
+    cerr << "alpha " << i << ": " << alphas1[i] << endl;
+  }
+  cerr << endl;
+
+  cerr << "partial updates:" << endl;
+  vector< ScoreComponentCollection> featureValueDiffs1(featureValueDiffs);
+  FVector totalUpdate1 = ScoreComponentCollection::CreateFVector();
+  for (size_t k = 0; k < featureValueDiffs1.size(); ++k) {
+    featureValueDiffs1[k].MultiplyEquals(alphas1[k]);
+    cerr << k << ": " << featureValueDiffs1[k].GetScoresVector() << endl;
+    FVector update = featureValueDiffs1[k].GetScoresVector();
+    totalUpdate1 += update;
+  }
+  cerr << endl;
+  cerr << "total update: " << totalUpdate1 << endl << endl;
+
+  ScoreComponentCollection weightsUpdate1(weights);
+  weightsUpdate1.PlusEquals(totalUpdate1);
+  cerr << "old weights: " << weights << endl;
+  cerr << "new weights: " << weightsUpdate1 << endl << endl;
+
+  vector<float> newModelScoreDiff;
+  for (int i = 0; i < numberOfConstraints; ++i) {
+    newModelScoreDiff.push_back(featureValueDiffs[i].InnerProduct(weightsUpdate1));
+  }
+
+  for (int i = 0; i < numberOfConstraints; ++i) {
+    cerr << "new model score diff: " << newModelScoreDiff[i] << ", loss: " << losses[i] << "\t" << (newModelScoreDiff[i] >= losses[i] ? 1 : 0) << endl;
+  }
+
+  cerr << "\n\nalphas with slack 0.01:" << endl;
+  for (size_t i = 0; i < alphas2.size(); ++i) {
+    cerr << "alpha " << i << ": " << alphas2[i] << endl;
+  }
+  cerr << endl;
+
+  cerr << "partial updates:" << endl;
+  vector< ScoreComponentCollection> featureValueDiffs2(featureValueDiffs);
+  FVector totalUpdate2 = ScoreComponentCollection::CreateFVector();
+  for (size_t k = 0; k < featureValueDiffs2.size(); ++k) {
+    featureValueDiffs2[k].MultiplyEquals(alphas2[k]);
+    cerr << k << ": " << featureValueDiffs2[k].GetScoresVector() << endl;
+    FVector update = featureValueDiffs2[k].GetScoresVector();
+    totalUpdate2 += update;
+  }
+  cerr << endl;
+  cerr << "total update: " << totalUpdate2 << endl << endl;
+
+  ScoreComponentCollection weightsUpdate2(weights);
+  weightsUpdate2.PlusEquals(totalUpdate2);
+  cerr << "old weights: " << weights << endl;
+  cerr << "new weights: " << weightsUpdate2 << endl << endl;
+
+  newModelScoreDiff.clear();
+  for (int i = 0; i < numberOfConstraints; ++i) {
+    newModelScoreDiff.push_back(featureValueDiffs[i].InnerProduct(weightsUpdate2));
+  }
+
+  for (int i = 0; i < numberOfConstraints; ++i) {
+    cerr << "new model score diff: " << newModelScoreDiff[i] << ", loss: " << losses[i] << endl;
+  }
 }
 
 BOOST_FIXTURE_TEST_CASE(test_hildreth_5, MockProducers)
 {
-	// Unfeasible example with 2 constraints
-	cerr << "\n>>>>>Hildreth test, without slack and with 0.01 slack" << endl << endl;
-	vector< ScoreComponentCollection> featureValueDiffs;
-	vector< float> lossMinusModelScoreDiff;
-
-	// initial weights
-	float w[] = { 1, 1, 0.638672, 1, 0 };
-	vector<float> vec(w,w+5);
-	ScoreComponentCollection weights;
-	weights.PlusEquals(&multi, vec);
-
-	int numberOfConstraints = 2;
-
-	// feature value differences (to oracle)
-	// NOTE: these feature values are only approximations
-	ScoreComponentCollection s1, s17;
-	float arr1[] = { 0, 0, -2.0672, 0, 0 };
-	float arr17[] = { 0, 0, 4.4283, 0, 0 };
-	vector<float> losses;
-	losses.push_back(2.73485);
-	losses.push_back(3.64118);
-
-	vector<float> vec1(arr1,arr1+5);
-	vector<float> vec17(arr17,arr17+5);
-
-	s1.PlusEquals(&multi,vec1);
-	s17.PlusEquals(&multi,vec17);
-
-	featureValueDiffs.push_back(s1);
-	featureValueDiffs.push_back(s17);
-
-	vector<float> oldModelScoreDiff;
-	for (int i = 0; i < numberOfConstraints; ++i) {
-		oldModelScoreDiff.push_back(featureValueDiffs[i].InnerProduct(weights));
-	}
-
-	float sumOfOldError = 0;
-	for (int i = 0; i < numberOfConstraints; ++i) {
-		cerr << "old model score diff: " << oldModelScoreDiff[i] << ", loss: " << losses[i] << "\t" << (oldModelScoreDiff[i] >= losses[i] ? 1 : 0) << endl;
-		sumOfOldError += (losses[i] - oldModelScoreDiff[i]);
-	}
-	cerr << "sum of old error: " << sumOfOldError << endl;
-
-	for (int i = 0; i < numberOfConstraints; ++i) {
-		lossMinusModelScoreDiff.push_back(losses[i] - oldModelScoreDiff[i]);
-	}
-
-	for (int i = 0; i < numberOfConstraints; ++i) {
-		cerr << "A: " << featureValueDiffs[i] << ", b: " << lossMinusModelScoreDiff[i] << endl;
-	}
-
-	vector< float> alphas1 = Hildreth::optimise(featureValueDiffs, lossMinusModelScoreDiff);
-	vector< float> alphas2 = Hildreth::optimise(featureValueDiffs, lossMinusModelScoreDiff, 0.01);
-	vector< float> alphas3 = Hildreth::optimise(featureValueDiffs, lossMinusModelScoreDiff, 0.1);
-
-	cerr << "\nalphas without slack:" << endl;
-	for (size_t i = 0; i < alphas1.size(); ++i) {
-		cerr << "alpha " << i << ": " << alphas1[i] << endl;
-	}
-	cerr << endl;
-
-	cerr << "partial updates:" << endl;
-	vector< ScoreComponentCollection> featureValueDiffs1(featureValueDiffs);
-	FVector totalUpdate1 = ScoreComponentCollection::CreateFVector();
-	for (size_t k = 0; k < featureValueDiffs1.size(); ++k) {
-		featureValueDiffs1[k].MultiplyEquals(alphas1[k]);
-		cerr << k << ": " << featureValueDiffs1[k].GetScoresVector() << endl;
-		FVector update = featureValueDiffs1[k].GetScoresVector();
-		totalUpdate1 += update;
-	}
-	cerr << endl;
-	cerr << "total update: " << totalUpdate1 << endl << endl;
-
-	ScoreComponentCollection weightsUpdate1(weights);
-	weightsUpdate1.PlusEquals(totalUpdate1);
-	cerr << "old weights: " << weights << endl;
-	cerr << "new weights: " << weightsUpdate1 << endl << endl;
-
-	vector<float> newModelScoreDiff;
-	for (int i = 0; i < numberOfConstraints; ++i) {
-		newModelScoreDiff.push_back(featureValueDiffs[i].InnerProduct(weightsUpdate1));
-	}
-
-	float sumOfNewError = 0;
-	for (int i = 0; i < numberOfConstraints; ++i) {
-		cerr << "new model score diff: " << newModelScoreDiff[i] << ", loss: " << losses[i] << "\t" << (newModelScoreDiff[i] >= losses[i] ? 1 : 0) << endl;
-		sumOfNewError += (losses[i] - newModelScoreDiff[i]);
-	}
-	cerr << "sum of new error: " << sumOfNewError << endl;
-
-	cerr << "\n\nalphas with slack 0.01:" << endl;
-	for (size_t i = 0; i < alphas2.size(); ++i) {
-		cerr << "alpha " << i << ": " << alphas2[i] << endl;
-	}
-	cerr << endl;
-
-	cerr << "partial updates:" << endl;
-	vector< ScoreComponentCollection> featureValueDiffs2(featureValueDiffs);
-	FVector totalUpdate2 = ScoreComponentCollection::CreateFVector();
-	for (size_t k = 0; k < featureValueDiffs2.size(); ++k) {
-		featureValueDiffs2[k].MultiplyEquals(alphas2[k]);
-		cerr << k << ": " << featureValueDiffs2[k].GetScoresVector() << endl;
-		FVector update = featureValueDiffs2[k].GetScoresVector();
-		totalUpdate2 += update;
-	}
-	cerr << endl;
-	cerr << "total update: " << totalUpdate2 << endl << endl;
-
-	ScoreComponentCollection weightsUpdate2(weights);
-	weightsUpdate2.PlusEquals(totalUpdate2);
-	cerr << "old weights: " << weights << endl;
-	cerr << "new weights: " << weightsUpdate2 << endl << endl;
-
-	newModelScoreDiff.clear();
-	for (int i = 0; i < numberOfConstraints; ++i) {
-		newModelScoreDiff.push_back(featureValueDiffs[i].InnerProduct(weightsUpdate2));
-	}
-
-	sumOfNewError = 0;
-	for (int i = 0; i < numberOfConstraints; ++i) {
-		cerr << "new model score diff: " << newModelScoreDiff[i] << ", loss: " << losses[i] << "\t" << (newModelScoreDiff[i] >= losses[i] ? 1 : 0) << endl;
-		sumOfNewError += (losses[i] - newModelScoreDiff[i]);
-	}
-	cerr << "sum of new error: " << sumOfNewError << endl;
-
-	cerr << "\n\nalphas with slack 0.1:" << endl;
-	for (size_t i = 0; i < alphas3.size(); ++i) {
-		cerr << "alpha " << i << ": " << alphas3[i] << endl;
-	}
-	cerr << endl;
-
-	cerr << "partial updates:" << endl;
-	vector< ScoreComponentCollection> featureValueDiffs3(featureValueDiffs);
-	FVector totalUpdate3 = ScoreComponentCollection::CreateFVector();
-	for (size_t k = 0; k < featureValueDiffs3.size(); ++k) {
-		featureValueDiffs3[k].MultiplyEquals(alphas3[k]);
-		cerr << k << ": " << featureValueDiffs3[k].GetScoresVector() << endl;
-		FVector update = featureValueDiffs3[k].GetScoresVector();
-		totalUpdate3 += update;
-	}
-	cerr << endl;
-	cerr << "total update: " << totalUpdate3 << endl << endl;
-
-	ScoreComponentCollection weightsUpdate3(weights);
-	weightsUpdate3.PlusEquals(totalUpdate3);
-	cerr << "old weights: " << weights << endl;
-	cerr << "new weights: " << weightsUpdate3 << endl << endl;
-
-	newModelScoreDiff.clear();
-	for (int i = 0; i < numberOfConstraints; ++i) {
-		newModelScoreDiff.push_back(featureValueDiffs[i].InnerProduct(weightsUpdate3));
-	}
-
-	sumOfNewError = 0;
-	for (int i = 0; i < numberOfConstraints; ++i) {
-		cerr << "new model score diff: " << newModelScoreDiff[i] << ", loss: " << losses[i] << "\t" << (newModelScoreDiff[i] >= losses[i] ? 1 : 0) << endl;
-		sumOfNewError += (losses[i] - newModelScoreDiff[i]);
-	}
-	cerr << "sum of new error: " << sumOfNewError << endl;
+  // Unfeasible example with 2 constraints
+  cerr << "\n>>>>>Hildreth test, without slack and with 0.01 slack" << endl << endl;
+  vector< ScoreComponentCollection> featureValueDiffs;
+  vector< float> lossMinusModelScoreDiff;
+
+  // initial weights
+  float w[] = { 1, 1, 0.638672, 1, 0 };
+  vector<float> vec(w,w+5);
+  ScoreComponentCollection weights;
+  weights.PlusEquals(&multi, vec);
+
+  int numberOfConstraints = 2;
+
+  // feature value differences (to oracle)
+  // NOTE: these feature values are only approximations
+  ScoreComponentCollection s1, s17;
+  float arr1[] = { 0, 0, -2.0672, 0, 0 };
+  float arr17[] = { 0, 0, 4.4283, 0, 0 };
+  vector<float> losses;
+  losses.push_back(2.73485);
+  losses.push_back(3.64118);
+
+  vector<float> vec1(arr1,arr1+5);
+  vector<float> vec17(arr17,arr17+5);
+
+  s1.PlusEquals(&multi,vec1);
+  s17.PlusEquals(&multi,vec17);
+
+  featureValueDiffs.push_back(s1);
+  featureValueDiffs.push_back(s17);
+
+  vector<float> oldModelScoreDiff;
+  for (int i = 0; i < numberOfConstraints; ++i) {
+    oldModelScoreDiff.push_back(featureValueDiffs[i].InnerProduct(weights));
+  }
+
+  float sumOfOldError = 0;
+  for (int i = 0; i < numberOfConstraints; ++i) {
+    cerr << "old model score diff: " << oldModelScoreDiff[i] << ", loss: " << losses[i] << "\t" << (oldModelScoreDiff[i] >= losses[i] ? 1 : 0) << endl;
+    sumOfOldError += (losses[i] - oldModelScoreDiff[i]);
+  }
+  cerr << "sum of old error: " << sumOfOldError << endl;
+
+  for (int i = 0; i < numberOfConstraints; ++i) {
+    lossMinusModelScoreDiff.push_back(losses[i] - oldModelScoreDiff[i]);
+  }
+
+  for (int i = 0; i < numberOfConstraints; ++i) {
+    cerr << "A: " << featureValueDiffs[i] << ", b: " << lossMinusModelScoreDiff[i] << endl;
+  }
+
+  vector< float> alphas1 = Hildreth::optimise(featureValueDiffs, lossMinusModelScoreDiff);
+  vector< float> alphas2 = Hildreth::optimise(featureValueDiffs, lossMinusModelScoreDiff, 0.01);
+  vector< float> alphas3 = Hildreth::optimise(featureValueDiffs, lossMinusModelScoreDiff, 0.1);
+
+  cerr << "\nalphas without slack:" << endl;
+  for (size_t i = 0; i < alphas1.size(); ++i) {
+    cerr << "alpha " << i << ": " << alphas1[i] << endl;
+  }
+  cerr << endl;
+
+  cerr << "partial updates:" << endl;
+  vector< ScoreComponentCollection> featureValueDiffs1(featureValueDiffs);
+  FVector totalUpdate1 = ScoreComponentCollection::CreateFVector();
+  for (size_t k = 0; k < featureValueDiffs1.size(); ++k) {
+    featureValueDiffs1[k].MultiplyEquals(alphas1[k]);
+    cerr << k << ": " << featureValueDiffs1[k].GetScoresVector() << endl;
+    FVector update = featureValueDiffs1[k].GetScoresVector();
+    totalUpdate1 += update;
+  }
+  cerr << endl;
+  cerr << "total update: " << totalUpdate1 << endl << endl;
+
+  ScoreComponentCollection weightsUpdate1(weights);
+  weightsUpdate1.PlusEquals(totalUpdate1);
+  cerr << "old weights: " << weights << endl;
+  cerr << "new weights: " << weightsUpdate1 << endl << endl;
+
+  vector<float> newModelScoreDiff;
+  for (int i = 0; i < numberOfConstraints; ++i) {
+    newModelScoreDiff.push_back(featureValueDiffs[i].InnerProduct(weightsUpdate1));
+  }
+
+  float sumOfNewError = 0;
+  for (int i = 0; i < numberOfConstraints; ++i) {
+    cerr << "new model score diff: " << newModelScoreDiff[i] << ", loss: " << losses[i] << "\t" << (newModelScoreDiff[i] >= losses[i] ? 1 : 0) << endl;
+    sumOfNewError += (losses[i] - newModelScoreDiff[i]);
+  }
+  cerr << "sum of new error: " << sumOfNewError << endl;
+
+  cerr << "\n\nalphas with slack 0.01:" << endl;
+  for (size_t i = 0; i < alphas2.size(); ++i) {
+    cerr << "alpha " << i << ": " << alphas2[i] << endl;
+  }
+  cerr << endl;
+
+  cerr << "partial updates:" << endl;
+  vector< ScoreComponentCollection> featureValueDiffs2(featureValueDiffs);
+  FVector totalUpdate2 = ScoreComponentCollection::CreateFVector();
+  for (size_t k = 0; k < featureValueDiffs2.size(); ++k) {
+    featureValueDiffs2[k].MultiplyEquals(alphas2[k]);
+    cerr << k << ": " << featureValueDiffs2[k].GetScoresVector() << endl;
+    FVector update = featureValueDiffs2[k].GetScoresVector();
+    totalUpdate2 += update;
+  }
+  cerr << endl;
+  cerr << "total update: " << totalUpdate2 << endl << endl;
+
+  ScoreComponentCollection weightsUpdate2(weights);
+  weightsUpdate2.PlusEquals(totalUpdate2);
+  cerr << "old weights: " << weights << endl;
+  cerr << "new weights: " << weightsUpdate2 << endl << endl;
+
+  newModelScoreDiff.clear();
+  for (int i = 0; i < numberOfConstraints; ++i) {
+    newModelScoreDiff.push_back(featureValueDiffs[i].InnerProduct(weightsUpdate2));
+  }
+
+  sumOfNewError = 0;
+  for (int i = 0; i < numberOfConstraints; ++i) {
+    cerr << "new model score diff: " << newModelScoreDiff[i] << ", loss: " << losses[i] << "\t" << (newModelScoreDiff[i] >= losses[i] ? 1 : 0) << endl;
+    sumOfNewError += (losses[i] - newModelScoreDiff[i]);
+  }
+  cerr << "sum of new error: " << sumOfNewError << endl;
+
+  cerr << "\n\nalphas with slack 0.1:" << endl;
+  for (size_t i = 0; i < alphas3.size(); ++i) {
+    cerr << "alpha " << i << ": " << alphas3[i] << endl;
+  }
+  cerr << endl;
+
+  cerr << "partial updates:" << endl;
+  vector< ScoreComponentCollection> featureValueDiffs3(featureValueDiffs);
+  FVector totalUpdate3 = ScoreComponentCollection::CreateFVector();
+  for (size_t k = 0; k < featureValueDiffs3.size(); ++k) {
+    featureValueDiffs3[k].MultiplyEquals(alphas3[k]);
+    cerr << k << ": " << featureValueDiffs3[k].GetScoresVector() << endl;
+    FVector update = featureValueDiffs3[k].GetScoresVector();
+    totalUpdate3 += update;
+  }
+  cerr << endl;
+  cerr << "total update: " << totalUpdate3 << endl << endl;
+
+  ScoreComponentCollection weightsUpdate3(weights);
+  weightsUpdate3.PlusEquals(totalUpdate3);
+  cerr << "old weights: " << weights << endl;
+  cerr << "new weights: " << weightsUpdate3 << endl << endl;
+
+  newModelScoreDiff.clear();
+  for (int i = 0; i < numberOfConstraints; ++i) {
+    newModelScoreDiff.push_back(featureValueDiffs[i].InnerProduct(weightsUpdate3));
+  }
+
+  sumOfNewError = 0;
+  for (int i = 0; i < numberOfConstraints; ++i) {
+    cerr << "new model score diff: " << newModelScoreDiff[i] << ", loss: " << losses[i] << "\t" << (newModelScoreDiff[i] >= losses[i] ? 1 : 0) << endl;
+    sumOfNewError += (losses[i] - newModelScoreDiff[i]);
+  }
+  cerr << "sum of new error: " << sumOfNewError << endl;
 }
 
 BOOST_AUTO_TEST_SUITE_END()
diff --git a/mira/HypothesisQueue.cpp b/mira/HypothesisQueue.cpp
index 43e082b92..8c8daa4da 100644
--- a/mira/HypothesisQueue.cpp
+++ b/mira/HypothesisQueue.cpp
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -22,13 +22,16 @@
 
 using namespace std;
 
-namespace Moses {
+namespace Moses
+{
 
-HypothesisQueue::~HypothesisQueue() {
+HypothesisQueue::~HypothesisQueue()
+{
   m_queue.clear();
 }
 
-void HypothesisQueue::Push(BleuIndexPair hypo) {
+void HypothesisQueue::Push(BleuIndexPair hypo)
+{
   //pair<set<BleuIndexPair>::iterator,bool> ret;
 
   if (m_capacity == 0 || m_queue.size() < m_capacity) {
@@ -52,7 +55,8 @@ void HypothesisQueue::Push(BleuIndexPair hypo) {
   }
 }
 
-BleuIndexPair HypothesisQueue::Pop() {
+BleuIndexPair HypothesisQueue::Pop()
+{
   HypoQueueType::iterator p = m_queue.begin();
   BleuIndexPair top = *p;
   m_queue.erase(p);
diff --git a/mira/HypothesisQueue.h b/mira/HypothesisQueue.h
index a926a40da..63cabbd0f 100644
--- a/mira/HypothesisQueue.h
+++ b/mira/HypothesisQueue.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -21,7 +21,8 @@
 
 #include <set>
 
-namespace Moses {
+namespace Moses
+{
 
 // pair of Bleu score and index
 typedef std::pair<float, size_t> BleuIndexPair;
@@ -30,14 +31,17 @@ typedef std::pair<float, size_t> BleuIndexPair;
 // the best scoring hypothesis.  The queue assumes ownership of pushed items and
 // relinquishes ownership when they are popped.  Any remaining items at the
 // time of the queue's destruction are deleted.
-class HypothesisQueue {
+class HypothesisQueue
+{
 
- public:
+public:
   // Create empty queue with fixed capacity of c.  Capacity 0 means unbounded.
   HypothesisQueue(size_t c) : m_capacity(c) {}
   ~HypothesisQueue();
 
-  bool Empty() { return m_queue.empty(); }
+  bool Empty() {
+    return m_queue.empty();
+  }
 
   // Add the hypo to the queue or delete it if the queue is full and the
   // score is no better than the queue's worst score.
@@ -47,17 +51,17 @@ class HypothesisQueue {
   // caller is responsible for deleting the object.
   BleuIndexPair Pop();
 
- private:
+private:
   struct HypothesisOrderer {
     bool operator()(BleuIndexPair a,
-                     BleuIndexPair b) {
+                    BleuIndexPair b) {
       return (a.first > b.first);
     }
   };
 
   typedef std::multiset<BleuIndexPair, HypothesisOrderer> HypoQueueType;
   //typedef std::set<BleuIndexPair, HypothesisOrderer> HypoQueueType;
-  
+
   HypoQueueType m_queue;
   const size_t m_capacity;
 };
diff --git a/mira/Main.cpp b/mira/Main.cpp
index 2c62256d9..0dbc9be43 100644
--- a/mira/Main.cpp
+++ b/mira/Main.cpp
@@ -54,7 +54,8 @@ using namespace std;
 using namespace Moses;
 namespace po = boost::program_options;
 
-int main(int argc, char** argv) {
+int main(int argc, char** argv)
+{
   size_t rank = 0;
   size_t size = 1;
 #ifdef MPI_ENABLE
@@ -141,113 +142,113 @@ int main(int argc, char** argv) {
   bool modelPlusBleu,  simpleHistoryBleu;
   po::options_description desc("Allowed options");
   desc.add_options()
-    ("continue-epoch", po::value<size_t>(&continue_epoch)->default_value(0), "Continue an interrupted experiment from this epoch on")
-    ("freq-reg", po::value<bool>(&reg_on_every_mix)->default_value(false), "Regularize after every weight mixing")
-    ("l1sparse", po::value<bool>(&l1_reg_sparse)->default_value(true), "L1-regularization for sparse weights only")
-    ("l2sparse", po::value<bool>(&l2_reg_sparse)->default_value(true), "L2-regularization for sparse weights only")
-    ("mv-reg", po::value<bool>(&most_violated_reg)->default_value(false), "Regularize most violated constraint")
-    ("dbg", po::value<bool>(&debug)->default_value(true), "More debug output")
-    ("make-pairs", po::value<bool>(&makePairs)->default_value(true), "Make pairs of hypotheses for 1slack")
-    ("debug", po::value<bool>(&debug)->default_value(true), "More debug output")
-    ("rescale-slack", po::value<bool>(&rescaleSlack)->default_value(false), "Rescale slack in 1-slack formulation")
-    ("disable-bleu-feature", po::value<bool>(&disableBleuFeature)->default_value(false), "Disable the Bleu feature")
-    ("real-bleu", po::value<bool>(&realBleu)->default_value(false), "Compute real sentence Bleu on complete translations")
-    ("add2lm", po::value<float>(&add2lm)->default_value(0.0), "Add the specified amount to all LM weights")
-    ("hildreth", po::value<bool>(&hildreth)->default_value(false), "Prefer Hildreth over analytical update")
-    ("selective", po::value<bool>(&selective)->default_value(false), "Build constraints for every feature")
-    ("summed", po::value<bool>(&summed)->default_value(false), "Sum up all constraints")
-    ("model-plus-bleu", po::value<bool>(&modelPlusBleu)->default_value(false), "Use the sum of model score and +/- bleu to select hope and fear translations")
-    ("simple-history-bleu", po::value<bool>(&simpleHistoryBleu)->default_value(false), "Simple history Bleu")
-
-    ("bleu-weight", po::value<float>(&bleuWeight)->default_value(1.0), "Bleu weight used in decoder objective")
-    ("bw-hope", po::value<float>(&bleuWeight_hope)->default_value(-1.0), "Bleu weight used in decoder objective for hope")
-    ("bw-fear", po::value<float>(&bleuWeight_fear)->default_value(-1.0), "Bleu weight used in decoder objective for fear")
-
-    ("core-r0", po::value<float>(&core_r0)->default_value(1.0), "Start learning rate for core features")
-    ("sparse-r0", po::value<float>(&sparse_r0)->default_value(1.0), "Start learning rate for sparse features")
-
-    ("tie-bw-to-lm", po::value<bool>(&bleu_weight_lm)->default_value(false), "Make bleu weight depend on lm weight")
-    ("adjust-bw", po::value<bool>(&bleu_weight_lm_adjust)->default_value(false), "Adjust bleu weight when lm weight changes")
-    ("bw-lm-factor", po::value<float>(&bleu_weight_lm_factor)->default_value(2.0), "Make bleu weight depend on lm weight by this factor")
-    ("bw-factor-fear", po::value<float>(&bleu_weight_fear_factor)->default_value(1.0), "Multiply fear weight by this factor")
-    ("accumulate-weights", po::value<bool>(&accumulateWeights)->default_value(false), "Accumulate and average weights over all epochs")
-    ("average-weights", po::value<bool>(&averageWeights)->default_value(false), "Set decoder weights to average weights after each update")
-    ("avg-ref-length", po::value<bool>(&avgRefLength)->default_value(false), "Use average reference length instead of shortest for BLEU score feature")
-    ("batch-equals-shard", po::value<bool>(&batchEqualsShard)->default_value(false), "Batch size is equal to shard size (purely batch)")
-    ("batch-size,b", po::value<size_t>(&batchSize)->default_value(1), "Size of batch that is send to optimiser for weight adjustments")
-    ("bleu-smoothing-scheme", po::value<size_t>(&bleu_smoothing_scheme)->default_value(1), "Set a smoothing scheme for sentence-Bleu: +1 (1), +0.1 (2), papineni (3) (default:1)")
-    ("boost", po::value<bool>(&boost)->default_value(false), "Apply boosting factor to updates on misranked candidates")
-    ("config,f", po::value<string>(&mosesConfigFile), "Moses ini-file")
-    ("configs-folds", po::value<vector<string> >(&mosesConfigFilesFolds), "Moses ini-files, one for each fold")
-    ("debug-model", po::value<bool>(&debug_model)->default_value(false), "Get best model translation for debugging purposes")
-    ("decode-hope", po::value<bool>(&decode_hope)->default_value(false), "Decode dev input set according to hope objective")
-    ("decode-fear", po::value<bool>(&decode_fear)->default_value(false), "Decode dev input set according to fear objective")
-    ("decode-model", po::value<bool>(&decode_model)->default_value(false), "Decode dev input set according to normal objective")
-    ("decode-filename", po::value<string>(&decode_filename), "Filename for Bleu objective translations")
-    ("decoder-settings", po::value<string>(&decoder_settings)->default_value(""), "Decoder settings for tuning runs")
-    ("distinct-nbest", po::value<bool>(&distinctNbest)->default_value(true), "Use n-best list with distinct translations in inference step")
-    ("dump-mixed-weights", po::value<bool>(&dumpMixedWeights)->default_value(false), "Dump mixed weights instead of averaged weights")
-    ("epochs,e", po::value<size_t>(&epochs)->default_value(10), "Number of epochs")
-    ("feature-cutoff", po::value<int>(&featureCutoff)->default_value(-1), "Feature cutoff as additional regularization for sparse features")
-    ("fear-n", po::value<int>(&fear_n)->default_value(1), "Number of fear translations used")
-    ("help", po::value(&help)->zero_tokens()->default_value(false), "Print this help message and exit")
-    ("history-bleu", po::value<bool>(&historyBleu)->default_value(false), "Use 1best translations to update the history")
-    ("history-smoothing", po::value<float>(&historySmoothing)->default_value(0.9), "Adjust the factor for history smoothing")
-    ("hope-fear", po::value<bool>(&hope_fear)->default_value(true), "Use only hope and fear translations for optimisation (not model)")
-    ("hope-n", po::value<int>(&hope_n)->default_value(2), "Number of hope translations used")
-    ("input-file,i", po::value<string>(&inputFile), "Input file containing tokenised source")
-    ("input-files-folds", po::value<vector<string> >(&inputFilesFolds), "Input files containing tokenised source, one for each fold")
-    ("learner,l", po::value<string>(&learner)->default_value("mira"), "Learning algorithm")
-    ("l1-lambda", po::value<float>(&l1_lambda)->default_value(0.0001), "Lambda for l1-regularization (w_i +/- lambda)")
-    ("l2-lambda", po::value<float>(&l2_lambda)->default_value(0.01), "Lambda for l2-regularization (w_i * (1 - lambda))")
-    ("l1-reg", po::value<bool>(&l1_regularize)->default_value(false), "L1-regularization")
-    ("l2-reg", po::value<bool>(&l2_regularize)->default_value(false), "L2-regularization")
-    ("min-bleu-ratio", po::value<float>(&minBleuRatio)->default_value(-1), "Set a minimum BLEU ratio between hope and fear")
-    ("max-bleu-ratio", po::value<float>(&maxBleuRatio)->default_value(-1), "Set a maximum BLEU ratio between hope and fear")
-    ("max-bleu-diff", po::value<bool>(&max_bleu_diff)->default_value(true), "Select hope/fear with maximum Bleu difference")
-    ("min-oracle-bleu", po::value<float>(&min_oracle_bleu)->default_value(0), "Set a minimum oracle BLEU score")
-    ("min-weight-change", po::value<float>(&min_weight_change)->default_value(0.0001), "Set minimum weight change for stopping criterion")
-    ("mira-learning-rate", po::value<float>(&mira_learning_rate)->default_value(1), "Learning rate for MIRA (fixed or flexible)")
-    ("mixing-frequency", po::value<size_t>(&mixingFrequency)->default_value(1), "How often per epoch to mix weights, when using mpi")
-    ("model-hope-fear", po::value<bool>(&model_hope_fear)->default_value(false), "Use model, hope and fear translations for optimisation")
-    ("moses-src", po::value<string>(&moses_src)->default_value(""), "Moses source directory")
-    ("nbest,n", po::value<size_t>(&n)->default_value(1), "Number of translations in n-best list")
-    ("normalise-weights", po::value<bool>(&normaliseWeights)->default_value(false), "Whether to normalise the updated weights before passing them to the decoder")
-    ("normalise-margin", po::value<bool>(&normaliseMargin)->default_value(false), "Normalise the margin: squash between 0 and 1")
-    ("perceptron-learning-rate", po::value<float>(&perceptron_learning_rate)->default_value(0.01), "Perceptron learning rate")
-    ("print-feature-values", po::value<bool>(&print_feature_values)->default_value(false), "Print out feature values")
-    ("print-feature-counts", po::value<bool>(&printFeatureCounts)->default_value(false), "Print out feature values, print feature list with hope counts after 1st epoch")
-    ("print-nbest-with-features", po::value<bool>(&printNbestWithFeatures)->default_value(false), "Print out feature values, print feature list with hope counts after 1st epoch")
-    ("print-weights", po::value<bool>(&print_weights)->default_value(false), "Print out current weights")
-    ("print-core-weights", po::value<bool>(&print_core_weights)->default_value(true), "Print out current core weights")
-    ("prune-zero-weights", po::value<bool>(&pruneZeroWeights)->default_value(false), "Prune zero-valued sparse feature weights")
-    ("reference-files,r", po::value<vector<string> >(&referenceFiles), "Reference translation files for training")
-    ("reference-files-folds", po::value<vector<string> >(&referenceFilesFolds), "Reference translation files for training, one for each fold")
-    ("kbest", po::value<bool>(&kbest)->default_value(false), "Select hope/fear pairs from a list of nbest translations")
-      
-    ("scale-by-inverse-length", po::value<bool>(&scaleByInverseLength)->default_value(false), "Scale BLEU by (history of) inverse input length")
-    ("scale-by-input-length", po::value<bool>(&scaleByInputLength)->default_value(false), "Scale BLEU by (history of) input length")
-    ("scale-by-avg-input-length", po::value<bool>(&scaleByAvgInputLength)->default_value(false), "Scale BLEU by average input length")
-    ("scale-by-avg-inverse-length", po::value<bool>(&scaleByAvgInverseLength)->default_value(false), "Scale BLEU by average inverse input length")
-    ("scale-by-x", po::value<float>(&scaleByX)->default_value(1), "Scale the BLEU score by value x")
-    ("scale-lm", po::value<bool>(&scale_lm)->default_value(false), "Scale the language model feature")
-    ("scale-factor-lm", po::value<float>(&scale_lm_factor)->default_value(2), "Scale the language model feature by this factor")
-    ("scale-wp", po::value<bool>(&scale_wp)->default_value(false), "Scale the word penalty feature")
-    ("scale-factor-wp", po::value<float>(&scale_wp_factor)->default_value(2), "Scale the word penalty feature by this factor")
-    ("scale-margin", po::value<bool>(&scale_margin)->default_value(0), "Scale the margin by the Bleu score of the oracle translation")
-    ("scale-margin-precision", po::value<bool>(&scale_margin_precision)->default_value(0), "Scale margin by precision of oracle")
-    ("scale-update", po::value<bool>(&scale_update)->default_value(0), "Scale update by Bleu score of oracle")
-    ("scale-update-precision", po::value<bool>(&scale_update_precision)->default_value(0), "Scale update by precision of oracle")
-    ("sentence-level-bleu", po::value<bool>(&sentenceBleu)->default_value(true), "Use a sentences level Bleu scoring function")
-    ("shuffle", po::value<bool>(&shuffle)->default_value(false), "Shuffle input sentences before processing")
-    ("sigmoid-param", po::value<float>(&sigmoidParam)->default_value(1), "y=sigmoidParam is the axis that this sigmoid approaches")
-    ("slack", po::value<float>(&slack)->default_value(0.01), "Use slack in optimiser")
-    ("sparse-average", po::value<bool>(&sparseAverage)->default_value(false), "Average weights by the number of processes")
-    ("sparse-no-average", po::value<bool>(&sparseNoAverage)->default_value(false), "Don't average sparse weights, just sum")
-    ("stop-weights", po::value<bool>(&weightConvergence)->default_value(true), "Stop when weights converge")
-    ("verbosity,v", po::value<int>(&verbosity)->default_value(0), "Verbosity level")
-    ("weight-dump-frequency", po::value<size_t>(&weightDumpFrequency)->default_value(1), "How often per epoch to dump weights (mpi)")
-    ("weight-dump-stem", po::value<string>(&weightDumpStem)->default_value("weights"), "Stem of filename to use for dumping weights");
+  ("continue-epoch", po::value<size_t>(&continue_epoch)->default_value(0), "Continue an interrupted experiment from this epoch on")
+  ("freq-reg", po::value<bool>(&reg_on_every_mix)->default_value(false), "Regularize after every weight mixing")
+  ("l1sparse", po::value<bool>(&l1_reg_sparse)->default_value(true), "L1-regularization for sparse weights only")
+  ("l2sparse", po::value<bool>(&l2_reg_sparse)->default_value(true), "L2-regularization for sparse weights only")
+  ("mv-reg", po::value<bool>(&most_violated_reg)->default_value(false), "Regularize most violated constraint")
+  ("dbg", po::value<bool>(&debug)->default_value(true), "More debug output")
+  ("make-pairs", po::value<bool>(&makePairs)->default_value(true), "Make pairs of hypotheses for 1slack")
+  ("debug", po::value<bool>(&debug)->default_value(true), "More debug output")
+  ("rescale-slack", po::value<bool>(&rescaleSlack)->default_value(false), "Rescale slack in 1-slack formulation")
+  ("disable-bleu-feature", po::value<bool>(&disableBleuFeature)->default_value(false), "Disable the Bleu feature")
+  ("real-bleu", po::value<bool>(&realBleu)->default_value(false), "Compute real sentence Bleu on complete translations")
+  ("add2lm", po::value<float>(&add2lm)->default_value(0.0), "Add the specified amount to all LM weights")
+  ("hildreth", po::value<bool>(&hildreth)->default_value(false), "Prefer Hildreth over analytical update")
+  ("selective", po::value<bool>(&selective)->default_value(false), "Build constraints for every feature")
+  ("summed", po::value<bool>(&summed)->default_value(false), "Sum up all constraints")
+  ("model-plus-bleu", po::value<bool>(&modelPlusBleu)->default_value(false), "Use the sum of model score and +/- bleu to select hope and fear translations")
+  ("simple-history-bleu", po::value<bool>(&simpleHistoryBleu)->default_value(false), "Simple history Bleu")
+
+  ("bleu-weight", po::value<float>(&bleuWeight)->default_value(1.0), "Bleu weight used in decoder objective")
+  ("bw-hope", po::value<float>(&bleuWeight_hope)->default_value(-1.0), "Bleu weight used in decoder objective for hope")
+  ("bw-fear", po::value<float>(&bleuWeight_fear)->default_value(-1.0), "Bleu weight used in decoder objective for fear")
+
+  ("core-r0", po::value<float>(&core_r0)->default_value(1.0), "Start learning rate for core features")
+  ("sparse-r0", po::value<float>(&sparse_r0)->default_value(1.0), "Start learning rate for sparse features")
+
+  ("tie-bw-to-lm", po::value<bool>(&bleu_weight_lm)->default_value(false), "Make bleu weight depend on lm weight")
+  ("adjust-bw", po::value<bool>(&bleu_weight_lm_adjust)->default_value(false), "Adjust bleu weight when lm weight changes")
+  ("bw-lm-factor", po::value<float>(&bleu_weight_lm_factor)->default_value(2.0), "Make bleu weight depend on lm weight by this factor")
+  ("bw-factor-fear", po::value<float>(&bleu_weight_fear_factor)->default_value(1.0), "Multiply fear weight by this factor")
+  ("accumulate-weights", po::value<bool>(&accumulateWeights)->default_value(false), "Accumulate and average weights over all epochs")
+  ("average-weights", po::value<bool>(&averageWeights)->default_value(false), "Set decoder weights to average weights after each update")
+  ("avg-ref-length", po::value<bool>(&avgRefLength)->default_value(false), "Use average reference length instead of shortest for BLEU score feature")
+  ("batch-equals-shard", po::value<bool>(&batchEqualsShard)->default_value(false), "Batch size is equal to shard size (purely batch)")
+  ("batch-size,b", po::value<size_t>(&batchSize)->default_value(1), "Size of batch that is send to optimiser for weight adjustments")
+  ("bleu-smoothing-scheme", po::value<size_t>(&bleu_smoothing_scheme)->default_value(1), "Set a smoothing scheme for sentence-Bleu: +1 (1), +0.1 (2), papineni (3) (default:1)")
+  ("boost", po::value<bool>(&boost)->default_value(false), "Apply boosting factor to updates on misranked candidates")
+  ("config,f", po::value<string>(&mosesConfigFile), "Moses ini-file")
+  ("configs-folds", po::value<vector<string> >(&mosesConfigFilesFolds), "Moses ini-files, one for each fold")
+  ("debug-model", po::value<bool>(&debug_model)->default_value(false), "Get best model translation for debugging purposes")
+  ("decode-hope", po::value<bool>(&decode_hope)->default_value(false), "Decode dev input set according to hope objective")
+  ("decode-fear", po::value<bool>(&decode_fear)->default_value(false), "Decode dev input set according to fear objective")
+  ("decode-model", po::value<bool>(&decode_model)->default_value(false), "Decode dev input set according to normal objective")
+  ("decode-filename", po::value<string>(&decode_filename), "Filename for Bleu objective translations")
+  ("decoder-settings", po::value<string>(&decoder_settings)->default_value(""), "Decoder settings for tuning runs")
+  ("distinct-nbest", po::value<bool>(&distinctNbest)->default_value(true), "Use n-best list with distinct translations in inference step")
+  ("dump-mixed-weights", po::value<bool>(&dumpMixedWeights)->default_value(false), "Dump mixed weights instead of averaged weights")
+  ("epochs,e", po::value<size_t>(&epochs)->default_value(10), "Number of epochs")
+  ("feature-cutoff", po::value<int>(&featureCutoff)->default_value(-1), "Feature cutoff as additional regularization for sparse features")
+  ("fear-n", po::value<int>(&fear_n)->default_value(1), "Number of fear translations used")
+  ("help", po::value(&help)->zero_tokens()->default_value(false), "Print this help message and exit")
+  ("history-bleu", po::value<bool>(&historyBleu)->default_value(false), "Use 1best translations to update the history")
+  ("history-smoothing", po::value<float>(&historySmoothing)->default_value(0.9), "Adjust the factor for history smoothing")
+  ("hope-fear", po::value<bool>(&hope_fear)->default_value(true), "Use only hope and fear translations for optimisation (not model)")
+  ("hope-n", po::value<int>(&hope_n)->default_value(2), "Number of hope translations used")
+  ("input-file,i", po::value<string>(&inputFile), "Input file containing tokenised source")
+  ("input-files-folds", po::value<vector<string> >(&inputFilesFolds), "Input files containing tokenised source, one for each fold")
+  ("learner,l", po::value<string>(&learner)->default_value("mira"), "Learning algorithm")
+  ("l1-lambda", po::value<float>(&l1_lambda)->default_value(0.0001), "Lambda for l1-regularization (w_i +/- lambda)")
+  ("l2-lambda", po::value<float>(&l2_lambda)->default_value(0.01), "Lambda for l2-regularization (w_i * (1 - lambda))")
+  ("l1-reg", po::value<bool>(&l1_regularize)->default_value(false), "L1-regularization")
+  ("l2-reg", po::value<bool>(&l2_regularize)->default_value(false), "L2-regularization")
+  ("min-bleu-ratio", po::value<float>(&minBleuRatio)->default_value(-1), "Set a minimum BLEU ratio between hope and fear")
+  ("max-bleu-ratio", po::value<float>(&maxBleuRatio)->default_value(-1), "Set a maximum BLEU ratio between hope and fear")
+  ("max-bleu-diff", po::value<bool>(&max_bleu_diff)->default_value(true), "Select hope/fear with maximum Bleu difference")
+  ("min-oracle-bleu", po::value<float>(&min_oracle_bleu)->default_value(0), "Set a minimum oracle BLEU score")
+  ("min-weight-change", po::value<float>(&min_weight_change)->default_value(0.0001), "Set minimum weight change for stopping criterion")
+  ("mira-learning-rate", po::value<float>(&mira_learning_rate)->default_value(1), "Learning rate for MIRA (fixed or flexible)")
+  ("mixing-frequency", po::value<size_t>(&mixingFrequency)->default_value(1), "How often per epoch to mix weights, when using mpi")
+  ("model-hope-fear", po::value<bool>(&model_hope_fear)->default_value(false), "Use model, hope and fear translations for optimisation")
+  ("moses-src", po::value<string>(&moses_src)->default_value(""), "Moses source directory")
+  ("nbest,n", po::value<size_t>(&n)->default_value(1), "Number of translations in n-best list")
+  ("normalise-weights", po::value<bool>(&normaliseWeights)->default_value(false), "Whether to normalise the updated weights before passing them to the decoder")
+  ("normalise-margin", po::value<bool>(&normaliseMargin)->default_value(false), "Normalise the margin: squash between 0 and 1")
+  ("perceptron-learning-rate", po::value<float>(&perceptron_learning_rate)->default_value(0.01), "Perceptron learning rate")
+  ("print-feature-values", po::value<bool>(&print_feature_values)->default_value(false), "Print out feature values")
+  ("print-feature-counts", po::value<bool>(&printFeatureCounts)->default_value(false), "Print out feature values, print feature list with hope counts after 1st epoch")
+  ("print-nbest-with-features", po::value<bool>(&printNbestWithFeatures)->default_value(false), "Print out feature values, print feature list with hope counts after 1st epoch")
+  ("print-weights", po::value<bool>(&print_weights)->default_value(false), "Print out current weights")
+  ("print-core-weights", po::value<bool>(&print_core_weights)->default_value(true), "Print out current core weights")
+  ("prune-zero-weights", po::value<bool>(&pruneZeroWeights)->default_value(false), "Prune zero-valued sparse feature weights")
+  ("reference-files,r", po::value<vector<string> >(&referenceFiles), "Reference translation files for training")
+  ("reference-files-folds", po::value<vector<string> >(&referenceFilesFolds), "Reference translation files for training, one for each fold")
+  ("kbest", po::value<bool>(&kbest)->default_value(false), "Select hope/fear pairs from a list of nbest translations")
+
+  ("scale-by-inverse-length", po::value<bool>(&scaleByInverseLength)->default_value(false), "Scale BLEU by (history of) inverse input length")
+  ("scale-by-input-length", po::value<bool>(&scaleByInputLength)->default_value(false), "Scale BLEU by (history of) input length")
+  ("scale-by-avg-input-length", po::value<bool>(&scaleByAvgInputLength)->default_value(false), "Scale BLEU by average input length")
+  ("scale-by-avg-inverse-length", po::value<bool>(&scaleByAvgInverseLength)->default_value(false), "Scale BLEU by average inverse input length")
+  ("scale-by-x", po::value<float>(&scaleByX)->default_value(1), "Scale the BLEU score by value x")
+  ("scale-lm", po::value<bool>(&scale_lm)->default_value(false), "Scale the language model feature")
+  ("scale-factor-lm", po::value<float>(&scale_lm_factor)->default_value(2), "Scale the language model feature by this factor")
+  ("scale-wp", po::value<bool>(&scale_wp)->default_value(false), "Scale the word penalty feature")
+  ("scale-factor-wp", po::value<float>(&scale_wp_factor)->default_value(2), "Scale the word penalty feature by this factor")
+  ("scale-margin", po::value<bool>(&scale_margin)->default_value(0), "Scale the margin by the Bleu score of the oracle translation")
+  ("scale-margin-precision", po::value<bool>(&scale_margin_precision)->default_value(0), "Scale margin by precision of oracle")
+  ("scale-update", po::value<bool>(&scale_update)->default_value(0), "Scale update by Bleu score of oracle")
+  ("scale-update-precision", po::value<bool>(&scale_update_precision)->default_value(0), "Scale update by precision of oracle")
+  ("sentence-level-bleu", po::value<bool>(&sentenceBleu)->default_value(true), "Use a sentences level Bleu scoring function")
+  ("shuffle", po::value<bool>(&shuffle)->default_value(false), "Shuffle input sentences before processing")
+  ("sigmoid-param", po::value<float>(&sigmoidParam)->default_value(1), "y=sigmoidParam is the axis that this sigmoid approaches")
+  ("slack", po::value<float>(&slack)->default_value(0.01), "Use slack in optimiser")
+  ("sparse-average", po::value<bool>(&sparseAverage)->default_value(false), "Average weights by the number of processes")
+  ("sparse-no-average", po::value<bool>(&sparseNoAverage)->default_value(false), "Don't average sparse weights, just sum")
+  ("stop-weights", po::value<bool>(&weightConvergence)->default_value(true), "Stop when weights converge")
+  ("verbosity,v", po::value<int>(&verbosity)->default_value(0), "Verbosity level")
+  ("weight-dump-frequency", po::value<size_t>(&weightDumpFrequency)->default_value(1), "How often per epoch to dump weights (mpi)")
+  ("weight-dump-stem", po::value<string>(&weightDumpStem)->default_value("weights"), "Stem of filename to use for dumping weights");
 
   po::options_description cmdline_options;
   cmdline_options.add(desc);
@@ -257,7 +258,7 @@ int main(int argc, char** argv) {
 
   if (help) {
     std::cout << "Usage: " + string(argv[0])
-      + " -f mosesini-file -i input-file -r reference-file(s) [options]" << std::endl;
+              + " -f mosesini-file -i input-file -r reference-file(s) [options]" << std::endl;
     std::cout << desc << std::endl;
     return 0;
   }
@@ -296,8 +297,7 @@ int main(int argc, char** argv) {
       cerr << "Error: No reference files specified for training with folds" << endl;
       exit(1);
     }
-  }
-  else {
+  } else {
     if (mosesConfigFile.empty()) {
       cerr << "Error: No moses ini file specified" << endl;
       return 1;
@@ -354,12 +354,11 @@ int main(int argc, char** argv) {
     }
     if (referenceSentences[myFold].size() != inputSentencesFolds[myFold].size()) {
       cerr << "Error: Input file length (" << inputSentencesFolds[myFold].size() << ") != ("
-	   << referenceSentences[myFold].size() << ") reference file length (rank " << rank << ")" << endl;
+           << referenceSentences[myFold].size() << ") reference file length (rank " << rank << ")" << endl;
       exit(1);
     }
     VERBOSE(1, "Rank " << rank << " reading references from " << referenceFilesFolds[myFold] << endl);
-  }
-  else {
+  } else {
     if (!loadSentences(inputFile, inputSentences)) {
       cerr << "Error: Failed to load input sentences from " << inputFile << endl;
       return 1;
@@ -367,15 +366,15 @@ int main(int argc, char** argv) {
 
     for (size_t i = 0; i < referenceFiles.size(); ++i) {
       if (!loadSentences(referenceFiles[i], referenceSentences[i])) {
-	cerr << "Error: Failed to load reference sentences from "
-	     << referenceFiles[i] << endl;
-	return 1;
+        cerr << "Error: Failed to load reference sentences from "
+             << referenceFiles[i] << endl;
+        return 1;
       }
       if (referenceSentences[i].size() != inputSentences.size()) {
-	cerr << "Error: Input file length (" << inputSentences.size() << ") != ("
-	     << referenceSentences[i].size() << ") length of reference file " << i
-	     << endl;
-	return 1;
+        cerr << "Error: Input file length (" << inputSentences.size() << ") != ("
+             << referenceSentences[i].size() << ") length of reference file " << i
+             << endl;
+        return 1;
       }
     }
   }
@@ -401,8 +400,7 @@ int main(int argc, char** argv) {
   if (trainWithMultipleFolds) {
     decoder_settings += " ";
     decoder_settings += referenceFilesFolds[myFold];
-  }
-  else {
+  } else {
     for (size_t i=0; i < referenceFiles.size(); ++i) {
       decoder_settings += " ";
       decoder_settings += referenceFiles[i];
@@ -416,8 +414,8 @@ int main(int argc, char** argv) {
   VERBOSE(1, "Rank " << rank << " reading config file from " << configFile << endl);
   MosesDecoder* decoder = new MosesDecoder(configFile, verbosity, decoder_params.size(), decoder_params);
   decoder->setBleuParameters(disableBleuFeature, sentenceBleu, scaleByInputLength, scaleByAvgInputLength,
-			     scaleByInverseLength, scaleByAvgInverseLength,
-			     scaleByX, historySmoothing, bleu_smoothing_scheme, simpleHistoryBleu);
+                             scaleByInverseLength, scaleByAvgInverseLength,
+                             scaleByX, historySmoothing, bleu_smoothing_scheme, simpleHistoryBleu);
   SearchAlgorithm searchAlgorithm = staticData.GetSearchAlgorithm();
   bool chartDecoding = (searchAlgorithm == ChartDecoding);
 
@@ -427,11 +425,10 @@ int main(int argc, char** argv) {
     for (size_t i = 0; i < inputSentencesFolds[myFold].size(); ++i) {
       order.push_back(i);
     }
-  }
-  else {
+  } else {
     if (rank == 0) {
       for (size_t i = 0; i < inputSentences.size(); ++i) {
-	order.push_back(i);
+        order.push_back(i);
       }
     }
   }
@@ -444,10 +441,10 @@ int main(int argc, char** argv) {
       cerr << "slack: " << slack << ", learning rate: " << mira_learning_rate << endl;
       cerr << "selective: " << selective << endl;
       if (normaliseMargin)
-	cerr << "sigmoid parameter: " << sigmoidParam << endl;
+        cerr << "sigmoid parameter: " << sigmoidParam << endl;
     }
     optimiser = new MiraOptimiser(slack, scale_margin, scale_margin_precision,
-				  scale_update, scale_update_precision, boost, normaliseMargin, sigmoidParam);
+                                  scale_update, scale_update_precision, boost, normaliseMargin, sigmoidParam);
     learning_rate = mira_learning_rate;
     perceptron_update = false;
   } else if (learner == "perceptron") {
@@ -466,30 +463,30 @@ int main(int argc, char** argv) {
     cerr << "Error: Unknown optimiser: " << learner << endl;
     return 1;
   }
-  
+
   // resolve parameter dependencies
   if (batchSize > 1 && perceptron_update) {
     batchSize = 1;
     cerr << "Info: Setting batch size to 1 for perceptron update" << endl;
   }
-  
+
   if (hope_n == -1)
     hope_n = n;
   if (fear_n == -1)
     fear_n = n;
-  
+
   if (model_hope_fear || kbest)
     hope_fear = false; // is true by default
   if (learner == "mira" && !(hope_fear || model_hope_fear || kbest)) {
     cerr << "Error: Need to select one of parameters --hope-fear/--model-hope-fear/--kbest for mira update." << endl;
     return 1;
   }
-  
+
 #ifdef MPI_ENABLE
   if (!trainWithMultipleFolds)
     mpi::broadcast(world, order, 0);
 #endif
-  
+
   // Create shards according to the number of processes used
   vector<size_t> shard;
   if (trainWithMultipleFolds) {
@@ -505,8 +502,7 @@ int main(int argc, char** argv) {
     shard.resize(shardSize);
     copy(order.begin() + shardStart, order.begin() + shardEnd, shard.begin());
     batchSize = 1;
-  }
-  else {
+  } else {
     size_t shardSize = order.size() / size;
     size_t shardStart = (size_t) (shardSize * rank);
     size_t shardEnd = (size_t) (shardSize * (rank + 1));
@@ -521,49 +517,49 @@ int main(int argc, char** argv) {
     if (batchEqualsShard)
       batchSize = shardSize;
   }
-  
+
   // get reference to feature functions
   const vector<FeatureFunction*> &featureFunctions = FeatureFunction::GetFeatureFunctions();
   ScoreComponentCollection initialWeights = decoder->getWeights();
-    
+
   if (add2lm != 0) {
-		const std::vector<const StatefulFeatureFunction*> &statefulFFs = StatefulFeatureFunction::GetStatefulFeatureFunctions();
-		for (size_t i = 0; i < statefulFFs.size(); ++i) {
-		  const StatefulFeatureFunction *ff = statefulFFs[i];
-		  const LanguageModel *lm = dynamic_cast<const LanguageModel*>(ff);
-
-		  if (lm) {
-		    float lmWeight = initialWeights.GetScoreForProducer(lm) + add2lm;
-		    initialWeights.Assign(lm, lmWeight);
-		    cerr << "Rank " << rank << ", add " << add2lm << " to lm weight." << endl;
-		  }
-		}
+    const std::vector<const StatefulFeatureFunction*> &statefulFFs = StatefulFeatureFunction::GetStatefulFeatureFunctions();
+    for (size_t i = 0; i < statefulFFs.size(); ++i) {
+      const StatefulFeatureFunction *ff = statefulFFs[i];
+      const LanguageModel *lm = dynamic_cast<const LanguageModel*>(ff);
+
+      if (lm) {
+        float lmWeight = initialWeights.GetScoreForProducer(lm) + add2lm;
+        initialWeights.Assign(lm, lmWeight);
+        cerr << "Rank " << rank << ", add " << add2lm << " to lm weight." << endl;
+      }
+    }
   }
-  
+
   if (normaliseWeights) {
     initialWeights.L1Normalise();
     cerr << "Rank " << rank << ", normalised initial weights: " << initialWeights << endl;
   }
 
   decoder->setWeights(initialWeights);
-  
+
   // set bleu weight to twice the size of the language model weight(s)
   if (bleu_weight_lm) {
     float lmSum = 0;
-		const std::vector<const StatefulFeatureFunction*> &statefulFFs = StatefulFeatureFunction::GetStatefulFeatureFunctions();
-		for (size_t i = 0; i < statefulFFs.size(); ++i) {
-		  const StatefulFeatureFunction *ff = statefulFFs[i];
-		  const LanguageModel *lm = dynamic_cast<const LanguageModel*>(ff);
+    const std::vector<const StatefulFeatureFunction*> &statefulFFs = StatefulFeatureFunction::GetStatefulFeatureFunctions();
+    for (size_t i = 0; i < statefulFFs.size(); ++i) {
+      const StatefulFeatureFunction *ff = statefulFFs[i];
+      const LanguageModel *lm = dynamic_cast<const LanguageModel*>(ff);
 
-		  if (lm) {
+      if (lm) {
         lmSum += abs(initialWeights.GetScoreForProducer(lm));
-			}
-		}
+      }
+    }
 
     bleuWeight = lmSum * bleu_weight_lm_factor;
     cerr << "Set bleu weight to lm weight * " << bleu_weight_lm_factor << endl;
   }
-  
+
   if (bleuWeight_hope == -1) {
     bleuWeight_hope = bleuWeight;
   }
@@ -573,35 +569,35 @@ int main(int argc, char** argv) {
   bleuWeight_fear *= bleu_weight_fear_factor;
   cerr << "Bleu weight: " << bleuWeight << endl;
   cerr << "Bleu weight fear: " << bleuWeight_fear << endl;
-  
+
   if (decode_hope || decode_fear || decode_model) {
     size_t decode = 1;
     if (decode_fear) decode = 2;
     if (decode_model) decode = 3;
     decodeHopeOrFear(rank, size, decode, decode_filename, inputSentences, decoder, n, bleuWeight);
   }
-  
+
   //Main loop:
   ScoreComponentCollection cumulativeWeights; // collect weights per epoch to produce an average
   ScoreComponentCollection cumulativeWeightsBinary;
   size_t numberOfUpdates = 0;
   size_t numberOfUpdatesThisEpoch = 0;
-  
+
   time_t now;
   time(&now);
   cerr << "Rank " << rank << ", " << ctime(&now);
-  
+
   float avgInputLength = 0;
   float sumOfInputs = 0;
   size_t numberOfInputs = 0;
-  
+
   ScoreComponentCollection mixedWeights;
   ScoreComponentCollection mixedWeightsPrevious;
   ScoreComponentCollection mixedWeightsBeforePrevious;
   ScoreComponentCollection mixedAverageWeights;
   ScoreComponentCollection mixedAverageWeightsPrevious;
   ScoreComponentCollection mixedAverageWeightsBeforePrevious;
-  
+
   bool stop = false;
 //	int sumStillViolatedConstraints;
   float epsilon = 0.0001;
@@ -610,66 +606,65 @@ int main(int argc, char** argv) {
   ScoreComponentCollection confidenceCounts, mixedConfidenceCounts, featureLearningRates;
   featureLearningRates.UpdateLearningRates(decay_core, decay_sparse, confidenceCounts, core_r0, sparse_r0); //initialise core learning rates
   cerr << "Initial learning rates, core: " << core_r0 << ", sparse: " << sparse_r0 << endl;
-  
+
   for (size_t epoch = continue_epoch; epoch < epochs && !stop; ++epoch) {
     if (shuffle) {
       if (trainWithMultipleFolds || rank == 0) {
-	cerr << "Rank " << rank << ", epoch " << epoch << ", shuffling input sentences.." << endl;
-	RandomIndex rindex;
-	random_shuffle(order.begin(), order.end(), rindex);
+        cerr << "Rank " << rank << ", epoch " << epoch << ", shuffling input sentences.." << endl;
+        RandomIndex rindex;
+        random_shuffle(order.begin(), order.end(), rindex);
       }
-      
+
 #ifdef MPI_ENABLE
       if (!trainWithMultipleFolds)
-	mpi::broadcast(world, order, 0);
+        mpi::broadcast(world, order, 0);
 #endif
-      
+
       // redo shards
       if (trainWithMultipleFolds) {
-	size_t shardSize = order.size()/coresPerFold;
-	size_t shardStart = (size_t) (shardSize * (rank % coresPerFold));
-	size_t shardEnd = shardStart + shardSize;
-	if (rank % coresPerFold == coresPerFold - 1) { // last rank of each fold
-	  shardEnd = order.size();
-	  shardSize = shardEnd - shardStart;
-	}
-	VERBOSE(1, "Rank: " << rank << ", shard size: " << shardSize << endl);
-	VERBOSE(1, "Rank: " << rank << ", shard start: " << shardStart << " shard end: " << shardEnd << endl);
-	shard.resize(shardSize);
-	copy(order.begin() + shardStart, order.begin() + shardEnd, shard.begin());
-	batchSize = 1;
-      }
-      else {
-	size_t shardSize = order.size()/size;
-	size_t shardStart = (size_t) (shardSize * rank);
-	size_t shardEnd = (size_t) (shardSize * (rank + 1));
-	if (rank == size - 1) {
-	  shardEnd = order.size();
-	  shardSize = shardEnd - shardStart;
-	}
-	VERBOSE(1, "Shard size: " << shardSize << endl);
-	VERBOSE(1, "Rank: " << rank << " Shard start: " << shardStart << " Shard end: " << shardEnd << endl);
-	shard.resize(shardSize);
-	copy(order.begin() + shardStart, order.begin() + shardEnd, shard.begin());
-	if (batchEqualsShard)
-	  batchSize = shardSize;
+        size_t shardSize = order.size()/coresPerFold;
+        size_t shardStart = (size_t) (shardSize * (rank % coresPerFold));
+        size_t shardEnd = shardStart + shardSize;
+        if (rank % coresPerFold == coresPerFold - 1) { // last rank of each fold
+          shardEnd = order.size();
+          shardSize = shardEnd - shardStart;
+        }
+        VERBOSE(1, "Rank: " << rank << ", shard size: " << shardSize << endl);
+        VERBOSE(1, "Rank: " << rank << ", shard start: " << shardStart << " shard end: " << shardEnd << endl);
+        shard.resize(shardSize);
+        copy(order.begin() + shardStart, order.begin() + shardEnd, shard.begin());
+        batchSize = 1;
+      } else {
+        size_t shardSize = order.size()/size;
+        size_t shardStart = (size_t) (shardSize * rank);
+        size_t shardEnd = (size_t) (shardSize * (rank + 1));
+        if (rank == size - 1) {
+          shardEnd = order.size();
+          shardSize = shardEnd - shardStart;
+        }
+        VERBOSE(1, "Shard size: " << shardSize << endl);
+        VERBOSE(1, "Rank: " << rank << " Shard start: " << shardStart << " Shard end: " << shardEnd << endl);
+        shard.resize(shardSize);
+        copy(order.begin() + shardStart, order.begin() + shardEnd, shard.begin());
+        if (batchEqualsShard)
+          batchSize = shardSize;
       }
     }
-    
+
     // sum of violated constraints in an epoch
     // sumStillViolatedConstraints = 0;
-    
+
     numberOfUpdatesThisEpoch = 0;
     // Sum up weights over one epoch, final average uses weights from last epoch
     if (!accumulateWeights) {
       cumulativeWeights.ZeroAll();
       cumulativeWeightsBinary.ZeroAll();
     }
-    
+
     // number of weight dumps this epoch
     size_t weightMixingThisEpoch = 0;
     size_t weightEpochDump = 0;
-    
+
     size_t shardPosition = 0;
     vector<size_t>::const_iterator sid = shard.begin();
     while (sid != shard.end()) {
@@ -677,7 +672,7 @@ int main(int argc, char** argv) {
       vector<vector<ScoreComponentCollection> > featureValues;
       vector<vector<float> > bleuScores;
       vector<vector<float> > modelScores;
-      
+
       // variables for hope-fear/perceptron setting
       vector<vector<ScoreComponentCollection> > featureValuesHope;
       vector<vector<ScoreComponentCollection> > featureValuesFear;
@@ -685,15 +680,15 @@ int main(int argc, char** argv) {
       vector<vector<float> > bleuScoresFear;
       vector<vector<float> > modelScoresHope;
       vector<vector<float> > modelScoresFear;
-      
+
       // get moses weights
       ScoreComponentCollection mosesWeights = decoder->getWeights();
       VERBOSE(1, "\nRank " << rank << ", epoch " << epoch << ", weights: " << mosesWeights << endl);
-      
+
       if (historyBleu || simpleHistoryBleu) {
-	decoder->printBleuFeatureHistory(cerr);
+        decoder->printBleuFeatureHistory(cerr);
       }
-      
+
       // BATCHING: produce nbest lists for all input sentences in batch
       vector<float> oracleBleuScores;
       vector<float> oracleModelScores;
@@ -702,926 +697,903 @@ int main(int argc, char** argv) {
       vector<size_t> inputLengths;
       vector<size_t> ref_ids;
       size_t actualBatchSize = 0;
-      
+
       vector<size_t>::const_iterator current_sid_start = sid;
       size_t examples_in_batch = 0;
       bool skip_example = false;
       for (size_t batchPosition = 0; batchPosition < batchSize && sid
-	     != shard.end(); ++batchPosition) {
-	string input;
-	if (trainWithMultipleFolds)
-	  input = inputSentencesFolds[myFold][*sid];
-	else
-	  input = inputSentences[*sid];
-	
-	Moses::Sentence *sentence = new Sentence();
-	stringstream in(input + "\n");
-	const vector<FactorType> inputFactorOrder = staticData.GetInputFactorOrder();
-	sentence->Read(in,inputFactorOrder);
-	cerr << "\nRank " << rank << ", epoch " << epoch << ", input sentence " << *sid << ": \"";
-	sentence->Print(cerr);
-	cerr << "\"" << " (batch pos " << batchPosition << ")" << endl;
-	size_t current_input_length = (*sentence).GetSize();
-	
-	if (epoch == 0 && (scaleByAvgInputLength || scaleByAvgInverseLength)) {
-	  sumOfInputs += current_input_length;
-	  ++numberOfInputs;
-	  avgInputLength = sumOfInputs/numberOfInputs;
-	  decoder->setAvgInputLength(avgInputLength);
-	  cerr << "Rank " << rank << ", epoch 0, average input length: " << avgInputLength << endl;
-	}
-	
-	vector<ScoreComponentCollection> newFeatureValues;
-	vector<float> newScores;
-	if (model_hope_fear) {
-	  featureValues.push_back(newFeatureValues);
-	  bleuScores.push_back(newScores);
-	  modelScores.push_back(newScores);
-	}
-	if (hope_fear || perceptron_update) {
-	  featureValuesHope.push_back(newFeatureValues);
-	  featureValuesFear.push_back(newFeatureValues);
-	  bleuScoresHope.push_back(newScores);
-	  bleuScoresFear.push_back(newScores);
-	  modelScoresHope.push_back(newScores);
-	  modelScoresFear.push_back(newScores);
-	  if (historyBleu || simpleHistoryBleu || debug_model) {
-	    featureValues.push_back(newFeatureValues);
-	    bleuScores.push_back(newScores);
-	    modelScores.push_back(newScores);
-	  }
-	}
-	if (kbest) {
-	  // for decoding
-	  featureValues.push_back(newFeatureValues);
-	  bleuScores.push_back(newScores);
-	  modelScores.push_back(newScores);
-	  
-	  // for storing selected examples
-	  featureValuesHope.push_back(newFeatureValues);
-	  featureValuesFear.push_back(newFeatureValues);
-	  bleuScoresHope.push_back(newScores);
-	  bleuScoresFear.push_back(newScores);
-	  modelScoresHope.push_back(newScores);
-	  modelScoresFear.push_back(newScores);
-	}
-	
-	size_t ref_length;
-	float avg_ref_length;
-	
-	if (print_weights)
-	  cerr << "Rank " << rank << ", epoch " << epoch << ", current weights: " << mosesWeights << endl;
-	if (print_core_weights) {
-	  cerr << "Rank " << rank << ", epoch " << epoch << ", current weights: ";
-	  mosesWeights.PrintCoreFeatures();
-	  cerr << endl;
-	}
-	
-	// check LM weight
-  const std::vector<const StatefulFeatureFunction*> &statefulFFs = StatefulFeatureFunction::GetStatefulFeatureFunctions();
-  for (size_t i = 0; i < statefulFFs.size(); ++i) {
-    const StatefulFeatureFunction *ff = statefulFFs[i];
-    const LanguageModel *lm = dynamic_cast<const LanguageModel*>(ff);
-
-    if (lm) {
-			float lmWeight = mosesWeights.GetScoreForProducer(lm);
-			cerr << "Rank " << rank << ", epoch " << epoch << ", lm weight: " << lmWeight << endl;
-			if (lmWeight <= 0) {
-			  cerr << "Rank " << rank << ", epoch " << epoch << ", ERROR: language model weight should never be <= 0." << endl;
-			  mosesWeights.Assign(lm, 0.1);
-			  cerr << "Rank " << rank << ", epoch " << epoch << ", assign lm weights of 0.1" << endl;
-			}
-		}
-	}
-	
-	// select inference scheme
-	cerr << "Rank " << rank << ", epoch " << epoch << ", real Bleu? " << realBleu << endl;
-	if (hope_fear || perceptron_update) {
-	  // HOPE
-	  cerr << "Rank " << rank << ", epoch " << epoch << ", " << hope_n <<
-	    "best hope translations" << endl;
-	  vector< vector<const Word*> > outputHope = decoder->getNBest(input, *sid, hope_n, 1.0, bleuWeight_hope,
-	       featureValuesHope[batchPosition], bleuScoresHope[batchPosition], modelScoresHope[batchPosition],
-	       1, realBleu, distinctNbest, avgRefLength, rank, epoch, "");
-	  vector<const Word*> oracle = outputHope[0];
-	  decoder->cleanup(chartDecoding);
-	  ref_length = decoder->getClosestReferenceLength(*sid, oracle.size());
-	  avg_ref_length = ref_length;
-	  float hope_length_ratio = (float)oracle.size()/ref_length;
-	  int oracleSize = (int)oracle.size();
-	  cerr << endl;
-	  
-	  // count sparse features occurring in hope translation
-	  featureValuesHope[batchPosition][0].IncrementSparseHopeFeatures();
-	  	  
-	  float precision = bleuScoresHope[batchPosition][0];
-	  if (historyBleu || simpleHistoryBleu) {
-	    precision /= decoder->getTargetLengthHistory();
-	  }
-	  else {
-	    if (scaleByAvgInputLength) precision /= decoder->getAverageInputLength();
-	    else if (scaleByAvgInverseLength) precision /= (100/decoder->getAverageInputLength());
-	    precision /= scaleByX;
-	  }
-	  if (scale_margin_precision || scale_update_precision) {
-	    if (historyBleu || simpleHistoryBleu || scaleByAvgInputLength || scaleByAvgInverseLength) {
-	      cerr << "Rank " << rank << ", epoch " << epoch << ", set hope precision: " << precision << endl;
-	      ((MiraOptimiser*) optimiser)->setPrecision(precision);
-	    }
-	  }
-	  
-	  vector<const Word*> bestModel;
-	  if (debug_model || historyBleu || simpleHistoryBleu) {
-	    // MODEL (for updating the history only, using dummy vectors)
-	    cerr << "Rank " << rank << ", epoch " << epoch << ", 1best wrt model score (debug or history)" << endl;
-	    vector< vector<const Word*> > outputModel = decoder->getNBest(input, *sid, n, 0.0, bleuWeight,
-		featureValues[batchPosition], bleuScores[batchPosition], modelScores[batchPosition],
-		1, realBleu, distinctNbest, avgRefLength, rank, epoch, "");
-	    bestModel = outputModel[0];
-	    decoder->cleanup(chartDecoding);
-	    cerr << endl;
-	    ref_length = decoder->getClosestReferenceLength(*sid, bestModel.size());
-	  }
-	  
-	  // FEAR
-	  float fear_length_ratio = 0;
-	  float bleuRatioHopeFear = 0;
-	  int fearSize = 0;
-	  cerr << "Rank " << rank << ", epoch " << epoch << ", " << fear_n << "best fear translations" << endl;
-	  vector< vector<const Word*> > outputFear = decoder->getNBest(input, *sid, fear_n, -1.0, bleuWeight_fear,
-	      featureValuesFear[batchPosition], bleuScoresFear[batchPosition], modelScoresFear[batchPosition],
-	      1, realBleu, distinctNbest, avgRefLength, rank, epoch, "");
-	  vector<const Word*> fear = outputFear[0];
-	  decoder->cleanup(chartDecoding);
-	  ref_length = decoder->getClosestReferenceLength(*sid, fear.size());
-	  avg_ref_length += ref_length;
-	  avg_ref_length /= 2;
-	  fear_length_ratio = (float)fear.size()/ref_length;
-	  fearSize = (int)fear.size();
-	  cerr << endl;
-	  for (size_t i = 0; i < fear.size(); ++i)
-	    delete fear[i];
-	  
-	  // count sparse features occurring in fear translation
-	  featureValuesFear[batchPosition][0].IncrementSparseFearFeatures();
-	  	  
-	  // Bleu-related example selection
-	  bool skip = false;
-	  bleuRatioHopeFear = bleuScoresHope[batchPosition][0] / bleuScoresFear[batchPosition][0];
-	  if (minBleuRatio != -1 && bleuRatioHopeFear < minBleuRatio)
-	    skip = true;
-	  if(maxBleuRatio != -1 && bleuRatioHopeFear > maxBleuRatio)
-	    skip = true;
-	  
-	  // sanity check
-	  if (historyBleu || simpleHistoryBleu) {
-	    if (bleuScores[batchPosition][0] > bleuScoresHope[batchPosition][0] &&
-		modelScores[batchPosition][0] > modelScoresHope[batchPosition][0]) {
-	      if (abs(bleuScores[batchPosition][0] - bleuScoresHope[batchPosition][0]) > epsilon &&
-		  abs(modelScores[batchPosition][0] - modelScoresHope[batchPosition][0]) > epsilon) {
-		cerr << "Rank " << rank << ", epoch " << epoch << ", ERROR: MODEL translation better than HOPE translation." << endl;
-		skip = true;
-	      }
-	    }
-	    if (bleuScoresFear[batchPosition][0] > bleuScores[batchPosition][0] &&
-		modelScoresFear[batchPosition][0] > modelScores[batchPosition][0]) {
-	      if (abs(bleuScoresFear[batchPosition][0] - bleuScores[batchPosition][0]) > epsilon &&
-		  abs(modelScoresFear[batchPosition][0] - modelScores[batchPosition][0]) > epsilon) {
-		cerr << "Rank " << rank << ", epoch " << epoch << ", ERROR: FEAR translation better than MODEL translation." << endl;
-		skip = true;
-	      }
-	    }
-	  }
-	  if (bleuScoresFear[batchPosition][0] > bleuScoresHope[batchPosition][0]) {
-	    if (abs(bleuScoresFear[batchPosition][0] - bleuScoresHope[batchPosition][0]) > epsilon) {
-	      // check if it's an error or a warning
-	      skip = true;
-	      if (modelScoresFear[batchPosition][0] > modelScoresHope[batchPosition][0] && abs(modelScoresFear[batchPosition][0] - modelScoresHope[batchPosition][0]) > epsilon) {
-		cerr << "Rank " << rank << ", epoch " << epoch << ", ERROR: FEAR translation better than HOPE translation. (abs-diff: " << abs(bleuScoresFear[batchPosition][0] - bleuScoresHope[batchPosition][0]) << ")" <<endl;
-	      }
-	      else {
-		cerr << "Rank " << rank << ", epoch " << epoch << ", WARNING: FEAR translation has better Bleu than HOPE translation. (abs-diff: " << abs(bleuScoresFear[batchPosition][0] - bleuScoresHope[batchPosition][0]) << ")" <<endl;
-	      }
-	    }
-	  }
-	  
-	  if (skip) {
-	    cerr << "Rank " << rank << ", epoch " << epoch << ", skip example (" << hope_length_ratio << ", " << bleuRatioHopeFear << ").. " << endl;
-	    featureValuesHope[batchPosition].clear();
-	    featureValuesFear[batchPosition].clear();
-	    bleuScoresHope[batchPosition].clear();
-	    bleuScoresFear[batchPosition].clear();
-	    if (historyBleu || simpleHistoryBleu || debug_model) {
-	      featureValues[batchPosition].clear();
-	      bleuScores[batchPosition].clear();
-	    }
-	  }
-	  else {
-	    examples_in_batch++;
-	    
-	    // needed for history
-	    if (historyBleu || simpleHistoryBleu)  {
-	      inputLengths.push_back(current_input_length);
-	      ref_ids.push_back(*sid);
-	      oneBests.push_back(bestModel);
-	    }
-	  }
-	}
-	if (model_hope_fear) {
-	  cerr << "Rank " << rank << ", epoch " << epoch << ", " << n << "best hope translations" << endl;
-	  size_t oraclePos = featureValues[batchPosition].size();
-	  decoder->getNBest(input, *sid, n, 1.0, bleuWeight_hope,
-	    featureValues[batchPosition], bleuScores[batchPosition], modelScores[batchPosition],
-	    0, realBleu, distinctNbest, avgRefLength, rank, epoch, "");
-	  //vector<const Word*> oracle = outputHope[0];
-	  // needed for history
-	  inputLengths.push_back(current_input_length);
-	  ref_ids.push_back(*sid);
-	  decoder->cleanup(chartDecoding);
-	  //ref_length = decoder->getClosestReferenceLength(*sid, oracle.size());
-	  //float hope_length_ratio = (float)oracle.size()/ref_length;
-	  cerr << endl;
-	  
-	  oracleFeatureValues.push_back(featureValues[batchPosition][oraclePos]);
-	  oracleBleuScores.push_back(bleuScores[batchPosition][oraclePos]);
-	  oracleModelScores.push_back(modelScores[batchPosition][oraclePos]);
-	  
-	  // MODEL
-	  cerr << "Rank " << rank << ", epoch " << epoch << ", " << n << "best wrt model score" << endl;
-	  if (historyBleu || simpleHistoryBleu) {
-	    vector< vector<const Word*> > outputModel = decoder->getNBest(input, *sid, n, 0.0,
-	       bleuWeight, featureValues[batchPosition], bleuScores[batchPosition],
-	       modelScores[batchPosition], 1, realBleu, distinctNbest, avgRefLength, rank, epoch, "");
-	    vector<const Word*> bestModel = outputModel[0];
-	    oneBests.push_back(bestModel);
-	    inputLengths.push_back(current_input_length);
-	    ref_ids.push_back(*sid);
-	  }
-	  else {
-	    decoder->getNBest(input, *sid, n, 0.0, bleuWeight,
-	      featureValues[batchPosition], bleuScores[batchPosition], modelScores[batchPosition],
-	      0, realBleu, distinctNbest, avgRefLength, rank, epoch, "");
-	  }
-	  decoder->cleanup(chartDecoding);
-	  //ref_length = decoder->getClosestReferenceLength(*sid, bestModel.size());
-	  //float model_length_ratio = (float)bestModel.size()/ref_length;
-	  cerr << endl;
-	  
-	  // FEAR
-	  cerr << "Rank " << rank << ", epoch " << epoch << ", " << n << "best fear translations" << endl;
-	  decoder->getNBest(input, *sid, n, -1.0, bleuWeight_fear,
-	    featureValues[batchPosition], bleuScores[batchPosition], modelScores[batchPosition],
-	    0, realBleu, distinctNbest, avgRefLength, rank, epoch, "");
-	  decoder->cleanup(chartDecoding);
-	  //ref_length = decoder->getClosestReferenceLength(*sid, fear.size());
-	  //float fear_length_ratio = (float)fear.size()/ref_length;
-	  
-	  examples_in_batch++;
-	}
-	if (kbest) {
-	  // MODEL
-	  cerr << "Rank " << rank << ", epoch " << epoch << ", " << n << "best wrt model score" << endl;
-	  if (historyBleu || simpleHistoryBleu) {
-	    vector< vector<const Word*> > outputModel = decoder->getNBest(input, *sid, n, 0.0,
-		  bleuWeight, featureValues[batchPosition], bleuScores[batchPosition],
-		  modelScores[batchPosition], 1, realBleu, distinctNbest, avgRefLength,	rank, epoch, "");
-	    vector<const Word*> bestModel = outputModel[0];
-	    oneBests.push_back(bestModel);
-	    inputLengths.push_back(current_input_length);
-	    ref_ids.push_back(*sid);
-	  }
-	  else {
-	    decoder->getNBest(input, *sid, n, 0.0, bleuWeight,
-	      featureValues[batchPosition], bleuScores[batchPosition],
-	      modelScores[batchPosition], 0, realBleu, distinctNbest, avgRefLength, rank, epoch, "");
-	  }
-	  decoder->cleanup(chartDecoding);
-	  //ref_length = decoder->getClosestReferenceLength(*sid, bestModel.size());
-	  //float model_length_ratio = (float)bestModel.size()/ref_length;
-	  cerr << endl;
-
-	  examples_in_batch++;
-	  
-	  HypothesisQueue queueHope(hope_n);
-	  HypothesisQueue queueFear(fear_n);
-	  cerr << endl;
-	  if (most_violated || all_violated || one_against_all) {
-	    float bleuHope = -1000;
-	    float bleuFear = 1000;
-	    size_t indexHope = -1;
-	    size_t indexFear = -1;
-	    
-	    vector<float> bleuHopeList;
-	    vector<float> bleuFearList;
-	    vector<float> indexHopeList;
-	    vector<float> indexFearList;
-	    
-	    if (most_violated)
-	      cerr << "Rank " << rank << ", epoch " << epoch << ", pick pair with most violated constraint" << endl;
-	    else if (all_violated)
-	      cerr << "Rank " << rank << ", epoch " << epoch << ", pick all pairs with violated constraints";
-	    else
-	      cerr << "Rank " << rank << ", epoch " << epoch << ", pick all pairs with hope";
-	    
-	    // find best hope, then find fear that violates our constraint most
-	    for (size_t i=0; i<bleuScores[batchPosition].size(); ++i) {
-	      if (abs(bleuScores[batchPosition][i] - bleuHope) < epsilon) { // equal bleu scores
-		if (modelScores[batchPosition][i] > modelScores[batchPosition][indexHope]) {
-		  if (abs(modelScores[batchPosition][i] - modelScores[batchPosition][indexHope]) > epsilon) {
-		    // better model score
-		    bleuHope = bleuScores[batchPosition][i];
-		    indexHope = i;
-		  }
-		}
-	      }
-	      else if (bleuScores[batchPosition][i] > bleuHope) { // better than current best
-		bleuHope = bleuScores[batchPosition][i];
-		indexHope = i;
-	      }
-	    }
-	    
-	    float currentViolation = 0;
-	    float minimum_bleu_diff = 0.01;
-	    for (size_t i=0; i<bleuScores[batchPosition].size(); ++i) {
-	      float bleuDiff = bleuHope - bleuScores[batchPosition][i];
-	      float modelDiff = modelScores[batchPosition][indexHope] - modelScores[batchPosition][i];
-	      if (bleuDiff > epsilon) {
-		if (one_against_all && bleuDiff > minimum_bleu_diff) {
-		  cerr << ".. adding pair";
-		  bleuHopeList.push_back(bleuHope);
-		  bleuFearList.push_back(bleuScores[batchPosition][i]);
-		  indexHopeList.push_back(indexHope);
-		  indexFearList.push_back(i);
-		}
-		else if (modelDiff < bleuDiff) {
-		  float diff = bleuDiff - modelDiff;
-		  if (diff > epsilon) {
-		    if (all_violated) {
-		      cerr << ".. adding pair";
-		      bleuHopeList.push_back(bleuHope);
-		      bleuFearList.push_back(bleuScores[batchPosition][i]);
-		      indexHopeList.push_back(indexHope);
-		      indexFearList.push_back(i);
-		    }
-		    else if (most_violated && diff > currentViolation) {
-		      currentViolation = diff;
-		      bleuFear = bleuScores[batchPosition][i];
-		      indexFear = i;
-		      cerr << "Rank " << rank << ", epoch " << epoch << ", current violation: " << currentViolation << " (" << modelDiff << " >= " << bleuDiff << ")" << endl;
-		    }
-		  }
-		}
-	      }
-	    }
-	    
-	    if (most_violated) {
-	      if (currentViolation > 0) {
-		cerr << "Rank " << rank << ", epoch " << epoch << ", adding pair with violation " << currentViolation << endl;
-		cerr << "Rank " << rank << ", epoch " << epoch << ", hope: " << bleuHope << " (" << indexHope  << "), fear: " << bleuFear << " (" << indexFear << ")" << endl;
-		bleuScoresHope[batchPosition].push_back(bleuHope);
-		bleuScoresFear[batchPosition].push_back(bleuFear);
-		featureValuesHope[batchPosition].push_back(featureValues[batchPosition][indexHope]);
-		featureValuesFear[batchPosition].push_back(featureValues[batchPosition][indexFear]);
-		float modelScoreHope = modelScores[batchPosition][indexHope];
-		float modelScoreFear = modelScores[batchPosition][indexFear];
-		if (most_violated_reg) {
-		  // reduce model score difference by factor ~0.5
-		  float reg = currentViolation/4;
-		  modelScoreHope += abs(reg);
-		  modelScoreFear -= abs(reg);
-		  float newViolation = (bleuHope - bleuFear) - (modelScoreHope - modelScoreFear);
-		  cerr << "Rank " << rank << ", epoch " << epoch << ", regularized violation: " << newViolation << endl;
-		}
-		modelScoresHope[batchPosition].push_back(modelScoreHope);
-		modelScoresFear[batchPosition].push_back(modelScoreFear);
-		
-		featureValues[batchPosition][indexHope].IncrementSparseHopeFeatures();
-		featureValues[batchPosition][indexFear].IncrementSparseFearFeatures();
-	      }
-	      else {
-		cerr << "Rank " << rank << ", epoch " << epoch << ", no violated constraint found." << endl;
-		skip_example = 1;
-	      }
-	    }
-	    else cerr << endl;
-	  }
-	  if (max_bleu_diff) {
-	    cerr << "Rank " << rank << ", epoch " << epoch << ", pick pair with max Bleu diff from list: " << bleuScores[batchPosition].size() << endl;
-	    for (size_t i=0; i<bleuScores[batchPosition].size(); ++i) {
-	      float hopeScore = bleuScores[batchPosition][i];
-	      if (modelPlusBleu) hopeScore += modelScores[batchPosition][i];
-	      BleuIndexPair hope(hopeScore, i);
-	      queueHope.Push(hope);
-	      
-	      float fearScore = -1*(bleuScores[batchPosition][i]);
-	      if (modelPlusBleu) fearScore += modelScores[batchPosition][i];
-	      BleuIndexPair fear(fearScore, i);
-	      queueFear.Push(fear);
-	    }
-	    skip_example = 0;
-	  }
-	  cerr << endl;
-
-	  vector<BleuIndexPair> hopeList, fearList;
-	  for (size_t i=0; i<hope_n && !queueHope.Empty(); ++i) hopeList.push_back(queueHope.Pop());
-	  for (size_t i=0; i<fear_n && !queueFear.Empty(); ++i) fearList.push_back(queueFear.Pop());
-	  for (size_t i=0; i<hopeList.size(); ++i) {
-	    //float bleuHope = hopeList[i].first;
-	    size_t indexHope = hopeList[i].second;
-	    float bleuHope = bleuScores[batchPosition][indexHope];
-	    for (size_t j=0; j<fearList.size(); ++j) {
-	      //float bleuFear = -1*(fearList[j].first);
-	      size_t indexFear = fearList[j].second;
-	      float bleuFear = bleuScores[batchPosition][indexFear];
-	      cerr << "Rank " << rank << ", epoch " << epoch << ", hope: " << bleuHope << " (" << indexHope  << "), fear: " << bleuFear << " (" << indexFear << ")" << endl;
-	      bleuScoresHope[batchPosition].push_back(bleuHope);
-	      bleuScoresFear[batchPosition].push_back(bleuFear);
-	      featureValuesHope[batchPosition].push_back(featureValues[batchPosition][indexHope]);
-	      featureValuesFear[batchPosition].push_back(featureValues[batchPosition][indexFear]);
-	      float modelScoreHope = modelScores[batchPosition][indexHope];
-	      float modelScoreFear = modelScores[batchPosition][indexFear];
-	      
-	      modelScoresHope[batchPosition].push_back(modelScoreHope);
-	      modelScoresFear[batchPosition].push_back(modelScoreFear);
-	      
-	      featureValues[batchPosition][indexHope].IncrementSparseHopeFeatures();
-	      featureValues[batchPosition][indexFear].IncrementSparseFearFeatures();
-	    }
-	  }
-	  if (!makePairs)
-	    cerr << "Rank " << rank << ", epoch " << epoch << "summing up hope and fear vectors, no pairs" << endl;
-	}
-	
-	// next input sentence
-	++sid;
-	++actualBatchSize;
-	++shardPosition;
+           != shard.end(); ++batchPosition) {
+        string input;
+        if (trainWithMultipleFolds)
+          input = inputSentencesFolds[myFold][*sid];
+        else
+          input = inputSentences[*sid];
+
+        Moses::Sentence *sentence = new Sentence();
+        stringstream in(input + "\n");
+        const vector<FactorType> inputFactorOrder = staticData.GetInputFactorOrder();
+        sentence->Read(in,inputFactorOrder);
+        cerr << "\nRank " << rank << ", epoch " << epoch << ", input sentence " << *sid << ": \"";
+        sentence->Print(cerr);
+        cerr << "\"" << " (batch pos " << batchPosition << ")" << endl;
+        size_t current_input_length = (*sentence).GetSize();
+
+        if (epoch == 0 && (scaleByAvgInputLength || scaleByAvgInverseLength)) {
+          sumOfInputs += current_input_length;
+          ++numberOfInputs;
+          avgInputLength = sumOfInputs/numberOfInputs;
+          decoder->setAvgInputLength(avgInputLength);
+          cerr << "Rank " << rank << ", epoch 0, average input length: " << avgInputLength << endl;
+        }
+
+        vector<ScoreComponentCollection> newFeatureValues;
+        vector<float> newScores;
+        if (model_hope_fear) {
+          featureValues.push_back(newFeatureValues);
+          bleuScores.push_back(newScores);
+          modelScores.push_back(newScores);
+        }
+        if (hope_fear || perceptron_update) {
+          featureValuesHope.push_back(newFeatureValues);
+          featureValuesFear.push_back(newFeatureValues);
+          bleuScoresHope.push_back(newScores);
+          bleuScoresFear.push_back(newScores);
+          modelScoresHope.push_back(newScores);
+          modelScoresFear.push_back(newScores);
+          if (historyBleu || simpleHistoryBleu || debug_model) {
+            featureValues.push_back(newFeatureValues);
+            bleuScores.push_back(newScores);
+            modelScores.push_back(newScores);
+          }
+        }
+        if (kbest) {
+          // for decoding
+          featureValues.push_back(newFeatureValues);
+          bleuScores.push_back(newScores);
+          modelScores.push_back(newScores);
+
+          // for storing selected examples
+          featureValuesHope.push_back(newFeatureValues);
+          featureValuesFear.push_back(newFeatureValues);
+          bleuScoresHope.push_back(newScores);
+          bleuScoresFear.push_back(newScores);
+          modelScoresHope.push_back(newScores);
+          modelScoresFear.push_back(newScores);
+        }
+
+        size_t ref_length;
+        float avg_ref_length;
+
+        if (print_weights)
+          cerr << "Rank " << rank << ", epoch " << epoch << ", current weights: " << mosesWeights << endl;
+        if (print_core_weights) {
+          cerr << "Rank " << rank << ", epoch " << epoch << ", current weights: ";
+          mosesWeights.PrintCoreFeatures();
+          cerr << endl;
+        }
+
+        // check LM weight
+        const std::vector<const StatefulFeatureFunction*> &statefulFFs = StatefulFeatureFunction::GetStatefulFeatureFunctions();
+        for (size_t i = 0; i < statefulFFs.size(); ++i) {
+          const StatefulFeatureFunction *ff = statefulFFs[i];
+          const LanguageModel *lm = dynamic_cast<const LanguageModel*>(ff);
+
+          if (lm) {
+            float lmWeight = mosesWeights.GetScoreForProducer(lm);
+            cerr << "Rank " << rank << ", epoch " << epoch << ", lm weight: " << lmWeight << endl;
+            if (lmWeight <= 0) {
+              cerr << "Rank " << rank << ", epoch " << epoch << ", ERROR: language model weight should never be <= 0." << endl;
+              mosesWeights.Assign(lm, 0.1);
+              cerr << "Rank " << rank << ", epoch " << epoch << ", assign lm weights of 0.1" << endl;
+            }
+          }
+        }
+
+        // select inference scheme
+        cerr << "Rank " << rank << ", epoch " << epoch << ", real Bleu? " << realBleu << endl;
+        if (hope_fear || perceptron_update) {
+          // HOPE
+          cerr << "Rank " << rank << ", epoch " << epoch << ", " << hope_n <<
+               "best hope translations" << endl;
+          vector< vector<const Word*> > outputHope = decoder->getNBest(input, *sid, hope_n, 1.0, bleuWeight_hope,
+              featureValuesHope[batchPosition], bleuScoresHope[batchPosition], modelScoresHope[batchPosition],
+              1, realBleu, distinctNbest, avgRefLength, rank, epoch, "");
+          vector<const Word*> oracle = outputHope[0];
+          decoder->cleanup(chartDecoding);
+          ref_length = decoder->getClosestReferenceLength(*sid, oracle.size());
+          avg_ref_length = ref_length;
+          float hope_length_ratio = (float)oracle.size()/ref_length;
+          int oracleSize = (int)oracle.size();
+          cerr << endl;
+
+          // count sparse features occurring in hope translation
+          featureValuesHope[batchPosition][0].IncrementSparseHopeFeatures();
+
+          float precision = bleuScoresHope[batchPosition][0];
+          if (historyBleu || simpleHistoryBleu) {
+            precision /= decoder->getTargetLengthHistory();
+          } else {
+            if (scaleByAvgInputLength) precision /= decoder->getAverageInputLength();
+            else if (scaleByAvgInverseLength) precision /= (100/decoder->getAverageInputLength());
+            precision /= scaleByX;
+          }
+          if (scale_margin_precision || scale_update_precision) {
+            if (historyBleu || simpleHistoryBleu || scaleByAvgInputLength || scaleByAvgInverseLength) {
+              cerr << "Rank " << rank << ", epoch " << epoch << ", set hope precision: " << precision << endl;
+              ((MiraOptimiser*) optimiser)->setPrecision(precision);
+            }
+          }
+
+          vector<const Word*> bestModel;
+          if (debug_model || historyBleu || simpleHistoryBleu) {
+            // MODEL (for updating the history only, using dummy vectors)
+            cerr << "Rank " << rank << ", epoch " << epoch << ", 1best wrt model score (debug or history)" << endl;
+            vector< vector<const Word*> > outputModel = decoder->getNBest(input, *sid, n, 0.0, bleuWeight,
+                featureValues[batchPosition], bleuScores[batchPosition], modelScores[batchPosition],
+                1, realBleu, distinctNbest, avgRefLength, rank, epoch, "");
+            bestModel = outputModel[0];
+            decoder->cleanup(chartDecoding);
+            cerr << endl;
+            ref_length = decoder->getClosestReferenceLength(*sid, bestModel.size());
+          }
+
+          // FEAR
+          float fear_length_ratio = 0;
+          float bleuRatioHopeFear = 0;
+          int fearSize = 0;
+          cerr << "Rank " << rank << ", epoch " << epoch << ", " << fear_n << "best fear translations" << endl;
+          vector< vector<const Word*> > outputFear = decoder->getNBest(input, *sid, fear_n, -1.0, bleuWeight_fear,
+              featureValuesFear[batchPosition], bleuScoresFear[batchPosition], modelScoresFear[batchPosition],
+              1, realBleu, distinctNbest, avgRefLength, rank, epoch, "");
+          vector<const Word*> fear = outputFear[0];
+          decoder->cleanup(chartDecoding);
+          ref_length = decoder->getClosestReferenceLength(*sid, fear.size());
+          avg_ref_length += ref_length;
+          avg_ref_length /= 2;
+          fear_length_ratio = (float)fear.size()/ref_length;
+          fearSize = (int)fear.size();
+          cerr << endl;
+          for (size_t i = 0; i < fear.size(); ++i)
+            delete fear[i];
+
+          // count sparse features occurring in fear translation
+          featureValuesFear[batchPosition][0].IncrementSparseFearFeatures();
+
+          // Bleu-related example selection
+          bool skip = false;
+          bleuRatioHopeFear = bleuScoresHope[batchPosition][0] / bleuScoresFear[batchPosition][0];
+          if (minBleuRatio != -1 && bleuRatioHopeFear < minBleuRatio)
+            skip = true;
+          if(maxBleuRatio != -1 && bleuRatioHopeFear > maxBleuRatio)
+            skip = true;
+
+          // sanity check
+          if (historyBleu || simpleHistoryBleu) {
+            if (bleuScores[batchPosition][0] > bleuScoresHope[batchPosition][0] &&
+                modelScores[batchPosition][0] > modelScoresHope[batchPosition][0]) {
+              if (abs(bleuScores[batchPosition][0] - bleuScoresHope[batchPosition][0]) > epsilon &&
+                  abs(modelScores[batchPosition][0] - modelScoresHope[batchPosition][0]) > epsilon) {
+                cerr << "Rank " << rank << ", epoch " << epoch << ", ERROR: MODEL translation better than HOPE translation." << endl;
+                skip = true;
+              }
+            }
+            if (bleuScoresFear[batchPosition][0] > bleuScores[batchPosition][0] &&
+                modelScoresFear[batchPosition][0] > modelScores[batchPosition][0]) {
+              if (abs(bleuScoresFear[batchPosition][0] - bleuScores[batchPosition][0]) > epsilon &&
+                  abs(modelScoresFear[batchPosition][0] - modelScores[batchPosition][0]) > epsilon) {
+                cerr << "Rank " << rank << ", epoch " << epoch << ", ERROR: FEAR translation better than MODEL translation." << endl;
+                skip = true;
+              }
+            }
+          }
+          if (bleuScoresFear[batchPosition][0] > bleuScoresHope[batchPosition][0]) {
+            if (abs(bleuScoresFear[batchPosition][0] - bleuScoresHope[batchPosition][0]) > epsilon) {
+              // check if it's an error or a warning
+              skip = true;
+              if (modelScoresFear[batchPosition][0] > modelScoresHope[batchPosition][0] && abs(modelScoresFear[batchPosition][0] - modelScoresHope[batchPosition][0]) > epsilon) {
+                cerr << "Rank " << rank << ", epoch " << epoch << ", ERROR: FEAR translation better than HOPE translation. (abs-diff: " << abs(bleuScoresFear[batchPosition][0] - bleuScoresHope[batchPosition][0]) << ")" <<endl;
+              } else {
+                cerr << "Rank " << rank << ", epoch " << epoch << ", WARNING: FEAR translation has better Bleu than HOPE translation. (abs-diff: " << abs(bleuScoresFear[batchPosition][0] - bleuScoresHope[batchPosition][0]) << ")" <<endl;
+              }
+            }
+          }
+
+          if (skip) {
+            cerr << "Rank " << rank << ", epoch " << epoch << ", skip example (" << hope_length_ratio << ", " << bleuRatioHopeFear << ").. " << endl;
+            featureValuesHope[batchPosition].clear();
+            featureValuesFear[batchPosition].clear();
+            bleuScoresHope[batchPosition].clear();
+            bleuScoresFear[batchPosition].clear();
+            if (historyBleu || simpleHistoryBleu || debug_model) {
+              featureValues[batchPosition].clear();
+              bleuScores[batchPosition].clear();
+            }
+          } else {
+            examples_in_batch++;
+
+            // needed for history
+            if (historyBleu || simpleHistoryBleu)  {
+              inputLengths.push_back(current_input_length);
+              ref_ids.push_back(*sid);
+              oneBests.push_back(bestModel);
+            }
+          }
+        }
+        if (model_hope_fear) {
+          cerr << "Rank " << rank << ", epoch " << epoch << ", " << n << "best hope translations" << endl;
+          size_t oraclePos = featureValues[batchPosition].size();
+          decoder->getNBest(input, *sid, n, 1.0, bleuWeight_hope,
+                            featureValues[batchPosition], bleuScores[batchPosition], modelScores[batchPosition],
+                            0, realBleu, distinctNbest, avgRefLength, rank, epoch, "");
+          //vector<const Word*> oracle = outputHope[0];
+          // needed for history
+          inputLengths.push_back(current_input_length);
+          ref_ids.push_back(*sid);
+          decoder->cleanup(chartDecoding);
+          //ref_length = decoder->getClosestReferenceLength(*sid, oracle.size());
+          //float hope_length_ratio = (float)oracle.size()/ref_length;
+          cerr << endl;
+
+          oracleFeatureValues.push_back(featureValues[batchPosition][oraclePos]);
+          oracleBleuScores.push_back(bleuScores[batchPosition][oraclePos]);
+          oracleModelScores.push_back(modelScores[batchPosition][oraclePos]);
+
+          // MODEL
+          cerr << "Rank " << rank << ", epoch " << epoch << ", " << n << "best wrt model score" << endl;
+          if (historyBleu || simpleHistoryBleu) {
+            vector< vector<const Word*> > outputModel = decoder->getNBest(input, *sid, n, 0.0,
+                bleuWeight, featureValues[batchPosition], bleuScores[batchPosition],
+                modelScores[batchPosition], 1, realBleu, distinctNbest, avgRefLength, rank, epoch, "");
+            vector<const Word*> bestModel = outputModel[0];
+            oneBests.push_back(bestModel);
+            inputLengths.push_back(current_input_length);
+            ref_ids.push_back(*sid);
+          } else {
+            decoder->getNBest(input, *sid, n, 0.0, bleuWeight,
+                              featureValues[batchPosition], bleuScores[batchPosition], modelScores[batchPosition],
+                              0, realBleu, distinctNbest, avgRefLength, rank, epoch, "");
+          }
+          decoder->cleanup(chartDecoding);
+          //ref_length = decoder->getClosestReferenceLength(*sid, bestModel.size());
+          //float model_length_ratio = (float)bestModel.size()/ref_length;
+          cerr << endl;
+
+          // FEAR
+          cerr << "Rank " << rank << ", epoch " << epoch << ", " << n << "best fear translations" << endl;
+          decoder->getNBest(input, *sid, n, -1.0, bleuWeight_fear,
+                            featureValues[batchPosition], bleuScores[batchPosition], modelScores[batchPosition],
+                            0, realBleu, distinctNbest, avgRefLength, rank, epoch, "");
+          decoder->cleanup(chartDecoding);
+          //ref_length = decoder->getClosestReferenceLength(*sid, fear.size());
+          //float fear_length_ratio = (float)fear.size()/ref_length;
+
+          examples_in_batch++;
+        }
+        if (kbest) {
+          // MODEL
+          cerr << "Rank " << rank << ", epoch " << epoch << ", " << n << "best wrt model score" << endl;
+          if (historyBleu || simpleHistoryBleu) {
+            vector< vector<const Word*> > outputModel = decoder->getNBest(input, *sid, n, 0.0,
+                bleuWeight, featureValues[batchPosition], bleuScores[batchPosition],
+                modelScores[batchPosition], 1, realBleu, distinctNbest, avgRefLength,	rank, epoch, "");
+            vector<const Word*> bestModel = outputModel[0];
+            oneBests.push_back(bestModel);
+            inputLengths.push_back(current_input_length);
+            ref_ids.push_back(*sid);
+          } else {
+            decoder->getNBest(input, *sid, n, 0.0, bleuWeight,
+                              featureValues[batchPosition], bleuScores[batchPosition],
+                              modelScores[batchPosition], 0, realBleu, distinctNbest, avgRefLength, rank, epoch, "");
+          }
+          decoder->cleanup(chartDecoding);
+          //ref_length = decoder->getClosestReferenceLength(*sid, bestModel.size());
+          //float model_length_ratio = (float)bestModel.size()/ref_length;
+          cerr << endl;
+
+          examples_in_batch++;
+
+          HypothesisQueue queueHope(hope_n);
+          HypothesisQueue queueFear(fear_n);
+          cerr << endl;
+          if (most_violated || all_violated || one_against_all) {
+            float bleuHope = -1000;
+            float bleuFear = 1000;
+            size_t indexHope = -1;
+            size_t indexFear = -1;
+
+            vector<float> bleuHopeList;
+            vector<float> bleuFearList;
+            vector<float> indexHopeList;
+            vector<float> indexFearList;
+
+            if (most_violated)
+              cerr << "Rank " << rank << ", epoch " << epoch << ", pick pair with most violated constraint" << endl;
+            else if (all_violated)
+              cerr << "Rank " << rank << ", epoch " << epoch << ", pick all pairs with violated constraints";
+            else
+              cerr << "Rank " << rank << ", epoch " << epoch << ", pick all pairs with hope";
+
+            // find best hope, then find fear that violates our constraint most
+            for (size_t i=0; i<bleuScores[batchPosition].size(); ++i) {
+              if (abs(bleuScores[batchPosition][i] - bleuHope) < epsilon) { // equal bleu scores
+                if (modelScores[batchPosition][i] > modelScores[batchPosition][indexHope]) {
+                  if (abs(modelScores[batchPosition][i] - modelScores[batchPosition][indexHope]) > epsilon) {
+                    // better model score
+                    bleuHope = bleuScores[batchPosition][i];
+                    indexHope = i;
+                  }
+                }
+              } else if (bleuScores[batchPosition][i] > bleuHope) { // better than current best
+                bleuHope = bleuScores[batchPosition][i];
+                indexHope = i;
+              }
+            }
+
+            float currentViolation = 0;
+            float minimum_bleu_diff = 0.01;
+            for (size_t i=0; i<bleuScores[batchPosition].size(); ++i) {
+              float bleuDiff = bleuHope - bleuScores[batchPosition][i];
+              float modelDiff = modelScores[batchPosition][indexHope] - modelScores[batchPosition][i];
+              if (bleuDiff > epsilon) {
+                if (one_against_all && bleuDiff > minimum_bleu_diff) {
+                  cerr << ".. adding pair";
+                  bleuHopeList.push_back(bleuHope);
+                  bleuFearList.push_back(bleuScores[batchPosition][i]);
+                  indexHopeList.push_back(indexHope);
+                  indexFearList.push_back(i);
+                } else if (modelDiff < bleuDiff) {
+                  float diff = bleuDiff - modelDiff;
+                  if (diff > epsilon) {
+                    if (all_violated) {
+                      cerr << ".. adding pair";
+                      bleuHopeList.push_back(bleuHope);
+                      bleuFearList.push_back(bleuScores[batchPosition][i]);
+                      indexHopeList.push_back(indexHope);
+                      indexFearList.push_back(i);
+                    } else if (most_violated && diff > currentViolation) {
+                      currentViolation = diff;
+                      bleuFear = bleuScores[batchPosition][i];
+                      indexFear = i;
+                      cerr << "Rank " << rank << ", epoch " << epoch << ", current violation: " << currentViolation << " (" << modelDiff << " >= " << bleuDiff << ")" << endl;
+                    }
+                  }
+                }
+              }
+            }
+
+            if (most_violated) {
+              if (currentViolation > 0) {
+                cerr << "Rank " << rank << ", epoch " << epoch << ", adding pair with violation " << currentViolation << endl;
+                cerr << "Rank " << rank << ", epoch " << epoch << ", hope: " << bleuHope << " (" << indexHope  << "), fear: " << bleuFear << " (" << indexFear << ")" << endl;
+                bleuScoresHope[batchPosition].push_back(bleuHope);
+                bleuScoresFear[batchPosition].push_back(bleuFear);
+                featureValuesHope[batchPosition].push_back(featureValues[batchPosition][indexHope]);
+                featureValuesFear[batchPosition].push_back(featureValues[batchPosition][indexFear]);
+                float modelScoreHope = modelScores[batchPosition][indexHope];
+                float modelScoreFear = modelScores[batchPosition][indexFear];
+                if (most_violated_reg) {
+                  // reduce model score difference by factor ~0.5
+                  float reg = currentViolation/4;
+                  modelScoreHope += abs(reg);
+                  modelScoreFear -= abs(reg);
+                  float newViolation = (bleuHope - bleuFear) - (modelScoreHope - modelScoreFear);
+                  cerr << "Rank " << rank << ", epoch " << epoch << ", regularized violation: " << newViolation << endl;
+                }
+                modelScoresHope[batchPosition].push_back(modelScoreHope);
+                modelScoresFear[batchPosition].push_back(modelScoreFear);
+
+                featureValues[batchPosition][indexHope].IncrementSparseHopeFeatures();
+                featureValues[batchPosition][indexFear].IncrementSparseFearFeatures();
+              } else {
+                cerr << "Rank " << rank << ", epoch " << epoch << ", no violated constraint found." << endl;
+                skip_example = 1;
+              }
+            } else cerr << endl;
+          }
+          if (max_bleu_diff) {
+            cerr << "Rank " << rank << ", epoch " << epoch << ", pick pair with max Bleu diff from list: " << bleuScores[batchPosition].size() << endl;
+            for (size_t i=0; i<bleuScores[batchPosition].size(); ++i) {
+              float hopeScore = bleuScores[batchPosition][i];
+              if (modelPlusBleu) hopeScore += modelScores[batchPosition][i];
+              BleuIndexPair hope(hopeScore, i);
+              queueHope.Push(hope);
+
+              float fearScore = -1*(bleuScores[batchPosition][i]);
+              if (modelPlusBleu) fearScore += modelScores[batchPosition][i];
+              BleuIndexPair fear(fearScore, i);
+              queueFear.Push(fear);
+            }
+            skip_example = 0;
+          }
+          cerr << endl;
+
+          vector<BleuIndexPair> hopeList, fearList;
+          for (size_t i=0; i<hope_n && !queueHope.Empty(); ++i) hopeList.push_back(queueHope.Pop());
+          for (size_t i=0; i<fear_n && !queueFear.Empty(); ++i) fearList.push_back(queueFear.Pop());
+          for (size_t i=0; i<hopeList.size(); ++i) {
+            //float bleuHope = hopeList[i].first;
+            size_t indexHope = hopeList[i].second;
+            float bleuHope = bleuScores[batchPosition][indexHope];
+            for (size_t j=0; j<fearList.size(); ++j) {
+              //float bleuFear = -1*(fearList[j].first);
+              size_t indexFear = fearList[j].second;
+              float bleuFear = bleuScores[batchPosition][indexFear];
+              cerr << "Rank " << rank << ", epoch " << epoch << ", hope: " << bleuHope << " (" << indexHope  << "), fear: " << bleuFear << " (" << indexFear << ")" << endl;
+              bleuScoresHope[batchPosition].push_back(bleuHope);
+              bleuScoresFear[batchPosition].push_back(bleuFear);
+              featureValuesHope[batchPosition].push_back(featureValues[batchPosition][indexHope]);
+              featureValuesFear[batchPosition].push_back(featureValues[batchPosition][indexFear]);
+              float modelScoreHope = modelScores[batchPosition][indexHope];
+              float modelScoreFear = modelScores[batchPosition][indexFear];
+
+              modelScoresHope[batchPosition].push_back(modelScoreHope);
+              modelScoresFear[batchPosition].push_back(modelScoreFear);
+
+              featureValues[batchPosition][indexHope].IncrementSparseHopeFeatures();
+              featureValues[batchPosition][indexFear].IncrementSparseFearFeatures();
+            }
+          }
+          if (!makePairs)
+            cerr << "Rank " << rank << ", epoch " << epoch << "summing up hope and fear vectors, no pairs" << endl;
+        }
+
+        // next input sentence
+        ++sid;
+        ++actualBatchSize;
+        ++shardPosition;
       } // end of batch loop
-      
+
       if (examples_in_batch == 0 || (kbest && skip_example)) {
-	cerr << "Rank " << rank << ", epoch " << epoch << ", batch is empty." << endl;
-      }
-      else {
-	vector<vector<float> > losses(actualBatchSize);
-	if (model_hope_fear) {
-	  // Set loss for each sentence as BLEU(oracle) - BLEU(hypothesis)
-	  for (size_t batchPosition = 0; batchPosition < actualBatchSize; ++batchPosition) {
-	    for (size_t j = 0; j < bleuScores[batchPosition].size(); ++j) {
-	      losses[batchPosition].push_back(oracleBleuScores[batchPosition] - bleuScores[batchPosition][j]);
-	    }
-	  }
-	}
-	
-	// set weight for bleu feature to 0 before optimizing
-	vector<FeatureFunction*>::const_iterator iter;
-	const vector<FeatureFunction*> &featureFunctions2 = FeatureFunction::GetFeatureFunctions();
-	for (iter = featureFunctions2.begin(); iter != featureFunctions2.end(); ++iter) {
-	  if ((*iter)->GetScoreProducerDescription() == "BleuScoreFeature") {
-	    mosesWeights.Assign(*iter, 0);
-	    break;
-	  }
-	}
-	
-	// scale LM feature (to avoid rapid changes)
-	if (scale_lm) {
-	  cerr << "scale lm" << endl;
-		const std::vector<const StatefulFeatureFunction*> &statefulFFs = StatefulFeatureFunction::GetStatefulFeatureFunctions();
-		for (size_t i = 0; i < statefulFFs.size(); ++i) {
-		  const StatefulFeatureFunction *ff = statefulFFs[i];
-		  const LanguageModel *lm = dynamic_cast<const LanguageModel*>(ff);
-
-		  if (lm) {
-			  // scale down score
-			  if (model_hope_fear) {
-			    scaleFeatureScore(lm, scale_lm_factor, featureValues, rank, epoch);
-			  }
-			  else {
-			    scaleFeatureScore(lm, scale_lm_factor, featureValuesHope, rank, epoch);
-			    scaleFeatureScore(lm, scale_lm_factor, featureValuesFear, rank, epoch);
-			  }
-			}
-		}
-	}
-	
-	// scale WP
-	if (scale_wp) {
-	  // scale up weight
-	  WordPenaltyProducer *wp = StaticData::InstanceNonConst().GetWordPenaltyProducer();
-	  
-	  // scale down score
-	  if (model_hope_fear) {
-	    scaleFeatureScore(wp, scale_wp_factor, featureValues, rank, epoch);
-	  }
-	  else {
-	    scaleFeatureScore(wp, scale_wp_factor, featureValuesHope, rank, epoch);
-	    scaleFeatureScore(wp, scale_wp_factor, featureValuesFear, rank, epoch);
-	  }
-	}
-		
-	// print out the feature values
-	if (print_feature_values) {
-	  cerr << "\nRank " << rank << ", epoch " << epoch << ", feature values: " << endl;
-	  if (model_hope_fear) printFeatureValues(featureValues);
-	  else {
-	    cerr << "hope: " << endl;
-	    printFeatureValues(featureValuesHope);
-	    cerr << "fear: " << endl;
-	    printFeatureValues(featureValuesFear);
-	  }
-	}
-	
-	// apply learning rates to feature vectors before optimization
-	if (feature_confidence) {
-	  cerr << "Rank " << rank << ", epoch " << epoch << ", apply feature learning rates with decays " << decay_core << "/" << decay_sparse << ": " << featureLearningRates << endl;
-	  if (model_hope_fear) {
-	    applyPerFeatureLearningRates(featureValues, featureLearningRates, sparse_r0);
-	  }
-	  else {
-	    applyPerFeatureLearningRates(featureValuesHope, featureLearningRates, sparse_r0);
-	    applyPerFeatureLearningRates(featureValuesFear, featureLearningRates, sparse_r0);
-	  }
-	}
-	else {
-	  // apply fixed learning rates
-	  cerr << "Rank " << rank << ", epoch " << epoch << ", apply fixed learning rates, core: " << core_r0 << ", sparse: " << sparse_r0 << endl;
-	  if (core_r0 != 1.0 || sparse_r0 != 1.0) {
-	    if (model_hope_fear) {
-	      applyLearningRates(featureValues, core_r0, sparse_r0);
-	    }
-	    else {
-	      applyLearningRates(featureValuesHope, core_r0, sparse_r0);
-	      applyLearningRates(featureValuesFear, core_r0, sparse_r0);
-	    }
-	  }
-	}
-	
-	// Run optimiser on batch:
-	VERBOSE(1, "\nRank " << rank << ", epoch " << epoch << ", run optimiser:" << endl);
-	size_t update_status = 1;
-	ScoreComponentCollection weightUpdate;
-	if (perceptron_update) {
-	  vector<vector<float> > dummy1;
-	  update_status = optimiser->updateWeightsHopeFear( weightUpdate, featureValuesHope,
-	    featureValuesFear, dummy1, dummy1, dummy1, dummy1, learning_rate, rank, epoch);
-	}
-	else if (hope_fear) {
-	  if (bleuScoresHope[0][0] >= min_oracle_bleu) {
-	    if (hope_n == 1 && fear_n ==1 && batchSize == 1 && !hildreth) {
-	      update_status = ((MiraOptimiser*) optimiser)->updateWeightsAnalytically(weightUpdate,
-	      featureValuesHope[0][0], featureValuesFear[0][0], bleuScoresHope[0][0],
-		 bleuScoresFear[0][0], modelScoresHope[0][0], modelScoresFear[0][0], learning_rate, rank, epoch);
-	    }
-	    else
-	      update_status = optimiser->updateWeightsHopeFear(weightUpdate, featureValuesHope,
-	       featureValuesFear, bleuScoresHope, bleuScoresFear, modelScoresHope,
-	       modelScoresFear, learning_rate, rank, epoch);
-	  }
-	  else
-	    update_status = 1;
-	}
-	else if (kbest) {
-	  if (selective)
-	    update_status = ((MiraOptimiser*)optimiser)->updateWeightsHopeFearSelective(
-		weightUpdate, featureValuesHope, featureValuesFear, bleuScoresHope, bleuScoresFear,
-		modelScoresHope, modelScoresFear, learning_rate, rank, epoch);
-	  else if (summed)
-	    update_status = ((MiraOptimiser*)optimiser)->updateWeightsHopeFearSummed(
-	     weightUpdate, featureValuesHope, featureValuesFear, bleuScoresHope, bleuScoresFear,
-	     modelScoresHope, modelScoresFear, learning_rate, rank, epoch, rescaleSlack, makePairs);
-	  else {
-	    if (batchSize == 1 && featureValuesHope[0].size() == 1 && !hildreth) {
-	      cerr << "Rank " << rank << ", epoch " << epoch << ", model score hope: " << modelScoresHope[0][0] << endl;
-	      cerr << "Rank " << rank << ", epoch " << epoch << ", model score fear: " << modelScoresFear[0][0] << endl;
-	      update_status = ((MiraOptimiser*) optimiser)->updateWeightsAnalytically(
-		      weightUpdate, featureValuesHope[0][0], featureValuesFear[0][0],
-		      bleuScoresHope[0][0], bleuScoresFear[0][0], modelScoresHope[0][0],
-		      modelScoresFear[0][0], learning_rate, rank, epoch);
-	    }
-	    else {
-	      cerr << "Rank " << rank << ", epoch " << epoch << ", model score hope: " << modelScoresHope[0][0] << endl;
-	      cerr << "Rank " << rank << ", epoch " << epoch << ", model score fear: " << modelScoresFear[0][0] << endl;
-	      update_status = optimiser->updateWeightsHopeFear(weightUpdate, featureValuesHope,
-		  featureValuesFear, bleuScoresHope, bleuScoresFear, modelScoresHope,
-		       modelScoresFear, learning_rate, rank, epoch);
-	    }
-	  }
-	}
-	else {
-	  // model_hope_fear
-	  update_status = ((MiraOptimiser*) optimiser)->updateWeights(weightUpdate,
-	      featureValues, losses, bleuScores, modelScores, oracleFeatureValues,
-	      oracleBleuScores, oracleModelScores, learning_rate, rank, epoch);
-	}
-	
-	// sumStillViolatedConstraints += update_status;
-	
-	if (update_status == 0) {	 // if weights were updated
-	  // apply weight update
-	  if (debug)
-	    cerr << "Rank " << rank << ", epoch " << epoch << ", update: " << weightUpdate << endl;
-	  
-	  if (feature_confidence) {
-	    // update confidence counts based on weight update
-	    confidenceCounts.UpdateConfidenceCounts(weightUpdate, signed_counts);
-	    
-	    // update feature learning rates
-	    featureLearningRates.UpdateLearningRates(decay_core, decay_sparse, confidenceCounts, core_r0, sparse_r0);
-	  }
-	  
-	  // apply weight update to Moses weights
-	  mosesWeights.PlusEquals(weightUpdate);
-	  
-	  if (normaliseWeights)
-	    mosesWeights.L1Normalise();
-	  
-	  cumulativeWeights.PlusEquals(mosesWeights);
-	  if (sparseAverage) {
-	    ScoreComponentCollection binary;
-	    binary.SetToBinaryOf(mosesWeights);
-	    cumulativeWeightsBinary.PlusEquals(binary);
-	  }
-	  
-	  ++numberOfUpdates;
-	  ++numberOfUpdatesThisEpoch;
-	  if (averageWeights) {
-	    ScoreComponentCollection averageWeights(cumulativeWeights);
-	    if (accumulateWeights) {
-	      averageWeights.DivideEquals(numberOfUpdates);
-	    } else {
-	      averageWeights.DivideEquals(numberOfUpdatesThisEpoch);
-	    }
-	    
-	    mosesWeights = averageWeights;
-	  }
-	  
-	  // set new Moses weights
-	  decoder->setWeights(mosesWeights);
-	  //cerr << "Rank " << rank << ", epoch " << epoch << ", new weights: " << mosesWeights << endl;
-	}
-	
-	// update history (for approximate document Bleu)
-	if (historyBleu || simpleHistoryBleu) {
-	  for (size_t i = 0; i < oneBests.size(); ++i)
-	    cerr << "Rank " << rank << ", epoch " << epoch << ", update history with 1best length: " << oneBests[i].size() << " ";
-	  decoder->updateHistory(oneBests, inputLengths, ref_ids, rank, epoch);
-	  deleteTranslations(oneBests);
-	}
+        cerr << "Rank " << rank << ", epoch " << epoch << ", batch is empty." << endl;
+      } else {
+        vector<vector<float> > losses(actualBatchSize);
+        if (model_hope_fear) {
+          // Set loss for each sentence as BLEU(oracle) - BLEU(hypothesis)
+          for (size_t batchPosition = 0; batchPosition < actualBatchSize; ++batchPosition) {
+            for (size_t j = 0; j < bleuScores[batchPosition].size(); ++j) {
+              losses[batchPosition].push_back(oracleBleuScores[batchPosition] - bleuScores[batchPosition][j]);
+            }
+          }
+        }
+
+        // set weight for bleu feature to 0 before optimizing
+        vector<FeatureFunction*>::const_iterator iter;
+        const vector<FeatureFunction*> &featureFunctions2 = FeatureFunction::GetFeatureFunctions();
+        for (iter = featureFunctions2.begin(); iter != featureFunctions2.end(); ++iter) {
+          if ((*iter)->GetScoreProducerDescription() == "BleuScoreFeature") {
+            mosesWeights.Assign(*iter, 0);
+            break;
+          }
+        }
+
+        // scale LM feature (to avoid rapid changes)
+        if (scale_lm) {
+          cerr << "scale lm" << endl;
+          const std::vector<const StatefulFeatureFunction*> &statefulFFs = StatefulFeatureFunction::GetStatefulFeatureFunctions();
+          for (size_t i = 0; i < statefulFFs.size(); ++i) {
+            const StatefulFeatureFunction *ff = statefulFFs[i];
+            const LanguageModel *lm = dynamic_cast<const LanguageModel*>(ff);
+
+            if (lm) {
+              // scale down score
+              if (model_hope_fear) {
+                scaleFeatureScore(lm, scale_lm_factor, featureValues, rank, epoch);
+              } else {
+                scaleFeatureScore(lm, scale_lm_factor, featureValuesHope, rank, epoch);
+                scaleFeatureScore(lm, scale_lm_factor, featureValuesFear, rank, epoch);
+              }
+            }
+          }
+        }
+
+        // scale WP
+        if (scale_wp) {
+          // scale up weight
+          WordPenaltyProducer *wp = StaticData::InstanceNonConst().GetWordPenaltyProducer();
+
+          // scale down score
+          if (model_hope_fear) {
+            scaleFeatureScore(wp, scale_wp_factor, featureValues, rank, epoch);
+          } else {
+            scaleFeatureScore(wp, scale_wp_factor, featureValuesHope, rank, epoch);
+            scaleFeatureScore(wp, scale_wp_factor, featureValuesFear, rank, epoch);
+          }
+        }
+
+        // print out the feature values
+        if (print_feature_values) {
+          cerr << "\nRank " << rank << ", epoch " << epoch << ", feature values: " << endl;
+          if (model_hope_fear) printFeatureValues(featureValues);
+          else {
+            cerr << "hope: " << endl;
+            printFeatureValues(featureValuesHope);
+            cerr << "fear: " << endl;
+            printFeatureValues(featureValuesFear);
+          }
+        }
+
+        // apply learning rates to feature vectors before optimization
+        if (feature_confidence) {
+          cerr << "Rank " << rank << ", epoch " << epoch << ", apply feature learning rates with decays " << decay_core << "/" << decay_sparse << ": " << featureLearningRates << endl;
+          if (model_hope_fear) {
+            applyPerFeatureLearningRates(featureValues, featureLearningRates, sparse_r0);
+          } else {
+            applyPerFeatureLearningRates(featureValuesHope, featureLearningRates, sparse_r0);
+            applyPerFeatureLearningRates(featureValuesFear, featureLearningRates, sparse_r0);
+          }
+        } else {
+          // apply fixed learning rates
+          cerr << "Rank " << rank << ", epoch " << epoch << ", apply fixed learning rates, core: " << core_r0 << ", sparse: " << sparse_r0 << endl;
+          if (core_r0 != 1.0 || sparse_r0 != 1.0) {
+            if (model_hope_fear) {
+              applyLearningRates(featureValues, core_r0, sparse_r0);
+            } else {
+              applyLearningRates(featureValuesHope, core_r0, sparse_r0);
+              applyLearningRates(featureValuesFear, core_r0, sparse_r0);
+            }
+          }
+        }
+
+        // Run optimiser on batch:
+        VERBOSE(1, "\nRank " << rank << ", epoch " << epoch << ", run optimiser:" << endl);
+        size_t update_status = 1;
+        ScoreComponentCollection weightUpdate;
+        if (perceptron_update) {
+          vector<vector<float> > dummy1;
+          update_status = optimiser->updateWeightsHopeFear( weightUpdate, featureValuesHope,
+                          featureValuesFear, dummy1, dummy1, dummy1, dummy1, learning_rate, rank, epoch);
+        } else if (hope_fear) {
+          if (bleuScoresHope[0][0] >= min_oracle_bleu) {
+            if (hope_n == 1 && fear_n ==1 && batchSize == 1 && !hildreth) {
+              update_status = ((MiraOptimiser*) optimiser)->updateWeightsAnalytically(weightUpdate,
+                              featureValuesHope[0][0], featureValuesFear[0][0], bleuScoresHope[0][0],
+                              bleuScoresFear[0][0], modelScoresHope[0][0], modelScoresFear[0][0], learning_rate, rank, epoch);
+            } else
+              update_status = optimiser->updateWeightsHopeFear(weightUpdate, featureValuesHope,
+                              featureValuesFear, bleuScoresHope, bleuScoresFear, modelScoresHope,
+                              modelScoresFear, learning_rate, rank, epoch);
+          } else
+            update_status = 1;
+        } else if (kbest) {
+          if (selective)
+            update_status = ((MiraOptimiser*)optimiser)->updateWeightsHopeFearSelective(
+                              weightUpdate, featureValuesHope, featureValuesFear, bleuScoresHope, bleuScoresFear,
+                              modelScoresHope, modelScoresFear, learning_rate, rank, epoch);
+          else if (summed)
+            update_status = ((MiraOptimiser*)optimiser)->updateWeightsHopeFearSummed(
+                              weightUpdate, featureValuesHope, featureValuesFear, bleuScoresHope, bleuScoresFear,
+                              modelScoresHope, modelScoresFear, learning_rate, rank, epoch, rescaleSlack, makePairs);
+          else {
+            if (batchSize == 1 && featureValuesHope[0].size() == 1 && !hildreth) {
+              cerr << "Rank " << rank << ", epoch " << epoch << ", model score hope: " << modelScoresHope[0][0] << endl;
+              cerr << "Rank " << rank << ", epoch " << epoch << ", model score fear: " << modelScoresFear[0][0] << endl;
+              update_status = ((MiraOptimiser*) optimiser)->updateWeightsAnalytically(
+                                weightUpdate, featureValuesHope[0][0], featureValuesFear[0][0],
+                                bleuScoresHope[0][0], bleuScoresFear[0][0], modelScoresHope[0][0],
+                                modelScoresFear[0][0], learning_rate, rank, epoch);
+            } else {
+              cerr << "Rank " << rank << ", epoch " << epoch << ", model score hope: " << modelScoresHope[0][0] << endl;
+              cerr << "Rank " << rank << ", epoch " << epoch << ", model score fear: " << modelScoresFear[0][0] << endl;
+              update_status = optimiser->updateWeightsHopeFear(weightUpdate, featureValuesHope,
+                              featureValuesFear, bleuScoresHope, bleuScoresFear, modelScoresHope,
+                              modelScoresFear, learning_rate, rank, epoch);
+            }
+          }
+        } else {
+          // model_hope_fear
+          update_status = ((MiraOptimiser*) optimiser)->updateWeights(weightUpdate,
+                          featureValues, losses, bleuScores, modelScores, oracleFeatureValues,
+                          oracleBleuScores, oracleModelScores, learning_rate, rank, epoch);
+        }
+
+        // sumStillViolatedConstraints += update_status;
+
+        if (update_status == 0) {	 // if weights were updated
+          // apply weight update
+          if (debug)
+            cerr << "Rank " << rank << ", epoch " << epoch << ", update: " << weightUpdate << endl;
+
+          if (feature_confidence) {
+            // update confidence counts based on weight update
+            confidenceCounts.UpdateConfidenceCounts(weightUpdate, signed_counts);
+
+            // update feature learning rates
+            featureLearningRates.UpdateLearningRates(decay_core, decay_sparse, confidenceCounts, core_r0, sparse_r0);
+          }
+
+          // apply weight update to Moses weights
+          mosesWeights.PlusEquals(weightUpdate);
+
+          if (normaliseWeights)
+            mosesWeights.L1Normalise();
+
+          cumulativeWeights.PlusEquals(mosesWeights);
+          if (sparseAverage) {
+            ScoreComponentCollection binary;
+            binary.SetToBinaryOf(mosesWeights);
+            cumulativeWeightsBinary.PlusEquals(binary);
+          }
+
+          ++numberOfUpdates;
+          ++numberOfUpdatesThisEpoch;
+          if (averageWeights) {
+            ScoreComponentCollection averageWeights(cumulativeWeights);
+            if (accumulateWeights) {
+              averageWeights.DivideEquals(numberOfUpdates);
+            } else {
+              averageWeights.DivideEquals(numberOfUpdatesThisEpoch);
+            }
+
+            mosesWeights = averageWeights;
+          }
+
+          // set new Moses weights
+          decoder->setWeights(mosesWeights);
+          //cerr << "Rank " << rank << ", epoch " << epoch << ", new weights: " << mosesWeights << endl;
+        }
+
+        // update history (for approximate document Bleu)
+        if (historyBleu || simpleHistoryBleu) {
+          for (size_t i = 0; i < oneBests.size(); ++i)
+            cerr << "Rank " << rank << ", epoch " << epoch << ", update history with 1best length: " << oneBests[i].size() << " ";
+          decoder->updateHistory(oneBests, inputLengths, ref_ids, rank, epoch);
+          deleteTranslations(oneBests);
+        }
       } // END TRANSLATE AND UPDATE BATCH
-      
+
       // size of all shards except for the last one
       size_t generalShardSize;
       if (trainWithMultipleFolds)
-	generalShardSize = order.size()/coresPerFold;
+        generalShardSize = order.size()/coresPerFold;
       else
-	generalShardSize = order.size()/size;
-      
+        generalShardSize = order.size()/size;
+
       size_t mixing_base = mixingFrequency == 0 ? 0 : generalShardSize / mixingFrequency;
       size_t dumping_base = weightDumpFrequency == 0 ? 0 : generalShardSize / weightDumpFrequency;
       bool mix = evaluateModulo(shardPosition, mixing_base, actualBatchSize);
-      
+
       // mix weights?
       if (mix) {
 #ifdef MPI_ENABLE
-	cerr << "Rank " << rank << ", epoch " << epoch << ", mixing weights.. " << endl;
-	// collect all weights in mixedWeights and divide by number of processes
-	mpi::reduce(world, mosesWeights, mixedWeights, SCCPlus(), 0);
-	
-	// mix confidence counts
-	//mpi::reduce(world, confidenceCounts, mixedConfidenceCounts, SCCPlus(), 0);
-	ScoreComponentCollection totalBinary;
-	if (sparseAverage) {
-	  ScoreComponentCollection binary;
-	  binary.SetToBinaryOf(mosesWeights);
-	  mpi::reduce(world, binary, totalBinary, SCCPlus(), 0);
-	}
-	if (rank == 0) {
-	  // divide by number of processes
-	  if (sparseNoAverage)
-	    mixedWeights.CoreDivideEquals(size); // average only core weights
-	  else if (sparseAverage)
-	    mixedWeights.DivideEquals(totalBinary);
-	  else
-	    mixedWeights.DivideEquals(size);
-	  
-	  // divide confidence counts
-	  //mixedConfidenceCounts.DivideEquals(size);
-	  
-	  // normalise weights after averaging
-	  if (normaliseWeights) {
-	    mixedWeights.L1Normalise();
-	  }
-	  
-	  ++weightMixingThisEpoch;
-
-	  if (pruneZeroWeights) {
-	    size_t pruned = mixedWeights.PruneZeroWeightFeatures();
-	    cerr << "Rank " << rank << ", epoch " << epoch << ", "
-		 << pruned << " zero-weighted features pruned from mixedWeights." << endl;
-	    
-	    pruned = cumulativeWeights.PruneZeroWeightFeatures();
-	    cerr << "Rank " << rank << ", epoch " << epoch << ", "
-		 << pruned << " zero-weighted features pruned from cumulativeWeights." << endl;
-	  }
-
-	  if (featureCutoff != -1 && weightMixingThisEpoch == mixingFrequency) {
-	    size_t pruned = mixedWeights.PruneSparseFeatures(featureCutoff);
-	    cerr << "Rank " << rank << ", epoch " << epoch << ", "
-		 << pruned << " features pruned from mixedWeights." << endl;
-	    
-	    pruned = cumulativeWeights.PruneSparseFeatures(featureCutoff);
-	    cerr << "Rank " << rank << ", epoch " << epoch << ", "
-		 << pruned << " features pruned from cumulativeWeights." << endl;
-	  }
-	  
-	  if (weightMixingThisEpoch == mixingFrequency || reg_on_every_mix) {
-	    if (l1_regularize) {
-	      size_t pruned;
-	      if (l1_reg_sparse)
-		pruned = mixedWeights.SparseL1Regularize(l1_lambda);
-	      else
-		pruned = mixedWeights.L1Regularize(l1_lambda);
-	      cerr << "Rank " << rank << ", epoch " << epoch << ", "
-		   << "l1-reg. on mixedWeights with lambda=" << l1_lambda << ", pruned: " << pruned << endl;
-	    }
-	    if (l2_regularize) {
-	      if (l2_reg_sparse)
-		mixedWeights.SparseL2Regularize(l2_lambda);
-	      else
-		mixedWeights.L2Regularize(l2_lambda);
-	      cerr << "Rank " << rank << ", epoch " << epoch << ", "
-		   << "l2-reg. on mixedWeights with lambda=" << l2_lambda << endl;
-	    }
-	  }
-	}
-	
-	// broadcast average weights from process 0
-	mpi::broadcast(world, mixedWeights, 0);
-	decoder->setWeights(mixedWeights);
-	mosesWeights = mixedWeights;
-	
-	// broadcast summed confidence counts
-	//mpi::broadcast(world, mixedConfidenceCounts, 0);
-	//confidenceCounts = mixedConfidenceCounts;
+        cerr << "Rank " << rank << ", epoch " << epoch << ", mixing weights.. " << endl;
+        // collect all weights in mixedWeights and divide by number of processes
+        mpi::reduce(world, mosesWeights, mixedWeights, SCCPlus(), 0);
+
+        // mix confidence counts
+        //mpi::reduce(world, confidenceCounts, mixedConfidenceCounts, SCCPlus(), 0);
+        ScoreComponentCollection totalBinary;
+        if (sparseAverage) {
+          ScoreComponentCollection binary;
+          binary.SetToBinaryOf(mosesWeights);
+          mpi::reduce(world, binary, totalBinary, SCCPlus(), 0);
+        }
+        if (rank == 0) {
+          // divide by number of processes
+          if (sparseNoAverage)
+            mixedWeights.CoreDivideEquals(size); // average only core weights
+          else if (sparseAverage)
+            mixedWeights.DivideEquals(totalBinary);
+          else
+            mixedWeights.DivideEquals(size);
+
+          // divide confidence counts
+          //mixedConfidenceCounts.DivideEquals(size);
+
+          // normalise weights after averaging
+          if (normaliseWeights) {
+            mixedWeights.L1Normalise();
+          }
+
+          ++weightMixingThisEpoch;
+
+          if (pruneZeroWeights) {
+            size_t pruned = mixedWeights.PruneZeroWeightFeatures();
+            cerr << "Rank " << rank << ", epoch " << epoch << ", "
+                 << pruned << " zero-weighted features pruned from mixedWeights." << endl;
+
+            pruned = cumulativeWeights.PruneZeroWeightFeatures();
+            cerr << "Rank " << rank << ", epoch " << epoch << ", "
+                 << pruned << " zero-weighted features pruned from cumulativeWeights." << endl;
+          }
+
+          if (featureCutoff != -1 && weightMixingThisEpoch == mixingFrequency) {
+            size_t pruned = mixedWeights.PruneSparseFeatures(featureCutoff);
+            cerr << "Rank " << rank << ", epoch " << epoch << ", "
+                 << pruned << " features pruned from mixedWeights." << endl;
+
+            pruned = cumulativeWeights.PruneSparseFeatures(featureCutoff);
+            cerr << "Rank " << rank << ", epoch " << epoch << ", "
+                 << pruned << " features pruned from cumulativeWeights." << endl;
+          }
+
+          if (weightMixingThisEpoch == mixingFrequency || reg_on_every_mix) {
+            if (l1_regularize) {
+              size_t pruned;
+              if (l1_reg_sparse)
+                pruned = mixedWeights.SparseL1Regularize(l1_lambda);
+              else
+                pruned = mixedWeights.L1Regularize(l1_lambda);
+              cerr << "Rank " << rank << ", epoch " << epoch << ", "
+                   << "l1-reg. on mixedWeights with lambda=" << l1_lambda << ", pruned: " << pruned << endl;
+            }
+            if (l2_regularize) {
+              if (l2_reg_sparse)
+                mixedWeights.SparseL2Regularize(l2_lambda);
+              else
+                mixedWeights.L2Regularize(l2_lambda);
+              cerr << "Rank " << rank << ", epoch " << epoch << ", "
+                   << "l2-reg. on mixedWeights with lambda=" << l2_lambda << endl;
+            }
+          }
+        }
+
+        // broadcast average weights from process 0
+        mpi::broadcast(world, mixedWeights, 0);
+        decoder->setWeights(mixedWeights);
+        mosesWeights = mixedWeights;
+
+        // broadcast summed confidence counts
+        //mpi::broadcast(world, mixedConfidenceCounts, 0);
+        //confidenceCounts = mixedConfidenceCounts;
 #endif
 #ifndef MPI_ENABLE
-	//cerr << "\nRank " << rank << ", no mixing, weights: " << mosesWeights << endl;
-	mixedWeights = mosesWeights;
+        //cerr << "\nRank " << rank << ", no mixing, weights: " << mosesWeights << endl;
+        mixedWeights = mosesWeights;
 #endif
       } // end mixing
-      
+
       // Dump weights?
       if (trainWithMultipleFolds || weightEpochDump == weightDumpFrequency) {
-	// dump mixed weights at end of every epoch to enable continuing a crashed experiment
-	// (for jackknife every time the weights are mixed)
-	ostringstream filename;
-	if (epoch < 10)
-	  filename << weightDumpStem << "_mixed_0" << epoch;
-	else
-	  filename << weightDumpStem << "_mixed_" << epoch;
-	
-	if (weightDumpFrequency > 1)
-	  filename << "_" << weightEpochDump;
-	
-	mixedWeights.Save(filename.str());
-	cerr << "Dumping mixed weights during epoch " << epoch << " to " << filename.str() << endl << endl;
+        // dump mixed weights at end of every epoch to enable continuing a crashed experiment
+        // (for jackknife every time the weights are mixed)
+        ostringstream filename;
+        if (epoch < 10)
+          filename << weightDumpStem << "_mixed_0" << epoch;
+        else
+          filename << weightDumpStem << "_mixed_" << epoch;
+
+        if (weightDumpFrequency > 1)
+          filename << "_" << weightEpochDump;
+
+        mixedWeights.Save(filename.str());
+        cerr << "Dumping mixed weights during epoch " << epoch << " to " << filename.str() << endl << endl;
       }
       if (dumpMixedWeights) {
-	if (mix && rank == 0 && !weightDumpStem.empty()) {
-	  // dump mixed weights instead of average weights
-	  ostringstream filename;
-	  if (epoch < 10)
-	    filename << weightDumpStem << "_0" << epoch;
-	  else
-	    filename << weightDumpStem << "_" << epoch;
-	  
-	  if (weightDumpFrequency > 1)
-	    filename << "_" << weightEpochDump;
-	  
-	  cerr << "Dumping mixed weights during epoch " << epoch << " to " << filename.str() << endl << endl;
-	  mixedWeights.Save(filename.str());
-	  ++weightEpochDump;
-	}
-      }
-      else {
-	if (evaluateModulo(shardPosition, dumping_base, actualBatchSize)) {
-	  cerr << "Rank " << rank << ", epoch " << epoch << ", dump weights.. (pos: " << shardPosition << ", base: " << dumping_base << ")" << endl;
-	  ScoreComponentCollection tmpAverageWeights(cumulativeWeights);
-	  bool proceed = false;
-	  if (accumulateWeights) {
-	    if (numberOfUpdates > 0) {
-	      tmpAverageWeights.DivideEquals(numberOfUpdates);
-	      proceed = true;
-	    }
-	  } else {
-	    if (numberOfUpdatesThisEpoch > 0) {
-	      if (sparseNoAverage) // average only core weights
-		tmpAverageWeights.CoreDivideEquals(numberOfUpdatesThisEpoch);
-	      else if (sparseAverage)
-		tmpAverageWeights.DivideEquals(cumulativeWeightsBinary);
-	      else
-		tmpAverageWeights.DivideEquals(numberOfUpdatesThisEpoch);
-	      proceed = true;
-	    }
-	  }
-	  
-	  if (proceed) {
+        if (mix && rank == 0 && !weightDumpStem.empty()) {
+          // dump mixed weights instead of average weights
+          ostringstream filename;
+          if (epoch < 10)
+            filename << weightDumpStem << "_0" << epoch;
+          else
+            filename << weightDumpStem << "_" << epoch;
+
+          if (weightDumpFrequency > 1)
+            filename << "_" << weightEpochDump;
+
+          cerr << "Dumping mixed weights during epoch " << epoch << " to " << filename.str() << endl << endl;
+          mixedWeights.Save(filename.str());
+          ++weightEpochDump;
+        }
+      } else {
+        if (evaluateModulo(shardPosition, dumping_base, actualBatchSize)) {
+          cerr << "Rank " << rank << ", epoch " << epoch << ", dump weights.. (pos: " << shardPosition << ", base: " << dumping_base << ")" << endl;
+          ScoreComponentCollection tmpAverageWeights(cumulativeWeights);
+          bool proceed = false;
+          if (accumulateWeights) {
+            if (numberOfUpdates > 0) {
+              tmpAverageWeights.DivideEquals(numberOfUpdates);
+              proceed = true;
+            }
+          } else {
+            if (numberOfUpdatesThisEpoch > 0) {
+              if (sparseNoAverage) // average only core weights
+                tmpAverageWeights.CoreDivideEquals(numberOfUpdatesThisEpoch);
+              else if (sparseAverage)
+                tmpAverageWeights.DivideEquals(cumulativeWeightsBinary);
+              else
+                tmpAverageWeights.DivideEquals(numberOfUpdatesThisEpoch);
+              proceed = true;
+            }
+          }
+
+          if (proceed) {
 #ifdef MPI_ENABLE
-	    // average across processes
-	    mpi::reduce(world, tmpAverageWeights, mixedAverageWeights, SCCPlus(), 0);
-	    ScoreComponentCollection totalBinary;
-	    if (sparseAverage) {
-	      ScoreComponentCollection binary;
-	      binary.SetToBinaryOf(mosesWeights);
-	      mpi::reduce(world, binary, totalBinary, SCCPlus(), 0);
-	    }
+            // average across processes
+            mpi::reduce(world, tmpAverageWeights, mixedAverageWeights, SCCPlus(), 0);
+            ScoreComponentCollection totalBinary;
+            if (sparseAverage) {
+              ScoreComponentCollection binary;
+              binary.SetToBinaryOf(mosesWeights);
+              mpi::reduce(world, binary, totalBinary, SCCPlus(), 0);
+            }
 #endif
 #ifndef MPI_ENABLE
-	    mixedAverageWeights = tmpAverageWeights;
-      //FIXME: What do to for non-mpi version
-	    ScoreComponentCollection totalBinary;
+            mixedAverageWeights = tmpAverageWeights;
+            //FIXME: What do to for non-mpi version
+            ScoreComponentCollection totalBinary;
 #endif
-	    if (rank == 0 && !weightDumpStem.empty()) {
-	      // divide by number of processes
-	      if (sparseNoAverage)
-		mixedAverageWeights.CoreDivideEquals(size); // average only core weights
-	      else if (sparseAverage)
-		mixedAverageWeights.DivideEquals(totalBinary);
-	      else
-		mixedAverageWeights.DivideEquals(size);
-	      
-	      // normalise weights after averaging
-	      if (normaliseWeights) {
-		mixedAverageWeights.L1Normalise();
-	      }
-	      
-	      // dump final average weights
-	      ostringstream filename;
-	      if (epoch < 10) {
-		filename << weightDumpStem << "_0" << epoch;
-	      } else {
-		filename << weightDumpStem << "_" << epoch;
-	      }
-	      
-	      if (weightDumpFrequency > 1) {
-		filename << "_" << weightEpochDump;
-	      }
-	      
-	      /*if (accumulateWeights) {
-		cerr << "\nMixed average weights (cumulative) during epoch "	<< epoch << ": " << mixedAverageWeights << endl;
-		} else {
-		cerr << "\nMixed average weights during epoch " << epoch << ": " << mixedAverageWeights << endl;
-		}*/
-	      
-	      cerr << "Dumping mixed average weights during epoch " << epoch << " to " << filename.str() << endl << endl;
-	      mixedAverageWeights.Save(filename.str());
-	      ++weightEpochDump;
-	      
-	      if (weightEpochDump == weightDumpFrequency) {
-		if (l1_regularize) {
-		  size_t pruned = mixedAverageWeights.SparseL1Regularize(l1_lambda);
-		  cerr << "Rank " << rank << ", epoch " << epoch << ", "
-		       << "l1-reg. on mixedAverageWeights with lambda=" << l1_lambda << ", pruned: " << pruned << endl;
-
-		}
-		if (l2_regularize) {
-		  mixedAverageWeights.SparseL2Regularize(l2_lambda);
-		  cerr << "Rank " << rank << ", epoch " << epoch << ", "
-		       << "l2-reg. on mixedAverageWeights with lambda=" << l2_lambda << endl;
-		}
-		
-		if (l1_regularize || l2_regularize) {
-		  filename << "_reg";
-		  cerr << "Dumping regularized mixed average weights during epoch " << epoch << " to " << filename.str() << endl << endl;
-		  mixedAverageWeights.Save(filename.str());
-		}
-	      }
-	      
-	      if (weightEpochDump == weightDumpFrequency && printFeatureCounts) {
-		// print out all features with counts
-		stringstream s1, s2;
-		s1 << "sparse_feature_hope_counts" << "_" << epoch;
-		s2 << "sparse_feature_fear_counts" << "_" << epoch;
-		ofstream sparseFeatureCountsHope(s1.str().c_str());
-		ofstream sparseFeatureCountsFear(s2.str().c_str());
-		
-		mixedAverageWeights.PrintSparseHopeFeatureCounts(sparseFeatureCountsHope);
-		mixedAverageWeights.PrintSparseFearFeatureCounts(sparseFeatureCountsFear);
-		sparseFeatureCountsHope.close();
-		sparseFeatureCountsFear.close();
-	      }
-	    }
-	  }
-	}// end dumping
+            if (rank == 0 && !weightDumpStem.empty()) {
+              // divide by number of processes
+              if (sparseNoAverage)
+                mixedAverageWeights.CoreDivideEquals(size); // average only core weights
+              else if (sparseAverage)
+                mixedAverageWeights.DivideEquals(totalBinary);
+              else
+                mixedAverageWeights.DivideEquals(size);
+
+              // normalise weights after averaging
+              if (normaliseWeights) {
+                mixedAverageWeights.L1Normalise();
+              }
+
+              // dump final average weights
+              ostringstream filename;
+              if (epoch < 10) {
+                filename << weightDumpStem << "_0" << epoch;
+              } else {
+                filename << weightDumpStem << "_" << epoch;
+              }
+
+              if (weightDumpFrequency > 1) {
+                filename << "_" << weightEpochDump;
+              }
+
+              /*if (accumulateWeights) {
+              cerr << "\nMixed average weights (cumulative) during epoch "	<< epoch << ": " << mixedAverageWeights << endl;
+              } else {
+              cerr << "\nMixed average weights during epoch " << epoch << ": " << mixedAverageWeights << endl;
+              }*/
+
+              cerr << "Dumping mixed average weights during epoch " << epoch << " to " << filename.str() << endl << endl;
+              mixedAverageWeights.Save(filename.str());
+              ++weightEpochDump;
+
+              if (weightEpochDump == weightDumpFrequency) {
+                if (l1_regularize) {
+                  size_t pruned = mixedAverageWeights.SparseL1Regularize(l1_lambda);
+                  cerr << "Rank " << rank << ", epoch " << epoch << ", "
+                       << "l1-reg. on mixedAverageWeights with lambda=" << l1_lambda << ", pruned: " << pruned << endl;
+
+                }
+                if (l2_regularize) {
+                  mixedAverageWeights.SparseL2Regularize(l2_lambda);
+                  cerr << "Rank " << rank << ", epoch " << epoch << ", "
+                       << "l2-reg. on mixedAverageWeights with lambda=" << l2_lambda << endl;
+                }
+
+                if (l1_regularize || l2_regularize) {
+                  filename << "_reg";
+                  cerr << "Dumping regularized mixed average weights during epoch " << epoch << " to " << filename.str() << endl << endl;
+                  mixedAverageWeights.Save(filename.str());
+                }
+              }
+
+              if (weightEpochDump == weightDumpFrequency && printFeatureCounts) {
+                // print out all features with counts
+                stringstream s1, s2;
+                s1 << "sparse_feature_hope_counts" << "_" << epoch;
+                s2 << "sparse_feature_fear_counts" << "_" << epoch;
+                ofstream sparseFeatureCountsHope(s1.str().c_str());
+                ofstream sparseFeatureCountsFear(s2.str().c_str());
+
+                mixedAverageWeights.PrintSparseHopeFeatureCounts(sparseFeatureCountsHope);
+                mixedAverageWeights.PrintSparseFearFeatureCounts(sparseFeatureCountsFear);
+                sparseFeatureCountsHope.close();
+                sparseFeatureCountsFear.close();
+              }
+            }
+          }
+        }// end dumping
       } // end if dump
     } // end of shard loop, end of this epoch
     cerr << "Rank " << rank << ", epoch " << epoch << ", end of epoch.." << endl;
-    
+
     if (historyBleu || simpleHistoryBleu) {
       cerr << "Bleu feature history after epoch " <<  epoch << endl;
       decoder->printBleuFeatureHistory(cerr);
     }
     //		cerr << "Rank " << rank << ", epoch " << epoch << ", sum of violated constraints: " << sumStillViolatedConstraints << endl;
-    
+
     // Check whether there were any weight updates during this epoch
     size_t sumUpdates;
     size_t *sendbuf_uint, *recvbuf_uint;
@@ -1643,63 +1615,62 @@ int main(int argc, char** argv) {
       mpi::broadcast(world, stop, 0);
 #endif
     }
-    
+
     if (!stop) {
       // Test if weights have converged
       if (weightConvergence) {
-	bool reached = true;
-	if (rank == 0 && (epoch >= 2)) {
-	  ScoreComponentCollection firstDiff, secondDiff;
-	  if (dumpMixedWeights) {
-	    firstDiff = mixedWeights;
-	    firstDiff.MinusEquals(mixedWeightsPrevious);
-	    secondDiff = mixedWeights;
-	    secondDiff.MinusEquals(mixedWeightsBeforePrevious);
-	  }
-	  else {
-	    firstDiff = mixedAverageWeights;
-	    firstDiff.MinusEquals(mixedAverageWeightsPrevious);
-	    secondDiff = mixedAverageWeights;
-	    secondDiff.MinusEquals(mixedAverageWeightsBeforePrevious);
-	  }
-	  VERBOSE(1, "Average weight changes since previous epoch: " << firstDiff << " (max: " << firstDiff.GetLInfNorm() << ")" << endl);
-	  VERBOSE(1, "Average weight changes since before previous epoch: " << secondDiff << " (max: " << secondDiff.GetLInfNorm() << ")" << endl << endl);
-	  
-	  // check whether stopping criterion has been reached
-	  // (both difference vectors must have all weight changes smaller than min_weight_change)
-	  if (firstDiff.GetLInfNorm() >= min_weight_change)
-	    reached = false;
-	  if (secondDiff.GetLInfNorm() >= min_weight_change)
-	    reached = false;
-	  if (reached) {
-	    // stop MIRA
-	    stop = true;
-	    cerr << "\nWeights have converged after epoch " << epoch << ".. stopping MIRA." << endl;
-	    ScoreComponentCollection dummy;
-	    ostringstream endfilename;
-	    endfilename << "stopping";
-	    dummy.Save(endfilename.str());
-	  }
-	}
-	
-	mixedWeightsBeforePrevious = mixedWeightsPrevious;
-	mixedWeightsPrevious = mixedWeights;
-	mixedAverageWeightsBeforePrevious = mixedAverageWeightsPrevious;
-	mixedAverageWeightsPrevious = mixedAverageWeights;
+        bool reached = true;
+        if (rank == 0 && (epoch >= 2)) {
+          ScoreComponentCollection firstDiff, secondDiff;
+          if (dumpMixedWeights) {
+            firstDiff = mixedWeights;
+            firstDiff.MinusEquals(mixedWeightsPrevious);
+            secondDiff = mixedWeights;
+            secondDiff.MinusEquals(mixedWeightsBeforePrevious);
+          } else {
+            firstDiff = mixedAverageWeights;
+            firstDiff.MinusEquals(mixedAverageWeightsPrevious);
+            secondDiff = mixedAverageWeights;
+            secondDiff.MinusEquals(mixedAverageWeightsBeforePrevious);
+          }
+          VERBOSE(1, "Average weight changes since previous epoch: " << firstDiff << " (max: " << firstDiff.GetLInfNorm() << ")" << endl);
+          VERBOSE(1, "Average weight changes since before previous epoch: " << secondDiff << " (max: " << secondDiff.GetLInfNorm() << ")" << endl << endl);
+
+          // check whether stopping criterion has been reached
+          // (both difference vectors must have all weight changes smaller than min_weight_change)
+          if (firstDiff.GetLInfNorm() >= min_weight_change)
+            reached = false;
+          if (secondDiff.GetLInfNorm() >= min_weight_change)
+            reached = false;
+          if (reached) {
+            // stop MIRA
+            stop = true;
+            cerr << "\nWeights have converged after epoch " << epoch << ".. stopping MIRA." << endl;
+            ScoreComponentCollection dummy;
+            ostringstream endfilename;
+            endfilename << "stopping";
+            dummy.Save(endfilename.str());
+          }
+        }
+
+        mixedWeightsBeforePrevious = mixedWeightsPrevious;
+        mixedWeightsPrevious = mixedWeights;
+        mixedAverageWeightsBeforePrevious = mixedAverageWeightsPrevious;
+        mixedAverageWeightsPrevious = mixedAverageWeights;
 #ifdef MPI_ENABLE
-	mpi::broadcast(world, stop, 0);
+        mpi::broadcast(world, stop, 0);
 #endif
       } //end if (weightConvergence)
     }
   } // end of epoch loop
-  
+
 #ifdef MPI_ENABLE
   MPI_Finalize();
 #endif
-  
+
   time(&now);
   cerr << "Rank " << rank << ", " << ctime(&now);
-  
+
   if (rank == 0) {
     ScoreComponentCollection dummy;
     ostringstream endfilename;
@@ -1711,7 +1682,8 @@ int main(int argc, char** argv) {
   exit(0);
 }
 
-bool loadSentences(const string& filename, vector<string>& sentences) {
+bool loadSentences(const string& filename, vector<string>& sentences)
+{
   ifstream in(filename.c_str());
   if (!in)
     return false;
@@ -1721,27 +1693,28 @@ bool loadSentences(const string& filename, vector<string>& sentences) {
   return true;
 }
 
-bool evaluateModulo(size_t shard_position, size_t mix_or_dump_base, size_t actual_batch_size) {
+bool evaluateModulo(size_t shard_position, size_t mix_or_dump_base, size_t actual_batch_size)
+{
   if (mix_or_dump_base == 0) return 0;
   if (actual_batch_size > 1) {
     bool mix_or_dump = false;
     size_t numberSubtracts = actual_batch_size;
     do {
       if (shard_position % mix_or_dump_base == 0) {
-	mix_or_dump = true;
-	break;
+        mix_or_dump = true;
+        break;
       }
       --shard_position;
       --numberSubtracts;
     } while (numberSubtracts > 0);
     return mix_or_dump;
-  }
-  else {
+  } else {
     return ((shard_position % mix_or_dump_base) == 0);
   }
 }
 
-void printFeatureValues(vector<vector<ScoreComponentCollection> > &featureValues) {
+void printFeatureValues(vector<vector<ScoreComponentCollection> > &featureValues)
+{
   for (size_t i = 0; i < featureValues.size(); ++i) {
     for (size_t j = 0; j < featureValues[i].size(); ++j) {
       cerr << featureValues[i][j] << endl;
@@ -1750,7 +1723,8 @@ void printFeatureValues(vector<vector<ScoreComponentCollection> > &featureValues
   cerr << endl;
 }
 
-void deleteTranslations(vector<vector<const Word*> > &translations) {
+void deleteTranslations(vector<vector<const Word*> > &translations)
+{
   for (size_t i = 0; i < translations.size(); ++i) {
     for (size_t j = 0; j < translations[i].size(); ++j) {
       delete translations[i][j];
@@ -1758,19 +1732,20 @@ void deleteTranslations(vector<vector<const Word*> > &translations) {
   }
 }
 
-void decodeHopeOrFear(size_t rank, size_t size, size_t decode, string filename, vector<string> &inputSentences, MosesDecoder* decoder, size_t n, float bleuWeight) {
+void decodeHopeOrFear(size_t rank, size_t size, size_t decode, string filename, vector<string> &inputSentences, MosesDecoder* decoder, size_t n, float bleuWeight)
+{
   if (decode == 1)
     cerr << "Rank " << rank << ", decoding dev input set according to hope objective.. " << endl;
   else if (decode == 2)
     cerr << "Rank " << rank << ", decoding dev input set according to fear objective.. " << endl;
   else
     cerr << "Rank " << rank << ", decoding dev input set according to normal objective.. " << endl;
-  
+
   // Create shards according to the number of processes used
   vector<size_t> order;
   for (size_t i = 0; i < inputSentences.size(); ++i)
     order.push_back(i);
-  
+
   vector<size_t> shard;
   float shardSize = (float) (order.size()) / size;
   size_t shardStart = (size_t) (shardSize * rank);
@@ -1783,7 +1758,7 @@ void decodeHopeOrFear(size_t rank, size_t size, size_t decode, string filename,
   VERBOSE(1, "Rank " << rank << ", shard size: " << shardSize << endl);
   shard.resize(shardSize);
   copy(order.begin() + shardStart, order.begin() + shardEnd, shard.begin());
-  
+
   // open files for writing
   stringstream fname;
   fname << filename << ".rank" << rank;
@@ -1802,76 +1777,79 @@ void decodeHopeOrFear(size_t rank, size_t size, size_t decode, string filename,
     msg << "Unable to open " << filename_nbest;
     throw runtime_error(msg.str());
   }
-  
+
   for (size_t i = 0; i < shard.size(); ++i) {
     size_t sid = shard[i];
     string& input = inputSentences[sid];
-    
+
     vector<vector<ScoreComponentCollection> > dummyFeatureValues;
     vector<vector<float> > dummyBleuScores;
     vector<vector<float> > dummyModelScores;
-    
+
     vector<ScoreComponentCollection> newFeatureValues;
     vector<float> newScores;
     dummyFeatureValues.push_back(newFeatureValues);
     dummyBleuScores.push_back(newScores);
     dummyModelScores.push_back(newScores);
-    
+
     float factor = 0.0;
     if (decode == 1) factor = 1.0;
     if (decode == 2) factor = -1.0;
     cerr << "Rank " << rank << ", translating sentence " << sid << endl;
     bool realBleu = false;
     vector< vector<const Word*> > nbestOutput = decoder->getNBest(input, sid, n, factor, bleuWeight, dummyFeatureValues[0],
-								  dummyBleuScores[0], dummyModelScores[0], n, realBleu, true, false, rank, 0, "");
+        dummyBleuScores[0], dummyModelScores[0], n, realBleu, true, false, rank, 0, "");
     cerr << endl;
     decoder->cleanup(StaticData::Instance().GetSearchAlgorithm() == ChartDecoding);
-    
+
     for (size_t i = 0; i < nbestOutput.size(); ++i) {
       vector<const Word*> output = nbestOutput[i];
       stringstream translation;
       for (size_t k = 0; k < output.size(); ++k) {
-	Word* w = const_cast<Word*>(output[k]);
-	translation << w->GetString(0);
-	translation << " ";
+        Word* w = const_cast<Word*>(output[k]);
+        translation << w->GetString(0);
+        translation << " ";
       }
-      
+
       if (i == 0)
-	out << translation.str() << endl;
+        out << translation.str() << endl;
       nbest_out << sid << " ||| " << translation.str() << " ||| " << dummyFeatureValues[0][i] <<
-	" ||| " << dummyModelScores[0][i] << " ||| sBleu=" << dummyBleuScores[0][i] << endl;
+                " ||| " << dummyModelScores[0][i] << " ||| sBleu=" << dummyBleuScores[0][i] << endl;
     }
   }
-  
+
   out.close();
   nbest_out.close();
   cerr << "Closing files " << filename << " and " << filename_nbest.str() << endl;
-  
+
 #ifdef MPI_ENABLE
   MPI_Finalize();
 #endif
-  
+
   time_t now;
   time(&now);
   cerr << "Rank " << rank << ", " << ctime(&now);
-  
+
   delete decoder;
   exit(0);
 }
 
-void applyLearningRates(vector<vector<ScoreComponentCollection> > &featureValues, float core_r0, float sparse_r0) {
+void applyLearningRates(vector<vector<ScoreComponentCollection> > &featureValues, float core_r0, float sparse_r0)
+{
   for (size_t i=0; i<featureValues.size(); ++i) // each item in batch
     for (size_t j=0; j<featureValues[i].size(); ++j) // each item in nbest
       featureValues[i][j].MultiplyEquals(core_r0, sparse_r0);
 }
 
-void applyPerFeatureLearningRates(vector<vector<ScoreComponentCollection> > &featureValues, ScoreComponentCollection featureLearningRates, float sparse_r0) {
+void applyPerFeatureLearningRates(vector<vector<ScoreComponentCollection> > &featureValues, ScoreComponentCollection featureLearningRates, float sparse_r0)
+{
   for (size_t i=0; i<featureValues.size(); ++i) // each item in batch
     for (size_t j=0; j<featureValues[i].size(); ++j) // each item in nbest
       featureValues[i][j].MultiplyEqualsBackoff(featureLearningRates, sparse_r0);
 }
 
-void scaleFeatureScore(const FeatureFunction *sp, float scaling_factor, vector<vector<ScoreComponentCollection> > &featureValues, size_t rank, size_t epoch) {
+void scaleFeatureScore(const FeatureFunction *sp, float scaling_factor, vector<vector<ScoreComponentCollection> > &featureValues, size_t rank, size_t epoch)
+{
   string name = sp->GetScoreProducerDescription();
 
   // scale down score
@@ -1885,7 +1863,8 @@ void scaleFeatureScore(const FeatureFunction *sp, float scaling_factor, vector<v
   }
 }
 
-void scaleFeatureScores(const FeatureFunction *sp, float scaling_factor, vector<vector<ScoreComponentCollection> > &featureValues, size_t rank, size_t epoch) {
+void scaleFeatureScores(const FeatureFunction *sp, float scaling_factor, vector<vector<ScoreComponentCollection> > &featureValues, size_t rank, size_t epoch)
+{
   string name = sp->GetScoreProducerDescription();
 
   // scale down score
@@ -1893,7 +1872,7 @@ void scaleFeatureScores(const FeatureFunction *sp, float scaling_factor, vector<
     for (size_t j=0; j<featureValues[i].size(); ++j) { // each item in nbest
       vector<float> featureScores = featureValues[i][j].GetScoresForProducer(sp);
       for (size_t k=0; k<featureScores.size(); ++k)
-	featureScores[k] *= scaling_factor;
+        featureScores[k] *= scaling_factor;
       featureValues[i][j].Assign(sp, featureScores);
       //cerr << "Rank " << rank << ", epoch " << epoch << ", " << name << " score scaled from " << featureScore << " to " << featureScore/scaling_factor << endl;
     }
diff --git a/mira/Main.h b/mira/Main.h
index 6ba375c2c..8736257f6 100644
--- a/mira/Main.h
+++ b/mira/Main.h
@@ -36,10 +36,10 @@ template <class T> bool from_string(T& t, const std::string& s, std::ios_base& (
 }
 
 struct RandomIndex {
-	ptrdiff_t operator()(ptrdiff_t max) {
-		srand(time(0));  // Initialize random number generator with current time.
-		return static_cast<ptrdiff_t> (rand() % max);
-	}
+  ptrdiff_t operator()(ptrdiff_t max) {
+    srand(time(0));  // Initialize random number generator with current time.
+    return static_cast<ptrdiff_t> (rand() % max);
+  }
 };
 
 //void OutputNBestList(const MosesChart::TrellisPathList &nBestList, const TranslationSystem* system, long translationId);
@@ -50,7 +50,7 @@ void ignoreCoreFeatures(std::vector<std::vector<Moses::ScoreComponentCollection>
 void takeLogs(std::vector<std::vector<Moses::ScoreComponentCollection> > &featureValues, size_t base);
 void deleteTranslations(std::vector<std::vector<const Moses::Word*> > &translations);
 void decodeHopeOrFear(size_t rank, size_t size, size_t decode, std::string decode_filename, std::vector<std::string> &inputSentences, Mira::MosesDecoder* decoder, size_t n, float bleuWeight);
-void applyLearningRates(std::vector<std::vector<Moses::ScoreComponentCollection> > &featureValues, float core_r0, float sparse_r0); 
+void applyLearningRates(std::vector<std::vector<Moses::ScoreComponentCollection> > &featureValues, float core_r0, float sparse_r0);
 void applyPerFeatureLearningRates(std::vector<std::vector<Moses::ScoreComponentCollection> > &featureValues, Moses::ScoreComponentCollection featureLearningRates, float sparse_r0);
 void scaleFeatureScore(const Moses::FeatureFunction *sp, float scaling_factor,  std::vector<std::vector<Moses::ScoreComponentCollection> > &featureValues, size_t rank, size_t epoch);
 void scaleFeatureScores(const Moses::FeatureFunction *sp, float scaling_factor,  std::vector<std::vector<Moses::ScoreComponentCollection> > &featureValues, size_t rank, size_t epoch);
diff --git a/mira/MiraOptimiser.cpp b/mira/MiraOptimiser.cpp
index 4cc7f3fc3..82e9d85fb 100644
--- a/mira/MiraOptimiser.cpp
+++ b/mira/MiraOptimiser.cpp
@@ -5,234 +5,236 @@
 using namespace Moses;
 using namespace std;
 
-namespace Mira {
+namespace Mira
+{
 
 size_t MiraOptimiser::updateWeights(
-		ScoreComponentCollection& weightUpdate,
-    const vector<vector<ScoreComponentCollection> >& featureValues,
-    const vector<vector<float> >& losses,
-    const vector<vector<float> >& bleuScores,
-    const vector<vector<float> >& modelScores,
-    const vector<ScoreComponentCollection>& oracleFeatureValues,
-    const vector<float> oracleBleuScores,
-    const vector<float> oracleModelScores,
-    float learning_rate,
-    size_t rank,
-    size_t epoch) {
-
-	// vector of feature values differences for all created constraints
-	vector<ScoreComponentCollection> featureValueDiffs;
-	vector<float> lossMinusModelScoreDiffs;
-	vector<float> all_losses;
-
-	// most violated constraint in batch
-	ScoreComponentCollection max_batch_featureValueDiff;
-
-	// Make constraints for new hypothesis translations
-	float epsilon = 0.0001;
-	int violatedConstraintsBefore = 0;
-	float oldDistanceFromOptimum = 0;
-	// iterate over input sentences (1 (online) or more (batch))
-	for (size_t i = 0; i < featureValues.size(); ++i) {
-		//size_t sentenceId = sentenceIds[i];
-		// iterate over hypothesis translations for one input sentence
-		for (size_t j = 0; j < featureValues[i].size(); ++j) {
-			ScoreComponentCollection featureValueDiff = oracleFeatureValues[i];
-			featureValueDiff.MinusEquals(featureValues[i][j]);
-
-			//			cerr << "Rank " << rank << ", epoch " << epoch << ", feature value diff: " << featureValueDiff << endl;
-			if (featureValueDiff.GetL1Norm() == 0) {
-				cerr << "Rank " << rank << ", epoch " << epoch << ", features equal --> skip" << endl;
-				continue;
-			}
-
-			float loss = losses[i][j];
-
-		  	// check if constraint is violated
-		    bool violated = false;
+  ScoreComponentCollection& weightUpdate,
+  const vector<vector<ScoreComponentCollection> >& featureValues,
+  const vector<vector<float> >& losses,
+  const vector<vector<float> >& bleuScores,
+  const vector<vector<float> >& modelScores,
+  const vector<ScoreComponentCollection>& oracleFeatureValues,
+  const vector<float> oracleBleuScores,
+  const vector<float> oracleModelScores,
+  float learning_rate,
+  size_t rank,
+  size_t epoch)
+{
+
+  // vector of feature values differences for all created constraints
+  vector<ScoreComponentCollection> featureValueDiffs;
+  vector<float> lossMinusModelScoreDiffs;
+  vector<float> all_losses;
+
+  // most violated constraint in batch
+  ScoreComponentCollection max_batch_featureValueDiff;
+
+  // Make constraints for new hypothesis translations
+  float epsilon = 0.0001;
+  int violatedConstraintsBefore = 0;
+  float oldDistanceFromOptimum = 0;
+  // iterate over input sentences (1 (online) or more (batch))
+  for (size_t i = 0; i < featureValues.size(); ++i) {
+    //size_t sentenceId = sentenceIds[i];
+    // iterate over hypothesis translations for one input sentence
+    for (size_t j = 0; j < featureValues[i].size(); ++j) {
+      ScoreComponentCollection featureValueDiff = oracleFeatureValues[i];
+      featureValueDiff.MinusEquals(featureValues[i][j]);
+
+      //			cerr << "Rank " << rank << ", epoch " << epoch << ", feature value diff: " << featureValueDiff << endl;
+      if (featureValueDiff.GetL1Norm() == 0) {
+        cerr << "Rank " << rank << ", epoch " << epoch << ", features equal --> skip" << endl;
+        continue;
+      }
+
+      float loss = losses[i][j];
+
+      // check if constraint is violated
+      bool violated = false;
 //		    float modelScoreDiff = featureValueDiff.InnerProduct(currWeights);
-		    float modelScoreDiff = oracleModelScores[i] - modelScores[i][j];
-		    float diff = 0;		    
-
-		    if (loss > modelScoreDiff) 
-		    	diff = loss - modelScoreDiff;
-		    cerr << "Rank " << rank << ", epoch " << epoch << ", constraint: " << modelScoreDiff << " >= " << loss << " (current violation: " << diff << ")" << endl;    
-		    if (diff > epsilon) 
-		    	violated = true;
-		    
-		    if (m_normaliseMargin) {
-		      modelScoreDiff = (2*m_sigmoidParam/(1 + exp(-modelScoreDiff))) - m_sigmoidParam;
-		      loss = (2*m_sigmoidParam/(1 + exp(-loss))) - m_sigmoidParam;
-		      diff = 0;
-		      if (loss > modelScoreDiff) {
-			diff = loss - modelScoreDiff;
-		      }
-		      cerr << "Rank " << rank << ", epoch " << epoch << ", normalised constraint: " << modelScoreDiff << " >= " << loss << " (current violation: " << diff << ")" << endl;
-		    }
-		    		    
-		    if (m_scale_margin) {
-		      diff *= oracleBleuScores[i];
-		      cerr << "Rank " << rank << ", epoch " << epoch << ", scaling margin with oracle bleu score "  << oracleBleuScores[i] << endl;
-		    }
-
-		    featureValueDiffs.push_back(featureValueDiff);
-		    lossMinusModelScoreDiffs.push_back(diff);
-		    all_losses.push_back(loss);
-		    if (violated) {      
-		      ++violatedConstraintsBefore;
-		      oldDistanceFromOptimum += diff;
-		    } 
-		}
-	}
-
-	// run optimisation: compute alphas for all given constraints
-	vector<float> alphas;
-	ScoreComponentCollection summedUpdate;
-	if (violatedConstraintsBefore > 0) {
-	  cerr << "Rank " << rank << ", epoch " << epoch << ", number of constraints passed to optimizer: " <<
-			  featureValueDiffs.size() << " (of which violated: " << violatedConstraintsBefore << ")" << endl;
-	  if (m_slack != 0) {
-	    alphas = Hildreth::optimise(featureValueDiffs, lossMinusModelScoreDiffs, m_slack);
-	  } else {
-	    alphas = Hildreth::optimise(featureValueDiffs, lossMinusModelScoreDiffs);
-	  }
-  
-	  // Update the weight vector according to the alphas and the feature value differences
-	  // * w' = w' + SUM alpha_i * (h_i(oracle) - h_i(hypothesis))
-	  for (size_t k = 0; k < featureValueDiffs.size(); ++k) {
-	  	float alpha = alphas[k];
-	  	cerr << "Rank " << rank << ", epoch " << epoch << ", alpha: " << alpha << endl;
-	  	ScoreComponentCollection update(featureValueDiffs[k]);
-	    update.MultiplyEquals(alpha);
-	    
-	    // sum updates
-	    summedUpdate.PlusEquals(update);
-	  }
-	} 
-	else {
-		cerr << "Rank " << rank << ", epoch " << epoch << ", no constraint violated for this batch" << endl;
+      float modelScoreDiff = oracleModelScores[i] - modelScores[i][j];
+      float diff = 0;
+
+      if (loss > modelScoreDiff)
+        diff = loss - modelScoreDiff;
+      cerr << "Rank " << rank << ", epoch " << epoch << ", constraint: " << modelScoreDiff << " >= " << loss << " (current violation: " << diff << ")" << endl;
+      if (diff > epsilon)
+        violated = true;
+
+      if (m_normaliseMargin) {
+        modelScoreDiff = (2*m_sigmoidParam/(1 + exp(-modelScoreDiff))) - m_sigmoidParam;
+        loss = (2*m_sigmoidParam/(1 + exp(-loss))) - m_sigmoidParam;
+        diff = 0;
+        if (loss > modelScoreDiff) {
+          diff = loss - modelScoreDiff;
+        }
+        cerr << "Rank " << rank << ", epoch " << epoch << ", normalised constraint: " << modelScoreDiff << " >= " << loss << " (current violation: " << diff << ")" << endl;
+      }
+
+      if (m_scale_margin) {
+        diff *= oracleBleuScores[i];
+        cerr << "Rank " << rank << ", epoch " << epoch << ", scaling margin with oracle bleu score "  << oracleBleuScores[i] << endl;
+      }
+
+      featureValueDiffs.push_back(featureValueDiff);
+      lossMinusModelScoreDiffs.push_back(diff);
+      all_losses.push_back(loss);
+      if (violated) {
+        ++violatedConstraintsBefore;
+        oldDistanceFromOptimum += diff;
+      }
+    }
+  }
+
+  // run optimisation: compute alphas for all given constraints
+  vector<float> alphas;
+  ScoreComponentCollection summedUpdate;
+  if (violatedConstraintsBefore > 0) {
+    cerr << "Rank " << rank << ", epoch " << epoch << ", number of constraints passed to optimizer: " <<
+         featureValueDiffs.size() << " (of which violated: " << violatedConstraintsBefore << ")" << endl;
+    if (m_slack != 0) {
+      alphas = Hildreth::optimise(featureValueDiffs, lossMinusModelScoreDiffs, m_slack);
+    } else {
+      alphas = Hildreth::optimise(featureValueDiffs, lossMinusModelScoreDiffs);
+    }
+
+    // Update the weight vector according to the alphas and the feature value differences
+    // * w' = w' + SUM alpha_i * (h_i(oracle) - h_i(hypothesis))
+    for (size_t k = 0; k < featureValueDiffs.size(); ++k) {
+      float alpha = alphas[k];
+      cerr << "Rank " << rank << ", epoch " << epoch << ", alpha: " << alpha << endl;
+      ScoreComponentCollection update(featureValueDiffs[k]);
+      update.MultiplyEquals(alpha);
+
+      // sum updates
+      summedUpdate.PlusEquals(update);
+    }
+  } else {
+    cerr << "Rank " << rank << ", epoch " << epoch << ", no constraint violated for this batch" << endl;
 //		return 0;
-		return 1;
-	}
-
-	// apply learning rate
-	if (learning_rate != 1) {
-		cerr << "Rank " << rank << ", epoch " << epoch << ", apply learning rate " << learning_rate << " to update." << endl;
-		summedUpdate.MultiplyEquals(learning_rate);
-	}
-
-	// scale update by BLEU of oracle (for batch size 1 only)
-	if (oracleBleuScores.size() == 1) {
-		if (m_scale_update) {
-			cerr << "Rank " << rank << ", epoch " << epoch << ", scaling summed update with oracle bleu score " << oracleBleuScores[0] << endl;
-			summedUpdate.MultiplyEquals(oracleBleuScores[0]);
-		}
-	}
-
-	//	cerr << "Rank " << rank << ", epoch " << epoch << ", update: " << summedUpdate << endl;
-	weightUpdate.PlusEquals(summedUpdate);
-
-	// Sanity check: are there still violated constraints after optimisation?
-/*	int violatedConstraintsAfter = 0;
-	float newDistanceFromOptimum = 0;
-	for (size_t i = 0; i < featureValueDiffs.size(); ++i) {
-		float modelScoreDiff = featureValueDiffs[i].InnerProduct(currWeights);
-		float loss = all_losses[i];
-		float diff = loss - modelScoreDiff;
-		if (diff > epsilon) {
-			++violatedConstraintsAfter;
-			newDistanceFromOptimum += diff;
-		}
-	}
-	VERBOSE(1, "Rank " << rank << ", epoch " << epoch << ", violated constraint before: " << violatedConstraintsBefore << ", after: " << violatedConstraintsAfter  << ", change: " << violatedConstraintsBefore - violatedConstraintsAfter << endl);
-	VERBOSE(1, "Rank " << rank << ", epoch " << epoch << ", error before: " << oldDistanceFromOptimum << ", after: " << newDistanceFromOptimum << ", change: " << oldDistanceFromOptimum - newDistanceFromOptimum << endl);*/
+    return 1;
+  }
+
+  // apply learning rate
+  if (learning_rate != 1) {
+    cerr << "Rank " << rank << ", epoch " << epoch << ", apply learning rate " << learning_rate << " to update." << endl;
+    summedUpdate.MultiplyEquals(learning_rate);
+  }
+
+  // scale update by BLEU of oracle (for batch size 1 only)
+  if (oracleBleuScores.size() == 1) {
+    if (m_scale_update) {
+      cerr << "Rank " << rank << ", epoch " << epoch << ", scaling summed update with oracle bleu score " << oracleBleuScores[0] << endl;
+      summedUpdate.MultiplyEquals(oracleBleuScores[0]);
+    }
+  }
+
+  //	cerr << "Rank " << rank << ", epoch " << epoch << ", update: " << summedUpdate << endl;
+  weightUpdate.PlusEquals(summedUpdate);
+
+  // Sanity check: are there still violated constraints after optimisation?
+  /*	int violatedConstraintsAfter = 0;
+  	float newDistanceFromOptimum = 0;
+  	for (size_t i = 0; i < featureValueDiffs.size(); ++i) {
+  		float modelScoreDiff = featureValueDiffs[i].InnerProduct(currWeights);
+  		float loss = all_losses[i];
+  		float diff = loss - modelScoreDiff;
+  		if (diff > epsilon) {
+  			++violatedConstraintsAfter;
+  			newDistanceFromOptimum += diff;
+  		}
+  	}
+  	VERBOSE(1, "Rank " << rank << ", epoch " << epoch << ", violated constraint before: " << violatedConstraintsBefore << ", after: " << violatedConstraintsAfter  << ", change: " << violatedConstraintsBefore - violatedConstraintsAfter << endl);
+  	VERBOSE(1, "Rank " << rank << ", epoch " << epoch << ", error before: " << oldDistanceFromOptimum << ", after: " << newDistanceFromOptimum << ", change: " << oldDistanceFromOptimum - newDistanceFromOptimum << endl);*/
 //	return violatedConstraintsAfter;
-	return 0;
+  return 0;
 }
 
 size_t MiraOptimiser::updateWeightsHopeFear(
-		Moses::ScoreComponentCollection& weightUpdate,
-		const std::vector< std::vector<Moses::ScoreComponentCollection> >& featureValuesHope,
-		const std::vector< std::vector<Moses::ScoreComponentCollection> >& featureValuesFear,
-		const std::vector<std::vector<float> >& bleuScoresHope,
-		const std::vector<std::vector<float> >& bleuScoresFear,
-		const std::vector<std::vector<float> >& modelScoresHope,
-		const std::vector<std::vector<float> >& modelScoresFear,
-		float learning_rate,
-		size_t rank,
-		size_t epoch,
-		int updatePosition) {
+  Moses::ScoreComponentCollection& weightUpdate,
+  const std::vector< std::vector<Moses::ScoreComponentCollection> >& featureValuesHope,
+  const std::vector< std::vector<Moses::ScoreComponentCollection> >& featureValuesFear,
+  const std::vector<std::vector<float> >& bleuScoresHope,
+  const std::vector<std::vector<float> >& bleuScoresFear,
+  const std::vector<std::vector<float> >& modelScoresHope,
+  const std::vector<std::vector<float> >& modelScoresFear,
+  float learning_rate,
+  size_t rank,
+  size_t epoch,
+  int updatePosition)
+{
 
   // vector of feature values differences for all created constraints
   vector<ScoreComponentCollection> featureValueDiffs;
   vector<float> lossMinusModelScoreDiffs;
   vector<float> modelScoreDiffs;
   vector<float> all_losses;
-  
+
   // most violated constraint in batch
   ScoreComponentCollection max_batch_featureValueDiff;
-  
+
   // Make constraints for new hypothesis translations
   float epsilon = 0.0001;
   int violatedConstraintsBefore = 0;
   float oldDistanceFromOptimum = 0;
-  
+
   // iterate over input sentences (1 (online) or more (batch))
   for (size_t i = 0; i < featureValuesHope.size(); ++i) {
     if (updatePosition != -1) {
       if (i < updatePosition)
-	continue;
+        continue;
       else if (i > updatePosition)
-	break;
+        break;
     }
-    
+
     // Pick all pairs[j,j] of hope and fear translations for one input sentence
     for (size_t j = 0; j < featureValuesHope[i].size(); ++j) {
       ScoreComponentCollection featureValueDiff = featureValuesHope[i][j];
       featureValueDiff.MinusEquals(featureValuesFear[i][j]);
       //cerr << "Rank " << rank << ", epoch " << epoch << ", feature value diff: " << featureValueDiff << endl;
       if (featureValueDiff.GetL1Norm() == 0) {
-	cerr << "Rank " << rank << ", epoch " << epoch << ", features equal --> skip" << endl;
-	continue;
+        cerr << "Rank " << rank << ", epoch " << epoch << ", features equal --> skip" << endl;
+        continue;
       }
-      
+
       float loss = bleuScoresHope[i][j] - bleuScoresFear[i][j];
-      
+
       // check if constraint is violated
       bool violated = false;
       //float modelScoreDiff = featureValueDiff.InnerProduct(currWeights);
       float modelScoreDiff = modelScoresHope[i][j] - modelScoresFear[i][j];
       float diff = 0;
-      if (loss > modelScoreDiff) 
-	diff = loss - modelScoreDiff;
-      cerr << "Rank " << rank << ", epoch " << epoch << ", constraint: " << modelScoreDiff << " >= " << loss << " (current violation: " << diff << ")" << endl;	
-      
-      if (diff > epsilon) 
-	violated = true;
-	    
+      if (loss > modelScoreDiff)
+        diff = loss - modelScoreDiff;
+      cerr << "Rank " << rank << ", epoch " << epoch << ", constraint: " << modelScoreDiff << " >= " << loss << " (current violation: " << diff << ")" << endl;
+
+      if (diff > epsilon)
+        violated = true;
+
       if (m_normaliseMargin) {
-	modelScoreDiff = (2*m_sigmoidParam/(1 + exp(-modelScoreDiff))) - m_sigmoidParam;
-	loss = (2*m_sigmoidParam/(1 + exp(-loss))) - m_sigmoidParam;
-	diff = 0;
-	if (loss > modelScoreDiff) {
-	  diff = loss - modelScoreDiff;
-	}
-	cerr << "Rank " << rank << ", epoch " << epoch << ", normalised constraint: " << modelScoreDiff << " >= " << loss << " (current violation: " << diff << ")" << endl;
+        modelScoreDiff = (2*m_sigmoidParam/(1 + exp(-modelScoreDiff))) - m_sigmoidParam;
+        loss = (2*m_sigmoidParam/(1 + exp(-loss))) - m_sigmoidParam;
+        diff = 0;
+        if (loss > modelScoreDiff) {
+          diff = loss - modelScoreDiff;
+        }
+        cerr << "Rank " << rank << ", epoch " << epoch << ", normalised constraint: " << modelScoreDiff << " >= " << loss << " (current violation: " << diff << ")" << endl;
       }
-      
+
       if (m_scale_margin) {
-	diff *= bleuScoresHope[i][j];
-	cerr << "Rank " << rank << ", epoch " << epoch << ", scaling margin with oracle bleu score "  << bleuScoresHope[i][j] << endl;
+        diff *= bleuScoresHope[i][j];
+        cerr << "Rank " << rank << ", epoch " << epoch << ", scaling margin with oracle bleu score "  << bleuScoresHope[i][j] << endl;
       }
-      
+
       featureValueDiffs.push_back(featureValueDiff);
       lossMinusModelScoreDiffs.push_back(diff);
       modelScoreDiffs.push_back(modelScoreDiff);
       all_losses.push_back(loss);
       if (violated) {
-	++violatedConstraintsBefore;
-	oldDistanceFromOptimum += diff;
-      }				
+        ++violatedConstraintsBefore;
+        oldDistanceFromOptimum += diff;
+      }
     }
   }
 
@@ -241,48 +243,47 @@ size_t MiraOptimiser::updateWeightsHopeFear(
   ScoreComponentCollection summedUpdate;
   if (violatedConstraintsBefore > 0) {
     cerr << "Rank " << rank << ", epoch " << epoch << ", number of constraints passed to optimizer: " <<
-      featureValueDiffs.size() << " (of which violated: " << violatedConstraintsBefore << ")" << endl;
+         featureValueDiffs.size() << " (of which violated: " << violatedConstraintsBefore << ")" << endl;
     if (m_slack != 0) {
       alphas = Hildreth::optimise(featureValueDiffs, lossMinusModelScoreDiffs, m_slack);
     } else {
       alphas = Hildreth::optimise(featureValueDiffs, lossMinusModelScoreDiffs);
     }
-    
+
     // Update the weight vector according to the alphas and the feature value differences
     // * w' = w' + SUM alpha_i * (h_i(oracle) - h_i(hypothesis))
     for (size_t k = 0; k < featureValueDiffs.size(); ++k) {
       float alpha = alphas[k];
       cerr << "Rank " << rank << ", epoch " << epoch << ", alpha: " << alpha << endl;
       if (alpha != 0) {
-	// apply boosting factor
-	if (m_boost && modelScoreDiffs[k] <= 0) {
-	  // factor between 1.5 and 3 (for Bleu scores between 5 and 20, the factor is within the boundaries)
-	  float factor = min(1.5, log2(bleuScoresHope[0][0])); // TODO: make independent of number of oracles!!
-	  factor = min(3.0f, factor);
-	  alpha = alpha * factor;
-	  cerr << "Rank " << rank << ", epoch " << epoch << ", apply boosting factor " << factor << " to update." << endl;
-	}
-	
-	ScoreComponentCollection update(featureValueDiffs[k]);
-	update.MultiplyEquals(alpha);
-	
-	// sum updates
-	summedUpdate.PlusEquals(update);
+        // apply boosting factor
+        if (m_boost && modelScoreDiffs[k] <= 0) {
+          // factor between 1.5 and 3 (for Bleu scores between 5 and 20, the factor is within the boundaries)
+          float factor = min(1.5, log2(bleuScoresHope[0][0])); // TODO: make independent of number of oracles!!
+          factor = min(3.0f, factor);
+          alpha = alpha * factor;
+          cerr << "Rank " << rank << ", epoch " << epoch << ", apply boosting factor " << factor << " to update." << endl;
+        }
+
+        ScoreComponentCollection update(featureValueDiffs[k]);
+        update.MultiplyEquals(alpha);
+
+        // sum updates
+        summedUpdate.PlusEquals(update);
       }
     }
-  }
-  else {
+  } else {
     cerr << "Rank " << rank << ", epoch " << epoch << ", no constraint violated for this batch" << endl;
     //	  return 0;
     return 1;
   }
-  
+
   // apply learning rate
   if (learning_rate != 1) {
     cerr << "Rank " << rank << ", epoch " << epoch << ", apply learning rate " << learning_rate << " to update." << endl;
     summedUpdate.MultiplyEquals(learning_rate);
   }
-  
+
   // scale update by BLEU of oracle (for batch size 1 only)
   if (featureValuesHope.size() == 1) {
     if (m_scale_update) {
@@ -290,46 +291,47 @@ size_t MiraOptimiser::updateWeightsHopeFear(
       summedUpdate.MultiplyEquals(bleuScoresHope[0][0]);
     }
   }
-  
+
   //cerr << "Rank " << rank << ", epoch " << epoch << ", update: " << summedUpdate << endl;
   weightUpdate.PlusEquals(summedUpdate);
-  
+
   // Sanity check: are there still violated constraints after optimisation?
-/*	int violatedConstraintsAfter = 0;
-	float newDistanceFromOptimum = 0;
-	for (size_t i = 0; i < featureValueDiffs.size(); ++i) {
-	float modelScoreDiff = featureValueDiffs[i].InnerProduct(currWeights);
-	float loss = all_losses[i];
-	float diff = loss - modelScoreDiff;
-	if (diff > epsilon) {
-	++violatedConstraintsAfter;
-	newDistanceFromOptimum += diff;
-	}
-	}
-	VERBOSE(1, "Rank " << rank << ", epoch " << epoch << ", violated constraint before: " << violatedConstraintsBefore << ", after: " << violatedConstraintsAfter  << ", change: " << violatedConstraintsBefore - violatedConstraintsAfter << endl);
-	VERBOSE(1, "Rank " << rank << ", epoch " << epoch << ", error before: " << oldDistanceFromOptimum << ", after: " << newDistanceFromOptimum << ", change: " << oldDistanceFromOptimum - newDistanceFromOptimum << endl);*/
+  /*	int violatedConstraintsAfter = 0;
+  	float newDistanceFromOptimum = 0;
+  	for (size_t i = 0; i < featureValueDiffs.size(); ++i) {
+  	float modelScoreDiff = featureValueDiffs[i].InnerProduct(currWeights);
+  	float loss = all_losses[i];
+  	float diff = loss - modelScoreDiff;
+  	if (diff > epsilon) {
+  	++violatedConstraintsAfter;
+  	newDistanceFromOptimum += diff;
+  	}
+  	}
+  	VERBOSE(1, "Rank " << rank << ", epoch " << epoch << ", violated constraint before: " << violatedConstraintsBefore << ", after: " << violatedConstraintsAfter  << ", change: " << violatedConstraintsBefore - violatedConstraintsAfter << endl);
+  	VERBOSE(1, "Rank " << rank << ", epoch " << epoch << ", error before: " << oldDistanceFromOptimum << ", after: " << newDistanceFromOptimum << ", change: " << oldDistanceFromOptimum - newDistanceFromOptimum << endl);*/
 //	return violatedConstraintsAfter;
-	return 0;
+  return 0;
 }
 
 size_t MiraOptimiser::updateWeightsAnalytically(
-		ScoreComponentCollection& weightUpdate,
-		ScoreComponentCollection& featureValuesHope,
-    ScoreComponentCollection& featureValuesFear,
-    float bleuScoreHope,
-    float bleuScoreFear,
-    float modelScoreHope,
-    float modelScoreFear,
-    float learning_rate,
-    size_t rank,
-    size_t epoch) {
+  ScoreComponentCollection& weightUpdate,
+  ScoreComponentCollection& featureValuesHope,
+  ScoreComponentCollection& featureValuesFear,
+  float bleuScoreHope,
+  float bleuScoreFear,
+  float modelScoreHope,
+  float modelScoreFear,
+  float learning_rate,
+  size_t rank,
+  size_t epoch)
+{
 
   float epsilon = 0.0001;
   float oldDistanceFromOptimum = 0;
   bool constraintViolatedBefore = false;
 
- // cerr << "Rank " << rank << ", epoch " << epoch << ", hope: " << featureValuesHope << endl;
- // cerr << "Rank " << rank << ", epoch " << epoch << ", fear: " << featureValuesFear << endl;
+// cerr << "Rank " << rank << ", epoch " << epoch << ", hope: " << featureValuesHope << endl;
+// cerr << "Rank " << rank << ", epoch " << epoch << ", fear: " << featureValuesFear << endl;
   ScoreComponentCollection featureValueDiff = featureValuesHope;
   featureValueDiff.MinusEquals(featureValuesFear);
   if (featureValueDiff.GetL1Norm() == 0) {
@@ -342,35 +344,35 @@ size_t MiraOptimiser::updateWeightsAnalytically(
   float modelScoreDiff = modelScoreHope - modelScoreFear;
   float loss = bleuScoreHope - bleuScoreFear;
   float diff = 0;
-  if (loss > modelScoreDiff) 
-    diff = loss - modelScoreDiff; 
+  if (loss > modelScoreDiff)
+    diff = loss - modelScoreDiff;
   cerr << "Rank " << rank << ", epoch " << epoch << ", constraint: " << modelScoreDiff << " >= " << loss << " (current violation: " << diff << ")" << endl;
 
   if (m_normaliseMargin) {
     modelScoreDiff = (2*m_sigmoidParam/(1 + exp(-modelScoreDiff))) - m_sigmoidParam;
     loss = (2*m_sigmoidParam/(1 + exp(-loss))) - m_sigmoidParam;
-    if (loss > modelScoreDiff) 
+    if (loss > modelScoreDiff)
       diff = loss - modelScoreDiff;
     cerr << "Rank " << rank << ", epoch " << epoch << ", normalised constraint: " << modelScoreDiff << " >= " << loss << " (current violation: " << diff << ")" << endl;
   }
-  
+
   if (m_scale_margin) {
-	  diff *= bleuScoreHope;
-	  cerr << "Rank " << rank << ", epoch " << epoch << ", scaling margin with oracle bleu score "  << bleuScoreHope << endl;
+    diff *= bleuScoreHope;
+    cerr << "Rank " << rank << ", epoch " << epoch << ", scaling margin with oracle bleu score "  << bleuScoreHope << endl;
   }
   if (m_scale_margin_precision) {
-	  diff *= (1+m_precision);
-	  cerr << "Rank " << rank << ", epoch " << epoch << ", scaling margin with 1+precision: "  << (1+m_precision) << endl;
+    diff *= (1+m_precision);
+    cerr << "Rank " << rank << ", epoch " << epoch << ", scaling margin with 1+precision: "  << (1+m_precision) << endl;
   }
 
   if (diff > epsilon) {
-  	// squash it between 0 and 1
-  	//diff = tanh(diff);
-  	//diff = (2/(1 + pow(2,-diff))) - 1;
+    // squash it between 0 and 1
+    //diff = tanh(diff);
+    //diff = (2/(1 + pow(2,-diff))) - 1;
     /*  	if (m_normaliseMargin) {
-  		diff = (2/(1 + exp(-diff))) - 1;
-  		cerr << "Rank " << rank << ", epoch " << epoch << ", new margin: " << diff << endl;
-		}*/
+    	diff = (2/(1 + exp(-diff))) - 1;
+    	cerr << "Rank " << rank << ", epoch " << epoch << ", new margin: " << diff << endl;
+    }*/
 
     // constraint violated
     oldDistanceFromOptimum += diff;
@@ -384,134 +386,134 @@ size_t MiraOptimiser::updateWeightsAnalytically(
     float alpha = diff / squaredNorm;
     cerr << "Rank " << rank << ", epoch " << epoch << ", unclipped alpha: " << alpha << endl;
     if (m_slack > 0 ) {
-    	if (alpha > m_slack) {
-    		alpha = m_slack;
-    	}
-    	else if (alpha < m_slack*(-1)) {
-    		alpha = m_slack*(-1);
-    	}
+      if (alpha > m_slack) {
+        alpha = m_slack;
+      } else if (alpha < m_slack*(-1)) {
+        alpha = m_slack*(-1);
+      }
     }
 
     // apply learning rate
     if (learning_rate != 1)
-    	alpha = alpha * learning_rate;
-    
+      alpha = alpha * learning_rate;
+
     if (m_scale_update) {
-  	  cerr << "Rank " << rank << ", epoch " << epoch << ", scaling update with oracle bleu score " << bleuScoreHope << endl;
-  	  alpha *= bleuScoreHope;
+      cerr << "Rank " << rank << ", epoch " << epoch << ", scaling update with oracle bleu score " << bleuScoreHope << endl;
+      alpha *= bleuScoreHope;
     }
     if (m_scale_update_precision) {
-  	  cerr << "Rank " << rank << ", epoch " << epoch << ", scaling update with 1+precision: " << (1+m_precision) << endl;
-  	  alpha *= (1+m_precision);	
+      cerr << "Rank " << rank << ", epoch " << epoch << ", scaling update with 1+precision: " << (1+m_precision) << endl;
+      alpha *= (1+m_precision);
     }
-    
+
     cerr << "Rank " << rank << ", epoch " << epoch << ", clipped/scaled alpha: " << alpha << endl;
 
     // apply boosting factor
     if (m_boost && modelScoreDiff <= 0) {
-    	// factor between 1.5 and 3 (for Bleu scores between 5 and 20, the factor is within the boundaries)
-    	float factor = min(1.5, log2(bleuScoreHope));
-    	factor = min(3.0f, factor);
-    	alpha = alpha * factor;
-    	cerr << "Rank " << rank << ", epoch " << epoch << ", boosted alpha: " << alpha << endl;
+      // factor between 1.5 and 3 (for Bleu scores between 5 and 20, the factor is within the boundaries)
+      float factor = min(1.5, log2(bleuScoreHope));
+      factor = min(3.0f, factor);
+      alpha = alpha * factor;
+      cerr << "Rank " << rank << ", epoch " << epoch << ", boosted alpha: " << alpha << endl;
     }
 
     featureValueDiff.MultiplyEquals(alpha);
     weightUpdate.PlusEquals(featureValueDiff);
 //  	cerr << "Rank " << rank << ", epoch " << epoch << ", update: " << weightUpdate << endl;
   }
-  
+
   if (!constraintViolatedBefore) {
     // constraint satisfied, nothing to do
-  	cerr << "Rank " << rank << ", epoch " << epoch << ", constraint already satisfied" << endl;
+    cerr << "Rank " << rank << ", epoch " << epoch << ", constraint already satisfied" << endl;
     return 1;
   }
 
   // sanity check: constraint still violated after optimisation?
-/*  ScoreComponentCollection newWeights(currWeights);
-  newWeights.PlusEquals(weightUpdate);
-  bool constraintViolatedAfter = false;
-  float newDistanceFromOptimum = 0;
-  featureValueDiff = featureValuesHope;
-  featureValueDiff.MinusEquals(featureValuesFear);
-  modelScoreDiff = featureValueDiff.InnerProduct(newWeights);
-  diff = loss - modelScoreDiff;
-  // approximate comparison between floats!
-  if (diff > epsilon) {
-    constraintViolatedAfter = true;
-    newDistanceFromOptimum += (loss - modelScoreDiff);
-  }
+  /*  ScoreComponentCollection newWeights(currWeights);
+    newWeights.PlusEquals(weightUpdate);
+    bool constraintViolatedAfter = false;
+    float newDistanceFromOptimum = 0;
+    featureValueDiff = featureValuesHope;
+    featureValueDiff.MinusEquals(featureValuesFear);
+    modelScoreDiff = featureValueDiff.InnerProduct(newWeights);
+    diff = loss - modelScoreDiff;
+    // approximate comparison between floats!
+    if (diff > epsilon) {
+      constraintViolatedAfter = true;
+      newDistanceFromOptimum += (loss - modelScoreDiff);
+    }
 
-  float hopeScore = featureValuesHope.InnerProduct(newWeights);
-  float fearScore = featureValuesFear.InnerProduct(newWeights);
-  cerr << "New hope score: " << hopeScore << endl;
-  cerr << "New fear score: " << fearScore << endl;
+    float hopeScore = featureValuesHope.InnerProduct(newWeights);
+    float fearScore = featureValuesFear.InnerProduct(newWeights);
+    cerr << "New hope score: " << hopeScore << endl;
+    cerr << "New fear score: " << fearScore << endl;
 
-  VERBOSE(0, "Rank " << rank << ", epoch " << epoch << ", check, constraint violated before? " << constraintViolatedBefore << ", after? " << constraintViolatedAfter << endl);
-  VERBOSE(0, "Rank " << rank << ", epoch " << epoch << ", check, error before: " << oldDistanceFromOptimum << ", after: " << newDistanceFromOptimum << ", change: " << oldDistanceFromOptimum - newDistanceFromOptimum << endl);
-*/
+    VERBOSE(0, "Rank " << rank << ", epoch " << epoch << ", check, constraint violated before? " << constraintViolatedBefore << ", after? " << constraintViolatedAfter << endl);
+    VERBOSE(0, "Rank " << rank << ", epoch " << epoch << ", check, error before: " << oldDistanceFromOptimum << ", after: " << newDistanceFromOptimum << ", change: " << oldDistanceFromOptimum - newDistanceFromOptimum << endl);
+  */
   return 0;
 }
 
 size_t MiraOptimiser::updateWeightsHopeFearSelective(
-		Moses::ScoreComponentCollection& weightUpdate,
-		const std::vector< std::vector<Moses::ScoreComponentCollection> >& featureValuesHope,
-		const std::vector< std::vector<Moses::ScoreComponentCollection> >& featureValuesFear,
-		const std::vector<std::vector<float> >& bleuScoresHope,
-		const std::vector<std::vector<float> >& bleuScoresFear,
-		const std::vector<std::vector<float> >& modelScoresHope,
-		const std::vector<std::vector<float> >& modelScoresFear,
-		float learning_rate,
-		size_t rank,
-		size_t epoch,
-		int updatePosition) {
+  Moses::ScoreComponentCollection& weightUpdate,
+  const std::vector< std::vector<Moses::ScoreComponentCollection> >& featureValuesHope,
+  const std::vector< std::vector<Moses::ScoreComponentCollection> >& featureValuesFear,
+  const std::vector<std::vector<float> >& bleuScoresHope,
+  const std::vector<std::vector<float> >& bleuScoresFear,
+  const std::vector<std::vector<float> >& modelScoresHope,
+  const std::vector<std::vector<float> >& modelScoresFear,
+  float learning_rate,
+  size_t rank,
+  size_t epoch,
+  int updatePosition)
+{
 
   // vector of feature values differences for all created constraints
   vector<ScoreComponentCollection> nonZeroFeatures;
   vector<float> lossMinusModelScoreDiffs;
- 
+
   // Make constraints for new hypothesis translations
   float epsilon = 0.0001;
   int violatedConstraintsBefore = 0;
-  
+
   // iterate over input sentences (1 (online) or more (batch))
   for (size_t i = 0; i < featureValuesHope.size(); ++i) {
     if (updatePosition != -1) {
       if (i < updatePosition)
-	continue;
+        continue;
       else if (i > updatePosition)
-	break;
+        break;
     }
-    
+
     // Pick all pairs[j,j] of hope and fear translations for one input sentence
     for (size_t j = 0; j < featureValuesHope[i].size(); ++j) {
       ScoreComponentCollection featureValueDiff = featureValuesHope[i][j];
       featureValueDiff.MinusEquals(featureValuesFear[i][j]);
       if (featureValueDiff.GetL1Norm() == 0) {
-	cerr << "Rank " << rank << ", epoch " << epoch << ", features equal --> skip" << endl;
-	continue;
+        cerr << "Rank " << rank << ", epoch " << epoch << ", features equal --> skip" << endl;
+        continue;
       }
-           
+
       // check if constraint is violated
       float loss = bleuScoresHope[i][j] - bleuScoresFear[i][j];
       float modelScoreDiff = modelScoresHope[i][j] - modelScoresFear[i][j];
       float diff = 0;
-      if (loss > modelScoreDiff) 
-	diff = loss - modelScoreDiff;
-      if (diff > epsilon) 
-	++violatedConstraintsBefore;   				
-      cerr << "Rank " << rank << ", epoch " << epoch << ", constraint: " << modelScoreDiff << " >= " << loss << " (current violation: " << diff << ")" << endl;	
-	    
+      if (loss > modelScoreDiff)
+        diff = loss - modelScoreDiff;
+      if (diff > epsilon)
+        ++violatedConstraintsBefore;
+      cerr << "Rank " << rank << ", epoch " << epoch << ", constraint: " << modelScoreDiff << " >= " << loss << " (current violation: " << diff << ")" << endl;
+
       // iterate over difference vector and add a constraint for every non-zero feature
       FVector features = featureValueDiff.GetScoresVector();
       size_t n_core = 0, n_sparse = 0, n_sparse_hope = 0, n_sparse_fear = 0;
       for (size_t i=0; i<features.coreSize(); ++i) {
-	if (features[i] != 0.0) {
-	  ++n_core;
-	  ScoreComponentCollection f;
-	  f.Assign(i, features[i]);
-	  nonZeroFeatures.push_back(f);
-	}
+        if (features[i] != 0.0) {
+          ++n_core;
+          ScoreComponentCollection f;
+          f.Assign(i, features[i]);
+          nonZeroFeatures.push_back(f);
+        }
       }
 
       vector<ScoreComponentCollection> nonZeroFeaturesHope;
@@ -522,27 +524,26 @@ size_t MiraOptimiser::updateWeightsHopeFearSelective(
           f.Assign((i->first).name(), i->second);
           cerr << "Rank " << rank << ", epoch " << epoch << ", f: " << f << endl;
 
-	  if (i->second > 0.0) {
-	    ++n_sparse_hope;
-	    nonZeroFeaturesHope.push_back(f);
-	  }
-	  else {
-	    ++n_sparse_fear;
-	    nonZeroFeaturesFear.push_back(f);
-	  }
+          if (i->second > 0.0) {
+            ++n_sparse_hope;
+            nonZeroFeaturesHope.push_back(f);
+          } else {
+            ++n_sparse_fear;
+            nonZeroFeaturesFear.push_back(f);
+          }
         }
       }
 
       float n = n_core + n_sparse_hope + n_sparse_fear;
       for (size_t i=0; i<n_core; ++i)
-        lossMinusModelScoreDiffs.push_back(diff/n);      
+        lossMinusModelScoreDiffs.push_back(diff/n);
       for (size_t i=0; i<n_sparse_hope; ++i) {
-	nonZeroFeatures.push_back(nonZeroFeaturesHope[i]);
+        nonZeroFeatures.push_back(nonZeroFeaturesHope[i]);
         lossMinusModelScoreDiffs.push_back((diff/n)*1.1);
       }
       for (size_t i=0; i<n_sparse_fear; ++i) {
-	nonZeroFeatures.push_back(nonZeroFeaturesFear[i]);
-	lossMinusModelScoreDiffs.push_back(diff/n);
+        nonZeroFeatures.push_back(nonZeroFeaturesFear[i]);
+        lossMinusModelScoreDiffs.push_back(diff/n);
       }
       cerr << "Rank " << rank << ", epoch " << epoch << ", core diff: " << diff/n << endl;
       cerr << "Rank " << rank << ", epoch " << epoch << ", hope diff: " << ((diff/n)*1.1) << endl;
@@ -558,33 +559,32 @@ size_t MiraOptimiser::updateWeightsHopeFearSelective(
   if (violatedConstraintsBefore > 0) {
     cerr << "Rank " << rank << ", epoch " << epoch << ", number of constraints passed to optimizer: " << nonZeroFeatures.size() << endl;
     alphas = Hildreth::optimise(nonZeroFeatures, lossMinusModelScoreDiffs, m_slack);
-    
+
     // Update the weight vector according to the alphas and the feature value differences
     // * w' = w' + SUM alpha_i * (h_i(oracle) - h_i(hypothesis))
     for (size_t k = 0; k < nonZeroFeatures.size(); ++k) {
       float alpha = alphas[k];
       cerr << "Rank " << rank << ", epoch " << epoch << ", alpha: " << alpha << endl;
       if (alpha != 0) {
-	ScoreComponentCollection update(nonZeroFeatures[k]);
-	update.MultiplyEquals(alpha);
-	
-	// sum updates
-	summedUpdate.PlusEquals(update);
+        ScoreComponentCollection update(nonZeroFeatures[k]);
+        update.MultiplyEquals(alpha);
+
+        // sum updates
+        summedUpdate.PlusEquals(update);
       }
     }
-  }
-  else {
+  } else {
     cerr << "Rank " << rank << ", epoch " << epoch << ", no constraint violated for this batch" << endl;
     //	  return 0;
     return 1;
   }
-  
+
   // apply learning rate
   if (learning_rate != 1) {
     cerr << "Rank " << rank << ", epoch " << epoch << ", apply learning rate " << learning_rate << " to update." << endl;
     summedUpdate.MultiplyEquals(learning_rate);
   }
-  
+
   // scale update by BLEU of oracle (for batch size 1 only)
   if (featureValuesHope.size() == 1) {
     if (m_scale_update) {
@@ -592,56 +592,57 @@ size_t MiraOptimiser::updateWeightsHopeFearSelective(
       summedUpdate.MultiplyEquals(bleuScoresHope[0][0]);
     }
   }
-  
+
   //cerr << "Rank " << rank << ", epoch " << epoch << ", update: " << summedUpdate << endl;
   weightUpdate.PlusEquals(summedUpdate);
   return 0;
 }
 
 size_t MiraOptimiser::updateWeightsHopeFearSummed(
-		Moses::ScoreComponentCollection& weightUpdate,
-		const std::vector< std::vector<Moses::ScoreComponentCollection> >& featureValuesHope,
-		const std::vector< std::vector<Moses::ScoreComponentCollection> >& featureValuesFear,
-		const std::vector<std::vector<float> >& bleuScoresHope,
-		const std::vector<std::vector<float> >& bleuScoresFear,
-		const std::vector<std::vector<float> >& modelScoresHope,
-		const std::vector<std::vector<float> >& modelScoresFear,
-		float learning_rate,
-		size_t rank,
-		size_t epoch,
-		bool rescaleSlack,
-		bool makePairs) {
+  Moses::ScoreComponentCollection& weightUpdate,
+  const std::vector< std::vector<Moses::ScoreComponentCollection> >& featureValuesHope,
+  const std::vector< std::vector<Moses::ScoreComponentCollection> >& featureValuesFear,
+  const std::vector<std::vector<float> >& bleuScoresHope,
+  const std::vector<std::vector<float> >& bleuScoresFear,
+  const std::vector<std::vector<float> >& modelScoresHope,
+  const std::vector<std::vector<float> >& modelScoresFear,
+  float learning_rate,
+  size_t rank,
+  size_t epoch,
+  bool rescaleSlack,
+  bool makePairs)
+{
 
   // vector of feature values differences for all created constraints
   ScoreComponentCollection averagedFeatureDiffs;
   float averagedViolations = 0;
- 
+
   // Make constraints for new hypothesis translations
   float epsilon = 0.0001;
   int violatedConstraintsBefore = 0;
-  
+
   if (!makePairs) {
     ScoreComponentCollection featureValueDiff;
     float lossHope = 0, lossFear = 0, modelScoreHope = 0, modelScoreFear = 0, hopeCount = 0, fearCount = 0;
     // add all hope vectors
     for (size_t i = 0; i < featureValuesHope.size(); ++i) {
       for (size_t j = 0; j < featureValuesHope[i].size(); ++j)  {
-	featureValueDiff.PlusEquals(featureValuesHope[i][j]);
-	lossHope += bleuScoresHope[i][j];
-	modelScoreHope += modelScoresHope[i][j];
-	++hopeCount;
+        featureValueDiff.PlusEquals(featureValuesHope[i][j]);
+        lossHope += bleuScoresHope[i][j];
+        modelScoreHope += modelScoresHope[i][j];
+        ++hopeCount;
       }
     }
     lossHope /= hopeCount;
     modelScoreHope /= hopeCount;
-    
+
     // subtract all fear  vectors
     for (size_t i = 0; i < featureValuesFear.size(); ++i) {
       for (size_t j = 0; j < featureValuesFear[i].size(); ++j) {
         featureValueDiff.MinusEquals(featureValuesFear[i][j]);
-	lossFear += bleuScoresFear[i][j];
+        lossFear += bleuScoresFear[i][j];
         modelScoreFear += modelScoresFear[i][j];
-	++fearCount;
+        ++fearCount;
       }
     }
     lossFear /= fearCount;
@@ -653,7 +654,7 @@ size_t MiraOptimiser::updateWeightsHopeFearSummed(
       return 1;
     }
 
-    // check if constraint is violated                                                                                                       
+    // check if constraint is violated
     float lossDiff = lossHope - lossFear;
     float modelScoreDiff = modelScoreHope - modelScoreFear;
     float diff = 0;
@@ -662,54 +663,52 @@ size_t MiraOptimiser::updateWeightsHopeFearSummed(
     if (diff > epsilon)
       ++violatedConstraintsBefore;
     cerr << "Rank " << rank << ", epoch " << epoch << ", constraint: " << modelScoreDiff << " >= " << lossDiff << " (current violation: " <<\
-      diff << ")" << endl;
+         diff << ")" << endl;
 
-    // add constraint                                                                                                                        
+    // add constraint
     averagedFeatureDiffs = featureValueDiff;
     averagedViolations = diff;
-  }
-  else {
-  // iterate over input sentences (1 (online) or more (batch))
-  for (size_t i = 0; i < featureValuesHope.size(); ++i) {    
-    // Pick all pairs[j,j] of hope and fear translations for one input sentence and add them up 
-    for (size_t j = 0; j < featureValuesHope[i].size(); ++j) {
-      ScoreComponentCollection featureValueDiff = featureValuesHope[i][j];
-      featureValueDiff.MinusEquals(featureValuesFear[i][j]);
-      if (featureValueDiff.GetL1Norm() == 0) {
-	cerr << "Rank " << rank << ", epoch " << epoch << ", features equal --> skip" << endl;
-	continue;
-      }
-           
-      // check if constraint is violated
-      float lossDiff = bleuScoresHope[i][j] - bleuScoresFear[i][j];
-      float modelScoreDiff = modelScoresHope[i][j] - modelScoresFear[i][j];
-      if (rescaleSlack) {
-	cerr << "Rank " << rank << ", epoch " << epoch << ", modelScoreDiff scaled by lossDiff: " << modelScoreDiff << " --> " << modelScoreDiff*lossDiff << endl;
-	modelScoreDiff *= lossDiff; 
-      }
-      float diff = 0;
-      if (lossDiff > modelScoreDiff) 
-	diff = lossDiff - modelScoreDiff;
-      if (diff > epsilon) 
-	++violatedConstraintsBefore;   				
-      cerr << "Rank " << rank << ", epoch " << epoch << ", constraint: " << modelScoreDiff << " >= " << lossDiff << " (current violation: " << diff << ")" << endl;	
-
-      // add constraint
-      if (rescaleSlack) {
-	averagedFeatureDiffs.MultiplyEquals(lossDiff);
-	cerr << "Rank " << rank << ", epoch " << epoch << ", featureValueDiff scaled by lossDiff." << endl;
+  } else {
+    // iterate over input sentences (1 (online) or more (batch))
+    for (size_t i = 0; i < featureValuesHope.size(); ++i) {
+      // Pick all pairs[j,j] of hope and fear translations for one input sentence and add them up
+      for (size_t j = 0; j < featureValuesHope[i].size(); ++j) {
+        ScoreComponentCollection featureValueDiff = featureValuesHope[i][j];
+        featureValueDiff.MinusEquals(featureValuesFear[i][j]);
+        if (featureValueDiff.GetL1Norm() == 0) {
+          cerr << "Rank " << rank << ", epoch " << epoch << ", features equal --> skip" << endl;
+          continue;
+        }
+
+        // check if constraint is violated
+        float lossDiff = bleuScoresHope[i][j] - bleuScoresFear[i][j];
+        float modelScoreDiff = modelScoresHope[i][j] - modelScoresFear[i][j];
+        if (rescaleSlack) {
+          cerr << "Rank " << rank << ", epoch " << epoch << ", modelScoreDiff scaled by lossDiff: " << modelScoreDiff << " --> " << modelScoreDiff*lossDiff << endl;
+          modelScoreDiff *= lossDiff;
+        }
+        float diff = 0;
+        if (lossDiff > modelScoreDiff)
+          diff = lossDiff - modelScoreDiff;
+        if (diff > epsilon)
+          ++violatedConstraintsBefore;
+        cerr << "Rank " << rank << ", epoch " << epoch << ", constraint: " << modelScoreDiff << " >= " << lossDiff << " (current violation: " << diff << ")" << endl;
+
+        // add constraint
+        if (rescaleSlack) {
+          averagedFeatureDiffs.MultiplyEquals(lossDiff);
+          cerr << "Rank " << rank << ", epoch " << epoch << ", featureValueDiff scaled by lossDiff." << endl;
+        }
+        averagedFeatureDiffs.PlusEquals(featureValueDiff);
+        averagedViolations += diff;
       }
-      averagedFeatureDiffs.PlusEquals(featureValueDiff);
-      averagedViolations += diff;
-    }	    
-  }
+    }
   }
 
   // divide by number of constraints (1/n)
   if (!makePairs) {
     averagedFeatureDiffs.DivideEquals(featureValuesHope[0].size());
-  }
-  else {
+  } else {
     averagedFeatureDiffs.DivideEquals(featureValuesHope[0].size());
     averagedViolations /= featureValuesHope[0].size();
   }
@@ -717,29 +716,27 @@ size_t MiraOptimiser::updateWeightsHopeFearSummed(
   cerr << "Rank " << rank << ", epoch " << epoch << ", averaged violations: " << averagedViolations << endl;
 
   if (violatedConstraintsBefore > 0) {
-    // compute alpha for given constraint: (loss diff - model score diff) / || feature value diff ||^2                                
-    // featureValueDiff.GetL2Norm() * featureValueDiff.GetL2Norm() == featureValueDiff.InnerProduct(featureValueDiff)                     
-    // from Crammer&Singer 2006: alpha = min {C , l_t/ ||x||^2}                                                         
+    // compute alpha for given constraint: (loss diff - model score diff) / || feature value diff ||^2
+    // featureValueDiff.GetL2Norm() * featureValueDiff.GetL2Norm() == featureValueDiff.InnerProduct(featureValueDiff)
+    // from Crammer&Singer 2006: alpha = min {C , l_t/ ||x||^2}
     // adjusted for 1 slack according to Joachims 2009, OP4 (margin rescaling), OP5 (slack rescaling)
     float squaredNorm = averagedFeatureDiffs.GetL2Norm() * averagedFeatureDiffs.GetL2Norm();
     float alpha = averagedViolations / squaredNorm;
     cerr << "Rank " << rank << ", epoch " << epoch << ", unclipped alpha: " << alpha << endl;
     if (m_slack > 0 ) {
       if (alpha > m_slack) {
-	alpha = m_slack;
-      }
-      else if (alpha < m_slack*(-1)) {
-	alpha = m_slack*(-1);
+        alpha = m_slack;
+      } else if (alpha < m_slack*(-1)) {
+        alpha = m_slack*(-1);
       }
     }
     cerr << "Rank " << rank << ", epoch " << epoch << ", clipped alpha: " << alpha << endl;
-  
+
     // compute update
     averagedFeatureDiffs.MultiplyEquals(alpha);
     weightUpdate.PlusEquals(averagedFeatureDiffs);
     return 0;
-  }
-  else {
+  } else {
     cerr << "Rank " << rank << ", epoch " << epoch << ", no constraint violated for this batch" << endl;
     return 1;
   }
diff --git a/mira/Optimiser.h b/mira/Optimiser.h
index a610268f3..d8afb8a0a 100644
--- a/mira/Optimiser.h
+++ b/mira/Optimiser.h
@@ -24,151 +24,155 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 #include "moses/ScoreComponentCollection.h"
 
 
-namespace Mira {
-  
-  class Optimiser {
-  public:
-    Optimiser() {}
-    
-    virtual size_t updateWeightsHopeFear(
-	 Moses::ScoreComponentCollection& weightUpdate,
-	 const std::vector<std::vector<Moses::ScoreComponentCollection> >& featureValuesHope,
-	 const std::vector<std::vector<Moses::ScoreComponentCollection> >& featureValuesFear,
-	 const std::vector<std::vector<float> >& bleuScoresHope,
-	 const std::vector<std::vector<float> >& bleuScoresFear,
-	 const std::vector<std::vector<float> >& modelScoresHope,
-	 const std::vector<std::vector<float> >& modelScoresFear,
-	 float learning_rate,
-	 size_t rank,
-	 size_t epoch,
-	 int updatePosition = -1) = 0;
-  };
- 
-  class Perceptron : public Optimiser {
-  public:
-    virtual size_t updateWeightsHopeFear(
-	 Moses::ScoreComponentCollection& weightUpdate,
-	 const std::vector<std::vector<Moses::ScoreComponentCollection> >& featureValuesHope,
-	 const std::vector<std::vector<Moses::ScoreComponentCollection> >& featureValuesFear,
-	 const std::vector<std::vector<float> >& bleuScoresHope,
-	 const std::vector<std::vector<float> >& bleuScoresFear,
-	 const std::vector<std::vector<float> >& modelScoresHope,
-	 const std::vector<std::vector<float> >& modelScoresFear,
-	 float learning_rate,
-	 size_t rank,
-	 size_t epoch,
-	 int updatePosition = -1);
-  };
-
-  class MiraOptimiser : public Optimiser {
-  public:
+namespace Mira
+{
+
+class Optimiser
+{
+public:
+  Optimiser() {}
+
+  virtual size_t updateWeightsHopeFear(
+    Moses::ScoreComponentCollection& weightUpdate,
+    const std::vector<std::vector<Moses::ScoreComponentCollection> >& featureValuesHope,
+    const std::vector<std::vector<Moses::ScoreComponentCollection> >& featureValuesFear,
+    const std::vector<std::vector<float> >& bleuScoresHope,
+    const std::vector<std::vector<float> >& bleuScoresFear,
+    const std::vector<std::vector<float> >& modelScoresHope,
+    const std::vector<std::vector<float> >& modelScoresFear,
+    float learning_rate,
+    size_t rank,
+    size_t epoch,
+    int updatePosition = -1) = 0;
+};
+
+class Perceptron : public Optimiser
+{
+public:
+  virtual size_t updateWeightsHopeFear(
+    Moses::ScoreComponentCollection& weightUpdate,
+    const std::vector<std::vector<Moses::ScoreComponentCollection> >& featureValuesHope,
+    const std::vector<std::vector<Moses::ScoreComponentCollection> >& featureValuesFear,
+    const std::vector<std::vector<float> >& bleuScoresHope,
+    const std::vector<std::vector<float> >& bleuScoresFear,
+    const std::vector<std::vector<float> >& modelScoresHope,
+    const std::vector<std::vector<float> >& modelScoresFear,
+    float learning_rate,
+    size_t rank,
+    size_t epoch,
+    int updatePosition = -1);
+};
+
+class MiraOptimiser : public Optimiser
+{
+public:
   MiraOptimiser() :
     Optimiser() { }
-    
+
   MiraOptimiser(
-	float slack, bool scale_margin, bool scale_margin_precision,
-	bool scale_update, bool scale_update_precision, bool boost, bool normaliseMargin, float sigmoidParam) :
-      Optimiser(),
-      m_slack(slack),
-      m_scale_margin(scale_margin),
-      m_scale_margin_precision(scale_margin_precision),
-      m_scale_update(scale_update),
-      m_scale_update_precision(scale_update_precision),
-      m_precision(1),
-      m_boost(boost),
-      m_normaliseMargin(normaliseMargin),
-      m_sigmoidParam(sigmoidParam) { }
-    
-      size_t updateWeights(
-	   Moses::ScoreComponentCollection& weightUpdate,
-	   const std::vector<std::vector<Moses::ScoreComponentCollection> >& featureValues,
-	   const std::vector<std::vector<float> >& losses,
-	   const std::vector<std::vector<float> >& bleuScores,
-	   const std::vector<std::vector<float> >& modelScores,
-	   const std::vector< Moses::ScoreComponentCollection>& oracleFeatureValues,
-	   const std::vector< float> oracleBleuScores,
-	   const std::vector< float> oracleModelScores,
-	   float learning_rate,
-	   size_t rank,
-	   size_t epoch);
-	virtual size_t updateWeightsHopeFear(
-	   Moses::ScoreComponentCollection& weightUpdate,
-	   const std::vector<std::vector<Moses::ScoreComponentCollection> >& featureValuesHope,
-	   const std::vector<std::vector<Moses::ScoreComponentCollection> >& featureValuesFear,
-	   const std::vector<std::vector<float> >& bleuScoresHope,
-	   const std::vector<std::vector<float> >& bleuScoresFear,
-	   const std::vector<std::vector<float> >& modelScoresHope,
-	   const std::vector<std::vector<float> >& modelScoresFear,
-	   float learning_rate,
-	   size_t rank,
-	   size_t epoch,
-	   int updatePosition = -1);
-	size_t updateWeightsHopeFearSelective(
-	   Moses::ScoreComponentCollection& weightUpdate,
-	   const std::vector<std::vector<Moses::ScoreComponentCollection> >& featureValuesHope,
-	   const std::vector<std::vector<Moses::ScoreComponentCollection> >& featureValuesFear,
-	   const std::vector<std::vector<float> >& bleuScoresHope,
-	   const std::vector<std::vector<float> >& bleuScoresFear,
-	   const std::vector<std::vector<float> >& modelScoresHope,
-	   const std::vector<std::vector<float> >& modelScoresFear,
-	   float learning_rate,
-	   size_t rank,
-	   size_t epoch,
-	   int updatePosition = -1);
-	size_t updateWeightsHopeFearSummed(
-	   Moses::ScoreComponentCollection& weightUpdate,
-	   const std::vector<std::vector<Moses::ScoreComponentCollection> >& featureValuesHope,
-	   const std::vector<std::vector<Moses::ScoreComponentCollection> >& featureValuesFear,
-	   const std::vector<std::vector<float> >& bleuScoresHope,
-	   const std::vector<std::vector<float> >& bleuScoresFear,
-	   const std::vector<std::vector<float> >& modelScoresHope,
-	   const std::vector<std::vector<float> >& modelScoresFear,
-	   float learning_rate,
-	   size_t rank,
-	   size_t epoch,
-	   bool rescaleSlack,
-	   bool makePairs);
-	size_t updateWeightsAnalytically(
-	   Moses::ScoreComponentCollection& weightUpdate,
-	   Moses::ScoreComponentCollection& featureValuesHope,
-	   Moses::ScoreComponentCollection& featureValuesFear,
-	   float bleuScoreHope,
-	   float bleuScoreFear,
-	   float modelScoreHope,
-	   float modelScoreFear,
-	   float learning_rate,
-	   size_t rank,
-	   size_t epoch);
-
-     void setSlack(float slack) {
-       m_slack = slack;
-     }
-     
-     void setPrecision(float precision) {
-       m_precision = precision;
-     }
-     
-  private:
-     // regularise Hildreth updates
-     float m_slack;
-     
-     // scale margin with BLEU score or precision
-     bool m_scale_margin, m_scale_margin_precision;
-     
-     // scale update with oracle BLEU score or precision
-     bool m_scale_update, m_scale_update_precision;
-     
-     float m_precision;
-     
-     // boosting of updates on misranked candidates
-     bool m_boost;
-     
-     // squash margin between 0 and 1 (or depending on m_sigmoidParam)
-     bool m_normaliseMargin;
-     
-     // y=sigmoidParam is the axis that this sigmoid approaches
-     float m_sigmoidParam ;
-  };
+    float slack, bool scale_margin, bool scale_margin_precision,
+    bool scale_update, bool scale_update_precision, bool boost, bool normaliseMargin, float sigmoidParam) :
+    Optimiser(),
+    m_slack(slack),
+    m_scale_margin(scale_margin),
+    m_scale_margin_precision(scale_margin_precision),
+    m_scale_update(scale_update),
+    m_scale_update_precision(scale_update_precision),
+    m_precision(1),
+    m_boost(boost),
+    m_normaliseMargin(normaliseMargin),
+    m_sigmoidParam(sigmoidParam) { }
+
+  size_t updateWeights(
+    Moses::ScoreComponentCollection& weightUpdate,
+    const std::vector<std::vector<Moses::ScoreComponentCollection> >& featureValues,
+    const std::vector<std::vector<float> >& losses,
+    const std::vector<std::vector<float> >& bleuScores,
+    const std::vector<std::vector<float> >& modelScores,
+    const std::vector< Moses::ScoreComponentCollection>& oracleFeatureValues,
+    const std::vector< float> oracleBleuScores,
+    const std::vector< float> oracleModelScores,
+    float learning_rate,
+    size_t rank,
+    size_t epoch);
+  virtual size_t updateWeightsHopeFear(
+    Moses::ScoreComponentCollection& weightUpdate,
+    const std::vector<std::vector<Moses::ScoreComponentCollection> >& featureValuesHope,
+    const std::vector<std::vector<Moses::ScoreComponentCollection> >& featureValuesFear,
+    const std::vector<std::vector<float> >& bleuScoresHope,
+    const std::vector<std::vector<float> >& bleuScoresFear,
+    const std::vector<std::vector<float> >& modelScoresHope,
+    const std::vector<std::vector<float> >& modelScoresFear,
+    float learning_rate,
+    size_t rank,
+    size_t epoch,
+    int updatePosition = -1);
+  size_t updateWeightsHopeFearSelective(
+    Moses::ScoreComponentCollection& weightUpdate,
+    const std::vector<std::vector<Moses::ScoreComponentCollection> >& featureValuesHope,
+    const std::vector<std::vector<Moses::ScoreComponentCollection> >& featureValuesFear,
+    const std::vector<std::vector<float> >& bleuScoresHope,
+    const std::vector<std::vector<float> >& bleuScoresFear,
+    const std::vector<std::vector<float> >& modelScoresHope,
+    const std::vector<std::vector<float> >& modelScoresFear,
+    float learning_rate,
+    size_t rank,
+    size_t epoch,
+    int updatePosition = -1);
+  size_t updateWeightsHopeFearSummed(
+    Moses::ScoreComponentCollection& weightUpdate,
+    const std::vector<std::vector<Moses::ScoreComponentCollection> >& featureValuesHope,
+    const std::vector<std::vector<Moses::ScoreComponentCollection> >& featureValuesFear,
+    const std::vector<std::vector<float> >& bleuScoresHope,
+    const std::vector<std::vector<float> >& bleuScoresFear,
+    const std::vector<std::vector<float> >& modelScoresHope,
+    const std::vector<std::vector<float> >& modelScoresFear,
+    float learning_rate,
+    size_t rank,
+    size_t epoch,
+    bool rescaleSlack,
+    bool makePairs);
+  size_t updateWeightsAnalytically(
+    Moses::ScoreComponentCollection& weightUpdate,
+    Moses::ScoreComponentCollection& featureValuesHope,
+    Moses::ScoreComponentCollection& featureValuesFear,
+    float bleuScoreHope,
+    float bleuScoreFear,
+    float modelScoreHope,
+    float modelScoreFear,
+    float learning_rate,
+    size_t rank,
+    size_t epoch);
+
+  void setSlack(float slack) {
+    m_slack = slack;
+  }
+
+  void setPrecision(float precision) {
+    m_precision = precision;
+  }
+
+private:
+  // regularise Hildreth updates
+  float m_slack;
+
+  // scale margin with BLEU score or precision
+  bool m_scale_margin, m_scale_margin_precision;
+
+  // scale update with oracle BLEU score or precision
+  bool m_scale_update, m_scale_update_precision;
+
+  float m_precision;
+
+  // boosting of updates on misranked candidates
+  bool m_boost;
+
+  // squash margin between 0 and 1 (or depending on m_sigmoidParam)
+  bool m_normaliseMargin;
+
+  // y=sigmoidParam is the axis that this sigmoid approaches
+  float m_sigmoidParam ;
+};
 }
 
 #endif
diff --git a/mira/Perceptron.cpp b/mira/Perceptron.cpp
index 569a83216..af61c28a9 100644
--- a/mira/Perceptron.cpp
+++ b/mira/Perceptron.cpp
@@ -22,30 +22,31 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 using namespace Moses;
 using namespace std;
 
-namespace Mira {
+namespace Mira
+{
 
 size_t Perceptron::updateWeightsHopeFear(
-		ScoreComponentCollection& weightUpdate,
-		const vector< vector<ScoreComponentCollection> >& featureValuesHope,
-		const vector< vector<ScoreComponentCollection> >& featureValuesFear,
-		const vector< vector<float> >& dummy1,
-		const vector< vector<float> >& dummy2,
-		const vector< vector<float> >& dummy3,
-		const vector< vector<float> >& dummy4,
-		float perceptron_learning_rate,
-		size_t rank,
-		size_t epoch,
-		int updatePosition)
+  ScoreComponentCollection& weightUpdate,
+  const vector< vector<ScoreComponentCollection> >& featureValuesHope,
+  const vector< vector<ScoreComponentCollection> >& featureValuesFear,
+  const vector< vector<float> >& dummy1,
+  const vector< vector<float> >& dummy2,
+  const vector< vector<float> >& dummy3,
+  const vector< vector<float> >& dummy4,
+  float perceptron_learning_rate,
+  size_t rank,
+  size_t epoch,
+  int updatePosition)
 {
-	cerr << "Rank " << rank << ", epoch " << epoch << ", hope: " << featureValuesHope[0][0] << endl;
-	cerr << "Rank " << rank << ", epoch " << epoch << ", fear: " << featureValuesFear[0][0] << endl;
-	ScoreComponentCollection featureValueDiff = featureValuesHope[0][0];
-	featureValueDiff.MinusEquals(featureValuesFear[0][0]);
-	cerr << "Rank " << rank << ", epoch " << epoch << ", hope - fear: " << featureValueDiff << endl;
-	featureValueDiff.MultiplyEquals(perceptron_learning_rate);
-	weightUpdate.PlusEquals(featureValueDiff);
-	cerr << "Rank " << rank << ", epoch " << epoch << ", update: " << featureValueDiff << endl;
-	return 0;
+  cerr << "Rank " << rank << ", epoch " << epoch << ", hope: " << featureValuesHope[0][0] << endl;
+  cerr << "Rank " << rank << ", epoch " << epoch << ", fear: " << featureValuesFear[0][0] << endl;
+  ScoreComponentCollection featureValueDiff = featureValuesHope[0][0];
+  featureValueDiff.MinusEquals(featureValuesFear[0][0]);
+  cerr << "Rank " << rank << ", epoch " << epoch << ", hope - fear: " << featureValueDiff << endl;
+  featureValueDiff.MultiplyEquals(perceptron_learning_rate);
+  weightUpdate.PlusEquals(featureValueDiff);
+  cerr << "Rank " << rank << ", epoch " << epoch << ", update: " << featureValueDiff << endl;
+  return 0;
 }
 
 }
diff --git a/misc/processLexicalTableMin.cpp b/misc/processLexicalTableMin.cpp
index 3f2887e55..04f6590b1 100644
--- a/misc/processLexicalTableMin.cpp
+++ b/misc/processLexicalTableMin.cpp
@@ -20,7 +20,7 @@ void printHelp(char **argv)
             "\t-T string         -- path to temporary directory (uses /tmp by default)\n"
 #ifdef WITH_THREADS
             "\t-threads int|all  -- number of threads used for conversion\n"
-#endif 
+#endif
             "\n  advanced:\n"
             "\t-landmark int     -- use landmark phrase every 2^n phrases\n"
             "\t-fingerprint int  -- number of bits used for phrase fingerprints\n"
@@ -44,11 +44,11 @@ void printHelp(char **argv)
 
 int main(int argc, char** argv)
 {
-  
+
   std::string inFilePath;
   std::string outFilePath("out");
   std::string tempfilePath;
-  
+
   size_t orderBits = 10;
   size_t fingerPrintBits = 16;
   bool multipleScoreTrees = true;
@@ -56,52 +56,36 @@ int main(int argc, char** argv)
 
 #ifdef WITH_THREADS
   size_t threads = 1;
-#endif   
+#endif
 
-  if(1 >= argc)
-  {
+  if(1 >= argc) {
     printHelp(argv);
     return 1;
   }
-  for(int i = 1; i < argc; ++i)
-  {
+  for(int i = 1; i < argc; ++i) {
     std::string arg(argv[i]);
-    if("-in" == arg && i+1 < argc)
-    {
+    if("-in" == arg && i+1 < argc) {
       ++i;
       inFilePath = argv[i];
-    }
-    else if("-out" == arg && i+1 < argc)
-    {
+    } else if("-out" == arg && i+1 < argc) {
       ++i;
       outFilePath = argv[i];
-    }
-    else if("-T" == arg && i+1 < argc) {
+    } else if("-T" == arg && i+1 < argc) {
       ++i;
       tempfilePath = argv[i];
       util::NormalizeTempPrefix(tempfilePath);
-    }
-    else if("-landmark" == arg && i+1 < argc)
-    {
+    } else if("-landmark" == arg && i+1 < argc) {
       ++i;
       orderBits = atoi(argv[i]);
-    }
-    else if("-fingerprint" == arg && i+1 < argc)
-    {
+    } else if("-fingerprint" == arg && i+1 < argc) {
       ++i;
       fingerPrintBits = atoi(argv[i]);
-    }
-    else if("-join-scores" == arg)
-    {
+    } else if("-join-scores" == arg) {
       multipleScoreTrees = false;
-    }
-    else if("-quantize" == arg && i+1 < argc)
-    {
+    } else if("-quantize" == arg && i+1 < argc) {
       ++i;
       quantize = atoi(argv[i]);
-    }
-    else if("-threads" == arg && i+1 < argc)
-    {
+    } else if("-threads" == arg && i+1 < argc) {
 #ifdef WITH_THREADS
       ++i;
       if(std::string(argv[i]) == "all") {
@@ -109,23 +93,20 @@ int main(int argc, char** argv)
         if(!threads) {
           std::cerr << "Could not determine number of hardware threads, setting to 1" << std::endl;
           threads = 1;
-        }  
-      }
-      else
+        }
+      } else
         threads = atoi(argv[i]);
 #else
       std::cerr << "Thread support not compiled in" << std::endl;
       exit(1);
 #endif
-    }
-    else
-    {
+    } else {
       //somethings wrong... print help
       printHelp(argv);
       return 1;
     }
   }
-  
+
   if(outFilePath.rfind(".minlexr") != outFilePath.size() - 8)
     outFilePath += ".minlexr";
 
@@ -135,6 +116,6 @@ int main(int argc, char** argv)
     multipleScoreTrees, quantize
 #ifdef WITH_THREADS
     , threads
-#endif   
+#endif
   );
 }
diff --git a/misc/processPhraseTableMin.cpp b/misc/processPhraseTableMin.cpp
index 5c25262b8..1ea42252c 100644
--- a/misc/processPhraseTableMin.cpp
+++ b/misc/processPhraseTableMin.cpp
@@ -2,7 +2,7 @@
 
 #ifdef WITH_THREADS
 #include <boost/thread/thread.hpp>
-#endif 
+#endif
 
 #include "moses/TypeDef.h"
 #include "moses/TranslationModel/CompactPT/PhraseTableCreator.h"
@@ -11,7 +11,8 @@
 
 using namespace Moses;
 
-void printHelp(char **argv) {
+void printHelp(char **argv)
+{
   std::cerr << "Usage " << argv[0] << ":\n"
             "  options: \n"
             "\t-in  string       -- input table file name\n"
@@ -21,7 +22,7 @@ void printHelp(char **argv) {
             "\t-no-alignment-info   -- do not include alignment info in the binary phrase table\n"
 #ifdef WITH_THREADS
             "\t-threads int|all  -- number of threads used for conversion\n"
-#endif 
+#endif
             "\n  advanced:\n"
             "\t-encoding string  -- encoding type: PREnc REnc None (default PREnc)\n"
             "\t-rankscore int    -- score index of P(t|s) (default 2)\n"
@@ -48,14 +49,15 @@ void printHelp(char **argv) {
 }
 
 
-int main(int argc, char **argv) {
-    
+int main(int argc, char **argv)
+{
+
   std::string inFilePath;
   std::string outFilePath("out");
   std::string tempfilePath;
   PhraseTableCreator::Coding coding = PhraseTableCreator::PREnc;
-  
-  size_t numScoreComponent = 5;  
+
+  size_t numScoreComponent = 5;
   size_t orderBits = 10;
   size_t fingerprintBits = 16;
   bool useAlignmentInfo = true;
@@ -63,10 +65,10 @@ int main(int argc, char **argv) {
   size_t quantize = 0;
   size_t maxRank = 100;
   bool sortScoreIndexSet = false;
-  size_t sortScoreIndex = 2; 
+  size_t sortScoreIndex = 2;
   bool warnMe = true;
   size_t threads = 1;
-  
+
   if(1 >= argc) {
     printHelp(argv);
     return 1;
@@ -76,64 +78,49 @@ int main(int argc, char **argv) {
     if("-in" == arg && i+1 < argc) {
       ++i;
       inFilePath = argv[i];
-    }
-    else if("-out" == arg && i+1 < argc) {
+    } else if("-out" == arg && i+1 < argc) {
       ++i;
       outFilePath = argv[i];
-    }
-    else if("-T" == arg && i+1 < argc) {
+    } else if("-T" == arg && i+1 < argc) {
       ++i;
       tempfilePath = argv[i];
       util::NormalizeTempPrefix(tempfilePath);
-    }
-    else if("-encoding" == arg && i+1 < argc) {
+    } else if("-encoding" == arg && i+1 < argc) {
       ++i;
       std::string val(argv[i]);
       if(val == "None" || val == "none") {
         coding = PhraseTableCreator::None;
-      }
-      else if(val == "REnc" || val == "renc") {
+      } else if(val == "REnc" || val == "renc") {
         coding = PhraseTableCreator::REnc;
-      }
-      else if(val == "PREnc" || val == "prenc") {
+      } else if(val == "PREnc" || val == "prenc") {
         coding = PhraseTableCreator::PREnc;
       }
-    }
-    else if("-maxrank" == arg && i+1 < argc) {
+    } else if("-maxrank" == arg && i+1 < argc) {
       ++i;
       maxRank = atoi(argv[i]);
-    }
-    else if("-nscores" == arg && i+1 < argc) {
+    } else if("-nscores" == arg && i+1 < argc) {
       ++i;
       numScoreComponent = atoi(argv[i]);
-    }
-    else if("-rankscore" == arg && i+1 < argc) {
+    } else if("-rankscore" == arg && i+1 < argc) {
       ++i;
       sortScoreIndex = atoi(argv[i]);
       sortScoreIndexSet = true;
-    }
-    else if("-no-alignment-info" == arg) {
+    } else if("-no-alignment-info" == arg) {
       useAlignmentInfo = false;
-    }
-    else if("-landmark" == arg && i+1 < argc) {
+    } else if("-landmark" == arg && i+1 < argc) {
       ++i;
       orderBits = atoi(argv[i]);
-    }
-    else if("-fingerprint" == arg && i+1 < argc) {
+    } else if("-fingerprint" == arg && i+1 < argc) {
       ++i;
       fingerprintBits = atoi(argv[i]);
-    }
-    else if("-join-scores" == arg) {
+    } else if("-join-scores" == arg) {
       multipleScoreTrees = false;
-    }
-    else if("-quantize" == arg && i+1 < argc) {
+    } else if("-quantize" == arg && i+1 < argc) {
       ++i;
       quantize = atoi(argv[i]);
-    }
-    else if("-no-warnings" == arg) {
+    } else if("-no-warnings" == arg) {
       warnMe = false;
-    }
-    else if("-threads" == arg && i+1 < argc) {
+    } else if("-threads" == arg && i+1 < argc) {
 #ifdef WITH_THREADS
       ++i;
       if(std::string(argv[i]) == "all") {
@@ -141,40 +128,36 @@ int main(int argc, char **argv) {
         if(!threads) {
           std::cerr << "Could not determine number of hardware threads, setting to 1" << std::endl;
           threads = 1;
-        }  
-      }
-      else
+        }
+      } else
         threads = atoi(argv[i]);
 #else
       std::cerr << "Thread support not compiled in" << std::endl;
       exit(1);
 #endif
-    }
-    else {
+    } else {
       //something's wrong... print help
       printHelp(argv);
       return 1;
     }
   }
-  
-  if(!sortScoreIndexSet && numScoreComponent != 5 && coding == PhraseTableCreator::PREnc)
-  {
+
+  if(!sortScoreIndexSet && numScoreComponent != 5 && coding == PhraseTableCreator::PREnc) {
     std::cerr << "WARNING: You are using a nonstandard number of scores ("
               << numScoreComponent << ") with PREnc. Set the index of P(t|s) "
               "with  -rankscore int  if it is not "
               << sortScoreIndex << "." << std::endl;
   }
-  
-  if(sortScoreIndex >= numScoreComponent)
-  {
+
+  if(sortScoreIndex >= numScoreComponent) {
     std::cerr << "ERROR: -rankscore " << sortScoreIndex << " is out of range (0 ... "
               << (numScoreComponent-1) << ")" << std::endl;
     abort();
   }
-  
+
   if(outFilePath.rfind(".minphr") != outFilePath.size() - 7)
     outFilePath += ".minphr";
-  
+
   PhraseTableCreator(inFilePath, outFilePath, tempfilePath,
                      numScoreComponent, sortScoreIndex,
                      coding, orderBits, fingerprintBits,
@@ -182,6 +165,6 @@ int main(int argc, char **argv) {
                      quantize, maxRank, warnMe
 #ifdef WITH_THREADS
                      , threads
-#endif                     
-                     );
+#endif
+                    );
 }
diff --git a/misc/queryPhraseTable.cpp b/misc/queryPhraseTable.cpp
index d8103f371..5e4f7755a 100644
--- a/misc/queryPhraseTable.cpp
+++ b/misc/queryPhraseTable.cpp
@@ -33,8 +33,7 @@ int main(int argc, char **argv)
       needAlignments = true;
     } else if (!strcmp(argv[i], "-c")) {
       reportCounts = true;
-    }
-    else
+    } else
       usage();
   }
 
diff --git a/misc/queryPhraseTableMin.cpp b/misc/queryPhraseTableMin.cpp
index f4dca8b6b..6b6f9beaf 100644
--- a/misc/queryPhraseTableMin.cpp
+++ b/misc/queryPhraseTableMin.cpp
@@ -36,8 +36,7 @@ int main(int argc, char **argv)
       useAlignments = true;
     } else if (!strcmp(argv[i], "-c")) {
       reportCounts = true;
-    }
-    else
+    } else
       usage();
   }
 
@@ -47,28 +46,28 @@ int main(int argc, char **argv)
   std::vector<FactorType> input(1, 0);
   std::vector<FactorType> output(1, 0);
   std::vector<float> weight(nscores, 0);
-    
+
   Parameter *parameter = new Parameter();
   const_cast<std::vector<std::string>&>(parameter->GetParam("factor-delimiter")).resize(1, "||dummy_string||");
   const_cast<std::vector<std::string>&>(parameter->GetParam("input-factors")).resize(1, "0");
   const_cast<std::vector<std::string>&>(parameter->GetParam("verbose")).resize(1, "0");
   const_cast<std::vector<std::string>&>(parameter->GetParam("weight-w")).resize(1, "0");
   const_cast<std::vector<std::string>&>(parameter->GetParam("weight-d")).resize(1, "0");
-  
+
   StaticData::InstanceNonConst().LoadData(parameter);
 
   PhraseDictionaryCompact pdc("input-factor=0 output-factor=0 num-features=5 path=" + ttable);
-  bool ret = pdc.InitDictionary(); 
+  bool ret = pdc.InitDictionary();
   assert(ret);
-  
+
   std::string line;
   while(getline(std::cin, line)) {
     Phrase sourcePhrase;
     sourcePhrase.CreateFromString(Input, input, line, "||dummy_string||", NULL);
-    
+
     TargetPhraseVectorPtr decodedPhraseColl
-      = pdc.GetTargetPhraseCollectionRaw(sourcePhrase);
-    
+    = pdc.GetTargetPhraseCollectionRaw(sourcePhrase);
+
     if(decodedPhraseColl != NULL) {
       if(reportCounts)
         std::cout << sourcePhrase << decodedPhraseColl->size() << std::endl;
@@ -77,19 +76,18 @@ int main(int argc, char **argv)
           TargetPhrase &tp = *it;
           std::cout << sourcePhrase << "||| ";
           std::cout << static_cast<const Phrase&>(tp) << "|||";
-          
+
           if(useAlignments)
-            std::cout << " " << tp.GetAlignTerm() << "|||"; 
-          
+            std::cout << " " << tp.GetAlignTerm() << "|||";
+
           std::vector<float> scores = tp.GetScoreBreakdown().GetScoresForProducer(&pdc);
           for(size_t i = 0; i < scores.size(); i++)
             std::cout << " " << exp(scores[i]);
           std::cout << std::endl;
         }
-    }
-    else if(reportCounts)
+    } else if(reportCounts)
       std::cout << sourcePhrase << 0 << std::endl;
-    
+
     std::cout.flush();
   }
 }
diff --git a/moses-chart-cmd/IOWrapper.cpp b/moses-chart-cmd/IOWrapper.cpp
index 92f68a84d..b130943a1 100644
--- a/moses-chart-cmd/IOWrapper.cpp
+++ b/moses-chart-cmd/IOWrapper.cpp
@@ -138,7 +138,8 @@ IOWrapper::~IOWrapper()
   delete m_alignmentInfoCollector;
 }
 
-void IOWrapper::ResetTranslationId() {
+void IOWrapper::ResetTranslationId()
+{
   m_translationId = StaticData::Instance().GetStartTranslationId();
 }
 
@@ -174,7 +175,7 @@ void OutputSurface(std::ostream &out, const Phrase &phrase, const std::vector<Fa
 
       for (size_t i = 1 ; i < outputFactorOrder.size() ; i++) {
         const Factor *factor = phrase.GetFactor(pos, outputFactorOrder[i]);
-	CHECK(factor);
+        CHECK(factor);
 
         out << "|" << *factor;
       }
@@ -245,8 +246,8 @@ void OutputInput(std::ostream& os, const ChartHypothesis* hypo)
 // Given a hypothesis and sentence, reconstructs the 'application context' --
 // the source RHS symbols of the SCFG rule that was applied, plus their spans.
 void IOWrapper::ReconstructApplicationContext(const ChartHypothesis &hypo,
-                                   const Sentence &sentence,
-                                   ApplicationContext &context)
+    const Sentence &sentence,
+    ApplicationContext &context)
 {
   context.clear();
   const std::vector<const ChartHypothesis*> &prevHypos = hypo.GetPrevHypos();
@@ -276,7 +277,7 @@ void IOWrapper::ReconstructApplicationContext(const ChartHypothesis &hypo,
 // but there are scripts and tools that expect the output of -T to look like
 // that.
 void IOWrapper::WriteApplicationContext(std::ostream &out,
-                             const ApplicationContext &context)
+                                        const ApplicationContext &context)
 {
   assert(!context.empty());
   ApplicationContext::const_reverse_iterator p = context.rbegin();
@@ -327,7 +328,7 @@ void IOWrapper::OutputDetailedTranslationReport(
   CHECK(m_detailOutputCollector);
   m_detailOutputCollector->Write(translationId, out.str());
 }
-  
+
 
 void IOWrapper::OutputBestHypo(const ChartHypothesis *hypo, long translationId)
 {
@@ -344,18 +345,18 @@ void IOWrapper::OutputBestHypo(const ChartHypothesis *hypo, long translationId)
     if (StaticData::Instance().GetOutputHypoScore()) {
       out << hypo->GetTotalScore() << " ";
     }
-    
+
     if (StaticData::Instance().IsPathRecoveryEnabled()) {
       out << "||| ";
     }
     Phrase outPhrase(ARRAY_SIZE_INCR);
     hypo->CreateOutputPhrase(outPhrase);
-    
+
     // delete 1st & last
     CHECK(outPhrase.GetSize() >= 2);
     outPhrase.RemoveWord(0);
     outPhrase.RemoveWord(outPhrase.GetSize() - 1);
-    
+
     const std::vector<FactorType> outputFactorOrder = StaticData::Instance().GetOutputFactorOrder();
     string output = outPhrase.GetStringRep(outputFactorOrder);
     out << output << endl;
@@ -371,7 +372,8 @@ void IOWrapper::OutputBestHypo(const ChartHypothesis *hypo, long translationId)
   m_singleBestOutputCollector->Write(translationId, out.str());
 }
 
-void IOWrapper::OutputBestHypo(search::Applied applied, long translationId) {
+void IOWrapper::OutputBestHypo(search::Applied applied, long translationId)
+{
   if (!m_singleBestOutputCollector) return;
   std::ostringstream out;
   IOWrapper::FixPrecision(out);
@@ -389,7 +391,8 @@ void IOWrapper::OutputBestHypo(search::Applied applied, long translationId) {
   m_singleBestOutputCollector->Write(translationId, out.str());
 }
 
-void IOWrapper::OutputBestNone(long translationId) {
+void IOWrapper::OutputBestNone(long translationId)
+{
   if (!m_singleBestOutputCollector) return;
   if (StaticData::Instance().GetOutputHypoScore()) {
     m_singleBestOutputCollector->Write(translationId, "0 \n");
@@ -443,7 +446,8 @@ void IOWrapper::OutputFeatureScores( std::ostream& out, const ScoreComponentColl
   }
 }
 
-void IOWrapper::OutputNBestList(const ChartTrellisPathList &nBestList, long translationId) {
+void IOWrapper::OutputNBestList(const ChartTrellisPathList &nBestList, long translationId)
+{
   std::ostringstream out;
 
   // Check if we're writing to std::cout.
@@ -452,7 +456,7 @@ void IOWrapper::OutputNBestList(const ChartTrellisPathList &nBestList, long tran
     // preserve existing behaviour, but should probably be done either way.
     IOWrapper::FixPrecision(out);
 
-    // Used to check StaticData's GetOutputHypoScore(), but it makes no sense with nbest output.  
+    // Used to check StaticData's GetOutputHypoScore(), but it makes no sense with nbest output.
   }
 
   //bool includeAlignment = StaticData::Instance().NBestIncludesAlignment();
@@ -528,7 +532,8 @@ void IOWrapper::OutputNBestList(const ChartTrellisPathList &nBestList, long tran
   m_nBestOutputCollector->Write(translationId, out.str());
 }
 
-void IOWrapper::OutputNBestList(const std::vector<search::Applied> &nbest, long translationId) {
+void IOWrapper::OutputNBestList(const std::vector<search::Applied> &nbest, long translationId)
+{
   std::ostringstream out;
   // wtf? copied from the original OutputNBestList
   if (m_nBestOutputCollector->OutputIsCout()) {
@@ -565,12 +570,11 @@ void ShiftOffsets(vector<T> &offsets, T shift)
   T currPos = shift;
   for (size_t i = 0; i < offsets.size(); ++i) {
     if (offsets[i] == 0) {
-	  offsets[i] = currPos;
-	  ++currPos;
-	}
-	else {
-	  currPos += offsets[i];
-	}
+      offsets[i] = currPos;
+      ++currPos;
+    } else {
+      currPos += offsets[i];
+    }
   }
 }
 
@@ -630,8 +634,7 @@ size_t IOWrapper::OutputAlignmentNBest(Alignments &retAlign, const Moses::ChartT
 
       totalTargetSize += targetSize;
       ++targetInd;
-    }
-    else {
+    } else {
       ++totalTargetSize;
     }
   }
@@ -666,15 +669,15 @@ void IOWrapper::OutputAlignment(size_t translationId , const Moses::ChartHypothe
   ostringstream out;
 
   if (hypo) {
-	Alignments retAlign;
-	OutputAlignment(retAlign, hypo, 0);
-
-	// output alignments
-	Alignments::const_iterator iter;
-	for (iter = retAlign.begin(); iter != retAlign.end(); ++iter) {
-	  const pair<size_t, size_t> &alignPoint = *iter;
-	  out << alignPoint.first << "-" << alignPoint.second << " ";
-	}
+    Alignments retAlign;
+    OutputAlignment(retAlign, hypo, 0);
+
+    // output alignments
+    Alignments::const_iterator iter;
+    for (iter = retAlign.begin(); iter != retAlign.end(); ++iter) {
+      const pair<size_t, size_t> &alignPoint = *iter;
+      out << alignPoint.first << "-" << alignPoint.second << " ";
+    }
   }
   out << endl;
 
@@ -724,8 +727,7 @@ size_t IOWrapper::OutputAlignment(Alignments &retAlign, const Moses::ChartHypoth
 
       totalTargetSize += targetSize;
       ++targetInd;
-    }
-    else {
+    } else {
       ++totalTargetSize;
     }
   }
diff --git a/moses-chart-cmd/IOWrapper.h b/moses-chart-cmd/IOWrapper.h
index 3178b6507..aba73e9a6 100644
--- a/moses-chart-cmd/IOWrapper.h
+++ b/moses-chart-cmd/IOWrapper.h
@@ -91,11 +91,11 @@ protected:
                                const ApplicationContext &context);
 
   void OutputAllFeatureScores(const Moses::ScoreComponentCollection &features
-                                , std::ostream &out);
+                              , std::ostream &out);
   void OutputFeatureScores( std::ostream& out
-                                , const Moses::ScoreComponentCollection &features
-                                , const Moses::FeatureFunction *ff
-                                , std::string &lastName );
+                            , const Moses::ScoreComponentCollection &features
+                            , const Moses::FeatureFunction *ff
+                            , std::string &lastName );
 
 public:
   IOWrapper(const std::vector<Moses::FactorType>	&inputFactorOrder
diff --git a/moses-chart-cmd/Main.cpp b/moses-chart-cmd/Main.cpp
index a7568f5fb..61b8b9f5e 100644
--- a/moses-chart-cmd/Main.cpp
+++ b/moses-chart-cmd/Main.cpp
@@ -190,7 +190,7 @@ static void PrintFeatureWeight(const FeatureFunction* ff)
   size_t numScoreComps = ff->GetNumScoreComponents();
   vector<float> values = StaticData::Instance().GetAllWeights().GetScoresForProducer(ff);
   for (size_t i = 0; i < numScoreComps; ++i) {
-  	cout << " " << values[i];
+    cout << " " << values[i];
   }
   cout << endl;
 
@@ -244,12 +244,12 @@ int main(int argc, char* argv[])
       ShowWeights();
       exit(0);
     }
-  
+
     CHECK(staticData.IsChart());
-  
+
     // set up read/writing class
     IOWrapper *ioWrapper = GetIOWrapper(staticData);
-  
+
     // check on weights
     const ScoreComponentCollection& weights = staticData.GetAllWeights();
     IFVERBOSE(2) {
@@ -264,7 +264,7 @@ int main(int argc, char* argv[])
 #ifdef WITH_THREADS
     ThreadPool pool(staticData.ThreadCount());
 #endif
-  
+
     // read each sentence & decode
     InputType *source=0;
     while(ReadInput(*ioWrapper,staticData.GetInputType(),source)) {
@@ -279,16 +279,16 @@ int main(int argc, char* argv[])
       delete task;
 #endif
     }
-  
+
 #ifdef WITH_THREADS
     pool.Stop(true);  // flush remaining jobs
 #endif
-  
+
     delete ioWrapper;
-  
+
     IFVERBOSE(1)
     PrintUserTime("End.");
-  
+
   } catch (const std::exception &e) {
     std::cerr << "Exception: " << e.what() << std::endl;
     return EXIT_FAILURE;
diff --git a/moses-chart-cmd/Main.h b/moses-chart-cmd/Main.h
index 4f2765695..319e3889c 100644
--- a/moses-chart-cmd/Main.h
+++ b/moses-chart-cmd/Main.h
@@ -36,8 +36,9 @@ POSSIBILITY OF SUCH DAMAGE.
 
 #include "moses/StaticData.h"
 
-namespace MosesChartCmd {
-  class IOWrapper;
+namespace MosesChartCmd
+{
+class IOWrapper;
 }
 
 int main(int argc, char* argv[]);
diff --git a/moses-cmd/IOWrapper.cpp b/moses-cmd/IOWrapper.cpp
index e5346852f..44e60ddf3 100644
--- a/moses-cmd/IOWrapper.cpp
+++ b/moses-cmd/IOWrapper.cpp
@@ -53,47 +53,47 @@ namespace MosesCmd
 {
 
 IOWrapper::IOWrapper(
-    const vector<FactorType>				&inputFactorOrder
-    , const vector<FactorType>			&outputFactorOrder
-    , const FactorMask							&inputFactorUsed
-    , size_t												nBestSize
-    , const string									&nBestFilePath)
-:m_inputFactorOrder(inputFactorOrder)
-,m_outputFactorOrder(outputFactorOrder)
-,m_inputFactorUsed(inputFactorUsed)
-,m_inputFile(NULL)
-,m_inputStream(&std::cin)
-,m_nBestStream(NULL)
-,m_outputWordGraphStream(NULL)
-,m_outputSearchGraphStream(NULL)
-,m_detailedTranslationReportingStream(NULL)
-,m_alignmentOutputStream(NULL)
+  const vector<FactorType>				&inputFactorOrder
+  , const vector<FactorType>			&outputFactorOrder
+  , const FactorMask							&inputFactorUsed
+  , size_t												nBestSize
+  , const string									&nBestFilePath)
+  :m_inputFactorOrder(inputFactorOrder)
+  ,m_outputFactorOrder(outputFactorOrder)
+  ,m_inputFactorUsed(inputFactorUsed)
+  ,m_inputFile(NULL)
+  ,m_inputStream(&std::cin)
+  ,m_nBestStream(NULL)
+  ,m_outputWordGraphStream(NULL)
+  ,m_outputSearchGraphStream(NULL)
+  ,m_detailedTranslationReportingStream(NULL)
+  ,m_alignmentOutputStream(NULL)
 {
   Initialization(inputFactorOrder, outputFactorOrder
-      , inputFactorUsed
-      , nBestSize, nBestFilePath);
+                 , inputFactorUsed
+                 , nBestSize, nBestFilePath);
 }
 
 IOWrapper::IOWrapper(const std::vector<FactorType>	&inputFactorOrder
-    , const std::vector<FactorType>	&outputFactorOrder
-    , const FactorMask							&inputFactorUsed
-    , size_t												nBestSize
-    , const std::string							&nBestFilePath
-    , const std::string							&inputFilePath)
-:m_inputFactorOrder(inputFactorOrder)
-,m_outputFactorOrder(outputFactorOrder)
-,m_inputFactorUsed(inputFactorUsed)
-,m_inputFilePath(inputFilePath)
-,m_inputFile(new InputFileStream(inputFilePath))
-,m_nBestStream(NULL)
-,m_outputWordGraphStream(NULL)
-,m_outputSearchGraphStream(NULL)
-,m_detailedTranslationReportingStream(NULL)
-,m_alignmentOutputStream(NULL)
+                     , const std::vector<FactorType>	&outputFactorOrder
+                     , const FactorMask							&inputFactorUsed
+                     , size_t												nBestSize
+                     , const std::string							&nBestFilePath
+                     , const std::string							&inputFilePath)
+  :m_inputFactorOrder(inputFactorOrder)
+  ,m_outputFactorOrder(outputFactorOrder)
+  ,m_inputFactorUsed(inputFactorUsed)
+  ,m_inputFilePath(inputFilePath)
+  ,m_inputFile(new InputFileStream(inputFilePath))
+  ,m_nBestStream(NULL)
+  ,m_outputWordGraphStream(NULL)
+  ,m_outputSearchGraphStream(NULL)
+  ,m_detailedTranslationReportingStream(NULL)
+  ,m_alignmentOutputStream(NULL)
 {
   Initialization(inputFactorOrder, outputFactorOrder
-      , inputFactorUsed
-      , nBestSize, nBestFilePath);
+                 , inputFactorUsed
+                 , nBestSize, nBestFilePath);
 
   m_inputStream = m_inputFile;
 }
@@ -117,10 +117,10 @@ IOWrapper::~IOWrapper()
 }
 
 void IOWrapper::Initialization(const std::vector<FactorType>	&/*inputFactorOrder*/
-    , const std::vector<FactorType>			&/*outputFactorOrder*/
-    , const FactorMask							&/*inputFactorUsed*/
-    , size_t												nBestSize
-    , const std::string							&nBestFilePath)
+                               , const std::vector<FactorType>			&/*outputFactorOrder*/
+                               , const FactorMask							&/*inputFactorUsed*/
+                               , size_t												nBestSize
+                               , const std::string							&nBestFilePath)
 {
   const StaticData &staticData = StaticData::Instance();
 
@@ -192,7 +192,7 @@ InputType*IOWrapper::GetInput(InputType* inputType)
  * print surface factor only for the given phrase
  */
 void OutputSurface(std::ostream &out, const Hypothesis &edge, const std::vector<FactorType> &outputFactorOrder,
-    bool reportSegmentation, bool reportAllFactors)
+                   bool reportSegmentation, bool reportAllFactors)
 {
   CHECK(outputFactorOrder.size() > 0);
   const Phrase& phrase = edge.GetCurrTargetPhrase();
@@ -218,12 +218,12 @@ void OutputSurface(std::ostream &out, const Hypothesis &edge, const std::vector<
   // trace option "-t"
   if (reportSegmentation == true && phrase.GetSize() > 0) {
     out << "|" << edge.GetCurrSourceWordsRange().GetStartPos()
-	    << "-" << edge.GetCurrSourceWordsRange().GetEndPos() << "| ";
+        << "-" << edge.GetCurrSourceWordsRange().GetEndPos() << "| ";
   }
 }
 
 void OutputBestSurface(std::ostream &out, const Hypothesis *hypo, const std::vector<FactorType> &outputFactorOrder,
-    bool reportSegmentation, bool reportAllFactors)
+                       bool reportSegmentation, bool reportAllFactors)
 {
   if (hypo != NULL) {
     // recursively retrace this best path through the lattice, starting from the end of the hypothesis sentence
@@ -377,10 +377,10 @@ void IOWrapper::OutputBestHypo(const Hypothesis *hypo, long /*translationId*/, b
 }
 
 void OutputNBest(std::ostream& out
-                  , const Moses::TrellisPathList &nBestList
-                  , const std::vector<Moses::FactorType>& outputFactorOrder
-                  , long translationId
-                  , bool reportSegmentation)
+                 , const Moses::TrellisPathList &nBestList
+                 , const std::vector<Moses::FactorType>& outputFactorOrder
+                 , long translationId
+                 , bool reportSegmentation)
 {
   const StaticData &staticData = StaticData::Instance();
   bool labeledOutput = staticData.IsLabeledNBestList();
@@ -473,9 +473,9 @@ void OutputAllFeatureScores(const Moses::ScoreComponentCollection &features
 }
 
 void OutputFeatureScores( std::ostream& out
-                                      , const ScoreComponentCollection &features
-                                      , const FeatureFunction *ff
-                                      , std::string &lastName )
+                          , const ScoreComponentCollection &features
+                          , const FeatureFunction *ff
+                          , std::string &lastName )
 {
   const StaticData &staticData = StaticData::Instance();
   bool labeledOutput = staticData.IsLabeledNBestList();
@@ -556,7 +556,7 @@ IOWrapper *GetIOWrapper(const StaticData &staticData)
 {
   IOWrapper *ioWrapper;
   const std::vector<FactorType> &inputFactorOrder = staticData.GetInputFactorOrder()
-          ,&outputFactorOrder = staticData.GetOutputFactorOrder();
+      ,&outputFactorOrder = staticData.GetOutputFactorOrder();
   FactorMask inputFactorUsed(inputFactorOrder);
 
   // io
@@ -565,14 +565,14 @@ IOWrapper *GetIOWrapper(const StaticData &staticData)
     string filePath = staticData.GetParam("input-file")[0];
 
     ioWrapper = new IOWrapper(inputFactorOrder, outputFactorOrder, inputFactorUsed
-        , staticData.GetNBestSize()
-        , staticData.GetNBestFilePath()
-        , filePath);
+                              , staticData.GetNBestSize()
+                              , staticData.GetNBestFilePath()
+                              , filePath);
   } else {
     VERBOSE(1,"IO from STDOUT/STDIN" << endl);
     ioWrapper = new IOWrapper(inputFactorOrder, outputFactorOrder, inputFactorUsed
-        , staticData.GetNBestSize()
-        , staticData.GetNBestFilePath());
+                              , staticData.GetNBestSize()
+                              , staticData.GetNBestFilePath());
   }
   ioWrapper->ResetTranslationId();
 
diff --git a/moses-cmd/IOWrapper.h b/moses-cmd/IOWrapper.h
index fac9ca307..66b9377dc 100644
--- a/moses-cmd/IOWrapper.h
+++ b/moses-cmd/IOWrapper.h
@@ -142,12 +142,12 @@ void OutputAlignment(Moses::OutputCollector* collector, size_t lineNo,  const Mo
 void OutputAlignment(std::ostream &out, const Moses::Hypothesis *hypo);
 
 void OutputNBest(std::ostream& out
-                  , const Moses::TrellisPathList &nBestList
-                  , const std::vector<Moses::FactorType>& outputFactorOrder
-                  , long translationId
-                  , bool reportSegmentation);
+                 , const Moses::TrellisPathList &nBestList
+                 , const std::vector<Moses::FactorType>& outputFactorOrder
+                 , long translationId
+                 , bool reportSegmentation);
 void OutputAllFeatureScores(const Moses::ScoreComponentCollection &features
-                              , std::ostream &out);
+                            , std::ostream &out);
 void OutputFeatureScores( std::ostream& out
                           , const Moses::ScoreComponentCollection &features
                           , const Moses::FeatureFunction *ff
diff --git a/moses-cmd/Main.cpp b/moses-cmd/Main.cpp
index 3a6f2856e..d70b64536 100644
--- a/moses-cmd/Main.cpp
+++ b/moses-cmd/Main.cpp
@@ -92,7 +92,7 @@ public:
                   OutputCollector* alignmentInfoCollector,
                   OutputCollector* unknownsCollector,
                   bool outputSearchGraphSLF,
-		  bool outputSearchGraphHypergraph) :
+                  bool outputSearchGraphHypergraph) :
     m_source(source), m_lineNumber(lineNumber),
     m_outputCollector(outputCollector), m_nbestCollector(nbestCollector),
     m_latticeSamplesCollector(latticeSamplesCollector),
@@ -103,7 +103,7 @@ public:
     m_outputSearchGraphSLF(outputSearchGraphSLF),
     m_outputSearchGraphHypergraph(outputSearchGraphHypergraph) {}
 
-	/** Translate one sentence
+  /** Translate one sentence
    * gets called by main function implemented at end of this source file */
   void Run() {
 
@@ -150,7 +150,7 @@ public:
         manager.SerializeSearchGraphPB(m_lineNumber, output);
       }
 #endif
-    }		
+    }
 
     // Output search graph in HTK standard lattice format (SLF)
     if (m_outputSearchGraphSLF) {
@@ -159,13 +159,13 @@ public:
       std::ofstream *file = new std::ofstream;
       file->open(fileName.str().c_str());
       if (file->is_open() && file->good()) {
-	ostringstream out;
-	fix(out,PRECISION);
-	manager.OutputSearchGraphAsSLF(m_lineNumber, out);
-	*file << out.str();
-	file -> flush();
+        ostringstream out;
+        fix(out,PRECISION);
+        manager.OutputSearchGraphAsSLF(m_lineNumber, out);
+        *file << out.str();
+        file -> flush();
       } else {
-	TRACE_ERR("Cannot output HTK standard lattice for line " << m_lineNumber << " because the output file is not open or not ready for writing" << std::endl);
+        TRACE_ERR("Cannot output HTK standard lattice for line " << m_lineNumber << " because the output file is not open or not ready for writing" << std::endl);
       }
     }
 
@@ -176,91 +176,91 @@ public:
 
       bool appendSuffix;
       if (hypergraphParameters.size() > 0 && hypergraphParameters[0] == "true") {
-	appendSuffix = true;
+        appendSuffix = true;
       } else {
-	appendSuffix = false;
+        appendSuffix = false;
       }
 
       string compression;
       if (hypergraphParameters.size() > 1) {
-	compression = hypergraphParameters[1];
+        compression = hypergraphParameters[1];
       } else {
-	compression = "txt";
+        compression = "txt";
       }
 
       string hypergraphDir;
       if ( hypergraphParameters.size() > 2 ) {
         hypergraphDir = hypergraphParameters[2];
       } else {
-	string nbestFile = staticData.GetNBestFilePath();
-	if ( ! nbestFile.empty() && nbestFile!="-" && !boost::starts_with(nbestFile,"/dev/stdout") ) {
-	  boost::filesystem::path nbestPath(nbestFile);
-
-	  // In the Boost filesystem API version 2, 
-	  //   which was the default prior to Boost 1.46,
-	  //   the filename() method returned a string.
-	  //
-	  // In the Boost filesystem API version 3,
-	  //   which is the default starting with Boost 1.46,
-	  //   the filename() method returns a path object.
-	  //
-	  // To get a string from the path object, 
-	  //   the native() method must be called.
-	  //	  hypergraphDir = nbestPath.parent_path().filename()
-	  //#if BOOST_VERSION >= 104600
-	  //	    .native()
-	  //#endif
-	  //;
-
-	  // Hopefully the following compiles under all versions of Boost.
-	  //
-	  // If this line gives you compile errors,
-	  //   contact Lane Schwartz on the Moses mailing list
-	  hypergraphDir = nbestPath.parent_path().string();
-
-	} else {
-	  stringstream hypergraphDirName;
-	  hypergraphDirName << boost::filesystem::current_path() << "/hypergraph";
-	  hypergraphDir = hypergraphDirName.str();
-	}
+        string nbestFile = staticData.GetNBestFilePath();
+        if ( ! nbestFile.empty() && nbestFile!="-" && !boost::starts_with(nbestFile,"/dev/stdout") ) {
+          boost::filesystem::path nbestPath(nbestFile);
+
+          // In the Boost filesystem API version 2,
+          //   which was the default prior to Boost 1.46,
+          //   the filename() method returned a string.
+          //
+          // In the Boost filesystem API version 3,
+          //   which is the default starting with Boost 1.46,
+          //   the filename() method returns a path object.
+          //
+          // To get a string from the path object,
+          //   the native() method must be called.
+          //	  hypergraphDir = nbestPath.parent_path().filename()
+          //#if BOOST_VERSION >= 104600
+          //	    .native()
+          //#endif
+          //;
+
+          // Hopefully the following compiles under all versions of Boost.
+          //
+          // If this line gives you compile errors,
+          //   contact Lane Schwartz on the Moses mailing list
+          hypergraphDir = nbestPath.parent_path().string();
+
+        } else {
+          stringstream hypergraphDirName;
+          hypergraphDirName << boost::filesystem::current_path() << "/hypergraph";
+          hypergraphDir = hypergraphDirName.str();
+        }
       }
 
       if ( ! boost::filesystem::exists(hypergraphDir) ) {
-	boost::filesystem::create_directory(hypergraphDir);
-      } 
+        boost::filesystem::create_directory(hypergraphDir);
+      }
 
       if ( ! boost::filesystem::exists(hypergraphDir) ) {
-	TRACE_ERR("Cannot output hypergraphs to " << hypergraphDir << " because the directory does not exist" << std::endl);
+        TRACE_ERR("Cannot output hypergraphs to " << hypergraphDir << " because the directory does not exist" << std::endl);
       } else if ( ! boost::filesystem::is_directory(hypergraphDir) ) {
-	TRACE_ERR("Cannot output hypergraphs to " << hypergraphDir << " because that path exists, but is not a directory" << std::endl);
+        TRACE_ERR("Cannot output hypergraphs to " << hypergraphDir << " because that path exists, but is not a directory" << std::endl);
       } else {
-	stringstream fileName;
-	fileName << hypergraphDir << "/" << m_lineNumber;
-	if ( appendSuffix ) {
-	  fileName << "." << compression;
-	}
-	boost::iostreams::filtering_ostream *file = new boost::iostreams::filtering_ostream;
-
-	if ( compression == "gz" ) {
-	  file->push( boost::iostreams::gzip_compressor() );
-	} else if ( compression == "bz2" ) {
-	  file->push( boost::iostreams::bzip2_compressor() );
-	} else if ( compression != "txt" ) {
-	  TRACE_ERR("Unrecognized hypergraph compression format (" << compression << ") - using uncompressed plain txt" << std::endl);
-	  compression = "txt";
-	}
-
-	file->push( boost::iostreams::file_sink(fileName.str(), ios_base::out) );
-
-	if (file->is_complete() && file->good()) {
-	  fix(*file,PRECISION);
-	  manager.OutputSearchGraphAsHypergraph(m_lineNumber, *file);
-	  file -> flush();
-	} else {
-	  TRACE_ERR("Cannot output hypergraph for line " << m_lineNumber << " because the output file " << fileName.str() << " is not open or not ready for writing" << std::endl);
-	}
-	file -> pop();
-	delete file;
+        stringstream fileName;
+        fileName << hypergraphDir << "/" << m_lineNumber;
+        if ( appendSuffix ) {
+          fileName << "." << compression;
+        }
+        boost::iostreams::filtering_ostream *file = new boost::iostreams::filtering_ostream;
+
+        if ( compression == "gz" ) {
+          file->push( boost::iostreams::gzip_compressor() );
+        } else if ( compression == "bz2" ) {
+          file->push( boost::iostreams::bzip2_compressor() );
+        } else if ( compression != "txt" ) {
+          TRACE_ERR("Unrecognized hypergraph compression format (" << compression << ") - using uncompressed plain txt" << std::endl);
+          compression = "txt";
+        }
+
+        file->push( boost::iostreams::file_sink(fileName.str(), ios_base::out) );
+
+        if (file->is_complete() && file->good()) {
+          fix(*file,PRECISION);
+          manager.OutputSearchGraphAsHypergraph(m_lineNumber, *file);
+          file -> flush();
+        } else {
+          TRACE_ERR("Cannot output hypergraph for line " << m_lineNumber << " because the output file " << fileName.str() << " is not open or not ready for writing" << std::endl);
+        }
+        file -> pop();
+        delete file;
       }
     }
 
@@ -277,8 +277,7 @@ public:
 
       // MAP decoding: best hypothesis
       const Hypothesis* bestHypo = NULL;
-      if (!staticData.UseMBR()) 
-	  {
+      if (!staticData.UseMBR()) {
         bestHypo = manager.GetBestHypothesis();
         if (bestHypo) {
           if (staticData.IsPathRecoveryEnabled()) {
@@ -296,7 +295,7 @@ public:
             staticData.GetReportSegmentation(),
             staticData.GetReportAllFactors());
           if (staticData.PrintAlignmentInfo()) {
-        	out << "||| ";
+            out << "||| ";
             OutputAlignment(out, bestHypo);
           }
 
@@ -306,11 +305,10 @@ public:
           }
         }
         out << endl;
-	  }
+      }
 
       // MBR decoding (n-best MBR, lattice MBR, consensus)
-      else 
-			{
+      else {
         // we first need the n-best translations
         size_t nBestSize = staticData.GetMBRSize();
         if (nBestSize <= 0) {
@@ -346,7 +344,7 @@ public:
         }
 
         // consensus decoding
-				else if (staticData.UseConsensusDecoding()) {
+        else if (staticData.UseConsensusDecoding()) {
           const TrellisPath &conBestHypo = doConsensusDecoding(manager,nBestList);
           OutputBestHypo(conBestHypo, m_lineNumber,
                          staticData.GetReportSegmentation(),
@@ -355,8 +353,8 @@ public:
           IFVERBOSE(2) {
             PrintUserTime("finished Consensus decoding");
           }
-				}
-				
+        }
+
         // n-best MBR decoding
         else {
           const Moses::TrellisPath &mbrBestHypo = doMBR(nBestList);
@@ -380,7 +378,7 @@ public:
       ostringstream out;
       manager.CalcNBest(staticData.GetNBestSize(), nBestList,staticData.GetDistinctNBest());
       OutputNBest(out, nBestList, staticData.GetOutputFactorOrder(), m_lineNumber,
-		  staticData.GetReportSegmentation());
+                  staticData.GetReportSegmentation());
       m_nbestCollector->Write(m_lineNumber, out.str());
     }
 
@@ -390,7 +388,7 @@ public:
       ostringstream out;
       manager.CalcLatticeSamples(staticData.GetLatticeSamplesSize(), latticeSamples);
       OutputNBest(out,latticeSamples, staticData.GetOutputFactorOrder(), m_lineNumber,
-		  staticData.GetReportSegmentation());
+                  staticData.GetReportSegmentation());
       m_latticeSamplesCollector->Write(m_lineNumber, out.str());
     }
 
@@ -450,7 +448,7 @@ static void PrintFeatureWeight(const FeatureFunction* ff)
   size_t numScoreComps = ff->GetNumScoreComponents();
   vector<float> values = StaticData::Instance().GetAllWeights().GetScoresForProducer(ff);
   for (size_t i = 0; i < numScoreComps; ++i) {
-	cout << " " << values[i];
+    cout << " " << values[i];
   }
   cout << endl;
 }
@@ -484,13 +482,13 @@ size_t OutputFeatureWeightsForHypergraph(size_t index, const FeatureFunction* ff
     vector<float> values = StaticData::Instance().GetAllWeights().GetScoresForProducer(ff);
     if (numScoreComps > 1) {
       for (size_t i = 0; i < numScoreComps; ++i) {
-	outputSearchGraphStream << ff->GetScoreProducerDescription()
-				<< i
-				<< "=" << values[i] << endl;
+        outputSearchGraphStream << ff->GetScoreProducerDescription()
+                                << i
+                                << "=" << values[i] << endl;
       }
     } else {
-	outputSearchGraphStream << ff->GetScoreProducerDescription()
-				<< "=" << values[0] << endl;
+      outputSearchGraphStream << ff->GetScoreProducerDescription()
+                              << "=" << values[0] << endl;
     }
     return index+numScoreComps;
   } else {
@@ -541,7 +539,7 @@ void OutputFeatureWeightsForHypergraph(std::ostream &outputSearchGraphStream)
 int main(int argc, char** argv)
 {
   try {
-  
+
 #ifdef HAVE_PROTOBUF
     GOOGLE_PROTOBUF_VERIFY_VERSION;
 #endif
@@ -601,20 +599,20 @@ int main(int argc, char** argv)
     if (staticData.GetOutputSearchGraphHypergraph()) {
       ofstream* weightsOut = new std::ofstream;
       stringstream weightsFilename;
-      if (staticData.GetParam("output-search-graph-hypergraph").size() > 3) { 
-	weightsFilename << staticData.GetParam("output-search-graph-hypergraph")[3];
+      if (staticData.GetParam("output-search-graph-hypergraph").size() > 3) {
+        weightsFilename << staticData.GetParam("output-search-graph-hypergraph")[3];
       } else {
-	string nbestFile = staticData.GetNBestFilePath();
-	if ( ! nbestFile.empty() && nbestFile!="-" && !boost::starts_with(nbestFile,"/dev/stdout") ) {
-	  boost::filesystem::path nbestPath(nbestFile);
-	  weightsFilename << nbestPath.parent_path().filename() << "/weights";
-	} else {
-	  weightsFilename << boost::filesystem::current_path() << "/hypergraph/weights";
-	}
+        string nbestFile = staticData.GetNBestFilePath();
+        if ( ! nbestFile.empty() && nbestFile!="-" && !boost::starts_with(nbestFile,"/dev/stdout") ) {
+          boost::filesystem::path nbestPath(nbestFile);
+          weightsFilename << nbestPath.parent_path().filename() << "/weights";
+        } else {
+          weightsFilename << boost::filesystem::current_path() << "/hypergraph/weights";
+        }
       }
       boost::filesystem::path weightsFilePath(weightsFilename.str());
       if ( ! boost::filesystem::exists(weightsFilePath.parent_path()) ) {
-	boost::filesystem::create_directory(weightsFilePath.parent_path());
+        boost::filesystem::create_directory(weightsFilePath.parent_path());
       }
       TRACE_ERR("The weights file is " << weightsFilename.str() << "\n");
       weightsOut->open(weightsFilename.str().c_str());
@@ -669,26 +667,26 @@ int main(int argc, char** argv)
     if (output1best) {
       outputCollector.reset(new OutputCollector());
     }
-  
+
     // initialize stream for word graph (aka: output lattice)
     auto_ptr<OutputCollector> wordGraphCollector;
     if (staticData.GetOutputWordGraph()) {
       wordGraphCollector.reset(new OutputCollector(&(ioWrapper->GetOutputWordGraphStream())));
     }
-  
+
     // initialize stream for search graph
     // note: this is essentially the same as above, but in a different format
     auto_ptr<OutputCollector> searchGraphCollector;
     if (staticData.GetOutputSearchGraph()) {
       searchGraphCollector.reset(new OutputCollector(&(ioWrapper->GetOutputSearchGraphStream())));
     }
-  
+
     // initialize stram for details about the decoder run
     auto_ptr<OutputCollector> detailedTranslationCollector;
     if (staticData.IsDetailedTranslationReportingEnabled()) {
       detailedTranslationCollector.reset(new OutputCollector(&(ioWrapper->GetDetailedTranslationReportingStream())));
     }
-  
+
     // initialize stram for word alignment between input and output
     auto_ptr<OutputCollector> alignmentInfoCollector;
     if (!staticData.GetAlignmentOutputFile().empty()) {
@@ -706,11 +704,11 @@ int main(int argc, char** argv)
       }
       unknownsCollector.reset(new OutputCollector(unknownsStream.get()));
     }
-  
+
 #ifdef WITH_THREADS
     ThreadPool pool(staticData.ThreadCount());
 #endif
-  
+
     // main loop over set of input sentences
     InputType* source = NULL;
     size_t lineCount = staticData.GetStartTranslationId();
@@ -728,21 +726,21 @@ int main(int argc, char** argv)
                             detailedTranslationCollector.get(),
                             alignmentInfoCollector.get(),
                             unknownsCollector.get(),
-			    staticData.GetOutputSearchGraphSLF(),
-			    staticData.GetOutputSearchGraphHypergraph());
+                            staticData.GetOutputSearchGraphSLF(),
+                            staticData.GetOutputSearchGraphHypergraph());
       // execute task
 #ifdef WITH_THREADS
-    pool.Submit(task);
+      pool.Submit(task);
 #else
       task->Run();
       delete task;
 #endif
-  
+
       source = NULL; //make sure it doesn't get deleted
       ++lineCount;
     }
-  
-  // we are done, finishing up
+
+    // we are done, finishing up
 #ifdef WITH_THREADS
     pool.Stop(true); //flush remaining jobs
 #endif
diff --git a/moses-cmd/TranslationAnalysis.cpp b/moses-cmd/TranslationAnalysis.cpp
index 4231001e9..bd7113096 100644
--- a/moses-cmd/TranslationAnalysis.cpp
+++ b/moses-cmd/TranslationAnalysis.cpp
@@ -57,7 +57,7 @@ void PrintTranslationAnalysis(std::ostream &os, const Hypothesis* hypo)
         }
       }
     }
-    
+
     bool epsilon = false;
     if (target == "") {
       target="<EPSILON>";
@@ -101,21 +101,21 @@ void PrintTranslationAnalysis(std::ostream &os, const Hypothesis* hypo)
   }
   os << std::endl << std::endl;
   if (doLMStats && lmCalls > 0) {
-	  std::vector<unsigned int>::iterator acc = lmAcc.begin();
+    std::vector<unsigned int>::iterator acc = lmAcc.begin();
 
-	  const std::vector<const StatefulFeatureFunction*> &statefulFFs = StatefulFeatureFunction::GetStatefulFeatureFunctions();
-	  for (size_t i = 0; i < statefulFFs.size(); ++i) {
-	    const StatefulFeatureFunction *ff = statefulFFs[i];
-	    const LanguageModel *lm = dynamic_cast<const LanguageModel*>(ff);
+    const std::vector<const StatefulFeatureFunction*> &statefulFFs = StatefulFeatureFunction::GetStatefulFeatureFunctions();
+    for (size_t i = 0; i < statefulFFs.size(); ++i) {
+      const StatefulFeatureFunction *ff = statefulFFs[i];
+      const LanguageModel *lm = dynamic_cast<const LanguageModel*>(ff);
 
-	    if (lm) {
-	        char buf[256];
-	        sprintf(buf, "%.4f", (float)(*acc)/(float)lmCalls);
-	        os << lm->GetScoreProducerDescription() <<", AVG N-GRAM LENGTH: " << buf << std::endl;
+      if (lm) {
+        char buf[256];
+        sprintf(buf, "%.4f", (float)(*acc)/(float)lmCalls);
+        os << lm->GetScoreProducerDescription() <<", AVG N-GRAM LENGTH: " << buf << std::endl;
 
-	    	++acc;
-	    }
-	  }
+        ++acc;
+      }
+    }
   }
 
   if (droppedWords.size() > 0) {
@@ -125,10 +125,10 @@ void PrintTranslationAnalysis(std::ostream &os, const Hypothesis* hypo)
       os << "\tdropped=" << *dwi << std::endl;
     }
   }
-	os << std::endl << "SCORES (UNWEIGHTED/WEIGHTED): ";
+  os << std::endl << "SCORES (UNWEIGHTED/WEIGHTED): ";
   os << translationPath.back()->GetScoreBreakdown();
   os << " weighted(TODO)";
-	os << std::endl;
+  os << std::endl;
 }
 
 }
diff --git a/moses/AlignmentInfo.cpp b/moses/AlignmentInfo.cpp
index 97eff59b5..178f3438a 100644
--- a/moses/AlignmentInfo.cpp
+++ b/moses/AlignmentInfo.cpp
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -46,17 +46,18 @@ void AlignmentInfo::BuildNonTermIndexMap()
   m_nonTermIndexMap.resize(maxIndex+1, NOT_FOUND);
   size_t i = 0;
   for (p = begin(); p != end(); ++p) {
-  	if (m_nonTermIndexMap[p->second] != NOT_FOUND) {
-  		// 1-to-many. Definitely a set of terminals. Don't bother storing 1-to-1 index map
-  		m_nonTermIndexMap.clear();
-  		return;
-  	}
+    if (m_nonTermIndexMap[p->second] != NOT_FOUND) {
+      // 1-to-many. Definitely a set of terminals. Don't bother storing 1-to-1 index map
+      m_nonTermIndexMap.clear();
+      return;
+    }
     m_nonTermIndexMap[p->second] = i++;
   }
-            
+
 }
 
-bool compare_target(const std::pair<size_t,size_t> *a, const std::pair<size_t,size_t> *b) {
+bool compare_target(const std::pair<size_t,size_t> *a, const std::pair<size_t,size_t> *b)
+{
   if(a->second < b->second)  return true;
   if(a->second == b->second) return (a->first < b->first);
   return false;
@@ -66,32 +67,30 @@ bool compare_target(const std::pair<size_t,size_t> *a, const std::pair<size_t,si
 std::vector< const std::pair<size_t,size_t>* > AlignmentInfo::GetSortedAlignments() const
 {
   std::vector< const std::pair<size_t,size_t>* > ret;
-  
+
   CollType::const_iterator iter;
-  for (iter = m_collection.begin(); iter != m_collection.end(); ++iter)
-  {
+  for (iter = m_collection.begin(); iter != m_collection.end(); ++iter) {
     const std::pair<size_t,size_t> &alignPair = *iter;
     ret.push_back(&alignPair);
   }
-  
+
   const StaticData &staticData = StaticData::Instance();
   WordAlignmentSort wordAlignmentSort = staticData.GetWordAlignmentSort();
-  
-  switch (wordAlignmentSort)
-  {
-    case NoSort:
-      break;
-      
-    case TargetOrder:
-      std::sort(ret.begin(), ret.end(), compare_target);
-      break;
-      
-    default:
-      CHECK(false);
+
+  switch (wordAlignmentSort) {
+  case NoSort:
+    break;
+
+  case TargetOrder:
+    std::sort(ret.begin(), ret.end(), compare_target);
+    break;
+
+  default:
+    CHECK(false);
   }
-  
+
   return ret;
-  
+
 }
 
 std::vector<size_t> AlignmentInfo::GetSourceIndex2PosMap() const
diff --git a/moses/AlignmentInfo.h b/moses/AlignmentInfo.h
index db92791aa..76d4d918a 100644
--- a/moses/AlignmentInfo.h
+++ b/moses/AlignmentInfo.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -42,16 +42,20 @@ class AlignmentInfo
   friend struct AlignmentInfoHasher;
   friend class AlignmentInfoCollection;
 
- public:
+public:
   typedef std::set<std::pair<size_t,size_t> > CollType;
   typedef std::vector<size_t> NonTermIndexMap;
   typedef CollType::const_iterator const_iterator;
 
-  const_iterator begin() const { return m_collection.begin(); }
-  const_iterator end() const { return m_collection.end(); }
+  const_iterator begin() const {
+    return m_collection.begin();
+  }
+  const_iterator end() const {
+    return m_collection.end();
+  }
 
   void Add(size_t sourcePos, size_t targetPos) {
-  	m_collection.insert(std::pair<size_t, size_t>(sourcePos, targetPos));
+    m_collection.insert(std::pair<size_t, size_t>(sourcePos, targetPos));
   }
   /** Provides a map from target-side to source-side non-terminal indices.
     * The target-side index should be the rule symbol index (COUNTING terminals).
@@ -64,20 +68,21 @@ class AlignmentInfo
   const CollType &GetAlignments() const {
     return m_collection;
   }
-  
-  size_t GetSize() const { return m_collection.size(); }
+
+  size_t GetSize() const {
+    return m_collection.size();
+  }
 
   std::vector< const std::pair<size_t,size_t>* > GetSortedAlignments() const;
 
   std::vector<size_t> GetSourceIndex2PosMap() const;
 
-  bool operator==(const AlignmentInfo& rhs) const 
-  {
+  bool operator==(const AlignmentInfo& rhs) const {
     return m_collection == rhs.m_collection &&
            m_nonTermIndexMap == rhs.m_nonTermIndexMap;
   }
-  
- private:
+
+private:
   //! AlignmentInfo objects should only be created by an AlignmentInfoCollection
   explicit AlignmentInfo(const std::set<std::pair<size_t,size_t> > &pairs);
 
@@ -90,25 +95,21 @@ class AlignmentInfo
 /** Define an arbitrary strict weak ordering between AlignmentInfo objects
  * for use by AlignmentInfoCollection.
  */
-struct AlignmentInfoOrderer
-{
+struct AlignmentInfoOrderer {
   bool operator()(const AlignmentInfo &a, const AlignmentInfo &b) const {
-		if (a.m_collection == b.m_collection) {
-			return a.m_nonTermIndexMap < b.m_nonTermIndexMap;
-		}
-		else {
-			return a.m_collection < b.m_collection;
-		}
+    if (a.m_collection == b.m_collection) {
+      return a.m_nonTermIndexMap < b.m_nonTermIndexMap;
+    } else {
+      return a.m_collection < b.m_collection;
+    }
   }
 };
 
-/** 
+/**
  * Hashing functoid
  **/
-struct AlignmentInfoHasher
-{
-  size_t operator()(const AlignmentInfo& a) const
-  {
+struct AlignmentInfoHasher {
+  size_t operator()(const AlignmentInfo& a) const {
     size_t seed = 0;
     boost::hash_combine(seed,a.m_collection);
     boost::hash_combine(seed,a.m_nonTermIndexMap);
@@ -117,7 +118,8 @@ struct AlignmentInfoHasher
 
 };
 
-inline size_t hash_value(const AlignmentInfo& a) {
+inline size_t hash_value(const AlignmentInfo& a)
+{
   static AlignmentInfoHasher hasher;
   return hasher(a);
 }
diff --git a/moses/AlignmentInfoCollection.cpp b/moses/AlignmentInfoCollection.cpp
index 53b83d8cd..ef6e62eb3 100644
--- a/moses/AlignmentInfoCollection.cpp
+++ b/moses/AlignmentInfoCollection.cpp
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -39,7 +39,7 @@ const AlignmentInfo &AlignmentInfoCollection::GetEmptyAlignmentInfo() const
 }
 
 const AlignmentInfo *AlignmentInfoCollection::Add(
-    const std::set<std::pair<size_t,size_t> > &pairs)
+  const std::set<std::pair<size_t,size_t> > &pairs)
 {
   AlignmentInfo pairsAlignmentInfo(pairs);
 #ifdef WITH_THREADS
diff --git a/moses/AlignmentInfoCollection.h b/moses/AlignmentInfoCollection.h
index 6185b32a9..37d717b0f 100644
--- a/moses/AlignmentInfoCollection.h
+++ b/moses/AlignmentInfoCollection.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -36,8 +36,10 @@ namespace Moses
  */
 class AlignmentInfoCollection
 {
- public:
-  static AlignmentInfoCollection &Instance() { return s_instance; }
+public:
+  static AlignmentInfoCollection &Instance() {
+    return s_instance;
+  }
 
   /** Returns a pointer to an AlignmentInfo object with the same source-target
     * alignment pairs as given in the argument.  If the collection already
@@ -49,7 +51,7 @@ class AlignmentInfoCollection
   //! Returns a pointer to an empty AlignmentInfo object.
   const AlignmentInfo &GetEmptyAlignmentInfo() const;
 
- private:
+private:
   typedef std::set<AlignmentInfo, AlignmentInfoOrderer> AlignmentInfoSet;
 
   //! Only a single static variable should be created.
@@ -62,7 +64,7 @@ class AlignmentInfoCollection
   //reader-writer lock
   mutable boost::shared_mutex m_accessLock;
 #endif
-  
+
   AlignmentInfoSet m_collection;
   const AlignmentInfo *m_emptyAlignmentInfo;
 };
diff --git a/moses/AlignmentInfoTest.cpp b/moses/AlignmentInfoTest.cpp
index 48c88db65..26127f3cf 100644
--- a/moses/AlignmentInfoTest.cpp
+++ b/moses/AlignmentInfoTest.cpp
@@ -35,8 +35,7 @@ struct AlignmentInfoFixture {
   const AlignmentInfo* ai2;
   const AlignmentInfo* ai3;
 
-  AlignmentInfoFixture()
-  {
+  AlignmentInfoFixture() {
     AlignmentInfoCollection& collection = AlignmentInfoCollection::Instance();
     IndexSet aligns1,aligns2,aligns3;
     aligns1.insert(IndexPair(1,1));
diff --git a/moses/BitmapContainer.cpp b/moses/BitmapContainer.cpp
index 7e8d470ee..64dd9081b 100644
--- a/moses/BitmapContainer.cpp
+++ b/moses/BitmapContainer.cpp
@@ -275,11 +275,11 @@ BitmapContainer::~BitmapContainer()
   // As we have created the square position objects we clean up now.
 
   while (!m_queue.empty()) {
-	HypothesisQueueItem *item = m_queue.top();
-	m_queue.pop();
+    HypothesisQueueItem *item = m_queue.top();
+    m_queue.pop();
 
-	FREEHYPO( item->GetHypothesis() );
-	delete item;
+    FREEHYPO( item->GetHypothesis() );
+    delete item;
   }
 
   // Delete all edges.
diff --git a/moses/ChartCell.cpp b/moses/ChartCell.cpp
index fd163450e..b57a4ab36 100644
--- a/moses/ChartCell.cpp
+++ b/moses/ChartCell.cpp
@@ -45,17 +45,18 @@ ChartCellBase::~ChartCellBase() {}
 
 /** Constructor
  * \param startPos endPos range of this cell
- * \param manager pointer back to the manager 
+ * \param manager pointer back to the manager
  */
 ChartCell::ChartCell(size_t startPos, size_t endPos, ChartManager &manager) :
-  ChartCellBase(startPos, endPos), m_manager(manager) {
+  ChartCellBase(startPos, endPos), m_manager(manager)
+{
   const StaticData &staticData = StaticData::Instance();
   m_nBestIsEnabled = staticData.IsNBestEnabled();
 }
 
 ChartCell::~ChartCell() {}
 
-/** Add the given hypothesis to the cell. 
+/** Add the given hypothesis to the cell.
  *  Returns true if added, false if not. Maybe it already exists in the collection or score falls below threshold etc.
  *  This function just calls the correspondind AddHypothesis() in ChartHypothesisCollection
  *  \param hypo Hypothesis to be added
@@ -98,8 +99,7 @@ void ChartCell::ProcessSentence(const ChartTranslationOptionList &transOptList
 
   // pluck things out of queue and add to hypo collection
   const size_t popLimit = staticData.GetCubePruningPopLimit();
-  for (size_t numPops = 0; numPops < popLimit && !queue.IsEmpty(); ++numPops) 
-  {
+  for (size_t numPops = 0; numPops < popLimit && !queue.IsEmpty(); ++numPops) {
     ChartHypothesis *hypo = queue.Pop();
     AddHypothesis(hypo);
   }
@@ -179,15 +179,15 @@ size_t ChartCell::GetSize() const
 
 const HypoList *ChartCell::GetAllSortedHypotheses() const
 {
-	HypoList *ret = new HypoList();
+  HypoList *ret = new HypoList();
 
-	MapType::const_iterator iter;
-	for (iter = m_hypoColl.begin(); iter != m_hypoColl.end(); ++iter) {
-	  const ChartHypothesisCollection &coll = iter->second;
-	  const HypoList &list = coll.GetSortedHypotheses();
+  MapType::const_iterator iter;
+  for (iter = m_hypoColl.begin(); iter != m_hypoColl.end(); ++iter) {
+    const ChartHypothesisCollection &coll = iter->second;
+    const HypoList &list = coll.GetSortedHypotheses();
     std::copy(list.begin(), list.end(), std::inserter(*ret, ret->end()));
-	}
-	return ret;
+  }
+  return ret;
 }
 
 //! call GetSearchGraph() for each hypo collection
diff --git a/moses/ChartCell.h b/moses/ChartCell.h
index 14ac8e3b4..1fed695ac 100644
--- a/moses/ChartCell.h
+++ b/moses/ChartCell.h
@@ -44,35 +44,43 @@ class ChartTranslationOptionList;
 class ChartCellCollection;
 class ChartManager;
 
-class ChartCellBase {
-  public:
-    ChartCellBase(size_t startPos, size_t endPos);
+class ChartCellBase
+{
+public:
+  ChartCellBase(size_t startPos, size_t endPos);
 
-    virtual ~ChartCellBase();
+  virtual ~ChartCellBase();
 
-    const ChartCellLabelSet &GetTargetLabelSet() const { return m_targetLabelSet; }
+  const ChartCellLabelSet &GetTargetLabelSet() const {
+    return m_targetLabelSet;
+  }
 
-    ChartCellLabelSet &MutableTargetLabelSet() { return m_targetLabelSet; }
+  ChartCellLabelSet &MutableTargetLabelSet() {
+    return m_targetLabelSet;
+  }
 
-    const WordsRange &GetCoverage() const { return m_coverage; }
+  const WordsRange &GetCoverage() const {
+    return m_coverage;
+  }
 
-  protected:
-    const WordsRange m_coverage;
-    ChartCellLabelSet m_targetLabelSet;
+protected:
+  const WordsRange m_coverage;
+  ChartCellLabelSet m_targetLabelSet;
 };
 
 /** 1 cell in chart decoder.
  *  Doesn't directly hold hypotheses. Each cell contain a map of ChartHypothesisCollection that have different constituent labels
  */
-class ChartCell : public ChartCellBase {
+class ChartCell : public ChartCellBase
+{
   friend std::ostream& operator<<(std::ostream&, const ChartCell&);
 public:
 #if defined(BOOST_VERSION) && (BOOST_VERSION >= 104200)
   typedef boost::unordered_map<Word,
-                               ChartHypothesisCollection,
-                               NonTerminalHasher,
-                               NonTerminalEqualityPred
-                              > MapType;
+          ChartHypothesisCollection,
+          NonTerminalHasher,
+          NonTerminalEqualityPred
+          > MapType;
 #else
   typedef std::map<Word, ChartHypothesisCollection> MapType;
 #endif
@@ -91,8 +99,7 @@ public:
                        ,const ChartCellCollection &allChartCells);
 
   //! Get all hypotheses in the cell that have the specified constituent label
-  const HypoList *GetSortedHypotheses(const Word &constituentLabel) const
-  {
+  const HypoList *GetSortedHypotheses(const Word &constituentLabel) const {
     MapType::const_iterator p = m_hypoColl.find(constituentLabel);
     return (p == m_hypoColl.end()) ? NULL : &(p->second.GetSortedHypotheses());
   }
diff --git a/moses/ChartCellCollection.cpp b/moses/ChartCellCollection.cpp
index a34687f59..46392261d 100644
--- a/moses/ChartCellCollection.cpp
+++ b/moses/ChartCellCollection.cpp
@@ -23,24 +23,27 @@
 #include "InputType.h"
 #include "WordsRange.h"
 
-namespace Moses {
+namespace Moses
+{
 
-ChartCellCollectionBase::~ChartCellCollectionBase() {
+ChartCellCollectionBase::~ChartCellCollectionBase()
+{
   m_source.clear();
-  for (std::vector<std::vector<ChartCellBase*> >::iterator i = m_cells.begin(); i != m_cells.end(); ++i) 
+  for (std::vector<std::vector<ChartCellBase*> >::iterator i = m_cells.begin(); i != m_cells.end(); ++i)
     RemoveAllInColl(*i);
 }
 
-class CubeCellFactory {
-  public:
-    explicit CubeCellFactory(ChartManager &manager) : m_manager(manager) {}
+class CubeCellFactory
+{
+public:
+  explicit CubeCellFactory(ChartManager &manager) : m_manager(manager) {}
 
-    ChartCell *operator()(size_t start, size_t end) const {
-      return new ChartCell(start, end, m_manager);
-    }
+  ChartCell *operator()(size_t start, size_t end) const {
+    return new ChartCell(start, end, m_manager);
+  }
 
-  private:
-    ChartManager &m_manager;
+private:
+  ChartManager &m_manager;
 };
 
 /** Costructor
diff --git a/moses/ChartCellCollection.h b/moses/ChartCellCollection.h
index 7532503d7..d0423b0b2 100644
--- a/moses/ChartCellCollection.h
+++ b/moses/ChartCellCollection.h
@@ -31,57 +31,59 @@ namespace Moses
 class InputType;
 class ChartManager;
 
-class ChartCellCollectionBase {
-  public:
-    template <class Factory> ChartCellCollectionBase(const InputType &input, const Factory &factory) :
-      m_cells(input.GetSize()) {
-      size_t size = input.GetSize();
-      for (size_t startPos = 0; startPos < size; ++startPos) {
-        std::vector<ChartCellBase*> &inner = m_cells[startPos];
-        inner.reserve(size - startPos);
-        for (size_t endPos = startPos; endPos < size; ++endPos) {
-          inner.push_back(factory(startPos, endPos));
-        }
-        /* Hack: ChartCellLabel shouldn't need to know its span, but the parser
-         * gets it from there :-(.  The span is actually stored as a reference,
-         * which needs to point somewhere, so I have it refer to the ChartCell.
-         */
-        m_source.push_back(new ChartCellLabel(inner[0]->GetCoverage(), input.GetWord(startPos)));
+class ChartCellCollectionBase
+{
+public:
+  template <class Factory> ChartCellCollectionBase(const InputType &input, const Factory &factory) :
+    m_cells(input.GetSize()) {
+    size_t size = input.GetSize();
+    for (size_t startPos = 0; startPos < size; ++startPos) {
+      std::vector<ChartCellBase*> &inner = m_cells[startPos];
+      inner.reserve(size - startPos);
+      for (size_t endPos = startPos; endPos < size; ++endPos) {
+        inner.push_back(factory(startPos, endPos));
       }
+      /* Hack: ChartCellLabel shouldn't need to know its span, but the parser
+       * gets it from there :-(.  The span is actually stored as a reference,
+       * which needs to point somewhere, so I have it refer to the ChartCell.
+       */
+      m_source.push_back(new ChartCellLabel(inner[0]->GetCoverage(), input.GetWord(startPos)));
     }
+  }
 
-    virtual ~ChartCellCollectionBase();
+  virtual ~ChartCellCollectionBase();
 
-    const ChartCellBase &GetBase(const WordsRange &coverage) const {
-      return *m_cells[coverage.GetStartPos()][coverage.GetEndPos() - coverage.GetStartPos()];
-    }
+  const ChartCellBase &GetBase(const WordsRange &coverage) const {
+    return *m_cells[coverage.GetStartPos()][coverage.GetEndPos() - coverage.GetStartPos()];
+  }
 
-    ChartCellBase &MutableBase(const WordsRange &coverage) {
-      return *m_cells[coverage.GetStartPos()][coverage.GetEndPos() - coverage.GetStartPos()];
-    }
+  ChartCellBase &MutableBase(const WordsRange &coverage) {
+    return *m_cells[coverage.GetStartPos()][coverage.GetEndPos() - coverage.GetStartPos()];
+  }
 
 
-    const ChartCellLabel &GetSourceWordLabel(size_t at) const {
-      return m_source[at];
-    }
+  const ChartCellLabel &GetSourceWordLabel(size_t at) const {
+    return m_source[at];
+  }
 
-  private:
-    std::vector<std::vector<ChartCellBase*> > m_cells;
+private:
+  std::vector<std::vector<ChartCellBase*> > m_cells;
 
-    boost::ptr_vector<ChartCellLabel> m_source;
+  boost::ptr_vector<ChartCellLabel> m_source;
 };
 
 /** Hold all the chart cells for 1 input sentence. A variable of this type is held by the ChartManager
  */
-class ChartCellCollection : public ChartCellCollectionBase {
-  public:
-    ChartCellCollection(const InputType &input, ChartManager &manager);
+class ChartCellCollection : public ChartCellCollectionBase
+{
+public:
+  ChartCellCollection(const InputType &input, ChartManager &manager);
 
   //! get a chart cell for a particular range
   ChartCell &Get(const WordsRange &coverage) {
     return static_cast<ChartCell&>(MutableBase(coverage));
   }
-  
+
   //! get a chart cell for a particular range
   const ChartCell &Get(const WordsRange &coverage) const {
     return static_cast<const ChartCell&>(GetBase(coverage));
diff --git a/moses/ChartCellLabel.h b/moses/ChartCellLabel.h
index 218a512c0..ad6e3565d 100644
--- a/moses/ChartCellLabel.h
+++ b/moses/ChartCellLabel.h
@@ -23,7 +23,10 @@
 #include "Word.h"
 #include "WordsRange.h"
 
-namespace search { class Vertex; }
+namespace search
+{
+class Vertex;
+}
 
 namespace Moses
 {
@@ -31,17 +34,17 @@ namespace Moses
 class Word;
 
 /** Contains a range, word (non-terms?) and a vector of hypotheses.
- * @todo This is probably incompatible with lattice decoding when the word that spans 
+ * @todo This is probably incompatible with lattice decoding when the word that spans
  *   a position (or positions) can vary.
  * @todo is this to hold sorted hypotheses that are in the queue for creating the next hypos?
  */
 class ChartCellLabel
 {
- public:
+public:
   union Stack {
     const HypoList *cube; // cube pruning
-    search::Vertex *incr; // incremental search after filling.  
-    void *incr_generator; // incremental search during filling.  
+    search::Vertex *incr; // incremental search after filling.
+    void *incr_generator; // incremental search during filling.
   };
 
 
@@ -52,13 +55,20 @@ class ChartCellLabel
     , m_stack(stack)
   {}
 
-  const WordsRange &GetCoverage() const { return m_coverage; }
-  const Word &GetLabel() const { return m_label; }
-  Stack GetStack() const { return m_stack; }
-  Stack &MutableStack() { return m_stack; }
+  const WordsRange &GetCoverage() const {
+    return m_coverage;
+  }
+  const Word &GetLabel() const {
+    return m_label;
+  }
+  Stack GetStack() const {
+    return m_stack;
+  }
+  Stack &MutableStack() {
+    return m_stack;
+  }
 
-  bool operator<(const ChartCellLabel &other) const
-  {
+  bool operator<(const ChartCellLabel &other) const {
     // m_coverage and m_label uniquely identify a ChartCellLabel, so don't
     // need to compare m_stack.
     if (m_coverage == other.m_coverage) {
@@ -67,7 +77,7 @@ class ChartCellLabel
     return m_coverage < other.m_coverage;
   }
 
- private:
+private:
   const WordsRange &m_coverage;
   const Word &m_label;
   Stack m_stack;
diff --git a/moses/ChartCellLabelSet.h b/moses/ChartCellLabelSet.h
index 5ea192e51..68c8b4263 100644
--- a/moses/ChartCellLabelSet.h
+++ b/moses/ChartCellLabelSet.h
@@ -35,46 +35,55 @@ class ChartHypothesisCollection;
  */
 class ChartCellLabelSet
 {
- private:
+private:
 #if defined(BOOST_VERSION) && (BOOST_VERSION >= 104200)
   typedef boost::unordered_map<Word, ChartCellLabel,
-                               NonTerminalHasher, NonTerminalEqualityPred
-                              > MapType;
+          NonTerminalHasher, NonTerminalEqualityPred
+          > MapType;
 #else
   typedef std::map<Word, ChartCellLabel> MapType;
 #endif
 
- public:
+public:
   typedef MapType::const_iterator const_iterator;
   typedef MapType::iterator iterator;
 
   ChartCellLabelSet(const WordsRange &coverage) : m_coverage(coverage) {}
 
-  const_iterator begin() const { return m_map.begin(); }
-  const_iterator end() const { return m_map.end(); }
-  
-  iterator mutable_begin() { return m_map.begin(); }
-  iterator mutable_end() { return m_map.end(); }
+  const_iterator begin() const {
+    return m_map.begin();
+  }
+  const_iterator end() const {
+    return m_map.end();
+  }
 
-  void AddWord(const Word &w)
-  {
+  iterator mutable_begin() {
+    return m_map.begin();
+  }
+  iterator mutable_end() {
+    return m_map.end();
+  }
+
+  void AddWord(const Word &w) {
     m_map.insert(std::make_pair(w, ChartCellLabel(m_coverage, w)));
   }
 
-  // Stack is a HypoList or whatever the search algorithm uses.  
-  void AddConstituent(const Word &w, const HypoList *stack)
-  {
+  // Stack is a HypoList or whatever the search algorithm uses.
+  void AddConstituent(const Word &w, const HypoList *stack) {
     ChartCellLabel::Stack s;
     s.cube = stack;
     m_map.insert(std::make_pair(w, ChartCellLabel(m_coverage, w, s)));
   }
 
-  bool Empty() const { return m_map.empty(); }
+  bool Empty() const {
+    return m_map.empty();
+  }
 
-  size_t GetSize() const { return m_map.size(); }
+  size_t GetSize() const {
+    return m_map.size();
+  }
 
-  const ChartCellLabel *Find(const Word &w) const
-  {
+  const ChartCellLabel *Find(const Word &w) const {
     MapType::const_iterator p = m_map.find(w);
     return p == m_map.end() ? 0 : &(p->second);
   }
@@ -83,7 +92,7 @@ class ChartCellLabelSet
     return m_map.insert(std::make_pair(w, ChartCellLabel(m_coverage, w))).first->second.MutableStack();
   }
 
- private:
+private:
   const WordsRange &m_coverage;
   MapType m_map;
 };
diff --git a/moses/ChartHypothesis.cpp b/moses/ChartHypothesis.cpp
index c7c1047f1..ce5a318ac 100644
--- a/moses/ChartHypothesis.cpp
+++ b/moses/ChartHypothesis.cpp
@@ -39,7 +39,7 @@ namespace Moses
 ObjectPool<ChartHypothesis> ChartHypothesis::s_objectPool("ChartHypothesis", 300000);
 #endif
 
-/** Create a hypothesis from a rule 
+/** Create a hypothesis from a rule
  * \param transOpt wrapper around the rule
  * \param item @todo dunno
  * \param manager reference back to manager
@@ -59,15 +59,14 @@ ChartHypothesis::ChartHypothesis(const ChartTranslationOptions &transOpt,
   const std::vector<HypothesisDimension> &childEntries = item.GetHypothesisDimensions();
   m_prevHypos.reserve(childEntries.size());
   std::vector<HypothesisDimension>::const_iterator iter;
-  for (iter = childEntries.begin(); iter != childEntries.end(); ++iter) 
-  {
+  for (iter = childEntries.begin(); iter != childEntries.end(); ++iter) {
     m_prevHypos.push_back(iter->GetHypothesis());
   }
 }
 
 ChartHypothesis::~ChartHypothesis()
 {
-	// delete feature function states
+  // delete feature function states
   for (unsigned i = 0; i < m_ffStates.size(); ++i) {
     delete m_ffStates[i];
   }
@@ -98,8 +97,7 @@ void ChartHypothesis::CreateOutputPhrase(Phrase &outPhrase) const
       size_t nonTermInd = GetCurrTargetPhrase().GetAlignNonTerm().GetNonTermIndexMap()[pos];
       const ChartHypothesis *prevHypo = m_prevHypos[nonTermInd];
       prevHypo->CreateOutputPhrase(outPhrase);
-    } 
-    else {
+    } else {
       outPhrase.AddWord(word);
     }
   }
@@ -124,17 +122,16 @@ Phrase ChartHypothesis::GetOutputPhrase() const
 */
 int ChartHypothesis::RecombineCompare(const ChartHypothesis &compare) const
 {
-	int comp = 0;
+  int comp = 0;
 
-  for (unsigned i = 0; i < m_ffStates.size(); ++i) 
-	{
-    if (m_ffStates[i] == NULL || compare.m_ffStates[i] == NULL) 
+  for (unsigned i = 0; i < m_ffStates.size(); ++i) {
+    if (m_ffStates[i] == NULL || compare.m_ffStates[i] == NULL)
       comp = m_ffStates[i] - compare.m_ffStates[i];
-		else 
+    else
       comp = m_ffStates[i]->Compare(*compare.m_ffStates[i]);
 
-		if (comp != 0) 
-			return comp;
+    if (comp != 0)
+      return comp;
   }
 
   return 0;
@@ -161,16 +158,16 @@ void ChartHypothesis::CalcScore()
   //Add pre-computed features
   m_manager.InsertPreCalculatedScores(GetCurrTargetPhrase(), &m_scoreBreakdown);
 
-	// compute values of stateless feature functions that were not
+  // compute values of stateless feature functions that were not
   // cached in the translation option-- there is no principled distinction
   const std::vector<const StatelessFeatureFunction*>& sfs =
-      StatelessFeatureFunction::GetStatelessFeatureFunctions();
+    StatelessFeatureFunction::GetStatelessFeatureFunctions();
   for (unsigned i = 0; i < sfs.size(); ++i) {
     sfs[i]->EvaluateChart(ChartBasedFeatureContext(this),&m_scoreBreakdown);
   }
 
   const std::vector<const StatefulFeatureFunction*>& ffs =
-      StatefulFeatureFunction::GetStatefulFeatureFunctions();
+    StatefulFeatureFunction::GetStatefulFeatureFunctions();
   for (unsigned i = 0; i < ffs.size(); ++i)
     m_ffStates[i] = ffs[i]->EvaluateChart(*this,i,&m_scoreBreakdown);
 
@@ -262,13 +259,12 @@ std::ostream& operator<<(std::ostream& out, const ChartHypothesis& hypo)
 {
 
   out << hypo.GetId();
-	
-	// recombination
-	if (hypo.GetWinningHypothesis() != NULL &&
-			hypo.GetWinningHypothesis() != &hypo)
-	{
-		out << "->" << hypo.GetWinningHypothesis()->GetId();
-	}
+
+  // recombination
+  if (hypo.GetWinningHypothesis() != NULL &&
+      hypo.GetWinningHypothesis() != &hypo) {
+    out << "->" << hypo.GetWinningHypothesis()->GetId();
+  }
 
   if (StaticData::Instance().GetIncludeLHSInSearchGraph()) {
     out << " " << hypo.GetTargetLHS() << "=>";
diff --git a/moses/ChartHypothesis.h b/moses/ChartHypothesis.h
index 9dc1cba92..61c2faae1 100644
--- a/moses/ChartHypothesis.h
+++ b/moses/ChartHypothesis.h
@@ -52,7 +52,7 @@ protected:
   const TargetPhrase &m_targetPhrase;
 
   WordsRange					m_currSourceWordsRange;
-	std::vector<const FFState*> m_ffStates; /*! stateful feature function states */
+  std::vector<const FFState*> m_ffStates; /*! stateful feature function states */
   ScoreComponentCollection m_scoreBreakdown /*! detailed score break-down by components (for instance language model, word penalty, etc) */
   ,m_lmNGram
   ,m_lmPrefix;
@@ -68,8 +68,8 @@ protected:
   unsigned m_id; /* pkoehn wants to log the order in which hypotheses were generated */
 
   //! not implemented
-  ChartHypothesis(); 
-  
+  ChartHypothesis();
+
   //! not implemented
   ChartHypothesis(const ChartHypothesis &copy);
 
@@ -96,35 +96,39 @@ public:
 
   ~ChartHypothesis();
 
-  unsigned GetId() const { return m_id; }
+  unsigned GetId() const {
+    return m_id;
+  }
 
   //! Get the rule that created this hypothesis
   const TargetPhrase &GetCurrTargetPhrase()const {
     return m_targetPhrase;
   }
-  
+
   //! the source range that this hypothesis spans
   const WordsRange &GetCurrSourceRange()const {
     return m_currSourceWordsRange;
   }
-  
+
   //! the arc list when creating n-best lists
   inline const ChartArcList* GetArcList() const {
     return m_arcList;
   }
-  
+
   //! the feature function states for a particular feature \param featureID
-	inline const FFState* GetFFState( size_t featureID ) const {
-		return m_ffStates[ featureID ];
-	}
-  
+  inline const FFState* GetFFState( size_t featureID ) const {
+    return m_ffStates[ featureID ];
+  }
+
   //! reference back to the manager
-	inline const ChartManager& GetManager() const { return m_manager; }
+  inline const ChartManager& GetManager() const {
+    return m_manager;
+  }
 
   void CreateOutputPhrase(Phrase &outPhrase) const;
   Phrase GetOutputPhrase() const;
 
-	int RecombineCompare(const ChartHypothesis &compare) const;
+  int RecombineCompare(const ChartHypothesis &compare) const;
 
   void CalcScore();
 
@@ -133,30 +137,34 @@ public:
   void SetWinningHypo(const ChartHypothesis *hypo);
 
   //! get the unweighted score for each feature function
-  const ScoreComponentCollection &GetScoreBreakdown() const 
-  { return m_scoreBreakdown; }
-  
+  const ScoreComponentCollection &GetScoreBreakdown() const {
+    return m_scoreBreakdown;
+  }
+
   //! Get the weighted total score
-  float GetTotalScore() const 
-  { return m_totalScore; }
+  float GetTotalScore() const {
+    return m_totalScore;
+  }
 
-  //! vector of previous hypotheses this hypo is built on 
-  const std::vector<const ChartHypothesis*> &GetPrevHypos() const
-  { return m_prevHypos; }
+  //! vector of previous hypotheses this hypo is built on
+  const std::vector<const ChartHypothesis*> &GetPrevHypos() const {
+    return m_prevHypos;
+  }
 
   //! get a particular previous hypos
-	const ChartHypothesis* GetPrevHypo(size_t pos) const {
-		return m_prevHypos[pos];
-	}
-  
+  const ChartHypothesis* GetPrevHypo(size_t pos) const {
+    return m_prevHypos[pos];
+  }
+
   //! get the constituency label that covers this hypo
   const Word &GetTargetLHS() const {
     return GetCurrTargetPhrase().GetTargetLHS();
   }
 
   //! get the best hypo in the arc list when doing n-best list creation. It's either this hypothesis, or the best hypo is this hypo is in the arc list
-	const ChartHypothesis* GetWinningHypothesis() const 
-  {	return m_winningHypo;	}
+  const ChartHypothesis* GetWinningHypothesis() const {
+    return m_winningHypo;
+  }
 
   TO_STRING();
 
diff --git a/moses/ChartHypothesisCollection.cpp b/moses/ChartHypothesisCollection.cpp
index 752bb7f6c..3b80f68dc 100644
--- a/moses/ChartHypothesisCollection.cpp
+++ b/moses/ChartHypothesisCollection.cpp
@@ -51,7 +51,7 @@ ChartHypothesisCollection::~ChartHypothesisCollection()
   //RemoveAllInColl(m_hypos);
 }
 
-/** public function to add hypothesis to this collection. 
+/** public function to add hypothesis to this collection.
  * Returns false if equiv hypo exists in collection, otherwise returns true.
  * Takes care of update arc list for n-best list creation.
  * Will delete hypo is it exist - once this function is call don't delete hypothesis.
@@ -108,8 +108,7 @@ bool ChartHypothesisCollection::AddHypothesis(ChartHypothesis *hypo, ChartManage
     VERBOSE(3,"worse than matching hyp " << hypoExisting->GetId() << ", recombining" << std::endl)
     if (m_nBestIsEnabled) {
       hypoExisting->AddArc(hypo);
-    } 
-    else {
+    } else {
       ChartHypothesis::Delete(hypo);
     }
     return false;
@@ -146,7 +145,7 @@ pair<ChartHypothesisCollection::HCType::iterator, bool> ChartHypothesisCollectio
   return ret;
 }
 
-/** Remove hypothesis pointed to by iterator but DOES NOT delete the object. 
+/** Remove hypothesis pointed to by iterator but DOES NOT delete the object.
  * \param iter iterator to delete
  */
 void ChartHypothesisCollection::Detach(const HCType::iterator &iter)
diff --git a/moses/ChartHypothesisCollection.h b/moses/ChartHypothesisCollection.h
index f88cb8302..fa707b46d 100644
--- a/moses/ChartHypothesisCollection.h
+++ b/moses/ChartHypothesisCollection.h
@@ -46,7 +46,7 @@ public:
   bool operator()(const ChartHypothesis* hypoA, const ChartHypothesis* hypoB) const {
     // assert in same cell
     const WordsRange &rangeA	= hypoA->GetCurrSourceRange()
-                                      , &rangeB	= hypoB->GetCurrSourceRange();
+                                , &rangeB	= hypoB->GetCurrSourceRange();
     CHECK(rangeA == rangeB);
 
     // shouldn't be mixing hypos with different lhs
@@ -115,7 +115,9 @@ public:
   }
 
   //! return the best total score of all hypos in this collection
-  float GetBestScore() const { return m_bestScore; }
+  float GetBestScore() const {
+    return m_bestScore;
+  }
 
   void GetSearchGraph(long translationId, std::ostream &outputSearchGraphStream, const std::map<unsigned,bool> &reachable) const;
 
diff --git a/moses/ChartManager.cpp b/moses/ChartManager.cpp
index fc4865af7..98f0e17f3 100644
--- a/moses/ChartManager.cpp
+++ b/moses/ChartManager.cpp
@@ -124,10 +124,13 @@ void ChartManager::ProcessSentence()
  *  Doesn't seem to do anything about walls and zones.
  *  @todo check walls & zones. Check that the implementation doesn't leak, xml options sometimes does if you're not careful
  */
-void ChartManager::AddXmlChartOptions() {
+void ChartManager::AddXmlChartOptions()
+{
   const StaticData &staticData = StaticData::Instance();
   const std::vector <ChartTranslationOptions*> xmlChartOptionsList = m_source.GetXmlChartTranslationOptions();
-  IFVERBOSE(2) { cerr << "AddXmlChartOptions " << xmlChartOptionsList.size() << endl; }
+  IFVERBOSE(2) {
+    cerr << "AddXmlChartOptions " << xmlChartOptionsList.size() << endl;
+  }
   if (xmlChartOptionsList.size() == 0) return;
 
   for(std::vector<ChartTranslationOptions*>::const_iterator i = xmlChartOptionsList.begin();
@@ -160,12 +163,12 @@ const ChartHypothesis *ChartManager::GetBestHypothesis() const
   }
 }
 
-  /** Calculate the n-best paths through the output hypergraph.
-   * Return the list of paths with the variable ret
-   * \param count how may paths to return
-   * \param ret return argument
-   * \param onlyDistinct whether to check for distinct output sentence or not (default - don't check, just return top n-paths)
-   */
+/** Calculate the n-best paths through the output hypergraph.
+ * Return the list of paths with the variable ret
+ * \param count how may paths to return
+ * \param ret return argument
+ * \param onlyDistinct whether to check for distinct output sentence or not (default - don't check, just return top n-paths)
+ */
 void ChartManager::CalcNBest(size_t count, ChartTrellisPathList &ret,bool onlyDistinct) const
 {
   size_t size = m_source.GetSize();
@@ -184,7 +187,7 @@ void ChartManager::CalcNBest(size_t count, ChartTrellisPathList &ret,bool onlyDi
 
   // Add it to the n-best list.
   if (count == 1) {
-	ret.Add(basePath);
+    ret.Add(basePath);
     return;
   }
 
@@ -210,21 +213,21 @@ void ChartManager::CalcNBest(size_t count, ChartTrellisPathList &ret,bool onlyDi
 
   // Get all complete translations
   const HypoList *topHypos = lastCell.GetAllSortedHypotheses();
-  
+
   // Create a ChartTrellisDetour for each complete translation and add it to the queue
   HypoList::const_iterator iter;
   for (iter = topHypos->begin(); iter != topHypos->end(); ++iter) {
-	  const ChartHypothesis &hypo = **iter;
-	  boost::shared_ptr<ChartTrellisPath> basePath(new ChartTrellisPath(hypo));
-	  ChartTrellisDetour *detour = new ChartTrellisDetour(basePath, basePath->GetFinalNode(), hypo);
-	  contenders.Push(detour);
+    const ChartHypothesis &hypo = **iter;
+    boost::shared_ptr<ChartTrellisPath> basePath(new ChartTrellisPath(hypo));
+    ChartTrellisDetour *detour = new ChartTrellisDetour(basePath, basePath->GetFinalNode(), hypo);
+    contenders.Push(detour);
   }
- 	
+
   delete topHypos;
 
   // Record the output phrase if distinct translations are required.
   set<Phrase> distinctHyps;
-  
+
   // MAIN loop
   for (size_t i = 0; ret.GetSize() < count && !contenders.Empty() && i < popLimit; ++i) {
     // Get the best detour from the queue.
@@ -234,7 +237,7 @@ void ChartManager::CalcNBest(size_t count, ChartTrellisPathList &ret,bool onlyDi
     // Create a full base path from the chosen detour.
     //basePath.reset(new ChartTrellisPath(*detour));
     boost::shared_ptr<ChartTrellisPath> path(new ChartTrellisPath(*detour));
-    
+
     // Generate new detours from this base path and add them to the queue of
     // contenders.  The new detours deviate from the base path by a single
     // replacement along the previous detour sub-path.
@@ -259,17 +262,17 @@ void ChartManager::GetSearchGraph(long translationId, std::ostream &outputSearch
 {
   size_t size = m_source.GetSize();
 
-	// which hypotheses are reachable?
-	std::map<unsigned,bool> reachable;
-	WordsRange fullRange(0, size-1);
-	const ChartCell &lastCell = m_hypoStackColl.Get(fullRange);
+  // which hypotheses are reachable?
+  std::map<unsigned,bool> reachable;
+  WordsRange fullRange(0, size-1);
+  const ChartCell &lastCell = m_hypoStackColl.Get(fullRange);
   const ChartHypothesis *hypo = lastCell.GetBestHypothesis();
 
   if (hypo == NULL) {
     // no hypothesis
     return;
   }
-	FindReachableHypotheses( hypo, reachable);
+  FindReachableHypotheses( hypo, reachable);
 
   for (size_t width = 1; width <= size; ++width) {
     for (size_t startPos = 0; startPos <= size-width; ++startPos) {
@@ -285,42 +288,40 @@ void ChartManager::GetSearchGraph(long translationId, std::ostream &outputSearch
 
 void ChartManager::FindReachableHypotheses( const ChartHypothesis *hypo, std::map<unsigned,bool> &reachable ) const
 {
-	// do not recurse, if already visited
-	if (reachable.find(hypo->GetId()) != reachable.end())
-	{
-		return;
-	}
-
-	// recurse
-	reachable[ hypo->GetId() ] = true;
-	const std::vector<const ChartHypothesis*> &previous = hypo->GetPrevHypos();
-	for(std::vector<const ChartHypothesis*>::const_iterator i = previous.begin(); i != previous.end(); ++i)
-	{
-		FindReachableHypotheses( *i, reachable );
-	}	
-
-	// also loop over recombined hypotheses (arcs)
-	const ChartArcList *arcList = hypo->GetArcList();
-	if (arcList) {
-		ChartArcList::const_iterator iterArc;
-		for (iterArc = arcList->begin(); iterArc != arcList->end(); ++iterArc) {
-			const ChartHypothesis &arc = **iterArc;
-			FindReachableHypotheses( &arc, reachable );
-		}
-	}
+  // do not recurse, if already visited
+  if (reachable.find(hypo->GetId()) != reachable.end()) {
+    return;
+  }
+
+  // recurse
+  reachable[ hypo->GetId() ] = true;
+  const std::vector<const ChartHypothesis*> &previous = hypo->GetPrevHypos();
+  for(std::vector<const ChartHypothesis*>::const_iterator i = previous.begin(); i != previous.end(); ++i) {
+    FindReachableHypotheses( *i, reachable );
+  }
+
+  // also loop over recombined hypotheses (arcs)
+  const ChartArcList *arcList = hypo->GetArcList();
+  if (arcList) {
+    ChartArcList::const_iterator iterArc;
+    for (iterArc = arcList->begin(); iterArc != arcList->end(); ++iterArc) {
+      const ChartHypothesis &arc = **iterArc;
+      FindReachableHypotheses( &arc, reachable );
+    }
+  }
 }
 
 void ChartManager::CreateDeviantPaths(
-    boost::shared_ptr<const ChartTrellisPath> basePath,
-    ChartTrellisDetourQueue &q)
+  boost::shared_ptr<const ChartTrellisPath> basePath,
+  ChartTrellisDetourQueue &q)
 {
   CreateDeviantPaths(basePath, basePath->GetFinalNode(), q);
 }
 
 void ChartManager::CreateDeviantPaths(
-    boost::shared_ptr<const ChartTrellisPath> basePath,
-    const ChartTrellisNode &substitutedNode,
-    ChartTrellisDetourQueue &queue)
+  boost::shared_ptr<const ChartTrellisPath> basePath,
+  const ChartTrellisNode &substitutedNode,
+  ChartTrellisDetourQueue &queue)
 {
   const ChartArcList *arcList = substitutedNode.GetHypothesis().GetArcList();
   if (arcList) {
@@ -340,18 +341,18 @@ void ChartManager::CreateDeviantPaths(
   }
 }
 
-  
-void ChartManager::PreCalculateScores() 
+
+void ChartManager::PreCalculateScores()
 {
   for (size_t i = 0; i < m_translationOptionList.GetSize(); ++i) {
     const ChartTranslationOptions& cto = m_translationOptionList.Get(i);
     for (TargetPhraseCollection::const_iterator j  = cto.GetTargetPhraseCollection().begin();
-     j != cto.GetTargetPhraseCollection().end(); ++j) {
+         j != cto.GetTargetPhraseCollection().end(); ++j) {
       const TargetPhrase* targetPhrase = *j;
       if (m_precalculatedScores.find(*targetPhrase) == m_precalculatedScores.end()) {
         ChartBasedFeatureContext context(*targetPhrase,m_source);
         const vector<const StatelessFeatureFunction*>& sfs =
-            StatelessFeatureFunction::GetStatelessFeatureFunctions();
+          StatelessFeatureFunction::GetStatelessFeatureFunctions();
         ScoreComponentCollection& breakdown = m_precalculatedScores[*targetPhrase];
         for (size_t k = 0; k < sfs.size(); ++k) {
           sfs[k]->EvaluateChart(context,&breakdown);
@@ -362,18 +363,18 @@ void ChartManager::PreCalculateScores()
 }
 
 void ChartManager::InsertPreCalculatedScores(
-    const TargetPhrase& targetPhrase, ScoreComponentCollection* scoreBreakdown) const 
+  const TargetPhrase& targetPhrase, ScoreComponentCollection* scoreBreakdown) const
 {
-  boost::unordered_map<TargetPhrase,ScoreComponentCollection>::const_iterator scoreIter = 
+  boost::unordered_map<TargetPhrase,ScoreComponentCollection>::const_iterator scoreIter =
     m_precalculatedScores.find(targetPhrase);
   if (scoreIter != m_precalculatedScores.end()) {
     scoreBreakdown->PlusEquals(scoreIter->second);
   } else {
     TRACE_ERR("ERROR: " << targetPhrase << " missing from precalculation cache" << endl);
-    assert(0);  
+    assert(0);
   }
 
 }
 
-  
+
 } // namespace Moses
diff --git a/moses/ChartManager.h b/moses/ChartManager.h
index 7f3f24a0b..736986e05 100644
--- a/moses/ChartManager.h
+++ b/moses/ChartManager.h
@@ -79,35 +79,37 @@ public:
   void CalcNBest(size_t count, ChartTrellisPathList &ret, bool onlyDistinct=0) const;
 
   void GetSearchGraph(long translationId, std::ostream &outputSearchGraphStream) const;
-	void FindReachableHypotheses( const ChartHypothesis *hypo, std::map<unsigned,bool> &reachable ) const; /* auxilliary function for GetSearchGraph */
+  void FindReachableHypotheses( const ChartHypothesis *hypo, std::map<unsigned,bool> &reachable ) const; /* auxilliary function for GetSearchGraph */
 
   //! the input sentence being decoded
   const InputType& GetSource() const {
     return m_source;
   }
-  
+
   //! debug data collected when decoding sentence
   SentenceStats& GetSentenceStats() const {
     return *m_sentenceStats;
   }
-  
+
   /***
    * to be called after processing a sentence (which may consist of more than just calling ProcessSentence() )
    * currently an empty function
    */
   void CalcDecoderStatistics() const
   { }
-  
+
   void ResetSentenceStats(const InputType& source) {
     m_sentenceStats = std::auto_ptr<SentenceStats>(new SentenceStats(source));
   }
 
   //! contigious hypo id for each input sentence. For debugging purposes
-  unsigned GetNextHypoId() { return m_hypothesisId++; }
+  unsigned GetNextHypoId() {
+    return m_hypothesisId++;
+  }
 
   //! Access the pre-calculated values
   void InsertPreCalculatedScores(const TargetPhrase& targetPhrase,
-      ScoreComponentCollection* scoreBreakdown) const;
+                                 ScoreComponentCollection* scoreBreakdown) const;
 
 };
 
diff --git a/moses/ChartParser.cpp b/moses/ChartParser.cpp
index 805bec7ab..0dba600e1 100644
--- a/moses/ChartParser.cpp
+++ b/moses/ChartParser.cpp
@@ -35,16 +35,18 @@ extern bool g_debug;
 
 ChartParserUnknown::ChartParserUnknown() {}
 
-ChartParserUnknown::~ChartParserUnknown() {
+ChartParserUnknown::~ChartParserUnknown()
+{
   RemoveAllInColl(m_unksrcs);
   RemoveAllInColl(m_cacheTargetPhraseCollection);
 }
 
-void ChartParserUnknown::Process(const Word &sourceWord, const WordsRange &range, ChartParserCallback &to) {
+void ChartParserUnknown::Process(const Word &sourceWord, const WordsRange &range, ChartParserCallback &to)
+{
   // unknown word, add as trans opt
   const StaticData &staticData = StaticData::Instance();
   const UnknownWordPenaltyProducer *unknownWordPenaltyProducer = staticData.GetUnknownWordPenaltyProducer();
-  
+
   size_t isDigit = 0;
   if (staticData.GetDropUnknown()) {
     const Factor *f = sourceWord[0]; // TODO hack. shouldn't know which factor is surface
@@ -56,11 +58,11 @@ void ChartParserUnknown::Process(const Word &sourceWord, const WordsRange &range
       isDigit = 1;
     // modify the starting bitmap
   }
-  
+
   Phrase* unksrc = new Phrase(1);
   unksrc->AddWord() = sourceWord;
   m_unksrcs.push_back(unksrc);
-  
+
   //TranslationOption *transOpt;
   if (! staticData.GetDropUnknown() || isDigit) {
     // loop
@@ -69,19 +71,19 @@ void ChartParserUnknown::Process(const Word &sourceWord, const WordsRange &range
     for (iterLHS = lhsList.begin(); iterLHS != lhsList.end(); ++iterLHS) {
       const string &targetLHSStr = iterLHS->first;
       float prob = iterLHS->second;
-      
+
       // lhs
       //const Word &sourceLHS = staticData.GetInputDefaultNonTerminal();
       Word *targetLHS = new Word(true);
-      
+
       targetLHS->CreateFromString(Output, staticData.GetOutputFactorOrder(), targetLHSStr, true);
       CHECK(targetLHS->GetFactor(0) != NULL);
-      
+
       // add to dictionary
       TargetPhrase *targetPhrase = new TargetPhrase();
       Word &targetWord = targetPhrase->AddWord();
       targetWord.CreateUnknownWord(sourceWord);
-      
+
       // scores
       float unknownScore = FloorScore(TransformScore(prob));
 
@@ -98,7 +100,7 @@ void ChartParserUnknown::Process(const Word &sourceWord, const WordsRange &range
   } else {
     // drop source word. create blank trans opt
     float unknownScore = FloorScore(-numeric_limits<float>::infinity());
-    
+
     TargetPhrase *targetPhrase = new TargetPhrase();
     // loop
     const UnknownLHSList &lhsList = staticData.GetUnknownLHS();
@@ -106,11 +108,11 @@ void ChartParserUnknown::Process(const Word &sourceWord, const WordsRange &range
     for (iterLHS = lhsList.begin(); iterLHS != lhsList.end(); ++iterLHS) {
       const string &targetLHSStr = iterLHS->first;
       //float prob = iterLHS->second;
-      
+
       Word *targetLHS = new Word(true);
       targetLHS->CreateFromString(Output, staticData.GetOutputFactorOrder(), targetLHSStr, true);
       CHECK(targetLHS->GetFactor(0) != NULL);
-      
+
       targetPhrase->GetScoreBreakdown().Assign(unknownWordPenaltyProducer, unknownScore);
       targetPhrase->Evaluate(*unksrc);
 
@@ -125,7 +127,8 @@ void ChartParserUnknown::Process(const Word &sourceWord, const WordsRange &range
 
 ChartParser::ChartParser(InputType const &source, ChartCellCollectionBase &cells) :
   m_decodeGraphList(StaticData::Instance().GetDecodeGraphs()),
-  m_source(source) {
+  m_source(source)
+{
   const StaticData &staticData = StaticData::Instance();
 
   staticData.InitializeForInput(source);
@@ -139,14 +142,16 @@ ChartParser::ChartParser(InputType const &source, ChartCellCollectionBase &cells
   }
 }
 
-ChartParser::~ChartParser() {
+ChartParser::~ChartParser()
+{
   RemoveAllInColl(m_ruleLookupManagers);
   StaticData::Instance().CleanUpAfterSentenceProcessing(m_source);
 }
 
-void ChartParser::Create(const WordsRange &wordsRange, ChartParserCallback &to) {
+void ChartParser::Create(const WordsRange &wordsRange, ChartParserCallback &to)
+{
   assert(m_decodeGraphList.size() == m_ruleLookupManagers.size());
-   
+
   std::vector <DecodeGraph*>::const_iterator iterDecodeGraph;
   std::vector <ChartRuleLookupManager*>::const_iterator iterRuleLookupManagers = m_ruleLookupManagers.begin();
   for (iterDecodeGraph = m_decodeGraphList.begin(); iterDecodeGraph != m_decodeGraphList.end(); ++iterDecodeGraph, ++iterRuleLookupManagers) {
@@ -158,7 +163,7 @@ void ChartParser::Create(const WordsRange &wordsRange, ChartParserCallback &to)
       ruleLookupManager.GetChartRuleCollection(wordsRange, to);
     }
   }
-  
+
   if (wordsRange.GetNumWordsCovered() == 1 && wordsRange.GetStartPos() != 0 && wordsRange.GetStartPos() != m_source.GetSize()-1) {
     bool alwaysCreateDirectTranslationOption = StaticData::Instance().IsAlwaysCreateDirectTranslationOption();
     if (to.Empty() || alwaysCreateDirectTranslationOption) {
@@ -166,7 +171,7 @@ void ChartParser::Create(const WordsRange &wordsRange, ChartParserCallback &to)
       const Word &sourceWord = m_source.GetWord(wordsRange.GetStartPos());
       m_unknown.Process(sourceWord, wordsRange, to);
     }
-  }  
+  }
 }
- 
+
 } // namespace Moses
diff --git a/moses/ChartParser.h b/moses/ChartParser.h
index 9d8baa649..1ff99480d 100644
--- a/moses/ChartParser.h
+++ b/moses/ChartParser.h
@@ -39,31 +39,33 @@ class Phrase;
 class TargetPhraseCollection;
 class DecodeGraph;
 
-class ChartParserUnknown {
-  public:
-    ChartParserUnknown();
-    ~ChartParserUnknown();
+class ChartParserUnknown
+{
+public:
+  ChartParserUnknown();
+  ~ChartParserUnknown();
 
-    void Process(const Word &sourceWord, const WordsRange &range, ChartParserCallback &to);
+  void Process(const Word &sourceWord, const WordsRange &range, ChartParserCallback &to);
 
-  private:
-    std::vector<Phrase*> m_unksrcs;
-    std::list<TargetPhraseCollection*> m_cacheTargetPhraseCollection;
-    StackVec m_emptyStackVec;
+private:
+  std::vector<Phrase*> m_unksrcs;
+  std::list<TargetPhraseCollection*> m_cacheTargetPhraseCollection;
+  StackVec m_emptyStackVec;
 };
 
-class ChartParser {
-  public:
-    ChartParser(const InputType &source, ChartCellCollectionBase &cells);
-    ~ChartParser();
+class ChartParser
+{
+public:
+  ChartParser(const InputType &source, ChartCellCollectionBase &cells);
+  ~ChartParser();
 
-    void Create(const WordsRange &range, ChartParserCallback &to);
+  void Create(const WordsRange &range, ChartParserCallback &to);
 
-  private:
-    ChartParserUnknown m_unknown;
-    std::vector <DecodeGraph*> m_decodeGraphList;
-    std::vector<ChartRuleLookupManager*> m_ruleLookupManagers;
-    InputType const& m_source; /**< source sentence to be translated */
+private:
+  ChartParserUnknown m_unknown;
+  std::vector <DecodeGraph*> m_decodeGraphList;
+  std::vector<ChartRuleLookupManager*> m_ruleLookupManagers;
+  InputType const& m_source; /**< source sentence to be translated */
 };
 
 }
diff --git a/moses/ChartParserCallback.h b/moses/ChartParserCallback.h
index 797a57156..84ddb8b75 100644
--- a/moses/ChartParserCallback.h
+++ b/moses/ChartParserCallback.h
@@ -4,21 +4,23 @@
 
 #include <list>
 
-namespace Moses {
+namespace Moses
+{
 
 class TargetPhraseCollection;
 class WordsRange;
 class TargetPhrase;
 
-class ChartParserCallback {
-  public:
-    virtual ~ChartParserCallback() {}
+class ChartParserCallback
+{
+public:
+  virtual ~ChartParserCallback() {}
 
-    virtual void Add(const TargetPhraseCollection &, const StackVec &, const WordsRange &) = 0;
+  virtual void Add(const TargetPhraseCollection &, const StackVec &, const WordsRange &) = 0;
 
-    virtual bool Empty() const = 0;
+  virtual bool Empty() const = 0;
 
-    virtual void AddPhraseOOV(TargetPhrase &phrase, std::list<TargetPhraseCollection*> &waste_memory, const WordsRange &range) = 0;
+  virtual void AddPhraseOOV(TargetPhrase &phrase, std::list<TargetPhraseCollection*> &waste_memory, const WordsRange &range) = 0;
 };
 
 } // namespace Moses
diff --git a/moses/ChartRuleLookupManager.h b/moses/ChartRuleLookupManager.h
index da8c98cb4..ad936ff9c 100644
--- a/moses/ChartRuleLookupManager.h
+++ b/moses/ChartRuleLookupManager.h
@@ -50,7 +50,7 @@ public:
   const InputType &GetSentence() const {
     return m_sentence;
   }
-  
+
   const ChartCellLabelSet &GetTargetLabelSet(size_t begin, size_t end) const {
     return m_cellCollection.GetBase(WordsRange(begin, end)).GetTargetLabelSet();
   }
diff --git a/moses/ChartTranslationOptionList.cpp b/moses/ChartTranslationOptionList.cpp
index 8f4422e23..5b72ea7a3 100644
--- a/moses/ChartTranslationOptionList.cpp
+++ b/moses/ChartTranslationOptionList.cpp
@@ -74,11 +74,11 @@ void ChartTranslationOptionList::Add(const TargetPhraseCollection &tpc,
   if (m_size == m_collection.size()) {
     // m_collection has reached capacity: create a new object.
     m_collection.push_back(new ChartTranslationOptions(tpc, stackVec,
-                                                      range, score));
+                           range, score));
   } else {
     // Overwrite an unused object.
     *(m_collection[m_size]) = ChartTranslationOptions(tpc, stackVec,
-                                                     range, score);
+                              range, score);
   }
   ++m_size;
 
@@ -98,7 +98,8 @@ void ChartTranslationOptionList::Add(const TargetPhraseCollection &tpc,
   }
 }
 
-void ChartTranslationOptionList::AddPhraseOOV(TargetPhrase &phrase, std::list<TargetPhraseCollection*> &waste_memory, const WordsRange &range) {
+void ChartTranslationOptionList::AddPhraseOOV(TargetPhrase &phrase, std::list<TargetPhraseCollection*> &waste_memory, const WordsRange &range)
+{
   TargetPhraseCollection *tpc = new TargetPhraseCollection();
   tpc->Add(&phrase);
   waste_memory.push_back(tpc);
@@ -106,7 +107,8 @@ void ChartTranslationOptionList::AddPhraseOOV(TargetPhrase &phrase, std::list<Ta
   Add(*tpc, empty, range);
 }
 
-void ChartTranslationOptionList::ApplyThreshold() {
+void ChartTranslationOptionList::ApplyThreshold()
+{
   if (m_size > m_ruleLimit) {
     // Something's gone wrong if the list has grown to m_ruleLimit * 2
     // without being pruned.
@@ -134,8 +136,8 @@ void ChartTranslationOptionList::ApplyThreshold() {
   scoreThreshold += StaticData::Instance().GetTranslationOptionThreshold();
 
   CollType::iterator bound = std::partition(m_collection.begin(),
-                                            m_collection.begin()+m_size,
-                                            ScoreThresholdPred(scoreThreshold));
+                             m_collection.begin()+m_size,
+                             ScoreThresholdPred(scoreThreshold));
 
   m_size = std::distance(m_collection.begin(), bound);
 }
diff --git a/moses/ChartTranslationOptionList.h b/moses/ChartTranslationOptionList.h
index 0b56b1f61..a2979fcbc 100644
--- a/moses/ChartTranslationOptionList.h
+++ b/moses/ChartTranslationOptionList.h
@@ -32,27 +32,34 @@ class TargetPhraseCollection;
 class WordsRange;
 
 //! a vector of translations options for a specific range, in a specific sentence
-class ChartTranslationOptionList : public ChartParserCallback {
- public:
+class ChartTranslationOptionList : public ChartParserCallback
+{
+public:
   ChartTranslationOptionList(size_t);
   ~ChartTranslationOptionList();
 
-  const ChartTranslationOptions &Get(size_t i) const { return *m_collection[i]; }
+  const ChartTranslationOptions &Get(size_t i) const {
+    return *m_collection[i];
+  }
 
   //! number of translation options
-  size_t GetSize() const { return m_size; }
+  size_t GetSize() const {
+    return m_size;
+  }
 
   void Add(const TargetPhraseCollection &, const StackVec &,
            const WordsRange &);
 
   void AddPhraseOOV(TargetPhrase &phrase, std::list<TargetPhraseCollection*> &waste_memory, const WordsRange &range);
 
-  bool Empty() const { return m_size == 0; }
+  bool Empty() const {
+    return m_size == 0;
+  }
 
   void Clear();
   void ApplyThreshold();
 
- private:
+private:
   typedef std::vector<ChartTranslationOptions*> CollType;
 
   struct ScoreThresholdPred {
diff --git a/moses/ChartTranslationOptions.cpp b/moses/ChartTranslationOptions.cpp
index c55948a82..5ba88a0db 100644
--- a/moses/ChartTranslationOptions.cpp
+++ b/moses/ChartTranslationOptions.cpp
@@ -27,8 +27,8 @@ namespace Moses
 {
 
 float ChartTranslationOptions::CalcEstimateOfBestScore(
-    const TargetPhraseCollection &tpc,
-    const StackVec &stackVec)
+  const TargetPhraseCollection &tpc,
+  const StackVec &stackVec)
 {
   const TargetPhrase &targetPhrase = **(tpc.begin());
   float estimateOfBestScore = targetPhrase.GetFutureScore();
diff --git a/moses/ChartTranslationOptions.h b/moses/ChartTranslationOptions.h
index 4910723f7..459c91659 100644
--- a/moses/ChartTranslationOptions.h
+++ b/moses/ChartTranslationOptions.h
@@ -35,7 +35,7 @@ namespace Moses
  */
 class ChartTranslationOptions
 {
- public:
+public:
   /** Constructor
       \param targetPhraseColl @todo dunno
       \param stackVec @todo dunno
@@ -43,13 +43,13 @@ class ChartTranslationOptions
       \param score @todo dunno
    */
   ChartTranslationOptions(const TargetPhraseCollection &targetPhraseColl,
-                         const StackVec &stackVec,
-                         const WordsRange &wordsRange,
-                         float score)
-      : m_stackVec(stackVec)
-      , m_targetPhraseCollection(&targetPhraseColl)
-      , m_wordsRange(&wordsRange)
-      , m_estimateOfBestScore(score) 
+                          const StackVec &stackVec,
+                          const WordsRange &wordsRange,
+                          float score)
+    : m_stackVec(stackVec)
+    , m_targetPhraseCollection(&targetPhraseColl)
+    , m_wordsRange(&wordsRange)
+    , m_estimateOfBestScore(score)
   {}
 
   ~ChartTranslationOptions() {}
@@ -58,10 +58,12 @@ class ChartTranslationOptions
                                        const StackVec &);
 
   //! @todo dunno
-  const StackVec &GetStackVec() const { return m_stackVec; }
+  const StackVec &GetStackVec() const {
+    return m_stackVec;
+  }
 
   //! @todo isn't the translation suppose to just contain 1 target phrase, not a whole collection of them?
-  const TargetPhraseCollection &GetTargetPhraseCollection() const { 
+  const TargetPhraseCollection &GetTargetPhraseCollection() const {
     return *m_targetPhraseCollection;
   }
 
@@ -74,9 +76,11 @@ class ChartTranslationOptions
     * the estimate is the sum of the top target phrase's estimated score plus the
     * scores of the best child hypotheses.
     */
-  inline float GetEstimateOfBestScore() const { return m_estimateOfBestScore; }
+  inline float GetEstimateOfBestScore() const {
+    return m_estimateOfBestScore;
+  }
 
- private:
+private:
 
   StackVec m_stackVec; //! vector of hypothesis list!
   const TargetPhraseCollection *m_targetPhraseCollection;
diff --git a/moses/ChartTrellisDetour.cpp b/moses/ChartTrellisDetour.cpp
index 550a44a2c..1a187396c 100644
--- a/moses/ChartTrellisDetour.cpp
+++ b/moses/ChartTrellisDetour.cpp
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -27,15 +27,15 @@ namespace Moses
 {
 
 ChartTrellisDetour::ChartTrellisDetour(
-    boost::shared_ptr<const ChartTrellisPath> basePath,
-    const ChartTrellisNode &substitutedNode,
-    const ChartHypothesis &replacementHypo)
+  boost::shared_ptr<const ChartTrellisPath> basePath,
+  const ChartTrellisNode &substitutedNode,
+  const ChartHypothesis &replacementHypo)
   : m_basePath(basePath)
   , m_substitutedNode(substitutedNode)
   , m_replacementHypo(replacementHypo)
 {
   float diff = replacementHypo.GetTotalScore()
-             - substitutedNode.GetHypothesis().GetTotalScore();
+               - substitutedNode.GetHypothesis().GetTotalScore();
   m_totalScore = basePath->GetTotalScore() + diff;
 }
 
diff --git a/moses/ChartTrellisDetour.h b/moses/ChartTrellisDetour.h
index 977ccb67d..26c98bef8 100644
--- a/moses/ChartTrellisDetour.h
+++ b/moses/ChartTrellisDetour.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -31,20 +31,24 @@ class ChartTrellisPath;
  */
 class ChartTrellisDetour
 {
- public:
+public:
   ChartTrellisDetour(boost::shared_ptr<const ChartTrellisPath>,
                      const ChartTrellisNode &, const ChartHypothesis &);
 
-  const ChartTrellisPath &GetBasePath() const { return *m_basePath; }
+  const ChartTrellisPath &GetBasePath() const {
+    return *m_basePath;
+  }
   const ChartTrellisNode &GetSubstitutedNode() const {
     return m_substitutedNode;
   }
   const ChartHypothesis &GetReplacementHypo() const {
     return m_replacementHypo;
   }
-  float GetTotalScore() const { return m_totalScore; }
+  float GetTotalScore() const {
+    return m_totalScore;
+  }
 
- private:
+private:
   boost::shared_ptr<const ChartTrellisPath> m_basePath;
   const ChartTrellisNode &m_substitutedNode;
   const ChartHypothesis &m_replacementHypo;
diff --git a/moses/ChartTrellisDetourQueue.cpp b/moses/ChartTrellisDetourQueue.cpp
index 9b359ca43..4bb81d20b 100644
--- a/moses/ChartTrellisDetourQueue.cpp
+++ b/moses/ChartTrellisDetourQueue.cpp
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -21,13 +21,16 @@
 
 #include "Util.h"
 
-namespace Moses {
+namespace Moses
+{
 
-ChartTrellisDetourQueue::~ChartTrellisDetourQueue() {
+ChartTrellisDetourQueue::~ChartTrellisDetourQueue()
+{
   RemoveAllInColl(m_queue);
 }
 
-void ChartTrellisDetourQueue::Push(const ChartTrellisDetour *detour) {
+void ChartTrellisDetourQueue::Push(const ChartTrellisDetour *detour)
+{
   if (m_capacity == 0 || m_queue.size() < m_capacity) {
     m_queue.insert(detour);
   } else if (detour->GetTotalScore() > (*m_queue.rbegin())->GetTotalScore()) {
@@ -43,7 +46,8 @@ void ChartTrellisDetourQueue::Push(const ChartTrellisDetour *detour) {
   }
 }
 
-const ChartTrellisDetour *ChartTrellisDetourQueue::Pop() {
+const ChartTrellisDetour *ChartTrellisDetourQueue::Pop()
+{
   QueueType::iterator p = m_queue.begin();
   const ChartTrellisDetour *top = *p;
   m_queue.erase(p);
diff --git a/moses/ChartTrellisDetourQueue.h b/moses/ChartTrellisDetourQueue.h
index d6505d8a2..2406a69f5 100644
--- a/moses/ChartTrellisDetourQueue.h
+++ b/moses/ChartTrellisDetourQueue.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -23,20 +23,24 @@
 
 #include <set>
 
-namespace Moses {
+namespace Moses
+{
 
 /** A bounded priority queue of ChartTrellisDetour pointers.  The top item is
  *  the best scoring detour.  The queue assumes ownership of pushed items and
  *  relinquishes ownership when they are popped.  Any remaining items at the
  *  time of the queue's destruction are deleted.
  */
-class ChartTrellisDetourQueue {
- public:
+class ChartTrellisDetourQueue
+{
+public:
   // Create empty queue with fixed capacity of c.  Capacity 0 means unbounded.
   ChartTrellisDetourQueue(size_t c) : m_capacity(c) {}
   ~ChartTrellisDetourQueue();
 
-  bool Empty() const { return m_queue.empty(); }
+  bool Empty() const {
+    return m_queue.empty();
+  }
 
   // Add the detour to the queue or delete it if the queue is full and the
   // score is no better than the queue's worst score.
@@ -46,7 +50,7 @@ class ChartTrellisDetourQueue {
   // caller is responsible for deleting the object.
   const ChartTrellisDetour *Pop();
 
- private:
+private:
   struct DetourOrderer {
     bool operator()(const ChartTrellisDetour* a,
                     const ChartTrellisDetour* b) const {
diff --git a/moses/ChartTrellisNode.cpp b/moses/ChartTrellisNode.cpp
index e55d4b1ab..73651f507 100644
--- a/moses/ChartTrellisNode.cpp
+++ b/moses/ChartTrellisNode.cpp
@@ -29,16 +29,16 @@ namespace Moses
 {
 
 ChartTrellisNode::ChartTrellisNode(const ChartHypothesis &hypo)
-    : m_hypo(hypo)
+  : m_hypo(hypo)
 {
   CreateChildren();
 }
 
 ChartTrellisNode::ChartTrellisNode(const ChartTrellisDetour &detour,
                                    ChartTrellisNode *&deviationPoint)
-    : m_hypo((&detour.GetBasePath().GetFinalNode() == &detour.GetSubstitutedNode())
-             ? detour.GetReplacementHypo()
-             : detour.GetBasePath().GetFinalNode().GetHypothesis())
+  : m_hypo((&detour.GetBasePath().GetFinalNode() == &detour.GetSubstitutedNode())
+           ? detour.GetReplacementHypo()
+           : detour.GetBasePath().GetFinalNode().GetHypothesis())
 {
   if (&m_hypo == &detour.GetReplacementHypo()) {
     deviationPoint = this;
@@ -54,9 +54,9 @@ ChartTrellisNode::ChartTrellisNode(const ChartTrellisNode &root,
                                    const ChartTrellisNode &substitutedNode,
                                    const ChartHypothesis &replacementHypo,
                                    ChartTrellisNode *&deviationPoint)
-    : m_hypo((&root == &substitutedNode)
-             ? replacementHypo
-             : root.GetHypothesis())
+  : m_hypo((&root == &substitutedNode)
+           ? replacementHypo
+           : root.GetHypothesis())
 {
   if (&root == &substitutedNode) {
     deviationPoint = this;
@@ -118,8 +118,8 @@ void ChartTrellisNode::CreateChildren(const ChartTrellisNode &rootNode,
   for (size_t ind = 0; ind < children.size(); ++ind) {
     const ChartTrellisNode *origChild = children[ind];
     ChartTrellisNode *child = new ChartTrellisNode(*origChild, substitutedNode,
-                                                   replacementHypo,
-                                                   deviationPoint);
+        replacementHypo,
+        deviationPoint);
     m_children.push_back(child);
   }
 }
diff --git a/moses/ChartTrellisNode.h b/moses/ChartTrellisNode.h
index 58203677e..643809728 100644
--- a/moses/ChartTrellisNode.h
+++ b/moses/ChartTrellisNode.h
@@ -34,7 +34,7 @@ class ChartTrellisDetour;
  */
 class ChartTrellisNode
 {
- public:
+public:
   typedef std::vector<ChartTrellisNode*> NodeChildren;
 
   ChartTrellisNode(const ChartHypothesis &hypo);
@@ -42,15 +42,21 @@ class ChartTrellisNode
 
   ~ChartTrellisNode();
 
-  const ChartHypothesis &GetHypothesis() const { return m_hypo; }
+  const ChartHypothesis &GetHypothesis() const {
+    return m_hypo;
+  }
 
-  const NodeChildren &GetChildren() const { return m_children; }
+  const NodeChildren &GetChildren() const {
+    return m_children;
+  }
 
-  const ChartTrellisNode &GetChild(size_t i) const { return *m_children[i]; }
+  const ChartTrellisNode &GetChild(size_t i) const {
+    return *m_children[i];
+  }
 
   Phrase GetOutputPhrase() const;
 
- private:
+private:
   ChartTrellisNode(const ChartTrellisNode &);  // Not implemented
   ChartTrellisNode& operator=(const ChartTrellisNode &);  // Not implemented
 
diff --git a/moses/ChartTrellisPath.cpp b/moses/ChartTrellisPath.cpp
index 231d4237a..c53e636e9 100644
--- a/moses/ChartTrellisPath.cpp
+++ b/moses/ChartTrellisPath.cpp
@@ -30,17 +30,17 @@ namespace Moses
 {
 
 ChartTrellisPath::ChartTrellisPath(const ChartHypothesis &hypo)
-    : m_finalNode(new ChartTrellisNode(hypo))
-    , m_deviationPoint(NULL)
-    , m_scoreBreakdown(hypo.GetScoreBreakdown())
-    , m_totalScore(hypo.GetTotalScore())
+  : m_finalNode(new ChartTrellisNode(hypo))
+  , m_deviationPoint(NULL)
+  , m_scoreBreakdown(hypo.GetScoreBreakdown())
+  , m_totalScore(hypo.GetTotalScore())
 {
 }
 
 ChartTrellisPath::ChartTrellisPath(const ChartTrellisDetour &detour)
-   : m_finalNode(new ChartTrellisNode(detour, m_deviationPoint))
-   , m_scoreBreakdown(detour.GetBasePath().m_scoreBreakdown)
-   , m_totalScore(0)
+  : m_finalNode(new ChartTrellisNode(detour, m_deviationPoint))
+  , m_scoreBreakdown(detour.GetBasePath().m_scoreBreakdown)
+  , m_totalScore(0)
 {
   CHECK(m_deviationPoint);
   ScoreComponentCollection scoreChange;
diff --git a/moses/ChartTrellisPath.h b/moses/ChartTrellisPath.h
index 6e5d50e0c..1023ad7b4 100644
--- a/moses/ChartTrellisPath.h
+++ b/moses/ChartTrellisPath.h
@@ -41,18 +41,24 @@ class ChartTrellisNode;
  */
 class ChartTrellisPath
 {
- public:
+public:
   ChartTrellisPath(const ChartHypothesis &hypo);
   ChartTrellisPath(const ChartTrellisDetour &detour);
 
   ~ChartTrellisPath();
 
-  const ChartTrellisNode &GetFinalNode() const { return *m_finalNode; }
+  const ChartTrellisNode &GetFinalNode() const {
+    return *m_finalNode;
+  }
 
-  const ChartTrellisNode *GetDeviationPoint() const { return m_deviationPoint; }
+  const ChartTrellisNode *GetDeviationPoint() const {
+    return m_deviationPoint;
+  }
 
   //! get score for this path throught trellis
-  float GetTotalScore() const { return m_totalScore; }
+  float GetTotalScore() const {
+    return m_totalScore;
+  }
 
   Phrase GetOutputPhrase() const;
 
@@ -61,7 +67,7 @@ class ChartTrellisPath
     return m_scoreBreakdown;
   }
 
- private:
+private:
   ChartTrellisPath(const ChartTrellisPath &);  // Not implemented
   ChartTrellisPath &operator=(const ChartTrellisPath &);  // Not implemented
 
diff --git a/moses/ConfusionNet.h b/moses/ConfusionNet.h
index 55fa0c8bf..c9c83e154 100644
--- a/moses/ConfusionNet.h
+++ b/moses/ConfusionNet.h
@@ -15,7 +15,7 @@ class FactorCollection;
 class TranslationOptionCollection;
 class Sentence;
 
-/** An input to the decoder where each position can be 1 of a number of words, 
+/** An input to the decoder where each position can be 1 of a number of words,
  *  each with an associated probability. Compared with a sentence, where each position is a word
  */
 class ConfusionNet : public InputType
diff --git a/moses/DecodeFeature.cpp b/moses/DecodeFeature.cpp
index ebec7a7e3..57137170e 100644
--- a/moses/DecodeFeature.cpp
+++ b/moses/DecodeFeature.cpp
@@ -30,8 +30,8 @@ using namespace std;
 namespace Moses
 {
 DecodeFeature::DecodeFeature(  const std::string& description
-                , const std::string &line)
-: StatelessFeatureFunction(description, line)
+                               , const std::string &line)
+  : StatelessFeatureFunction(description, line)
 {
   VERBOSE(2,"DecodeFeature:" << std::endl);
   for (size_t i = 0; i < m_args.size(); ++i) {
@@ -40,8 +40,7 @@ DecodeFeature::DecodeFeature(  const std::string& description
     if (args[0] == "input-factor") {
       m_input =Tokenize<FactorType>(args[1], ",");
       m_inputFactors = FactorMask(m_input);
-    }
-    else if (args[0] == "output-factor") {
+    } else if (args[0] == "output-factor") {
       m_output =Tokenize<FactorType>(args[1], ",");
       m_outputFactors = FactorMask(m_output);
     }
@@ -50,20 +49,20 @@ DecodeFeature::DecodeFeature(  const std::string& description
 }
 
 DecodeFeature::DecodeFeature(  const std::string& description
-                            , size_t numScoreComponents
-                            , const std::string &line)
-: StatelessFeatureFunction(description,numScoreComponents, line)
+                               , size_t numScoreComponents
+                               , const std::string &line)
+  : StatelessFeatureFunction(description,numScoreComponents, line)
 {
   VERBOSE(2,"DecodeFeature: no factors yet" << std::endl);
 }
 
 DecodeFeature::DecodeFeature(const std::string& description
-                            , size_t numScoreComponents
-                            , const std::vector<FactorType> &input
-                            , const std::vector<FactorType> &output
-                            , const std::string &line)
-: StatelessFeatureFunction(description,numScoreComponents, line)
-, m_input(input), m_output(output)
+                             , size_t numScoreComponents
+                             , const std::vector<FactorType> &input
+                             , const std::vector<FactorType> &output
+                             , const std::string &line)
+  : StatelessFeatureFunction(description,numScoreComponents, line)
+  , m_input(input), m_output(output)
 {
   m_inputFactors = FactorMask(input);
   m_outputFactors = FactorMask(output);
diff --git a/moses/DecodeFeature.h b/moses/DecodeFeature.h
index b6352b181..d6cf3a323 100644
--- a/moses/DecodeFeature.h
+++ b/moses/DecodeFeature.h
@@ -34,9 +34,10 @@ namespace Moses
 /**
   * Baseclass for phrase-table or generation table feature function
  **/
-class DecodeFeature : public StatelessFeatureFunction {
+class DecodeFeature : public StatelessFeatureFunction
+{
 
-  public:
+public:
   DecodeFeature(  const std::string& description
                   , const std::string &line);
 
@@ -45,28 +46,29 @@ class DecodeFeature : public StatelessFeatureFunction {
                   , const std::string &line);
 
   DecodeFeature(  const std::string& description
-                    , size_t numScoreComponents
-                    , const std::vector<FactorType> &input
-                    , const std::vector<FactorType> &output
-                    , const std::string &line);
-    
-    //! returns output factor types as specified by the ini file
-    const FactorMask& GetOutputFactorMask() const;
-    
-    //! returns input factor types as specified by the ini file
-    const FactorMask& GetInputFactorMask() const;
-    
-    const std::vector<FactorType>& GetInput() const;
-    const std::vector<FactorType>& GetOutput() const;
-
-    bool IsDecodeFeature() const
-    { return true; }
-
-  protected:
-    std::vector<FactorType> m_input;
-    std::vector<FactorType> m_output;
-    FactorMask m_inputFactors;
-    FactorMask m_outputFactors;
+                  , size_t numScoreComponents
+                  , const std::vector<FactorType> &input
+                  , const std::vector<FactorType> &output
+                  , const std::string &line);
+
+  //! returns output factor types as specified by the ini file
+  const FactorMask& GetOutputFactorMask() const;
+
+  //! returns input factor types as specified by the ini file
+  const FactorMask& GetInputFactorMask() const;
+
+  const std::vector<FactorType>& GetInput() const;
+  const std::vector<FactorType>& GetOutput() const;
+
+  bool IsDecodeFeature() const {
+    return true;
+  }
+
+protected:
+  std::vector<FactorType> m_input;
+  std::vector<FactorType> m_output;
+  FactorMask m_inputFactors;
+  FactorMask m_outputFactors;
 };
 
 }
diff --git a/moses/DecodeStepTranslation.cpp b/moses/DecodeStepTranslation.cpp
index 0acd3479f..e4dbb673d 100644
--- a/moses/DecodeStepTranslation.cpp
+++ b/moses/DecodeStepTranslation.cpp
@@ -94,9 +94,9 @@ void DecodeStepTranslation::Process(const TranslationOption &inputPartialTranslO
 
 
 void DecodeStepTranslation::ProcessInitialTranslation(
-    const InputType &source
-    ,PartialTranslOptColl &outputPartialTranslOptColl
-    , size_t startPos, size_t endPos, bool adhereTableLimit) const
+  const InputType &source
+  ,PartialTranslOptColl &outputPartialTranslOptColl
+  , size_t startPos, size_t endPos, bool adhereTableLimit) const
 {
   const PhraseDictionary* phraseDictionary = GetPhraseDictionaryFeature();
   const size_t tableLimit = phraseDictionary->GetTableLimit();
diff --git a/moses/FF/BleuScoreFeature.cpp b/moses/FF/BleuScoreFeature.cpp
index 091035b0f..7808d6012 100644
--- a/moses/FF/BleuScoreFeature.cpp
+++ b/moses/FF/BleuScoreFeature.cpp
@@ -5,90 +5,94 @@
 
 using namespace std;
 
-namespace Moses {
+namespace Moses
+{
 
 size_t BleuScoreState::bleu_order = 4;
 
 BleuScoreState::BleuScoreState(): m_words(1),
-                                  m_source_length(0),
-                                  m_target_length(0),
-                                  m_scaled_ref_length(0),
-                                  m_ngram_counts(bleu_order),
-                                  m_ngram_matches(bleu_order)
+  m_source_length(0),
+  m_target_length(0),
+  m_scaled_ref_length(0),
+  m_ngram_counts(bleu_order),
+  m_ngram_matches(bleu_order)
 {
 }
 
 int BleuScoreState::Compare(const FFState& o) const
 {
-    if (&o == this)
-      return 0;
-
-    const StaticData &staticData = StaticData::Instance();
-    SearchAlgorithm searchAlgorithm = staticData.GetSearchAlgorithm();
-    bool chartDecoding = (searchAlgorithm == ChartDecoding);
-    if (chartDecoding) 
-      return 0;
-
-    const BleuScoreState& other = dynamic_cast<const BleuScoreState&>(o);
-    int c = m_words.Compare(other.m_words);
-    if (c != 0)
-      return c;
-
-    /*for(size_t i = 0; i < m_ngram_counts.size(); i++) {
-      if (m_ngram_counts[i] < other.m_ngram_counts[i])
-	return -1;
-      if (m_ngram_counts[i] > other.m_ngram_counts[i])
-	return 1;
-      if (m_ngram_matches[i] < other.m_ngram_matches[i])
-	return -1;
-      if (m_ngram_matches[i] > other.m_ngram_matches[i])
-	return 1;
-	}*/
+  if (&o == this)
+    return 0;
 
+  const StaticData &staticData = StaticData::Instance();
+  SearchAlgorithm searchAlgorithm = staticData.GetSearchAlgorithm();
+  bool chartDecoding = (searchAlgorithm == ChartDecoding);
+  if (chartDecoding)
     return 0;
+
+  const BleuScoreState& other = dynamic_cast<const BleuScoreState&>(o);
+  int c = m_words.Compare(other.m_words);
+  if (c != 0)
+    return c;
+
+  /*for(size_t i = 0; i < m_ngram_counts.size(); i++) {
+    if (m_ngram_counts[i] < other.m_ngram_counts[i])
+  return -1;
+    if (m_ngram_counts[i] > other.m_ngram_counts[i])
+  return 1;
+    if (m_ngram_matches[i] < other.m_ngram_matches[i])
+  return -1;
+    if (m_ngram_matches[i] > other.m_ngram_matches[i])
+  return 1;
+  }*/
+
+  return 0;
 }
-std::ostream& operator<<(std::ostream& out, const BleuScoreState& state) {
+std::ostream& operator<<(std::ostream& out, const BleuScoreState& state)
+{
   state.print(out);
   return out;
 }
 
-void BleuScoreState::print(std::ostream& out) const {
+void BleuScoreState::print(std::ostream& out) const
+{
   out << "ref=" << m_scaled_ref_length
-  	<< ";source=" << m_source_length
-	  << ";target=" << m_target_length << ";counts=";
+      << ";source=" << m_source_length
+      << ";target=" << m_target_length << ";counts=";
   for (size_t i = 0; i < bleu_order; ++i) {
     out << m_ngram_matches[i] << "/" << m_ngram_counts[i] << ",";
   }
   out << "ctxt=" << m_words;
-    
+
 }
 
 void BleuScoreState::AddNgramCountAndMatches(std::vector< size_t >& counts,
-																									std::vector< size_t >& matches) {
-	for (size_t order = 0; order < BleuScoreState::bleu_order; ++order) {
-		m_ngram_counts[order] += counts[order];
-		m_ngram_matches[order] += matches[order];
-	}
+    std::vector< size_t >& matches)
+{
+  for (size_t order = 0; order < BleuScoreState::bleu_order; ++order) {
+    m_ngram_counts[order] += counts[order];
+    m_ngram_matches[order] += matches[order];
+  }
 }
 
 
 BleuScoreFeature::BleuScoreFeature(const std::string &line)
-:StatefulFeatureFunction("BleuScoreFeature",1, line),
-m_enabled(true),
-m_sentence_bleu(true),
-m_simple_history_bleu(false),
-m_count_history(BleuScoreState::bleu_order),
-m_match_history(BleuScoreState::bleu_order),
-m_source_length_history(0),
-m_target_length_history(0),
-m_ref_length_history(0),
-m_scale_by_input_length(true),
-m_scale_by_avg_input_length(false),
-m_scale_by_inverse_length(false),
-m_scale_by_avg_inverse_length(false),
-m_scale_by_x(1),
-m_historySmoothing(0.9),
-m_smoothing_scheme(PLUS_POINT_ONE)
+  :StatefulFeatureFunction("BleuScoreFeature",1, line),
+   m_enabled(true),
+   m_sentence_bleu(true),
+   m_simple_history_bleu(false),
+   m_count_history(BleuScoreState::bleu_order),
+   m_match_history(BleuScoreState::bleu_order),
+   m_source_length_history(0),
+   m_target_length_history(0),
+   m_ref_length_history(0),
+   m_scale_by_input_length(true),
+   m_scale_by_avg_input_length(false),
+   m_scale_by_inverse_length(false),
+   m_scale_by_avg_inverse_length(false),
+   m_scale_by_x(1),
+   m_historySmoothing(0.9),
+   m_smoothing_scheme(PLUS_POINT_ONE)
 {
   for (size_t i = 0; i < m_args.size(); ++i) {
     const vector<string> &args = m_args[i];
@@ -131,10 +135,11 @@ m_smoothing_scheme(PLUS_POINT_ONE)
   } // for (size_t i = 0; i < toks.size(); ++i) {
 }
 
-void BleuScoreFeature::PrintHistory(std::ostream& out) const {
-	out << "source length history=" << m_source_length_history << endl;
-	out << "target length history=" << m_target_length_history << endl;
-	out << "ref length history=" << m_ref_length_history << endl;
+void BleuScoreFeature::PrintHistory(std::ostream& out) const
+{
+  out << "source length history=" << m_source_length_history << endl;
+  out << "target length history=" << m_target_length_history << endl;
+  out << "ref length history=" << m_ref_length_history << endl;
 
   for (size_t i = 0; i < BleuScoreState::bleu_order; ++i) {
     out << "match history/count history (" << i << "):" << m_match_history[i] << "/" << m_count_history[i] << endl;
@@ -142,48 +147,49 @@ void BleuScoreFeature::PrintHistory(std::ostream& out) const {
 }
 
 void BleuScoreFeature::SetBleuParameters(bool disable, bool sentenceBleu, bool scaleByInputLength, bool scaleByAvgInputLength,
-		bool scaleByInverseLength, bool scaleByAvgInverseLength,
-					 float scaleByX, float historySmoothing, size_t scheme, bool simpleHistoryBleu) {
-	m_enabled = !disable;
-	m_sentence_bleu = sentenceBleu;
-	m_simple_history_bleu = simpleHistoryBleu;
-	m_scale_by_input_length = scaleByInputLength;
-	m_scale_by_avg_input_length = scaleByAvgInputLength;
-	m_scale_by_inverse_length = scaleByInverseLength;
-	m_scale_by_avg_inverse_length = scaleByAvgInverseLength;
-	m_scale_by_x = scaleByX;
-	m_historySmoothing = historySmoothing;
-	m_smoothing_scheme = (SmoothingScheme)scheme;
+    bool scaleByInverseLength, bool scaleByAvgInverseLength,
+    float scaleByX, float historySmoothing, size_t scheme, bool simpleHistoryBleu)
+{
+  m_enabled = !disable;
+  m_sentence_bleu = sentenceBleu;
+  m_simple_history_bleu = simpleHistoryBleu;
+  m_scale_by_input_length = scaleByInputLength;
+  m_scale_by_avg_input_length = scaleByAvgInputLength;
+  m_scale_by_inverse_length = scaleByInverseLength;
+  m_scale_by_avg_inverse_length = scaleByAvgInverseLength;
+  m_scale_by_x = scaleByX;
+  m_historySmoothing = historySmoothing;
+  m_smoothing_scheme = (SmoothingScheme)scheme;
 }
 
 // Incoming references (refs) are stored as refs[file_id][[sent_id][reference]]
 // This data structure: m_refs[sent_id][[vector<length>][ngrams]]
 void BleuScoreFeature::LoadReferences(const std::vector< std::vector< std::string > >& refs)
 {
-	m_refs.clear();
-	FactorCollection& fc = FactorCollection::Instance();
-	for (size_t file_id = 0; file_id < refs.size(); file_id++) {
-		for (size_t sent_id = 0; sent_id < refs[file_id].size(); sent_id++) {
-			const string& ref = refs[file_id][sent_id];
-			vector<string> refTokens  = Tokenize(ref);
-			if (file_id == 0)
-				m_refs[sent_id] = RefValue(); 
-			pair<vector<size_t>,NGrams>& ref_pair = m_refs[sent_id];
-			(ref_pair.first).push_back(refTokens.size());
-			for (size_t order = 1; order <= BleuScoreState::bleu_order; order++) {
-				for (size_t end_idx = order; end_idx <= refTokens.size(); end_idx++) {
-					Phrase ngram(1);
-					for (size_t s_idx = end_idx - order; s_idx < end_idx; s_idx++) {
-						const Factor* f = fc.AddFactor(Output, 0, refTokens[s_idx]);
-						Word w;
-						w.SetFactor(0, f);
-						ngram.AddWord(w);
-					}
-					ref_pair.second[ngram] += 1;
-				}
-			}
-   	}
-	}
+  m_refs.clear();
+  FactorCollection& fc = FactorCollection::Instance();
+  for (size_t file_id = 0; file_id < refs.size(); file_id++) {
+    for (size_t sent_id = 0; sent_id < refs[file_id].size(); sent_id++) {
+      const string& ref = refs[file_id][sent_id];
+      vector<string> refTokens  = Tokenize(ref);
+      if (file_id == 0)
+        m_refs[sent_id] = RefValue();
+      pair<vector<size_t>,NGrams>& ref_pair = m_refs[sent_id];
+      (ref_pair.first).push_back(refTokens.size());
+      for (size_t order = 1; order <= BleuScoreState::bleu_order; order++) {
+        for (size_t end_idx = order; end_idx <= refTokens.size(); end_idx++) {
+          Phrase ngram(1);
+          for (size_t s_idx = end_idx - order; s_idx < end_idx; s_idx++) {
+            const Factor* f = fc.AddFactor(Output, 0, refTokens[s_idx]);
+            Word w;
+            w.SetFactor(0, f);
+            ngram.AddWord(w);
+          }
+          ref_pair.second[ngram] += 1;
+        }
+      }
+    }
+  }
 
 //	cerr << "Number of ref files: " << refs.size() << endl;
 //	for (size_t i = 0; i < m_refs.size(); ++i) {
@@ -191,51 +197,57 @@ void BleuScoreFeature::LoadReferences(const std::vector< std::vector< std::strin
 //	}
 }
 
-void BleuScoreFeature::SetCurrSourceLength(size_t source_length) {
-    m_cur_source_length = source_length;
+void BleuScoreFeature::SetCurrSourceLength(size_t source_length)
+{
+  m_cur_source_length = source_length;
 }
-void BleuScoreFeature::SetCurrNormSourceLength(size_t source_length) {
-    m_cur_norm_source_length = source_length;
+void BleuScoreFeature::SetCurrNormSourceLength(size_t source_length)
+{
+  m_cur_norm_source_length = source_length;
 }
 
 // m_refs[sent_id][[vector<length>][ngrams]]
-void BleuScoreFeature::SetCurrShortestRefLength(size_t sent_id) {
-		// look for shortest reference
-		int shortestRef = -1;
-		for (size_t i = 0; i < (m_refs[sent_id].first).size(); ++i) {
-			if (shortestRef == -1 || (m_refs[sent_id].first)[i] < shortestRef)
-				shortestRef = (m_refs[sent_id].first)[i];
-		}
-		m_cur_ref_length = shortestRef;
+void BleuScoreFeature::SetCurrShortestRefLength(size_t sent_id)
+{
+  // look for shortest reference
+  int shortestRef = -1;
+  for (size_t i = 0; i < (m_refs[sent_id].first).size(); ++i) {
+    if (shortestRef == -1 || (m_refs[sent_id].first)[i] < shortestRef)
+      shortestRef = (m_refs[sent_id].first)[i];
+  }
+  m_cur_ref_length = shortestRef;
 //		cerr << "Set shortest cur_ref_length: " << m_cur_ref_length << endl;
 }
 
-void BleuScoreFeature::SetCurrAvgRefLength(size_t sent_id) {
-		// compute average reference length
-		size_t sum = 0;
-		size_t numberRefs = (m_refs[sent_id].first).size();
-		for (size_t i = 0; i < numberRefs; ++i) {
-			sum += (m_refs[sent_id].first)[i];
-		}
-		m_cur_ref_length = (float)sum/numberRefs;
+void BleuScoreFeature::SetCurrAvgRefLength(size_t sent_id)
+{
+  // compute average reference length
+  size_t sum = 0;
+  size_t numberRefs = (m_refs[sent_id].first).size();
+  for (size_t i = 0; i < numberRefs; ++i) {
+    sum += (m_refs[sent_id].first)[i];
+  }
+  m_cur_ref_length = (float)sum/numberRefs;
 //		cerr << "Set average cur_ref_length: " << m_cur_ref_length << endl;
 }
 
-void BleuScoreFeature::SetCurrReferenceNgrams(size_t sent_id) {
-    m_cur_ref_ngrams = m_refs[sent_id].second;
+void BleuScoreFeature::SetCurrReferenceNgrams(size_t sent_id)
+{
+  m_cur_ref_ngrams = m_refs[sent_id].second;
 }
 
-size_t BleuScoreFeature::GetShortestRefIndex(size_t ref_id) {
-		// look for shortest reference
-		int shortestRef = -1;
-		size_t shortestRefIndex = 0;
-		for (size_t i = 0; i < (m_refs[ref_id].first).size(); ++i) {
-			if (shortestRef == -1 || (m_refs[ref_id].first)[i] < shortestRef) {
-				shortestRef = (m_refs[ref_id].first)[i];
-				shortestRefIndex = i;
-			}
-		}
-    return shortestRefIndex;
+size_t BleuScoreFeature::GetShortestRefIndex(size_t ref_id)
+{
+  // look for shortest reference
+  int shortestRef = -1;
+  size_t shortestRefIndex = 0;
+  for (size_t i = 0; i < (m_refs[ref_id].first).size(); ++i) {
+    if (shortestRef == -1 || (m_refs[ref_id].first)[i] < shortestRef) {
+      shortestRef = (m_refs[ref_id].first)[i];
+      shortestRefIndex = i;
+    }
+  }
+  return shortestRefIndex;
 }
 
 /*
@@ -244,73 +256,75 @@ size_t BleuScoreFeature::GetShortestRefIndex(size_t ref_id) {
  * O = m_historySmoothing * (O + c(e_oracle))
  * O_f = m_historySmoothing * (O_f + |f|)		input length of pseudo-document
  */
-void BleuScoreFeature::UpdateHistory(const vector< const Word* >& hypo) {
-    Phrase phrase(hypo);
+void BleuScoreFeature::UpdateHistory(const vector< const Word* >& hypo)
+{
+  Phrase phrase(hypo);
+  std::vector< size_t > ngram_counts(BleuScoreState::bleu_order);
+  std::vector< size_t > ngram_matches(BleuScoreState::bleu_order);
+
+  // compute vector c(e;{r_k}):
+  // vector of effective reference length, number of ngrams in e, number of ngram matches between e and r_k
+  GetNgramMatchCounts(phrase, m_cur_ref_ngrams, ngram_counts, ngram_matches, 0);
+
+  // update counts and matches for every ngram length with counts from hypo
+  for (size_t i = 0; i < BleuScoreState::bleu_order; i++) {
+    m_count_history[i] = m_historySmoothing * (m_count_history[i] + ngram_counts[i]);
+    m_match_history[i] = m_historySmoothing * (m_match_history[i] + ngram_matches[i]);
+  }
+
+  // update counts for reference and target length
+  m_source_length_history = m_historySmoothing * (m_source_length_history + m_cur_source_length);
+  m_target_length_history = m_historySmoothing * (m_target_length_history + hypo.size());
+  m_ref_length_history = m_historySmoothing * (m_ref_length_history + m_cur_ref_length);
+}
+
+/*
+ * Update history with a batch of translations
+ */
+void BleuScoreFeature::UpdateHistory(const vector< vector< const Word* > >& hypos, vector<size_t>& sourceLengths, vector<size_t>& ref_ids, size_t rank, size_t epoch)
+{
+  for (size_t ref_id = 0; ref_id < hypos.size(); ++ref_id) {
+    Phrase phrase(hypos[ref_id]);
     std::vector< size_t > ngram_counts(BleuScoreState::bleu_order);
     std::vector< size_t > ngram_matches(BleuScoreState::bleu_order);
 
+    // set current source and reference information for each oracle in the batch
+    size_t cur_source_length = sourceLengths[ref_id];
+    size_t hypo_length = hypos[ref_id].size();
+    size_t cur_ref_length = GetClosestRefLength(ref_ids[ref_id], hypo_length);
+    NGrams cur_ref_ngrams = m_refs[ref_ids[ref_id]].second;
+    cerr << "reference length: " << cur_ref_length << endl;
+
     // compute vector c(e;{r_k}):
     // vector of effective reference length, number of ngrams in e, number of ngram matches between e and r_k
-    GetNgramMatchCounts(phrase, m_cur_ref_ngrams, ngram_counts, ngram_matches, 0);
+    GetNgramMatchCounts(phrase, cur_ref_ngrams, ngram_counts, ngram_matches, 0);
 
     // update counts and matches for every ngram length with counts from hypo
     for (size_t i = 0; i < BleuScoreState::bleu_order; i++) {
-        m_count_history[i] = m_historySmoothing * (m_count_history[i] + ngram_counts[i]);
-        m_match_history[i] = m_historySmoothing * (m_match_history[i] + ngram_matches[i]);
+      m_count_history[i] += ngram_counts[i];
+      m_match_history[i] += ngram_matches[i];
+
+      // do this for last position in batch
+      if (ref_id == hypos.size() - 1) {
+        m_count_history[i] *= m_historySmoothing;
+        m_match_history[i] *= m_historySmoothing;
+      }
     }
 
     // update counts for reference and target length
-    m_source_length_history = m_historySmoothing * (m_source_length_history + m_cur_source_length);
-    m_target_length_history = m_historySmoothing * (m_target_length_history + hypo.size());
-    m_ref_length_history = m_historySmoothing * (m_ref_length_history + m_cur_ref_length);
-}
-
-/*
- * Update history with a batch of translations
- */
-void BleuScoreFeature::UpdateHistory(const vector< vector< const Word* > >& hypos, vector<size_t>& sourceLengths, vector<size_t>& ref_ids, size_t rank, size_t epoch) {
-	for (size_t ref_id = 0; ref_id < hypos.size(); ++ref_id){
-	    Phrase phrase(hypos[ref_id]);
-	    std::vector< size_t > ngram_counts(BleuScoreState::bleu_order);
-	    std::vector< size_t > ngram_matches(BleuScoreState::bleu_order);
-
-	    // set current source and reference information for each oracle in the batch
-	    size_t cur_source_length = sourceLengths[ref_id];
-	    size_t hypo_length = hypos[ref_id].size();
-	    size_t cur_ref_length = GetClosestRefLength(ref_ids[ref_id], hypo_length);
-	    NGrams cur_ref_ngrams = m_refs[ref_ids[ref_id]].second;
-	    cerr << "reference length: " << cur_ref_length << endl;
-
-	    // compute vector c(e;{r_k}):
-	    // vector of effective reference length, number of ngrams in e, number of ngram matches between e and r_k
-	    GetNgramMatchCounts(phrase, cur_ref_ngrams, ngram_counts, ngram_matches, 0);
-
-	    // update counts and matches for every ngram length with counts from hypo
-	    for (size_t i = 0; i < BleuScoreState::bleu_order; i++) {
-	        m_count_history[i] += ngram_counts[i];
-	        m_match_history[i] += ngram_matches[i];
-
-	        // do this for last position in batch
-	        if (ref_id == hypos.size() - 1) {
-	        	m_count_history[i] *= m_historySmoothing;
-	        	m_match_history[i] *= m_historySmoothing;
-	        }
-	    }
-
-	    // update counts for reference and target length
-	    m_source_length_history += cur_source_length;
-	    m_target_length_history += hypos[ref_id].size();
-	    m_ref_length_history += cur_ref_length;
-
-	    // do this for last position in batch
-	    if (ref_id == hypos.size() - 1) {
-	    	cerr << "Rank " << rank << ", epoch " << epoch << " ,source length history: " << m_source_length_history << " --> " << m_source_length_history * m_historySmoothing << endl;
-	    	cerr << "Rank " << rank << ", epoch " << epoch << " ,target length history: " << m_target_length_history << " --> " << m_target_length_history * m_historySmoothing << endl;
-	    	m_source_length_history *= m_historySmoothing;
-	    	m_target_length_history *= m_historySmoothing;
-	    	m_ref_length_history *= m_historySmoothing;
-	    }
-	}
+    m_source_length_history += cur_source_length;
+    m_target_length_history += hypos[ref_id].size();
+    m_ref_length_history += cur_ref_length;
+
+    // do this for last position in batch
+    if (ref_id == hypos.size() - 1) {
+      cerr << "Rank " << rank << ", epoch " << epoch << " ,source length history: " << m_source_length_history << " --> " << m_source_length_history * m_historySmoothing << endl;
+      cerr << "Rank " << rank << ", epoch " << epoch << " ,target length history: " << m_target_length_history << " --> " << m_target_length_history * m_historySmoothing << endl;
+      m_source_length_history *= m_historySmoothing;
+      m_target_length_history *= m_historySmoothing;
+      m_ref_length_history *= m_historySmoothing;
+    }
+  }
 }
 
 /*
@@ -323,17 +337,18 @@ void BleuScoreFeature::UpdateHistory(const vector< vector< const Word* > >& hypo
 	}
 }*/
 
-size_t BleuScoreFeature::GetClosestRefLength(size_t ref_id, int hypoLength) {
-	// look for closest reference
-	int currentDist = -1;
-	int closestRefLength = -1;
-	for (size_t i = 0; i < (m_refs[ref_id].first).size(); ++i) {
-		if (closestRefLength == -1 || abs(hypoLength - (int)(m_refs[ref_id].first)[i]) < currentDist) {
-			closestRefLength = (m_refs[ref_id].first)[i];
-			currentDist = abs(hypoLength - (int)(m_refs[ref_id].first)[i]);
-		}
-	}
-	return (size_t)closestRefLength;
+size_t BleuScoreFeature::GetClosestRefLength(size_t ref_id, int hypoLength)
+{
+  // look for closest reference
+  int currentDist = -1;
+  int closestRefLength = -1;
+  for (size_t i = 0; i < (m_refs[ref_id].first).size(); ++i) {
+    if (closestRefLength == -1 || abs(hypoLength - (int)(m_refs[ref_id].first)[i]) < currentDist) {
+      closestRefLength = (m_refs[ref_id].first)[i];
+      currentDist = abs(hypoLength - (int)(m_refs[ref_id].first)[i]);
+    }
+  }
+  return (size_t)closestRefLength;
 }
 
 /*
@@ -341,206 +356,206 @@ size_t BleuScoreFeature::GetClosestRefLength(size_t ref_id, int hypoLength) {
  * its ngram matches against the ngrams in the reference translation
  */
 void BleuScoreFeature::GetNgramMatchCounts(Phrase& phrase,
-                                           const NGrams& ref_ngram_counts,
-                                           std::vector< size_t >& ret_counts,
-                                           std::vector< size_t >& ret_matches,
-                                           size_t skip_first) const
+    const NGrams& ref_ngram_counts,
+    std::vector< size_t >& ret_counts,
+    std::vector< size_t >& ret_matches,
+    size_t skip_first) const
 {
-    NGrams::const_iterator ref_ngram_counts_iter;
-    size_t ngram_start_idx, ngram_end_idx;
+  NGrams::const_iterator ref_ngram_counts_iter;
+  size_t ngram_start_idx, ngram_end_idx;
 
-    // Chiang et al (2008) use unclipped counts of ngram matches
-    for (size_t end_idx = skip_first; end_idx < phrase.GetSize(); end_idx++) {
-        for (size_t order = 0; order < BleuScoreState::bleu_order; order++) {
-            if (order > end_idx) break;
+  // Chiang et al (2008) use unclipped counts of ngram matches
+  for (size_t end_idx = skip_first; end_idx < phrase.GetSize(); end_idx++) {
+    for (size_t order = 0; order < BleuScoreState::bleu_order; order++) {
+      if (order > end_idx) break;
 
-            ngram_end_idx = end_idx;
-            ngram_start_idx = end_idx - order;
+      ngram_end_idx = end_idx;
+      ngram_start_idx = end_idx - order;
 
-            Phrase ngram = phrase.GetSubString(WordsRange(ngram_start_idx, ngram_end_idx), 0);
-            ret_counts[order]++;
+      Phrase ngram = phrase.GetSubString(WordsRange(ngram_start_idx, ngram_end_idx), 0);
+      ret_counts[order]++;
 
-            ref_ngram_counts_iter = ref_ngram_counts.find(ngram);
-            if (ref_ngram_counts_iter != ref_ngram_counts.end())
-                ret_matches[order]++;
-        }
+      ref_ngram_counts_iter = ref_ngram_counts.find(ngram);
+      if (ref_ngram_counts_iter != ref_ngram_counts.end())
+        ret_matches[order]++;
     }
+  }
 }
 
 // score ngrams of words that have been added before the previous word span
 void BleuScoreFeature::GetNgramMatchCounts_prefix(Phrase& phrase,
-                                           const NGrams& ref_ngram_counts,
-                                           std::vector< size_t >& ret_counts,
-                                           std::vector< size_t >& ret_matches,
-                                           size_t new_start_indices,
-                                           size_t last_end_index) const
+    const NGrams& ref_ngram_counts,
+    std::vector< size_t >& ret_counts,
+    std::vector< size_t >& ret_matches,
+    size_t new_start_indices,
+    size_t last_end_index) const
 {
-    NGrams::const_iterator ref_ngram_counts_iter;
-    size_t ngram_start_idx, ngram_end_idx;
-
-    // Chiang et al (2008) use unclipped counts of ngram matches
-    for (size_t start_idx = 0; start_idx < new_start_indices; start_idx++) {
-        for (size_t order = 0; order < BleuScoreState::bleu_order; order++) {
-        		ngram_start_idx = start_idx;
-            ngram_end_idx = start_idx + order;
-            if (order > ngram_end_idx) break;
-            if (ngram_end_idx > last_end_index) break;
-
-            Phrase ngram = phrase.GetSubString(WordsRange(ngram_start_idx, ngram_end_idx), 0);
-            ret_counts[order]++;
-
-            ref_ngram_counts_iter = ref_ngram_counts.find(ngram);
-            if (ref_ngram_counts_iter != ref_ngram_counts.end())
-                ret_matches[order]++;
-        }
+  NGrams::const_iterator ref_ngram_counts_iter;
+  size_t ngram_start_idx, ngram_end_idx;
+
+  // Chiang et al (2008) use unclipped counts of ngram matches
+  for (size_t start_idx = 0; start_idx < new_start_indices; start_idx++) {
+    for (size_t order = 0; order < BleuScoreState::bleu_order; order++) {
+      ngram_start_idx = start_idx;
+      ngram_end_idx = start_idx + order;
+      if (order > ngram_end_idx) break;
+      if (ngram_end_idx > last_end_index) break;
+
+      Phrase ngram = phrase.GetSubString(WordsRange(ngram_start_idx, ngram_end_idx), 0);
+      ret_counts[order]++;
+
+      ref_ngram_counts_iter = ref_ngram_counts.find(ngram);
+      if (ref_ngram_counts_iter != ref_ngram_counts.end())
+        ret_matches[order]++;
     }
+  }
 }
 
 // score ngrams around the overlap of two previously scored phrases
 void BleuScoreFeature::GetNgramMatchCounts_overlap(Phrase& phrase,
-                                           const NGrams& ref_ngram_counts,
-                                           std::vector< size_t >& ret_counts,
-                                           std::vector< size_t >& ret_matches,
-                                           size_t overlap_index) const
+    const NGrams& ref_ngram_counts,
+    std::vector< size_t >& ret_counts,
+    std::vector< size_t >& ret_matches,
+    size_t overlap_index) const
 {
-    NGrams::const_iterator ref_ngram_counts_iter;
-    size_t ngram_start_idx, ngram_end_idx;
+  NGrams::const_iterator ref_ngram_counts_iter;
+  size_t ngram_start_idx, ngram_end_idx;
 
-    // Chiang et al (2008) use unclipped counts of ngram matches
-    for (size_t end_idx = overlap_index; end_idx < phrase.GetSize(); end_idx++) {
-    	if (end_idx >= (overlap_index+BleuScoreState::bleu_order-1)) break;
-    	for (size_t order = 0; order < BleuScoreState::bleu_order; order++) {
-            if (order > end_idx) break;
+  // Chiang et al (2008) use unclipped counts of ngram matches
+  for (size_t end_idx = overlap_index; end_idx < phrase.GetSize(); end_idx++) {
+    if (end_idx >= (overlap_index+BleuScoreState::bleu_order-1)) break;
+    for (size_t order = 0; order < BleuScoreState::bleu_order; order++) {
+      if (order > end_idx) break;
 
-            ngram_end_idx = end_idx;
-            ngram_start_idx = end_idx - order;
-            if (ngram_start_idx >= overlap_index) continue; // only score ngrams that span the overlap point
+      ngram_end_idx = end_idx;
+      ngram_start_idx = end_idx - order;
+      if (ngram_start_idx >= overlap_index) continue; // only score ngrams that span the overlap point
 
-            Phrase ngram = phrase.GetSubString(WordsRange(ngram_start_idx, ngram_end_idx), 0);
-            ret_counts[order]++;
+      Phrase ngram = phrase.GetSubString(WordsRange(ngram_start_idx, ngram_end_idx), 0);
+      ret_counts[order]++;
 
-            ref_ngram_counts_iter = ref_ngram_counts.find(ngram);
-            if (ref_ngram_counts_iter != ref_ngram_counts.end())
-                ret_matches[order]++;
-        }
+      ref_ngram_counts_iter = ref_ngram_counts.find(ngram);
+      if (ref_ngram_counts_iter != ref_ngram_counts.end())
+        ret_matches[order]++;
     }
+  }
 }
 
 void BleuScoreFeature::GetClippedNgramMatchesAndCounts(Phrase& phrase,
-                                           const NGrams& ref_ngram_counts,
-                                           std::vector< size_t >& ret_counts,
-                                           std::vector< size_t >& ret_matches,
-                                           size_t skip_first) const
+    const NGrams& ref_ngram_counts,
+    std::vector< size_t >& ret_counts,
+    std::vector< size_t >& ret_matches,
+    size_t skip_first) const
 {
-	NGrams::const_iterator ref_ngram_counts_iter;
-	size_t ngram_start_idx, ngram_end_idx;
+  NGrams::const_iterator ref_ngram_counts_iter;
+  size_t ngram_start_idx, ngram_end_idx;
 
-	Matches ngram_matches;
-	for (size_t end_idx = skip_first; end_idx < phrase.GetSize(); end_idx++) {
-		for (size_t order = 0; order < BleuScoreState::bleu_order; order++) {
-			if (order > end_idx) break;
+  Matches ngram_matches;
+  for (size_t end_idx = skip_first; end_idx < phrase.GetSize(); end_idx++) {
+    for (size_t order = 0; order < BleuScoreState::bleu_order; order++) {
+      if (order > end_idx) break;
 
-			ngram_end_idx = end_idx;
-			ngram_start_idx = end_idx - order;
+      ngram_end_idx = end_idx;
+      ngram_start_idx = end_idx - order;
 
-			Phrase ngram = phrase.GetSubString(WordsRange(ngram_start_idx, ngram_end_idx), 0);
-			ret_counts[order]++;
+      Phrase ngram = phrase.GetSubString(WordsRange(ngram_start_idx, ngram_end_idx), 0);
+      ret_counts[order]++;
 
-			ref_ngram_counts_iter = ref_ngram_counts.find(ngram);
-			if (ref_ngram_counts_iter != ref_ngram_counts.end()) {
-				ngram_matches[order][ngram]++;
-			}
-		}
-	}
+      ref_ngram_counts_iter = ref_ngram_counts.find(ngram);
+      if (ref_ngram_counts_iter != ref_ngram_counts.end()) {
+        ngram_matches[order][ngram]++;
+      }
+    }
+  }
 
-	// clip ngram matches
-	for (size_t order = 0; order < BleuScoreState::bleu_order; order++) {
-		NGrams::const_iterator iter;
-
-		// iterate over ngram counts for every ngram order
-		for (iter=ngram_matches[order].begin(); iter != ngram_matches[order].end(); ++iter) {
-			ref_ngram_counts_iter = ref_ngram_counts.find(iter->first);
-			if (iter->second > ref_ngram_counts_iter->second) {
-				ret_matches[order] += ref_ngram_counts_iter->second;
-			}
-			else {
-				ret_matches[order] += iter->second;
-			}
+  // clip ngram matches
+  for (size_t order = 0; order < BleuScoreState::bleu_order; order++) {
+    NGrams::const_iterator iter;
+
+    // iterate over ngram counts for every ngram order
+    for (iter=ngram_matches[order].begin(); iter != ngram_matches[order].end(); ++iter) {
+      ref_ngram_counts_iter = ref_ngram_counts.find(iter->first);
+      if (iter->second > ref_ngram_counts_iter->second) {
+        ret_matches[order] += ref_ngram_counts_iter->second;
+      } else {
+        ret_matches[order] += iter->second;
+      }
     }
-	}
+  }
 }
 
 /*
  * Given a previous state, compute Bleu score for the updated state with an additional target
  * phrase translated.
  */
-FFState* BleuScoreFeature::Evaluate(const Hypothesis& cur_hypo, 
-                                    const FFState* prev_state, 
+FFState* BleuScoreFeature::Evaluate(const Hypothesis& cur_hypo,
+                                    const FFState* prev_state,
                                     ScoreComponentCollection* accumulator) const
 {
-	if (!m_enabled) return new BleuScoreState();
-	
-	NGrams::const_iterator reference_ngrams_iter;
-    const BleuScoreState& ps = dynamic_cast<const BleuScoreState&>(*prev_state);
-    BleuScoreState* new_state = new BleuScoreState(ps);
-    
-    float old_bleu, new_bleu;
-    size_t num_new_words, ctx_start_idx, ctx_end_idx;
-
-    // Calculate old bleu;
-    old_bleu = CalculateBleu(new_state);
-
-    // Get context and append new words.
-    num_new_words = cur_hypo.GetCurrTargetLength();
-    if (num_new_words == 0) {
-    	return new_state;
-    }
- 
-    Phrase new_words = ps.m_words;
-    new_words.Append(cur_hypo.GetCurrTargetPhrase());
-    //cerr << "NW: " << new_words << endl;
+  if (!m_enabled) return new BleuScoreState();
 
-    // get ngram matches for new words
-    GetNgramMatchCounts(new_words,
-                        m_cur_ref_ngrams,
-                        new_state->m_ngram_counts,
-                        new_state->m_ngram_matches,
-                        new_state->m_words.GetSize()); // number of words in previous states
+  NGrams::const_iterator reference_ngrams_iter;
+  const BleuScoreState& ps = dynamic_cast<const BleuScoreState&>(*prev_state);
+  BleuScoreState* new_state = new BleuScoreState(ps);
 
-    // Update state variables
-    ctx_end_idx = new_words.GetSize()-1;
-    size_t bleu_context_length = BleuScoreState::bleu_order -1;
-    if (ctx_end_idx > bleu_context_length) {
-      ctx_start_idx = ctx_end_idx - bleu_context_length;
-    } else {
-      ctx_start_idx = 0;
-    }
+  float old_bleu, new_bleu;
+  size_t num_new_words, ctx_start_idx, ctx_end_idx;
 
-    WordsBitmap coverageVector = cur_hypo.GetWordsBitmap();
-    new_state->m_source_length = coverageVector.GetNumWordsCovered();
+  // Calculate old bleu;
+  old_bleu = CalculateBleu(new_state);
 
-    new_state->m_words = new_words.GetSubString(WordsRange(ctx_start_idx,
-                                                           ctx_end_idx));
-    new_state->m_target_length += cur_hypo.GetCurrTargetLength();
+  // Get context and append new words.
+  num_new_words = cur_hypo.GetCurrTargetLength();
+  if (num_new_words == 0) {
+    return new_state;
+  }
 
-    // we need a scaled reference length to compare the current target phrase to the corresponding reference phrase
-    new_state->m_scaled_ref_length = m_cur_ref_length * 
-        ((float)coverageVector.GetNumWordsCovered()/coverageVector.GetSize());
+  Phrase new_words = ps.m_words;
+  new_words.Append(cur_hypo.GetCurrTargetPhrase());
+  //cerr << "NW: " << new_words << endl;
 
-    // Calculate new bleu.
-    new_bleu = CalculateBleu(new_state);
+  // get ngram matches for new words
+  GetNgramMatchCounts(new_words,
+                      m_cur_ref_ngrams,
+                      new_state->m_ngram_counts,
+                      new_state->m_ngram_matches,
+                      new_state->m_words.GetSize()); // number of words in previous states
 
-    // Set score to new Bleu score
-    accumulator->PlusEquals(this, new_bleu - old_bleu);
-    return new_state;
+  // Update state variables
+  ctx_end_idx = new_words.GetSize()-1;
+  size_t bleu_context_length = BleuScoreState::bleu_order -1;
+  if (ctx_end_idx > bleu_context_length) {
+    ctx_start_idx = ctx_end_idx - bleu_context_length;
+  } else {
+    ctx_start_idx = 0;
+  }
+
+  WordsBitmap coverageVector = cur_hypo.GetWordsBitmap();
+  new_state->m_source_length = coverageVector.GetNumWordsCovered();
+
+  new_state->m_words = new_words.GetSubString(WordsRange(ctx_start_idx,
+                       ctx_end_idx));
+  new_state->m_target_length += cur_hypo.GetCurrTargetLength();
+
+  // we need a scaled reference length to compare the current target phrase to the corresponding reference phrase
+  new_state->m_scaled_ref_length = m_cur_ref_length *
+                                   ((float)coverageVector.GetNumWordsCovered()/coverageVector.GetSize());
+
+  // Calculate new bleu.
+  new_bleu = CalculateBleu(new_state);
+
+  // Set score to new Bleu score
+  accumulator->PlusEquals(this, new_bleu - old_bleu);
+  return new_state;
 }
 
 FFState* BleuScoreFeature::EvaluateChart(const ChartHypothesis& cur_hypo, int featureID,
-		ScoreComponentCollection* accumulator ) const {
+    ScoreComponentCollection* accumulator ) const
+{
   if (!m_enabled) return new BleuScoreState();
-	
+
   NGrams::const_iterator reference_ngrams_iter;
-  
+
   const Phrase& curr_target_phrase = static_cast<const Phrase&>(cur_hypo.GetCurrTargetPhrase());
 //  cerr << "\nCur target phrase: " << cur_hypo.GetTargetLHS() << " --> " << curr_target_phrase << endl;
 
@@ -553,35 +568,35 @@ FFState* BleuScoreFeature::EvaluateChart(const ChartHypothesis& cur_hypo, int fe
   assert(cur_hypo.GetPrevHypos().size() <= 2);
   BleuScoreState* new_state;
   if (cur_hypo.GetPrevHypos().size() == 0)
-  	new_state = new BleuScoreState();
+    new_state = new BleuScoreState();
   else {
-  	const FFState* prev_state_zero = cur_hypo.GetPrevHypo(0)->GetFFState(featureID);
-  	const BleuScoreState& ps_zero = dynamic_cast<const BleuScoreState&>(*prev_state_zero);
-  	new_state = new BleuScoreState(ps_zero);
-  	num_words_first_prev = ps_zero.m_target_length;
-
-  	for (size_t i = 0; i < cur_hypo.GetPrevHypos().size(); ++i) {
-  		const FFState* prev_state = cur_hypo.GetPrevHypo(i)->GetFFState(featureID);
-  		const BleuScoreState* ps = dynamic_cast<const BleuScoreState*>(prev_state);
-  		BleuScoreState* ps_nonConst = const_cast<BleuScoreState*>(ps);
+    const FFState* prev_state_zero = cur_hypo.GetPrevHypo(0)->GetFFState(featureID);
+    const BleuScoreState& ps_zero = dynamic_cast<const BleuScoreState&>(*prev_state_zero);
+    new_state = new BleuScoreState(ps_zero);
+    num_words_first_prev = ps_zero.m_target_length;
+
+    for (size_t i = 0; i < cur_hypo.GetPrevHypos().size(); ++i) {
+      const FFState* prev_state = cur_hypo.GetPrevHypo(i)->GetFFState(featureID);
+      const BleuScoreState* ps = dynamic_cast<const BleuScoreState*>(prev_state);
+      BleuScoreState* ps_nonConst = const_cast<BleuScoreState*>(ps);
 //  		cerr << "prev phrase: " << cur_hypo.GetPrevHypo(i)->GetOutputPhrase()
 //  				<< " ( " << cur_hypo.GetPrevHypo(i)->GetTargetLHS() << ")" << endl;
 
-  		old_bleu += CalculateBleu(ps_nonConst);
-  		num_old_words += ps->m_target_length;
+      old_bleu += CalculateBleu(ps_nonConst);
+      num_old_words += ps->m_target_length;
 
-  		if (i > 0)
-  			// add ngram matches from other previous states
-  			new_state->AddNgramCountAndMatches(ps_nonConst->m_ngram_counts, ps_nonConst->m_ngram_matches);
-  	}
+      if (i > 0)
+        // add ngram matches from other previous states
+        new_state->AddNgramCountAndMatches(ps_nonConst->m_ngram_counts, ps_nonConst->m_ngram_matches);
+    }
   }
-  
+
   // check if we are already done (don't add <s> and </s>)
   size_t numWordsCovered = cur_hypo.GetCurrSourceRange().GetNumWordsCovered();
   if (numWordsCovered == m_cur_source_length) {
-	  // Bleu score stays the same, do not need to add anything
-	  //accumulator->PlusEquals(this, 0);
-	  return new_state;
+    // Bleu score stays the same, do not need to add anything
+    //accumulator->PlusEquals(this, 0);
+    return new_state;
   }
 
   // set new context
@@ -592,55 +607,52 @@ FFState* BleuScoreFeature::EvaluateChart(const ChartHypothesis& cur_hypo, int fe
   // get ngram matches for new words
   if (num_old_words == 0) {
 //  	cerr << "compute right ngram context" << endl;
-  	GetNgramMatchCounts(new_words,
-  											m_cur_ref_ngrams,
-  											new_state->m_ngram_counts,
-  											new_state->m_ngram_matches,
-  											0);
-  }
-  else if (new_words.GetSize() == num_old_words) {
-  	// two hypotheses were glued together, compute new ngrams on the basis of first hypothesis
-  	num_words_added_right = num_curr_words - num_words_first_prev;
-  	// score around overlap point
+    GetNgramMatchCounts(new_words,
+                        m_cur_ref_ngrams,
+                        new_state->m_ngram_counts,
+                        new_state->m_ngram_matches,
+                        0);
+  } else if (new_words.GetSize() == num_old_words) {
+    // two hypotheses were glued together, compute new ngrams on the basis of first hypothesis
+    num_words_added_right = num_curr_words - num_words_first_prev;
+    // score around overlap point
 //  	cerr << "compute overlap ngram context (" << (num_words_first_prev) << ")" << endl;
-  	GetNgramMatchCounts_overlap(new_words,
-  											m_cur_ref_ngrams,
-  											new_state->m_ngram_counts,
-  											new_state->m_ngram_matches,
-  											num_words_first_prev);
-  }
-  else if (num_old_words + curr_target_phrase.GetNumTerminals() == num_curr_words) {
-  	assert(curr_target_phrase.GetSize() == curr_target_phrase.GetNumTerminals()+1);
-  	// previous hypothesis + rule with 1 non-terminal were combined (NT substituted by Ts)
-  	for (size_t i = 0; i < curr_target_phrase.GetSize(); ++i)
-  		if (curr_target_phrase.GetWord(i).IsNonTerminal()) {
-  			num_words_added_left = i;
-  			num_words_added_right = curr_target_phrase.GetSize() - (i+1);
-  			break;
-  		}
-
-  	// left context
+    GetNgramMatchCounts_overlap(new_words,
+                                m_cur_ref_ngrams,
+                                new_state->m_ngram_counts,
+                                new_state->m_ngram_matches,
+                                num_words_first_prev);
+  } else if (num_old_words + curr_target_phrase.GetNumTerminals() == num_curr_words) {
+    assert(curr_target_phrase.GetSize() == curr_target_phrase.GetNumTerminals()+1);
+    // previous hypothesis + rule with 1 non-terminal were combined (NT substituted by Ts)
+    for (size_t i = 0; i < curr_target_phrase.GetSize(); ++i)
+      if (curr_target_phrase.GetWord(i).IsNonTerminal()) {
+        num_words_added_left = i;
+        num_words_added_right = curr_target_phrase.GetSize() - (i+1);
+        break;
+      }
+
+    // left context
 //  	cerr << "compute left ngram context" << endl;
-  	if (num_words_added_left > 0)
-  		GetNgramMatchCounts_prefix(new_words,
-  											m_cur_ref_ngrams,
-  											new_state->m_ngram_counts,
-  											new_state->m_ngram_matches,
-  											num_words_added_left,
-  											num_curr_words - num_words_added_right - 1);
-
-  	// right context
+    if (num_words_added_left > 0)
+      GetNgramMatchCounts_prefix(new_words,
+                                 m_cur_ref_ngrams,
+                                 new_state->m_ngram_counts,
+                                 new_state->m_ngram_matches,
+                                 num_words_added_left,
+                                 num_curr_words - num_words_added_right - 1);
+
+    // right context
 //  	cerr << "compute right ngram context" << endl;
-  	if (num_words_added_right > 0)
-  		GetNgramMatchCounts(new_words,
-  											m_cur_ref_ngrams,
-  											new_state->m_ngram_counts,
-  											new_state->m_ngram_matches,
-  											num_words_added_left + num_old_words);
-  }
-  else {
-  	cerr << "undefined state.. " << endl;
-  	exit(1);
+    if (num_words_added_right > 0)
+      GetNgramMatchCounts(new_words,
+                          m_cur_ref_ngrams,
+                          new_state->m_ngram_counts,
+                          new_state->m_ngram_matches,
+                          num_words_added_left + num_old_words);
+  } else {
+    cerr << "undefined state.. " << endl;
+    exit(1);
   }
 
   // Update state variables
@@ -659,7 +671,7 @@ FFState* BleuScoreFeature::EvaluateChart(const ChartHypothesis& cur_hypo, int fe
   // reference phrase
   size_t cur_source_length = m_cur_source_length;
   new_state->m_scaled_ref_length = m_cur_ref_length * (float(new_state->m_source_length)/cur_source_length);
-  
+
   // Calculate new bleu.
   new_bleu = CalculateBleu(new_state);
 
@@ -675,28 +687,28 @@ float BleuScoreFeature::CalculateBleu(Phrase translation) const
 {
   if (translation.GetSize() == 0)
     return 0.0;
-	
+
   Phrase normTranslation = translation;
   // remove start and end symbol for chart decoding
   if (m_cur_source_length != m_cur_norm_source_length) {
     WordsRange* range = new WordsRange(1, translation.GetSize()-2);
     normTranslation = translation.GetSubString(*range);
   }
-  
+
   // get ngram matches for translation
   BleuScoreState* state = new BleuScoreState();
   GetClippedNgramMatchesAndCounts(normTranslation,
-                        m_cur_ref_ngrams,
-                        state->m_ngram_counts,
-                        state->m_ngram_matches,
-                        0); // number of words in previous states
+                                  m_cur_ref_ngrams,
+                                  state->m_ngram_counts,
+                                  state->m_ngram_matches,
+                                  0); // number of words in previous states
 
   // set state variables
   state->m_words = normTranslation;
   state->m_source_length = m_cur_norm_source_length;
   state->m_target_length = normTranslation.GetSize();
   state->m_scaled_ref_length = m_cur_ref_length;
-  
+
   // Calculate bleu.
   return CalculateBleu(state);
 }
@@ -704,52 +716,53 @@ float BleuScoreFeature::CalculateBleu(Phrase translation) const
 /*
  * Calculate Bleu score for a partial hypothesis given as state.
  */
-float BleuScoreFeature::CalculateBleu(BleuScoreState* state) const {
+float BleuScoreFeature::CalculateBleu(BleuScoreState* state) const
+{
   if (!state->m_ngram_counts[0]) return 0;
   if (!state->m_ngram_matches[0]) return 0;      	// if we have no unigram matches, score should be 0
-  
+
   float precision = 1.0;
   float smooth = 1;
   float smoothed_count, smoothed_matches;
-  
+
   if (m_sentence_bleu || m_simple_history_bleu) {
     // Calculate geometric mean of modified ngram precisions
     // BLEU = BP * exp(SUM_1_4 1/4 * log p_n)
     // 		= BP * 4th root(PRODUCT_1_4 p_n)
     for (size_t i = 0; i < BleuScoreState::bleu_order; i++) {
       if (state->m_ngram_counts[i]) {
-      	smoothed_matches = state->m_ngram_matches[i];
-      	smoothed_count = state->m_ngram_counts[i];
-
-      	switch (m_smoothing_scheme) {
-      	case PLUS_ONE:
-      	default:
-      		if (i > 0) {
-      			// smoothing for all n > 1
-      			smoothed_matches += 1;
-      			smoothed_count += 1;
-      		}
-      		break;
-      	case PLUS_POINT_ONE:
-      		if (i > 0) {
-      			// smoothing for all n > 1
-      			smoothed_matches += 0.1;
-      			smoothed_count += 0.1;
-      		}
-      		break;
-      	case PAPINENI:
-      		if (state->m_ngram_matches[i] == 0) {
-      			smooth *= 0.5;
-      			smoothed_matches += smooth;
-      			smoothed_count += smooth;
-      		}
-      		break;
-      	}
-
-	if (m_simple_history_bleu) {
-	  smoothed_matches += m_match_history[i];
-	  smoothed_count += m_count_history[i];
-	}
+        smoothed_matches = state->m_ngram_matches[i];
+        smoothed_count = state->m_ngram_counts[i];
+
+        switch (m_smoothing_scheme) {
+        case PLUS_ONE:
+        default:
+          if (i > 0) {
+            // smoothing for all n > 1
+            smoothed_matches += 1;
+            smoothed_count += 1;
+          }
+          break;
+        case PLUS_POINT_ONE:
+          if (i > 0) {
+            // smoothing for all n > 1
+            smoothed_matches += 0.1;
+            smoothed_count += 0.1;
+          }
+          break;
+        case PAPINENI:
+          if (state->m_ngram_matches[i] == 0) {
+            smooth *= 0.5;
+            smoothed_matches += smooth;
+            smoothed_count += smooth;
+          }
+          break;
+        }
+
+        if (m_simple_history_bleu) {
+          smoothed_matches += m_match_history[i];
+          smoothed_count += m_count_history[i];
+        }
 
         precision *= smoothed_matches/smoothed_count;
       }
@@ -766,40 +779,35 @@ float BleuScoreFeature::CalculateBleu(BleuScoreState* state) const {
     // r: effective reference length (sum of best match lengths for each candidate sentence)
     if (m_simple_history_bleu) {
       if ((m_target_length_history + state->m_target_length) < (m_ref_length_history + state->m_scaled_ref_length)) {
-	float smoothed_target_length = m_target_length_history + state->m_target_length;
-	float smoothed_ref_length = m_ref_length_history + state->m_scaled_ref_length;
-	precision *= exp(1 - (smoothed_ref_length/smoothed_target_length));
+        float smoothed_target_length = m_target_length_history + state->m_target_length;
+        float smoothed_ref_length = m_ref_length_history + state->m_scaled_ref_length;
+        precision *= exp(1 - (smoothed_ref_length/smoothed_target_length));
       }
-    }
-    else {
+    } else {
       if (state->m_target_length < state->m_scaled_ref_length) {
-	float target_length = state->m_target_length;
-	float ref_length = state->m_scaled_ref_length;
-	precision *= exp(1 - (ref_length/target_length));
+        float target_length = state->m_target_length;
+        float ref_length = state->m_scaled_ref_length;
+        precision *= exp(1 - (ref_length/target_length));
       }
     }
-    
+
     //cerr << "precision: " << precision << endl;
-    
+
     // Approximate bleu score as of Chiang/Resnik is scaled by the size of the input:
     // B(e;f,{r_k}) = (O_f + |f|) * BLEU(O + c(e;{r_k}))
     // where c(e;) is a vector of reference length, ngram counts and ngram matches
     if (m_scale_by_input_length) {
       precision *= m_cur_norm_source_length;
-    }
-    else if (m_scale_by_avg_input_length) {
+    } else if (m_scale_by_avg_input_length) {
       precision *= m_avg_input_length;
-    }
-    else if (m_scale_by_inverse_length) {
+    } else if (m_scale_by_inverse_length) {
       precision *= (100/m_cur_norm_source_length);
-    }
-    else if (m_scale_by_avg_inverse_length) {
+    } else if (m_scale_by_avg_inverse_length) {
       precision *= (100/m_avg_input_length);
     }
-    
+
     return precision * m_scale_by_x;
-  }
-  else {
+  } else {
     // Revised history BLEU: compute Bleu in the context of the pseudo-document
     // B(b) = size_of_oracle_doc * (Bleu(B_hist + b) - Bleu(B_hist))
     // Calculate geometric mean of modified ngram precisions
@@ -807,12 +815,12 @@ float BleuScoreFeature::CalculateBleu(BleuScoreState* state) const {
     // 		= BP * 4th root(PRODUCT_1_4 p_n)
     for (size_t i = 0; i < BleuScoreState::bleu_order; i++) {
       if (state->m_ngram_counts[i]) {
-      	smoothed_matches = m_match_history[i] + state->m_ngram_matches[i] + 0.1;
-      	smoothed_count = m_count_history[i] + state->m_ngram_counts[i] + 0.1;
-      	precision *= smoothed_matches/smoothed_count;
+        smoothed_matches = m_match_history[i] + state->m_ngram_matches[i] + 0.1;
+        smoothed_count = m_count_history[i] + state->m_ngram_counts[i] + 0.1;
+        precision *= smoothed_matches/smoothed_count;
       }
     }
-    
+
     // take geometric mean
     precision = pow(precision, (float)1/4);
 
@@ -826,25 +834,24 @@ float BleuScoreFeature::CalculateBleu(BleuScoreState* state) const {
     float precision_pd = 1.0;
     if (m_target_length_history > 0) {
       for (size_t i = 0; i < BleuScoreState::bleu_order; i++)
-	if (m_count_history[i] != 0)
-	  precision_pd *= (m_match_history[i] + 0.1)/(m_count_history[i] + 0.1);
-      
+        if (m_count_history[i] != 0)
+          precision_pd *= (m_match_history[i] + 0.1)/(m_count_history[i] + 0.1);
+
       // take geometric mean
       precision_pd = pow(precision_pd, (float)1/4);
 
       // Apply brevity penalty if applicable.
       if (m_target_length_history < m_ref_length_history)
-    	  precision_pd *= exp(1 - (m_ref_length_history/m_target_length_history));
-    }
-    else
+        precision_pd *= exp(1 - (m_ref_length_history/m_target_length_history));
+    } else
       precision_pd = 0;
     // **end BLEU of pseudo-document**
 
     cerr << "precision pd: " << precision_pd << endl;
 
     float sentence_impact;
-    if (m_target_length_history > 0) 
-      sentence_impact = m_target_length_history * (precision - precision_pd);    
+    if (m_target_length_history > 0)
+      sentence_impact = m_target_length_history * (precision - precision_pd);
     else
       sentence_impact = precision;
 
@@ -855,7 +862,7 @@ float BleuScoreFeature::CalculateBleu(BleuScoreState* state) const {
 
 const FFState* BleuScoreFeature::EmptyHypothesisState(const InputType& input) const
 {
-    return new BleuScoreState();
+  return new BleuScoreState();
 }
 
 } // namespace.
diff --git a/moses/FF/BleuScoreFeature.h b/moses/FF/BleuScoreFeature.h
index dc4495506..96e273672 100644
--- a/moses/FF/BleuScoreFeature.h
+++ b/moses/FF/BleuScoreFeature.h
@@ -13,31 +13,33 @@
 #include "moses/Phrase.h"
 #include "moses/ChartHypothesis.h"
 
-namespace Moses {
+namespace Moses
+{
 
 class BleuScoreFeature;
 
-class BleuScoreState : public FFState {
+class BleuScoreState : public FFState
+{
 public:
-    friend class BleuScoreFeature;
-    static size_t bleu_order;
+  friend class BleuScoreFeature;
+  static size_t bleu_order;
 
-    BleuScoreState();
-    virtual int Compare(const FFState& other) const;
-    void print(std::ostream& out) const;
+  BleuScoreState();
+  virtual int Compare(const FFState& other) const;
+  void print(std::ostream& out) const;
 
 private:
-    Phrase m_words;
-    size_t m_source_length;
-    size_t m_target_length;
+  Phrase m_words;
+  size_t m_source_length;
+  size_t m_target_length;
 
-    // scaled reference length is needed for scoring incomplete hypotheses against reference translation
-    float m_scaled_ref_length;
+  // scaled reference length is needed for scoring incomplete hypotheses against reference translation
+  float m_scaled_ref_length;
 
-    std::vector< size_t > m_ngram_counts;
-    std::vector< size_t > m_ngram_matches;
+  std::vector< size_t > m_ngram_counts;
+  std::vector< size_t > m_ngram_matches;
 
-    void AddNgramCountAndMatches(std::vector< size_t >& counts, std::vector< size_t >& matches);
+  void AddNgramCountAndMatches(std::vector< size_t >& counts, std::vector< size_t >& matches);
 };
 
 
@@ -56,7 +58,8 @@ public:
 };
 
 
-class BleuScoreFeature : public StatefulFeatureFunction {
+class BleuScoreFeature : public StatefulFeatureFunction
+{
 public:
 
   typedef boost::unordered_map<size_t, RefValue > RefCounts;
@@ -64,95 +67,105 @@ public:
 
   BleuScoreFeature(const std::string &line);
 
-    void PrintHistory(std::ostream& out) const;
-    void LoadReferences(const std::vector< std::vector< std::string > > &);
-    void SetCurrSourceLength(size_t);
-    void SetCurrNormSourceLength(size_t);
-    void SetCurrShortestRefLength(size_t);
-    void SetCurrAvgRefLength(size_t sent_id);
-    void SetAvgInputLength (float l) { m_avg_input_length = l; }
-    void SetCurrReferenceNgrams(size_t sent_id);
-    size_t GetShortestRefIndex(size_t ref_id);
-    size_t GetClosestRefLength(size_t ref_id, int hypoLength);
-    void UpdateHistory(const std::vector< const Word* >&);
-    void UpdateHistory(const std::vector< std::vector< const Word* > >& hypos, std::vector<size_t>& sourceLengths, std::vector<size_t>& ref_ids, size_t rank, size_t epoch);
-    void PrintRefLength(const std::vector<size_t>& ref_ids);
-    void SetBleuParameters(bool disable, bool sentenceBleu, bool scaleByInputLength, bool scaleByAvgInputLength,
-    		bool scaleByInverseLength, bool scaleByAvgInverseLength,
-			   float scaleByX, float historySmoothing, size_t scheme, bool simpleHistoryBleu);
-
-    void GetNgramMatchCounts(Phrase&,
-                             const NGrams&,
-                             std::vector< size_t >&,
-                             std::vector< size_t >&,
-                             size_t skip = 0) const;
-    void GetNgramMatchCounts_prefix(Phrase&,
-                             const NGrams&,
-                             std::vector< size_t >&,
-                             std::vector< size_t >&,
-                             size_t new_start_indices,
-                             size_t last_end_index) const;
-    void GetNgramMatchCounts_overlap(Phrase& phrase,
-    												 const NGrams& ref_ngram_counts,
-    												 std::vector< size_t >& ret_counts,
-    												 std::vector< size_t >& ret_matches,
-    												 size_t overlap_index) const;
-    void GetClippedNgramMatchesAndCounts(Phrase&,
-    												 const NGrams&,
-    												 std::vector< size_t >&,
-    												 std::vector< size_t >&,
-    												 size_t skip = 0) const;
-
-    FFState* Evaluate( const Hypothesis& cur_hypo, 
-                       const FFState* prev_state, 
-                       ScoreComponentCollection* accumulator) const;
-    FFState* EvaluateChart(const ChartHypothesis& cur_hypo,
-    										int featureID,
-    										ScoreComponentCollection* accumulator) const;
-    bool Enabled() const { return m_enabled; }
-    float CalculateBleu(BleuScoreState*) const;
-    float CalculateBleu(Phrase translation) const;
-    const FFState* EmptyHypothesisState(const InputType&) const;
-
-    float GetSourceLengthHistory() { return m_source_length_history; }
-    float GetTargetLengthHistory() { return m_target_length_history; }
-    float GetAverageInputLength() { return m_avg_input_length; }
+  void PrintHistory(std::ostream& out) const;
+  void LoadReferences(const std::vector< std::vector< std::string > > &);
+  void SetCurrSourceLength(size_t);
+  void SetCurrNormSourceLength(size_t);
+  void SetCurrShortestRefLength(size_t);
+  void SetCurrAvgRefLength(size_t sent_id);
+  void SetAvgInputLength (float l) {
+    m_avg_input_length = l;
+  }
+  void SetCurrReferenceNgrams(size_t sent_id);
+  size_t GetShortestRefIndex(size_t ref_id);
+  size_t GetClosestRefLength(size_t ref_id, int hypoLength);
+  void UpdateHistory(const std::vector< const Word* >&);
+  void UpdateHistory(const std::vector< std::vector< const Word* > >& hypos, std::vector<size_t>& sourceLengths, std::vector<size_t>& ref_ids, size_t rank, size_t epoch);
+  void PrintRefLength(const std::vector<size_t>& ref_ids);
+  void SetBleuParameters(bool disable, bool sentenceBleu, bool scaleByInputLength, bool scaleByAvgInputLength,
+                         bool scaleByInverseLength, bool scaleByAvgInverseLength,
+                         float scaleByX, float historySmoothing, size_t scheme, bool simpleHistoryBleu);
+
+  void GetNgramMatchCounts(Phrase&,
+                           const NGrams&,
+                           std::vector< size_t >&,
+                           std::vector< size_t >&,
+                           size_t skip = 0) const;
+  void GetNgramMatchCounts_prefix(Phrase&,
+                                  const NGrams&,
+                                  std::vector< size_t >&,
+                                  std::vector< size_t >&,
+                                  size_t new_start_indices,
+                                  size_t last_end_index) const;
+  void GetNgramMatchCounts_overlap(Phrase& phrase,
+                                   const NGrams& ref_ngram_counts,
+                                   std::vector< size_t >& ret_counts,
+                                   std::vector< size_t >& ret_matches,
+                                   size_t overlap_index) const;
+  void GetClippedNgramMatchesAndCounts(Phrase&,
+                                       const NGrams&,
+                                       std::vector< size_t >&,
+                                       std::vector< size_t >&,
+                                       size_t skip = 0) const;
+
+  FFState* Evaluate( const Hypothesis& cur_hypo,
+                     const FFState* prev_state,
+                     ScoreComponentCollection* accumulator) const;
+  FFState* EvaluateChart(const ChartHypothesis& cur_hypo,
+                         int featureID,
+                         ScoreComponentCollection* accumulator) const;
+  bool Enabled() const {
+    return m_enabled;
+  }
+  float CalculateBleu(BleuScoreState*) const;
+  float CalculateBleu(Phrase translation) const;
+  const FFState* EmptyHypothesisState(const InputType&) const;
+
+  float GetSourceLengthHistory() {
+    return m_source_length_history;
+  }
+  float GetTargetLengthHistory() {
+    return m_target_length_history;
+  }
+  float GetAverageInputLength() {
+    return m_avg_input_length;
+  }
 
 private:
-    bool m_enabled;
-    bool m_sentence_bleu;
-    bool m_simple_history_bleu;
+  bool m_enabled;
+  bool m_sentence_bleu;
+  bool m_simple_history_bleu;
 
-    // counts for pseudo-document
-    std::vector< float > m_count_history;
-    std::vector< float > m_match_history;
-    float m_source_length_history;
-    float m_target_length_history;
-    float m_ref_length_history;
+  // counts for pseudo-document
+  std::vector< float > m_count_history;
+  std::vector< float > m_match_history;
+  float m_source_length_history;
+  float m_target_length_history;
+  float m_ref_length_history;
 
-    size_t m_cur_source_length;
-    size_t m_cur_norm_source_length; // length without <s>, </s>
-    RefCounts m_refs;
-    NGrams m_cur_ref_ngrams;
-    float m_cur_ref_length;
+  size_t m_cur_source_length;
+  size_t m_cur_norm_source_length; // length without <s>, </s>
+  RefCounts m_refs;
+  NGrams m_cur_ref_ngrams;
+  float m_cur_ref_length;
 
-    // scale BLEU score by history of input length
-    bool m_scale_by_input_length;
-    bool m_scale_by_avg_input_length;
+  // scale BLEU score by history of input length
+  bool m_scale_by_input_length;
+  bool m_scale_by_avg_input_length;
 
-    // scale by the inverse of the input length * 100
-    bool m_scale_by_inverse_length;
-    bool m_scale_by_avg_inverse_length;
+  // scale by the inverse of the input length * 100
+  bool m_scale_by_inverse_length;
+  bool m_scale_by_avg_inverse_length;
 
-    float m_avg_input_length;
+  float m_avg_input_length;
 
-    float m_scale_by_x;
+  float m_scale_by_x;
 
-    // smoothing factor for history counts
-    float m_historySmoothing;
+  // smoothing factor for history counts
+  float m_historySmoothing;
 
-    enum SmoothingScheme { PLUS_ONE = 1, PLUS_POINT_ONE = 2, PAPINENI = 3 };
-    SmoothingScheme m_smoothing_scheme;
+  enum SmoothingScheme { PLUS_ONE = 1, PLUS_POINT_ONE = 2, PAPINENI = 3 };
+  SmoothingScheme m_smoothing_scheme;
 };
 
 } // Namespace.
diff --git a/moses/FF/ChartBasedFeatureContext.cpp b/moses/FF/ChartBasedFeatureContext.cpp
index 803f81deb..a74cce50c 100644
--- a/moses/FF/ChartBasedFeatureContext.cpp
+++ b/moses/FF/ChartBasedFeatureContext.cpp
@@ -5,15 +5,15 @@
 namespace Moses
 {
 ChartBasedFeatureContext::ChartBasedFeatureContext
-                        (const ChartHypothesis* hypothesis):
+(const ChartHypothesis* hypothesis):
   m_hypothesis(hypothesis),
   m_targetPhrase(hypothesis->GetCurrTargetPhrase()),
   m_source(hypothesis->GetManager().GetSource())
 {}
 
 ChartBasedFeatureContext::ChartBasedFeatureContext(
-                         const TargetPhrase& targetPhrase,
-                         const InputType& source):
+  const TargetPhrase& targetPhrase,
+  const InputType& source):
   m_hypothesis(NULL),
   m_targetPhrase(targetPhrase),
   m_source(source)
diff --git a/moses/FF/ChartBasedFeatureContext.h b/moses/FF/ChartBasedFeatureContext.h
index 7649effde..a204f7c77 100644
--- a/moses/FF/ChartBasedFeatureContext.h
+++ b/moses/FF/ChartBasedFeatureContext.h
@@ -11,7 +11,7 @@ class TargetPhrase;
  **/
 class ChartBasedFeatureContext
 {
-  //The context either has a hypothesis (during search) or a 
+  //The context either has a hypothesis (during search) or a
   //TargetPhrase and source sentence (during pre-calculation)
   //TODO: should the context also include some info on where the TargetPhrase
   //is anchored (assuming it's lexicalised), which is available at pre-calc?
@@ -24,11 +24,13 @@ public:
   ChartBasedFeatureContext(const TargetPhrase& targetPhrase,
                            const InputType& source);
 
-  const InputType& GetSource() const
-  { return m_source; }
+  const InputType& GetSource() const {
+    return m_source;
+  }
 
-  const TargetPhrase& GetTargetPhrase() const
-  { return m_targetPhrase; }
+  const TargetPhrase& GetTargetPhrase() const {
+    return m_targetPhrase;
+  }
 
 };
 
diff --git a/moses/FF/DistortionScoreProducer.cpp b/moses/FF/DistortionScoreProducer.cpp
index 413679779..328c833c8 100644
--- a/moses/FF/DistortionScoreProducer.cpp
+++ b/moses/FF/DistortionScoreProducer.cpp
@@ -39,8 +39,7 @@ float DistortionScoreProducer::CalculateDistortionScore(const Hypothesis& hypo,
 {
   if(!StaticData::Instance().UseEarlyDistortionCost()) {
     return - (float) hypo.GetInput().ComputeDistortionDistance(prev, curr);
-  }
-  else {
+  } else {
     /* Pay distortion score as soon as possible, from Moore and Quirk MT Summit 2007
        Definitions:
        S   : current source range
@@ -50,23 +49,23 @@ float DistortionScoreProducer::CalculateDistortionScore(const Hypothesis& hypo,
 
     int prefixEndPos = (int)FirstGap-1;
     if((int)FirstGap==-1)
-    prefixEndPos = -1;
+      prefixEndPos = -1;
 
     // case1: S is adjacent to S'' => return 0
     if ((int) curr.GetStartPos() == prefixEndPos+1) {
-    IFVERBOSE(4) std::cerr<< "MQ07disto:case1" << std::endl;
+      IFVERBOSE(4) std::cerr<< "MQ07disto:case1" << std::endl;
       return 0;
     }
 
     // case2: S is to the left of S' => return 2(length(S))
     if ((int) curr.GetEndPos() < (int) prev.GetEndPos()) {
-    IFVERBOSE(4) std::cerr<< "MQ07disto:case2" << std::endl;
+      IFVERBOSE(4) std::cerr<< "MQ07disto:case2" << std::endl;
       return (float) -2*(int)curr.GetNumWordsCovered();
     }
 
     // case3: S' is a subsequence of S'' => return 2(nbWordBetween(S,S'')+length(S))
     if ((int) prev.GetEndPos() <= prefixEndPos) {
-    IFVERBOSE(4) std::cerr<< "MQ07disto:case3" << std::endl;
+      IFVERBOSE(4) std::cerr<< "MQ07disto:case3" << std::endl;
       int z = (int)curr.GetStartPos()-prefixEndPos - 1;
       return (float) -2*(z + (int)curr.GetNumWordsCovered());
     }
diff --git a/moses/FF/DistortionScoreProducer.h b/moses/FF/DistortionScoreProducer.h
index 394e7f2e1..2601e6398 100644
--- a/moses/FF/DistortionScoreProducer.h
+++ b/moses/FF/DistortionScoreProducer.h
@@ -17,12 +17,12 @@ class WordsRange;
 class DistortionScoreProducer : public StatefulFeatureFunction
 {
 public:
-	DistortionScoreProducer(const std::string &line)
-	: StatefulFeatureFunction("Distortion", 1, line)
-	{}
+  DistortionScoreProducer(const std::string &line)
+    : StatefulFeatureFunction("Distortion", 1, line)
+  {}
 
   static float CalculateDistortionScore(const Hypothesis& hypo,
-                                 const WordsRange &prev, const WordsRange &curr, const int FirstGapPosition);
+                                        const WordsRange &prev, const WordsRange &curr, const int FirstGapPosition);
 
   virtual const FFState* EmptyHypothesisState(const InputType &input) const;
 
@@ -35,8 +35,8 @@ public:
     const ChartHypothesis& /* cur_hypo */,
     int /* featureID - used to index the state in the previous hypotheses */,
     ScoreComponentCollection*) const {
-		throw std::logic_error("DistortionScoreProducer not supported in chart decoder, yet");
-	}
+    throw std::logic_error("DistortionScoreProducer not supported in chart decoder, yet");
+  }
 };
 }
 
diff --git a/moses/FF/FFState.h b/moses/FF/FFState.h
index 49b0e55a8..bb3a119ef 100644
--- a/moses/FF/FFState.h
+++ b/moses/FF/FFState.h
@@ -15,11 +15,12 @@ public:
   virtual int Compare(const FFState& other) const = 0;
 };
 
-class DummyState : public FFState {
+class DummyState : public FFState
+{
 public:
   DummyState()  {}
   int Compare(const FFState& other) const {
-  	return 0;
+    return 0;
   }
 };
 
diff --git a/moses/FF/FeatureFunction.cpp b/moses/FF/FeatureFunction.cpp
index d1a73e1a9..ea4441522 100644
--- a/moses/FF/FeatureFunction.cpp
+++ b/moses/FF/FeatureFunction.cpp
@@ -19,7 +19,7 @@ std::vector<const StatelessFeatureFunction*> StatelessFeatureFunction::m_statele
 std::vector<const StatefulFeatureFunction*>  StatefulFeatureFunction::m_statefulFFs;
 
 FeatureFunction::FeatureFunction(const std::string& description, const std::string &line)
-: m_tuneable(true)
+  : m_tuneable(true)
 {
   ParseLine(description, line);
 
@@ -35,13 +35,13 @@ FeatureFunction::FeatureFunction(const std::string& description, const std::stri
     m_description = dstream.str();
   }
 
-	ScoreComponentCollection::RegisterScoreProducer(this);
+  ScoreComponentCollection::RegisterScoreProducer(this);
   m_producers.push_back(this);
 }
 
 FeatureFunction::FeatureFunction(const std::string& description, size_t numScoreComponents, const std::string &line)
-: m_numScoreComponents(numScoreComponents)
-, m_tuneable(true)
+  : m_numScoreComponents(numScoreComponents)
+  , m_tuneable(true)
 {
   ParseLine(description, line);
 
@@ -75,14 +75,11 @@ void FeatureFunction::ParseLine(const std::string& description, const std::strin
 
     if (args[0] == "num-features") {
       m_numScoreComponents = Scan<size_t>(args[1]);
-    }
-    else if (args[0] == "name") {
+    } else if (args[0] == "name") {
       m_description = args[1];
-    }
-    else if (args[0] == "tuneable") {
+    } else if (args[0] == "tuneable") {
       m_tuneable = Scan<bool>(args[1]);
-    }
-    else {
+    } else {
       m_args.push_back(args);
     }
   }
diff --git a/moses/FF/FeatureFunction.h b/moses/FF/FeatureFunction.h
index 6e1fa67a8..97e7d754d 100644
--- a/moses/FF/FeatureFunction.h
+++ b/moses/FF/FeatureFunction.h
@@ -42,26 +42,33 @@ protected:
   void ParseLine(const std::string& description, const std::string &line);
 
 public:
-  static const std::vector<FeatureFunction*>& GetFeatureFunctions() { return m_producers; }
+  static const std::vector<FeatureFunction*>& GetFeatureFunctions() {
+    return m_producers;
+  }
 
   FeatureFunction(const std::string& description, const std::string &line);
   FeatureFunction(const std::string& description, size_t numScoreComponents, const std::string &line);
-  virtual bool IsStateless() const = 0;	
+  virtual bool IsStateless() const = 0;
   virtual ~FeatureFunction();
-  
+
   static void ResetDescriptionCounts() {
     description_counts.clear();
   }
 
   //! returns the number of scores that a subclass produces.
   //! For example, a language model conventionally produces 1, a translation table some arbitrary number, etc
-  size_t GetNumScoreComponents() const {return m_numScoreComponents;}
+  size_t GetNumScoreComponents() const {
+    return m_numScoreComponents;
+  }
 
   //! returns a string description of this producer
-  const std::string& GetScoreProducerDescription() const
-  { return m_description; }
+  const std::string& GetScoreProducerDescription() const {
+    return m_description;
+  }
 
-  virtual bool IsTuneable() const { return m_tuneable; }
+  virtual bool IsTuneable() const {
+    return m_tuneable;
+  }
 
   //!
   virtual void InitializeForInput(InputType const& source)
@@ -71,17 +78,18 @@ public:
   virtual void CleanUpAfterSentenceProcessing(const InputType& source)
   {}
 
-  const std::string &GetArgLine() const
-  { return m_argLine; }
+  const std::string &GetArgLine() const {
+    return m_argLine;
+  }
 
   virtual void Evaluate(const Phrase &source
-		  	  	  	  , const TargetPhrase &targetPhrase
-                      , ScoreComponentCollection &scoreBreakdown
-                      , ScoreComponentCollection &estimatedFutureScore) const
+                        , const TargetPhrase &targetPhrase
+                        , ScoreComponentCollection &scoreBreakdown
+                        , ScoreComponentCollection &estimatedFutureScore) const
   {}
 
   virtual void Evaluate(const InputType &source
-                      , ScoreComponentCollection &scoreBreakdown) const
+                        , ScoreComponentCollection &scoreBreakdown) const
   {}
 };
 
diff --git a/moses/FF/GlobalLexicalModel.cpp b/moses/FF/GlobalLexicalModel.cpp
index 5724f6598..cbc6811ee 100644
--- a/moses/FF/GlobalLexicalModel.cpp
+++ b/moses/FF/GlobalLexicalModel.cpp
@@ -10,7 +10,7 @@ using namespace std;
 namespace Moses
 {
 GlobalLexicalModel::GlobalLexicalModel(const std::string &line)
-: StatelessFeatureFunction("GlobalLexicalModel",1, line)
+  : StatelessFeatureFunction("GlobalLexicalModel",1, line)
 {
   std::cerr << "Creating global lexical model...\n";
 
@@ -23,14 +23,11 @@ GlobalLexicalModel::GlobalLexicalModel(const std::string &line)
     if (args[0] == "file") {
       CHECK(args.size() == 2);
       filePath = args[1];
-    }
-    else if (args[0] == "inputFactors") {
+    } else if (args[0] == "inputFactors") {
       inputFactors = Tokenize<FactorType>(args[1],",");
-    }
-    else if (args[0] == "outputFactors") {
+    } else if (args[0] == "outputFactors") {
       outputFactors = Tokenize<FactorType>(args[1],",");
-    }
-    else {
+    } else {
       throw "Unknown argument " + args[0];
     }
   }
@@ -179,11 +176,11 @@ float GlobalLexicalModel::GetFromCacheOrScorePhrase( const TargetPhrase& targetP
 }
 
 void GlobalLexicalModel::Evaluate
-               (const PhraseBasedFeatureContext& context,
-  							ScoreComponentCollection* accumulator) const
+(const PhraseBasedFeatureContext& context,
+ ScoreComponentCollection* accumulator) const
 {
-  accumulator->PlusEquals( this,  
-      GetFromCacheOrScorePhrase(context.GetTargetPhrase()) );
+  accumulator->PlusEquals( this,
+                           GetFromCacheOrScorePhrase(context.GetTargetPhrase()) );
 }
 
 }
diff --git a/moses/FF/GlobalLexicalModel.h b/moses/FF/GlobalLexicalModel.h
index 03659b7f2..b3bf79b53 100644
--- a/moses/FF/GlobalLexicalModel.h
+++ b/moses/FF/GlobalLexicalModel.h
@@ -37,8 +37,7 @@ class GlobalLexicalModel : public StatelessFeatureFunction
   typedef std::map< const Word*, float, WordComparer > SingleHash;
   typedef std::map< const TargetPhrase*, float > LexiconCache;
 
-  struct ThreadLocalStorage
-  {
+  struct ThreadLocalStorage {
     LexiconCache cache;
     const Sentence *input;
   };
@@ -64,18 +63,17 @@ private:
 
 public:
   GlobalLexicalModel(const std::string &line);
-	virtual ~GlobalLexicalModel();
+  virtual ~GlobalLexicalModel();
 
   void InitializeForInput( Sentence const& in );
 
   void Evaluate(const PhraseBasedFeatureContext& context,
-  							ScoreComponentCollection* accumulator) const;
+                ScoreComponentCollection* accumulator) const;
 
 
   void EvaluateChart(
     const ChartBasedFeatureContext& context,
-    ScoreComponentCollection* accumulator) const
-  {
+    ScoreComponentCollection* accumulator) const {
     throw std::logic_error("GlobalLexicalModel not supported in chart decoder, yet");
   }
 
diff --git a/moses/FF/GlobalLexicalModelUnlimited.cpp b/moses/FF/GlobalLexicalModelUnlimited.cpp
index d4b1aeb37..5c096e43f 100644
--- a/moses/FF/GlobalLexicalModelUnlimited.cpp
+++ b/moses/FF/GlobalLexicalModelUnlimited.cpp
@@ -10,7 +10,7 @@ using namespace std;
 namespace Moses
 {
 GlobalLexicalModelUnlimited::GlobalLexicalModelUnlimited(const std::string &line)
-:StatelessFeatureFunction("GlobalLexicalModelUnlimited", 0, line)
+  :StatelessFeatureFunction("GlobalLexicalModelUnlimited", 0, line)
 {
   const vector<string> modelSpec = Tokenize(line);
 
@@ -25,7 +25,7 @@ GlobalLexicalModelUnlimited::GlobalLexicalModelUnlimited(const std::string &line
     if (spec.size() > 0) {
       if (spec.size() != 2 && spec.size() != 3 && spec.size() != 4 && spec.size() != 6) {
         UserMessage::Add("Format of glm feature is <factor-src>-<factor-tgt> [ignore-punct] [use-bias] "
-            "[context-type] [filename-src filename-tgt]");
+                         "[context-type] [filename-src filename-tgt]");
         //return false;
       }
 
@@ -41,8 +41,7 @@ GlobalLexicalModelUnlimited::GlobalLexicalModelUnlimited(const std::string &line
         filenameTarget = spec[5];
         restricted = true;
       }
-    }
-    else
+    } else
       factors = Tokenize(modelSpec[i],"-");
 
     if ( factors.size() != 2 ) {
@@ -66,14 +65,13 @@ GlobalLexicalModelUnlimited::GlobalLexicalModelUnlimited(const std::string &line
 }
 
 bool GlobalLexicalModelUnlimited::Load(const std::string &filePathSource,
-																			 const std::string &filePathTarget)
+                                       const std::string &filePathTarget)
 {
   // restricted source word vocabulary
   ifstream inFileSource(filePathSource.c_str());
-  if (!inFileSource)
-  {
-      cerr << "could not open file " << filePathSource << endl;
-      return false;
+  if (!inFileSource) {
+    cerr << "could not open file " << filePathSource << endl;
+    return false;
   }
 
   std::string line;
@@ -85,10 +83,9 @@ bool GlobalLexicalModelUnlimited::Load(const std::string &filePathSource,
 
   // restricted target word vocabulary
   ifstream inFileTarget(filePathTarget.c_str());
-  if (!inFileTarget)
-  {
-      cerr << "could not open file " << filePathTarget << endl;
-      return false;
+  if (!inFileTarget) {
+    cerr << "could not open file " << filePathTarget << endl;
+    return false;
   }
 
   while (getline(inFileTarget, line)) {
@@ -109,228 +106,222 @@ void GlobalLexicalModelUnlimited::InitializeForInput( Sentence const& in )
 
 void GlobalLexicalModelUnlimited::Evaluate(const Hypothesis& cur_hypo, ScoreComponentCollection* accumulator) const
 {
-	const Sentence& input = *(m_local->input);
-	const TargetPhrase& targetPhrase = cur_hypo.GetCurrTargetPhrase();
-
-	for(int targetIndex = 0; targetIndex < targetPhrase.GetSize(); targetIndex++ ) {
-	  StringPiece targetString = targetPhrase.GetWord(targetIndex).GetString(0); // TODO: change for other factors
-
-  	if (m_ignorePunctuation) {
-  		// check if first char is punctuation
-  		char firstChar = targetString[0];
-  		CharHash::const_iterator charIterator = m_punctuationHash.find( firstChar );
-  		if(charIterator != m_punctuationHash.end())
-  			continue;
-  	}
-
-  	if (m_biasFeature) {
-  		stringstream feature;
-  		feature << "glm_";
-  		feature << targetString;
-  		feature << "~";
-  		feature << "**BIAS**";
-  		accumulator->SparsePlusEquals(feature.str(), 1);
-  	}
-
-  	boost::unordered_set<uint64_t> alreadyScored;
-  	for(int sourceIndex = 0; sourceIndex < input.GetSize(); sourceIndex++ ) {
-  		const StringPiece sourceString = input.GetWord(sourceIndex).GetString(0); // TODO: change for other factors
-
-  		if (m_ignorePunctuation) {
-  			// check if first char is punctuation
-  			char firstChar = sourceString[0];
-  			CharHash::const_iterator charIterator = m_punctuationHash.find( firstChar );
-  			if(charIterator != m_punctuationHash.end()) 
-			  continue;			
-  		}
-  		const uint64_t sourceHash = util::MurmurHashNative(sourceString.data(), sourceString.size());
-
-  		if ( alreadyScored.find(sourceHash) == alreadyScored.end()) {
-  			bool sourceExists, targetExists;
-  			if (!m_unrestricted) {
-  			  sourceExists = FindStringPiece(m_vocabSource, sourceString ) != m_vocabSource.end();
-  			  targetExists = FindStringPiece(m_vocabTarget, targetString) != m_vocabTarget.end();
-  			}
-
-  			// no feature if vocab is in use and both words are not in restricted vocabularies
-  			if (m_unrestricted || (sourceExists && targetExists)) {
-  				if (m_sourceContext) {
-  					if (sourceIndex == 0) {
-  						// add <s> trigger feature for source
-	  					stringstream feature;
-	  					feature << "glm_";
-	  					feature << targetString;
-	  					feature << "~";
-	  					feature << "<s>,";
-	  					feature << sourceString;
-	  					accumulator->SparsePlusEquals(feature.str(), 1);
-	  					alreadyScored.insert(sourceHash);
-  					}
-
-  					// add source words to the right of current source word as context
-  					for(int contextIndex = sourceIndex+1; contextIndex < input.GetSize(); contextIndex++ ) {
-  						StringPiece contextString = input.GetWord(contextIndex).GetString(0); // TODO: change for other factors
-  						bool contextExists;
-  						if (!m_unrestricted)
-  							contextExists = FindStringPiece(m_vocabSource, contextString ) != m_vocabSource.end();
-
-  						if (m_unrestricted || contextExists) {
-  	  					stringstream feature;
-  	  					feature << "glm_";
-  	  					feature << targetString;
-  	  					feature << "~";
-  	  					feature << sourceString;
-  	  					feature << ",";
-  	  					feature << contextString;
-  	  					accumulator->SparsePlusEquals(feature.str(), 1);
-  	  					alreadyScored.insert(sourceHash);
-  						}
-  					}
-  				}
-  				else if (m_biphrase) {
-  					// --> look backwards for constructing context
-  					int globalTargetIndex = cur_hypo.GetSize() - targetPhrase.GetSize() + targetIndex;
-
-  					// 1) source-target pair, trigger source word (can be discont.) and adjacent target word (bigram)
-  					StringPiece targetContext;
-						if (globalTargetIndex > 0)
-							targetContext = cur_hypo.GetWord(globalTargetIndex-1).GetString(0); // TODO: change for other factors
-						else
-							targetContext = "<s>";
-
-  					if (sourceIndex == 0) {
-  						StringPiece sourceTrigger = "<s>";
-  						AddFeature(accumulator, sourceTrigger, sourceString,
-  						  						targetContext, targetString);
-  					}
-  					else
-  						for(int contextIndex = sourceIndex-1; contextIndex >= 0; contextIndex-- ) {
-  							StringPiece sourceTrigger = input.GetWord(contextIndex).GetString(0); // TODO: change for other factors
-  							bool sourceTriggerExists = false;
-  							if (!m_unrestricted)
-  								sourceTriggerExists = FindStringPiece(m_vocabSource, sourceTrigger ) != m_vocabSource.end();
-
-  							if (m_unrestricted || sourceTriggerExists)
-  								AddFeature(accumulator, sourceTrigger, sourceString,
-  										targetContext, targetString);
-  						}
-
-  					// 2) source-target pair, adjacent source word (bigram) and trigger target word (can be discont.)
-  					StringPiece sourceContext;
-  					if (sourceIndex-1 >= 0)
-  						sourceContext = input.GetWord(sourceIndex-1).GetString(0); // TODO: change for other factors
-  					else
-  						sourceContext = "<s>";
-
-  					if (globalTargetIndex == 0) {
-	  					string targetTrigger = "<s>";
-	  					AddFeature(accumulator, sourceContext, sourceString,
-	  					  			targetTrigger, targetString);
-  					}
-  					else
-  						for(int globalContextIndex = globalTargetIndex-1; globalContextIndex >= 0; globalContextIndex-- ) {
-  							StringPiece targetTrigger = cur_hypo.GetWord(globalContextIndex).GetString(0); // TODO: change for other factors
-  							bool targetTriggerExists = false;
-  							if (!m_unrestricted)
-  								targetTriggerExists = FindStringPiece(m_vocabTarget, targetTrigger ) != m_vocabTarget.end();
-
-  							if (m_unrestricted || targetTriggerExists)
-  								AddFeature(accumulator, sourceContext, sourceString,
-  										targetTrigger, targetString);
-  						}
-  				}
-  				else if (m_bitrigger) {
-  					// allow additional discont. triggers on both sides
-  					int globalTargetIndex = cur_hypo.GetSize() - targetPhrase.GetSize() + targetIndex;
-
-  					if (sourceIndex == 0) {
-  						StringPiece sourceTrigger = "<s>";
-  						bool sourceTriggerExists = true;
-
-  						if (globalTargetIndex == 0) {
-  							string targetTrigger = "<s>";
-  							bool targetTriggerExists = true;
-
-  							if (m_unrestricted || (sourceTriggerExists && targetTriggerExists))
-  								AddFeature(accumulator, sourceTrigger, sourceString,
-  										targetTrigger, targetString);
-  						}
-  						else {
-  							// iterate backwards over target
-  							for(int globalContextIndex = globalTargetIndex-1; globalContextIndex >= 0; globalContextIndex-- ) {
-  								StringPiece targetTrigger = cur_hypo.GetWord(globalContextIndex).GetString(0); // TODO: change for other factors
-  								bool targetTriggerExists = false;
-  								if (!m_unrestricted)
-  									targetTriggerExists = FindStringPiece(m_vocabTarget, targetTrigger ) != m_vocabTarget.end();
-
-  								if (m_unrestricted || (sourceTriggerExists && targetTriggerExists))
-  									AddFeature(accumulator, sourceTrigger, sourceString,
-  											targetTrigger, targetString);
-  							}
-  						}
-  					}
-  					// iterate over both source and target
-  					else {
-  						// iterate backwards over source
-  						for(int contextIndex = sourceIndex-1; contextIndex >= 0; contextIndex-- ) {
-  							StringPiece sourceTrigger = input.GetWord(contextIndex).GetString(0); // TODO: change for other factors
-  							bool sourceTriggerExists = false;
-  							if (!m_unrestricted)
-  								sourceTriggerExists = FindStringPiece(m_vocabSource, sourceTrigger ) != m_vocabSource.end();
-
-    						if (globalTargetIndex == 0) {
-    							string targetTrigger = "<s>";
-    							bool targetTriggerExists = true;
-
-    							if (m_unrestricted || (sourceTriggerExists && targetTriggerExists))
-    								AddFeature(accumulator, sourceTrigger, sourceString,
-    										targetTrigger, targetString);
-    						}
-    						else {
-    							// iterate backwards over target
-    							for(int globalContextIndex = globalTargetIndex-1; globalContextIndex >= 0; globalContextIndex-- ) {
-    								StringPiece targetTrigger = cur_hypo.GetWord(globalContextIndex).GetString(0); // TODO: change for other factors
-    								bool targetTriggerExists = false;
-    								if (!m_unrestricted)
-    									targetTriggerExists = FindStringPiece(m_vocabTarget, targetTrigger ) != m_vocabTarget.end();
-
-    								if (m_unrestricted || (sourceTriggerExists && targetTriggerExists))
-    									AddFeature(accumulator, sourceTrigger, sourceString,
-    											targetTrigger, targetString);
-    							}
-    						}
-  						}
-						}
-  				}
-  				else {
-  					stringstream feature;
-  					feature << "glm_";
-  					feature << targetString;
-  					feature << "~";
-  					feature << sourceString;
-  					accumulator->SparsePlusEquals(feature.str(), 1);
-  					alreadyScored.insert(sourceHash);
-
-  				}
-  			}
-  		}
-  	}
+  const Sentence& input = *(m_local->input);
+  const TargetPhrase& targetPhrase = cur_hypo.GetCurrTargetPhrase();
+
+  for(int targetIndex = 0; targetIndex < targetPhrase.GetSize(); targetIndex++ ) {
+    StringPiece targetString = targetPhrase.GetWord(targetIndex).GetString(0); // TODO: change for other factors
+
+    if (m_ignorePunctuation) {
+      // check if first char is punctuation
+      char firstChar = targetString[0];
+      CharHash::const_iterator charIterator = m_punctuationHash.find( firstChar );
+      if(charIterator != m_punctuationHash.end())
+        continue;
+    }
+
+    if (m_biasFeature) {
+      stringstream feature;
+      feature << "glm_";
+      feature << targetString;
+      feature << "~";
+      feature << "**BIAS**";
+      accumulator->SparsePlusEquals(feature.str(), 1);
+    }
+
+    boost::unordered_set<uint64_t> alreadyScored;
+    for(int sourceIndex = 0; sourceIndex < input.GetSize(); sourceIndex++ ) {
+      const StringPiece sourceString = input.GetWord(sourceIndex).GetString(0); // TODO: change for other factors
+
+      if (m_ignorePunctuation) {
+        // check if first char is punctuation
+        char firstChar = sourceString[0];
+        CharHash::const_iterator charIterator = m_punctuationHash.find( firstChar );
+        if(charIterator != m_punctuationHash.end())
+          continue;
+      }
+      const uint64_t sourceHash = util::MurmurHashNative(sourceString.data(), sourceString.size());
+
+      if ( alreadyScored.find(sourceHash) == alreadyScored.end()) {
+        bool sourceExists, targetExists;
+        if (!m_unrestricted) {
+          sourceExists = FindStringPiece(m_vocabSource, sourceString ) != m_vocabSource.end();
+          targetExists = FindStringPiece(m_vocabTarget, targetString) != m_vocabTarget.end();
+        }
+
+        // no feature if vocab is in use and both words are not in restricted vocabularies
+        if (m_unrestricted || (sourceExists && targetExists)) {
+          if (m_sourceContext) {
+            if (sourceIndex == 0) {
+              // add <s> trigger feature for source
+              stringstream feature;
+              feature << "glm_";
+              feature << targetString;
+              feature << "~";
+              feature << "<s>,";
+              feature << sourceString;
+              accumulator->SparsePlusEquals(feature.str(), 1);
+              alreadyScored.insert(sourceHash);
+            }
+
+            // add source words to the right of current source word as context
+            for(int contextIndex = sourceIndex+1; contextIndex < input.GetSize(); contextIndex++ ) {
+              StringPiece contextString = input.GetWord(contextIndex).GetString(0); // TODO: change for other factors
+              bool contextExists;
+              if (!m_unrestricted)
+                contextExists = FindStringPiece(m_vocabSource, contextString ) != m_vocabSource.end();
+
+              if (m_unrestricted || contextExists) {
+                stringstream feature;
+                feature << "glm_";
+                feature << targetString;
+                feature << "~";
+                feature << sourceString;
+                feature << ",";
+                feature << contextString;
+                accumulator->SparsePlusEquals(feature.str(), 1);
+                alreadyScored.insert(sourceHash);
+              }
+            }
+          } else if (m_biphrase) {
+            // --> look backwards for constructing context
+            int globalTargetIndex = cur_hypo.GetSize() - targetPhrase.GetSize() + targetIndex;
+
+            // 1) source-target pair, trigger source word (can be discont.) and adjacent target word (bigram)
+            StringPiece targetContext;
+            if (globalTargetIndex > 0)
+              targetContext = cur_hypo.GetWord(globalTargetIndex-1).GetString(0); // TODO: change for other factors
+            else
+              targetContext = "<s>";
+
+            if (sourceIndex == 0) {
+              StringPiece sourceTrigger = "<s>";
+              AddFeature(accumulator, sourceTrigger, sourceString,
+                         targetContext, targetString);
+            } else
+              for(int contextIndex = sourceIndex-1; contextIndex >= 0; contextIndex-- ) {
+                StringPiece sourceTrigger = input.GetWord(contextIndex).GetString(0); // TODO: change for other factors
+                bool sourceTriggerExists = false;
+                if (!m_unrestricted)
+                  sourceTriggerExists = FindStringPiece(m_vocabSource, sourceTrigger ) != m_vocabSource.end();
+
+                if (m_unrestricted || sourceTriggerExists)
+                  AddFeature(accumulator, sourceTrigger, sourceString,
+                             targetContext, targetString);
+              }
+
+            // 2) source-target pair, adjacent source word (bigram) and trigger target word (can be discont.)
+            StringPiece sourceContext;
+            if (sourceIndex-1 >= 0)
+              sourceContext = input.GetWord(sourceIndex-1).GetString(0); // TODO: change for other factors
+            else
+              sourceContext = "<s>";
+
+            if (globalTargetIndex == 0) {
+              string targetTrigger = "<s>";
+              AddFeature(accumulator, sourceContext, sourceString,
+                         targetTrigger, targetString);
+            } else
+              for(int globalContextIndex = globalTargetIndex-1; globalContextIndex >= 0; globalContextIndex-- ) {
+                StringPiece targetTrigger = cur_hypo.GetWord(globalContextIndex).GetString(0); // TODO: change for other factors
+                bool targetTriggerExists = false;
+                if (!m_unrestricted)
+                  targetTriggerExists = FindStringPiece(m_vocabTarget, targetTrigger ) != m_vocabTarget.end();
+
+                if (m_unrestricted || targetTriggerExists)
+                  AddFeature(accumulator, sourceContext, sourceString,
+                             targetTrigger, targetString);
+              }
+          } else if (m_bitrigger) {
+            // allow additional discont. triggers on both sides
+            int globalTargetIndex = cur_hypo.GetSize() - targetPhrase.GetSize() + targetIndex;
+
+            if (sourceIndex == 0) {
+              StringPiece sourceTrigger = "<s>";
+              bool sourceTriggerExists = true;
+
+              if (globalTargetIndex == 0) {
+                string targetTrigger = "<s>";
+                bool targetTriggerExists = true;
+
+                if (m_unrestricted || (sourceTriggerExists && targetTriggerExists))
+                  AddFeature(accumulator, sourceTrigger, sourceString,
+                             targetTrigger, targetString);
+              } else {
+                // iterate backwards over target
+                for(int globalContextIndex = globalTargetIndex-1; globalContextIndex >= 0; globalContextIndex-- ) {
+                  StringPiece targetTrigger = cur_hypo.GetWord(globalContextIndex).GetString(0); // TODO: change for other factors
+                  bool targetTriggerExists = false;
+                  if (!m_unrestricted)
+                    targetTriggerExists = FindStringPiece(m_vocabTarget, targetTrigger ) != m_vocabTarget.end();
+
+                  if (m_unrestricted || (sourceTriggerExists && targetTriggerExists))
+                    AddFeature(accumulator, sourceTrigger, sourceString,
+                               targetTrigger, targetString);
+                }
+              }
+            }
+            // iterate over both source and target
+            else {
+              // iterate backwards over source
+              for(int contextIndex = sourceIndex-1; contextIndex >= 0; contextIndex-- ) {
+                StringPiece sourceTrigger = input.GetWord(contextIndex).GetString(0); // TODO: change for other factors
+                bool sourceTriggerExists = false;
+                if (!m_unrestricted)
+                  sourceTriggerExists = FindStringPiece(m_vocabSource, sourceTrigger ) != m_vocabSource.end();
+
+                if (globalTargetIndex == 0) {
+                  string targetTrigger = "<s>";
+                  bool targetTriggerExists = true;
+
+                  if (m_unrestricted || (sourceTriggerExists && targetTriggerExists))
+                    AddFeature(accumulator, sourceTrigger, sourceString,
+                               targetTrigger, targetString);
+                } else {
+                  // iterate backwards over target
+                  for(int globalContextIndex = globalTargetIndex-1; globalContextIndex >= 0; globalContextIndex-- ) {
+                    StringPiece targetTrigger = cur_hypo.GetWord(globalContextIndex).GetString(0); // TODO: change for other factors
+                    bool targetTriggerExists = false;
+                    if (!m_unrestricted)
+                      targetTriggerExists = FindStringPiece(m_vocabTarget, targetTrigger ) != m_vocabTarget.end();
+
+                    if (m_unrestricted || (sourceTriggerExists && targetTriggerExists))
+                      AddFeature(accumulator, sourceTrigger, sourceString,
+                                 targetTrigger, targetString);
+                  }
+                }
+              }
+            }
+          } else {
+            stringstream feature;
+            feature << "glm_";
+            feature << targetString;
+            feature << "~";
+            feature << sourceString;
+            accumulator->SparsePlusEquals(feature.str(), 1);
+            alreadyScored.insert(sourceHash);
+
+          }
+        }
+      }
+    }
   }
 }
 
 void GlobalLexicalModelUnlimited::AddFeature(ScoreComponentCollection* accumulator,
-		StringPiece sourceTrigger, StringPiece sourceWord,
-		StringPiece targetTrigger, StringPiece targetWord) const {
-	stringstream feature;
-	feature << "glm_";
-	feature << targetTrigger;
-	feature << ",";
-	feature << targetWord;
-	feature << "~";
-	feature << sourceTrigger;
-	feature << ",";
-	feature << sourceWord;
-	accumulator->SparsePlusEquals(feature.str(), 1);
+    StringPiece sourceTrigger, StringPiece sourceWord,
+    StringPiece targetTrigger, StringPiece targetWord) const
+{
+  stringstream feature;
+  feature << "glm_";
+  feature << targetTrigger;
+  feature << ",";
+  feature << targetWord;
+  feature << "~";
+  feature << sourceTrigger;
+  feature << ",";
+  feature << sourceWord;
+  accumulator->SparsePlusEquals(feature.str(), 1);
 
 }
 
diff --git a/moses/FF/GlobalLexicalModelUnlimited.h b/moses/FF/GlobalLexicalModelUnlimited.h
index 42b7abae9..28579f55c 100644
--- a/moses/FF/GlobalLexicalModelUnlimited.h
+++ b/moses/FF/GlobalLexicalModelUnlimited.h
@@ -38,11 +38,10 @@ class InputType;
 
 class GlobalLexicalModelUnlimited : public StatelessFeatureFunction
 {
-	typedef std::map< char, short > CharHash;
-	typedef std::map< std::string, short > StringHash;
+  typedef std::map< char, short > CharHash;
+  typedef std::map< std::string, short > StringHash;
 
-  struct ThreadLocalStorage
-  {
+  struct ThreadLocalStorage {
     const Sentence *input;
   };
 
@@ -77,23 +76,23 @@ public:
   void InitializeForInput( Sentence const& in );
 
   const FFState* EmptyHypothesisState(const InputType &) const {
-  	return new DummyState();
+    return new DummyState();
   }
 
   //TODO: This implements the old interface, but cannot be updated because
   //it appears to be stateful
   void Evaluate(const Hypothesis& cur_hypo,
-  							ScoreComponentCollection* accumulator) const;
+                ScoreComponentCollection* accumulator) const;
 
   void EvaluateChart(const ChartHypothesis& /* cur_hypo */,
-  									 int /* featureID */,
-  									 ScoreComponentCollection* ) const {
+                     int /* featureID */,
+                     ScoreComponentCollection* ) const {
     throw std::logic_error("GlobalLexicalModelUnlimited not supported in chart decoder, yet");
   }
 
-	void AddFeature(ScoreComponentCollection* accumulator,
-			StringPiece sourceTrigger, StringPiece sourceWord, StringPiece targetTrigger,
-			StringPiece targetWord) const;
+  void AddFeature(ScoreComponentCollection* accumulator,
+                  StringPiece sourceTrigger, StringPiece sourceWord, StringPiece targetTrigger,
+                  StringPiece targetWord) const;
 
 };
 
diff --git a/moses/FF/InputFeature.cpp b/moses/FF/InputFeature.cpp
index 6dc60f94a..1ef394f9f 100644
--- a/moses/FF/InputFeature.cpp
+++ b/moses/FF/InputFeature.cpp
@@ -7,7 +7,7 @@ using namespace std;
 namespace Moses
 {
 InputFeature::InputFeature(const std::string &line)
-:StatelessFeatureFunction("InputFeature", line)
+  :StatelessFeatureFunction("InputFeature", line)
 {
 
 }
@@ -17,19 +17,19 @@ const InputFeature &InputFeature::GetInputFeature()
   static const InputFeature *staticObj = NULL;
 
   if (staticObj) {
-	return *staticObj;
+    return *staticObj;
   }
 
   // 1st time looking up the feature
   const std::vector<const StatelessFeatureFunction*> &statefulFFs = StatelessFeatureFunction::GetStatelessFeatureFunctions();
   for (size_t i = 0; i < statefulFFs.size(); ++i) {
-	const StatelessFeatureFunction *ff = statefulFFs[i];
-	const InputFeature *lm = dynamic_cast<const InputFeature*>(ff);
+    const StatelessFeatureFunction *ff = statefulFFs[i];
+    const InputFeature *lm = dynamic_cast<const InputFeature*>(ff);
 
-	if (lm) {
-		staticObj = lm;
-	  return *staticObj;
-	}
+    if (lm) {
+      staticObj = lm;
+      return *staticObj;
+    }
   }
 
   throw std::logic_error("No input feature.");
diff --git a/moses/FF/PhraseBasedFeatureContext.cpp b/moses/FF/PhraseBasedFeatureContext.cpp
index 46e754801..4127a587c 100644
--- a/moses/FF/PhraseBasedFeatureContext.cpp
+++ b/moses/FF/PhraseBasedFeatureContext.cpp
@@ -11,7 +11,7 @@ PhraseBasedFeatureContext::PhraseBasedFeatureContext(const Hypothesis* hypothesi
   m_source(m_hypothesis->GetManager().GetSource()) {}
 
 PhraseBasedFeatureContext::PhraseBasedFeatureContext
-      (const TranslationOption& translationOption, const InputType& source) :
+(const TranslationOption& translationOption, const InputType& source) :
   m_hypothesis(NULL),
   m_translationOption(translationOption),
   m_source(source)
diff --git a/moses/FF/PhraseBasedFeatureContext.h b/moses/FF/PhraseBasedFeatureContext.h
index b2c7052f6..0c41712ca 100644
--- a/moses/FF/PhraseBasedFeatureContext.h
+++ b/moses/FF/PhraseBasedFeatureContext.h
@@ -17,7 +17,7 @@ class WordsBitmap;
  **/
 class PhraseBasedFeatureContext
 {
-  // The context either has a hypothesis (during search), or a TranslationOption and 
+  // The context either has a hypothesis (during search), or a TranslationOption and
   // source sentence (during pre-calculation).
   const Hypothesis* m_hypothesis;
   const TranslationOption& m_translationOption;
@@ -28,10 +28,12 @@ public:
   PhraseBasedFeatureContext(const TranslationOption& translationOption,
                             const InputType& source);
 
-  const TranslationOption& GetTranslationOption() const
-  { return m_translationOption; }
-  const InputType& GetSource() const
-  { return m_source; }
+  const TranslationOption& GetTranslationOption() const {
+    return m_translationOption;
+  }
+  const InputType& GetSource() const {
+    return m_source;
+  }
   const TargetPhrase& GetTargetPhrase() const; //convenience method
   const WordsBitmap& GetWordsBitmap() const;
 
diff --git a/moses/FF/PhraseBoundaryFeature.cpp b/moses/FF/PhraseBoundaryFeature.cpp
index 671cc903e..ff73c760e 100644
--- a/moses/FF/PhraseBoundaryFeature.cpp
+++ b/moses/FF/PhraseBoundaryFeature.cpp
@@ -4,9 +4,10 @@
 
 using namespace std;
 
-namespace Moses {
+namespace Moses
+{
 
-int PhraseBoundaryState::Compare(const FFState& other) const 
+int PhraseBoundaryState::Compare(const FFState& other) const
 {
   const PhraseBoundaryState& rhs = dynamic_cast<const PhraseBoundaryState&>(other);
   int tgt = Word::Compare(*m_targetWord,*(rhs.m_targetWord));
@@ -15,7 +16,7 @@ int PhraseBoundaryState::Compare(const FFState& other) const
 }
 
 PhraseBoundaryFeature::PhraseBoundaryFeature(const std::string &line)
-: StatefulFeatureFunction("PhraseBoundaryFeature", 0, line)
+  : StatefulFeatureFunction("PhraseBoundaryFeature", 0, line)
 {
   std::cerr << "Initializing source word deletion feature.." << std::endl;
 
@@ -24,17 +25,15 @@ PhraseBoundaryFeature::PhraseBoundaryFeature(const std::string &line)
 
     if (args[0] == "source") {
       m_sourceFactors = Tokenize<FactorType>(args[1], ",");
-    }
-    else if (args[0] == "target") {
+    } else if (args[0] == "target") {
       m_targetFactors = Tokenize<FactorType>(args[1], ",");
-    }
-    else {
+    } else {
       throw "Unknown argument " + args[0];
     }
   }
 }
 
-const FFState* PhraseBoundaryFeature::EmptyHypothesisState(const InputType &) const 
+const FFState* PhraseBoundaryFeature::EmptyHypothesisState(const InputType &) const
 {
   return new PhraseBoundaryState(NULL,NULL);
 }
@@ -42,31 +41,32 @@ const FFState* PhraseBoundaryFeature::EmptyHypothesisState(const InputType &) co
 
 void PhraseBoundaryFeature::AddFeatures(
   const Word* leftWord, const Word* rightWord, const FactorList& factors, const string& side,
-  ScoreComponentCollection* scores) const {
-   for (size_t i = 0; i < factors.size(); ++i) {
-      ostringstream name;
-      name << side << ":";
-      name << factors[i];
-      name << ":";
-      if (leftWord) {
-        name << leftWord->GetFactor(factors[i])->GetString();
-      } else {
-        name << BOS_;
-      }
-      name << ":";
-      if (rightWord) {
-        name << rightWord->GetFactor(factors[i])->GetString();
-      } else {
-        name << EOS_;
-      }
-      scores->PlusEquals(this,name.str(),1);
+  ScoreComponentCollection* scores) const
+{
+  for (size_t i = 0; i < factors.size(); ++i) {
+    ostringstream name;
+    name << side << ":";
+    name << factors[i];
+    name << ":";
+    if (leftWord) {
+      name << leftWord->GetFactor(factors[i])->GetString();
+    } else {
+      name << BOS_;
+    }
+    name << ":";
+    if (rightWord) {
+      name << rightWord->GetFactor(factors[i])->GetString();
+    } else {
+      name << EOS_;
     }
+    scores->PlusEquals(this,name.str(),1);
+  }
 
 }
 
 FFState* PhraseBoundaryFeature::Evaluate
-  (const Hypothesis& cur_hypo, const FFState* prev_state,
-      ScoreComponentCollection* scores) const
+(const Hypothesis& cur_hypo, const FFState* prev_state,
+ ScoreComponentCollection* scores) const
 {
   const PhraseBoundaryState* pbState = dynamic_cast<const PhraseBoundaryState*>(prev_state);
   const Phrase& targetPhrase = cur_hypo.GetCurrTargetPhrase();
diff --git a/moses/FF/PhraseBoundaryFeature.h b/moses/FF/PhraseBoundaryFeature.h
index 34b12abf6..b06e66eea 100644
--- a/moses/FF/PhraseBoundaryFeature.h
+++ b/moses/FF/PhraseBoundaryFeature.h
@@ -12,12 +12,17 @@
 namespace Moses
 {
 
-class PhraseBoundaryState : public FFState {
+class PhraseBoundaryState : public FFState
+{
 public:
   PhraseBoundaryState(const Word* sourceWord, const Word* targetWord) :
-     m_sourceWord(sourceWord), m_targetWord(targetWord) {}
-  const Word* GetSourceWord() const {return m_sourceWord;}
-  const Word* GetTargetWord() const {return m_targetWord;}
+    m_sourceWord(sourceWord), m_targetWord(targetWord) {}
+  const Word* GetSourceWord() const {
+    return m_sourceWord;
+  }
+  const Word* GetTargetWord() const {
+    return m_targetWord;
+  }
   virtual int Compare(const FFState& other) const;
 
 
@@ -30,7 +35,8 @@ private:
 /**
  * Concatenations of factors on boundaries of phrases.
  **/
-class PhraseBoundaryFeature : public StatefulFeatureFunction {
+class PhraseBoundaryFeature : public StatefulFeatureFunction
+{
 public:
   PhraseBoundaryFeature(const std::string &line);
 
@@ -39,7 +45,7 @@ public:
   virtual const FFState* EmptyHypothesisState(const InputType &) const;
 
   virtual FFState* Evaluate(const Hypothesis& cur_hypo, const FFState* prev_state,
-                          ScoreComponentCollection* accumulator) const;
+                            ScoreComponentCollection* accumulator) const;
 
   virtual FFState* EvaluateChart( const ChartHypothesis& /* cur_hypo */,
                                   int /* featureID */,
@@ -49,7 +55,7 @@ public:
 
 private:
   void AddFeatures(
-    const Word* leftWord, const Word* rightWord, const FactorList& factors, 
+    const Word* leftWord, const Word* rightWord, const FactorList& factors,
     const std::string& side, ScoreComponentCollection* scores) const ;
   FactorList m_sourceFactors;
   FactorList m_targetFactors;
diff --git a/moses/FF/PhraseLengthFeature.cpp b/moses/FF/PhraseLengthFeature.cpp
index b9e8e9e1d..2efeb07d2 100644
--- a/moses/FF/PhraseLengthFeature.cpp
+++ b/moses/FF/PhraseLengthFeature.cpp
@@ -4,20 +4,21 @@
 #include "moses/ScoreComponentCollection.h"
 #include "moses/TranslationOption.h"
 
-namespace Moses {
+namespace Moses
+{
 
 using namespace std;
 
 PhraseLengthFeature::PhraseLengthFeature(const std::string &line)
-:StatelessFeatureFunction("PhraseLengthFeature", 0, line)
+  :StatelessFeatureFunction("PhraseLengthFeature", 0, line)
 {
 
 }
 
 void PhraseLengthFeature::Evaluate(const Phrase &source
-								  , const TargetPhrase &targetPhrase
-								  , ScoreComponentCollection &scoreBreakdown
-								  , ScoreComponentCollection &estimatedFutureScore) const
+                                   , const TargetPhrase &targetPhrase
+                                   , ScoreComponentCollection &scoreBreakdown
+                                   , ScoreComponentCollection &estimatedFutureScore) const
 {
   // get length of source and target phrase
   size_t targetLength = targetPhrase.GetSize();
diff --git a/moses/FF/PhraseLengthFeature.h b/moses/FF/PhraseLengthFeature.h
index 327865558..23c168417 100644
--- a/moses/FF/PhraseLengthFeature.h
+++ b/moses/FF/PhraseLengthFeature.h
@@ -15,7 +15,8 @@ namespace Moses
 
 /** Sets the features for length of source phrase, target phrase, both.
  */
-class PhraseLengthFeature : public StatelessFeatureFunction {
+class PhraseLengthFeature : public StatelessFeatureFunction
+{
 public:
   PhraseLengthFeature(const std::string &line);
 
@@ -25,9 +26,9 @@ public:
   }
 
   virtual void Evaluate(const Phrase &source
-	  	  	  	  	  , const TargetPhrase &targetPhrase
-                      , ScoreComponentCollection &scoreBreakdown
-                      , ScoreComponentCollection &estimatedFutureScore) const;
+                        , const TargetPhrase &targetPhrase
+                        , ScoreComponentCollection &scoreBreakdown
+                        , ScoreComponentCollection &estimatedFutureScore) const;
 
 };
 
diff --git a/moses/FF/PhrasePairFeature.cpp b/moses/FF/PhrasePairFeature.cpp
index 58f71271f..9fce7ff4e 100644
--- a/moses/FF/PhrasePairFeature.cpp
+++ b/moses/FF/PhrasePairFeature.cpp
@@ -9,10 +9,11 @@
 
 using namespace std;
 
-namespace Moses {
+namespace Moses
+{
 
 PhrasePairFeature::PhrasePairFeature(const std::string &line)
-:StatelessFeatureFunction("PhrasePairFeature", 0, line)
+  :StatelessFeatureFunction("PhrasePairFeature", 0, line)
 {
   std::cerr << "Initializing PhrasePairFeature.." << std::endl;
 
@@ -44,47 +45,44 @@ PhrasePairFeature::PhrasePairFeature(const std::string &line)
   Load(filePathSource);
 }
 
-bool PhrasePairFeature::Load(const std::string &filePathSource/*, const std::string &filePathTarget*/) 
+bool PhrasePairFeature::Load(const std::string &filePathSource/*, const std::string &filePathTarget*/)
 {
   if (m_domainTrigger) {
     // domain trigger terms for each input document
     ifstream inFileSource(filePathSource.c_str());
-    if (!inFileSource)
-      {
-	cerr << "could not open file " << filePathSource << endl;
-	return false;
-      }
-    
+    if (!inFileSource) {
+      cerr << "could not open file " << filePathSource << endl;
+      return false;
+    }
+
     std::string line;
     while (getline(inFileSource, line)) {
       std::set<std::string> terms;
       vector<string> termVector;
       boost::split(termVector, line, boost::is_any_of("\t "));
-      for (size_t i=0; i < termVector.size(); ++i) 
+      for (size_t i=0; i < termVector.size(); ++i)
         terms.insert(termVector[i]);
-      
+
       // add term set for current document
       m_vocabDomain.push_back(terms);
     }
-    
+
     inFileSource.close();
-  }
-  else {
+  } else {
     // restricted source word vocabulary
     ifstream inFileSource(filePathSource.c_str());
-    if (!inFileSource)
-      {
-	cerr << "could not open file " << filePathSource << endl;
-	return false;
-      }
-    
+    if (!inFileSource) {
+      cerr << "could not open file " << filePathSource << endl;
+      return false;
+    }
+
     std::string line;
     while (getline(inFileSource, line)) {
       m_vocabSource.insert(line);
     }
-    
+
     inFileSource.close();
-    
+
     /*  // restricted target word vocabulary
     ifstream inFileTarget(filePathTarget.c_str());
     if (!inFileTarget)
@@ -105,11 +103,11 @@ bool PhrasePairFeature::Load(const std::string &filePathSource/*, const std::str
 }
 
 void PhrasePairFeature::Evaluate(
-            const PhraseBasedFeatureContext& context,
-            ScoreComponentCollection* accumulator) const
+  const PhraseBasedFeatureContext& context,
+  ScoreComponentCollection* accumulator) const
 {
   const TargetPhrase& target = context.GetTargetPhrase();
-  const Phrase& source = *(context.GetTranslationOption().GetSourcePhrase()); 
+  const Phrase& source = *(context.GetTranslationOption().GetSourcePhrase());
   if (m_simple) {
     ostringstream namestr;
     namestr << "pp_";
@@ -126,11 +124,11 @@ void PhrasePairFeature::Evaluate(
       namestr << ",";
       namestr << targetFactor->GetString();
     }
-    
+
     accumulator->SparsePlusEquals(namestr.str(),1);
   }
   if (m_domainTrigger) {
-    const Sentence& input = static_cast<const Sentence&>(context.GetSource());  
+    const Sentence& input = static_cast<const Sentence&>(context.GetSource());
     const bool use_topicid = input.GetUseTopicId();
     const bool use_topicid_prob = input.GetUseTopicIdAndProb();
 
@@ -149,95 +147,92 @@ void PhrasePairFeature::Evaluate(
       pair << ",";
       pair << targetFactor->GetString();
     }
-    
+
     if (use_topicid || use_topicid_prob) {
       if(use_topicid) {
-	// use topicid as trigger    
-	const long topicid = input.GetTopicId();
-	stringstream feature;
-	feature << "pp_";
-	if (topicid == -1)
-	  feature << "unk";
-	else
-	  feature << topicid;
-	
-	feature << "_";
-	feature << pair.str();
-	accumulator->SparsePlusEquals(feature.str(), 1);
+        // use topicid as trigger
+        const long topicid = input.GetTopicId();
+        stringstream feature;
+        feature << "pp_";
+        if (topicid == -1)
+          feature << "unk";
+        else
+          feature << topicid;
+
+        feature << "_";
+        feature << pair.str();
+        accumulator->SparsePlusEquals(feature.str(), 1);
+      } else {
+        // use topic probabilities
+        const vector<string> &topicid_prob = *(input.GetTopicIdAndProb());
+        if (atol(topicid_prob[0].c_str()) == -1) {
+          stringstream feature;
+          feature << "pp_unk_";
+          feature << pair.str();
+          accumulator->SparsePlusEquals(feature.str(), 1);
+        } else {
+          for (size_t i=0; i+1 < topicid_prob.size(); i+=2) {
+            stringstream feature;
+            feature << "pp_";
+            feature << topicid_prob[i];
+            feature << "_";
+            feature << pair.str();
+            accumulator->SparsePlusEquals(feature.str(), atof((topicid_prob[i+1]).c_str()));
+          }
+        }
       }
-      else {
-	// use topic probabilities                                                                                        
-	const vector<string> &topicid_prob = *(input.GetTopicIdAndProb());
-	if (atol(topicid_prob[0].c_str()) == -1) {
-	  stringstream feature;
-	  feature << "pp_unk_";
-	  feature << pair.str();
-	  accumulator->SparsePlusEquals(feature.str(), 1);
-	}
-	else {
-	  for (size_t i=0; i+1 < topicid_prob.size(); i+=2) {
-	    stringstream feature;
-	    feature << "pp_";
-	    feature << topicid_prob[i];
-	    feature << "_";
-	    feature << pair.str();
-	    accumulator->SparsePlusEquals(feature.str(), atof((topicid_prob[i+1]).c_str()));
-	  }
-	}
-      }
-    }
-    else {
+    } else {
       // range over domain trigger words
       const long docid = input.GetDocumentId();
       for (set<string>::const_iterator p = m_vocabDomain[docid].begin(); p != m_vocabDomain[docid].end(); ++p) {
-	string sourceTrigger = *p;
-	ostringstream namestr;
-	namestr << "pp_"; 
-	namestr << sourceTrigger;
-	namestr << "_";
-	namestr << pair.str();	
-	accumulator->SparsePlusEquals(namestr.str(),1);
+        string sourceTrigger = *p;
+        ostringstream namestr;
+        namestr << "pp_";
+        namestr << sourceTrigger;
+        namestr << "_";
+        namestr << pair.str();
+        accumulator->SparsePlusEquals(namestr.str(),1);
       }
     }
   }
   if (m_sourceContext) {
     const Sentence& input = static_cast<const Sentence&>(context.GetSource());
-    
+
     // range over source words to get context
     for(size_t contextIndex = 0; contextIndex < input.GetSize(); contextIndex++ ) {
       StringPiece sourceTrigger = input.GetWord(contextIndex).GetFactor(m_sourceFactorId)->GetString();
       if (m_ignorePunctuation) {
-	// check if trigger is punctuation
-	char firstChar = sourceTrigger[0];
-	CharHash::const_iterator charIterator = m_punctuationHash.find( firstChar );
-	if(charIterator != m_punctuationHash.end())
-	  continue;
+        // check if trigger is punctuation
+        char firstChar = sourceTrigger[0];
+        CharHash::const_iterator charIterator = m_punctuationHash.find( firstChar );
+        if(charIterator != m_punctuationHash.end())
+          continue;
       }
-      
+
       bool sourceTriggerExists = false;
       if (!m_unrestricted)
-	sourceTriggerExists = FindStringPiece(m_vocabSource, sourceTrigger ) != m_vocabSource.end();
-      
+        sourceTriggerExists = FindStringPiece(m_vocabSource, sourceTrigger ) != m_vocabSource.end();
+
       if (m_unrestricted || sourceTriggerExists) {
-	ostringstream namestr;
-	namestr << "pp_"; 
-	namestr << sourceTrigger;
-	namestr << "~";
-	namestr << source.GetWord(0).GetFactor(m_sourceFactorId)->GetString();
-	for (size_t i = 1; i < source.GetSize(); ++i) {
-	  const Factor* sourceFactor = source.GetWord(i).GetFactor(m_sourceFactorId);
-	  namestr << ",";
-	  namestr << sourceFactor->GetString();
-	}
-	namestr << "~";
-	namestr << target.GetWord(0).GetFactor(m_targetFactorId)->GetString();
-	for (size_t i = 1; i < target.GetSize(); ++i) {
-	  const Factor* targetFactor = target.GetWord(i).GetFactor(m_targetFactorId);
-	  namestr << ",";
-	  namestr << targetFactor->GetString();
-	}
-	
-	accumulator->SparsePlusEquals(namestr.str(),1);
+        ostringstream namestr;
+        namestr << "pp_";
+        namestr << sourceTrigger;
+        namestr << "~";
+        namestr << source.GetWord(0).GetFactor(m_sourceFactorId)->GetString();
+        for (size_t i = 1; i < source.GetSize(); ++i) {
+          const Factor* sourceFactor = source.GetWord(i).GetFactor(m_sourceFactorId);
+          namestr << ",";
+          namestr << sourceFactor->GetString();
+        }
+        namestr << "~";
+        namestr << target.GetWord(0).GetFactor(m_targetFactorId)->GetString();
+        for (size_t i = 1; i < target.GetSize(); ++i) {
+          const Factor* targetFactor = target.GetWord(i).GetFactor(m_targetFactorId);
+          namestr << ",";
+          namestr << targetFactor->GetString();
+        }
+
+        accumulator->SparsePlusEquals(namestr.str(),1);
       }
     }
   }
diff --git a/moses/FF/PhrasePairFeature.h b/moses/FF/PhrasePairFeature.h
index e895110f8..d7aa80be7 100644
--- a/moses/FF/PhrasePairFeature.h
+++ b/moses/FF/PhrasePairFeature.h
@@ -8,39 +8,41 @@
 #include "moses/Factor.h"
 #include "moses/Sentence.h"
 
-namespace Moses {
+namespace Moses
+{
 
 /**
   * Phrase pair feature: complete source/target phrase pair
   **/
-class PhrasePairFeature: public StatelessFeatureFunction {
-    
-    typedef std::map< char, short > CharHash;
-    typedef std::vector< std::set<std::string> > DocumentVector;
-       
-    boost::unordered_set<std::string> m_vocabSource;
-    DocumentVector m_vocabDomain;
-    FactorType m_sourceFactorId;
-    FactorType m_targetFactorId;
-    bool m_unrestricted;
-    bool m_simple;
-    bool m_sourceContext;
-    bool m_domainTrigger;
-    bool m_ignorePunctuation;
-    CharHash m_punctuationHash;
-    
-  public:
-    PhrasePairFeature(const std::string &line);
-
-    void Evaluate(const PhraseBasedFeatureContext& context,
-                  ScoreComponentCollection* accumulator) const;
-    
-    void EvaluateChart(const ChartBasedFeatureContext& context,
-                       ScoreComponentCollection*) const {
-      throw std::logic_error("PhrasePairFeature not valid in chart decoder");
-    }
-
-    bool Load(const std::string &filePathSource/*, const std::string &filePathTarget*/);
+class PhrasePairFeature: public StatelessFeatureFunction
+{
+
+  typedef std::map< char, short > CharHash;
+  typedef std::vector< std::set<std::string> > DocumentVector;
+
+  boost::unordered_set<std::string> m_vocabSource;
+  DocumentVector m_vocabDomain;
+  FactorType m_sourceFactorId;
+  FactorType m_targetFactorId;
+  bool m_unrestricted;
+  bool m_simple;
+  bool m_sourceContext;
+  bool m_domainTrigger;
+  bool m_ignorePunctuation;
+  CharHash m_punctuationHash;
+
+public:
+  PhrasePairFeature(const std::string &line);
+
+  void Evaluate(const PhraseBasedFeatureContext& context,
+                ScoreComponentCollection* accumulator) const;
+
+  void EvaluateChart(const ChartBasedFeatureContext& context,
+                     ScoreComponentCollection*) const {
+    throw std::logic_error("PhrasePairFeature not valid in chart decoder");
+  }
+
+  bool Load(const std::string &filePathSource/*, const std::string &filePathTarget*/);
 
 };
 
diff --git a/moses/FF/SourceWordDeletionFeature.cpp b/moses/FF/SourceWordDeletionFeature.cpp
index 085dbbeea..693812105 100644
--- a/moses/FF/SourceWordDeletionFeature.cpp
+++ b/moses/FF/SourceWordDeletionFeature.cpp
@@ -11,13 +11,14 @@
 
 #include "util/string_piece_hash.hh"
 
-namespace Moses {
+namespace Moses
+{
 
 using namespace std;
 
 SourceWordDeletionFeature::SourceWordDeletionFeature(const std::string &line)
-:StatelessFeatureFunction("SourceWordDeletionFeature", 0, line),
-m_unrestricted(true)
+  :StatelessFeatureFunction("SourceWordDeletionFeature", 0, line),
+   m_unrestricted(true)
 {
   std::cerr << "Initializing source word deletion feature.." << std::endl;
 
@@ -27,11 +28,9 @@ m_unrestricted(true)
 
     if (args[0] == "factor") {
       m_factorType = Scan<FactorType>(args[1]);
-    }
-    else if (args[0] == "path") {
+    } else if (args[0] == "path") {
       filename = args[1];
-    }
-    else {
+    } else {
       throw "Unknown argument " + args[0];
     }
   }
@@ -40,19 +39,18 @@ m_unrestricted(true)
   if (filename != "") {
     cerr << "loading source word deletion word list from " << filename << endl;
     if (!Load(filename)) {
-  	UserMessage::Add("Unable to load word list for source word deletion feature from file " + filename);
-	  //return false;
+      UserMessage::Add("Unable to load word list for source word deletion feature from file " + filename);
+      //return false;
     }
   }
 }
 
-bool SourceWordDeletionFeature::Load(const std::string &filePath) 
+bool SourceWordDeletionFeature::Load(const std::string &filePath)
 {
   ifstream inFile(filePath.c_str());
-  if (!inFile)
-  {
-      cerr << "could not open file " << filePath << endl;
-      return false;
+  if (!inFile) {
+    cerr << "could not open file " << filePath << endl;
+    return false;
   }
 
   std::string line;
@@ -67,23 +65,23 @@ bool SourceWordDeletionFeature::Load(const std::string &filePath)
 }
 
 void SourceWordDeletionFeature::Evaluate(const Phrase &source
-  	  	  	  	  	  , const TargetPhrase &targetPhrase
-                      , ScoreComponentCollection &scoreBreakdown
-                      , ScoreComponentCollection &estimatedFutureScore) const
+    , const TargetPhrase &targetPhrase
+    , ScoreComponentCollection &scoreBreakdown
+    , ScoreComponentCollection &estimatedFutureScore) const
 {
   const AlignmentInfo &alignmentInfo = targetPhrase.GetAlignTerm();
   ComputeFeatures(source, targetPhrase, &scoreBreakdown, alignmentInfo);
 }
 
 void SourceWordDeletionFeature::ComputeFeatures(const Phrase &source,
-  	  	  	  	  	  	  	  	  	  	  	  	const TargetPhrase& targetPhrase,
-		                   	 	 	 	 	 	ScoreComponentCollection* accumulator,
-		                   	 	 	 	 	 	const AlignmentInfo &alignmentInfo) const
+    const TargetPhrase& targetPhrase,
+    ScoreComponentCollection* accumulator,
+    const AlignmentInfo &alignmentInfo) const
 {
   // handle special case: unknown words (they have no word alignment)
-	size_t targetLength = targetPhrase.GetSize();
-	size_t sourceLength = source.GetSize();
-	if (targetLength == 1 && sourceLength == 1 && !alignmentInfo.GetSize()) return;
+  size_t targetLength = targetPhrase.GetSize();
+  size_t sourceLength = source.GetSize();
+  if (targetLength == 1 && sourceLength == 1 && !alignmentInfo.GetSize()) return;
 
   // flag aligned words
   bool aligned[16];
@@ -92,22 +90,21 @@ void SourceWordDeletionFeature::ComputeFeatures(const Phrase &source,
     aligned[i] = false;
   for (AlignmentInfo::const_iterator alignmentPoint = alignmentInfo.begin(); alignmentPoint != alignmentInfo.end(); alignmentPoint++)
     aligned[ alignmentPoint->first ] = true;
-      
+
   // process unaligned source words
   for(size_t i=0; i<sourceLength; i++) {
     if (!aligned[i]) {
-    	const Word &w = source.GetWord(i);
-    	if (!w.IsNonTerminal()) {
-    		const StringPiece word = w.GetFactor(m_factorType)->GetString();
-    		if (word != "<s>" && word != "</s>") {
-    			if (!m_unrestricted && FindStringPiece(m_vocab, word ) == m_vocab.end()) {
-    				accumulator->PlusEquals(this, StringPiece("OTHER"),1);
-    			}
-    			else {
-    			  accumulator->PlusEquals(this,word,1);
-    			}
-    		}
-    	}
+      const Word &w = source.GetWord(i);
+      if (!w.IsNonTerminal()) {
+        const StringPiece word = w.GetFactor(m_factorType)->GetString();
+        if (word != "<s>" && word != "</s>") {
+          if (!m_unrestricted && FindStringPiece(m_vocab, word ) == m_vocab.end()) {
+            accumulator->PlusEquals(this, StringPiece("OTHER"),1);
+          } else {
+            accumulator->PlusEquals(this,word,1);
+          }
+        }
+      }
     }
   }
 }
diff --git a/moses/FF/SourceWordDeletionFeature.h b/moses/FF/SourceWordDeletionFeature.h
index 1bf6323be..7a25ee6e1 100644
--- a/moses/FF/SourceWordDeletionFeature.h
+++ b/moses/FF/SourceWordDeletionFeature.h
@@ -13,7 +13,8 @@ namespace Moses
 
 /** Sets the features for source word deletion
  */
-class SourceWordDeletionFeature : public StatelessFeatureFunction {
+class SourceWordDeletionFeature : public StatelessFeatureFunction
+{
 private:
   boost::unordered_set<std::string> m_vocab;
   FactorType m_factorType;
@@ -21,18 +22,18 @@ private:
 
 public:
   SourceWordDeletionFeature(const std::string &line);
-      
+
   bool Load(const std::string &filePath);
 
   virtual void Evaluate(const Phrase &source
-	  	  	  	  	  , const TargetPhrase &targetPhrase
-                      , ScoreComponentCollection &scoreBreakdown
-                      , ScoreComponentCollection &estimatedFutureScore) const;
+                        , const TargetPhrase &targetPhrase
+                        , ScoreComponentCollection &scoreBreakdown
+                        , ScoreComponentCollection &estimatedFutureScore) const;
 
   void ComputeFeatures(const Phrase &source,
-	  	  	  	  	   const TargetPhrase& targetPhrase,
-		  	           ScoreComponentCollection* accumulator, 
-		  	           const AlignmentInfo &alignmentInfo) const;
+                       const TargetPhrase& targetPhrase,
+                       ScoreComponentCollection* accumulator,
+                       const AlignmentInfo &alignmentInfo) const;
 };
 
 }
diff --git a/moses/FF/StatefulFeatureFunction.cpp b/moses/FF/StatefulFeatureFunction.cpp
index a97846311..0aeeed62c 100644
--- a/moses/FF/StatefulFeatureFunction.cpp
+++ b/moses/FF/StatefulFeatureFunction.cpp
@@ -4,13 +4,13 @@ namespace Moses
 {
 
 StatefulFeatureFunction::StatefulFeatureFunction(const std::string& description, const std::string &line)
-: FeatureFunction(description, line)
+  : FeatureFunction(description, line)
 {
   m_statefulFFs.push_back(this);
 }
 
 StatefulFeatureFunction::StatefulFeatureFunction(const std::string& description, size_t numScoreComponents, const std::string &line)
-: FeatureFunction(description,numScoreComponents, line)
+  : FeatureFunction(description,numScoreComponents, line)
 {
   m_statefulFFs.push_back(this);
 }
diff --git a/moses/FF/StatefulFeatureFunction.h b/moses/FF/StatefulFeatureFunction.h
index d2721d4ae..fc5cd4faf 100644
--- a/moses/FF/StatefulFeatureFunction.h
+++ b/moses/FF/StatefulFeatureFunction.h
@@ -6,7 +6,7 @@ namespace Moses
 {
 
 /** base class for all stateful feature functions.
- * eg. LM, distortion penalty 
+ * eg. LM, distortion penalty
  */
 class StatefulFeatureFunction: public FeatureFunction
 {
@@ -14,7 +14,9 @@ class StatefulFeatureFunction: public FeatureFunction
   static std::vector<const StatefulFeatureFunction*> m_statefulFFs;
 
 public:
-  static const std::vector<const StatefulFeatureFunction*>& GetStatefulFeatureFunctions() {return m_statefulFFs;}
+  static const std::vector<const StatefulFeatureFunction*>& GetStatefulFeatureFunctions() {
+    return m_statefulFFs;
+  }
 
   StatefulFeatureFunction(const std::string& description, const std::string &line);
   StatefulFeatureFunction(const std::string& description, size_t numScoreComponents, const std::string &line);
@@ -39,8 +41,9 @@ public:
   //! return the state associated with the empty hypothesis for a given sentence
   virtual const FFState* EmptyHypothesisState(const InputType &input) const = 0;
 
-  bool IsStateless() const
-  { return false; }
+  bool IsStateless() const {
+    return false;
+  }
 
 };
 
diff --git a/moses/FF/StatelessFeatureFunction.cpp b/moses/FF/StatelessFeatureFunction.cpp
index 1c5e604de..278a90c54 100644
--- a/moses/FF/StatelessFeatureFunction.cpp
+++ b/moses/FF/StatelessFeatureFunction.cpp
@@ -4,13 +4,13 @@ namespace Moses
 {
 
 StatelessFeatureFunction::StatelessFeatureFunction(const std::string& description, const std::string &line)
-:FeatureFunction(description, line)
+  :FeatureFunction(description, line)
 {
   m_statelessFFs.push_back(this);
 }
 
 StatelessFeatureFunction::StatelessFeatureFunction(const std::string& description, size_t numScoreComponents, const std::string &line)
-:FeatureFunction(description, numScoreComponents, line)
+  :FeatureFunction(description, numScoreComponents, line)
 {
   m_statelessFFs.push_back(this);
 }
diff --git a/moses/FF/StatelessFeatureFunction.h b/moses/FF/StatelessFeatureFunction.h
index d8db7f514..3f120a1de 100644
--- a/moses/FF/StatelessFeatureFunction.h
+++ b/moses/FF/StatelessFeatureFunction.h
@@ -14,7 +14,9 @@ class StatelessFeatureFunction: public FeatureFunction
   static std::vector<const StatelessFeatureFunction*> m_statelessFFs;
 
 public:
-  static const std::vector<const StatelessFeatureFunction*>& GetStatelessFeatureFunctions() {return m_statelessFFs;}
+  static const std::vector<const StatelessFeatureFunction*>& GetStatelessFeatureFunctions() {
+    return m_statelessFFs;
+  }
 
   StatelessFeatureFunction(const std::string& description, const std::string &line);
   StatelessFeatureFunction(const std::string& description, size_t numScoreComponents, const std::string &line);
@@ -22,7 +24,7 @@ public:
     * This should be implemented for features that apply to phrase-based models.
     **/
   virtual void Evaluate(const PhraseBasedFeatureContext& context,
-  											ScoreComponentCollection* accumulator) const
+                        ScoreComponentCollection* accumulator) const
   {}
 
   /**
@@ -32,8 +34,9 @@ public:
                              ScoreComponentCollection* accumulator) const
   {}
 
-  virtual bool IsStateless() const
-  { return true; }
+  virtual bool IsStateless() const {
+    return true;
+  }
 
 };
 
diff --git a/moses/FF/TargetBigramFeature.cpp b/moses/FF/TargetBigramFeature.cpp
index 441cf9e15..fc30a737f 100644
--- a/moses/FF/TargetBigramFeature.cpp
+++ b/moses/FF/TargetBigramFeature.cpp
@@ -7,15 +7,17 @@
 
 using namespace std;
 
-namespace Moses {
+namespace Moses
+{
 
-int TargetBigramState::Compare(const FFState& other) const {
+int TargetBigramState::Compare(const FFState& other) const
+{
   const TargetBigramState& rhs = dynamic_cast<const TargetBigramState&>(other);
   return Word::Compare(m_word,rhs.m_word);
 }
 
 TargetBigramFeature::TargetBigramFeature(const std::string &line)
-:StatefulFeatureFunction("TargetBigramFeature", 0, line)
+  :StatefulFeatureFunction("TargetBigramFeature", 0, line)
 {
   std::cerr << "Initializing target bigram feature.." << std::endl;
 
@@ -27,7 +29,7 @@ TargetBigramFeature::TargetBigramFeature(const std::string &line)
 
   FactorCollection& factorCollection = FactorCollection::Instance();
   const Factor* bosFactor =
-     factorCollection.AddFactor(Output,m_factorType,BOS_);
+    factorCollection.AddFactor(Output,m_factorType,BOS_);
   m_bos.SetFactor(m_factorType,bosFactor);
 
   const string &filePath = tokens[2];
@@ -35,13 +37,12 @@ TargetBigramFeature::TargetBigramFeature(const std::string &line)
 
 }
 
-bool TargetBigramFeature::Load(const std::string &filePath) 
+bool TargetBigramFeature::Load(const std::string &filePath)
 {
   if (filePath == "*") return true; //allow all
   ifstream inFile(filePath.c_str());
-  if (!inFile)
-  {
-      return false;
+  if (!inFile) {
+    return false;
   }
 
   std::string line;
@@ -87,7 +88,7 @@ FFState* TargetBigramFeature::Evaluate(const Hypothesis& cur_hypo,
     const StringPiece w2 = f2->GetString();
 
     // skip bigrams if they don't belong to a given restricted vocabulary
-    if (m_vocab.size() && 
+    if (m_vocab.size() &&
         (FindStringPiece(m_vocab, w1) == m_vocab.end() || FindStringPiece(m_vocab, w2) == m_vocab.end())) {
       continue;
     }
diff --git a/moses/FF/TargetBigramFeature.h b/moses/FF/TargetBigramFeature.h
index f514f2405..e29eace14 100644
--- a/moses/FF/TargetBigramFeature.h
+++ b/moses/FF/TargetBigramFeature.h
@@ -13,35 +13,38 @@
 namespace Moses
 {
 
-class TargetBigramState : public FFState {
-  public:
-    TargetBigramState(const Word& word): m_word(word) {}
-    const Word& GetWord() const {return m_word;}
-    virtual int Compare(const FFState& other) const;
-
-  private:
-    Word m_word;
+class TargetBigramState : public FFState
+{
+public:
+  TargetBigramState(const Word& word): m_word(word) {}
+  const Word& GetWord() const {
+    return m_word;
+  }
+  virtual int Compare(const FFState& other) const;
+
+private:
+  Word m_word;
 };
 
 /** Sets the features of observed bigrams.
  */
-class TargetBigramFeature : public StatefulFeatureFunction {
+class TargetBigramFeature : public StatefulFeatureFunction
+{
 public:
-	TargetBigramFeature(const std::string &line);
+  TargetBigramFeature(const std::string &line);
 
-	bool Load(const std::string &filePath);
+  bool Load(const std::string &filePath);
 
-	virtual const FFState* EmptyHypothesisState(const InputType &input) const;
+  virtual const FFState* EmptyHypothesisState(const InputType &input) const;
 
-	virtual FFState* Evaluate(const Hypothesis& cur_hypo, const FFState* prev_state,
-	                          ScoreComponentCollection* accumulator) const;
+  virtual FFState* Evaluate(const Hypothesis& cur_hypo, const FFState* prev_state,
+                            ScoreComponentCollection* accumulator) const;
 
   virtual FFState* EvaluateChart( const ChartHypothesis& /* cur_hypo */,
                                   int /* featureID */,
-                                  ScoreComponentCollection* ) const
-                                  {
-                                    abort();
-                                  }
+                                  ScoreComponentCollection* ) const {
+    abort();
+  }
 
 private:
   FactorType m_factorType;
diff --git a/moses/FF/TargetNgramFeature.cpp b/moses/FF/TargetNgramFeature.cpp
index 174fcfa1a..3c36aef0e 100644
--- a/moses/FF/TargetNgramFeature.cpp
+++ b/moses/FF/TargetNgramFeature.cpp
@@ -7,38 +7,38 @@
 
 #include "util/string_piece_hash.hh"
 
-namespace Moses {
+namespace Moses
+{
 
 using namespace std;
 
-int TargetNgramState::Compare(const FFState& other) const {
+int TargetNgramState::Compare(const FFState& other) const
+{
   const TargetNgramState& rhs = dynamic_cast<const TargetNgramState&>(other);
   int result;
   if (m_words.size() == rhs.m_words.size()) {
-        for (size_t i = 0; i < m_words.size(); ++i) {
-                result = Word::Compare(m_words[i],rhs.m_words[i]);
-                if (result != 0) return result;
-        }
+    for (size_t i = 0; i < m_words.size(); ++i) {
+      result = Word::Compare(m_words[i],rhs.m_words[i]);
+      if (result != 0) return result;
+    }
     return 0;
-  }
-  else if (m_words.size() < rhs.m_words.size()) {
-        for (size_t i = 0; i < m_words.size(); ++i) {
-                result = Word::Compare(m_words[i],rhs.m_words[i]);
-                if (result != 0) return result;
-        }
-        return -1;
-  }
-  else {
-        for (size_t i = 0; i < rhs.m_words.size(); ++i) {
-                result = Word::Compare(m_words[i],rhs.m_words[i]);
-                if (result != 0) return result;
-        }
-        return 1;
+  } else if (m_words.size() < rhs.m_words.size()) {
+    for (size_t i = 0; i < m_words.size(); ++i) {
+      result = Word::Compare(m_words[i],rhs.m_words[i]);
+      if (result != 0) return result;
+    }
+    return -1;
+  } else {
+    for (size_t i = 0; i < rhs.m_words.size(); ++i) {
+      result = Word::Compare(m_words[i],rhs.m_words[i]);
+      if (result != 0) return result;
+    }
+    return 1;
   }
 }
 
 TargetNgramFeature::TargetNgramFeature(const std::string &line)
-:StatefulFeatureFunction("TargetNgramFeature", 0, line)
+  :StatefulFeatureFunction("TargetNgramFeature", 0, line)
 {
   std::cerr << "Initializing target ngram feature.." << std::endl;
 
@@ -56,9 +56,8 @@ bool TargetNgramFeature::Load(const std::string &filePath)
 {
   if (filePath == "*") return true; //allow all
   ifstream inFile(filePath.c_str());
-  if (!inFile)
-  {
-      return false;
+  if (!inFile) {
+    return false;
   }
 
   std::string line;
@@ -74,13 +73,13 @@ bool TargetNgramFeature::Load(const std::string &filePath)
 
 const FFState* TargetNgramFeature::EmptyHypothesisState(const InputType &/*input*/) const
 {
-	vector<Word> bos(1,m_bos);
+  vector<Word> bos(1,m_bos);
   return new TargetNgramState(bos);
 }
 
 FFState* TargetNgramFeature::Evaluate(const Hypothesis& cur_hypo,
-                                       const FFState* prev_state,
-                                       ScoreComponentCollection* accumulator) const
+                                      const FFState* prev_state,
+                                      ScoreComponentCollection* accumulator) const
 {
   const TargetNgramState* tnState = static_cast<const TargetNgramState*>(prev_state);
   assert(tnState);
@@ -99,92 +98,92 @@ FFState* TargetNgramFeature::Evaluate(const Hypothesis& cur_hypo,
   if (m_lower_ngrams) smallest_n = 1;
 
   for (size_t n = m_n; n >= smallest_n; --n) { // iterate over ngram size
-  	for (size_t i = 0; i < targetPhrase.GetSize(); ++i) {
+    for (size_t i = 0; i < targetPhrase.GetSize(); ++i) {
 //  		const string& curr_w = targetPhrase.GetWord(i).GetFactor(m_factorType)->GetString();
-  		const StringPiece& curr_w = targetPhrase.GetWord(i).GetString(m_factorType);
-
-  		if (m_vocab.size() && (FindStringPiece(m_vocab, curr_w) == m_vocab.end())) continue; // skip ngrams
-
-  		if (n > 1) {
-  			// can we build an ngram at this position? ("<s> this" --> cannot build 3gram at this position)
-  			size_t pos_in_translation = cur_hypo.GetSize() - targetPhrase.GetSize() + i;
-  			if (pos_in_translation < n - 2) continue; // need at least m_n - 1 words
-
-  			// how many words needed from previous state?
-  			int from_prev_state = n - (i+1);
-  			skip = false;
-  			if (from_prev_state > 0) {
-  				if (prev_words.size() < from_prev_state) {
-  					// context is too short, make new state from previous state and target phrase
-  					vector<Word> new_prev_words;
-  					for (size_t i = 0; i < prev_words.size(); ++i)
-  						new_prev_words.push_back(prev_words[i]);
-        	  for (size_t i = 0; i < targetPhrase.GetSize(); ++i)
-        	  	new_prev_words.push_back(targetPhrase.GetWord(i));
-        	 	return new TargetNgramState(new_prev_words);
-  				}
-
-  				// add words from previous state
-  				for (size_t j = prev_words.size()-from_prev_state; j < prev_words.size() && !skip; ++j)
-  					appendNgram(prev_words[j], skip, curr_ngram);
+      const StringPiece& curr_w = targetPhrase.GetWord(i).GetString(m_factorType);
+
+      if (m_vocab.size() && (FindStringPiece(m_vocab, curr_w) == m_vocab.end())) continue; // skip ngrams
+
+      if (n > 1) {
+        // can we build an ngram at this position? ("<s> this" --> cannot build 3gram at this position)
+        size_t pos_in_translation = cur_hypo.GetSize() - targetPhrase.GetSize() + i;
+        if (pos_in_translation < n - 2) continue; // need at least m_n - 1 words
+
+        // how many words needed from previous state?
+        int from_prev_state = n - (i+1);
+        skip = false;
+        if (from_prev_state > 0) {
+          if (prev_words.size() < from_prev_state) {
+            // context is too short, make new state from previous state and target phrase
+            vector<Word> new_prev_words;
+            for (size_t i = 0; i < prev_words.size(); ++i)
+              new_prev_words.push_back(prev_words[i]);
+            for (size_t i = 0; i < targetPhrase.GetSize(); ++i)
+              new_prev_words.push_back(targetPhrase.GetWord(i));
+            return new TargetNgramState(new_prev_words);
+          }
+
+          // add words from previous state
+          for (size_t j = prev_words.size()-from_prev_state; j < prev_words.size() && !skip; ++j)
+            appendNgram(prev_words[j], skip, curr_ngram);
         }
 
-  			// add words from current target phrase
-  			int start = i - n + 1; // add m_n-1 previous words
-  			if (start < 0) start = 0; // or less
-  			for (size_t j = start; j < i && !skip; ++j)
-  				appendNgram(targetPhrase.GetWord(j), skip, curr_ngram);
+        // add words from current target phrase
+        int start = i - n + 1; // add m_n-1 previous words
+        if (start < 0) start = 0; // or less
+        for (size_t j = start; j < i && !skip; ++j)
+          appendNgram(targetPhrase.GetWord(j), skip, curr_ngram);
       }
 
-  		if (!skip) {
-  			curr_ngram << curr_w;
-  			accumulator->PlusEquals(this,curr_ngram.str(),1);
+      if (!skip) {
+        curr_ngram << curr_w;
+        accumulator->PlusEquals(this,curr_ngram.str(),1);
       }
-  		curr_ngram.str("");
-  	}
+      curr_ngram.str("");
+    }
   }
 
   if (cur_hypo.GetWordsBitmap().IsComplete()) {
-  	for (size_t n = m_n; n >= smallest_n; --n) {
-  		stringstream last_ngram;
-  		skip = false;
-  		for (size_t i = cur_hypo.GetSize() - n + 1; i <  cur_hypo.GetSize() && !skip; ++i)
-  			appendNgram(cur_hypo.GetWord(i), skip, last_ngram);
-
-  		if (n > 1 && !skip) {
-  			last_ngram << EOS_;
-  			accumulator->PlusEquals(this, last_ngram.str(), 1);
-    	}
-  	}
-  	return NULL;
+    for (size_t n = m_n; n >= smallest_n; --n) {
+      stringstream last_ngram;
+      skip = false;
+      for (size_t i = cur_hypo.GetSize() - n + 1; i <  cur_hypo.GetSize() && !skip; ++i)
+        appendNgram(cur_hypo.GetWord(i), skip, last_ngram);
+
+      if (n > 1 && !skip) {
+        last_ngram << EOS_;
+        accumulator->PlusEquals(this, last_ngram.str(), 1);
+      }
+    }
+    return NULL;
   }
 
   // prepare new state
   vector<Word> new_prev_words;
   if (targetPhrase.GetSize() >= m_n-1) {
-  	// take subset of target words
-  	for (size_t i = targetPhrase.GetSize() - m_n + 1; i < targetPhrase.GetSize(); ++i)
-  		new_prev_words.push_back(targetPhrase.GetWord(i));
-  }
-  else {
-  	// take words from previous state and from target phrase
-  	int from_prev_state = m_n - 1 - targetPhrase.GetSize();
-  	for (size_t i = prev_words.size()-from_prev_state; i < prev_words.size(); ++i)
-  		new_prev_words.push_back(prev_words[i]);
-  	for (size_t i = 0; i < targetPhrase.GetSize(); ++i)
-  		new_prev_words.push_back(targetPhrase.GetWord(i));
+    // take subset of target words
+    for (size_t i = targetPhrase.GetSize() - m_n + 1; i < targetPhrase.GetSize(); ++i)
+      new_prev_words.push_back(targetPhrase.GetWord(i));
+  } else {
+    // take words from previous state and from target phrase
+    int from_prev_state = m_n - 1 - targetPhrase.GetSize();
+    for (size_t i = prev_words.size()-from_prev_state; i < prev_words.size(); ++i)
+      new_prev_words.push_back(prev_words[i]);
+    for (size_t i = 0; i < targetPhrase.GetSize(); ++i)
+      new_prev_words.push_back(targetPhrase.GetWord(i));
   }
   return new TargetNgramState(new_prev_words);
 }
 
-void TargetNgramFeature::appendNgram(const Word& word, bool& skip, stringstream &ngram) const {
+void TargetNgramFeature::appendNgram(const Word& word, bool& skip, stringstream &ngram) const
+{
 //	const string& w = word.GetFactor(m_factorType)->GetString();
-	const StringPiece& w = word.GetString(m_factorType);
-	if (m_vocab.size() && (FindStringPiece(m_vocab, w) == m_vocab.end())) skip = true;
-	else {
-		ngram << w;
-		ngram << ":";
-	}
+  const StringPiece& w = word.GetString(m_factorType);
+  if (m_vocab.size() && (FindStringPiece(m_vocab, w) == m_vocab.end())) skip = true;
+  else {
+    ngram << w;
+    ngram << ":";
+  }
 }
 
 FFState* TargetNgramFeature::EvaluateChart(const ChartHypothesis& cur_hypo, int featureId, ScoreComponentCollection* accumulator) const
@@ -205,159 +204,149 @@ FFState* TargetNgramFeature::EvaluateChart(const ChartHypothesis& cur_hypo, int
   bool onlyTerminals = true;
   bool prev_is_NT = false;
   size_t prev_subPhraseLength = 0;
-  for (size_t phrasePos = 0; phrasePos < cur_hypo.GetCurrTargetPhrase().GetSize(); phrasePos++)
-  {
+  for (size_t phrasePos = 0; phrasePos < cur_hypo.GetCurrTargetPhrase().GetSize(); phrasePos++) {
     // consult rule for either word or non-terminal
     const Word &word = cur_hypo.GetCurrTargetPhrase().GetWord(phrasePos);
 //    cerr << "word: " << word << endl;
 
     // regular word
     if (!word.IsNonTerminal()) {
-    	contextFactor.push_back(&word);
-    	prev_is_NT = false;
+      contextFactor.push_back(&word);
+      prev_is_NT = false;
 
       if (phrasePos==0)
-      	makePrefix = true;
+        makePrefix = true;
       if (phrasePos==cur_hypo.GetCurrTargetPhrase().GetSize()-1 || prev_is_NT)
-      	makeSuffix = true;
-      
+        makeSuffix = true;
+
       // beginning/end of sentence symbol <s>,</s>?
       StringPiece factorZero = word.GetString(0);
       if (factorZero.compare("<s>") == 0)
-      	prefixTerminals++;
+        prefixTerminals++;
       // end of sentence symbol </s>?
       else if (factorZero.compare("</s>") == 0)
-      	suffixTerminals++;
+        suffixTerminals++;
       // everything else
       else {
-      	stringstream ngram;
-      	ngram << m_baseName;
-      	if (m_factorType == 0)
-      		ngram << factorZero;
-      	else
-      		ngram << word.GetString(m_factorType);
-      	accumulator->SparsePlusEquals(ngram.str(), 1);
-
-      	if (collectForPrefix)
-      		prefixTerminals++;
-      	else
-      		suffixTerminals++;
+        stringstream ngram;
+        ngram << m_baseName;
+        if (m_factorType == 0)
+          ngram << factorZero;
+        else
+          ngram << word.GetString(m_factorType);
+        accumulator->SparsePlusEquals(ngram.str(), 1);
+
+        if (collectForPrefix)
+          prefixTerminals++;
+        else
+          suffixTerminals++;
       }
     }
 
     // non-terminal, add phrase from underlying hypothesis
-    else if (m_n > 1)
-    {
+    else if (m_n > 1) {
       // look up underlying hypothesis
       size_t nonTermIndex = nonTermIndexMap[phrasePos];
       const ChartHypothesis *prevHypo = cur_hypo.GetPrevHypo(nonTermIndex);
 
       const TargetNgramChartState* prevState =
-      		static_cast<const TargetNgramChartState*>(prevHypo->GetFFState(featureId));
+        static_cast<const TargetNgramChartState*>(prevHypo->GetFFState(featureId));
       size_t subPhraseLength = prevState->GetNumTargetTerminals();
 
       // special case: rule starts with non-terminal
       if (phrasePos == 0) {
-      	if (subPhraseLength == 1) {
-      		makePrefix = true;
-      		++prefixTerminals;
+        if (subPhraseLength == 1) {
+          makePrefix = true;
+          ++prefixTerminals;
 
-      		const Word &word = prevState->GetSuffix().GetWord(0);
+          const Word &word = prevState->GetSuffix().GetWord(0);
 //      		cerr << "NT0 --> : " << word << endl;
-      		contextFactor.push_back(&word);
-      	}
-      	else {
-      		onlyTerminals = false;
-      		collectForPrefix = false;
-      		int suffixPos = prevState->GetSuffix().GetSize() - (m_n-1);
-      		if (suffixPos < 0) suffixPos = 0; // push all words if less than order
-      		for(;(size_t)suffixPos < prevState->GetSuffix().GetSize(); suffixPos++)
-      		{
-      			const Word &word = prevState->GetSuffix().GetWord(suffixPos);
+          contextFactor.push_back(&word);
+        } else {
+          onlyTerminals = false;
+          collectForPrefix = false;
+          int suffixPos = prevState->GetSuffix().GetSize() - (m_n-1);
+          if (suffixPos < 0) suffixPos = 0; // push all words if less than order
+          for(; (size_t)suffixPos < prevState->GetSuffix().GetSize(); suffixPos++) {
+            const Word &word = prevState->GetSuffix().GetWord(suffixPos);
 //      			cerr << "NT0 --> : " << word << endl;
-      			contextFactor.push_back(&word);
-      		}
-      	}
+            contextFactor.push_back(&word);
+          }
+        }
       }
 
       // internal non-terminal
-      else
-      {
-      	// push its prefix
-      	for(size_t prefixPos = 0; prefixPos < m_n-1
-              && prefixPos < subPhraseLength; prefixPos++)
-        {
+      else {
+        // push its prefix
+        for(size_t prefixPos = 0; prefixPos < m_n-1
+            && prefixPos < subPhraseLength; prefixPos++) {
           const Word &word = prevState->GetPrefix().GetWord(prefixPos);
 //          cerr << "NT --> " << word << endl;
           contextFactor.push_back(&word);
         }
 
-      	if (subPhraseLength==1) {
-      		if (collectForPrefix)
-      			++prefixTerminals;
-      		else
-      			++suffixTerminals;
-
-      		if (phrasePos == cur_hypo.GetCurrTargetPhrase().GetSize()-1)
-      			makeSuffix = true;
-      	}
-      	else {
-      		onlyTerminals = false;
-      		collectForPrefix = true;
-
-      		// check if something follows this NT
-      		bool wordFollowing = (phrasePos < cur_hypo.GetCurrTargetPhrase().GetSize() - 1)? true : false;
-
-      		// check if we are dealing with a large sub-phrase
-      		if (wordFollowing && subPhraseLength > m_n - 1)
-      		{
-      			// clear up pending ngrams
-      			MakePrefixNgrams(contextFactor, accumulator, prefixTerminals);
-      			contextFactor.clear();
-      			makePrefix = false;
-      			makeSuffix = true;
-      			collectForPrefix = false;
-      			prefixTerminals = 0;
-      			suffixTerminals = 0;
-
-      			// push its suffix
-      			size_t remainingWords = (remainingWords > m_n-1) ? m_n-1 : subPhraseLength - (m_n-1);
-      			for(size_t suffixPos = 0; suffixPos < prevState->GetSuffix().GetSize(); suffixPos++) {
-      				const Word &word = prevState->GetSuffix().GetWord(suffixPos);
+        if (subPhraseLength==1) {
+          if (collectForPrefix)
+            ++prefixTerminals;
+          else
+            ++suffixTerminals;
+
+          if (phrasePos == cur_hypo.GetCurrTargetPhrase().GetSize()-1)
+            makeSuffix = true;
+        } else {
+          onlyTerminals = false;
+          collectForPrefix = true;
+
+          // check if something follows this NT
+          bool wordFollowing = (phrasePos < cur_hypo.GetCurrTargetPhrase().GetSize() - 1)? true : false;
+
+          // check if we are dealing with a large sub-phrase
+          if (wordFollowing && subPhraseLength > m_n - 1) {
+            // clear up pending ngrams
+            MakePrefixNgrams(contextFactor, accumulator, prefixTerminals);
+            contextFactor.clear();
+            makePrefix = false;
+            makeSuffix = true;
+            collectForPrefix = false;
+            prefixTerminals = 0;
+            suffixTerminals = 0;
+
+            // push its suffix
+            size_t remainingWords = (remainingWords > m_n-1) ? m_n-1 : subPhraseLength - (m_n-1);
+            for(size_t suffixPos = 0; suffixPos < prevState->GetSuffix().GetSize(); suffixPos++) {
+              const Word &word = prevState->GetSuffix().GetWord(suffixPos);
 //      				cerr << "NT --> : " << word << endl;
-      				contextFactor.push_back(&word);
-      			}
-      		}
-      		// subphrase can be used as suffix and as prefix for the next part
-      		else if (wordFollowing && subPhraseLength == m_n - 1)
-      		{
-      			// clear up pending ngrams
-      			MakePrefixNgrams(contextFactor, accumulator, prefixTerminals);
-      			makePrefix = false;
-      			makeSuffix = true;
-      			collectForPrefix = false;
-      			prefixTerminals = 0;
-      			suffixTerminals = 0;
-      		}
-      		else if (prev_is_NT && prev_subPhraseLength > 1 && subPhraseLength > 1) {
-      			// two NTs in a row: make transition
-      			MakePrefixNgrams(contextFactor, accumulator, 1, m_n-2);
-      			MakeSuffixNgrams(contextFactor, accumulator, 1, m_n-2);
-      			makePrefix = false;
-      			makeSuffix = false;
-      			collectForPrefix = false;
-      			prefixTerminals = 0;
-      			suffixTerminals = 0;
-		
-      			// remove duplicates
-      			stringstream curr_ngram;
-      			curr_ngram << m_baseName;
-      			curr_ngram << (*contextFactor[m_n-2]).GetString(m_factorType);
-      			curr_ngram << ":";
-      			curr_ngram << (*contextFactor[m_n-1]).GetString(m_factorType);
-      			accumulator->SparseMinusEquals(curr_ngram.str(),1);
-      		}
-      	}
+              contextFactor.push_back(&word);
+            }
+          }
+          // subphrase can be used as suffix and as prefix for the next part
+          else if (wordFollowing && subPhraseLength == m_n - 1) {
+            // clear up pending ngrams
+            MakePrefixNgrams(contextFactor, accumulator, prefixTerminals);
+            makePrefix = false;
+            makeSuffix = true;
+            collectForPrefix = false;
+            prefixTerminals = 0;
+            suffixTerminals = 0;
+          } else if (prev_is_NT && prev_subPhraseLength > 1 && subPhraseLength > 1) {
+            // two NTs in a row: make transition
+            MakePrefixNgrams(contextFactor, accumulator, 1, m_n-2);
+            MakeSuffixNgrams(contextFactor, accumulator, 1, m_n-2);
+            makePrefix = false;
+            makeSuffix = false;
+            collectForPrefix = false;
+            prefixTerminals = 0;
+            suffixTerminals = 0;
+
+            // remove duplicates
+            stringstream curr_ngram;
+            curr_ngram << m_baseName;
+            curr_ngram << (*contextFactor[m_n-2]).GetString(m_factorType);
+            curr_ngram << ":";
+            curr_ngram << (*contextFactor[m_n-1]).GetString(m_factorType);
+            accumulator->SparseMinusEquals(curr_ngram.str(),1);
+          }
+        }
       }
       prev_is_NT = true;
       prev_subPhraseLength = subPhraseLength;
@@ -366,25 +355,24 @@ FFState* TargetNgramFeature::EvaluateChart(const ChartHypothesis& cur_hypo, int
 
   if (m_n > 1) {
     if (onlyTerminals) {
-    	MakePrefixNgrams(contextFactor, accumulator, prefixTerminals-1);
-    }
-    else {
+      MakePrefixNgrams(contextFactor, accumulator, prefixTerminals-1);
+    } else {
       if (makePrefix)
-      	MakePrefixNgrams(contextFactor, accumulator, prefixTerminals);
+        MakePrefixNgrams(contextFactor, accumulator, prefixTerminals);
       if (makeSuffix)
-      	MakeSuffixNgrams(contextFactor, accumulator, suffixTerminals);
+        MakeSuffixNgrams(contextFactor, accumulator, suffixTerminals);
 
       // remove duplicates
       size_t size = contextFactor.size();
       if (makePrefix && makeSuffix && (size <= m_n)) {
-      	stringstream curr_ngram;
-      	curr_ngram << m_baseName;
-      	for (size_t i = 0; i < size; ++i) {
-      		curr_ngram << (*contextFactor[i]).GetString(m_factorType);
-      		if (i < size-1)
-      			curr_ngram << ":";
-      	}
-      	accumulator->SparseMinusEquals(curr_ngram.str(), 1);
+        stringstream curr_ngram;
+        curr_ngram << m_baseName;
+        for (size_t i = 0; i < size; ++i) {
+          curr_ngram << (*contextFactor[i]).GetString(m_factorType);
+          if (i < size-1)
+            curr_ngram << ":";
+        }
+        accumulator->SparseMinusEquals(curr_ngram.str(), 1);
       }
     }
   }
@@ -393,22 +381,23 @@ FFState* TargetNgramFeature::EvaluateChart(const ChartHypothesis& cur_hypo, int
   return new TargetNgramChartState(cur_hypo, featureId, m_n);
 }
 
-void TargetNgramFeature::MakePrefixNgrams(std::vector<const Word*> &contextFactor, ScoreComponentCollection* accumulator, size_t numberOfStartPos, size_t offset) const {
-	stringstream ngram;
-	size_t size = contextFactor.size();
+void TargetNgramFeature::MakePrefixNgrams(std::vector<const Word*> &contextFactor, ScoreComponentCollection* accumulator, size_t numberOfStartPos, size_t offset) const
+{
+  stringstream ngram;
+  size_t size = contextFactor.size();
   for (size_t k = 0; k < numberOfStartPos; ++k) {
     size_t max_end = (size < m_n+k+offset)? size: m_n+k+offset;
     for (size_t end_pos = 1+k+offset; end_pos < max_end; ++end_pos) {
       ngram << m_baseName;
-    	for (size_t i=k+offset; i <= end_pos; ++i) {
-      	if (i > k+offset)
-      		ngram << ":";
+      for (size_t i=k+offset; i <= end_pos; ++i) {
+        if (i > k+offset)
+          ngram << ":";
         StringPiece factorZero = (*contextFactor[i]).GetString(0);
         if (m_factorType == 0 || factorZero.compare("<s>") == 0 || factorZero.compare("</s>") == 0)
-      		ngram << factorZero;
-      	else
-      		ngram << (*contextFactor[i]).GetString(m_factorType);
-      	const Word w = *contextFactor[i];
+          ngram << factorZero;
+        else
+          ngram << (*contextFactor[i]).GetString(m_factorType);
+        const Word w = *contextFactor[i];
       }
 //      cerr << "p-ngram: " << ngram.str() << endl;
       accumulator->SparsePlusEquals(ngram.str(), 1);
@@ -417,21 +406,22 @@ void TargetNgramFeature::MakePrefixNgrams(std::vector<const Word*> &contextFacto
   }
 }
 
-void TargetNgramFeature::MakeSuffixNgrams(std::vector<const Word*> &contextFactor, ScoreComponentCollection* accumulator, size_t numberOfEndPos, size_t offset) const {
-	stringstream ngram;
+void TargetNgramFeature::MakeSuffixNgrams(std::vector<const Word*> &contextFactor, ScoreComponentCollection* accumulator, size_t numberOfEndPos, size_t offset) const
+{
+  stringstream ngram;
   for (size_t k = 0; k < numberOfEndPos; ++k) {
     size_t end_pos = contextFactor.size()-1-k-offset;
     for (int start_pos=end_pos-1; (start_pos >= 0) && (end_pos-start_pos < m_n); --start_pos) {
-    	ngram << m_baseName;
-    	for (size_t j=start_pos; j <= end_pos; ++j){
-    		StringPiece factorZero = (*contextFactor[j]).GetString(0);
-    		if (m_factorType == 0 || factorZero.compare("<s>") == 0 || factorZero.compare("</s>") == 0)
-    			ngram << factorZero;
-    		else
-    			ngram << (*contextFactor[j]).GetString(m_factorType);
-    		if (j < end_pos)
-      		ngram << ":";
-    	}
+      ngram << m_baseName;
+      for (size_t j=start_pos; j <= end_pos; ++j) {
+        StringPiece factorZero = (*contextFactor[j]).GetString(0);
+        if (m_factorType == 0 || factorZero.compare("<s>") == 0 || factorZero.compare("</s>") == 0)
+          ngram << factorZero;
+        else
+          ngram << (*contextFactor[j]).GetString(m_factorType);
+        if (j < end_pos)
+          ngram << ":";
+      }
 //      cerr << "s-ngram: " << ngram.str() << endl;
       accumulator->SparsePlusEquals(ngram.str(), 1);
       ngram.str("");
diff --git a/moses/FF/TargetNgramFeature.h b/moses/FF/TargetNgramFeature.h
index b50391d43..8001f2f87 100644
--- a/moses/FF/TargetNgramFeature.h
+++ b/moses/FF/TargetNgramFeature.h
@@ -16,14 +16,17 @@
 namespace Moses
 {
 
-class TargetNgramState : public FFState {
-  public:
-		TargetNgramState(std::vector<Word> &words): m_words(words) {}
-		const std::vector<Word> GetWords() const {return m_words;}
-    virtual int Compare(const FFState& other) const;
-
-  private:
-    std::vector<Word> m_words;
+class TargetNgramState : public FFState
+{
+public:
+  TargetNgramState(std::vector<Word> &words): m_words(words) {}
+  const std::vector<Word> GetWords() const {
+    return m_words;
+  }
+  virtual int Compare(const FFState& other) const;
+
+private:
+  std::vector<Word> m_words;
 };
 
 class TargetNgramChartState : public FFState
@@ -39,8 +42,7 @@ private:
    * \param ret prefix string
    * \param size maximum size (typically max lm context window)
    */
-  size_t CalcPrefix(const ChartHypothesis &hypo, const int featureId, Phrase &ret, size_t size) const
-  {
+  size_t CalcPrefix(const ChartHypothesis &hypo, const int featureId, Phrase &ret, size_t size) const {
     const TargetPhrase &target = hypo.GetCurrTargetPhrase();
     const AlignmentInfo::NonTermIndexMap &nonTermIndexMap =
       target.GetAlignNonTerm().GetNonTermIndexMap();
@@ -76,9 +78,8 @@ private:
    * \param ret suffix phrase
    * \param size maximum size of suffix
    */
-  size_t CalcSuffix(const ChartHypothesis &hypo, int featureId, Phrase &ret, size_t size) const
-  {
-  	size_t prefixSize = m_contextPrefix.GetSize();
+  size_t CalcSuffix(const ChartHypothesis &hypo, int featureId, Phrase &ret, size_t size) const {
+    size_t prefixSize = m_contextPrefix.GetSize();
     assert(prefixSize <= m_numTargetTerminals);
 
     // special handling for small hypotheses
@@ -98,9 +99,9 @@ private:
     }
     // construct suffix analogous to prefix
     else {
-    	const TargetPhrase targetPhrase = hypo.GetCurrTargetPhrase();
+      const TargetPhrase targetPhrase = hypo.GetCurrTargetPhrase();
       const AlignmentInfo::NonTermIndexMap &nonTermIndexMap =
-      		targetPhrase.GetAlignTerm().GetNonTermIndexMap();
+        targetPhrase.GetAlignTerm().GetNonTermIndexMap();
       for (int pos = (int) targetPhrase.GetSize() - 1; pos >= 0 ; --pos) {
         const Word &word = targetPhrase.GetWord(pos);
 
@@ -108,8 +109,7 @@ private:
           size_t nonTermInd = nonTermIndexMap[pos];
           const ChartHypothesis *prevHypo = hypo.GetPrevHypo(nonTermInd);
           size = static_cast<const TargetNgramChartState*>(prevHypo->GetFFState(featureId))->CalcSuffix(*prevHypo, featureId, ret, size);
-        }
-        else {
+        } else {
           ret.PrependWord(word);
           size--;
         }
@@ -124,9 +124,8 @@ private:
 
 public:
   TargetNgramChartState(const ChartHypothesis &hypo, int featureId, size_t order)
-      :m_contextPrefix(order - 1),
-      m_contextSuffix(order - 1)
-  {
+    :m_contextPrefix(order - 1),
+     m_contextSuffix(order - 1) {
     m_numTargetTerminals = hypo.GetCurrTargetPhrase().GetNumTerminals();
     const WordsRange range = hypo.GetCurrSourceRange();
     m_startPos = range.GetStartPos();
@@ -159,15 +158,13 @@ public:
       static_cast<const TargetNgramChartState &>( o );
 
     // prefix
-    if (m_startPos > 0) // not for "<s> ..."
-    {
+    if (m_startPos > 0) { // not for "<s> ..."
       int ret = GetPrefix().Compare(other.GetPrefix());
       if (ret != 0)
         return ret;
     }
 
-    if (m_endPos < m_inputSize - 1)// not for "... </s>"
-    {
+    if (m_endPos < m_inputSize - 1) { // not for "... </s>"
       int ret = GetSuffix().Compare(other.GetSuffix());
       if (ret != 0)
         return ret;
@@ -178,34 +175,35 @@ public:
 
 /** Sets the features of observed ngrams.
  */
-class TargetNgramFeature : public StatefulFeatureFunction {
+class TargetNgramFeature : public StatefulFeatureFunction
+{
 public:
   TargetNgramFeature(const std::string &line);
 
-	bool Load(const std::string &filePath);
+  bool Load(const std::string &filePath);
 
-	virtual const FFState* EmptyHypothesisState(const InputType &input) const;
+  virtual const FFState* EmptyHypothesisState(const InputType &input) const;
 
-	virtual FFState* Evaluate(const Hypothesis& cur_hypo, const FFState* prev_state,
-	                          ScoreComponentCollection* accumulator) const;
+  virtual FFState* Evaluate(const Hypothesis& cur_hypo, const FFState* prev_state,
+                            ScoreComponentCollection* accumulator) const;
 
   virtual FFState* EvaluateChart(const ChartHypothesis& cur_hypo, int featureId,
-                                  ScoreComponentCollection* accumulator) const;
+                                 ScoreComponentCollection* accumulator) const;
 
 private:
   FactorType m_factorType;
   Word m_bos;
   boost::unordered_set<std::string> m_vocab;
-	size_t m_n;
-	bool m_lower_ngrams;
+  size_t m_n;
+  bool m_lower_ngrams;
 
-	std::string m_baseName;
+  std::string m_baseName;
 
-	void appendNgram(const Word& word, bool& skip, std::stringstream& ngram) const;
-	void MakePrefixNgrams(std::vector<const Word*> &contextFactor, ScoreComponentCollection* accumulator,
-			      size_t numberOfStartPos = 1, size_t offset = 0) const;
-	void MakeSuffixNgrams(std::vector<const Word*> &contextFactor, ScoreComponentCollection* accumulator,
-			      size_t numberOfEndPos = 1, size_t offset = 0) const;
+  void appendNgram(const Word& word, bool& skip, std::stringstream& ngram) const;
+  void MakePrefixNgrams(std::vector<const Word*> &contextFactor, ScoreComponentCollection* accumulator,
+                        size_t numberOfStartPos = 1, size_t offset = 0) const;
+  void MakeSuffixNgrams(std::vector<const Word*> &contextFactor, ScoreComponentCollection* accumulator,
+                        size_t numberOfEndPos = 1, size_t offset = 0) const;
 };
 
 }
diff --git a/moses/FF/TargetWordInsertionFeature.cpp b/moses/FF/TargetWordInsertionFeature.cpp
index 386e943be..f20a652e4 100644
--- a/moses/FF/TargetWordInsertionFeature.cpp
+++ b/moses/FF/TargetWordInsertionFeature.cpp
@@ -9,13 +9,14 @@
 #include "moses/UserMessage.h"
 #include "util/string_piece_hash.hh"
 
-namespace Moses {
+namespace Moses
+{
 
 using namespace std;
 
 TargetWordInsertionFeature::TargetWordInsertionFeature(const std::string &line)
-:StatelessFeatureFunction("TargetWordInsertionFeature", 0, line),
-m_unrestricted(true)
+  :StatelessFeatureFunction("TargetWordInsertionFeature", 0, line),
+   m_unrestricted(true)
 {
   std::cerr << "Initializing target word insertion feature.." << std::endl;
 
@@ -26,11 +27,9 @@ m_unrestricted(true)
 
     if (args[0] == "factor") {
       m_factorType = Scan<FactorType>(args[1]);
-    }
-    else if (args[0] == "path") {
+    } else if (args[0] == "path") {
       filename = args[1];
-    }
-    else {
+    } else {
       throw "Unknown argument " + args[0];
     }
   }
@@ -46,13 +45,12 @@ m_unrestricted(true)
 
 }
 
-bool TargetWordInsertionFeature::Load(const std::string &filePath) 
+bool TargetWordInsertionFeature::Load(const std::string &filePath)
 {
   ifstream inFile(filePath.c_str());
-  if (!inFile)
-  {
-      cerr << "could not open file " << filePath << endl;
-      return false;
+  if (!inFile) {
+    cerr << "could not open file " << filePath << endl;
+    return false;
   }
 
   std::string line;
@@ -67,18 +65,18 @@ bool TargetWordInsertionFeature::Load(const std::string &filePath)
 }
 
 void TargetWordInsertionFeature::Evaluate(const Phrase &source
-  	  	  	  	  	  , const TargetPhrase &targetPhrase
-                      , ScoreComponentCollection &scoreBreakdown
-                      , ScoreComponentCollection &estimatedFutureScore) const
+    , const TargetPhrase &targetPhrase
+    , ScoreComponentCollection &scoreBreakdown
+    , ScoreComponentCollection &estimatedFutureScore) const
 {
   const AlignmentInfo &alignmentInfo = targetPhrase.GetAlignTerm();
   ComputeFeatures(source, targetPhrase, &scoreBreakdown, alignmentInfo);
 }
 
 void TargetWordInsertionFeature::ComputeFeatures(const Phrase &source,
-												 const TargetPhrase& targetPhrase,
-    											 ScoreComponentCollection* accumulator,
-    											 const AlignmentInfo &alignmentInfo) const
+    const TargetPhrase& targetPhrase,
+    ScoreComponentCollection* accumulator,
+    const AlignmentInfo &alignmentInfo) const
 {
   // handle special case: unknown words (they have no word alignment)
   size_t targetLength = targetPhrase.GetSize();
@@ -100,15 +98,14 @@ void TargetWordInsertionFeature::ComputeFeatures(const Phrase &source,
     if (!aligned[i]) {
       Word w = targetPhrase.GetWord(i);
       if (!w.IsNonTerminal()) {
-    	const StringPiece word = w.GetFactor(m_factorType)->GetString();
-    	if (word != "<s>" && word != "</s>") {
-      	  if (!m_unrestricted && FindStringPiece(m_vocab, word ) == m_vocab.end()) {
-      		accumulator->PlusEquals(this,StringPiece("OTHER"),1);
-      	  }
-      	  else {
-      		accumulator->PlusEquals(this,word,1);
-      	  }
-    	}
+        const StringPiece word = w.GetFactor(m_factorType)->GetString();
+        if (word != "<s>" && word != "</s>") {
+          if (!m_unrestricted && FindStringPiece(m_vocab, word ) == m_vocab.end()) {
+            accumulator->PlusEquals(this,StringPiece("OTHER"),1);
+          } else {
+            accumulator->PlusEquals(this,word,1);
+          }
+        }
       }
     }
   }
diff --git a/moses/FF/TargetWordInsertionFeature.h b/moses/FF/TargetWordInsertionFeature.h
index aabc4cffc..50f7e5f88 100644
--- a/moses/FF/TargetWordInsertionFeature.h
+++ b/moses/FF/TargetWordInsertionFeature.h
@@ -13,7 +13,8 @@ namespace Moses
 
 /** Sets the features for length of source phrase, target phrase, both.
  */
-class TargetWordInsertionFeature : public StatelessFeatureFunction {
+class TargetWordInsertionFeature : public StatelessFeatureFunction
+{
 private:
   boost::unordered_set<std::string> m_vocab;
   FactorType m_factorType;
@@ -21,18 +22,18 @@ private:
 
 public:
   TargetWordInsertionFeature(const std::string &line);
-      
+
   bool Load(const std::string &filePath);
 
   virtual void Evaluate(const Phrase &source
-	  	  	  	  	  , const TargetPhrase &targetPhrase
-                      , ScoreComponentCollection &scoreBreakdown
-                      , ScoreComponentCollection &estimatedFutureScore) const;
+                        , const TargetPhrase &targetPhrase
+                        , ScoreComponentCollection &scoreBreakdown
+                        , ScoreComponentCollection &estimatedFutureScore) const;
 
   void ComputeFeatures(const Phrase &source,
-	  	  	  	  	   const TargetPhrase& targetPhrase,
-		           	   ScoreComponentCollection* accumulator,
-		           	   const AlignmentInfo &alignmentInfo) const;
+                       const TargetPhrase& targetPhrase,
+                       ScoreComponentCollection* accumulator,
+                       const AlignmentInfo &alignmentInfo) const;
 
 };
 
diff --git a/moses/FF/UnknownWordPenaltyProducer.h b/moses/FF/UnknownWordPenaltyProducer.h
index b60967746..200033cfc 100644
--- a/moses/FF/UnknownWordPenaltyProducer.h
+++ b/moses/FF/UnknownWordPenaltyProducer.h
@@ -14,10 +14,9 @@ class WordsRange;
 class UnknownWordPenaltyProducer : public StatelessFeatureFunction
 {
 public:
-	UnknownWordPenaltyProducer(const std::string &line)
-  : StatelessFeatureFunction("UnknownWordPenalty",1, line)
-  {
-	  m_tuneable = false;
+  UnknownWordPenaltyProducer(const std::string &line)
+    : StatelessFeatureFunction("UnknownWordPenalty",1, line) {
+    m_tuneable = false;
   }
 
 };
diff --git a/moses/FF/WordPenaltyProducer.cpp b/moses/FF/WordPenaltyProducer.cpp
index ba97852e4..1dc425742 100644
--- a/moses/FF/WordPenaltyProducer.cpp
+++ b/moses/FF/WordPenaltyProducer.cpp
@@ -5,9 +5,9 @@
 namespace Moses
 {
 void WordPenaltyProducer::Evaluate(const Phrase &source
-  	  	  	  	  	  , const TargetPhrase &targetPhrase
-  	  	  	  	  	  , ScoreComponentCollection &scoreBreakdown
-  	  	  	  	  	  , ScoreComponentCollection &estimatedFutureScore) const
+                                   , const TargetPhrase &targetPhrase
+                                   , ScoreComponentCollection &scoreBreakdown
+                                   , ScoreComponentCollection &estimatedFutureScore) const
 {
   float score = - (float) targetPhrase.GetNumTerminals();
   scoreBreakdown.Assign(this, score);
diff --git a/moses/FF/WordPenaltyProducer.h b/moses/FF/WordPenaltyProducer.h
index fc824dd84..1892c459c 100644
--- a/moses/FF/WordPenaltyProducer.h
+++ b/moses/FF/WordPenaltyProducer.h
@@ -14,12 +14,12 @@ class ScoreComponentCollection;
 class WordPenaltyProducer : public StatelessFeatureFunction
 {
 public:
-	WordPenaltyProducer(const std::string &line) : StatelessFeatureFunction("WordPenalty",1, line) {}
+  WordPenaltyProducer(const std::string &line) : StatelessFeatureFunction("WordPenalty",1, line) {}
 
   virtual void Evaluate(const Phrase &source
-	  	  	  	  	  , const TargetPhrase &targetPhrase
-                      , ScoreComponentCollection &scoreBreakdown
-                      , ScoreComponentCollection &estimatedFutureScore) const;
+                        , const TargetPhrase &targetPhrase
+                        , ScoreComponentCollection &scoreBreakdown
+                        , ScoreComponentCollection &estimatedFutureScore) const;
 
 };
 
diff --git a/moses/FF/WordTranslationFeature.cpp b/moses/FF/WordTranslationFeature.cpp
index 2648ac9f1..3f282609f 100644
--- a/moses/FF/WordTranslationFeature.cpp
+++ b/moses/FF/WordTranslationFeature.cpp
@@ -10,18 +10,19 @@
 #include "moses/UserMessage.h"
 #include "util/string_piece_hash.hh"
 
-namespace Moses {
+namespace Moses
+{
 
 using namespace std;
 
 WordTranslationFeature::WordTranslationFeature(const std::string &line)
-:StatelessFeatureFunction("WordTranslationFeature", 0, line)
-,m_unrestricted(true)
-,m_simple(true)
-,m_sourceContext(false)
-,m_targetContext(false)
-,m_ignorePunctuation(false)
-,m_domainTrigger(false)
+  :StatelessFeatureFunction("WordTranslationFeature", 0, line)
+  ,m_unrestricted(true)
+  ,m_simple(true)
+  ,m_sourceContext(false)
+  ,m_targetContext(false)
+  ,m_ignorePunctuation(false)
+  ,m_domainTrigger(false)
 {
   std::cerr << "Initializing word translation feature.. " << endl;
 
@@ -34,35 +35,25 @@ WordTranslationFeature::WordTranslationFeature(const std::string &line)
 
     if (args[0] == "input-factor") {
       m_factorTypeSource = Scan<FactorType>(args[1]);
-    }
-    else if (args[0] == "output-factor") {
+    } else if (args[0] == "output-factor") {
       m_factorTypeTarget = Scan<FactorType>(args[1]);
-    }
-    else if (args[0] == "simple") {
+    } else if (args[0] == "simple") {
       m_simple = Scan<bool>(args[1]);
-    }
-    else if (args[0] == "source-context") {
+    } else if (args[0] == "source-context") {
       m_sourceContext = Scan<bool>(args[1]);
-    }
-    else if (args[0] == "target-context") {
+    } else if (args[0] == "target-context") {
       m_targetContext = Scan<bool>(args[1]);
-    }
-    else if (args[0] == "ignore-punctuation") {
+    } else if (args[0] == "ignore-punctuation") {
       m_ignorePunctuation = Scan<bool>(args[1]);
-    }
-    else if (args[0] == "domain-trigger") {
+    } else if (args[0] == "domain-trigger") {
       m_domainTrigger = Scan<bool>(args[1]);
-    }
-    else if (args[0] == "texttype") {
+    } else if (args[0] == "texttype") {
       texttype = args[1];
-    }
-    else if (args[0] == "source-path") {
+    } else if (args[0] == "source-path") {
       filenameSource = args[1];
-    }
-    else if (args[0] == "target-path") {
+    } else if (args[0] == "target-path") {
       filenameTarget = args[1];
-    }
-    else {
+    } else {
       throw "Unknown argument " + args[0];
     }
   }
@@ -108,65 +99,62 @@ WordTranslationFeature::WordTranslationFeature(const std::string &line)
 
 }
 
-bool WordTranslationFeature::Load(const std::string &filePathSource, const std::string &filePathTarget) 
+bool WordTranslationFeature::Load(const std::string &filePathSource, const std::string &filePathTarget)
 {
   if (m_domainTrigger) {
     // domain trigger terms for each input document
     ifstream inFileSource(filePathSource.c_str());
-    if (!inFileSource){
+    if (!inFileSource) {
       cerr << "could not open file " << filePathSource << endl;
       return false;
     }
-    
+
     std::string line;
     while (getline(inFileSource, line)) {
-	  m_vocabDomain.resize(m_vocabDomain.size() + 1);
-  	  vector<string> termVector;
-	  boost::split(termVector, line, boost::is_any_of("\t "));
-	  for (size_t i=0; i < termVector.size(); ++i)
-	    m_vocabDomain.back().insert(termVector[i]);
+      m_vocabDomain.resize(m_vocabDomain.size() + 1);
+      vector<string> termVector;
+      boost::split(termVector, line, boost::is_any_of("\t "));
+      for (size_t i=0; i < termVector.size(); ++i)
+        m_vocabDomain.back().insert(termVector[i]);
     }
-    
+
     inFileSource.close();
-  }
-  else {
+  } else {
     // restricted source word vocabulary
     ifstream inFileSource(filePathSource.c_str());
-    if (!inFileSource)
-      {
-	cerr << "could not open file " << filePathSource << endl;
-	return false;
-      }
-    
+    if (!inFileSource) {
+      cerr << "could not open file " << filePathSource << endl;
+      return false;
+    }
+
     std::string line;
     while (getline(inFileSource, line)) {
       m_vocabSource.insert(line);
     }
-    
+
     inFileSource.close();
-    
+
     // restricted target word vocabulary
     ifstream inFileTarget(filePathTarget.c_str());
-    if (!inFileTarget)
-      {
-	cerr << "could not open file " << filePathTarget << endl;
-	return false;
-      }
-    
+    if (!inFileTarget) {
+      cerr << "could not open file " << filePathTarget << endl;
+      return false;
+    }
+
     while (getline(inFileTarget, line)) {
       m_vocabTarget.insert(line);
     }
-    
+
     inFileTarget.close();
-    
+
     m_unrestricted = false;
   }
   return true;
 }
 
 void WordTranslationFeature::Evaluate
-                     (const PhraseBasedFeatureContext& context,
-                      ScoreComponentCollection* accumulator) const
+(const PhraseBasedFeatureContext& context,
+ ScoreComponentCollection* accumulator) const
 {
   const Sentence& input = static_cast<const Sentence&>(context.GetSource());
   const TargetPhrase& targetPhrase = context.GetTargetPhrase();
@@ -188,7 +176,7 @@ void WordTranslationFeature::Evaluate
       char firstChar = sourceWord[0];
       CharHash::const_iterator charIterator = m_punctuationHash.find( firstChar );
       if(charIterator != m_punctuationHash.end())
-      	continue;
+        continue;
       firstChar = targetWord[0];
       charIterator = m_punctuationHash.find( firstChar );
       if(charIterator != m_punctuationHash.end())
@@ -197,9 +185,9 @@ void WordTranslationFeature::Evaluate
 
     if (!m_unrestricted) {
       if (FindStringPiece(m_vocabSource, sourceWord) == m_vocabSource.end())
-	sourceWord = "OTHER";
+        sourceWord = "OTHER";
       if (FindStringPiece(m_vocabTarget, targetWord) == m_vocabTarget.end())
-	targetWord = "OTHER";
+        targetWord = "OTHER";
     }
 
     if (m_simple) {
@@ -215,174 +203,169 @@ void WordTranslationFeature::Evaluate
       const bool use_topicid = input.GetUseTopicId();
       const bool use_topicid_prob = input.GetUseTopicIdAndProb();
       if (use_topicid || use_topicid_prob) {
-	if(use_topicid) {
-	  // use topicid as trigger
-	  const long topicid = input.GetTopicId();
-	  stringstream feature;
-	  feature << m_description << "_";
-	  if (topicid == -1)
-	    feature << "unk";
-	  else
-	    feature << topicid;
-
-	  feature << "_";
-	  feature << sourceWord;
-	  feature << "~";
-	  feature << targetWord;
-	  accumulator->SparsePlusEquals(feature.str(), 1);
-	}
-	else {
-	  // use topic probabilities
-	  const vector<string> &topicid_prob = *(input.GetTopicIdAndProb());
-	  if (atol(topicid_prob[0].c_str()) == -1) {
-	    stringstream feature;
-	    feature << m_description << "_unk_";
-	    feature << sourceWord;
-	    feature << "~";
-	    feature << targetWord;
-	    accumulator->SparsePlusEquals(feature.str(), 1);
-	  }
-	  else {
-	    for (size_t i=0; i+1 < topicid_prob.size(); i+=2) {
-	      stringstream feature;
-	      feature << m_description << "_";
-	      feature << topicid_prob[i];
-	      feature << "_";
-	      feature << sourceWord;
-	      feature << "~";
-	      feature << targetWord;
-	      accumulator->SparsePlusEquals(feature.str(), atof((topicid_prob[i+1]).c_str()));
-	    }
-	  }
-	}
-      }
-      else {
-	// range over domain trigger words (keywords)
-	const long docid = input.GetDocumentId();
-	for (boost::unordered_set<std::string>::const_iterator p = m_vocabDomain[docid].begin(); p != m_vocabDomain[docid].end(); ++p) {
-	  string sourceTrigger = *p;
-	  stringstream feature;
-	  feature << m_description << "_";
-	  feature << sourceTrigger;
-	  feature << "_";
-	  feature << sourceWord;
-	  feature << "~";
-	  feature << targetWord;
-	  accumulator->SparsePlusEquals(feature.str(), 1);
-	}
+        if(use_topicid) {
+          // use topicid as trigger
+          const long topicid = input.GetTopicId();
+          stringstream feature;
+          feature << m_description << "_";
+          if (topicid == -1)
+            feature << "unk";
+          else
+            feature << topicid;
+
+          feature << "_";
+          feature << sourceWord;
+          feature << "~";
+          feature << targetWord;
+          accumulator->SparsePlusEquals(feature.str(), 1);
+        } else {
+          // use topic probabilities
+          const vector<string> &topicid_prob = *(input.GetTopicIdAndProb());
+          if (atol(topicid_prob[0].c_str()) == -1) {
+            stringstream feature;
+            feature << m_description << "_unk_";
+            feature << sourceWord;
+            feature << "~";
+            feature << targetWord;
+            accumulator->SparsePlusEquals(feature.str(), 1);
+          } else {
+            for (size_t i=0; i+1 < topicid_prob.size(); i+=2) {
+              stringstream feature;
+              feature << m_description << "_";
+              feature << topicid_prob[i];
+              feature << "_";
+              feature << sourceWord;
+              feature << "~";
+              feature << targetWord;
+              accumulator->SparsePlusEquals(feature.str(), atof((topicid_prob[i+1]).c_str()));
+            }
+          }
+        }
+      } else {
+        // range over domain trigger words (keywords)
+        const long docid = input.GetDocumentId();
+        for (boost::unordered_set<std::string>::const_iterator p = m_vocabDomain[docid].begin(); p != m_vocabDomain[docid].end(); ++p) {
+          string sourceTrigger = *p;
+          stringstream feature;
+          feature << m_description << "_";
+          feature << sourceTrigger;
+          feature << "_";
+          feature << sourceWord;
+          feature << "~";
+          feature << targetWord;
+          accumulator->SparsePlusEquals(feature.str(), 1);
+        }
       }
     }
     if (m_sourceContext) {
       size_t globalSourceIndex = context.GetTranslationOption().GetStartPos() + sourceIndex;
       if (!m_domainTrigger && globalSourceIndex == 0) {
-	// add <s> trigger feature for source
-	stringstream feature;
-	feature << m_description << "_";
-	feature << "<s>,";
-	feature << sourceWord;
-	feature << "~";
-	feature << targetWord;
-	accumulator->SparsePlusEquals(feature.str(), 1);
+        // add <s> trigger feature for source
+        stringstream feature;
+        feature << m_description << "_";
+        feature << "<s>,";
+        feature << sourceWord;
+        feature << "~";
+        feature << targetWord;
+        accumulator->SparsePlusEquals(feature.str(), 1);
       }
 
       // range over source words to get context
       for(size_t contextIndex = 0; contextIndex < input.GetSize(); contextIndex++ ) {
-	if (contextIndex == globalSourceIndex) continue;
-	StringPiece sourceTrigger = input.GetWord(contextIndex).GetFactor(m_factorTypeSource)->GetString();
-	if (m_ignorePunctuation) {
-	  // check if trigger is punctuation
-	  char firstChar = sourceTrigger[0];
-	  CharHash::const_iterator charIterator = m_punctuationHash.find( firstChar );
-	  if(charIterator != m_punctuationHash.end())
-	    continue;
-	}
-
-	const long docid = input.GetDocumentId();
-	bool sourceTriggerExists = false;
-	if (m_domainTrigger)
-	  sourceTriggerExists = FindStringPiece(m_vocabDomain[docid], sourceTrigger ) != m_vocabDomain[docid].end();
-	else if (!m_unrestricted)
-	  sourceTriggerExists = FindStringPiece(m_vocabSource, sourceTrigger ) != m_vocabSource.end();
-
-	if (m_domainTrigger) {
-	  if (sourceTriggerExists) {
-	    stringstream feature;
-	    feature << m_description << "_";
-	    feature << sourceTrigger;
-	    feature << "_";
-	    feature << sourceWord;
-	    feature << "~";
-	    feature << targetWord;
-	    accumulator->SparsePlusEquals(feature.str(), 1);
-	  }
-	}
-	else if (m_unrestricted || sourceTriggerExists) {
-	  stringstream feature;
-	  feature << m_description << "_";
-	  if (contextIndex < globalSourceIndex) {
-	    feature << sourceTrigger;
-	    feature << ",";
-	    feature << sourceWord;
-	  }
-	  else {
-	    feature << sourceWord;
-	    feature << ",";
-	    feature << sourceTrigger;
-	  }
-	  feature << "~";
-	  feature << targetWord;
-	  accumulator->SparsePlusEquals(feature.str(), 1);
-	}
+        if (contextIndex == globalSourceIndex) continue;
+        StringPiece sourceTrigger = input.GetWord(contextIndex).GetFactor(m_factorTypeSource)->GetString();
+        if (m_ignorePunctuation) {
+          // check if trigger is punctuation
+          char firstChar = sourceTrigger[0];
+          CharHash::const_iterator charIterator = m_punctuationHash.find( firstChar );
+          if(charIterator != m_punctuationHash.end())
+            continue;
+        }
+
+        const long docid = input.GetDocumentId();
+        bool sourceTriggerExists = false;
+        if (m_domainTrigger)
+          sourceTriggerExists = FindStringPiece(m_vocabDomain[docid], sourceTrigger ) != m_vocabDomain[docid].end();
+        else if (!m_unrestricted)
+          sourceTriggerExists = FindStringPiece(m_vocabSource, sourceTrigger ) != m_vocabSource.end();
+
+        if (m_domainTrigger) {
+          if (sourceTriggerExists) {
+            stringstream feature;
+            feature << m_description << "_";
+            feature << sourceTrigger;
+            feature << "_";
+            feature << sourceWord;
+            feature << "~";
+            feature << targetWord;
+            accumulator->SparsePlusEquals(feature.str(), 1);
+          }
+        } else if (m_unrestricted || sourceTriggerExists) {
+          stringstream feature;
+          feature << m_description << "_";
+          if (contextIndex < globalSourceIndex) {
+            feature << sourceTrigger;
+            feature << ",";
+            feature << sourceWord;
+          } else {
+            feature << sourceWord;
+            feature << ",";
+            feature << sourceTrigger;
+          }
+          feature << "~";
+          feature << targetWord;
+          accumulator->SparsePlusEquals(feature.str(), 1);
+        }
       }
     }
     if (m_targetContext) {
       throw runtime_error("Can't use target words outside current translation option in a stateless feature");
       /*
-    	size_t globalTargetIndex = cur_hypo.GetCurrTargetWordsRange().GetStartPos() + targetIndex;
-    	if (globalTargetIndex == 0) {
-    		// add <s> trigger feature for source
-    		stringstream feature;
-    		feature << "wt_";
-    		feature << sourceWord;
-    		feature << "~";
-    		feature << "<s>,";
-    		feature << targetWord;
-    		accumulator->SparsePlusEquals(feature.str(), 1);
-    	}
-
-    	// range over target words (up to current position) to get context
-    	for(size_t contextIndex = 0; contextIndex < globalTargetIndex; contextIndex++ ) {
-    		string targetTrigger = cur_hypo.GetWord(contextIndex).GetFactor(m_factorTypeTarget)->GetString();
-    		if (m_ignorePunctuation) {
-    			// check if trigger is punctuation
-    			char firstChar = targetTrigger.at(0);
-    			CharHash::const_iterator charIterator = m_punctuationHash.find( firstChar );
-    			if(charIterator != m_punctuationHash.end())
-    				continue;
-    		}
-
-    		bool targetTriggerExists = false;
-    		if (!m_unrestricted)
-    			targetTriggerExists = m_vocabTarget.find( targetTrigger ) != m_vocabTarget.end();
-
-    		if (m_unrestricted || targetTriggerExists) {
-    			stringstream feature;
-    			feature << "wt_";
-    			feature << sourceWord;
-    			feature << "~";
-    			feature << targetTrigger;
-    			feature << ",";
-    			feature << targetWord;
-    			accumulator->SparsePlusEquals(feature.str(), 1);
-    		}
-    	}*/
+      size_t globalTargetIndex = cur_hypo.GetCurrTargetWordsRange().GetStartPos() + targetIndex;
+      if (globalTargetIndex == 0) {
+      	// add <s> trigger feature for source
+      	stringstream feature;
+      	feature << "wt_";
+      	feature << sourceWord;
+      	feature << "~";
+      	feature << "<s>,";
+      	feature << targetWord;
+      	accumulator->SparsePlusEquals(feature.str(), 1);
+      }
+
+      // range over target words (up to current position) to get context
+      for(size_t contextIndex = 0; contextIndex < globalTargetIndex; contextIndex++ ) {
+      	string targetTrigger = cur_hypo.GetWord(contextIndex).GetFactor(m_factorTypeTarget)->GetString();
+      	if (m_ignorePunctuation) {
+      		// check if trigger is punctuation
+      		char firstChar = targetTrigger.at(0);
+      		CharHash::const_iterator charIterator = m_punctuationHash.find( firstChar );
+      		if(charIterator != m_punctuationHash.end())
+      			continue;
+      	}
+
+      	bool targetTriggerExists = false;
+      	if (!m_unrestricted)
+      		targetTriggerExists = m_vocabTarget.find( targetTrigger ) != m_vocabTarget.end();
+
+      	if (m_unrestricted || targetTriggerExists) {
+      		stringstream feature;
+      		feature << "wt_";
+      		feature << sourceWord;
+      		feature << "~";
+      		feature << targetTrigger;
+      		feature << ",";
+      		feature << targetWord;
+      		accumulator->SparsePlusEquals(feature.str(), 1);
+      	}
+      }*/
     }
   }
 }
 
 void WordTranslationFeature::EvaluateChart(
-            const ChartBasedFeatureContext& context,
-    				ScoreComponentCollection* accumulator) const
+  const ChartBasedFeatureContext& context,
+  ScoreComponentCollection* accumulator) const
 {
   const TargetPhrase& targetPhrase = context.GetTargetPhrase();
   const AlignmentInfo &alignmentInfo = targetPhrase.GetAlignTerm();
@@ -403,7 +386,7 @@ void WordTranslationFeature::EvaluateChart(
       char firstChar = sourceWord[0];
       CharHash::const_iterator charIterator = m_punctuationHash.find( firstChar );
       if(charIterator != m_punctuationHash.end())
-      	continue;
+        continue;
       firstChar = targetWord[0];
       charIterator = m_punctuationHash.find( firstChar );
       if(charIterator != m_punctuationHash.end())
@@ -411,118 +394,118 @@ void WordTranslationFeature::EvaluateChart(
     }
 
     if (!m_unrestricted) {
-    	if (FindStringPiece(m_vocabSource, sourceWord) == m_vocabSource.end())
-    		sourceWord = "OTHER";
-    	if (FindStringPiece(m_vocabTarget, targetWord) == m_vocabTarget.end())
-    		targetWord = "OTHER";
+      if (FindStringPiece(m_vocabSource, sourceWord) == m_vocabSource.end())
+        sourceWord = "OTHER";
+      if (FindStringPiece(m_vocabTarget, targetWord) == m_vocabTarget.end())
+        targetWord = "OTHER";
     }
-    
+
     if (m_simple) {
-    	// construct feature name
-    	stringstream featureName;
-    	featureName << m_description << "_";
-    	//featureName << ((sourceExists||m_unrestricted) ? sourceWord : "OTHER");
-    	featureName << sourceWord;
-    	featureName << "~";
-    	//featureName << ((targetExists||m_unrestricted) ? targetWord : "OTHER");
-    	featureName << targetWord;
-    	accumulator->SparsePlusEquals(featureName.str(), 1);
+      // construct feature name
+      stringstream featureName;
+      featureName << m_description << "_";
+      //featureName << ((sourceExists||m_unrestricted) ? sourceWord : "OTHER");
+      featureName << sourceWord;
+      featureName << "~";
+      //featureName << ((targetExists||m_unrestricted) ? targetWord : "OTHER");
+      featureName << targetWord;
+      accumulator->SparsePlusEquals(featureName.str(), 1);
     }
-  /*  if (m_sourceContext) {
-    	size_t globalSourceIndex = cur_hypo.GetCurrSourceRange().GetStartPos() + sourceIndex;
-    	if (globalSourceIndex == 0) {
-    		// add <s> trigger feature for source
-    		stringstream feature;
-    		feature << "wt_";
-    		feature << "<s>,";
-    		feature << sourceWord;
-    		feature << "~";
-    		feature << targetWord;
-    		accumulator->SparsePlusEquals(feature.str(), 1);
-    		cerr << feature.str() << endl;
-    	}
-
-    	// range over source words to get context
-    	for(size_t contextIndex = 0; contextIndex < input.GetSize(); contextIndex++ ) {
-    		if (contextIndex == globalSourceIndex) continue;
-    		string sourceTrigger = input.GetWord(contextIndex).GetFactor(m_factorTypeSource)->GetString();
-    		if (m_ignorePunctuation) {
-    			// check if trigger is punctuation
-    			char firstChar = sourceTrigger.at(0);
-    			CharHash::const_iterator charIterator = m_punctuationHash.find( firstChar );
-    			if(charIterator != m_punctuationHash.end())
-    				continue;
-    		}
-
-    		bool sourceTriggerExists = false;
-    		if (!m_unrestricted)
-    			sourceTriggerExists = m_vocabSource.find( sourceTrigger ) != m_vocabSource.end();
-
-    		if (m_unrestricted || sourceTriggerExists) {
-    			stringstream feature;
-    			feature << "wt_";
-    			if (contextIndex < globalSourceIndex) {
-    				feature << sourceTrigger;
-    				feature << ",";
-    				feature << sourceWord;
-	    		}
-    			else {
-    				feature << sourceWord;
-    				feature << ",";
-    				feature << sourceTrigger;
-	    		}
-    			feature << "~";
-    			feature << targetWord;
-    			accumulator->SparsePlusEquals(feature.str(), 1);
-    			cerr << feature.str() << endl;
-    		}
-    	}
-	}*/
-/*    if (m_targetContext) {
-    	size_t globalTargetIndex = 0; // TODO
-//    	size_t globalTargetIndex = cur_hypo.GetCurrTargetWordsRange().GetStartPos() + targetIndex;
-    	if (globalTargetIndex == 0) {
-    		// add <s> trigger feature for source
-    		stringstream feature;
-    		feature << "wt_";
-    		feature << sourceWord;
-    		feature << "~";
-    		feature << "<s>,";
-    		feature << targetWord;
-    		accumulator->SparsePlusEquals(feature.str(), 1);
-    		cerr << feature.str() << endl;
-    	}
-
-    	// range over target words (up to current position) to get context
-    	for(size_t contextIndex = 0; contextIndex < globalTargetIndex; contextIndex++ ) {
-    		Phrase outputPhrase = cur_hypo.GetOutputPhrase();
-    		string targetTrigger = outputPhrase.GetWord(contextIndex).GetFactor(m_factorTypeTarget)->GetString();
-    		//string targetTrigger = cur_hypo.GetWord(contextIndex).GetFactor(m_factorTypeTarget)->GetString();
-    		if (m_ignorePunctuation) {
-    			// check if trigger is punctuation
-    			char firstChar = targetTrigger.at(0);
-    			CharHash::const_iterator charIterator = m_punctuationHash.find( firstChar );
-    			if(charIterator != m_punctuationHash.end())
-    				continue;
-    		}
-
-    		bool targetTriggerExists = false;
-    		if (!m_unrestricted)
-    			targetTriggerExists = m_vocabTarget.find( targetTrigger ) != m_vocabTarget.end();
-
-    		if (m_unrestricted || targetTriggerExists) {
-    			stringstream feature;
-    			feature << "wt_";
-    			feature << sourceWord;
-    			feature << "~";
-    			feature << targetTrigger;
-    			feature << ",";
-    			feature << targetWord;
-    			accumulator->SparsePlusEquals(feature.str(), 1);
-    			cerr << feature.str() << endl;
-    		}
-    	}
+    /*  if (m_sourceContext) {
+      	size_t globalSourceIndex = cur_hypo.GetCurrSourceRange().GetStartPos() + sourceIndex;
+      	if (globalSourceIndex == 0) {
+      		// add <s> trigger feature for source
+      		stringstream feature;
+      		feature << "wt_";
+      		feature << "<s>,";
+      		feature << sourceWord;
+      		feature << "~";
+      		feature << targetWord;
+      		accumulator->SparsePlusEquals(feature.str(), 1);
+      		cerr << feature.str() << endl;
+      	}
+
+      	// range over source words to get context
+      	for(size_t contextIndex = 0; contextIndex < input.GetSize(); contextIndex++ ) {
+      		if (contextIndex == globalSourceIndex) continue;
+      		string sourceTrigger = input.GetWord(contextIndex).GetFactor(m_factorTypeSource)->GetString();
+      		if (m_ignorePunctuation) {
+      			// check if trigger is punctuation
+      			char firstChar = sourceTrigger.at(0);
+      			CharHash::const_iterator charIterator = m_punctuationHash.find( firstChar );
+      			if(charIterator != m_punctuationHash.end())
+      				continue;
+      		}
+
+      		bool sourceTriggerExists = false;
+      		if (!m_unrestricted)
+      			sourceTriggerExists = m_vocabSource.find( sourceTrigger ) != m_vocabSource.end();
+
+      		if (m_unrestricted || sourceTriggerExists) {
+      			stringstream feature;
+      			feature << "wt_";
+      			if (contextIndex < globalSourceIndex) {
+      				feature << sourceTrigger;
+      				feature << ",";
+      				feature << sourceWord;
+        		}
+      			else {
+      				feature << sourceWord;
+      				feature << ",";
+      				feature << sourceTrigger;
+        		}
+      			feature << "~";
+      			feature << targetWord;
+      			accumulator->SparsePlusEquals(feature.str(), 1);
+      			cerr << feature.str() << endl;
+      		}
+      	}
     }*/
+    /*    if (m_targetContext) {
+        	size_t globalTargetIndex = 0; // TODO
+    //    	size_t globalTargetIndex = cur_hypo.GetCurrTargetWordsRange().GetStartPos() + targetIndex;
+        	if (globalTargetIndex == 0) {
+        		// add <s> trigger feature for source
+        		stringstream feature;
+        		feature << "wt_";
+        		feature << sourceWord;
+        		feature << "~";
+        		feature << "<s>,";
+        		feature << targetWord;
+        		accumulator->SparsePlusEquals(feature.str(), 1);
+        		cerr << feature.str() << endl;
+        	}
+
+        	// range over target words (up to current position) to get context
+        	for(size_t contextIndex = 0; contextIndex < globalTargetIndex; contextIndex++ ) {
+        		Phrase outputPhrase = cur_hypo.GetOutputPhrase();
+        		string targetTrigger = outputPhrase.GetWord(contextIndex).GetFactor(m_factorTypeTarget)->GetString();
+        		//string targetTrigger = cur_hypo.GetWord(contextIndex).GetFactor(m_factorTypeTarget)->GetString();
+        		if (m_ignorePunctuation) {
+        			// check if trigger is punctuation
+        			char firstChar = targetTrigger.at(0);
+        			CharHash::const_iterator charIterator = m_punctuationHash.find( firstChar );
+        			if(charIterator != m_punctuationHash.end())
+        				continue;
+        		}
+
+        		bool targetTriggerExists = false;
+        		if (!m_unrestricted)
+        			targetTriggerExists = m_vocabTarget.find( targetTrigger ) != m_vocabTarget.end();
+
+        		if (m_unrestricted || targetTriggerExists) {
+        			stringstream feature;
+        			feature << "wt_";
+        			feature << sourceWord;
+        			feature << "~";
+        			feature << targetTrigger;
+        			feature << ",";
+        			feature << targetWord;
+        			accumulator->SparsePlusEquals(feature.str(), 1);
+        			cerr << feature.str() << endl;
+        		}
+        	}
+        }*/
   }
 
 }
diff --git a/moses/FF/WordTranslationFeature.h b/moses/FF/WordTranslationFeature.h
index 3379e8c84..b3a434325 100644
--- a/moses/FF/WordTranslationFeature.h
+++ b/moses/FF/WordTranslationFeature.h
@@ -14,11 +14,12 @@ namespace Moses
 
 /** Sets the features for word translation
  */
-class WordTranslationFeature : public StatelessFeatureFunction {
+class WordTranslationFeature : public StatelessFeatureFunction
+{
 
   typedef std::map< char, short > CharHash;
   typedef std::vector< boost::unordered_set<std::string> > DocumentVector;
-	
+
 private:
   boost::unordered_set<std::string> m_vocabSource;
   boost::unordered_set<std::string> m_vocabTarget;
@@ -32,18 +33,18 @@ private:
   bool m_domainTrigger;
   bool m_ignorePunctuation;
   CharHash m_punctuationHash;
-  
+
 public:
   WordTranslationFeature(const std::string &line);
-  
+
   bool Load(const std::string &filePathSource, const std::string &filePathTarget);
-  
+
   const FFState* EmptyHypothesisState(const InputType &) const {
     return new DummyState();
   }
-  
-  void Evaluate(const PhraseBasedFeatureContext& context,                       
-		ScoreComponentCollection* accumulator) const;
+
+  void Evaluate(const PhraseBasedFeatureContext& context,
+                ScoreComponentCollection* accumulator) const;
 
   void EvaluateChart(const ChartBasedFeatureContext& context,
                      ScoreComponentCollection* accumulator) const;
diff --git a/moses/Factor.h b/moses/Factor.h
index 87e8f8028..f4bb2074d 100644
--- a/moses/Factor.h
+++ b/moses/Factor.h
@@ -34,8 +34,8 @@ namespace Moses
 struct FactorFriend;
 class FactorCollection;
 
-/** Represents a factor (word, POS, etc).  
- * A Factor has a contiguous identifier and string value.  
+/** Represents a factor (word, POS, etc).
+ * A Factor has a contiguous identifier and string value.
  */
 class Factor
 {
@@ -53,10 +53,10 @@ class Factor
   //! protected constructor. only friend class, FactorCollection, is allowed to create Factor objects
   Factor() {}
 
-  // Needed for STL containers.  They'll delegate through FactorFriend, which is never exposed publicly.  
+  // Needed for STL containers.  They'll delegate through FactorFriend, which is never exposed publicly.
   Factor(const Factor &factor) : m_string(factor.m_string), m_id(factor.m_id) {}
 
-  // Not implemented.  Shouldn't be called.  
+  // Not implemented.  Shouldn't be called.
   Factor &operator=(const Factor &factor);
 
 public:
diff --git a/moses/FactorCollection.cpp b/moses/FactorCollection.cpp
index 969bb39d1..5d6eb1c53 100644
--- a/moses/FactorCollection.cpp
+++ b/moses/FactorCollection.cpp
@@ -38,11 +38,12 @@ FactorCollection FactorCollection::s_instance;
 const Factor *FactorCollection::AddFactor(const StringPiece &factorString)
 {
   FactorFriend to_ins;
-  to_ins.in.m_string = factorString; 
+  to_ins.in.m_string = factorString;
   to_ins.in.m_id = m_factorId;
   // If we're threaded, hope a read-only lock is sufficient.
 #ifdef WITH_THREADS
-  { // read=lock scope
+  {
+    // read=lock scope
     boost::shared_lock<boost::shared_mutex> read_lock(m_accessLock);
     Set::const_iterator i = m_set.find(to_ins);
     if (i != m_set.end()) return &i->in;
@@ -52,8 +53,8 @@ const Factor *FactorCollection::AddFactor(const StringPiece &factorString)
   std::pair<Set::iterator, bool> ret(m_set.insert(to_ins));
   if (ret.second) {
     ret.first->in.m_string.set(
-        memcpy(m_string_backing.Allocate(factorString.size()), factorString.data(), factorString.size()),
-        factorString.size());
+      memcpy(m_string_backing.Allocate(factorString.size()), factorString.data(), factorString.size()),
+      factorString.size());
     m_factorId++;
   }
   return &ret.first->in;
diff --git a/moses/FactorCollection.h b/moses/FactorCollection.h
index e7749244f..8c3db5da9 100644
--- a/moses/FactorCollection.h
+++ b/moses/FactorCollection.h
@@ -44,7 +44,7 @@ namespace Moses
  * private and friended to FactorFriend.  The STL containers can delegate
  * copying, so friending the container isn't sufficient.  STL containers see
  * FactorFriend's public copy constructor and everybody else sees Factor's
- * private copy constructor.  
+ * private copy constructor.
  */
 struct FactorFriend {
   Factor in;
diff --git a/moses/FeatureVector.cpp b/moses/FeatureVector.cpp
index f58bb5cab..96dd9a0ce 100644
--- a/moses/FeatureVector.cpp
+++ b/moses/FeatureVector.cpp
@@ -1,22 +1,22 @@
 /*
  Moses - factored phrase-based language decoder
  Copyright (C) 2010 University of Edinburgh
- 
- 
+
+
  This program is free software; you can redistribute it and/or modify
  it under the terms of the GNU General Public License as published by
  the Free Software Foundation; either version 2 of the License, or
  (at your option) any later version.
- 
+
  This program is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  GNU General Public License for more details.
- 
+
  You should have received a copy of the GNU General Public License along
  with this program; if not, write to the Free Software Foundation, Inc.,
  51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- 
+
  */
 
 #include <algorithm>
@@ -31,744 +31,815 @@
 using namespace std;
 
 
-namespace Moses {
-  
-  const string FName::SEP = "_";
-  FName::Name2Id FName::name2id;
-  vector<string> FName::id2name;
-  FName::Id2Count FName::id2hopeCount;
-  FName::Id2Count FName::id2fearCount;
+namespace Moses
+{
+
+const string FName::SEP = "_";
+FName::Name2Id FName::name2id;
+vector<string> FName::id2name;
+FName::Id2Count FName::id2hopeCount;
+FName::Id2Count FName::id2fearCount;
 #ifdef WITH_THREADS
-  boost::shared_mutex FName::m_idLock;
+boost::shared_mutex FName::m_idLock;
 #endif
-  
-  void FName::init(const StringPiece &name)  {
+
+void FName::init(const StringPiece &name)
+{
 #ifdef WITH_THREADS
-    //reader lock
-    boost::shared_lock<boost::shared_mutex> lock(m_idLock);
+  //reader lock
+  boost::shared_lock<boost::shared_mutex> lock(m_idLock);
 #endif
-    Name2Id::iterator i = FindStringPiece(name2id, name);
-    if (i != name2id.end()) {
-      m_id = i->second;
-    } else {
+  Name2Id::iterator i = FindStringPiece(name2id, name);
+  if (i != name2id.end()) {
+    m_id = i->second;
+  } else {
 #ifdef WITH_THREADS
-      //release the reader lock, and upgrade to writer lock
-      lock.unlock();
-      boost::unique_lock<boost::shared_mutex> write_lock(m_idLock);
+    //release the reader lock, and upgrade to writer lock
+    lock.unlock();
+    boost::unique_lock<boost::shared_mutex> write_lock(m_idLock);
 #endif
-      std::pair<std::string, size_t> to_ins;
-      to_ins.first.assign(name.data(), name.size());
-      to_ins.second = name2id.size();
-      std::pair<Name2Id::iterator, bool> res(name2id.insert(to_ins));
-      if (res.second) {
-        // TODO this should be string pointers backed by the hash table.
-        id2name.push_back(to_ins.first);
-      }
-      m_id = res.first->second;
+    std::pair<std::string, size_t> to_ins;
+    to_ins.first.assign(name.data(), name.size());
+    to_ins.second = name2id.size();
+    std::pair<Name2Id::iterator, bool> res(name2id.insert(to_ins));
+    if (res.second) {
+      // TODO this should be string pointers backed by the hash table.
+      id2name.push_back(to_ins.first);
     }
+    m_id = res.first->second;
+  }
+}
+
+size_t FName::getId(const string& name)
+{
+  Name2Id::iterator i = name2id.find(name);
+  assert (i != name2id.end());
+  return i->second;
+}
+
+size_t FName::getHopeIdCount(const string& name)
+{
+  Name2Id::iterator i = name2id.find(name);
+  if (i != name2id.end()) {
+    float id = i->second;
+    return id2hopeCount[id];
+  }
+  return 0;
+}
+
+size_t FName::getFearIdCount(const string& name)
+{
+  Name2Id::iterator i = name2id.find(name);
+  if (i != name2id.end()) {
+    float id = i->second;
+    return id2fearCount[id];
   }
-  
-  size_t FName::getId(const string& name) {
-	  Name2Id::iterator i = name2id.find(name);
-	  assert (i != name2id.end());
-	  return i->second;
-  }
-  
-  size_t FName::getHopeIdCount(const string& name) {
-	  Name2Id::iterator i = name2id.find(name);
-	  if (i != name2id.end()) {
-		  float id = i->second;
-		  return id2hopeCount[id];
-	  }
-	  return 0;
-  }
-
-  size_t FName::getFearIdCount(const string& name) {
-	  Name2Id::iterator i = name2id.find(name);
-	  if (i != name2id.end()) {
-		  float id = i->second;
-		  return id2fearCount[id];
-	  }
-	  return 0;
-  }
-  
-  void FName::incrementHopeId(const string& name) {
-	  Name2Id::iterator i = name2id.find(name);
-	  assert(i != name2id.end());
+  return 0;
+}
+
+void FName::incrementHopeId(const string& name)
+{
+  Name2Id::iterator i = name2id.find(name);
+  assert(i != name2id.end());
 #ifdef WITH_THREADS
-      // get upgradable lock and upgrade to writer lock
-      boost::upgrade_lock<boost::shared_mutex> upgradeLock(m_idLock);
-      boost::upgrade_to_unique_lock<boost::shared_mutex> uniqueLock(upgradeLock);
+  // get upgradable lock and upgrade to writer lock
+  boost::upgrade_lock<boost::shared_mutex> upgradeLock(m_idLock);
+  boost::upgrade_to_unique_lock<boost::shared_mutex> uniqueLock(upgradeLock);
 #endif
-      id2hopeCount[i->second] += 1; 
-  }
+  id2hopeCount[i->second] += 1;
+}
 
-    void FName::incrementFearId(const string& name) {
-	  Name2Id::iterator i = name2id.find(name);
-	  assert(i != name2id.end());
+void FName::incrementFearId(const string& name)
+{
+  Name2Id::iterator i = name2id.find(name);
+  assert(i != name2id.end());
 #ifdef WITH_THREADS
-      // get upgradable lock and upgrade to writer lock
-      boost::upgrade_lock<boost::shared_mutex> upgradeLock(m_idLock);
-      boost::upgrade_to_unique_lock<boost::shared_mutex> uniqueLock(upgradeLock);
+  // get upgradable lock and upgrade to writer lock
+  boost::upgrade_lock<boost::shared_mutex> upgradeLock(m_idLock);
+  boost::upgrade_to_unique_lock<boost::shared_mutex> uniqueLock(upgradeLock);
 #endif
-      id2fearCount[i->second] += 1; 
-  }
-  
-  void FName::eraseId(size_t id) {
+  id2fearCount[i->second] += 1;
+}
+
+void FName::eraseId(size_t id)
+{
 #ifdef WITH_THREADS
-      // get upgradable lock and upgrade to writer lock
-      boost::upgrade_lock<boost::shared_mutex> upgradeLock(m_idLock);
-      boost::upgrade_to_unique_lock<boost::shared_mutex> uniqueLock(upgradeLock);
+  // get upgradable lock and upgrade to writer lock
+  boost::upgrade_lock<boost::shared_mutex> upgradeLock(m_idLock);
+  boost::upgrade_to_unique_lock<boost::shared_mutex> uniqueLock(upgradeLock);
 #endif
-      id2hopeCount.erase(id);
-      id2fearCount.erase(id);
-  }
-   
-  std::ostream& operator<<( std::ostream& out, const FName& name) {
-    out << name.name();
-    return out;
-  }
-  
-  size_t FName::hash() const {
-    return boost::hash_value(m_id);
-  }
-  
-  const std::string& FName::name() const {
-    return id2name[m_id];
-  }
-  
-  
-  bool FName::operator==(const FName& rhs) const {
-    return m_id == rhs.m_id;
-  }
-  
-  bool FName::operator!=(const FName& rhs) const {
-    return ! (*this == rhs);
-  }
-  
-  FVector::FVector(size_t coreFeatures) : m_coreFeatures(coreFeatures) {}
-
-  void FVector::resize(size_t newsize) {
-      valarray<FValue> oldValues(m_coreFeatures);
-      m_coreFeatures.resize(newsize);
-      for (size_t i = 0; i < min(m_coreFeatures.size(), oldValues.size()); ++i) {
-        m_coreFeatures[i] = oldValues[i];
-      }
-    }
-	
-  void FVector::clear() {
-    m_coreFeatures.resize(0);
-    m_features.clear();
-  }
-	
-  bool FVector::load(const std::string& filename) {
-    clear();
-    ifstream in (filename.c_str());
-    if (!in) {
-      return false;
-    }
-    string line;
-    while(getline(in,line)) {
-      if (line[0] == '#') continue;
-      istringstream linestream(line);
-      string namestring;
-      FValue value;
-      linestream >> namestring;
-      linestream >> value;
-      FName fname(namestring);
-      //cerr << "Setting sparse weight " << fname << " to value " << value << "." << endl;
-      set(fname,value);
-    }
-    return true;
-  }
+  id2hopeCount.erase(id);
+  id2fearCount.erase(id);
+}
 
-  void FVector::save(const string& filename) const {
-    ofstream out(filename.c_str());
-    if (!out) {
-      ostringstream msg;
-      msg << "Unable to open " << filename;
-      throw runtime_error(msg.str());
-    }
-    write(out);
-    out.close();
+std::ostream& operator<<( std::ostream& out, const FName& name)
+{
+  out << name.name();
+  return out;
+}
+
+size_t FName::hash() const
+{
+  return boost::hash_value(m_id);
+}
+
+const std::string& FName::name() const
+{
+  return id2name[m_id];
+}
+
+
+bool FName::operator==(const FName& rhs) const
+{
+  return m_id == rhs.m_id;
+}
+
+bool FName::operator!=(const FName& rhs) const
+{
+  return ! (*this == rhs);
+}
+
+FVector::FVector(size_t coreFeatures) : m_coreFeatures(coreFeatures) {}
+
+void FVector::resize(size_t newsize)
+{
+  valarray<FValue> oldValues(m_coreFeatures);
+  m_coreFeatures.resize(newsize);
+  for (size_t i = 0; i < min(m_coreFeatures.size(), oldValues.size()); ++i) {
+    m_coreFeatures[i] = oldValues[i];
   }
+}
 
-  void FVector::write(ostream& out) const {
-    for (const_iterator i = cbegin(); i != cend(); ++i) {
-      out << i->first << " " << i->second << endl;
-    }
+void FVector::clear()
+{
+  m_coreFeatures.resize(0);
+  m_features.clear();
+}
+
+bool FVector::load(const std::string& filename)
+{
+  clear();
+  ifstream in (filename.c_str());
+  if (!in) {
+    return false;
+  }
+  string line;
+  while(getline(in,line)) {
+    if (line[0] == '#') continue;
+    istringstream linestream(line);
+    string namestring;
+    FValue value;
+    linestream >> namestring;
+    linestream >> value;
+    FName fname(namestring);
+    //cerr << "Setting sparse weight " << fname << " to value " << value << "." << endl;
+    set(fname,value);
+  }
+  return true;
+}
+
+void FVector::save(const string& filename) const
+{
+  ofstream out(filename.c_str());
+  if (!out) {
+    ostringstream msg;
+    msg << "Unable to open " << filename;
+    throw runtime_error(msg.str());
   }
+  write(out);
+  out.close();
+}
 
-  static bool equalsTolerance(FValue lhs, FValue rhs) {
-    if (lhs == rhs) return true;
-    static const FValue TOLERANCE = 1e-4;
-    FValue diff = abs(lhs-rhs);
-    FValue mean = (abs(lhs)+abs(rhs))/2;
-    //cerr << "ET " << lhs << " " << rhs << " " << diff << " " << mean << " " << endl;
-    return diff/mean < TOLERANCE ;
+void FVector::write(ostream& out) const
+{
+  for (const_iterator i = cbegin(); i != cend(); ++i) {
+    out << i->first << " " << i->second << endl;
   }
-  
-  bool FVector::operator== (const FVector& rhs) const {
-    if (this == &rhs) {
-      return true;
-    }
-    if (m_coreFeatures.size() != rhs.m_coreFeatures.size()) {
-      return false;
-    }
-    for (size_t i = 0; i < m_coreFeatures.size(); ++i) {
-      if (!equalsTolerance(m_coreFeatures[i], rhs.m_coreFeatures[i])) return false;
-    }
-    for (const_iterator i  = cbegin(); i != cend(); ++i) {
-      if (!equalsTolerance(i->second,rhs.get(i->first))) return false;
-    }
-    for (const_iterator i = rhs.cbegin(); i != rhs.cend(); ++i) {
-      if (!equalsTolerance(i->second, get(i->first))) return false;
-    }
+}
+
+static bool equalsTolerance(FValue lhs, FValue rhs)
+{
+  if (lhs == rhs) return true;
+  static const FValue TOLERANCE = 1e-4;
+  FValue diff = abs(lhs-rhs);
+  FValue mean = (abs(lhs)+abs(rhs))/2;
+  //cerr << "ET " << lhs << " " << rhs << " " << diff << " " << mean << " " << endl;
+  return diff/mean < TOLERANCE ;
+}
+
+bool FVector::operator== (const FVector& rhs) const
+{
+  if (this == &rhs) {
     return true;
   }
-  
-  bool FVector::operator!= (const FVector& rhs) const {
-    return ! (*this == rhs);
+  if (m_coreFeatures.size() != rhs.m_coreFeatures.size()) {
+    return false;
   }
-	
-  ProxyFVector FVector::operator[](const FName& name) {
-	  // At this point, we don't know whether operator[] was called, so we return
-	  // a proxy object and defer the decision until later
-	  return ProxyFVector(this, name);
+  for (size_t i = 0; i < m_coreFeatures.size(); ++i) {
+    if (!equalsTolerance(m_coreFeatures[i], rhs.m_coreFeatures[i])) return false;
   }
+  for (const_iterator i  = cbegin(); i != cend(); ++i) {
+    if (!equalsTolerance(i->second,rhs.get(i->first))) return false;
+  }
+  for (const_iterator i = rhs.cbegin(); i != rhs.cend(); ++i) {
+    if (!equalsTolerance(i->second, get(i->first))) return false;
+  }
+  return true;
+}
+
+bool FVector::operator!= (const FVector& rhs) const
+{
+  return ! (*this == rhs);
+}
+
+ProxyFVector FVector::operator[](const FName& name)
+{
+  // At this point, we don't know whether operator[] was called, so we return
+  // a proxy object and defer the decision until later
+  return ProxyFVector(this, name);
+}
 
-  /** Equivalent for core features. */
-  FValue& FVector::operator[](size_t index) {
-    return m_coreFeatures[index];
+/** Equivalent for core features. */
+FValue& FVector::operator[](size_t index)
+{
+  return m_coreFeatures[index];
+}
+
+
+FValue FVector::operator[](const FName& name) const
+{
+  return get(name);
+}
+
+FValue FVector::operator[](size_t index) const
+{
+  return m_coreFeatures[index];
+}
+
+ostream& FVector::print(ostream& out) const
+{
+  out << "core=(";
+  for (size_t i = 0; i < m_coreFeatures.size(); ++i) {
+    out << m_coreFeatures[i];
+    if (i + 1 < m_coreFeatures.size()) {
+      out << ",";
+    }
   }
+  out << ") ";
+  for (const_iterator i = cbegin(); i != cend(); ++i) {
+    if (i != cbegin())
+      out << " ";
+    out << i->first << "=" << i->second;
+  }
+  return out;
+}
+
+ostream& operator<<(ostream& out, const FVector& fv)
+{
+  return fv.print(out);
+}
 
-	
-  FValue FVector::operator[](const FName& name) const {
-	  return get(name);
+const FValue& FVector::get(const FName& name) const
+{
+  static const FValue DEFAULT = 0;
+  const_iterator fi = m_features.find(name);
+  if (fi == m_features.end()) {
+    return DEFAULT;
+  } else {
+    return fi->second;
   }
+}
 
-  FValue FVector::operator[](size_t index) const {
-    return m_coreFeatures[index];
+FValue FVector::getBackoff(const FName& name, float backoff) const
+{
+  const_iterator fi = m_features.find(name);
+  if (fi == m_features.end()) {
+    return backoff;
+  } else {
+    return fi->second;
   }
+}
 
-  ostream& FVector::print(ostream& out) const {
-    out << "core=(";
-    for (size_t i = 0; i < m_coreFeatures.size(); ++i) {
-      out << m_coreFeatures[i];
-      if (i + 1 < m_coreFeatures.size()) {
-        out << ",";
-      }
-    }
-    out << ") ";
-    for (const_iterator i = cbegin(); i != cend(); ++i) {
-      if (i != cbegin())
-	out << " ";
-      out << i->first << "=" << i->second;
-    }
-    return out;
-  }
-  
-  ostream& operator<<(ostream& out, const FVector& fv) {
-    return fv.print(out);
-  }
-	
-  const FValue& FVector::get(const FName& name) const {
-    static const FValue DEFAULT = 0;
-    const_iterator fi = m_features.find(name);
-    if (fi == m_features.end()) {
-      return DEFAULT;
-    } else {
-      return fi->second;
+void FVector::thresholdScale(FValue maxValue )
+{
+  FValue factor = 1.0;
+  for (const_iterator i = cbegin(); i != cend(); ++i) {
+    FValue value = i->second;
+    if (abs(value)*factor > maxValue) {
+      factor = abs(value) / maxValue;
     }
   }
+  operator*=(factor);
+}
 
-  FValue FVector::getBackoff(const FName& name, float backoff) const {
-    const_iterator fi = m_features.find(name);
-    if (fi == m_features.end()) {
-      return backoff;
-    } else {
-      return fi->second;
+void FVector::capMax(FValue maxValue)
+{
+  for (const_iterator i = cbegin(); i != cend(); ++i)
+    if (i->second > maxValue)
+      set(i->first, maxValue);
+}
+
+void FVector::capMin(FValue minValue)
+{
+  for (const_iterator i = cbegin(); i != cend(); ++i)
+    if (i->second < minValue)
+      set(i->first, minValue);
+}
+
+void FVector::set(const FName& name, const FValue& value)
+{
+  m_features[name] = value;
+}
+
+void FVector::printCoreFeatures()
+{
+  cerr << "core=(";
+  for (size_t i = 0; i < m_coreFeatures.size(); ++i) {
+    cerr << m_coreFeatures[i];
+    if (i + 1 < m_coreFeatures.size()) {
+      cerr << ",";
     }
   }
+  cerr << ") ";
+}
 
-  void FVector::thresholdScale(FValue maxValue ) {
-    FValue factor = 1.0;
-    for (const_iterator i = cbegin(); i != cend(); ++i) {
-      FValue value = i->second;
-      if (abs(value)*factor > maxValue) {
-        factor = abs(value) / maxValue;
-      }
+FVector& FVector::operator+= (const FVector& rhs)
+{
+  if (rhs.m_coreFeatures.size() > m_coreFeatures.size())
+    resize(rhs.m_coreFeatures.size());
+  for (const_iterator i = rhs.cbegin(); i != rhs.cend(); ++i)
+    set(i->first, get(i->first) + i->second);
+  for (size_t i = 0; i < rhs.m_coreFeatures.size(); ++i)
+    m_coreFeatures[i] += rhs.m_coreFeatures[i];
+  return *this;
+}
+
+// add only sparse features
+void FVector::sparsePlusEquals(const FVector& rhs)
+{
+  for (const_iterator i = rhs.cbegin(); i != rhs.cend(); ++i)
+    set(i->first, get(i->first) + i->second);
+}
+
+// assign only core features
+void FVector::coreAssign(const FVector& rhs)
+{
+  for (size_t i = 0; i < rhs.m_coreFeatures.size(); ++i)
+    m_coreFeatures[i] = rhs.m_coreFeatures[i];
+}
+
+void FVector::incrementSparseHopeFeatures()
+{
+  for (const_iterator i = cbegin(); i != cend(); ++i)
+    FName::incrementHopeId((i->first).name());
+}
+
+void FVector::incrementSparseFearFeatures()
+{
+  for (const_iterator i = cbegin(); i != cend(); ++i)
+    FName::incrementFearId((i->first).name());
+}
+
+void FVector::printSparseHopeFeatureCounts(std::ofstream& out)
+{
+  for (const_iterator i = cbegin(); i != cend(); ++i)
+    out << (i->first).name() << ": " << FName::getHopeIdCount((i->first).name()) << std::endl;
+}
+
+void FVector::printSparseFearFeatureCounts(std::ofstream& out)
+{
+  for (const_iterator i = cbegin(); i != cend(); ++i)
+    out << (i->first).name() << ": " << FName::getFearIdCount((i->first).name()) << std::endl;
+}
+
+void FVector::printSparseHopeFeatureCounts()
+{
+  for (const_iterator i = cbegin(); i != cend(); ++i)
+    std::cerr << (i->first).name() << ": " << FName::getHopeIdCount((i->first).name()) << std::endl;
+}
+
+void FVector::printSparseFearFeatureCounts()
+{
+  for (const_iterator i = cbegin(); i != cend(); ++i)
+    std::cerr << (i->first).name() << ": " << FName::getFearIdCount((i->first).name()) << std::endl;
+}
+
+size_t FVector::pruneSparseFeatures(size_t threshold)
+{
+  size_t count = 0;
+  vector<FName> toErase;
+  for (const_iterator i = cbegin(); i != cend(); ++i) {
+    const std::string& fname = (i->first).name();
+    if (FName::getHopeIdCount(fname) < threshold && FName::getFearIdCount(fname) < threshold) {
+      toErase.push_back(i->first);
+      std::cerr << "pruning: " << fname << " (" << FName::getHopeIdCount(fname) << ", " << FName::getFearIdCount(fname) << ")" << std::endl;
+      FName::eraseId(FName::getId(fname));
+      ++count;
     }
-    operator*=(factor);
   }
 
-  void FVector::capMax(FValue maxValue) {
-    for (const_iterator i = cbegin(); i != cend(); ++i)
-      if (i->second > maxValue)
-         set(i->first, maxValue);
-  }
+  for (size_t i = 0; i < toErase.size(); ++i)
+    m_features.erase(toErase[i]);
 
-  void FVector::capMin(FValue minValue) {
-    for (const_iterator i = cbegin(); i != cend(); ++i)
-      if (i->second < minValue)
-         set(i->first, minValue);
-  }
+  return count;
+}
 
-  void FVector::set(const FName& name, const FValue& value) {
-    m_features[name] = value;
-  }
-  
-  void FVector::printCoreFeatures() {
-    cerr << "core=(";
-    for (size_t i = 0; i < m_coreFeatures.size(); ++i) {
-      cerr << m_coreFeatures[i];
-      if (i + 1 < m_coreFeatures.size()) {
-	cerr << ",";
-      }
+size_t FVector::pruneZeroWeightFeatures()
+{
+  size_t count = 0;
+  vector<FName> toErase;
+  for (const_iterator i = cbegin(); i != cend(); ++i) {
+    const std::string& fname = (i->first).name();
+    if (i->second == 0) {
+      toErase.push_back(i->first);
+      //std::cerr << "prune: " << fname << std::endl;
+      FName::eraseId(FName::getId(fname));
+      ++count;
     }
-    cerr << ") ";
   }
 
-  FVector& FVector::operator+= (const FVector& rhs) {
-    if (rhs.m_coreFeatures.size() > m_coreFeatures.size())
-      resize(rhs.m_coreFeatures.size());
-    for (const_iterator i = rhs.cbegin(); i != rhs.cend(); ++i)
-        set(i->first, get(i->first) + i->second);
-    for (size_t i = 0; i < rhs.m_coreFeatures.size(); ++i)
-      m_coreFeatures[i] += rhs.m_coreFeatures[i];
-    return *this;
-  }
-  
-  // add only sparse features
-  void FVector::sparsePlusEquals(const FVector& rhs) {
-    for (const_iterator i = rhs.cbegin(); i != rhs.cend(); ++i)
-	  set(i->first, get(i->first) + i->second);
-  }
-  
-  // assign only core features                                                                                    
-  void FVector::coreAssign(const FVector& rhs) {
-    for (size_t i = 0; i < rhs.m_coreFeatures.size(); ++i)
-      m_coreFeatures[i] = rhs.m_coreFeatures[i];
+  for (size_t i = 0; i < toErase.size(); ++i)
+    m_features.erase(toErase[i]);
+
+  return count;
+}
+
+void FVector::updateConfidenceCounts(const FVector& weightUpdate, bool signedCounts)
+{
+  for (size_t i = 0; i < weightUpdate.m_coreFeatures.size(); ++i) {
+    if (signedCounts) {
+      //int sign = weightUpdate.m_coreFeatures[i] >= 0 ? 1 : -1;
+      //m_coreFeatures[i] += (weightUpdate.m_coreFeatures[i] * weightUpdate.m_coreFeatures[i]) * sign;
+      m_coreFeatures[i] += weightUpdate.m_coreFeatures[i];
+    } else
+      //m_coreFeatures[i] += (weightUpdate.m_coreFeatures[i] * weightUpdate.m_coreFeatures[i]);
+      m_coreFeatures[i] += abs(weightUpdate.m_coreFeatures[i]);
+  }
+
+  for (const_iterator i = weightUpdate.cbegin(); i != weightUpdate.cend(); ++i) {
+    if (weightUpdate[i->first] == 0)
+      continue;
+    float value = get(i->first);
+    if (signedCounts) {
+      //int sign = weightUpdate[i->first] >= 0 ? 1 : -1;
+      //value += (weightUpdate[i->first] * weightUpdate[i->first]) * sign;
+      value += weightUpdate[i->first];
+    } else
+      //value += (weightUpdate[i->first] * weightUpdate[i->first]);
+      value += abs(weightUpdate[i->first]);
+    set(i->first, value);
   }
-  
-  void FVector::incrementSparseHopeFeatures() {
-    for (const_iterator i = cbegin(); i != cend(); ++i) 
-      FName::incrementHopeId((i->first).name());
+}
+
+void FVector::updateLearningRates(float decay_core, float decay_sparse, const FVector &confidenceCounts, float core_r0, float sparse_r0)
+{
+  for (size_t i = 0; i < confidenceCounts.m_coreFeatures.size(); ++i) {
+    m_coreFeatures[i] = 1.0/(1.0/core_r0 + decay_core * abs(confidenceCounts.m_coreFeatures[i]));
   }
 
-  void FVector::incrementSparseFearFeatures() {
-    for (const_iterator i = cbegin(); i != cend(); ++i) 
-      FName::incrementFearId((i->first).name());
+  for (const_iterator i = confidenceCounts.cbegin(); i != confidenceCounts.cend(); ++i) {
+    float value = 1.0/(1.0/sparse_r0 + decay_sparse * abs(i->second));
+    set(i->first, value);
   }
-  
-  void FVector::printSparseHopeFeatureCounts(std::ofstream& out) {
-    for (const_iterator i = cbegin(); i != cend(); ++i) 
-      out << (i->first).name() << ": " << FName::getHopeIdCount((i->first).name()) << std::endl;
+}
+
+// count non-zero occurrences for all sparse features
+void FVector::setToBinaryOf(const FVector& rhs)
+{
+  for (const_iterator i = rhs.cbegin(); i != rhs.cend(); ++i)
+    if (rhs.get(i->first) != 0)
+      set(i->first, 1);
+  for (size_t i = 0; i < rhs.m_coreFeatures.size(); ++i)
+    m_coreFeatures[i] = 1;
+}
+
+// divide only core features by scalar
+FVector& FVector::coreDivideEquals(float scalar)
+{
+  for (size_t i = 0; i < m_coreFeatures.size(); ++i)
+    m_coreFeatures[i] /= scalar;
+  return *this;
+}
+
+// lhs vector is a sum of vectors, rhs vector holds number of non-zero summands
+FVector& FVector::divideEquals(const FVector& rhs)
+{
+  assert(m_coreFeatures.size() == rhs.m_coreFeatures.size());
+  for (const_iterator i = rhs.cbegin(); i != rhs.cend(); ++i)
+    set(i->first, get(i->first)/rhs.get(i->first)); // divide by number of summands
+  for (size_t i = 0; i < rhs.m_coreFeatures.size(); ++i)
+    m_coreFeatures[i] /= rhs.m_coreFeatures[i]; // divide by number of summands
+  return *this;
+}
+
+FVector& FVector::operator-= (const FVector& rhs)
+{
+  if (rhs.m_coreFeatures.size() > m_coreFeatures.size())
+    resize(rhs.m_coreFeatures.size());
+  for (const_iterator i = rhs.cbegin(); i != rhs.cend(); ++i)
+    set(i->first, get(i->first) -(i->second));
+  for (size_t i = 0; i < m_coreFeatures.size(); ++i) {
+    if (i < rhs.m_coreFeatures.size()) {
+      m_coreFeatures[i] -= rhs.m_coreFeatures[i];
+    }
   }
+  return *this;
+}
 
-  void FVector::printSparseFearFeatureCounts(std::ofstream& out) {
-    for (const_iterator i = cbegin(); i != cend(); ++i) 
-      out << (i->first).name() << ": " << FName::getFearIdCount((i->first).name()) << std::endl;
+FVector& FVector::operator*= (const FVector& rhs)
+{
+  if (rhs.m_coreFeatures.size() > m_coreFeatures.size()) {
+    resize(rhs.m_coreFeatures.size());
   }
-  
-  void FVector::printSparseHopeFeatureCounts() {
-    for (const_iterator i = cbegin(); i != cend(); ++i)
-      std::cerr << (i->first).name() << ": " << FName::getHopeIdCount((i->first).name()) << std::endl;
+  for (iterator i = begin(); i != end(); ++i) {
+    FValue lhsValue = i->second;
+    FValue rhsValue = rhs.get(i->first);
+    set(i->first,lhsValue*rhsValue);
   }
-
-  void FVector::printSparseFearFeatureCounts() {
-    for (const_iterator i = cbegin(); i != cend(); ++i)
-      std::cerr << (i->first).name() << ": " << FName::getFearIdCount((i->first).name()) << std::endl;
+  for (size_t i = 0; i < m_coreFeatures.size(); ++i) {
+    if (i < rhs.m_coreFeatures.size()) {
+      m_coreFeatures[i] *= rhs.m_coreFeatures[i];
+    } else {
+      m_coreFeatures[i] = 0;
+    }
   }
+  return *this;
+}
 
-  size_t FVector::pruneSparseFeatures(size_t threshold) {
-    size_t count = 0;
-    vector<FName> toErase;
-    for (const_iterator i = cbegin(); i != cend(); ++i) {
-      const std::string& fname = (i->first).name();
-      if (FName::getHopeIdCount(fname) < threshold && FName::getFearIdCount(fname) < threshold) {
-        toErase.push_back(i->first);
-        std::cerr << "pruning: " << fname << " (" << FName::getHopeIdCount(fname) << ", " << FName::getFearIdCount(fname) << ")" << std::endl;
-        FName::eraseId(FName::getId(fname));
-    	++count;
-      }
-    }
-    
-    for (size_t i = 0; i < toErase.size(); ++i) 
-    	m_features.erase(toErase[i]);	
-        
-    return count;
-  }
-  
-  size_t FVector::pruneZeroWeightFeatures() {
-	size_t count = 0;
-	vector<FName> toErase;
-    for (const_iterator i = cbegin(); i != cend(); ++i) {
-      const std::string& fname = (i->first).name();
-      if (i->second == 0) {
-        toErase.push_back(i->first);
-        //std::cerr << "prune: " << fname << std::endl;
-        FName::eraseId(FName::getId(fname));
-    	++count;
-      }
-    }
-    
-    for (size_t i = 0; i < toErase.size(); ++i)
-    	m_features.erase(toErase[i]);
-    
-    return count;
-  }
-
-  void FVector::updateConfidenceCounts(const FVector& weightUpdate, bool signedCounts) {
-    for (size_t i = 0; i < weightUpdate.m_coreFeatures.size(); ++i) {
-      if (signedCounts) {
-	//int sign = weightUpdate.m_coreFeatures[i] >= 0 ? 1 : -1;
-	//m_coreFeatures[i] += (weightUpdate.m_coreFeatures[i] * weightUpdate.m_coreFeatures[i]) * sign;
-	m_coreFeatures[i] += weightUpdate.m_coreFeatures[i];
-      }
-      else
-	//m_coreFeatures[i] += (weightUpdate.m_coreFeatures[i] * weightUpdate.m_coreFeatures[i]);
-	m_coreFeatures[i] += abs(weightUpdate.m_coreFeatures[i]);
-    }
-    
-    for (const_iterator i = weightUpdate.cbegin(); i != weightUpdate.cend(); ++i) {
-      if (weightUpdate[i->first] == 0)
-	continue;
-      float value = get(i->first);	  
-      if (signedCounts) {
-	//int sign = weightUpdate[i->first] >= 0 ? 1 : -1;
-	//value += (weightUpdate[i->first] * weightUpdate[i->first]) * sign;
-	value += weightUpdate[i->first];
+FVector& FVector::operator/= (const FVector& rhs)
+{
+  if (rhs.m_coreFeatures.size() > m_coreFeatures.size()) {
+    resize(rhs.m_coreFeatures.size());
+  }
+  for (iterator i = begin(); i != end(); ++i) {
+    FValue lhsValue = i->second;
+    FValue rhsValue = rhs.get(i->first);
+    set(i->first, lhsValue / rhsValue) ;
+  }
+  for (size_t i = 0; i < m_coreFeatures.size(); ++i) {
+    if (i < rhs.m_coreFeatures.size()) {
+      m_coreFeatures[i] /= rhs.m_coreFeatures[i];
+    } else {
+      if (m_coreFeatures[i] < 0) {
+        m_coreFeatures[i] = -numeric_limits<FValue>::infinity();
+      } else if (m_coreFeatures[i] > 0) {
+        m_coreFeatures[i] = numeric_limits<FValue>::infinity();
       }
-      else 
-	//value += (weightUpdate[i->first] * weightUpdate[i->first]);
-	value += abs(weightUpdate[i->first]);
-      set(i->first, value);
     }
   }
+  return *this;
+}
 
-  void FVector::updateLearningRates(float decay_core, float decay_sparse, const FVector &confidenceCounts, float core_r0, float sparse_r0) {
-    for (size_t i = 0; i < confidenceCounts.m_coreFeatures.size(); ++i) {
-      m_coreFeatures[i] = 1.0/(1.0/core_r0 + decay_core * abs(confidenceCounts.m_coreFeatures[i]));     
-    }
-
-    for (const_iterator i = confidenceCounts.cbegin(); i != confidenceCounts.cend(); ++i) {
-      float value = 1.0/(1.0/sparse_r0 + decay_sparse * abs(i->second));
-      set(i->first, value);
-    }
+FVector& FVector::operator*= (const FValue& rhs)
+{
+  //NB Could do this with boost::bind ?
+  for (iterator i = begin(); i != end(); ++i) {
+    i->second *= rhs;
   }
+  m_coreFeatures *= rhs;
+  return *this;
+}
 
-  // count non-zero occurrences for all sparse features
-  void FVector::setToBinaryOf(const FVector& rhs) {
-    for (const_iterator i = rhs.cbegin(); i != rhs.cend(); ++i)
-    	if (rhs.get(i->first) != 0)
-        	set(i->first, 1);
-    for (size_t i = 0; i < rhs.m_coreFeatures.size(); ++i)
-    	m_coreFeatures[i] = 1;
-  }
-
-  // divide only core features by scalar
-  FVector& FVector::coreDivideEquals(float scalar) {
-    for (size_t i = 0; i < m_coreFeatures.size(); ++i)
-    	m_coreFeatures[i] /= scalar;
-	  return *this;
-  }
-
-  // lhs vector is a sum of vectors, rhs vector holds number of non-zero summands
-  FVector& FVector::divideEquals(const FVector& rhs) {
-	  assert(m_coreFeatures.size() == rhs.m_coreFeatures.size());
-	    for (const_iterator i = rhs.cbegin(); i != rhs.cend(); ++i)
-	    	set(i->first, get(i->first)/rhs.get(i->first)); // divide by number of summands
-	    for (size_t i = 0; i < rhs.m_coreFeatures.size(); ++i)
-	    	m_coreFeatures[i] /= rhs.m_coreFeatures[i]; // divide by number of summands
-	  return *this;
-  }
-
-  FVector& FVector::operator-= (const FVector& rhs) {
-    if (rhs.m_coreFeatures.size() > m_coreFeatures.size())
-      resize(rhs.m_coreFeatures.size());
-    for (const_iterator i = rhs.cbegin(); i != rhs.cend(); ++i)
-    	set(i->first, get(i->first) -(i->second));
-    for (size_t i = 0; i < m_coreFeatures.size(); ++i) {
-      if (i < rhs.m_coreFeatures.size()) {
-        m_coreFeatures[i] -= rhs.m_coreFeatures[i];
-      }
-    }
-    return *this;
+FVector& FVector::operator/= (const FValue& rhs)
+{
+  for (iterator i = begin(); i != end(); ++i) {
+    i->second /= rhs;
   }
-  
-  FVector& FVector::operator*= (const FVector& rhs) {
-    if (rhs.m_coreFeatures.size() > m_coreFeatures.size()) {
-      resize(rhs.m_coreFeatures.size());
-    }
-    for (iterator i = begin(); i != end(); ++i) {
-      FValue lhsValue = i->second;
-      FValue rhsValue = rhs.get(i->first);
-      set(i->first,lhsValue*rhsValue);
-    }
-    for (size_t i = 0; i < m_coreFeatures.size(); ++i) {
-      if (i < rhs.m_coreFeatures.size()) {
-        m_coreFeatures[i] *= rhs.m_coreFeatures[i];
-      } else {
-        m_coreFeatures[i] = 0;
-      }
-    }
-    return *this;
+  m_coreFeatures /= rhs;
+  return *this;
+}
+
+FVector& FVector::multiplyEqualsBackoff(const FVector& rhs, float backoff)
+{
+  if (rhs.m_coreFeatures.size() > m_coreFeatures.size()) {
+    resize(rhs.m_coreFeatures.size());
   }
-  
-  FVector& FVector::operator/= (const FVector& rhs) {
-    if (rhs.m_coreFeatures.size() > m_coreFeatures.size()) {
-      resize(rhs.m_coreFeatures.size());
-    }
-    for (iterator i = begin(); i != end(); ++i) {
-      FValue lhsValue = i->second;
-      FValue rhsValue = rhs.get(i->first);
-      set(i->first, lhsValue / rhsValue) ;
-    }
-    for (size_t i = 0; i < m_coreFeatures.size(); ++i) {
-      if (i < rhs.m_coreFeatures.size()) {
-        m_coreFeatures[i] /= rhs.m_coreFeatures[i];
-      } else {
-        if (m_coreFeatures[i] < 0) {
-          m_coreFeatures[i] = -numeric_limits<FValue>::infinity();
-        } else if (m_coreFeatures[i] > 0) {
-          m_coreFeatures[i] = numeric_limits<FValue>::infinity();
-        }
-      }
-    }
-    return *this;
+  for (iterator i = begin(); i != end(); ++i) {
+    FValue lhsValue = i->second;
+    FValue rhsValue = rhs.getBackoff(i->first, backoff);
+    set(i->first,lhsValue*rhsValue);
   }
-  
-  FVector& FVector::operator*= (const FValue& rhs) {
-    //NB Could do this with boost::bind ?
-    for (iterator i = begin(); i != end(); ++i) {
-      i->second *= rhs;
+  for (size_t i = 0; i < m_coreFeatures.size(); ++i) {
+    if (i < rhs.m_coreFeatures.size()) {
+      m_coreFeatures[i] *= rhs.m_coreFeatures[i];
+    } else {
+      m_coreFeatures[i] = 0;
     }
-    m_coreFeatures *= rhs;
-    return *this;
   }
-  
-  FVector& FVector::operator/= (const FValue& rhs) {
-    for (iterator i = begin(); i != end(); ++i) {
-      i->second /= rhs;
-    }
-    m_coreFeatures /= rhs;
-    return *this;
+  return *this;
+}
+
+FVector& FVector::multiplyEquals(float core_r0, float sparse_r0)
+{
+  for (size_t i = 0; i < m_coreFeatures.size(); ++i) {
+    m_coreFeatures[i] *= core_r0;
   }
+  for (iterator i = begin(); i != end(); ++i)
+    set(i->first,(i->second)*sparse_r0);
+  return *this;
+}
 
-  FVector& FVector::multiplyEqualsBackoff(const FVector& rhs, float backoff) {
-    if (rhs.m_coreFeatures.size() > m_coreFeatures.size()) {
-      resize(rhs.m_coreFeatures.size());
-    }
-    for (iterator i = begin(); i != end(); ++i) {
-      FValue lhsValue = i->second;
-      FValue rhsValue = rhs.getBackoff(i->first, backoff);
-      set(i->first,lhsValue*rhsValue);
-    }
-    for (size_t i = 0; i < m_coreFeatures.size(); ++i) {
-      if (i < rhs.m_coreFeatures.size()) {
-        m_coreFeatures[i] *= rhs.m_coreFeatures[i];
-      } else {
-        m_coreFeatures[i] = 0;
-      }
-    }
-    return *this;
+FValue FVector::l1norm() const
+{
+  FValue norm = 0;
+  for (const_iterator i = cbegin(); i != cend(); ++i) {
+    norm += abs(i->second);
   }
-  
-  FVector& FVector::multiplyEquals(float core_r0, float sparse_r0) {
-    for (size_t i = 0; i < m_coreFeatures.size(); ++i) {
-      m_coreFeatures[i] *= core_r0;
-    }
-    for (iterator i = begin(); i != end(); ++i) 
-      set(i->first,(i->second)*sparse_r0);   
-    return *this;
-  }
-  
-  FValue FVector::l1norm() const {
-    FValue norm = 0;
-    for (const_iterator i = cbegin(); i != cend(); ++i) {
-      norm += abs(i->second);
-    }
-    for (size_t i = 0; i < m_coreFeatures.size(); ++i) {
-      norm += abs(m_coreFeatures[i]);
-    }
-    return norm;
+  for (size_t i = 0; i < m_coreFeatures.size(); ++i) {
+    norm += abs(m_coreFeatures[i]);
   }
+  return norm;
+}
+
+FValue FVector::l1norm_coreFeatures() const
+{
+  FValue norm = 0;
+  // ignore Bleu score feature (last feature)
+  for (size_t i = 0; i < m_coreFeatures.size()-1; ++i)
+    norm += abs(m_coreFeatures[i]);
+  return norm;
+}
+
+FValue FVector::l2norm() const
+{
+  return sqrt(inner_product(*this));
+}
 
-  FValue FVector::l1norm_coreFeatures() const {
-    FValue norm = 0;
-    // ignore Bleu score feature (last feature)
-    for (size_t i = 0; i < m_coreFeatures.size()-1; ++i) 
-      norm += abs(m_coreFeatures[i]);
-    return norm;
+FValue FVector::linfnorm() const
+{
+  FValue norm = 0;
+  for (const_iterator i = cbegin(); i != cend(); ++i) {
+    float absValue = abs(i->second);
+    if (absValue > norm)
+      norm = absValue;
   }
-  
-  FValue FVector::l2norm() const {
-    return sqrt(inner_product(*this));
+  for (size_t i = 0; i < m_coreFeatures.size(); ++i) {
+    float absValue = abs(m_coreFeatures[i]);
+    if (absValue > norm)
+      norm = absValue;
   }
+  return norm;
+}
 
-  FValue FVector::linfnorm() const {
-    FValue norm = 0;
-    for (const_iterator i = cbegin(); i != cend(); ++i) {
-      float absValue = abs(i->second);
-      if (absValue > norm)
-	norm = absValue;
-    }
-    for (size_t i = 0; i < m_coreFeatures.size(); ++i) {
-      float absValue = abs(m_coreFeatures[i]);
-      if (absValue > norm)
-	norm = absValue;
+size_t FVector::l1regularize(float lambda)
+{
+  for (size_t i = 0; i < m_coreFeatures.size(); ++i) {
+    float value = m_coreFeatures[i];
+    if (value > 0) {
+      m_coreFeatures[i] = max(0.0f, value - lambda);
+    } else {
+      m_coreFeatures[i] = min(0.0f, value + lambda);
     }
-    return norm;
   }
 
-  size_t FVector::l1regularize(float lambda) {
-    for (size_t i = 0; i < m_coreFeatures.size(); ++i) {
-      float value = m_coreFeatures[i];
-      if (value > 0) {
-        m_coreFeatures[i] = max(0.0f, value - lambda);
-      }
-      else {
-        m_coreFeatures[i] = min(0.0f, value + lambda);
-      }
-    }
+  size_t numberPruned = size();
+  vector<FName> toErase;
+  for (iterator i = begin(); i != end(); ++i) {
+    float value = i->second;
+    if (value != 0.0f) {
+      if (value > 0)
+        value = max(0.0f, value - lambda);
+      else
+        value = min(0.0f, value + lambda);
 
-    size_t numberPruned = size();
-    vector<FName> toErase;
-    for (iterator i = begin(); i != end(); ++i) {
-      float value = i->second;
-      if (value != 0.0f) {
-	if (value > 0) 
-	  value = max(0.0f, value - lambda);
-	else 
-	  value = min(0.0f, value + lambda);
-	
-	if (value != 0.0f) 
-	  i->second = value;
-	else {
-	  toErase.push_back(i->first);
-	  const std::string& fname = (i->first).name();
-	  FName::eraseId(FName::getId(fname));
-	}
+      if (value != 0.0f)
+        i->second = value;
+      else {
+        toErase.push_back(i->first);
+        const std::string& fname = (i->first).name();
+        FName::eraseId(FName::getId(fname));
       }
     }
-    
-    // erase features that have become zero
-    for (size_t i = 0; i < toErase.size(); ++i)
-      m_features.erase(toErase[i]);
-    numberPruned -= size();
-    return numberPruned;
   }
 
-  void FVector::l2regularize(float lambda)  {
-    for (size_t i = 0; i < m_coreFeatures.size(); ++i) {
-      m_coreFeatures[i] *= (1 - lambda);
-    }
+  // erase features that have become zero
+  for (size_t i = 0; i < toErase.size(); ++i)
+    m_features.erase(toErase[i]);
+  numberPruned -= size();
+  return numberPruned;
+}
 
-    for (iterator i = begin(); i != end(); ++i) {
-      i->second *= (1 - lambda);            
-    }
+void FVector::l2regularize(float lambda)
+{
+  for (size_t i = 0; i < m_coreFeatures.size(); ++i) {
+    m_coreFeatures[i] *= (1 - lambda);
   }
 
-  size_t FVector::sparseL1regularize(float lambda) {
-    /*for (size_t i = 0; i < m_coreFeatures.size(); ++i) {
-      float value = m_coreFeatures[i];
-      if (value > 0) {
-        m_coreFeatures[i] = max(0.0f, value - lambda);
-      }
+  for (iterator i = begin(); i != end(); ++i) {
+    i->second *= (1 - lambda);
+  }
+}
+
+size_t FVector::sparseL1regularize(float lambda)
+{
+  /*for (size_t i = 0; i < m_coreFeatures.size(); ++i) {
+    float value = m_coreFeatures[i];
+    if (value > 0) {
+      m_coreFeatures[i] = max(0.0f, value - lambda);
+    }
+    else {
+      m_coreFeatures[i] = min(0.0f, value + lambda);
+    }
+    }*/
+
+  size_t numberPruned = size();
+  vector<FName> toErase;
+  for (iterator i = begin(); i != end(); ++i) {
+    float value = i->second;
+    if (value != 0.0f) {
+      if (value > 0)
+        value = max(0.0f, value - lambda);
+      else
+        value = min(0.0f, value + lambda);
+
+      if (value != 0.0f)
+        i->second = value;
       else {
-        m_coreFeatures[i] = min(0.0f, value + lambda);
-      }
-      }*/
-
-    size_t numberPruned = size();
-    vector<FName> toErase;
-    for (iterator i = begin(); i != end(); ++i) {
-      float value = i->second;
-      if (value != 0.0f) {
-	if (value > 0) 
-	  value = max(0.0f, value - lambda);
-	else 
-	  value = min(0.0f, value + lambda);
-	
-	if (value != 0.0f) 
-	  i->second = value;
-	else {
-	  toErase.push_back(i->first);
-	  const std::string& fname = (i->first).name();
-	  FName::eraseId(FName::getId(fname));
-	}
+        toErase.push_back(i->first);
+        const std::string& fname = (i->first).name();
+        FName::eraseId(FName::getId(fname));
       }
     }
-    
-    // erase features that have become zero
-    for (size_t i = 0; i < toErase.size(); ++i)
-      m_features.erase(toErase[i]);
-    numberPruned -= size();
-    return numberPruned;
   }
 
-  void FVector::sparseL2regularize(float lambda)  {
-    /*for (size_t i = 0; i < m_coreFeatures.size(); ++i) {
-      m_coreFeatures[i] *= (1 - lambda);
-      }*/
+  // erase features that have become zero
+  for (size_t i = 0; i < toErase.size(); ++i)
+    m_features.erase(toErase[i]);
+  numberPruned -= size();
+  return numberPruned;
+}
 
-    for (iterator i = begin(); i != end(); ++i) {
-      i->second *= (1 - lambda);            
-    }
-  }
+void FVector::sparseL2regularize(float lambda)
+{
+  /*for (size_t i = 0; i < m_coreFeatures.size(); ++i) {
+    m_coreFeatures[i] *= (1 - lambda);
+    }*/
 
-  FValue FVector::sum() const {
-    FValue sum = 0;
-    for (const_iterator i = cbegin(); i != cend(); ++i) {
-      sum += i->second;
-    }
-    sum += m_coreFeatures.sum();
-    return sum;
-  }
-    
-  FValue FVector::inner_product(const FVector& rhs) const {
-    CHECK(m_coreFeatures.size() == rhs.m_coreFeatures.size());
-    FValue product = 0.0;
-    for (const_iterator i = cbegin(); i != cend(); ++i) {
-        product += ((i->second)*(rhs.get(i->first)));
-    }
-    for (size_t i = 0; i < m_coreFeatures.size(); ++i) {
-      product += m_coreFeatures[i]*rhs.m_coreFeatures[i];
-    }
-    return product;
+  for (iterator i = begin(); i != end(); ++i) {
+    i->second *= (1 - lambda);
   }
+}
 
-  const FVector operator+(const FVector& lhs, const FVector& rhs) {
-    return FVector(lhs) += rhs;
-  }
-  
-  const FVector operator-(const FVector& lhs, const FVector& rhs) {
-    return FVector(lhs) -= rhs;
+FValue FVector::sum() const
+{
+  FValue sum = 0;
+  for (const_iterator i = cbegin(); i != cend(); ++i) {
+    sum += i->second;
   }
-  
-	const FVector operator*(const FVector& lhs, const FVector& rhs) {
-    return FVector(lhs) *= rhs;
-  }
-  
-  const FVector operator/(const FVector& lhs, const FVector& rhs) {
-    return FVector(lhs) /= rhs;
-  }
-  
-  
-  const FVector operator*(const FVector& lhs, const FValue& rhs) {
-    return FVector(lhs) *= rhs;
+  sum += m_coreFeatures.sum();
+  return sum;
+}
+
+FValue FVector::inner_product(const FVector& rhs) const
+{
+  CHECK(m_coreFeatures.size() == rhs.m_coreFeatures.size());
+  FValue product = 0.0;
+  for (const_iterator i = cbegin(); i != cend(); ++i) {
+    product += ((i->second)*(rhs.get(i->first)));
   }
-  
-  const FVector operator/(const FVector& lhs, const FValue& rhs) {
-    return FVector(lhs) /= rhs;
+  for (size_t i = 0; i < m_coreFeatures.size(); ++i) {
+    product += m_coreFeatures[i]*rhs.m_coreFeatures[i];
   }
+  return product;
+}
 
-  FValue inner_product(const FVector& lhs, const FVector& rhs) {
-    if (lhs.size() >= rhs.size()) {
-      return rhs.inner_product(lhs);
-    } else {
-      return lhs.inner_product(rhs);
-    }
+const FVector operator+(const FVector& lhs, const FVector& rhs)
+{
+  return FVector(lhs) += rhs;
+}
+
+const FVector operator-(const FVector& lhs, const FVector& rhs)
+{
+  return FVector(lhs) -= rhs;
+}
+
+const FVector operator*(const FVector& lhs, const FVector& rhs)
+{
+  return FVector(lhs) *= rhs;
+}
+
+const FVector operator/(const FVector& lhs, const FVector& rhs)
+{
+  return FVector(lhs) /= rhs;
+}
+
+
+const FVector operator*(const FVector& lhs, const FValue& rhs)
+{
+  return FVector(lhs) *= rhs;
+}
+
+const FVector operator/(const FVector& lhs, const FValue& rhs)
+{
+  return FVector(lhs) /= rhs;
+}
+
+FValue inner_product(const FVector& lhs, const FVector& rhs)
+{
+  if (lhs.size() >= rhs.size()) {
+    return rhs.inner_product(lhs);
+  } else {
+    return lhs.inner_product(rhs);
   }
 }
+}
diff --git a/moses/FeatureVector.h b/moses/FeatureVector.h
index 9c15ba4f7..f4261b520 100644
--- a/moses/FeatureVector.h
+++ b/moses/FeatureVector.h
@@ -1,21 +1,21 @@
 /*
  Moses - factored phrase-based language decoder
  Copyright (C) 2010 University of Edinburgh
- 
+
  This program is free software; you can redistribute it and/or modify
  it under the terms of the GNU General Public License as published by
  the Free Software Foundation; either version 2 of the License, or
  (at your option) any later version.
- 
+
  This program is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  GNU General Public License for more details.
- 
+
  You should have received a copy of the GNU General Public License along
  with this program; if not, write to the Free Software Foundation, Inc.,
  51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- 
+
  */
 #pragma once
 
@@ -47,325 +47,336 @@
 #include "util/check.hh"
 #include "util/string_piece.hh"
 
-namespace Moses {
-	
-	typedef float FValue;
-	
-	/**
-	 * Feature name
-	 **/
-	struct FName {
-		
-    static const std::string SEP;
-    
-    typedef boost::unordered_map<std::string,size_t> Name2Id;
-    typedef boost::unordered_map<size_t,size_t> Id2Count;
-    //typedef std::map<std::string, size_t> Name2Id;
-    static Name2Id name2id;
-    static std::vector<std::string> id2name;
-    static Id2Count id2hopeCount;
-    static Id2Count id2fearCount;
-    
-    //A feature name can either be initialised as a pair of strings,
-    //which will be concatenated with a SEP between them, or as
-    //a single string, which will be used as-is.
-    FName(const StringPiece &root, const StringPiece &name) {
-      std::string assembled(root.data(), root.size());
-      assembled += SEP;
-      assembled.append(name.data(), name.size());
-      init(assembled);
-    }
-    explicit FName(const StringPiece &name)
-		{init(name);}
-    
-    const std::string& name() const;
-    //const std::string& root() const {return m_root;}
-    
-    size_t hash() const;
-
-    bool operator==(const FName& rhs) const ;
-    bool operator!=(const FName& rhs) const ;
-		
-    static size_t getId(const std::string& name);
-    static size_t getHopeIdCount(const std::string& name);
-    static size_t getFearIdCount(const std::string& name);
-    static void incrementHopeId(const std::string& name);
-    static void incrementFearId(const std::string& name);
-    static void eraseId(size_t id);
-        
-  private:
-    void init(const StringPiece& name);
-    size_t m_id;
+namespace Moses
+{
+
+typedef float FValue;
+
+/**
+ * Feature name
+ **/
+struct FName {
+
+  static const std::string SEP;
+
+  typedef boost::unordered_map<std::string,size_t> Name2Id;
+  typedef boost::unordered_map<size_t,size_t> Id2Count;
+  //typedef std::map<std::string, size_t> Name2Id;
+  static Name2Id name2id;
+  static std::vector<std::string> id2name;
+  static Id2Count id2hopeCount;
+  static Id2Count id2fearCount;
+
+  //A feature name can either be initialised as a pair of strings,
+  //which will be concatenated with a SEP between them, or as
+  //a single string, which will be used as-is.
+  FName(const StringPiece &root, const StringPiece &name) {
+    std::string assembled(root.data(), root.size());
+    assembled += SEP;
+    assembled.append(name.data(), name.size());
+    init(assembled);
+  }
+  explicit FName(const StringPiece &name) {
+    init(name);
+  }
+
+  const std::string& name() const;
+  //const std::string& root() const {return m_root;}
+
+  size_t hash() const;
+
+  bool operator==(const FName& rhs) const ;
+  bool operator!=(const FName& rhs) const ;
+
+  static size_t getId(const std::string& name);
+  static size_t getHopeIdCount(const std::string& name);
+  static size_t getFearIdCount(const std::string& name);
+  static void incrementHopeId(const std::string& name);
+  static void incrementFearId(const std::string& name);
+  static void eraseId(size_t id);
+
+private:
+  void init(const StringPiece& name);
+  size_t m_id;
 #ifdef WITH_THREADS
-    //reader-writer lock
-    static boost::shared_mutex m_idLock;
+  //reader-writer lock
+  static boost::shared_mutex m_idLock;
 #endif
-	};
-	
-	std::ostream& operator<<(std::ostream& out,const FName& name);
-	
-	struct FNameEquals {
-		inline bool operator() (const FName& lhs, const FName& rhs) const {
-			return (lhs == rhs);
-		}
-	};
-	
-	struct FNameHash
-  : std::unary_function<FName, std::size_t>
-	{
-		std::size_t operator()(const FName& x) const
-		{
-			return x.hash();
-		}
-	};
-	
-	class ProxyFVector;
-	
-	/**
-	 * A sparse feature (or weight) vector.
-	 **/
-	class FVector
-	{
-  public:
-    /** Empty feature vector */
-    FVector(size_t coreFeatures = 0);
-
-    FVector& operator=( const FVector& rhs ) {
-      m_features = rhs.m_features;
-      m_coreFeatures = rhs.m_coreFeatures;
-      return *this;
-    }
+};
 
-    /* 
-     * Change the number of core features
-    **/
-    void resize(size_t newsize);
-
-    typedef boost::unordered_map<FName,FValue,FNameHash, FNameEquals> FNVmap;
-    /** Iterators */
-    typedef FNVmap::iterator iterator;
-    typedef FNVmap::const_iterator const_iterator;
-    iterator begin() {return m_features.begin();}
-    iterator end() {return m_features.end();}
-    const_iterator cbegin() const {return m_features.cbegin();}
-    const_iterator cend() const {return m_features.cend();}
-		
-	bool hasNonDefaultValue(FName name) const { return m_features.find(name) != m_features.end();}
-    void clear();
-    
-    
-    /** Load from file - each line should be 'root[_name] value' */
-    bool load(const std::string& filename);
-    void save(const std::string& filename) const;
-    void write(std::ostream& out) const ;
-    
-    /** Element access */
-    ProxyFVector operator[](const FName& name);
-    FValue& operator[](size_t index);
-    FValue operator[](const FName& name) const;
-    FValue operator[](size_t index) const;
-
-    /** Size */
-    size_t size() const {
-      return m_features.size() + m_coreFeatures.size();
-    }
+std::ostream& operator<<(std::ostream& out,const FName& name);
 
-    size_t coreSize() const {
-      return m_coreFeatures.size();
-    }
-    
-    const std::valarray<FValue> &getCoreFeatures() const {
-      return m_coreFeatures;
-    }
-    
-    /** Equality */
-    bool operator== (const FVector& rhs) const;
-    bool operator!= (const FVector& rhs) const;
-
-    FValue inner_product(const FVector& rhs) const;
-    
-    friend class ProxyFVector;
-    
-    /**arithmetic */
-    //Element-wise
-    //If one side has fewer core features, take the missing ones to be 0.
-    FVector& operator+= (const FVector& rhs);
-    FVector& operator-= (const FVector& rhs);
-    FVector& operator*= (const FVector& rhs);
-    FVector& operator/= (const FVector& rhs);
-    //Scalar
-    FVector& operator*= (const FValue& rhs);
-    FVector& operator/= (const FValue& rhs);
-    
-    FVector& multiplyEqualsBackoff(const FVector& rhs, float backoff);
-    FVector& multiplyEquals(float core_r0, float sparse_r0);
-
-    FVector& max_equals(const FVector& rhs);
-
-    /** norms and sums */
-    FValue l1norm() const;
-    FValue l1norm_coreFeatures() const;
-    FValue l2norm() const;
-    FValue linfnorm() const;
-    size_t l1regularize(float lambda);
-    void l2regularize(float lambda);
-    size_t sparseL1regularize(float lambda);
-    void sparseL2regularize(float lambda);
-    FValue sum() const;
-    
-    /** pretty printing */
-    std::ostream& print(std::ostream& out) const;
-
-    /** additional */
-    void printCoreFeatures();
-    //scale so that abs. value is less than maxvalue
-    void thresholdScale(float maxValue );
-
-    void capMax(FValue maxValue);
-    void capMin(FValue minValue);
-
-    void sparsePlusEquals(const FVector& rhs);
-    void coreAssign(const FVector& rhs);
-    
-    void incrementSparseHopeFeatures();
-    void incrementSparseFearFeatures();
-    void printSparseHopeFeatureCounts(std::ofstream& out);
-    void printSparseFearFeatureCounts(std::ofstream& out);
-    void printSparseHopeFeatureCounts();
-    void printSparseFearFeatureCounts();
-    size_t pruneSparseFeatures(size_t threshold);
-    size_t pruneZeroWeightFeatures();
-    void updateConfidenceCounts(const FVector& weightUpdate, bool signedCounts);
-    void updateLearningRates(float decay_core, float decay_sparse, const FVector& confidence_counts, float core_r0, float sparse_r0);
-    
-    // vector which, for each element of the original vector, reflects whether an element is zero or non-zero
-    void setToBinaryOf(const FVector& rhs);
-
-    // divide only core features by scalar
-    FVector& coreDivideEquals(float scalar);
-
-    // divide each element by the number given in the rhs vector
-    FVector& divideEquals(const FVector& rhs);
+struct FNameEquals {
+  inline bool operator() (const FName& lhs, const FName& rhs) const {
+    return (lhs == rhs);
+  }
+};
+
+struct FNameHash
+    : std::unary_function<FName, std::size_t> {
+  std::size_t operator()(const FName& x) const {
+    return x.hash();
+  }
+};
+
+class ProxyFVector;
+
+/**
+ * A sparse feature (or weight) vector.
+ **/
+class FVector
+{
+public:
+  /** Empty feature vector */
+  FVector(size_t coreFeatures = 0);
+
+  FVector& operator=( const FVector& rhs ) {
+    m_features = rhs.m_features;
+    m_coreFeatures = rhs.m_coreFeatures;
+    return *this;
+  }
+
+  /*
+   * Change the number of core features
+  **/
+  void resize(size_t newsize);
+
+  typedef boost::unordered_map<FName,FValue,FNameHash, FNameEquals> FNVmap;
+  /** Iterators */
+  typedef FNVmap::iterator iterator;
+  typedef FNVmap::const_iterator const_iterator;
+  iterator begin() {
+    return m_features.begin();
+  }
+  iterator end() {
+    return m_features.end();
+  }
+  const_iterator cbegin() const {
+    return m_features.cbegin();
+  }
+  const_iterator cend() const {
+    return m_features.cend();
+  }
+
+  bool hasNonDefaultValue(FName name) const {
+    return m_features.find(name) != m_features.end();
+  }
+  void clear();
+
+
+  /** Load from file - each line should be 'root[_name] value' */
+  bool load(const std::string& filename);
+  void save(const std::string& filename) const;
+  void write(std::ostream& out) const ;
+
+  /** Element access */
+  ProxyFVector operator[](const FName& name);
+  FValue& operator[](size_t index);
+  FValue operator[](const FName& name) const;
+  FValue operator[](size_t index) const;
+
+  /** Size */
+  size_t size() const {
+    return m_features.size() + m_coreFeatures.size();
+  }
+
+  size_t coreSize() const {
+    return m_coreFeatures.size();
+  }
+
+  const std::valarray<FValue> &getCoreFeatures() const {
+    return m_coreFeatures;
+  }
+
+  /** Equality */
+  bool operator== (const FVector& rhs) const;
+  bool operator!= (const FVector& rhs) const;
+
+  FValue inner_product(const FVector& rhs) const;
+
+  friend class ProxyFVector;
+
+  /**arithmetic */
+  //Element-wise
+  //If one side has fewer core features, take the missing ones to be 0.
+  FVector& operator+= (const FVector& rhs);
+  FVector& operator-= (const FVector& rhs);
+  FVector& operator*= (const FVector& rhs);
+  FVector& operator/= (const FVector& rhs);
+  //Scalar
+  FVector& operator*= (const FValue& rhs);
+  FVector& operator/= (const FValue& rhs);
+
+  FVector& multiplyEqualsBackoff(const FVector& rhs, float backoff);
+  FVector& multiplyEquals(float core_r0, float sparse_r0);
+
+  FVector& max_equals(const FVector& rhs);
+
+  /** norms and sums */
+  FValue l1norm() const;
+  FValue l1norm_coreFeatures() const;
+  FValue l2norm() const;
+  FValue linfnorm() const;
+  size_t l1regularize(float lambda);
+  void l2regularize(float lambda);
+  size_t sparseL1regularize(float lambda);
+  void sparseL2regularize(float lambda);
+  FValue sum() const;
+
+  /** pretty printing */
+  std::ostream& print(std::ostream& out) const;
+
+  /** additional */
+  void printCoreFeatures();
+  //scale so that abs. value is less than maxvalue
+  void thresholdScale(float maxValue );
+
+  void capMax(FValue maxValue);
+  void capMin(FValue minValue);
+
+  void sparsePlusEquals(const FVector& rhs);
+  void coreAssign(const FVector& rhs);
+
+  void incrementSparseHopeFeatures();
+  void incrementSparseFearFeatures();
+  void printSparseHopeFeatureCounts(std::ofstream& out);
+  void printSparseFearFeatureCounts(std::ofstream& out);
+  void printSparseHopeFeatureCounts();
+  void printSparseFearFeatureCounts();
+  size_t pruneSparseFeatures(size_t threshold);
+  size_t pruneZeroWeightFeatures();
+  void updateConfidenceCounts(const FVector& weightUpdate, bool signedCounts);
+  void updateLearningRates(float decay_core, float decay_sparse, const FVector& confidence_counts, float core_r0, float sparse_r0);
+
+  // vector which, for each element of the original vector, reflects whether an element is zero or non-zero
+  void setToBinaryOf(const FVector& rhs);
+
+  // divide only core features by scalar
+  FVector& coreDivideEquals(float scalar);
+
+  // divide each element by the number given in the rhs vector
+  FVector& divideEquals(const FVector& rhs);
 
 #ifdef MPI_ENABLE
-    friend class boost::serialization::access;
-#endif  
-    
-  private:
-    
-    /** Internal get and set. */
-    const FValue& get(const FName& name) const;
-    FValue getBackoff(const FName& name, float backoff) const;
-    void set(const FName& name, const FValue& value);
-	       
-    FNVmap m_features;
-    std::valarray<FValue> m_coreFeatures;
-		
+  friend class boost::serialization::access;
+#endif
+
+private:
+
+  /** Internal get and set. */
+  const FValue& get(const FName& name) const;
+  FValue getBackoff(const FName& name, float backoff) const;
+  void set(const FName& name, const FValue& value);
+
+  FNVmap m_features;
+  std::valarray<FValue> m_coreFeatures;
+
 #ifdef MPI_ENABLE
-    //serialization
-    template<class Archive>
-    void save(Archive &ar, const unsigned int version) const {
-			std::vector<std::string> names;
-			std::vector<FValue> values;
-			for (const_iterator i = cbegin(); i != cend(); ++i) {
-				std::ostringstream ostr;
-				ostr << i->first;
-				names.push_back(ostr.str());
-				values.push_back(i->second);
-			}
-			ar << names;
-			ar << values;
-      ar << m_coreFeatures;
+  //serialization
+  template<class Archive>
+  void save(Archive &ar, const unsigned int version) const {
+    std::vector<std::string> names;
+    std::vector<FValue> values;
+    for (const_iterator i = cbegin(); i != cend(); ++i) {
+      std::ostringstream ostr;
+      ostr << i->first;
+      names.push_back(ostr.str());
+      values.push_back(i->second);
     }
-		
-    template<class Archive>
-    void load(Archive &ar, const unsigned int version) {
-			clear();
-			std::vector<std::string> names;
-			std::vector<FValue> values;
-			ar >> names;
-			ar >> values;
-      ar >> m_coreFeatures;
-			CHECK(names.size() == values.size());
-			for (size_t i = 0; i < names.size(); ++i) {
-				set(FName(names[i]), values[i]);
-			}
+    ar << names;
+    ar << values;
+    ar << m_coreFeatures;
+  }
+
+  template<class Archive>
+  void load(Archive &ar, const unsigned int version) {
+    clear();
+    std::vector<std::string> names;
+    std::vector<FValue> values;
+    ar >> names;
+    ar >> values;
+    ar >> m_coreFeatures;
+    CHECK(names.size() == values.size());
+    for (size_t i = 0; i < names.size(); ++i) {
+      set(FName(names[i]), values[i]);
     }
-		
-    BOOST_SERIALIZATION_SPLIT_MEMBER()
-		
+  }
+
+  BOOST_SERIALIZATION_SPLIT_MEMBER()
+
 #endif
-    
-	};
-	
-	std::ostream& operator<<( std::ostream& out, const FVector& fv);
-	//Element-wise operations
-	const FVector operator+(const FVector& lhs, const FVector& rhs);
-	const FVector operator-(const FVector& lhs, const FVector& rhs);
-	const FVector operator*(const FVector& lhs, const FVector& rhs);
-	const FVector operator/(const FVector& lhs, const FVector& rhs);
-	
-	//Scalar operations
-	const FVector operator*(const FVector& lhs, const FValue& rhs);
-	const FVector operator/(const FVector& lhs, const FValue& rhs);
-	
-	const FVector fvmax(const FVector& lhs, const FVector& rhs);
-	
-	FValue inner_product(const FVector& lhs, const FVector& rhs);
-	
-	struct FVectorPlus {
-    FVector operator()(const FVector& lhs, const FVector& rhs) const {
-			return lhs + rhs;
-    }
-	};
-	
-	/**
-	 * Used to help with subscript operator overloading.
-	 * See http://stackoverflow.com/questions/1386075/overloading-operator-for-a-sparse-vector
-	 **/
-	class ProxyFVector {
-  public:
-    ProxyFVector(FVector *fv, const FName& name ) : m_fv(fv), m_name(name) {}
-    ProxyFVector &operator=(const FValue& value) {
-      // If we get here, we know that operator[] was called to perform a write access,
-      // so we can insert an item in the vector if needed
-      //std::cerr << "Inserting " << value << " into " << m_name << std::endl;
-      m_fv->set(m_name,value);
-      return *this;
-      
-    }
-		
-    operator FValue() {
-      // If we get here, we know that operator[] was called to perform a read access,
-      // so we can simply return the value from the vector
-      return m_fv->get(m_name);
-    }
-    
-    /*operator FValue&() {
-		 return m_fv->m_features[m_name];
-		 }*/
-    
-    FValue operator++() {
-      return ++m_fv->m_features[m_name];
-    }
-    
-    FValue operator +=(FValue lhs) {
-      return (m_fv->m_features[m_name] += lhs);
-    }
-    
-    FValue operator -=(FValue lhs) {
-      return (m_fv->m_features[m_name] -= lhs);
-    }
 
-  private:
-    FValue m_tmp;
-    
-  private:
-    FVector* m_fv;
-    const FName& m_name;
-    
-	};
-	
+};
+
+std::ostream& operator<<( std::ostream& out, const FVector& fv);
+//Element-wise operations
+const FVector operator+(const FVector& lhs, const FVector& rhs);
+const FVector operator-(const FVector& lhs, const FVector& rhs);
+const FVector operator*(const FVector& lhs, const FVector& rhs);
+const FVector operator/(const FVector& lhs, const FVector& rhs);
+
+//Scalar operations
+const FVector operator*(const FVector& lhs, const FValue& rhs);
+const FVector operator/(const FVector& lhs, const FValue& rhs);
+
+const FVector fvmax(const FVector& lhs, const FVector& rhs);
+
+FValue inner_product(const FVector& lhs, const FVector& rhs);
+
+struct FVectorPlus {
+  FVector operator()(const FVector& lhs, const FVector& rhs) const {
+    return lhs + rhs;
+  }
+};
+
+/**
+ * Used to help with subscript operator overloading.
+ * See http://stackoverflow.com/questions/1386075/overloading-operator-for-a-sparse-vector
+ **/
+class ProxyFVector
+{
+public:
+  ProxyFVector(FVector *fv, const FName& name ) : m_fv(fv), m_name(name) {}
+  ProxyFVector &operator=(const FValue& value) {
+    // If we get here, we know that operator[] was called to perform a write access,
+    // so we can insert an item in the vector if needed
+    //std::cerr << "Inserting " << value << " into " << m_name << std::endl;
+    m_fv->set(m_name,value);
+    return *this;
+
+  }
+
+  operator FValue() {
+    // If we get here, we know that operator[] was called to perform a read access,
+    // so we can simply return the value from the vector
+    return m_fv->get(m_name);
+  }
+
+  /*operator FValue&() {
+   return m_fv->m_features[m_name];
+   }*/
+
+  FValue operator++() {
+    return ++m_fv->m_features[m_name];
+  }
+
+  FValue operator +=(FValue lhs) {
+    return (m_fv->m_features[m_name] += lhs);
+  }
+
+  FValue operator -=(FValue lhs) {
+    return (m_fv->m_features[m_name] -= lhs);
+  }
+
+private:
+  FValue m_tmp;
+
+private:
+  FVector* m_fv;
+  const FName& m_name;
+
+};
+
 }
 
 #endif
diff --git a/moses/FeatureVectorTest.cpp b/moses/FeatureVectorTest.cpp
index af1829e62..2e00b276e 100644
--- a/moses/FeatureVectorTest.cpp
+++ b/moses/FeatureVectorTest.cpp
@@ -28,41 +28,49 @@ static const float TOL = 0.00001;
 
 BOOST_AUTO_TEST_SUITE(fv)
 
-BOOST_AUTO_TEST_CASE(vector_sum_diff) 
+BOOST_AUTO_TEST_CASE(vector_sum_diff)
 {
   FVector f1,f2,f3;
   FName n1("a");
   FName n2("b");
   FName n3("c");
   FName n4("d");
-  f1[n1] = 1.2; f1[n2] = 1.4; f1[n3] = -0.1;
-  f2[n1] = 0.01; f2[n3] = 5.6; f2[n4] = 0.6;
+  f1[n1] = 1.2;
+  f1[n2] = 1.4;
+  f1[n3] = -0.1;
+  f2[n1] = 0.01;
+  f2[n3] = 5.6;
+  f2[n4] = 0.6;
   f3[n1] =1.2;
   FVector sum = f1 + f2;
   FVector diff = f1 - f2;
-  BOOST_CHECK_CLOSE((FValue)sum[n1], 1.21, TOL); 
-  BOOST_CHECK_CLOSE((FValue)sum[n2], 1.4, TOL); 
-  BOOST_CHECK_CLOSE((FValue)sum[n3], 5.5, TOL); 
-  BOOST_CHECK_CLOSE((FValue)sum[n4], 0.6, TOL); 
-  BOOST_CHECK_CLOSE((FValue)diff[n1], 1.19, TOL); 
-  BOOST_CHECK_CLOSE((FValue)diff[n2], 1.4, TOL); 
-  BOOST_CHECK_CLOSE((FValue)diff[n3], -5.7, TOL); 
-  BOOST_CHECK_CLOSE((FValue)diff[n4], -0.6, TOL); 
+  BOOST_CHECK_CLOSE((FValue)sum[n1], 1.21, TOL);
+  BOOST_CHECK_CLOSE((FValue)sum[n2], 1.4, TOL);
+  BOOST_CHECK_CLOSE((FValue)sum[n3], 5.5, TOL);
+  BOOST_CHECK_CLOSE((FValue)sum[n4], 0.6, TOL);
+  BOOST_CHECK_CLOSE((FValue)diff[n1], 1.19, TOL);
+  BOOST_CHECK_CLOSE((FValue)diff[n2], 1.4, TOL);
+  BOOST_CHECK_CLOSE((FValue)diff[n3], -5.7, TOL);
+  BOOST_CHECK_CLOSE((FValue)diff[n4], -0.6, TOL);
   f1 -= f3;
   cerr << f1 << endl << f3 << endl ;
   BOOST_CHECK_CLOSE((FValue)f1[n1],0,TOL);
 }
 
 
-BOOST_AUTO_TEST_CASE(scalar) 
+BOOST_AUTO_TEST_CASE(scalar)
 {
   FVector f1,f2;
   FName n1("a");
   FName n2("b");
   FName n3("c");
   FName n4("d");
-  f1[n1] = 0.2; f1[n2] = 9.178; f1[n3] = -0.1;
-  f2[n1] = 0.01; f2[n3] = 5.6; f2[n4] = 0.6;
+  f1[n1] = 0.2;
+  f1[n2] = 9.178;
+  f1[n3] = -0.1;
+  f2[n1] = 0.01;
+  f2[n3] = 5.6;
+  f2[n4] = 0.6;
   FVector prod1 = f1 * 2;
   FVector prod2 = f1 * -0.1;
   FVector quot = f2 / 2;
@@ -80,12 +88,13 @@ BOOST_AUTO_TEST_CASE(scalar)
   BOOST_CHECK_CLOSE((FValue)quot[n4], 0.3, TOL);
 }
 
-BOOST_AUTO_TEST_CASE(inc) 
+BOOST_AUTO_TEST_CASE(inc)
 {
   FVector f1;
   FName n1("a");
   FName n2("b");
-  f1[n1] = 2.3; f1[n2] = -0.4;
+  f1[n1] = 2.3;
+  f1[n2] = -0.4;
   f1[n1]+=2;
   BOOST_CHECK_CLOSE((FValue)f1[n1], 4.3, TOL);
   BOOST_CHECK_CLOSE((FValue)f1[n2], -0.4, TOL);
@@ -103,8 +112,13 @@ BOOST_AUTO_TEST_CASE(vector_mult)
   FName n2("b");
   FName n3("c");
   FName n4("d");
-  f1[n1] = 0.2; f1[n2] = 9.178;  f1[n3] = -0.1;
-  f2[n1] = 0.01; f2[n2] = 5.6; f2[n3] = 1; f2[n4] = 0.6;
+  f1[n1] = 0.2;
+  f1[n2] = 9.178;
+  f1[n3] = -0.1;
+  f2[n1] = 0.01;
+  f2[n2] = 5.6;
+  f2[n3] = 1;
+  f2[n4] = 0.6;
   FVector prod = f1 * f2;
   FVector quot = f1/f2;
   BOOST_CHECK_CLOSE((FValue)prod[n1], 0.002, TOL);
@@ -118,7 +132,7 @@ BOOST_AUTO_TEST_CASE(vector_mult)
   BOOST_CHECK_CLOSE((FValue)quot[n4], 0, TOL);
 }
 
-BOOST_AUTO_TEST_CASE(core) 
+BOOST_AUTO_TEST_CASE(core)
 {
   FVector f1(2);
   f1[0] = 1.3;
@@ -127,7 +141,7 @@ BOOST_AUTO_TEST_CASE(core)
   BOOST_CHECK_CLOSE(f1[1],-1.9,TOL);
   f1[1] = 0.1;
   BOOST_CHECK_CLOSE(f1[1],0.1,TOL);
-  
+
   BOOST_CHECK_EQUAL(f1.size(),2);
 
   f1[FName("a")] = 1.2;
@@ -140,8 +154,13 @@ BOOST_AUTO_TEST_CASE(core_arith)
   FVector f2(2);
   FName n1("a");
   FName n2("b");
-  f1[0] = 1.1; f1[1] = 0.25; f1[n1] = 3.6; f1[n2] = -1.5;
-  f2[0] = 0.5; f2[1] = -0.1; f2[n1] = 1;
+  f1[0] = 1.1;
+  f1[1] = 0.25;
+  f1[n1] = 3.6;
+  f1[n2] = -1.5;
+  f2[0] = 0.5;
+  f2[1] = -0.1;
+  f2[n1] = 1;
 
   //vector ops
   FVector sum = f1+f2;
@@ -172,9 +191,10 @@ BOOST_AUTO_TEST_CASE(core_arith)
   //with different length vectors
   FVector f3(2);
   FVector f4(1);
-  f3[0] = 2; f3[1] = -1;
+  f3[0] = 2;
+  f3[1] = -1;
   f4[0] = 5;
-  
+
   FVector sum1 = f3 + f4;
   FVector sum2 = f4 + f3;
   BOOST_CHECK_EQUAL(sum1,sum2);
@@ -200,14 +220,17 @@ BOOST_AUTO_TEST_CASE(core_arith)
   BOOST_CHECK_EQUAL(quot1[1], -numeric_limits<float>::infinity());
   BOOST_CHECK_CLOSE(quot2[0], 2.5, TOL);
   BOOST_CHECK_CLOSE(quot2[1], 0, TOL);
-  
+
 }
 
 BOOST_AUTO_TEST_CASE(core_scalar)
 {
   FVector f1(3);
   FName n1("a");
-  f1[0] = 1.5; f1[1] = 2.1; f1[2] = 4; f1[n1] = -0.5;
+  f1[0] = 1.5;
+  f1[1] = 2.1;
+  f1[2] = 4;
+  f1[n1] = -0.5;
 
   FVector prod = f1*2;
   FVector quot = f1/5;
@@ -224,31 +247,41 @@ BOOST_AUTO_TEST_CASE(core_scalar)
 
 }
 
-BOOST_AUTO_TEST_CASE(l1norm) 
+BOOST_AUTO_TEST_CASE(l1norm)
 {
   FVector f1(3);
   FName n1("a");
-  f1[0] = 1.5; f1[1] = 2.1; f1[2] = 4; f1[n1] = -0.5;
+  f1[0] = 1.5;
+  f1[1] = 2.1;
+  f1[2] = 4;
+  f1[n1] = -0.5;
   FValue n = f1.l1norm();
   BOOST_CHECK_CLOSE((FValue)n, abs(1.5)+abs(2.1)+abs(4)+abs(-0.5), TOL);
 }
 
 
-BOOST_AUTO_TEST_CASE(sum) 
+BOOST_AUTO_TEST_CASE(sum)
 {
   FVector f1(3);
   FName n1("a");
   FName n2("b");
-  f1[0] = 1.5; f1[1] = 2.1; f1[2] = 4; f1[n1] = -0.5; f1[n2] = 2.7;
+  f1[0] = 1.5;
+  f1[1] = 2.1;
+  f1[2] = 4;
+  f1[n1] = -0.5;
+  f1[n2] = 2.7;
   FValue n = f1.sum();
   BOOST_CHECK_CLOSE((FValue)n, 1.5+2.1+4-0.5+2.7, TOL);
 }
 
-BOOST_AUTO_TEST_CASE(l2norm) 
+BOOST_AUTO_TEST_CASE(l2norm)
 {
   FVector f1(3);
   FName n1("a");
-  f1[0] = 1.5; f1[1] = 2.1; f1[2] = 4; f1[n1] = -0.5;
+  f1[0] = 1.5;
+  f1[1] = 2.1;
+  f1[2] = 4;
+  f1[n1] = -0.5;
   FValue n = f1.l2norm();
   BOOST_CHECK_CLOSE((FValue)n, sqrt((1.5*1.5)+(2.1*2.1)+(4*4)+(-0.5*-0.5)), TOL);
 }
@@ -260,8 +293,14 @@ BOOST_AUTO_TEST_CASE(ip)
   FName n1("a");
   FName n2("b");
   FName n3("c");
-  f1[0] = 1.1; f1[1] = -0.1; ; f1[n2] = -1.5; f1[n3] = 2.2;
-  f2[0] = 0.5; f2[1] = 0.25; f2[n1] = 1; f2[n3] = 2.4;
+  f1[0] = 1.1;
+  f1[1] = -0.1; ;
+  f1[n2] = -1.5;
+  f1[n3] = 2.2;
+  f2[0] = 0.5;
+  f2[1] = 0.25;
+  f2[n1] = 1;
+  f2[n3] = 2.4;
   FValue p1 = inner_product(f1,f2);
   FValue p2 = inner_product(f2,f1);
   BOOST_CHECK_CLOSE(p1,p2,TOL);
diff --git a/moses/GenerationDictionary.cpp b/moses/GenerationDictionary.cpp
index f9f418197..dbc0eedb3 100644
--- a/moses/GenerationDictionary.cpp
+++ b/moses/GenerationDictionary.cpp
@@ -35,7 +35,7 @@ namespace Moses
 {
 
 GenerationDictionary::GenerationDictionary(const std::string &line)
-: DecodeFeature("Generation", line)
+  : DecodeFeature("Generation", line)
 {
   string filePath;
 
@@ -44,8 +44,7 @@ GenerationDictionary::GenerationDictionary(const std::string &line)
 
     if (args[0] == "path") {
       filePath = args[1];
-    }
-    else {
+    } else {
       //UserMessage::Add("Unknown argument " + args[0]);
       //abort();
     }
diff --git a/moses/GenerationDictionary.h b/moses/GenerationDictionary.h
index 6a1e4de9a..b2aeb0d96 100644
--- a/moses/GenerationDictionary.h
+++ b/moses/GenerationDictionary.h
@@ -53,22 +53,21 @@ protected:
 
 public:
   GenerationDictionary(const std::string &line);
-	virtual ~GenerationDictionary();
-	
-	//! load data file
-	bool Load(const std::string &filePath, FactorDirection direction);
-
-	/** number of unique input entries in the generation table. 
-	* NOT the number of lines in the generation table
-	*/
-	size_t GetSize() const
-	{
-		return m_collection.size();
-	}
-	/** returns a bag of output words, OutputWordCollection, for a particular input word. 
-	*	Or NULL if the input word isn't found. The search function used is the WordComparer functor
-	*/
-	const OutputWordCollection *FindWord(const Word &word) const;
+  virtual ~GenerationDictionary();
+
+  //! load data file
+  bool Load(const std::string &filePath, FactorDirection direction);
+
+  /** number of unique input entries in the generation table.
+  * NOT the number of lines in the generation table
+  */
+  size_t GetSize() const {
+    return m_collection.size();
+  }
+  /** returns a bag of output words, OutputWordCollection, for a particular input word.
+  *	Or NULL if the input word isn't found. The search function used is the WordComparer functor
+  */
+  const OutputWordCollection *FindWord(const Word &word) const;
 
 };
 
diff --git a/moses/Hypothesis.cpp b/moses/Hypothesis.cpp
index 7bc3e6a75..50443904c 100644
--- a/moses/Hypothesis.cpp
+++ b/moses/Hypothesis.cpp
@@ -60,8 +60,8 @@ Hypothesis::Hypothesis(Manager& manager, InputType const& source, const TargetPh
   , m_arcList(NULL)
   , m_transOpt(NULL)
   , m_manager(manager)
-,	m_totalScore(0.0f)
-,	m_futureScore(0.0f)
+  ,	m_totalScore(0.0f)
+  ,	m_futureScore(0.0f)
 
   , m_id(m_manager.GetNextHypoId())
 {
@@ -248,20 +248,22 @@ int Hypothesis::RecombineCompare(const Hypothesis &compare) const
     }
     if (comp != 0) return comp;
   }
-  
+
   return 0;
 }
 
 void Hypothesis::EvaluateWith(const StatefulFeatureFunction &sfff,
-                              int state_idx) {
+                              int state_idx)
+{
   m_ffStates[state_idx] = sfff.Evaluate(
-      *this,
-      m_prevHypo ? m_prevHypo->m_ffStates[state_idx] : NULL,
-      &m_scoreBreakdown);
-            
+                            *this,
+                            m_prevHypo ? m_prevHypo->m_ffStates[state_idx] : NULL,
+                            &m_scoreBreakdown);
+
 }
 
-void Hypothesis::EvaluateWith(const StatelessFeatureFunction& slff) {
+void Hypothesis::EvaluateWith(const StatelessFeatureFunction& slff)
+{
   slff.Evaluate(PhraseBasedFeatureContext(this), &m_scoreBreakdown);
 }
 
@@ -280,14 +282,14 @@ void Hypothesis::CalcScore(const SquareMatrix &futureScore)
   // compute values of stateless feature functions that were not
   // cached in the translation option
   const vector<const StatelessFeatureFunction*>& sfs =
-      StatelessFeatureFunction::GetStatelessFeatureFunctions();
+    StatelessFeatureFunction::GetStatelessFeatureFunctions();
   for (unsigned i = 0; i < sfs.size(); ++i) {
-	const StatelessFeatureFunction &ff = *sfs[i];
+    const StatelessFeatureFunction &ff = *sfs[i];
     EvaluateWith(ff);
   }
 
   const vector<const StatefulFeatureFunction*>& ffs =
-      StatefulFeatureFunction::GetStatefulFeatureFunctions();
+    StatefulFeatureFunction::GetStatefulFeatureFunctions();
   for (unsigned i = 0; i < ffs.size(); ++i) {
     const StatefulFeatureFunction &ff = *ffs[i];
     m_ffStates[i] = ff.Evaluate(
diff --git a/moses/HypothesisStack.h b/moses/HypothesisStack.h
index 26e6ed21b..0c3d4198f 100644
--- a/moses/HypothesisStack.h
+++ b/moses/HypothesisStack.h
@@ -11,7 +11,7 @@ namespace Moses
 
 class Manager;
 
-/** abstract unique set of hypotheses that cover a certain number of words, 
+/** abstract unique set of hypotheses that cover a certain number of words,
  *  ie. a stack in phrase-based decoding
  */
 class HypothesisStack
diff --git a/moses/Incremental.cpp b/moses/Incremental.cpp
index 3eb66fb0e..e4159063c 100644
--- a/moses/Incremental.cpp
+++ b/moses/Incremental.cpp
@@ -19,90 +19,98 @@
 
 #include <boost/lexical_cast.hpp>
 
-namespace Moses {
-namespace Incremental {
-namespace {
+namespace Moses
+{
+namespace Incremental
+{
+namespace
+{
 
 // This is called by EdgeGenerator.  Route hypotheses to separate vertices for
-// each left hand side label, populating ChartCellLabelSet out.  
-template <class Best> class HypothesisCallback {
-  private:
-    typedef search::VertexGenerator<Best> Gen;
-  public:
-    HypothesisCallback(search::ContextBase &context, Best &best, ChartCellLabelSet &out, boost::object_pool<search::Vertex> &vertex_pool)
-      : context_(context), best_(best), out_(out), vertex_pool_(vertex_pool) {}
-
-    void NewHypothesis(search::PartialEdge partial) {
-      // Get the LHS, look it up in the output ChartCellLabel, and upcast it.  
-      // It's not part of the union because it would have been ugly to expose template types in ChartCellLabel.
-      ChartCellLabel::Stack &stack = out_.FindOrInsert(static_cast<const TargetPhrase *>(partial.GetNote().vp)->GetTargetLHS());
-      Gen *entry = static_cast<Gen*>(stack.incr_generator);
-      if (!entry) {
-        entry = generator_pool_.construct(context_, *vertex_pool_.construct(), best_);
-        stack.incr_generator = entry;
-      }
-      entry->NewHypothesis(partial);
+// each left hand side label, populating ChartCellLabelSet out.
+template <class Best> class HypothesisCallback
+{
+private:
+  typedef search::VertexGenerator<Best> Gen;
+public:
+  HypothesisCallback(search::ContextBase &context, Best &best, ChartCellLabelSet &out, boost::object_pool<search::Vertex> &vertex_pool)
+    : context_(context), best_(best), out_(out), vertex_pool_(vertex_pool) {}
+
+  void NewHypothesis(search::PartialEdge partial) {
+    // Get the LHS, look it up in the output ChartCellLabel, and upcast it.
+    // It's not part of the union because it would have been ugly to expose template types in ChartCellLabel.
+    ChartCellLabel::Stack &stack = out_.FindOrInsert(static_cast<const TargetPhrase *>(partial.GetNote().vp)->GetTargetLHS());
+    Gen *entry = static_cast<Gen*>(stack.incr_generator);
+    if (!entry) {
+      entry = generator_pool_.construct(context_, *vertex_pool_.construct(), best_);
+      stack.incr_generator = entry;
     }
+    entry->NewHypothesis(partial);
+  }
 
-    void FinishedSearch() {
-      for (ChartCellLabelSet::iterator i(out_.mutable_begin()); i != out_.mutable_end(); ++i) {
-        ChartCellLabel::Stack &stack = i->second.MutableStack();
-        Gen *gen = static_cast<Gen*>(stack.incr_generator);
-        gen->FinishedSearch();
-        stack.incr = &gen->Generating();
-      }
+  void FinishedSearch() {
+    for (ChartCellLabelSet::iterator i(out_.mutable_begin()); i != out_.mutable_end(); ++i) {
+      ChartCellLabel::Stack &stack = i->second.MutableStack();
+      Gen *gen = static_cast<Gen*>(stack.incr_generator);
+      gen->FinishedSearch();
+      stack.incr = &gen->Generating();
     }
+  }
 
-  private:
-    search::ContextBase &context_;
+private:
+  search::ContextBase &context_;
 
-    Best &best_;
+  Best &best_;
 
-    ChartCellLabelSet &out_;
+  ChartCellLabelSet &out_;
 
-    boost::object_pool<search::Vertex> &vertex_pool_;
-    boost::object_pool<Gen> generator_pool_;
+  boost::object_pool<search::Vertex> &vertex_pool_;
+  boost::object_pool<Gen> generator_pool_;
 };
 
 // This is called by the moses parser to collect hypotheses.  It converts to my
-// edges (search::PartialEdge).  
-template <class Model> class Fill : public ChartParserCallback {
-  public:
-    Fill(search::Context<Model> &context, const std::vector<lm::WordIndex> &vocab_mapping, search::Score oov_weight)
-      : context_(context), vocab_mapping_(vocab_mapping), oov_weight_(oov_weight) {}
+// edges (search::PartialEdge).
+template <class Model> class Fill : public ChartParserCallback
+{
+public:
+  Fill(search::Context<Model> &context, const std::vector<lm::WordIndex> &vocab_mapping, search::Score oov_weight)
+    : context_(context), vocab_mapping_(vocab_mapping), oov_weight_(oov_weight) {}
 
-    void Add(const TargetPhraseCollection &targets, const StackVec &nts, const WordsRange &ignored);
+  void Add(const TargetPhraseCollection &targets, const StackVec &nts, const WordsRange &ignored);
 
-    void AddPhraseOOV(TargetPhrase &phrase, std::list<TargetPhraseCollection*> &waste_memory, const WordsRange &range);
+  void AddPhraseOOV(TargetPhrase &phrase, std::list<TargetPhraseCollection*> &waste_memory, const WordsRange &range);
 
-    bool Empty() const { return edges_.Empty(); }
+  bool Empty() const {
+    return edges_.Empty();
+  }
 
-    template <class Best> void Search(Best &best, ChartCellLabelSet &out, boost::object_pool<search::Vertex> &vertex_pool) {
-      HypothesisCallback<Best> callback(context_, best, out, vertex_pool);
-      edges_.Search(context_, callback);
-    }
+  template <class Best> void Search(Best &best, ChartCellLabelSet &out, boost::object_pool<search::Vertex> &vertex_pool) {
+    HypothesisCallback<Best> callback(context_, best, out, vertex_pool);
+    edges_.Search(context_, callback);
+  }
 
-    // Root: everything into one vertex.  
-    template <class Best> search::History RootSearch(Best &best) {
-      search::Vertex vertex;
-      search::RootVertexGenerator<Best> gen(vertex, best);
-      edges_.Search(context_, gen);
-      return vertex.BestChild();
-    }
+  // Root: everything into one vertex.
+  template <class Best> search::History RootSearch(Best &best) {
+    search::Vertex vertex;
+    search::RootVertexGenerator<Best> gen(vertex, best);
+    edges_.Search(context_, gen);
+    return vertex.BestChild();
+  }
 
-  private:
-    lm::WordIndex Convert(const Word &word) const;
+private:
+  lm::WordIndex Convert(const Word &word) const;
 
-    search::Context<Model> &context_;
+  search::Context<Model> &context_;
 
-    const std::vector<lm::WordIndex> &vocab_mapping_;
+  const std::vector<lm::WordIndex> &vocab_mapping_;
 
-    search::EdgeGenerator edges_;
+  search::EdgeGenerator edges_;
 
-    const search::Score oov_weight_;
+  const search::Score oov_weight_;
 };
 
-template <class Model> void Fill<Model>::Add(const TargetPhraseCollection &targets, const StackVec &nts, const WordsRange &) {
+template <class Model> void Fill<Model>::Add(const TargetPhraseCollection &targets, const StackVec &nts, const WordsRange &)
+{
   std::vector<search::PartialVertex> vertices;
   vertices.reserve(nts.size());
   float below_score = 0.0;
@@ -131,7 +139,7 @@ template <class Model> void Fill<Model>::Add(const TargetPhraseCollection &targe
     }
 
     edge.SetScore(phrase.GetFutureScore() + below_score);
-    // prob and oov were already accounted for.  
+    // prob and oov were already accounted for.
     search::ScoreRule(context_.LanguageModel(), words, edge.Between());
 
     search::Note note;
@@ -142,14 +150,15 @@ template <class Model> void Fill<Model>::Add(const TargetPhraseCollection &targe
   }
 }
 
-template <class Model> void Fill<Model>::AddPhraseOOV(TargetPhrase &phrase, std::list<TargetPhraseCollection*> &, const WordsRange &) {
+template <class Model> void Fill<Model>::AddPhraseOOV(TargetPhrase &phrase, std::list<TargetPhraseCollection*> &, const WordsRange &)
+{
   std::vector<lm::WordIndex> words;
   CHECK(phrase.GetSize() <= 1);
   if (phrase.GetSize())
     words.push_back(Convert(phrase.GetWord(0)));
 
   search::PartialEdge edge(edges_.AllocateEdge(0));
-  // Appears to be a bug that FutureScore does not already include language model. 
+  // Appears to be a bug that FutureScore does not already include language model.
   search::ScoreRuleRet scored(search::ScoreRule(context_.LanguageModel(), words, edge.Between()));
   edge.SetScore(phrase.GetFutureScore() + scored.prob * context_.LMWeight() + static_cast<search::Score>(scored.oov) * oov_weight_);
 
@@ -160,8 +169,9 @@ template <class Model> void Fill<Model>::AddPhraseOOV(TargetPhrase &phrase, std:
   edges_.AddEdge(edge);
 }
 
-// TODO: factors (but chart doesn't seem to support factors anyway). 
-template <class Model> lm::WordIndex Fill<Model>::Convert(const Word &word) const {
+// TODO: factors (but chart doesn't seem to support factors anyway).
+template <class Model> lm::WordIndex Fill<Model>::Convert(const Word &word) const
+{
   std::size_t factor = word.GetFactor(0)->GetId();
   return (factor >= vocab_mapping_.size() ? 0 : vocab_mapping_[factor]);
 }
@@ -180,10 +190,12 @@ Manager::Manager(const InputType &source) :
   parser_(source, cells_),
   n_best_(search::NBestConfig(StaticData::Instance().GetNBestSize())) {}
 
-Manager::~Manager() {
+Manager::~Manager()
+{
 }
 
-template <class Model, class Best> search::History Manager::PopulateBest(const Model &model, const std::vector<lm::WordIndex> &words, Best &out) {
+template <class Model, class Best> search::History Manager::PopulateBest(const Model &model, const std::vector<lm::WordIndex> &words, Best &out)
+{
   const LanguageModel &abstract = LanguageModel::GetFirstLM();
   const float oov_weight = abstract.OOVFeatureEnabled() ? abstract.GetOOVWeight() : 0.0;
   const StaticData &data = StaticData::Instance();
@@ -192,7 +204,7 @@ template <class Model, class Best> search::History Manager::PopulateBest(const M
 
   size_t size = source_.GetSize();
   boost::object_pool<search::Vertex> vertex_pool(std::max<size_t>(size * size / 2, 32));
-  
+
   for (size_t width = 1; width < size; ++width) {
     for (size_t startPos = 0; startPos <= size-width; ++startPos) {
       WordsRange range(startPos, startPos + width - 1);
@@ -208,7 +220,8 @@ template <class Model, class Best> search::History Manager::PopulateBest(const M
   return filler.RootSearch(out);
 }
 
-template <class Model> void Manager::LMCallback(const Model &model, const std::vector<lm::WordIndex> &words) {
+template <class Model> void Manager::LMCallback(const Model &model, const std::vector<lm::WordIndex> &words)
+{
   std::size_t nbest = StaticData::Instance().GetNBestSize();
   if (nbest <= 1) {
     search::History ret = PopulateBest(model, words, single_best_);
@@ -237,12 +250,14 @@ template void Manager::LMCallback<lm::ngram::QuantTrieModel>(const lm::ngram::Qu
 template void Manager::LMCallback<lm::ngram::ArrayTrieModel>(const lm::ngram::ArrayTrieModel &model, const std::vector<lm::WordIndex> &words);
 template void Manager::LMCallback<lm::ngram::QuantArrayTrieModel>(const lm::ngram::QuantArrayTrieModel &model, const std::vector<lm::WordIndex> &words);
 
-const std::vector<search::Applied> &Manager::ProcessSentence() {
+const std::vector<search::Applied> &Manager::ProcessSentence()
+{
   LanguageModel::GetFirstLM().IncrementalCallback(*this);
   return *completed_nbest_;
 }
 
-namespace {
+namespace
+{
 
 struct NoOp {
   void operator()(const TargetPhrase &) const {}
@@ -254,7 +269,8 @@ struct AccumScore {
   }
   ScoreComponentCollection *out_;
 };
-template <class Action> void AppendToPhrase(const search::Applied final, Phrase &out, Action action) {
+template <class Action> void AppendToPhrase(const search::Applied final, Phrase &out, Action action)
+{
   assert(final.Valid());
   const TargetPhrase &phrase = *static_cast<const TargetPhrase*>(final.GetNote().vp);
   action(phrase);
@@ -271,23 +287,25 @@ template <class Action> void AppendToPhrase(const search::Applied final, Phrase
 
 } // namespace
 
-void ToPhrase(const search::Applied final, Phrase &out) {
+void ToPhrase(const search::Applied final, Phrase &out)
+{
   out.Clear();
   AppendToPhrase(final, out, NoOp());
 }
 
-void PhraseAndFeatures(const search::Applied final, Phrase &phrase, ScoreComponentCollection &features) {
+void PhraseAndFeatures(const search::Applied final, Phrase &phrase, ScoreComponentCollection &features)
+{
   phrase.Clear();
   features.ZeroAll();
   AppendToPhrase(final, phrase, AccumScore(features));
 
-  // If we made it this far, there is only one language model.  
+  // If we made it this far, there is only one language model.
   float full, ignored_ngram;
   std::size_t ignored_oov;
 
   const LanguageModel &model = LanguageModel::GetFirstLM();
   model.CalcScore(phrase, full, ignored_ngram, ignored_oov);
-  // CalcScore transforms, but EvaluateChart doesn't.  
+  // CalcScore transforms, but EvaluateChart doesn't.
   features.Assign(&model, full);
 }
 
diff --git a/moses/Incremental.h b/moses/Incremental.h
index 30f7c588c..20040bf45 100644
--- a/moses/Incremental.h
+++ b/moses/Incremental.h
@@ -10,49 +10,52 @@
 #include <vector>
 #include <string>
 
-namespace Moses {
+namespace Moses
+{
 class ScoreComponentCollection;
 class InputType;
 class LanguageModel;
 
-namespace Incremental {
+namespace Incremental
+{
 
-class Manager {
-  public:
-    Manager(const InputType &source);
+class Manager
+{
+public:
+  Manager(const InputType &source);
 
-    ~Manager();
+  ~Manager();
 
-    template <class Model> void LMCallback(const Model &model, const std::vector<lm::WordIndex> &words);
-    
-    const std::vector<search::Applied> &ProcessSentence();
+  template <class Model> void LMCallback(const Model &model, const std::vector<lm::WordIndex> &words);
 
-    // Call to get the same value as ProcessSentence returned.  
-    const std::vector<search::Applied> &Completed() const {
-      return *completed_nbest_;
-    }
+  const std::vector<search::Applied> &ProcessSentence();
 
-  private:
-    template <class Model, class Best> search::History PopulateBest(const Model &model, const std::vector<lm::WordIndex> &words, Best &out);
+  // Call to get the same value as ProcessSentence returned.
+  const std::vector<search::Applied> &Completed() const {
+    return *completed_nbest_;
+  }
 
-    const InputType &source_;
-    ChartCellCollectionBase cells_;
-    ChartParser parser_;
+private:
+  template <class Model, class Best> search::History PopulateBest(const Model &model, const std::vector<lm::WordIndex> &words, Best &out);
 
-    // Only one of single_best_ or n_best_ will be used, but it was easier to do this than a template. 
-    search::SingleBest single_best_;
-    // ProcessSentence returns a reference to a vector.  ProcessSentence
-    // doesn't have one, so this is populated and returned.  
-    std::vector<search::Applied> backing_for_single_;
+  const InputType &source_;
+  ChartCellCollectionBase cells_;
+  ChartParser parser_;
 
-    search::NBest n_best_;
-    
-    const std::vector<search::Applied> *completed_nbest_;
+  // Only one of single_best_ or n_best_ will be used, but it was easier to do this than a template.
+  search::SingleBest single_best_;
+  // ProcessSentence returns a reference to a vector.  ProcessSentence
+  // doesn't have one, so this is populated and returned.
+  std::vector<search::Applied> backing_for_single_;
+
+  search::NBest n_best_;
+
+  const std::vector<search::Applied> *completed_nbest_;
 };
 
 // Just get the phrase.
 void ToPhrase(const search::Applied final, Phrase &out);
-// Get the phrase and the features.  
+// Get the phrase and the features.
 void PhraseAndFeatures(const search::Applied final, Phrase &phrase, ScoreComponentCollection &features);
 
 
diff --git a/moses/InputType.cpp b/moses/InputType.cpp
index 64dc9a7fd..1ca3da63b 100644
--- a/moses/InputType.cpp
+++ b/moses/InputType.cpp
@@ -67,7 +67,7 @@ std::vector <ChartTranslationOptions*> InputType::GetXmlChartTranslationOptions(
   std::vector <ChartTranslationOptions*> ret;
   return ret;
 }
-  
+
 }
 
 
diff --git a/moses/InputType.h b/moses/InputType.h
index a065c0bf0..d0106e5ca 100644
--- a/moses/InputType.h
+++ b/moses/InputType.h
@@ -38,9 +38,9 @@ class Factor;
 class PhraseDictionary;
 class TranslationOptionCollection;
 class ChartTranslationOptions;
-  
+
 /** base class for all types of inputs to the decoder,
- *  eg. sentences, confusion networks, lattices and tree 
+ *  eg. sentences, confusion networks, lattices and tree
  */
 class InputType
 {
@@ -81,7 +81,7 @@ public:
   }
   void SetDocumentId(long documentId) {
     m_documentId = documentId;
-  }  
+  }
   long GetTopicId() const {
     return m_topicId;
   }
@@ -111,7 +111,7 @@ public:
   }
   void SetTextType(std::string type) {
     m_textType = type;
-  }  
+  }
   std::string GetPassthroughInformation() const {
     return m_passthrough;
   }
diff --git a/moses/LM/Backward.cpp b/moses/LM/Backward.cpp
index a9fca1c75..263c90fec 100644
--- a/moses/LM/Backward.cpp
+++ b/moses/LM/Backward.cpp
@@ -35,281 +35,288 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //#include "moses/StaticData.h"
 //#include <iostream>
 
-namespace Moses {
-
-  /** Constructs a new backward language model. */
-  template <class Model> BackwardLanguageModel<Model>::BackwardLanguageModel(const std::string &file, FactorType factorType, bool lazy) : LanguageModelKen<Model>(file,factorType,lazy) {
-    //
-    // This space intentionally left blank
-    //
-  }
-
-  /** 
-   * Constructs an empty backward language model state.
-   *
-   * This state will correspond with a translation hypothesis 
-   * where no source words have been translated.
-   *
-   * In a forward language model, the language model state of an empty hypothesis 
-   * would store the beginning of sentence marker <s>.
-   *
-   * Because this is a backward language model, the language model state returned by this method
-   * instead stores the end of sentence marker </s>.
-   */
-  template <class Model> const FFState *BackwardLanguageModel<Model>::EmptyHypothesisState(const InputType &/*input*/) const {
-    BackwardLMState *ret = new BackwardLMState();
-    lm::ngram::RuleScore<Model> ruleScore(*m_ngram, ret->state);
-    ruleScore.Terminal(m_ngram->GetVocabulary().EndSentence());
-    //    float score = 
-    ruleScore.Finish();
-    //    VERBOSE(1, "BackwardLM EmptyHypothesisState has score " << score);
-    return ret;
-  }
-  /*
-  template <class Model> double BackwardLanguageModel<Model>::Score(FFState *ffState) {
-    BackwardLMState *lmState = static_cast< BackwardLMState* >(ffState);
-    lm::ngram::ChartState &state = lmState->state;
-    lm::ngram::RuleScore<Model> ruleScore(*m_ngram, lmState);
-    return ruleScore.Finish();
-  }
+namespace Moses
+{
+
+/** Constructs a new backward language model. */
+template <class Model> BackwardLanguageModel<Model>::BackwardLanguageModel(const std::string &file, FactorType factorType, bool lazy) : LanguageModelKen<Model>(file,factorType,lazy)
+{
+  //
+  // This space intentionally left blank
+  //
+}
+
+/**
+ * Constructs an empty backward language model state.
+ *
+ * This state will correspond with a translation hypothesis
+ * where no source words have been translated.
+ *
+ * In a forward language model, the language model state of an empty hypothesis
+ * would store the beginning of sentence marker <s>.
+ *
+ * Because this is a backward language model, the language model state returned by this method
+ * instead stores the end of sentence marker </s>.
+ */
+template <class Model> const FFState *BackwardLanguageModel<Model>::EmptyHypothesisState(const InputType &/*input*/) const
+{
+  BackwardLMState *ret = new BackwardLMState();
+  lm::ngram::RuleScore<Model> ruleScore(*m_ngram, ret->state);
+  ruleScore.Terminal(m_ngram->GetVocabulary().EndSentence());
+  //    float score =
+  ruleScore.Finish();
+  //    VERBOSE(1, "BackwardLM EmptyHypothesisState has score " << score);
+  return ret;
+}
+/*
+template <class Model> double BackwardLanguageModel<Model>::Score(FFState *ffState) {
+  BackwardLMState *lmState = static_cast< BackwardLMState* >(ffState);
+  lm::ngram::ChartState &state = lmState->state;
+  lm::ngram::RuleScore<Model> ruleScore(*m_ngram, lmState);
+  return ruleScore.Finish();
+}
 */
-  /**
-   * Pre-calculate the n-gram probabilities for the words in the specified phrase.
-   * 
-   * Note that when this method is called, we do not have access to the context
-   * in which this phrase will eventually be applied. 
-   *
-   * In other words, we know what words are in this phrase,
-   * but we do not know what words will come before or after this phrase.
-   *
-   * The parameters fullScore, ngramScore, and oovCount are all output parameters.
-   *
-   * The value stored in oovCount is the number of words in the phrase
-   * that are not in the language model's vocabulary.
-   *
-   * The sum of the ngram scores for all words in this phrase are stored in fullScore.
-   *
-   * The value stored in ngramScore is similar, but only full-order ngram scores are included.
-   *
-   * This is best shown by example:
-   * 
-   * Assume a trigram backward language model and a phrase "a b c d e f g"
-   *
-   * fullScore would represent the sum of the logprob scores for the following values:
-   *
-   * p(g)
-   * p(f | g)
-   * p(e | g f)
-   * p(d | f e)
-   * p(c | e d)
-   * p(b | d c)
-   * p(a | c b)
-   *
-   * ngramScore would represent the sum of the logprob scores for the following values:
-   *
-   * p(g)
-   * p(f | g)
-   * p(e | g f)
-   * p(d | f e)
-   * p(c | e d)
-   * p(b | d c)
-   * p(a | c b)
-   */
-  template <class Model> void BackwardLanguageModel<Model>::CalcScore(const Phrase &phrase, float &fullScore, float &ngramScore, size_t &oovCount) const {
-    fullScore = 0;
-    ngramScore = 0;
-    oovCount = 0;
-    
-    if (!phrase.GetSize()) return;
-
-    lm::ngram::ChartState discarded_sadly;
-    lm::ngram::RuleScore<Model> scorer(*m_ngram, discarded_sadly);
-    
+/**
+ * Pre-calculate the n-gram probabilities for the words in the specified phrase.
+ *
+ * Note that when this method is called, we do not have access to the context
+ * in which this phrase will eventually be applied.
+ *
+ * In other words, we know what words are in this phrase,
+ * but we do not know what words will come before or after this phrase.
+ *
+ * The parameters fullScore, ngramScore, and oovCount are all output parameters.
+ *
+ * The value stored in oovCount is the number of words in the phrase
+ * that are not in the language model's vocabulary.
+ *
+ * The sum of the ngram scores for all words in this phrase are stored in fullScore.
+ *
+ * The value stored in ngramScore is similar, but only full-order ngram scores are included.
+ *
+ * This is best shown by example:
+ *
+ * Assume a trigram backward language model and a phrase "a b c d e f g"
+ *
+ * fullScore would represent the sum of the logprob scores for the following values:
+ *
+ * p(g)
+ * p(f | g)
+ * p(e | g f)
+ * p(d | f e)
+ * p(c | e d)
+ * p(b | d c)
+ * p(a | c b)
+ *
+ * ngramScore would represent the sum of the logprob scores for the following values:
+ *
+ * p(g)
+ * p(f | g)
+ * p(e | g f)
+ * p(d | f e)
+ * p(c | e d)
+ * p(b | d c)
+ * p(a | c b)
+ */
+template <class Model> void BackwardLanguageModel<Model>::CalcScore(const Phrase &phrase, float &fullScore, float &ngramScore, size_t &oovCount) const
+{
+  fullScore = 0;
+  ngramScore = 0;
+  oovCount = 0;
+
+  if (!phrase.GetSize()) return;
+
+  lm::ngram::ChartState discarded_sadly;
+  lm::ngram::RuleScore<Model> scorer(*m_ngram, discarded_sadly);
+
+  UTIL_THROW_IF(
+    (m_beginSentenceFactor == phrase.GetWord(0).GetFactor(m_factorType)),
+    util::Exception,
+    "BackwardLanguageModel does not currently support rules that include <s>"
+  );
+
+  float before_boundary = 0.0f;
+
+  int lastWord = phrase.GetSize() - 1;
+  int ngramBoundary = m_ngram->Order() - 1;
+  int boundary = ( lastWord < ngramBoundary ) ? 0 : ngramBoundary;
+
+  int position;
+  for (position = lastWord; position >= 0; position-=1) {
+    const Word &word = phrase.GetWord(position);
     UTIL_THROW_IF(
-		  (m_beginSentenceFactor == phrase.GetWord(0).GetFactor(m_factorType)),
-		  util::Exception,
-		  "BackwardLanguageModel does not currently support rules that include <s>"
-		  );
-  
-    float before_boundary = 0.0f;
-    
-    int lastWord = phrase.GetSize() - 1;
-    int ngramBoundary = m_ngram->Order() - 1;
-    int boundary = ( lastWord < ngramBoundary ) ? 0 : ngramBoundary; 
-
-    int position;
-    for (position = lastWord; position >= 0; position-=1) {
-      const Word &word = phrase.GetWord(position);
-      UTIL_THROW_IF(
-		    (word.IsNonTerminal()),
-		    util::Exception,
-		    "BackwardLanguageModel does not currently support rules that include non-terminals "
-		    );
-  
-      lm::WordIndex index = TranslateID(word);
-      scorer.Terminal(index);
-      if (!index) ++oovCount;
-
-      if (position==boundary) {
-	before_boundary = scorer.Finish();
-      }
+      (word.IsNonTerminal()),
+      util::Exception,
+      "BackwardLanguageModel does not currently support rules that include non-terminals "
+    );
 
-    }
+    lm::WordIndex index = TranslateID(word);
+    scorer.Terminal(index);
+    if (!index) ++oovCount;
 
-    fullScore = scorer.Finish();
-    
-    ngramScore = TransformLMScore(fullScore - before_boundary);
-    fullScore = TransformLMScore(fullScore);
+    if (position==boundary) {
+      before_boundary = scorer.Finish();
+    }
 
   }
 
-  /**
-   * Calculate the ngram probabilities for the words at the beginning 
-   * (and under some circumstances, also at the end)
-   * of the phrase represented by the provided hypothesis.
-   *
-   * Additionally, calculate a new language model state.
-   *
-   * This is best shown by example:
-   *
-   * Assume a trigram language model.
-   *
-   * Assume the previous phrase was "a b c d e f g", 
-   * which means the previous language model state is "g f".
-   *
-   * When the phrase corresponding to "a b c d e f g" was previously processed by CalcScore
-   * the following full-order ngrams would have been calculated:
-   *
-   * p(a | c b)
-   * p(b | d c)
-   * p(c | e d)
-   * p(d | f e)
-   * p(e | g f)
-   *
-   * The following less-than-full-order ngrams would also have been calculated by CalcScore:
-   *
-   * p(f | g)
-   * p(g)
-   *
-   * In this method, we now have access to additional context which may allow
-   * us to compute the full-order ngrams for f and g.
-   *
-   * Assume the new provided hypothesis contains the new phrase "h i j k"
-   * 
-   * Given these assumptions, this method is responsible 
-   * for calculating the scores for the following:
-   * 
-   * p(f | h g)
-   * p(g | i h)
-   *
-   * This method must also calculate and return a new language model state.
-   *
-   * In this example, the returned language model state would be "k j"
-   *
-   * If the provided hypothesis represents the end of a completed translation
-   * (all source words have been translated)
-   * then this method is additionally responsible for calculating the following:
-   *
-   * p(j | <s> k)
-   * p(k | <s>)
-   *
-   */
-  template <class Model> FFState *BackwardLanguageModel<Model>::Evaluate(const Hypothesis &hypo, const FFState *ps, ScoreComponentCollection *out) const {
-
-    // If the current hypothesis contains zero target words
-    if (!hypo.GetCurrTargetLength()) {
-
-      // reuse and return the previous state
-      std::auto_ptr<BackwardLMState> ret(new BackwardLMState());
-      ret->state = static_cast<const BackwardLMState&>(*ps).state;
-      return ret.release();
+  fullScore = scorer.Finish();
+
+  ngramScore = TransformLMScore(fullScore - before_boundary);
+  fullScore = TransformLMScore(fullScore);
+
+}
+
+/**
+ * Calculate the ngram probabilities for the words at the beginning
+ * (and under some circumstances, also at the end)
+ * of the phrase represented by the provided hypothesis.
+ *
+ * Additionally, calculate a new language model state.
+ *
+ * This is best shown by example:
+ *
+ * Assume a trigram language model.
+ *
+ * Assume the previous phrase was "a b c d e f g",
+ * which means the previous language model state is "g f".
+ *
+ * When the phrase corresponding to "a b c d e f g" was previously processed by CalcScore
+ * the following full-order ngrams would have been calculated:
+ *
+ * p(a | c b)
+ * p(b | d c)
+ * p(c | e d)
+ * p(d | f e)
+ * p(e | g f)
+ *
+ * The following less-than-full-order ngrams would also have been calculated by CalcScore:
+ *
+ * p(f | g)
+ * p(g)
+ *
+ * In this method, we now have access to additional context which may allow
+ * us to compute the full-order ngrams for f and g.
+ *
+ * Assume the new provided hypothesis contains the new phrase "h i j k"
+ *
+ * Given these assumptions, this method is responsible
+ * for calculating the scores for the following:
+ *
+ * p(f | h g)
+ * p(g | i h)
+ *
+ * This method must also calculate and return a new language model state.
+ *
+ * In this example, the returned language model state would be "k j"
+ *
+ * If the provided hypothesis represents the end of a completed translation
+ * (all source words have been translated)
+ * then this method is additionally responsible for calculating the following:
+ *
+ * p(j | <s> k)
+ * p(k | <s>)
+ *
+ */
+template <class Model> FFState *BackwardLanguageModel<Model>::Evaluate(const Hypothesis &hypo, const FFState *ps, ScoreComponentCollection *out) const
+{
+
+  // If the current hypothesis contains zero target words
+  if (!hypo.GetCurrTargetLength()) {
+
+    // reuse and return the previous state
+    std::auto_ptr<BackwardLMState> ret(new BackwardLMState());
+    ret->state = static_cast<const BackwardLMState&>(*ps).state;
+    return ret.release();
 
-    } else {
+  } else {
 
-      float returnedScore;
+    float returnedScore;
 
-      FFState *returnedState = this->Evaluate(hypo.GetCurrTargetPhrase(), ps, returnedScore);
+    FFState *returnedState = this->Evaluate(hypo.GetCurrTargetPhrase(), ps, returnedScore);
 
-      out->PlusEquals(this, returnedScore);
+    out->PlusEquals(this, returnedScore);
 
-      return returnedState;
+    return returnedState;
 
-    }
   }
+}
 
 
-  template <class Model> FFState *BackwardLanguageModel<Model>::Evaluate(const Phrase &phrase, const FFState *ps, float &returnedScore) const {
-    
-    returnedScore = 0.0f;
+template <class Model> FFState *BackwardLanguageModel<Model>::Evaluate(const Phrase &phrase, const FFState *ps, float &returnedScore) const
+{
 
-    const lm::ngram::ChartState &previous = static_cast<const BackwardLMState&>(*ps).state;
+  returnedScore = 0.0f;
 
-    std::auto_ptr<BackwardLMState> ret(new BackwardLMState());
-    
-    lm::ngram::RuleScore<Model> scorer(*m_ngram, ret->state);
-
-    int ngramBoundary = m_ngram->Order() - 1;
-    int lastWord = phrase.GetSize() - 1;
-
-    // Get scores for words at the end of the previous phrase
-    // that are now adjacent to words at the the beginning of this phrase
-    for (int position=std::min( lastWord,  ngramBoundary - 1); position >= 0; position-=1) {
-      const Word &word = phrase.GetWord(position);
-      UTIL_THROW_IF(
-		    (word.IsNonTerminal()),
-		    util::Exception,
-		    "BackwardLanguageModel does not currently support rules that include non-terminals "
-		    );
-  
-      lm::WordIndex index = TranslateID(word);
-      scorer.Terminal(index);
-    }
-    scorer.NonTerminal(previous);
-    returnedScore = scorer.Finish();
-    /*      
-    out->PlusEquals(this, score);
-    
-    
-      UTIL_THROW_IF(
-		    (1==1),
-		    util::Exception,
-		    "This method (BackwardLanguageModel<Model>::Evaluate) is not yet fully implemented"
-		    );   
-    */
-    return ret.release();
+  const lm::ngram::ChartState &previous = static_cast<const BackwardLMState&>(*ps).state;
+
+  std::auto_ptr<BackwardLMState> ret(new BackwardLMState());
+
+  lm::ngram::RuleScore<Model> scorer(*m_ngram, ret->state);
 
-    
+  int ngramBoundary = m_ngram->Order() - 1;
+  int lastWord = phrase.GetSize() - 1;
 
+  // Get scores for words at the end of the previous phrase
+  // that are now adjacent to words at the the beginning of this phrase
+  for (int position=std::min( lastWord,  ngramBoundary - 1); position >= 0; position-=1) {
+    const Word &word = phrase.GetWord(position);
+    UTIL_THROW_IF(
+      (word.IsNonTerminal()),
+      util::Exception,
+      "BackwardLanguageModel does not currently support rules that include non-terminals "
+    );
+
+    lm::WordIndex index = TranslateID(word);
+    scorer.Terminal(index);
   }
+  scorer.NonTerminal(previous);
+  returnedScore = scorer.Finish();
+  /*
+  out->PlusEquals(this, score);
 
-  LanguageModel *ConstructBackwardLM(const std::string &file, FactorType factorType, bool lazy) {
-    try {
-      lm::ngram::ModelType model_type;
-      if (lm::ngram::RecognizeBinary(file.c_str(), model_type)) {
-	switch(model_type) {
-        case lm::ngram::PROBING:
-          return new BackwardLanguageModel<lm::ngram::ProbingModel>(file,  factorType, lazy);
-        case lm::ngram::REST_PROBING:
-          return new BackwardLanguageModel<lm::ngram::RestProbingModel>(file, factorType, lazy);
-        case lm::ngram::TRIE:
-          return new BackwardLanguageModel<lm::ngram::TrieModel>(file, factorType, lazy);
-        case lm::ngram::QUANT_TRIE:
-          return new BackwardLanguageModel<lm::ngram::QuantTrieModel>(file, factorType, lazy);
-        case lm::ngram::ARRAY_TRIE:
-          return new BackwardLanguageModel<lm::ngram::ArrayTrieModel>(file, factorType, lazy);
-        case lm::ngram::QUANT_ARRAY_TRIE:
-          return new BackwardLanguageModel<lm::ngram::QuantArrayTrieModel>(file, factorType, lazy);
-        default:
-          std::cerr << "Unrecognized kenlm model type " << model_type << std::endl;
-          abort();
-	}
-      } else {
-	return new BackwardLanguageModel<lm::ngram::ProbingModel>(file, factorType, lazy);
+
+    UTIL_THROW_IF(
+      (1==1),
+      util::Exception,
+      "This method (BackwardLanguageModel<Model>::Evaluate) is not yet fully implemented"
+      );
+  */
+  return ret.release();
+
+
+
+}
+
+LanguageModel *ConstructBackwardLM(const std::string &file, FactorType factorType, bool lazy)
+{
+  try {
+    lm::ngram::ModelType model_type;
+    if (lm::ngram::RecognizeBinary(file.c_str(), model_type)) {
+      switch(model_type) {
+      case lm::ngram::PROBING:
+        return new BackwardLanguageModel<lm::ngram::ProbingModel>(file,  factorType, lazy);
+      case lm::ngram::REST_PROBING:
+        return new BackwardLanguageModel<lm::ngram::RestProbingModel>(file, factorType, lazy);
+      case lm::ngram::TRIE:
+        return new BackwardLanguageModel<lm::ngram::TrieModel>(file, factorType, lazy);
+      case lm::ngram::QUANT_TRIE:
+        return new BackwardLanguageModel<lm::ngram::QuantTrieModel>(file, factorType, lazy);
+      case lm::ngram::ARRAY_TRIE:
+        return new BackwardLanguageModel<lm::ngram::ArrayTrieModel>(file, factorType, lazy);
+      case lm::ngram::QUANT_ARRAY_TRIE:
+        return new BackwardLanguageModel<lm::ngram::QuantArrayTrieModel>(file, factorType, lazy);
+      default:
+        std::cerr << "Unrecognized kenlm model type " << model_type << std::endl;
+        abort();
       }
-    } catch (std::exception &e) {
-      std::cerr << e.what() << std::endl;
-      abort();
+    } else {
+      return new BackwardLanguageModel<lm::ngram::ProbingModel>(file, factorType, lazy);
     }
+  } catch (std::exception &e) {
+    std::cerr << e.what() << std::endl;
+    abort();
   }
+}
 
 } // namespace Moses
diff --git a/moses/LM/Backward.h b/moses/LM/Backward.h
index 1bf6b560c..c81c0633d 100644
--- a/moses/LM/Backward.h
+++ b/moses/LM/Backward.h
@@ -29,53 +29,55 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 
 #include "lm/state.hh"
 
-namespace Moses {
+namespace Moses
+{
 
 //! This will also load. Returns a templated backward LM.
 LanguageModel *ConstructBackwardLM(const std::string &file, FactorType factorType, bool lazy);
 
- class FFState;
- // template<typename M> class BackwardLanguageModelTest;
- class BackwardLanguageModelTest;
+class FFState;
+// template<typename M> class BackwardLanguageModelTest;
+class BackwardLanguageModelTest;
 
 /*
  * An implementation of single factor backward LM using Kenneth's code.
  */
-template <class Model> class BackwardLanguageModel : public LanguageModelKen<Model> {
-  public:
-    BackwardLanguageModel(const std::string &file, FactorType factorType, bool lazy);
-
-    virtual const FFState *EmptyHypothesisState(const InputType &/*input*/) const;
-
-    virtual void CalcScore(const Phrase &phrase, float &fullScore, float &ngramScore, size_t &oovCount) const;
-
-    virtual FFState *Evaluate(const Hypothesis &hypo, const FFState *ps, ScoreComponentCollection *out) const;
-
-    FFState *Evaluate(const Phrase &phrase, const FFState *ps, float &returnedScore) const;
-
-  private:
-
-    // These lines are required to make the parent class's protected members visible to this class
-    using LanguageModelKen<Model>::m_ngram;
-    using LanguageModelKen<Model>::m_beginSentenceFactor;
-    using LanguageModelKen<Model>::m_factorType;
-    using LanguageModelKen<Model>::TranslateID;
-
-    //    friend class Moses::BackwardLanguageModelTest<Model>;
-    friend class Moses::BackwardLanguageModelTest;
-    /*
-    lm::ngram::ChartState* GetState(FFState *ffState) {
-      return NULL;
-    }
-    */
-    /*
-    double Score(FFState *ffState) {
-    BackwardLMState *lmState = static_cast< BackwardLMState* >(ffState);
-    lm::ngram::ChartState &state = lmState->state;
-    lm::ngram::RuleScore<Model> ruleScore(*m_ngram, lmState);
-    return ruleScore.Finish();
+template <class Model> class BackwardLanguageModel : public LanguageModelKen<Model>
+{
+public:
+  BackwardLanguageModel(const std::string &file, FactorType factorType, bool lazy);
+
+  virtual const FFState *EmptyHypothesisState(const InputType &/*input*/) const;
+
+  virtual void CalcScore(const Phrase &phrase, float &fullScore, float &ngramScore, size_t &oovCount) const;
+
+  virtual FFState *Evaluate(const Hypothesis &hypo, const FFState *ps, ScoreComponentCollection *out) const;
+
+  FFState *Evaluate(const Phrase &phrase, const FFState *ps, float &returnedScore) const;
+
+private:
+
+  // These lines are required to make the parent class's protected members visible to this class
+  using LanguageModelKen<Model>::m_ngram;
+  using LanguageModelKen<Model>::m_beginSentenceFactor;
+  using LanguageModelKen<Model>::m_factorType;
+  using LanguageModelKen<Model>::TranslateID;
+
+  //    friend class Moses::BackwardLanguageModelTest<Model>;
+  friend class Moses::BackwardLanguageModelTest;
+  /*
+  lm::ngram::ChartState* GetState(FFState *ffState) {
+    return NULL;
   }
-    */
+  */
+  /*
+  double Score(FFState *ffState) {
+  BackwardLMState *lmState = static_cast< BackwardLMState* >(ffState);
+  lm::ngram::ChartState &state = lmState->state;
+  lm::ngram::RuleScore<Model> ruleScore(*m_ngram, lmState);
+  return ruleScore.Finish();
+  }
+  */
 };
 
 } // namespace Moses
@@ -83,7 +85,7 @@ template <class Model> class BackwardLanguageModel : public LanguageModelKen<Mod
 #endif
 
 // To create a sample backward language model using SRILM:
-// 
+//
 // (ngram-count and reverse-text are SRILM programs)
 //
 // head -n 49 ./contrib/synlm/hhmm/LICENSE | tail -n 45 | tr '\n' ' ' | ./scripts/ems/support/split-sentences.perl | ./scripts/tokenizer/lowercase.perl | ./scripts/tokenizer/tokenizer.perl | reverse-text | ngram-count -order 3 -text - -lm - > lm/backward.arpa
diff --git a/moses/LM/BackwardLMState.cpp b/moses/LM/BackwardLMState.cpp
index 37a3ab7da..466c4b655 100644
--- a/moses/LM/BackwardLMState.cpp
+++ b/moses/LM/BackwardLMState.cpp
@@ -22,11 +22,13 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 #include "moses/LM/BackwardLMState.h"
 #include "lm/state.hh"
 
-namespace Moses {
+namespace Moses
+{
 
-  int BackwardLMState::Compare(const FFState &o) const {
-    const BackwardLMState &other = static_cast<const BackwardLMState &>(o);
-    return state.left.Compare(other.state.left);
-  }
+int BackwardLMState::Compare(const FFState &o) const
+{
+  const BackwardLMState &other = static_cast<const BackwardLMState &>(o);
+  return state.left.Compare(other.state.left);
+}
 
 }
diff --git a/moses/LM/BackwardLMState.h b/moses/LM/BackwardLMState.h
index 7c6ebff62..e6d1f325a 100644
--- a/moses/LM/BackwardLMState.h
+++ b/moses/LM/BackwardLMState.h
@@ -36,14 +36,16 @@ namespace lm {
 
 //#include "lm/state.hh"
 
-namespace Moses {
+namespace Moses
+{
 
-  //template<typename M> 
+//template<typename M>
 class BackwardLanguageModelTest;
 
-class BackwardLMState : public FFState {
+class BackwardLMState : public FFState
+{
 
-  public:
+public:
 
   /*
     int Compare(const FFState &o) const {
@@ -53,14 +55,14 @@ class BackwardLMState : public FFState {
   */
   int Compare(const FFState &o) const;
 
-    // Allow BackwardLanguageModel to access the private members of this class
-    template <class Model> friend class BackwardLanguageModel;
+  // Allow BackwardLanguageModel to access the private members of this class
+  template <class Model> friend class BackwardLanguageModel;
 
   //    template <class Model> friend class Moses::BackwardLanguageModelTest;
-    friend class Moses::BackwardLanguageModelTest;
+  friend class Moses::BackwardLanguageModelTest;
 
-  private:
-    lm::ngram::ChartState state;
+private:
+  lm::ngram::ChartState state;
 
 };
 
diff --git a/moses/LM/BackwardTest.cpp b/moses/LM/BackwardTest.cpp
index 5f58c9f32..dc5de32bd 100644
--- a/moses/LM/BackwardTest.cpp
+++ b/moses/LM/BackwardTest.cpp
@@ -47,7 +47,7 @@ template <class M> void Foo() {
 
   Moses::BackwardLanguageModel<M> *backwardLM;
   // = new Moses::BackwardLanguageModel<M>( filename, factorType, lazy );
-  
+
 
 }
 template <class M> void Everything() {
@@ -55,159 +55,160 @@ template <class M> void Everything() {
 }
 */
 
-namespace Moses {
+namespace Moses
+{
 
-// Apparently some Boost versions use templates and are pretty strict about types matching.  
+// Apparently some Boost versions use templates and are pretty strict about types matching.
 #define SLOPPY_CHECK_CLOSE(ref, value, tol) BOOST_CHECK_CLOSE(static_cast<double>(ref), static_cast<double>(value), static_cast<double>(tol));
 
-class BackwardLanguageModelTest {
-
-  public:
-    BackwardLanguageModelTest() : 
-      dummyInput(new Sentence()),
-      backwardLM(
-		 static_cast< BackwardLanguageModel<lm::ngram::ProbingModel> * >(
-			 ConstructBackwardLM( 
-				boost::unit_test::framework::master_test_suite().argv[1], 
-				0,
-				false)
-			 )
-		 )
+class BackwardLanguageModelTest
+{
+
+public:
+  BackwardLanguageModelTest() :
+    dummyInput(new Sentence()),
+    backwardLM(
+      static_cast< BackwardLanguageModel<lm::ngram::ProbingModel> * >(
+        ConstructBackwardLM(
+          boost::unit_test::framework::master_test_suite().argv[1],
+          0,
+          false)
+      )
+    ) {
+    // This space intentionally left blank
+  }
+
+  ~BackwardLanguageModelTest() {
+    delete dummyInput;
+    delete backwardLM;
+  }
+
+  void testEmptyHypothesis() {
+    FFState *ffState = const_cast< FFState * >(backwardLM->EmptyHypothesisState( *dummyInput ));
+
+    BOOST_CHECK( ffState != NULL );
+
+    delete ffState;
+  }
+
+  void testCalcScore() {
+
+    double p_the      = -1.383059;
+    double p_licenses = -2.360783;
+    double p_for      = -1.661813;
+    double p_most     = -2.360783;
+    //      double p_software = -1.62042;
+
+    double p_the_licenses  = -0.9625873;
+    double p_licenses_for  = -1.661557;
+    double p_for_most      = -0.4526253;
+    //      double p_most_software = -1.70295;
+
+    double p_the_licenses_for  = p_the_licenses + p_licenses_for;
+    //      double p_licenses_for_most = p_licenses_for + p_for_most;
+
+    // the
     {
-      // This space intentionally left blank
+      Phrase phrase;
+      BOOST_CHECK( phrase.GetSize() == 0 );
+
+      std::vector<FactorType> outputFactorOrder;
+      outputFactorOrder.push_back(0);
+
+      phrase.CreateFromString(
+        outputFactorOrder,
+        "the",
+        StaticData::Instance().GetFactorDelimiter());
+
+      BOOST_CHECK( phrase.GetSize() == 1 );
+
+      float fullScore;
+      float ngramScore;
+      size_t oovCount;
+      backwardLM->CalcScore(phrase, fullScore, ngramScore, oovCount);
+
+      BOOST_CHECK( oovCount == 0 );
+      SLOPPY_CHECK_CLOSE( TransformLMScore(p_the), fullScore, 0.01);
+      SLOPPY_CHECK_CLOSE( TransformLMScore( 0.0 ), ngramScore, 0.01);
     }
 
-    ~BackwardLanguageModelTest() {
-      delete dummyInput;
-      delete backwardLM;
+    // the licenses
+    {
+      Phrase phrase;
+      BOOST_CHECK( phrase.GetSize() == 0 );
+
+      std::vector<FactorType> outputFactorOrder;
+      outputFactorOrder.push_back(0);
+
+      phrase.CreateFromString(
+        outputFactorOrder,
+        "the licenses",
+        StaticData::Instance().GetFactorDelimiter());
+
+      BOOST_CHECK( phrase.GetSize() == 2 );
+
+      float fullScore;
+      float ngramScore;
+      size_t oovCount;
+      backwardLM->CalcScore(phrase, fullScore, ngramScore, oovCount);
+
+      BOOST_CHECK( oovCount == 0 );
+      SLOPPY_CHECK_CLOSE( TransformLMScore(p_licenses + p_the_licenses), fullScore, 0.01);
+      SLOPPY_CHECK_CLOSE( TransformLMScore( 0.0 ), ngramScore, 0.01);
     }
 
-    void testEmptyHypothesis() {
-      FFState *ffState = const_cast< FFState * >(backwardLM->EmptyHypothesisState( *dummyInput ));
+    // the licenses for
+    {
+      Phrase phrase;
+      BOOST_CHECK( phrase.GetSize() == 0 );
+
+      std::vector<FactorType> outputFactorOrder;
+      outputFactorOrder.push_back(0);
+
+      phrase.CreateFromString(
+        outputFactorOrder,
+        "the licenses for",
+        StaticData::Instance().GetFactorDelimiter());
 
-      BOOST_CHECK( ffState != NULL );
+      BOOST_CHECK( phrase.GetSize() == 3 );
 
-      delete ffState;
+      float fullScore;
+      float ngramScore;
+      size_t oovCount;
+      backwardLM->CalcScore(phrase, fullScore, ngramScore, oovCount);
+
+      BOOST_CHECK( oovCount == 0 );
+      SLOPPY_CHECK_CLOSE( TransformLMScore( p_the_licenses_for ), ngramScore, 0.01);
+      SLOPPY_CHECK_CLOSE( TransformLMScore(p_for + p_licenses_for + p_the_licenses), fullScore, 0.01);
     }
 
-    void testCalcScore() {
-
-      double p_the      = -1.383059;
-      double p_licenses = -2.360783;
-      double p_for      = -1.661813;
-      double p_most     = -2.360783;
-      //      double p_software = -1.62042;
-
-      double p_the_licenses  = -0.9625873;
-      double p_licenses_for  = -1.661557;
-      double p_for_most      = -0.4526253;
-      //      double p_most_software = -1.70295; 
-
-      double p_the_licenses_for  = p_the_licenses + p_licenses_for;
-      //      double p_licenses_for_most = p_licenses_for + p_for_most;
- 
-      // the
-      {
-	Phrase phrase;
-	BOOST_CHECK( phrase.GetSize() == 0 );
-
-	std::vector<FactorType> outputFactorOrder;
-	outputFactorOrder.push_back(0);
-
-	phrase.CreateFromString(
-				outputFactorOrder,
-				"the", 
-				StaticData::Instance().GetFactorDelimiter());
-
-	BOOST_CHECK( phrase.GetSize() == 1 );
-      
-	float fullScore;
-	float ngramScore;
-	size_t oovCount;
-	backwardLM->CalcScore(phrase, fullScore, ngramScore, oovCount);
-
-	BOOST_CHECK( oovCount == 0 );
-	SLOPPY_CHECK_CLOSE( TransformLMScore(p_the), fullScore, 0.01);
-	SLOPPY_CHECK_CLOSE( TransformLMScore( 0.0 ), ngramScore, 0.01);
-      }
-
-      // the licenses
-      {
-	Phrase phrase;
-	BOOST_CHECK( phrase.GetSize() == 0 );
-
-	std::vector<FactorType> outputFactorOrder;
-	outputFactorOrder.push_back(0);
-
-	phrase.CreateFromString(
-				outputFactorOrder,
-				"the licenses", 
-				StaticData::Instance().GetFactorDelimiter());
-
-	BOOST_CHECK( phrase.GetSize() == 2 );
-      
-	float fullScore;
-	float ngramScore;
-	size_t oovCount;
-	backwardLM->CalcScore(phrase, fullScore, ngramScore, oovCount);
-
-	BOOST_CHECK( oovCount == 0 );
-	SLOPPY_CHECK_CLOSE( TransformLMScore(p_licenses + p_the_licenses), fullScore, 0.01);
-	SLOPPY_CHECK_CLOSE( TransformLMScore( 0.0 ), ngramScore, 0.01);
-      }
-      
-      // the licenses for
-      {
-	Phrase phrase;
-	BOOST_CHECK( phrase.GetSize() == 0 );
-
-	std::vector<FactorType> outputFactorOrder;
-	outputFactorOrder.push_back(0);
-
-	phrase.CreateFromString(
-				outputFactorOrder,
-				"the licenses for", 
-				StaticData::Instance().GetFactorDelimiter());
-
-	BOOST_CHECK( phrase.GetSize() == 3 );
-      
-	float fullScore;
-	float ngramScore;
-	size_t oovCount;
-	backwardLM->CalcScore(phrase, fullScore, ngramScore, oovCount);
-
-	BOOST_CHECK( oovCount == 0 );
-	SLOPPY_CHECK_CLOSE( TransformLMScore( p_the_licenses_for ), ngramScore, 0.01);
-	SLOPPY_CHECK_CLOSE( TransformLMScore(p_for + p_licenses_for + p_the_licenses), fullScore, 0.01);
-      }
-     
-      // the licenses for most
-      {
-	Phrase phrase;
-	BOOST_CHECK( phrase.GetSize() == 0 );
-
-	std::vector<FactorType> outputFactorOrder;
-	outputFactorOrder.push_back(0);
-
-	phrase.CreateFromString(
-				outputFactorOrder,
-				"the licenses for most", 
-				StaticData::Instance().GetFactorDelimiter());
-
-	BOOST_CHECK( phrase.GetSize() == 4 );
-      
-	float fullScore;
-	float ngramScore;
-	size_t oovCount;
-	backwardLM->CalcScore(phrase, fullScore, ngramScore, oovCount);
-
-	BOOST_CHECK( oovCount == 0 );
-	SLOPPY_CHECK_CLOSE( TransformLMScore( p_the_licenses + p_licenses_for ), ngramScore, 0.01);
-	SLOPPY_CHECK_CLOSE( TransformLMScore(p_most + p_for_most + p_licenses_for + p_the_licenses), fullScore, 0.01);
-      }
- 
+    // the licenses for most
+    {
+      Phrase phrase;
+      BOOST_CHECK( phrase.GetSize() == 0 );
+
+      std::vector<FactorType> outputFactorOrder;
+      outputFactorOrder.push_back(0);
+
+      phrase.CreateFromString(
+        outputFactorOrder,
+        "the licenses for most",
+        StaticData::Instance().GetFactorDelimiter());
+
+      BOOST_CHECK( phrase.GetSize() == 4 );
+
+      float fullScore;
+      float ngramScore;
+      size_t oovCount;
+      backwardLM->CalcScore(phrase, fullScore, ngramScore, oovCount);
+
+      BOOST_CHECK( oovCount == 0 );
+      SLOPPY_CHECK_CLOSE( TransformLMScore( p_the_licenses + p_licenses_for ), ngramScore, 0.01);
+      SLOPPY_CHECK_CLOSE( TransformLMScore(p_most + p_for_most + p_licenses_for + p_the_licenses), fullScore, 0.01);
     }
-  
+
+  }
+
   void testEvaluate() {
 
     FFState *nextState;
@@ -223,132 +224,134 @@ class BackwardLanguageModelTest {
     double p_for_licenses  = -1.661557;
     double p_licenses_the = -0.9625873;
     double p_the_eos = -1.940311;
-    
-
-      // the
-      {
-	Phrase phrase;
-	BOOST_CHECK( phrase.GetSize() == 0 );
-
-	std::vector<FactorType> outputFactorOrder;
-	outputFactorOrder.push_back(0);
-
-	phrase.CreateFromString(
-				outputFactorOrder,
-				"the", 
-				StaticData::Instance().GetFactorDelimiter());
-
-	BOOST_CHECK( phrase.GetSize() == 1 );
-      
-	float score;
-	nextState = backwardLM->Evaluate(phrase, prevState, score);
-
-	// p(the) * p(</s> | the) / p(</s>)
-	SLOPPY_CHECK_CLOSE( (p_the + p_the_eos - p_eos), score, 0.01);
-	
-	delete prevState;
-	prevState = nextState;
-
-      }
-
-      // the licenses
-      {
-	Phrase phrase;
-	BOOST_CHECK( phrase.GetSize() == 0 );
-
-	std::vector<FactorType> outputFactorOrder;
-	outputFactorOrder.push_back(0);
-
-	phrase.CreateFromString(
-				outputFactorOrder,
-				"licenses", 
-				StaticData::Instance().GetFactorDelimiter());
-
-	BOOST_CHECK( phrase.GetSize() == 1 );
-      
-	float score;
-	nextState = backwardLM->Evaluate(phrase, prevState, score);
-
-	// p(licenses) * p(licenses | the) / p(the)
-	SLOPPY_CHECK_CLOSE( (p_licenses + p_licenses_the - p_the), score, 0.01);
-	
-	delete prevState;
-	prevState = nextState;
-
-      }
-
-      // the licenses for
-      {
-	Phrase phrase;
-	BOOST_CHECK( phrase.GetSize() == 0 );
-
-	std::vector<FactorType> outputFactorOrder;
-	outputFactorOrder.push_back(0);
-
-	phrase.CreateFromString(
-				outputFactorOrder,
-				"for", 
-				StaticData::Instance().GetFactorDelimiter());
-
-	BOOST_CHECK( phrase.GetSize() == 1 );
-      
-	float score;
-	nextState = backwardLM->Evaluate(phrase, prevState, score);
-
-	// p(for) * p(for | licenses) / p(licenses)
-	SLOPPY_CHECK_CLOSE( (p_for + p_for_licenses - p_licenses), score, 0.01);
-	
-	delete prevState;
-	prevState = nextState;
-
-      }
-
-      // the licenses for most
-      {
-	Phrase phrase;
-	BOOST_CHECK( phrase.GetSize() == 0 );
-
-	std::vector<FactorType> outputFactorOrder;
-	outputFactorOrder.push_back(0);
-
-	phrase.CreateFromString(
-				outputFactorOrder,
-				"most", 
-				StaticData::Instance().GetFactorDelimiter());
-
-	BOOST_CHECK( phrase.GetSize() == 1 );
-      
-	float score;
-	nextState = backwardLM->Evaluate(phrase, prevState, score);
-
-	// p(most) * p(most | for) / p(for)
-	SLOPPY_CHECK_CLOSE( (p_most + p_most_for - p_for), score, 0.01);
-	
-	delete prevState;
-	prevState = nextState;
-
-      }
+
+
+    // the
+    {
+      Phrase phrase;
+      BOOST_CHECK( phrase.GetSize() == 0 );
+
+      std::vector<FactorType> outputFactorOrder;
+      outputFactorOrder.push_back(0);
+
+      phrase.CreateFromString(
+        outputFactorOrder,
+        "the",
+        StaticData::Instance().GetFactorDelimiter());
+
+      BOOST_CHECK( phrase.GetSize() == 1 );
+
+      float score;
+      nextState = backwardLM->Evaluate(phrase, prevState, score);
+
+      // p(the) * p(</s> | the) / p(</s>)
+      SLOPPY_CHECK_CLOSE( (p_the + p_the_eos - p_eos), score, 0.01);
+
+      delete prevState;
+      prevState = nextState;
+
+    }
+
+    // the licenses
+    {
+      Phrase phrase;
+      BOOST_CHECK( phrase.GetSize() == 0 );
+
+      std::vector<FactorType> outputFactorOrder;
+      outputFactorOrder.push_back(0);
+
+      phrase.CreateFromString(
+        outputFactorOrder,
+        "licenses",
+        StaticData::Instance().GetFactorDelimiter());
+
+      BOOST_CHECK( phrase.GetSize() == 1 );
+
+      float score;
+      nextState = backwardLM->Evaluate(phrase, prevState, score);
+
+      // p(licenses) * p(licenses | the) / p(the)
+      SLOPPY_CHECK_CLOSE( (p_licenses + p_licenses_the - p_the), score, 0.01);
 
       delete prevState;
+      prevState = nextState;
+
+    }
+
+    // the licenses for
+    {
+      Phrase phrase;
+      BOOST_CHECK( phrase.GetSize() == 0 );
+
+      std::vector<FactorType> outputFactorOrder;
+      outputFactorOrder.push_back(0);
+
+      phrase.CreateFromString(
+        outputFactorOrder,
+        "for",
+        StaticData::Instance().GetFactorDelimiter());
+
+      BOOST_CHECK( phrase.GetSize() == 1 );
+
+      float score;
+      nextState = backwardLM->Evaluate(phrase, prevState, score);
+
+      // p(for) * p(for | licenses) / p(licenses)
+      SLOPPY_CHECK_CLOSE( (p_for + p_for_licenses - p_licenses), score, 0.01);
+
+      delete prevState;
+      prevState = nextState;
+
+    }
+
+    // the licenses for most
+    {
+      Phrase phrase;
+      BOOST_CHECK( phrase.GetSize() == 0 );
+
+      std::vector<FactorType> outputFactorOrder;
+      outputFactorOrder.push_back(0);
+
+      phrase.CreateFromString(
+        outputFactorOrder,
+        "most",
+        StaticData::Instance().GetFactorDelimiter());
+
+      BOOST_CHECK( phrase.GetSize() == 1 );
+
+      float score;
+      nextState = backwardLM->Evaluate(phrase, prevState, score);
+
+      // p(most) * p(most | for) / p(for)
+      SLOPPY_CHECK_CLOSE( (p_most + p_most_for - p_for), score, 0.01);
+
+      delete prevState;
+      prevState = nextState;
+
+    }
+
+    delete prevState;
   }
-  
-  private:
-    const Sentence *dummyInput;
-    BackwardLanguageModel<lm::ngram::ProbingModel> *backwardLM;
+
+private:
+  const Sentence *dummyInput;
+  BackwardLanguageModel<lm::ngram::ProbingModel> *backwardLM;
 
 };
 
 
 }
 
-const char *FileLocation() {
+const char *FileLocation()
+{
   if (boost::unit_test::framework::master_test_suite().argc < 2) {
     BOOST_FAIL("Jamfile must specify arpa file for this test, but did not");
   }
   return boost::unit_test::framework::master_test_suite().argv[1];
 }
 
-BOOST_AUTO_TEST_CASE(ProbingAll) {
+BOOST_AUTO_TEST_CASE(ProbingAll)
+{
 
   BackwardLanguageModelTest test;
   test.testEmptyHypothesis();
diff --git a/moses/LM/Base.cpp b/moses/LM/Base.cpp
index fe35604b0..37dc704de 100644
--- a/moses/LM/Base.cpp
+++ b/moses/LM/Base.cpp
@@ -31,63 +31,67 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 
 using namespace std;
 
-namespace Moses {
+namespace Moses
+{
 
 LanguageModel::LanguageModel(const std::string& description, const std::string &line) :
   StatefulFeatureFunction(description, StaticData::Instance().GetLMEnableOOVFeature() ? 2 : 1, line )
 {
-  m_enableOOVFeature = StaticData::Instance().GetLMEnableOOVFeature(); 
+  m_enableOOVFeature = StaticData::Instance().GetLMEnableOOVFeature();
 }
 
 
 LanguageModel::~LanguageModel() {}
 
-float LanguageModel::GetWeight() const {
+float LanguageModel::GetWeight() const
+{
   //return StaticData::Instance().GetAllWeights().GetScoresForProducer(this)[0];
   return StaticData::Instance().GetWeights(this)[0];
 }
 
-float LanguageModel::GetOOVWeight() const {
+float LanguageModel::GetOOVWeight() const
+{
   if (m_enableOOVFeature) {
     //return StaticData::Instance().GetAllWeights().GetScoresForProducer(this)[1];
-	return StaticData::Instance().GetWeights(this)[1];
+    return StaticData::Instance().GetWeights(this)[1];
   } else {
     return 0;
   }
 }
 
-void LanguageModel::IncrementalCallback(Incremental::Manager &manager) const {
+void LanguageModel::IncrementalCallback(Incremental::Manager &manager) const
+{
   UTIL_THROW(util::Exception, "Incremental search is only supported by KenLM.");
 }
 
 void LanguageModel::Evaluate(const Phrase &source
-					  , const TargetPhrase &targetPhrase
-                      , ScoreComponentCollection &scoreBreakdown
-                      , ScoreComponentCollection &estimatedFutureScore) const
+                             , const TargetPhrase &targetPhrase
+                             , ScoreComponentCollection &scoreBreakdown
+                             , ScoreComponentCollection &estimatedFutureScore) const
 {
-   if (Useable(targetPhrase)) {
-     // contains factors used by this LM
-     float fullScore, nGramScore;
-     size_t oovCount;
-
-     CalcScore(targetPhrase, fullScore, nGramScore, oovCount);
-     float estimateScore = fullScore - nGramScore;
-
-     if (StaticData::Instance().GetLMEnableOOVFeature()) {
-       vector<float> scores(2), estimateScores(2);
-       scores[0] = nGramScore;
-       scores[1] = oovCount;
-       scoreBreakdown.Assign(this, scores);
-
-       estimateScores[0] = estimateScore;
-       estimateScores[1] = 0;
-       estimatedFutureScore.Assign(this, estimateScores);
-     } else {
-       scoreBreakdown.Assign(this, nGramScore);
-       estimatedFutureScore.Assign(this, estimateScore);
-     }
-
-   }
+  if (Useable(targetPhrase)) {
+    // contains factors used by this LM
+    float fullScore, nGramScore;
+    size_t oovCount;
+
+    CalcScore(targetPhrase, fullScore, nGramScore, oovCount);
+    float estimateScore = fullScore - nGramScore;
+
+    if (StaticData::Instance().GetLMEnableOOVFeature()) {
+      vector<float> scores(2), estimateScores(2);
+      scores[0] = nGramScore;
+      scores[1] = oovCount;
+      scoreBreakdown.Assign(this, scores);
+
+      estimateScores[0] = estimateScore;
+      estimateScores[1] = 0;
+      estimatedFutureScore.Assign(this, estimateScores);
+    } else {
+      scoreBreakdown.Assign(this, nGramScore);
+      estimatedFutureScore.Assign(this, estimateScore);
+    }
+
+  }
 }
 
 const LanguageModel &LanguageModel::GetFirstLM()
diff --git a/moses/LM/Base.h b/moses/LM/Base.h
index 961fead5f..1f976ee53 100644
--- a/moses/LM/Base.h
+++ b/moses/LM/Base.h
@@ -30,21 +30,25 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 namespace Moses
 {
 
-namespace Incremental { class Manager; }
+namespace Incremental
+{
+class Manager;
+}
 
 class FactorCollection;
 class Factor;
 class Phrase;
 
 //! Abstract base class which represent a language model on a contiguous phrase
-class LanguageModel : public StatefulFeatureFunction {
+class LanguageModel : public StatefulFeatureFunction
+{
 protected:
   LanguageModel(const std::string& description, const std::string &line);
 
   // This can't be in the constructor for virual function dispatch reasons
 
   bool m_enableOOVFeature;
-  
+
 public:
   static const LanguageModel &GetFirstLM();
 
@@ -89,9 +93,9 @@ public:
   virtual void IncrementalCallback(Incremental::Manager &manager) const;
 
   virtual void Evaluate(const Phrase &source
-	  	  	  	  	  , const TargetPhrase &targetPhrase
-                      , ScoreComponentCollection &scoreBreakdown
-                      , ScoreComponentCollection &estimatedFutureScore) const;
+                        , const TargetPhrase &targetPhrase
+                        , ScoreComponentCollection &scoreBreakdown
+                        , ScoreComponentCollection &estimatedFutureScore) const;
 
 };
 
diff --git a/moses/LM/ChartState.h b/moses/LM/ChartState.h
index b6bdd8f7c..186694927 100644
--- a/moses/LM/ChartState.h
+++ b/moses/LM/ChartState.h
@@ -19,16 +19,15 @@ private:
 
   const ChartHypothesis &m_hypo;
 
-  /** Construct the prefix string of up to specified size 
+  /** Construct the prefix string of up to specified size
    * \param ret prefix string
    * \param size maximum size (typically max lm context window)
    */
-  size_t CalcPrefix(const ChartHypothesis &hypo, int featureID, Phrase &ret, size_t size) const
-  {
+  size_t CalcPrefix(const ChartHypothesis &hypo, int featureID, Phrase &ret, size_t size) const {
     const TargetPhrase &target = hypo.GetCurrTargetPhrase();
     const AlignmentInfo::NonTermIndexMap &nonTermIndexMap =
-          target.GetAlignNonTerm().GetNonTermIndexMap();
-    
+      target.GetAlignNonTerm().GetNonTermIndexMap();
+
     // loop over the rule that is being applied
     for (size_t pos = 0; pos < target.GetSize(); ++pos) {
       const Word &word = target.GetWord(pos);
@@ -53,13 +52,12 @@ private:
     return size;
   }
 
-  /** Construct the suffix phrase of up to specified size 
+  /** Construct the suffix phrase of up to specified size
    * will always be called after the construction of prefix phrase
    * \param ret suffix phrase
    * \param size maximum size of suffix
    */
-  size_t CalcSuffix(const ChartHypothesis &hypo, int featureID, Phrase &ret, size_t size) const
-  {
+  size_t CalcSuffix(const ChartHypothesis &hypo, int featureID, Phrase &ret, size_t size) const {
     CHECK(m_contextPrefix.GetSize() <= m_numTargetTerminals);
 
     // special handling for small hypotheses
@@ -81,7 +79,7 @@ private:
     else {
       const TargetPhrase& target = hypo.GetCurrTargetPhrase();
       const AlignmentInfo::NonTermIndexMap &nonTermIndexMap =
-            target.GetAlignNonTerm().GetNonTermIndexMap();
+        target.GetAlignNonTerm().GetNonTermIndexMap();
       for (int pos = (int) target.GetSize() - 1; pos >= 0 ; --pos) {
         const Word &word = target.GetWord(pos);
 
@@ -89,8 +87,7 @@ private:
           size_t nonTermInd = nonTermIndexMap[pos];
           const ChartHypothesis *prevHypo = hypo.GetPrevHypo(nonTermInd);
           size = static_cast<const LanguageModelChartState*>(prevHypo->GetFFState(featureID))->CalcSuffix(*prevHypo, featureID, ret, size);
-        }
-        else {
+        } else {
           ret.PrependWord(hypo.GetCurrTargetPhrase().GetWord(pos));
           size--;
         }
@@ -106,11 +103,10 @@ private:
 
 public:
   LanguageModelChartState(const ChartHypothesis &hypo, int featureID, size_t order)
-      :m_lmRightContext(NULL)
-      ,m_contextPrefix(order - 1)
-      ,m_contextSuffix( order - 1)
-      ,m_hypo(hypo)
-  {
+    :m_lmRightContext(NULL)
+    ,m_contextPrefix(order - 1)
+    ,m_contextSuffix( order - 1)
+    ,m_hypo(hypo) {
     m_numTargetTerminals = hypo.GetCurrTargetPhrase().GetNumTerminals();
 
     for (std::vector<const ChartHypothesis*>::const_iterator i = hypo.GetPrevHypos().begin(); i != hypo.GetPrevHypos().end(); ++i) {
@@ -131,8 +127,12 @@ public:
     m_lmRightContext = rightState;
   }
 
-  float GetPrefixScore() const { return m_prefixScore; }
-  FFState* GetRightContext() const { return m_lmRightContext; }
+  float GetPrefixScore() const {
+    return m_prefixScore;
+  }
+  FFState* GetRightContext() const {
+    return m_lmRightContext;
+  }
 
   size_t GetNumTargetTerminals() const {
     return m_numTargetTerminals;
@@ -150,8 +150,7 @@ public:
       dynamic_cast<const LanguageModelChartState &>( o );
 
     // prefix
-    if (m_hypo.GetCurrSourceRange().GetStartPos() > 0) // not for "<s> ..."
-    {
+    if (m_hypo.GetCurrSourceRange().GetStartPos() > 0) { // not for "<s> ..."
       int ret = GetPrefix().Compare(other.GetPrefix());
       if (ret != 0)
         return ret;
@@ -159,8 +158,7 @@ public:
 
     // suffix
     size_t inputSize = m_hypo.GetManager().GetSource().GetSize();
-    if (m_hypo.GetCurrSourceRange().GetEndPos() < inputSize - 1)// not for "... </s>"
-    {
+    if (m_hypo.GetCurrSourceRange().GetEndPos() < inputSize - 1) { // not for "... </s>"
       int ret = other.GetRightContext()->Compare(*m_lmRightContext);
       if (ret != 0)
         return ret;
diff --git a/moses/LM/IRST.cpp b/moses/LM/IRST.cpp
index 2d58bd310..ae1bb677d 100644
--- a/moses/LM/IRST.cpp
+++ b/moses/LM/IRST.cpp
@@ -40,25 +40,22 @@ using namespace std;
 namespace Moses
 {
 LanguageModelIRST::LanguageModelIRST(const std::string &line)
-:LanguageModelSingleFactor("IRSTLM", line)
+  :LanguageModelSingleFactor("IRSTLM", line)
 {
   FactorType factorType;
   size_t nGramOrder;
   string filePath;
 
   for (size_t i = 0; i < m_args.size(); ++i) {
-	const vector<string> &args = m_args[i];
+    const vector<string> &args = m_args[i];
 
     if (args[0] == "factor") {
       factorType = Scan<FactorType>(args[1]);
-    }
-    else if (args[0] == "order") {
+    } else if (args[0] == "order") {
       nGramOrder = Scan<size_t>(args[1]);
-    }
-    else if (args[0] == "path") {
+    } else if (args[0] == "path") {
       filePath = args[1];
-    }
-    else {
+    } else {
       throw "Unknown argument " + args[0];
     }
   }
@@ -86,8 +83,7 @@ bool LanguageModelIRST::Load(const std::string &filePath,
 
   const StaticData &staticData = StaticData::Instance();
   int threadCount = staticData.ThreadCount();
-  if (threadCount != 1)
-  {
+  if (threadCount != 1) {
     UserMessage::Add(threadCount + " number of threads specified but IRST LM is not threadsafe.");
     return false;
   }
@@ -99,7 +95,7 @@ bool LanguageModelIRST::Load(const std::string &filePath,
   m_filePath = filePath;
 
 
-  m_lmtb = m_lmtb->CreateLanguageModel(m_filePath); 
+  m_lmtb = m_lmtb->CreateLanguageModel(m_filePath);
   m_lmtb->setMaxLoadedLevel(1000);
   m_lmtb->load(m_filePath);
   d=m_lmtb->getDict();
@@ -170,7 +166,7 @@ int LanguageModelIRST::GetLmID( const std::string &str ) const
 }
 
 int LanguageModelIRST::GetLmID( const Factor *factor ) const
-{  
+{
   size_t factorId = factor->GetId();
 
   if  ((factorId >= m_lmIdLookup.size()) || (m_lmIdLookup[factorId] == m_empty)) {
@@ -180,12 +176,12 @@ int LanguageModelIRST::GetLmID( const Factor *factor ) const
 
       //////////
       ///poiche' non c'e' distinzione tra i factorIDs delle parole sorgenti
-      ///e delle parole target in Moses, puo' accadere che una parola target 
+      ///e delle parole target in Moses, puo' accadere che una parola target
       ///di cui non sia stato ancora calcolato il suo codice target abbia
       ///comunque un factorID noto (e quindi minore di m_lmIdLookup.size())
       ///E' necessario dunque identificare questi casi di indeterminatezza
       ///del codice target. Attualamente, questo controllo e' stato implementato
-      ///impostando a    m_empty     tutti i termini che non hanno ancora 
+      ///impostando a    m_empty     tutti i termini che non hanno ancora
       //ricevuto un codice target effettivo
       ///////////
 
@@ -197,7 +193,7 @@ int LanguageModelIRST::GetLmID( const Factor *factor ) const
 /// IN POSIZIONE (factorID-1) invece che in posizione factrID dove dopo andiamo a leggerlo (vedi caso C
 /// Cosi' funziona ....
 /// ho un dubbio su cosa c'e' nelle prime posizioni di m_lmIdLookup
-/// quindi 
+/// quindi
 /// e scopro che rimane vuota una entry ogni due
 /// perche' factorID cresce di due in due (perche' codifica sia source che target) "vuota" la posizione (factorID-1)
 /// non da problemi di correttezza, ma solo di "spreco" di memoria
@@ -207,10 +203,10 @@ int LanguageModelIRST::GetLmID( const Factor *factor ) const
 ////////////////
 
 
-      if (factorId >= m_lmIdLookup.size()){
-	//resize and fill with m_empty  
-	//increment the array more than needed to avoid too many resizing operation.
-	m_lmIdLookup.resize(factorId+10, m_empty); 
+      if (factorId >= m_lmIdLookup.size()) {
+        //resize and fill with m_empty
+        //increment the array more than needed to avoid too many resizing operation.
+        m_lmIdLookup.resize(factorId+10, m_empty);
       }
 
       //insert new code
diff --git a/moses/LM/Implementation.cpp b/moses/LM/Implementation.cpp
index 798a12775..e9c651089 100644
--- a/moses/LM/Implementation.cpp
+++ b/moses/LM/Implementation.cpp
@@ -69,8 +69,9 @@ void LanguageModelImplementation::GetState(
   GetValueForgotState(contextFactor, state);
 }
 
-// Calculate score of a phrase.  
-void LanguageModelImplementation::CalcScore(const Phrase &phrase, float &fullScore, float &ngramScore, size_t &oovCount) const {
+// Calculate score of a phrase.
+void LanguageModelImplementation::CalcScore(const Phrase &phrase, float &fullScore, float &ngramScore, size_t &oovCount) const
+{
   fullScore  = 0;
   ngramScore = 0;
 
@@ -82,7 +83,7 @@ void LanguageModelImplementation::CalcScore(const Phrase &phrase, float &fullSco
   vector<const Word*> contextFactor;
   contextFactor.reserve(GetNGramOrder());
   std::auto_ptr<FFState> state(NewState((phrase.GetWord(0) == GetSentenceStartWord()) ?
-                               GetBeginSentenceState() : GetNullContextState()));
+                                        GetBeginSentenceState() : GetNullContextState()));
   size_t currPos = 0;
   while (currPos < phraseSize) {
     const Word &word = phrase.GetWord(currPos);
@@ -109,7 +110,7 @@ void LanguageModelImplementation::CalcScore(const Phrase &phrase, float &fullSco
         fullScore += result.score;
         if (contextFactor.size() == GetNGramOrder())
           ngramScore += result.score;
-        if (result.unknown) ++oovCount;  
+        if (result.unknown) ++oovCount;
       }
     }
 
@@ -117,7 +118,8 @@ void LanguageModelImplementation::CalcScore(const Phrase &phrase, float &fullSco
   }
 }
 
-FFState *LanguageModelImplementation::Evaluate(const Hypothesis &hypo, const FFState *ps, ScoreComponentCollection *out) const {
+FFState *LanguageModelImplementation::Evaluate(const Hypothesis &hypo, const FFState *ps, ScoreComponentCollection *out) const
+{
   // In this function, we only compute the LM scores of n-grams that overlap a
   // phrase boundary. Phrase-internal scores are taken directly from the
   // translation option.
@@ -179,9 +181,7 @@ FFState *LanguageModelImplementation::Evaluate(const Hypothesis &hypo, const FFS
         contextFactor[i] = &hypo.GetWord((size_t)currPos);
     }
     lmScore += GetValueForgotState(contextFactor, *res).score;
-  }
-  else
-  {
+  } else {
     if (endPos < currEndPos) {
       //need to get the LM state (otherwise the last LM state is fine)
       for (size_t currPos = endPos+1; currPos <= currEndPos; currPos++) {
@@ -208,7 +208,8 @@ FFState *LanguageModelImplementation::Evaluate(const Hypothesis &hypo, const FFS
   return res;
 }
 
-FFState* LanguageModelImplementation::EvaluateChart(const ChartHypothesis& hypo, int featureID, ScoreComponentCollection* out) const {
+FFState* LanguageModelImplementation::EvaluateChart(const ChartHypothesis& hypo, int featureID, ScoreComponentCollection* out) const
+{
   LanguageModelChartState *ret = new LanguageModelChartState(hypo, featureID, GetNGramOrder());
   // data structure for factored context phrase (history and predicted word)
   vector<const Word*> contextFactor;
@@ -223,38 +224,33 @@ FFState* LanguageModelImplementation::EvaluateChart(const ChartHypothesis& hypo,
 
   // get index map for underlying hypotheses
   const AlignmentInfo::NonTermIndexMap &nonTermIndexMap =
-      hypo.GetCurrTargetPhrase().GetAlignNonTerm().GetNonTermIndexMap();
+    hypo.GetCurrTargetPhrase().GetAlignNonTerm().GetNonTermIndexMap();
 
   // loop over rule
   for (size_t phrasePos = 0, wordPos = 0;
        phrasePos < hypo.GetCurrTargetPhrase().GetSize();
-       phrasePos++)
-  {
+       phrasePos++) {
     // consult rule for either word or non-terminal
     const Word &word = hypo.GetCurrTargetPhrase().GetWord(phrasePos);
 
     // regular word
-    if (!word.IsNonTerminal())
-    {
+    if (!word.IsNonTerminal()) {
       ShiftOrPush(contextFactor, word);
 
       // beginning of sentence symbol <s>? -> just update state
-      if (word == GetSentenceStartWord())
-      {        
+      if (word == GetSentenceStartWord()) {
         CHECK(phrasePos == 0);
         delete lmState;
         lmState = NewState( GetBeginSentenceState() );
       }
       // score a regular word added by the rule
-      else
-      {
+      else {
         updateChartScore( &prefixScore, &finalizedScore, GetValueGivenState(contextFactor, *lmState).score, ++wordPos );
       }
     }
 
     // non-terminal, add phrase from underlying hypothesis
-    else
-    {
+    else {
       // look up underlying hypothesis
       size_t nonTermIndex = nonTermIndexMap[phrasePos];
       const ChartHypothesis *prevHypo = hypo.GetPrevHypo(nonTermIndex);
@@ -278,8 +274,7 @@ FFState* LanguageModelImplementation::EvaluateChart(const ChartHypothesis& hypo,
         // push suffix
         int suffixPos = prevState->GetSuffix().GetSize() - (GetNGramOrder()-1);
         if (suffixPos < 0) suffixPos = 0; // push all words if less than order
-        for(;(size_t)suffixPos < prevState->GetSuffix().GetSize(); suffixPos++)
-        {
+        for(; (size_t)suffixPos < prevState->GetSuffix().GetSize(); suffixPos++) {
           const Word &word = prevState->GetSuffix().GetWord(suffixPos);
           ShiftOrPush(contextFactor, word);
           wordPos++;
@@ -287,22 +282,19 @@ FFState* LanguageModelImplementation::EvaluateChart(const ChartHypothesis& hypo,
       }
 
       // internal non-terminal
-      else
-      {
+      else {
         // score its prefix
         for(size_t prefixPos = 0;
             prefixPos < GetNGramOrder()-1 // up to LM order window
-              && prefixPos < subPhraseLength; // up to length
-            prefixPos++)
-        {
+            && prefixPos < subPhraseLength; // up to length
+            prefixPos++) {
           const Word &word = prevState->GetPrefix().GetWord(prefixPos);
           ShiftOrPush(contextFactor, word);
           updateChartScore( &prefixScore, &finalizedScore, GetValueGivenState(contextFactor, *lmState).score, ++wordPos );
         }
 
         // check if we are dealing with a large sub-phrase
-        if (subPhraseLength > GetNGramOrder() - 1)
-        {
+        if (subPhraseLength > GetNGramOrder() - 1) {
           // add its finalized language model score
           finalizedScore +=
             prevHypo->GetScoreBreakdown().GetScoresForProducer(this)[0] // full score
@@ -337,11 +329,11 @@ FFState* LanguageModelImplementation::EvaluateChart(const ChartHypothesis& hypo,
   return ret;
 }
 
-void LanguageModelImplementation::updateChartScore(float *prefixScore, float *finalizedScore, float score, size_t wordPos) const {
+void LanguageModelImplementation::updateChartScore(float *prefixScore, float *finalizedScore, float score, size_t wordPos) const
+{
   if (wordPos < GetNGramOrder()) {
     *prefixScore += score;
-  }
-  else {
+  } else {
     *finalizedScore += score;
   }
 }
diff --git a/moses/LM/Implementation.h b/moses/LM/Implementation.h
index d3f83dfe1..fa6619208 100644
--- a/moses/LM/Implementation.h
+++ b/moses/LM/Implementation.h
@@ -44,7 +44,7 @@ class Phrase;
 struct LMResult {
   // log probability
   float score;
-  // Is the word unknown?  
+  // Is the word unknown?
   bool unknown;
 };
 
@@ -62,7 +62,7 @@ protected:
   //! Usually <s> and </s>
 
   LanguageModelImplementation(const std::string& description, const std::string &line)
-  :LanguageModel(description, line)
+    :LanguageModel(description, line)
   {}
 public:
 
@@ -108,8 +108,7 @@ public:
     return m_sentenceEndWord;
   }
 
-  const FFState* EmptyHypothesisState(const InputType &/*input*/) const
-  {
+  const FFState* EmptyHypothesisState(const InputType &/*input*/) const {
     return NewState(GetBeginSentenceState());
   }
 
diff --git a/moses/LM/Joint.h b/moses/LM/Joint.h
index 5bc52e2da..3a675cbd6 100644
--- a/moses/LM/Joint.h
+++ b/moses/LM/Joint.h
@@ -50,8 +50,7 @@ protected:
   size_t m_implFactor;
 public:
   LanguageModelJoint(const std::string &line, LanguageModelSingleFactor *lmImpl)
-  :LanguageModelMultiFactor("JointLM", line)
-  {
+    :LanguageModelMultiFactor("JointLM", line) {
     m_lmImpl = lmImpl;
   }
 
diff --git a/moses/LM/Ken.cpp b/moses/LM/Ken.cpp
index e251661c3..af24ad858 100644
--- a/moses/LM/Ken.cpp
+++ b/moses/LM/Ken.cpp
@@ -45,8 +45,10 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 
 using namespace std;
 
-namespace Moses {
-namespace {
+namespace Moses
+{
+namespace
+{
 
 struct KenLMState : public FFState {
   lm::ngram::State state;
@@ -61,63 +63,65 @@ struct KenLMState : public FFState {
 /*
  * An implementation of single factor LM using Ken's code.
  */
-template <class Model> class LanguageModelKen : public LanguageModel {
-  public:
-    LanguageModelKen(const std::string &description, const std::string &line, const std::string &file, FactorType factorType, bool lazy);
+template <class Model> class LanguageModelKen : public LanguageModel
+{
+public:
+  LanguageModelKen(const std::string &description, const std::string &line, const std::string &file, FactorType factorType, bool lazy);
 
-    bool Useable(const Phrase &phrase) const {
-      return (phrase.GetSize()>0 && phrase.GetFactor(0, m_factorType) != NULL);
-    }
+  bool Useable(const Phrase &phrase) const {
+    return (phrase.GetSize()>0 && phrase.GetFactor(0, m_factorType) != NULL);
+  }
 
-    const FFState *EmptyHypothesisState(const InputType &/*input*/) const {
-      KenLMState *ret = new KenLMState();
-      ret->state = m_ngram->BeginSentenceState();
-      return ret;
-    }
+  const FFState *EmptyHypothesisState(const InputType &/*input*/) const {
+    KenLMState *ret = new KenLMState();
+    ret->state = m_ngram->BeginSentenceState();
+    return ret;
+  }
 
-    void CalcScore(const Phrase &phrase, float &fullScore, float &ngramScore, size_t &oovCount) const;
+  void CalcScore(const Phrase &phrase, float &fullScore, float &ngramScore, size_t &oovCount) const;
 
-    FFState *Evaluate(const Hypothesis &hypo, const FFState *ps, ScoreComponentCollection *out) const;
+  FFState *Evaluate(const Hypothesis &hypo, const FFState *ps, ScoreComponentCollection *out) const;
 
-    FFState *EvaluateChart(const ChartHypothesis& cur_hypo, int featureID, ScoreComponentCollection *accumulator) const;
+  FFState *EvaluateChart(const ChartHypothesis& cur_hypo, int featureID, ScoreComponentCollection *accumulator) const;
 
-    void IncrementalCallback(Incremental::Manager &manager) const {
-      manager.LMCallback(*m_ngram, m_lmIdLookup);
-    }
+  void IncrementalCallback(Incremental::Manager &manager) const {
+    manager.LMCallback(*m_ngram, m_lmIdLookup);
+  }
 
-  private:
-    LanguageModelKen(const LanguageModelKen<Model> &copy_from);
+private:
+  LanguageModelKen(const LanguageModelKen<Model> &copy_from);
 
-    lm::WordIndex TranslateID(const Word &word) const {
-      std::size_t factor = word.GetFactor(m_factorType)->GetId();
-      return (factor >= m_lmIdLookup.size() ? 0 : m_lmIdLookup[factor]);
-    }
+  lm::WordIndex TranslateID(const Word &word) const {
+    std::size_t factor = word.GetFactor(m_factorType)->GetId();
+    return (factor >= m_lmIdLookup.size() ? 0 : m_lmIdLookup[factor]);
+  }
 
-    // Convert last words of hypothesis into vocab ids, returning an end pointer.  
-    lm::WordIndex *LastIDs(const Hypothesis &hypo, lm::WordIndex *indices) const {
-      lm::WordIndex *index = indices;
-      lm::WordIndex *end = indices + m_ngram->Order() - 1;
-      int position = hypo.GetCurrTargetWordsRange().GetEndPos();
-      for (; ; ++index, --position) {
-        if (index == end) return index;
-        if (position == -1) {
-          *index = m_ngram->GetVocabulary().BeginSentence();
-          return index + 1;
-        }
-        *index = TranslateID(hypo.GetWord(position));
+  // Convert last words of hypothesis into vocab ids, returning an end pointer.
+  lm::WordIndex *LastIDs(const Hypothesis &hypo, lm::WordIndex *indices) const {
+    lm::WordIndex *index = indices;
+    lm::WordIndex *end = indices + m_ngram->Order() - 1;
+    int position = hypo.GetCurrTargetWordsRange().GetEndPos();
+    for (; ; ++index, --position) {
+      if (index == end) return index;
+      if (position == -1) {
+        *index = m_ngram->GetVocabulary().BeginSentence();
+        return index + 1;
       }
+      *index = TranslateID(hypo.GetWord(position));
     }
+  }
 
-    boost::shared_ptr<Model> m_ngram;
-    
-    std::vector<lm::WordIndex> m_lmIdLookup;
+  boost::shared_ptr<Model> m_ngram;
 
-    FactorType m_factorType;
+  std::vector<lm::WordIndex> m_lmIdLookup;
 
-    const Factor *m_beginSentenceFactor;
+  FactorType m_factorType;
+
+  const Factor *m_beginSentenceFactor;
 };
 
-class MappingBuilder : public lm::EnumerateVocab {
+class MappingBuilder : public lm::EnumerateVocab
+{
 public:
   MappingBuilder(FactorCollection &factorCollection, std::vector<lm::WordIndex> &mapping)
     : m_factorCollection(factorCollection), m_mapping(mapping) {}
@@ -137,13 +141,14 @@ private:
 };
 
 template <class Model> LanguageModelKen<Model>::LanguageModelKen(const std::string &description, const std::string &line, const std::string &file, FactorType factorType, bool lazy)
-:LanguageModel(description, line)
-,m_factorType(factorType)
+  :LanguageModel(description, line)
+  ,m_factorType(factorType)
 {
   lm::ngram::Config config;
   IFVERBOSE(1) {
     config.messages = &std::cerr;
-  } else {
+  }
+  else {
     config.messages = NULL;
   }
   FactorCollection &collection = FactorCollection::Instance();
@@ -157,15 +162,17 @@ template <class Model> LanguageModelKen<Model>::LanguageModelKen(const std::stri
 }
 
 template <class Model> LanguageModelKen<Model>::LanguageModelKen(const LanguageModelKen<Model> &copy_from)
-:LanguageModel(copy_from.GetScoreProducerDescription(), copy_from.GetArgLine()),
-m_ngram(copy_from.m_ngram),
+  :LanguageModel(copy_from.GetScoreProducerDescription(), copy_from.GetArgLine()),
+   m_ngram(copy_from.m_ngram),
 // TODO: don't copy this.
-m_lmIdLookup(copy_from.m_lmIdLookup),
-m_factorType(copy_from.m_factorType),
-m_beginSentenceFactor(copy_from.m_beginSentenceFactor) {
+   m_lmIdLookup(copy_from.m_lmIdLookup),
+   m_factorType(copy_from.m_factorType),
+   m_beginSentenceFactor(copy_from.m_beginSentenceFactor)
+{
 }
 
-template <class Model> void LanguageModelKen<Model>::CalcScore(const Phrase &phrase, float &fullScore, float &ngramScore, size_t &oovCount) const {
+template <class Model> void LanguageModelKen<Model>::CalcScore(const Phrase &phrase, float &fullScore, float &ngramScore, size_t &oovCount) const
+{
   fullScore = 0;
   ngramScore = 0;
   oovCount = 0;
@@ -174,7 +181,7 @@ template <class Model> void LanguageModelKen<Model>::CalcScore(const Phrase &phr
 
   lm::ngram::ChartState discarded_sadly;
   lm::ngram::RuleScore<Model> scorer(*m_ngram, discarded_sadly);
-  
+
   size_t position;
   if (m_beginSentenceFactor == phrase.GetWord(0).GetFactor(m_factorType)) {
     scorer.BeginSentence();
@@ -182,7 +189,7 @@ template <class Model> void LanguageModelKen<Model>::CalcScore(const Phrase &phr
   } else {
     position = 0;
   }
-  
+
   size_t ngramBoundary = m_ngram->Order() - 1;
 
   size_t end_loop = std::min(ngramBoundary, phrase.GetSize());
@@ -199,7 +206,7 @@ template <class Model> void LanguageModelKen<Model>::CalcScore(const Phrase &phr
   }
   float before_boundary = fullScore + scorer.Finish();
   for (; position < phrase.GetSize(); ++position) {
-     const Word &word = phrase.GetWord(position);
+    const Word &word = phrase.GetWord(position);
     if (word.IsNonTerminal()) {
       fullScore += scorer.Finish();
       scorer.Reset();
@@ -207,7 +214,7 @@ template <class Model> void LanguageModelKen<Model>::CalcScore(const Phrase &phr
       lm::WordIndex index = TranslateID(word);
       scorer.Terminal(index);
       if (!index) ++oovCount;
-    }   
+    }
   }
   fullScore += scorer.Finish();
 
@@ -215,11 +222,12 @@ template <class Model> void LanguageModelKen<Model>::CalcScore(const Phrase &phr
   fullScore = TransformLMScore(fullScore);
 }
 
-template <class Model> FFState *LanguageModelKen<Model>::Evaluate(const Hypothesis &hypo, const FFState *ps, ScoreComponentCollection *out) const {
+template <class Model> FFState *LanguageModelKen<Model>::Evaluate(const Hypothesis &hypo, const FFState *ps, ScoreComponentCollection *out) const
+{
   const lm::ngram::State &in_state = static_cast<const KenLMState&>(*ps).state;
 
   std::auto_ptr<KenLMState> ret(new KenLMState());
-  
+
   if (!hypo.GetCurrTargetLength()) {
     ret->state = in_state;
     return ret.release();
@@ -242,17 +250,17 @@ template <class Model> FFState *LanguageModelKen<Model>::Evaluate(const Hypothes
   }
 
   if (hypo.IsSourceCompleted()) {
-    // Score end of sentence.  
+    // Score end of sentence.
     std::vector<lm::WordIndex> indices(m_ngram->Order() - 1);
     const lm::WordIndex *last = LastIDs(hypo, &indices.front());
     score += m_ngram->FullScoreForgotState(&indices.front(), last, m_ngram->GetVocabulary().EndSentence(), ret->state).prob;
   } else if (adjust_end < end) {
-    // Get state after adding a long phrase.  
+    // Get state after adding a long phrase.
     std::vector<lm::WordIndex> indices(m_ngram->Order() - 1);
     const lm::WordIndex *last = LastIDs(hypo, &indices.front());
     m_ngram->GetState(&indices.front(), last, ret->state);
   } else if (state0 != &ret->state) {
-    // Short enough phrase that we can just reuse the state.  
+    // Short enough phrase that we can just reuse the state.
     ret->state = *state0;
   }
 
@@ -270,34 +278,39 @@ template <class Model> FFState *LanguageModelKen<Model>::Evaluate(const Hypothes
   return ret.release();
 }
 
-class LanguageModelChartStateKenLM : public FFState {
-  public:
-    LanguageModelChartStateKenLM() {}
+class LanguageModelChartStateKenLM : public FFState
+{
+public:
+  LanguageModelChartStateKenLM() {}
 
-    const lm::ngram::ChartState &GetChartState() const { return m_state; }
-    lm::ngram::ChartState &GetChartState() { return m_state; }
+  const lm::ngram::ChartState &GetChartState() const {
+    return m_state;
+  }
+  lm::ngram::ChartState &GetChartState() {
+    return m_state;
+  }
 
-    int Compare(const FFState& o) const
-    {
-      const LanguageModelChartStateKenLM &other = static_cast<const LanguageModelChartStateKenLM&>(o);
-      int ret = m_state.Compare(other.m_state);
-      return ret;
-    }
+  int Compare(const FFState& o) const {
+    const LanguageModelChartStateKenLM &other = static_cast<const LanguageModelChartStateKenLM&>(o);
+    int ret = m_state.Compare(other.m_state);
+    return ret;
+  }
 
-  private:
-    lm::ngram::ChartState m_state;
+private:
+  lm::ngram::ChartState m_state;
 };
 
-template <class Model> FFState *LanguageModelKen<Model>::EvaluateChart(const ChartHypothesis& hypo, int featureID, ScoreComponentCollection *accumulator) const {
+template <class Model> FFState *LanguageModelKen<Model>::EvaluateChart(const ChartHypothesis& hypo, int featureID, ScoreComponentCollection *accumulator) const
+{
   LanguageModelChartStateKenLM *newState = new LanguageModelChartStateKenLM();
   lm::ngram::RuleScore<Model> ruleScore(*m_ngram, newState->GetChartState());
   const TargetPhrase &target = hypo.GetCurrTargetPhrase();
   const AlignmentInfo::NonTermIndexMap &nonTermIndexMap =
-        target.GetAlignNonTerm().GetNonTermIndexMap();
+    target.GetAlignNonTerm().GetNonTermIndexMap();
 
   const size_t size = hypo.GetCurrTargetPhrase().GetSize();
   size_t phrasePos = 0;
-  // Special cases for first word.  
+  // Special cases for first word.
   if (size) {
     const Word &word = hypo.GetCurrTargetPhrase().GetWord(0);
     if (word.GetFactor(m_factorType) == m_beginSentenceFactor) {
@@ -305,7 +318,7 @@ template <class Model> FFState *LanguageModelKen<Model>::EvaluateChart(const Cha
       ruleScore.BeginSentence();
       phrasePos++;
     } else if (word.IsNonTerminal()) {
-      // Non-terminal is first so we can copy instead of rescoring.  
+      // Non-terminal is first so we can copy instead of rescoring.
       const ChartHypothesis *prevHypo = hypo.GetPrevHypo(nonTermIndexMap[phrasePos]);
       const lm::ngram::ChartState &prevState = static_cast<const LanguageModelChartStateKenLM*>(prevHypo->GetFFState(featureID))->GetChartState();
       float prob = UntransformLMScore(prevHypo->GetScoreBreakdown().GetScoresForProducer(this)[0]);
@@ -347,20 +360,15 @@ LanguageModel *ConstructKenLM(const std::string &description, const std::string
 
     if (args[0] == "factor") {
       factorType = Scan<FactorType>(args[1]);
-    }
-    else if (args[0] == "order") {
+    } else if (args[0] == "order") {
       //nGramOrder = Scan<size_t>(args[1]);
-    }
-    else if (args[0] == "path") {
+    } else if (args[0] == "path") {
       filePath = args[1];
-    }
-    else if (args[0] == "lazyken") {
+    } else if (args[0] == "lazyken") {
       lazy = Scan<bool>(args[1]);
-    }
-    else if (args[0] == "name") {
+    } else if (args[0] == "name") {
       // that's ok. do nothing, passes onto LM constructor
-    }
-    else {
+    } else {
       throw "Unknown argument " + args[0];
     }
   }
@@ -368,26 +376,27 @@ LanguageModel *ConstructKenLM(const std::string &description, const std::string
   return ConstructKenLM(description, line, filePath, factorType, lazy);
 }
 
-LanguageModel *ConstructKenLM(const std::string &description, const std::string &line, const std::string &file, FactorType factorType, bool lazy) {
+LanguageModel *ConstructKenLM(const std::string &description, const std::string &line, const std::string &file, FactorType factorType, bool lazy)
+{
   try {
     lm::ngram::ModelType model_type;
     if (lm::ngram::RecognizeBinary(file.c_str(), model_type)) {
       switch(model_type) {
-        case lm::ngram::PROBING:
-          return new LanguageModelKen<lm::ngram::ProbingModel>(description, line, file,  factorType, lazy);
-        case lm::ngram::REST_PROBING:
-          return new LanguageModelKen<lm::ngram::RestProbingModel>(description, line, file, factorType, lazy);
-        case lm::ngram::TRIE:
-          return new LanguageModelKen<lm::ngram::TrieModel>(description, line, file, factorType, lazy);
-        case lm::ngram::QUANT_TRIE:
-          return new LanguageModelKen<lm::ngram::QuantTrieModel>(description, line, file, factorType, lazy);
-        case lm::ngram::ARRAY_TRIE:
-          return new LanguageModelKen<lm::ngram::ArrayTrieModel>(description, line, file, factorType, lazy);
-        case lm::ngram::QUANT_ARRAY_TRIE:
-          return new LanguageModelKen<lm::ngram::QuantArrayTrieModel>(description, line, file, factorType, lazy);
-        default:
-          std::cerr << "Unrecognized kenlm model type " << model_type << std::endl;
-          abort();
+      case lm::ngram::PROBING:
+        return new LanguageModelKen<lm::ngram::ProbingModel>(description, line, file,  factorType, lazy);
+      case lm::ngram::REST_PROBING:
+        return new LanguageModelKen<lm::ngram::RestProbingModel>(description, line, file, factorType, lazy);
+      case lm::ngram::TRIE:
+        return new LanguageModelKen<lm::ngram::TrieModel>(description, line, file, factorType, lazy);
+      case lm::ngram::QUANT_TRIE:
+        return new LanguageModelKen<lm::ngram::QuantTrieModel>(description, line, file, factorType, lazy);
+      case lm::ngram::ARRAY_TRIE:
+        return new LanguageModelKen<lm::ngram::ArrayTrieModel>(description, line, file, factorType, lazy);
+      case lm::ngram::QUANT_ARRAY_TRIE:
+        return new LanguageModelKen<lm::ngram::QuantArrayTrieModel>(description, line, file, factorType, lazy);
+      default:
+        std::cerr << "Unrecognized kenlm model type " << model_type << std::endl;
+        abort();
       }
     } else {
       return new LanguageModelKen<lm::ngram::ProbingModel>(description, line, file, factorType, lazy);
diff --git a/moses/LM/Ken.h b/moses/LM/Ken.h
index 3c2ceb774..360ac7be8 100644
--- a/moses/LM/Ken.h
+++ b/moses/LM/Ken.h
@@ -26,7 +26,8 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 
 #include "moses/TypeDef.h"
 
-namespace Moses {
+namespace Moses
+{
 
 class LanguageModel;
 
diff --git a/moses/LM/LDHT.cpp b/moses/LM/LDHT.cpp
index 5f52b2514..1b4e70661 100644
--- a/moses/LM/LDHT.cpp
+++ b/moses/LM/LDHT.cpp
@@ -16,7 +16,8 @@
 
 #include <boost/thread/tss.hpp>
 
-namespace Moses {
+namespace Moses
+{
 
 struct LDHTLMState : public FFState {
   LDHT::NewNgram gram_fingerprints;
@@ -60,338 +61,358 @@ struct LDHTLMState : public FFState {
   }
 };
 
-class LanguageModelLDHT : public LanguageModel {
+class LanguageModelLDHT : public LanguageModel
+{
 public:
-    LanguageModelLDHT();
-    LanguageModelLDHT(const std::string& path,
-                      ScoreIndexManager& manager,
-                      FactorType factorType);
-    LanguageModelLDHT(ScoreIndexManager& manager,
-                      LanguageModelLDHT& copyFrom);
-
-    LDHT::Client* getClientUnsafe() const;
-    LDHT::Client* getClientSafe();
-    LDHT::Client* initTSSClient();
-    virtual ~LanguageModelLDHT();
-    virtual void InitializeForInput(InputType const& source);
-    virtual void CleanUpAfterSentenceProcessing(const InputType &source);
-    virtual const FFState* EmptyHypothesisState(const InputType& input) const;
-    virtual bool Useable(const Phrase& phrase) const;
-    virtual void CalcScore(const Phrase& phrase,
-                           float& fullScore,
-                           float& ngramScore,
-                           std::size_t& oovCount) const;
-    virtual void CalcScoreFromCache(const Phrase& phrase,
-                                    float& fullScore,
-                                    float& ngramScore,
-                                    std::size_t& oovCount) const;
-    FFState* Evaluate(const Hypothesis& hypo,
-                      const FFState* input_state,
-                      ScoreComponentCollection* score_output) const;
-    FFState* EvaluateChart(const ChartHypothesis& hypo,
-                           int featureID,
-                           ScoreComponentCollection* accumulator) const;
-
-    virtual void IssueRequestsFor(Hypothesis& hypo,
-                                  const FFState* input_state);
-    float calcScoreFromState(LDHTLMState* hypo) const;
-    void sync();
-    void SetFFStateIdx(int state_idx);
+  LanguageModelLDHT();
+  LanguageModelLDHT(const std::string& path,
+                    ScoreIndexManager& manager,
+                    FactorType factorType);
+  LanguageModelLDHT(ScoreIndexManager& manager,
+                    LanguageModelLDHT& copyFrom);
+
+  LDHT::Client* getClientUnsafe() const;
+  LDHT::Client* getClientSafe();
+  LDHT::Client* initTSSClient();
+  virtual ~LanguageModelLDHT();
+  virtual void InitializeForInput(InputType const& source);
+  virtual void CleanUpAfterSentenceProcessing(const InputType &source);
+  virtual const FFState* EmptyHypothesisState(const InputType& input) const;
+  virtual bool Useable(const Phrase& phrase) const;
+  virtual void CalcScore(const Phrase& phrase,
+                         float& fullScore,
+                         float& ngramScore,
+                         std::size_t& oovCount) const;
+  virtual void CalcScoreFromCache(const Phrase& phrase,
+                                  float& fullScore,
+                                  float& ngramScore,
+                                  std::size_t& oovCount) const;
+  FFState* Evaluate(const Hypothesis& hypo,
+                    const FFState* input_state,
+                    ScoreComponentCollection* score_output) const;
+  FFState* EvaluateChart(const ChartHypothesis& hypo,
+                         int featureID,
+                         ScoreComponentCollection* accumulator) const;
+
+  virtual void IssueRequestsFor(Hypothesis& hypo,
+                                const FFState* input_state);
+  float calcScoreFromState(LDHTLMState* hypo) const;
+  void sync();
+  void SetFFStateIdx(int state_idx);
 
 protected:
-    boost::thread_specific_ptr<LDHT::Client> m_client;
-    std::string m_configPath;
-    FactorType m_factorType;
-    int m_state_idx;
-    int m_calc_score_count;
-    uint64_t m_start_tick;
+  boost::thread_specific_ptr<LDHT::Client> m_client;
+  std::string m_configPath;
+  FactorType m_factorType;
+  int m_state_idx;
+  int m_calc_score_count;
+  uint64_t m_start_tick;
 
 };
 
 LanguageModel* ConstructLDHTLM(const std::string& path,
                                ScoreIndexManager& manager,
-                               FactorType factorType) {
-    return new LanguageModelLDHT(path, manager, factorType);
+                               FactorType factorType)
+{
+  return new LanguageModelLDHT(path, manager, factorType);
 }
 
-LanguageModelLDHT::LanguageModelLDHT() : LanguageModel(), m_client(NULL) {
-    m_enableOOVFeature = false;
+LanguageModelLDHT::LanguageModelLDHT() : LanguageModel(), m_client(NULL)
+{
+  m_enableOOVFeature = false;
 }
 
 LanguageModelLDHT::LanguageModelLDHT(ScoreIndexManager& manager,
-                                     LanguageModelLDHT& copyFrom) {
-    m_calc_score_count = 0;
-    //m_client = copyFrom.m_client;
-    m_factorType = copyFrom.m_factorType;
-    m_configPath = copyFrom.m_configPath;
-    Init(manager);
+                                     LanguageModelLDHT& copyFrom)
+{
+  m_calc_score_count = 0;
+  //m_client = copyFrom.m_client;
+  m_factorType = copyFrom.m_factorType;
+  m_configPath = copyFrom.m_configPath;
+  Init(manager);
 }
 
 LanguageModelLDHT::LanguageModelLDHT(const std::string& path,
                                      ScoreIndexManager& manager,
                                      FactorType factorType)
-                                            : m_factorType(factorType) {
-    m_configPath = path;
-    Init(manager);
+  : m_factorType(factorType)
+{
+  m_configPath = path;
+  Init(manager);
 }
 
-LanguageModelLDHT::~LanguageModelLDHT() {
-    // TODO(wilson): should cleanup for each individual thread.
-    //delete getClientSafe();
+LanguageModelLDHT::~LanguageModelLDHT()
+{
+  // TODO(wilson): should cleanup for each individual thread.
+  //delete getClientSafe();
 }
 
 // Check that there is a TSS Client instance, and instantiate one if
 // there isn't.
-LDHT::Client* LanguageModelLDHT::getClientSafe() {
-    if (m_client.get() == NULL)
-        m_client.reset(initTSSClient());
-    return m_client.get();
+LDHT::Client* LanguageModelLDHT::getClientSafe()
+{
+  if (m_client.get() == NULL)
+    m_client.reset(initTSSClient());
+  return m_client.get();
 }
 
 // Do not check that there is a TSS Client instance.
-LDHT::Client* LanguageModelLDHT::getClientUnsafe() const {
-    return m_client.get();
+LDHT::Client* LanguageModelLDHT::getClientUnsafe() const
+{
+  return m_client.get();
 }
 
-LDHT::Client* LanguageModelLDHT::initTSSClient() {
-    std::ifstream config_file(m_configPath.c_str());
-    std::string ldht_config_path;
-    getline(config_file, ldht_config_path);
-    std::string ldhtlm_config_path;
-    getline(config_file, ldhtlm_config_path);
-
-    LDHT::FactoryCollection* factory_collection =
-            LDHT::FactoryCollection::createDefaultFactoryCollection();
-
-    LDHT::Client* client;
-    //client = new LDHT::ClientLocal();
-    client = new LDHT::Client();
-    client->fromXmlFiles(*factory_collection,
-                           ldht_config_path,
-                           ldhtlm_config_path);
-    return client;
+LDHT::Client* LanguageModelLDHT::initTSSClient()
+{
+  std::ifstream config_file(m_configPath.c_str());
+  std::string ldht_config_path;
+  getline(config_file, ldht_config_path);
+  std::string ldhtlm_config_path;
+  getline(config_file, ldhtlm_config_path);
+
+  LDHT::FactoryCollection* factory_collection =
+    LDHT::FactoryCollection::createDefaultFactoryCollection();
+
+  LDHT::Client* client;
+  //client = new LDHT::ClientLocal();
+  client = new LDHT::Client();
+  client->fromXmlFiles(*factory_collection,
+                       ldht_config_path,
+                       ldhtlm_config_path);
+  return client;
 }
 
-void LanguageModelLDHT::InitializeForInput(InputType const& source) {
-    getClientSafe()->clearCache();
-    m_start_tick = LDHT::Util::rdtsc();
+void LanguageModelLDHT::InitializeForInput(InputType const& source)
+{
+  getClientSafe()->clearCache();
+  m_start_tick = LDHT::Util::rdtsc();
 }
 
-void LanguageModelLDHT::CleanUpAfterSentenceProcessing(const InputType &source) {
-    LDHT::Client* client = getClientSafe();
-
-    std::cerr << "LDHT sentence stats:" << std::endl;
-    std::cerr << "  ngrams submitted: " << client->getNumNgramsSubmitted() << std::endl
-              << "  ngrams requested: " << client->getNumNgramsRequested() << std::endl
-              << "  ngrams not found: " << client->getKeyNotFoundCount() << std::endl
-              << "        cache hits: " << client->getCacheHitCount() << std::endl
-              << "        inferences: " << client->getInferenceCount() << std::endl
-              << "      pcnt latency: " << (float)client->getLatencyTicks() / (float)(LDHT::Util::rdtsc() - m_start_tick) * 100.0 << std::endl;
-    m_start_tick = 0;
-    client->resetLatencyTicks();
-    client->resetNumNgramsSubmitted();
-    client->resetNumNgramsRequested();
-    client->resetInferenceCount();
-    client->resetCacheHitCount();
-    client->resetKeyNotFoundCount();
+void LanguageModelLDHT::CleanUpAfterSentenceProcessing(const InputType &source)
+{
+  LDHT::Client* client = getClientSafe();
+
+  std::cerr << "LDHT sentence stats:" << std::endl;
+  std::cerr << "  ngrams submitted: " << client->getNumNgramsSubmitted() << std::endl
+            << "  ngrams requested: " << client->getNumNgramsRequested() << std::endl
+            << "  ngrams not found: " << client->getKeyNotFoundCount() << std::endl
+            << "        cache hits: " << client->getCacheHitCount() << std::endl
+            << "        inferences: " << client->getInferenceCount() << std::endl
+            << "      pcnt latency: " << (float)client->getLatencyTicks() / (float)(LDHT::Util::rdtsc() - m_start_tick) * 100.0 << std::endl;
+  m_start_tick = 0;
+  client->resetLatencyTicks();
+  client->resetNumNgramsSubmitted();
+  client->resetNumNgramsRequested();
+  client->resetInferenceCount();
+  client->resetCacheHitCount();
+  client->resetKeyNotFoundCount();
 }
 
 const FFState* LanguageModelLDHT::EmptyHypothesisState(
-        const InputType& input) const {
-    return NULL;
+  const InputType& input) const
+{
+  return NULL;
 }
 
-bool LanguageModelLDHT::Useable(const Phrase& phrase) const {
-    return (phrase.GetSize() > 0 && phrase.GetFactor(0, m_factorType) != NULL);
+bool LanguageModelLDHT::Useable(const Phrase& phrase) const
+{
+  return (phrase.GetSize() > 0 && phrase.GetFactor(0, m_factorType) != NULL);
 }
 
 void LanguageModelLDHT::CalcScore(const Phrase& phrase,
                                   float& fullScore,
                                   float& ngramScore,
-                                  std::size_t& oovCount) const {
-    const_cast<LanguageModelLDHT*>(this)->m_calc_score_count++;
-    if (m_calc_score_count > 10000) {
-        const_cast<LanguageModelLDHT*>(this)->m_calc_score_count = 0;
-        const_cast<LanguageModelLDHT*>(this)->sync();
-    }
+                                  std::size_t& oovCount) const
+{
+  const_cast<LanguageModelLDHT*>(this)->m_calc_score_count++;
+  if (m_calc_score_count > 10000) {
+    const_cast<LanguageModelLDHT*>(this)->m_calc_score_count = 0;
+    const_cast<LanguageModelLDHT*>(this)->sync();
+  }
 
-    // TODO(wilson): handle nonterminal words.
-    LDHT::Client* client = getClientUnsafe();
-    // Score the first order - 1 words of the phrase.
-    int order = LDHT::NewNgram::k_max_order;
-    int prefix_start = 0;
-    int prefix_end = std::min(phrase.GetSize(), static_cast<size_t>(order - 1));
-    LDHT::NewNgram ngram;
-    for (int word_idx = prefix_start; word_idx < prefix_end; ++word_idx) {
-        ngram.appendGram(phrase.GetWord(word_idx)
-                .GetFactor(m_factorType)->GetString().c_str());
-        client->requestNgram(ngram);
-    }
-    // Now score all subsequent ngrams to end of phrase.
-    int internal_start = prefix_end;
-    int internal_end = phrase.GetSize();
-    for (int word_idx = internal_start; word_idx < internal_end; ++word_idx) {
-        ngram.appendGram(phrase.GetWord(word_idx)
-                .GetFactor(m_factorType)->GetString().c_str());
-        client->requestNgram(ngram);
-    }
+  // TODO(wilson): handle nonterminal words.
+  LDHT::Client* client = getClientUnsafe();
+  // Score the first order - 1 words of the phrase.
+  int order = LDHT::NewNgram::k_max_order;
+  int prefix_start = 0;
+  int prefix_end = std::min(phrase.GetSize(), static_cast<size_t>(order - 1));
+  LDHT::NewNgram ngram;
+  for (int word_idx = prefix_start; word_idx < prefix_end; ++word_idx) {
+    ngram.appendGram(phrase.GetWord(word_idx)
+                     .GetFactor(m_factorType)->GetString().c_str());
+    client->requestNgram(ngram);
+  }
+  // Now score all subsequent ngrams to end of phrase.
+  int internal_start = prefix_end;
+  int internal_end = phrase.GetSize();
+  for (int word_idx = internal_start; word_idx < internal_end; ++word_idx) {
+    ngram.appendGram(phrase.GetWord(word_idx)
+                     .GetFactor(m_factorType)->GetString().c_str());
+    client->requestNgram(ngram);
+  }
 
-    fullScore = 0;
-    ngramScore = 0;
-    oovCount = 0;
+  fullScore = 0;
+  ngramScore = 0;
+  oovCount = 0;
 }
 
 void LanguageModelLDHT::CalcScoreFromCache(const Phrase& phrase,
-                                           float& fullScore,
-                                           float& ngramScore,
-                                           std::size_t& oovCount) const {
-    // Issue requests for phrase internal ngrams.
-    // Sync if necessary. (or autosync).
-    const_cast<LanguageModelLDHT*>(this)->sync();
-
-    // TODO(wilson): handle nonterminal words.
-    LDHT::Client* client = getClientUnsafe();
-    // Score the first order - 1 words of the phrase.
-    int order = LDHT::NewNgram::k_max_order;
-    int prefix_start = 0;
-    int prefix_end = std::min(phrase.GetSize(), static_cast<size_t>(order - 1));
-    LDHT::NewNgram ngram;
-    std::deque<int> full_score_tags;
-    for (int word_idx = prefix_start; word_idx < prefix_end; ++word_idx) {
-        ngram.appendGram(phrase.GetWord(word_idx)
-                .GetFactor(m_factorType)->GetString().c_str());
-        full_score_tags.push_back(client->requestNgram(ngram));
-    }
-    // Now score all subsequent ngrams to end of phrase.
-    int internal_start = prefix_end;
-    int internal_end = phrase.GetSize();
-    std::deque<int> internal_score_tags;
-    for (int word_idx = internal_start; word_idx < internal_end; ++word_idx) {
-        ngram.appendGram(phrase.GetWord(word_idx)
-                .GetFactor(m_factorType)->GetString().c_str());
-        internal_score_tags.push_back(client->requestNgram(ngram));
-    }
+    float& fullScore,
+    float& ngramScore,
+    std::size_t& oovCount) const
+{
+  // Issue requests for phrase internal ngrams.
+  // Sync if necessary. (or autosync).
+  const_cast<LanguageModelLDHT*>(this)->sync();
+
+  // TODO(wilson): handle nonterminal words.
+  LDHT::Client* client = getClientUnsafe();
+  // Score the first order - 1 words of the phrase.
+  int order = LDHT::NewNgram::k_max_order;
+  int prefix_start = 0;
+  int prefix_end = std::min(phrase.GetSize(), static_cast<size_t>(order - 1));
+  LDHT::NewNgram ngram;
+  std::deque<int> full_score_tags;
+  for (int word_idx = prefix_start; word_idx < prefix_end; ++word_idx) {
+    ngram.appendGram(phrase.GetWord(word_idx)
+                     .GetFactor(m_factorType)->GetString().c_str());
+    full_score_tags.push_back(client->requestNgram(ngram));
+  }
+  // Now score all subsequent ngrams to end of phrase.
+  int internal_start = prefix_end;
+  int internal_end = phrase.GetSize();
+  std::deque<int> internal_score_tags;
+  for (int word_idx = internal_start; word_idx < internal_end; ++word_idx) {
+    ngram.appendGram(phrase.GetWord(word_idx)
+                     .GetFactor(m_factorType)->GetString().c_str());
+    internal_score_tags.push_back(client->requestNgram(ngram));
+  }
 
-    // Wait for resposes from the servers.
-    //client->awaitResponses();
+  // Wait for resposes from the servers.
+  //client->awaitResponses();
 
-    // Calculate the full phrase score, and the internal score.
-    fullScore = 0.0;
-    while (!full_score_tags.empty()) {
-        fullScore += client->getNgramScore(full_score_tags.front());
-        full_score_tags.pop_front();
-    }
-    ngramScore = 0.0;
-    while (!internal_score_tags.empty()) {
-        float score = client->getNgramScore(internal_score_tags.front());
-        internal_score_tags.pop_front();
-        fullScore += score;
-        ngramScore += score;
-    }
-    fullScore = TransformLMScore(fullScore);
-    ngramScore = TransformLMScore(ngramScore);
-    oovCount = 0;
+  // Calculate the full phrase score, and the internal score.
+  fullScore = 0.0;
+  while (!full_score_tags.empty()) {
+    fullScore += client->getNgramScore(full_score_tags.front());
+    full_score_tags.pop_front();
+  }
+  ngramScore = 0.0;
+  while (!internal_score_tags.empty()) {
+    float score = client->getNgramScore(internal_score_tags.front());
+    internal_score_tags.pop_front();
+    fullScore += score;
+    ngramScore += score;
+  }
+  fullScore = TransformLMScore(fullScore);
+  ngramScore = TransformLMScore(ngramScore);
+  oovCount = 0;
 }
 
 void LanguageModelLDHT::IssueRequestsFor(Hypothesis& hypo,
-                                         const FFState* input_state) {
-    // TODO(wilson): handle nonterminal words.
-    LDHT::Client* client = getClientUnsafe();
-
-    // Create a new state and copy the contents of the input_state if
-    // supplied.
-    LDHTLMState* new_state = new LDHTLMState();
-    if (input_state == NULL) {
-        if (hypo.GetCurrTargetWordsRange().GetStartPos() != 0) {
-            V("got a null state but not at start of sentence");
-            abort();
-        }
-        new_state->gram_fingerprints.appendGram(BOS_);
+    const FFState* input_state)
+{
+  // TODO(wilson): handle nonterminal words.
+  LDHT::Client* client = getClientUnsafe();
+
+  // Create a new state and copy the contents of the input_state if
+  // supplied.
+  LDHTLMState* new_state = new LDHTLMState();
+  if (input_state == NULL) {
+    if (hypo.GetCurrTargetWordsRange().GetStartPos() != 0) {
+      V("got a null state but not at start of sentence");
+      abort();
     }
-    else {
-        if (hypo.GetCurrTargetWordsRange().GetStartPos() == 0) {
-            V("got a non null state but at start of sentence");
-            abort();
-        }
-        new_state->copyFrom(static_cast<const LDHTLMState&>(*input_state));
+    new_state->gram_fingerprints.appendGram(BOS_);
+  } else {
+    if (hypo.GetCurrTargetWordsRange().GetStartPos() == 0) {
+      V("got a non null state but at start of sentence");
+      abort();
     }
+    new_state->copyFrom(static_cast<const LDHTLMState&>(*input_state));
+  }
 
-    // Score ngrams that overlap with the previous phrase.
-    int order = LDHT::NewNgram::k_max_order;
-    int phrase_start = hypo.GetCurrTargetWordsRange().GetStartPos();
-    int phrase_end = hypo.GetCurrTargetWordsRange().GetEndPos() + 1;
-    int overlap_start = phrase_start;
-    int overlap_end = std::min(phrase_end, phrase_start + order - 1);
-    int word_idx = overlap_start;
-    LDHT::NewNgram& ngram = new_state->gram_fingerprints;
-    for (; word_idx < overlap_end; ++word_idx) {
-        ngram.appendGram(
-                hypo.GetFactor(word_idx, m_factorType)->GetString().c_str());
-        new_state->appendRequestTag(client->requestNgram(ngram));
-    }
-    // No need to score phrase internal ngrams, but keep track of them
-    // in the state (which in this case is the NewNgram containing the
-    // hashes of the individual grams).
-    for (; word_idx < phrase_end; ++word_idx) {
-        ngram.appendGram(
-                hypo.GetFactor(word_idx, m_factorType)->GetString().c_str());
-    }
-    // If this is the last phrase in the sentence, score the last ngram
-    // with the end of sentence marker on it.
-    if (hypo.IsSourceCompleted()) {
-        ngram.appendGram(EOS_);
-        //request_tags.push_back(client->requestNgram(ngram));
-        new_state->appendRequestTag(client->requestNgram(ngram));
-    }
-    hypo.SetFFState(m_state_idx, new_state);
+  // Score ngrams that overlap with the previous phrase.
+  int order = LDHT::NewNgram::k_max_order;
+  int phrase_start = hypo.GetCurrTargetWordsRange().GetStartPos();
+  int phrase_end = hypo.GetCurrTargetWordsRange().GetEndPos() + 1;
+  int overlap_start = phrase_start;
+  int overlap_end = std::min(phrase_end, phrase_start + order - 1);
+  int word_idx = overlap_start;
+  LDHT::NewNgram& ngram = new_state->gram_fingerprints;
+  for (; word_idx < overlap_end; ++word_idx) {
+    ngram.appendGram(
+      hypo.GetFactor(word_idx, m_factorType)->GetString().c_str());
+    new_state->appendRequestTag(client->requestNgram(ngram));
+  }
+  // No need to score phrase internal ngrams, but keep track of them
+  // in the state (which in this case is the NewNgram containing the
+  // hashes of the individual grams).
+  for (; word_idx < phrase_end; ++word_idx) {
+    ngram.appendGram(
+      hypo.GetFactor(word_idx, m_factorType)->GetString().c_str());
+  }
+  // If this is the last phrase in the sentence, score the last ngram
+  // with the end of sentence marker on it.
+  if (hypo.IsSourceCompleted()) {
+    ngram.appendGram(EOS_);
+    //request_tags.push_back(client->requestNgram(ngram));
+    new_state->appendRequestTag(client->requestNgram(ngram));
+  }
+  hypo.SetFFState(m_state_idx, new_state);
 }
 
-void LanguageModelLDHT::sync() {
-    m_calc_score_count = 0;
-    getClientUnsafe()->awaitResponses();
+void LanguageModelLDHT::sync()
+{
+  m_calc_score_count = 0;
+  getClientUnsafe()->awaitResponses();
 }
 
-void LanguageModelLDHT::SetFFStateIdx(int state_idx) {
-    m_state_idx = state_idx;
+void LanguageModelLDHT::SetFFStateIdx(int state_idx)
+{
+  m_state_idx = state_idx;
 }
 
 FFState* LanguageModelLDHT::Evaluate(
-        const Hypothesis& hypo,
-        const FFState* input_state_ignored,
-        ScoreComponentCollection* score_output) const {
-    // Input state is the state from the previous hypothesis, which
-    // we are not interested in. The requests for this hypo should
-    // already have been issued via IssueRequestsFor() and the LM then
-    // synced and all responses processed, and the tags placed in our
-    // FFState of hypo.
-    LDHTLMState* state = const_cast<LDHTLMState*>(static_cast<const LDHTLMState*>(hypo.GetFFState(m_state_idx)));
-
-    float score = calcScoreFromState(state);
-    score = FloorScore(TransformLMScore(score));
-    score_output->PlusEquals(this, score);
-
-    return state;
+  const Hypothesis& hypo,
+  const FFState* input_state_ignored,
+  ScoreComponentCollection* score_output) const
+{
+  // Input state is the state from the previous hypothesis, which
+  // we are not interested in. The requests for this hypo should
+  // already have been issued via IssueRequestsFor() and the LM then
+  // synced and all responses processed, and the tags placed in our
+  // FFState of hypo.
+  LDHTLMState* state = const_cast<LDHTLMState*>(static_cast<const LDHTLMState*>(hypo.GetFFState(m_state_idx)));
+
+  float score = calcScoreFromState(state);
+  score = FloorScore(TransformLMScore(score));
+  score_output->PlusEquals(this, score);
+
+  return state;
 }
 
 FFState* LanguageModelLDHT::EvaluateChart(
-        const ChartHypothesis& hypo,
-        int featureID,
-        ScoreComponentCollection* accumulator) const {
-    return NULL;
+  const ChartHypothesis& hypo,
+  int featureID,
+  ScoreComponentCollection* accumulator) const
+{
+  return NULL;
 }
 
-float LanguageModelLDHT::calcScoreFromState(LDHTLMState* state) const {
-    float score = 0.0;
-    std::vector<int>::iterator tag_iter;
-    LDHT::Client* client = getClientUnsafe();
-    for (tag_iter = state->requestTagsBegin();
-         tag_iter != state->requestTagsEnd();
-         ++tag_iter) {
-        score += client->getNgramScore(*tag_iter);
-    }
-    state->clearRequestTags();
-    state->setFinalised();
-    return score;
+float LanguageModelLDHT::calcScoreFromState(LDHTLMState* state) const
+{
+  float score = 0.0;
+  std::vector<int>::iterator tag_iter;
+  LDHT::Client* client = getClientUnsafe();
+  for (tag_iter = state->requestTagsBegin();
+       tag_iter != state->requestTagsEnd();
+       ++tag_iter) {
+    score += client->getNgramScore(*tag_iter);
+  }
+  state->clearRequestTags();
+  state->setFinalised();
+  return score;
 }
 
 }  // namespace Moses.
diff --git a/moses/LM/LDHT.h b/moses/LM/LDHT.h
index a8489c0e3..8c5c3c36b 100644
--- a/moses/LM/LDHT.h
+++ b/moses/LM/LDHT.h
@@ -7,7 +7,8 @@
 
 #include "moses/TypeDef.h"
 
-namespace Moses {
+namespace Moses
+{
 
 class ScoreIndexManager;
 class LanguageModel;
diff --git a/moses/LM/MultiFactor.h b/moses/LM/MultiFactor.h
index 491da4abe..21a9d493b 100644
--- a/moses/LM/MultiFactor.h
+++ b/moses/LM/MultiFactor.h
@@ -33,7 +33,7 @@ namespace Moses
 
 class Phrase;
 
-/* Abstract class for for multi factor LM. Only inherited by the JointLM at the moment. 
+/* Abstract class for for multi factor LM. Only inherited by the JointLM at the moment.
  * Could use this when factored LM are implemented
  */
 class LanguageModelMultiFactor : public LanguageModelImplementation
@@ -41,16 +41,16 @@ class LanguageModelMultiFactor : public LanguageModelImplementation
 protected:
   FactorMask m_factorTypes;
 
-	LanguageModelMultiFactor(const std::string& description, const std::string &line)
-  :LanguageModelImplementation(description, line)
+  LanguageModelMultiFactor(const std::string& description, const std::string &line)
+    :LanguageModelImplementation(description, line)
   {}
-	
+
 public:
   virtual bool Load(const std::string &filePath
                     , const std::vector<FactorType> &factorTypes
                     , size_t nGramOrder) = 0;
 
-	bool Useable(const Phrase &phrase) const;	
+  bool Useable(const Phrase &phrase) const;
 };
 
 }
diff --git a/moses/LM/ORLM.cpp b/moses/LM/ORLM.cpp
index 226267ee2..44fd64efb 100644
--- a/moses/LM/ORLM.cpp
+++ b/moses/LM/ORLM.cpp
@@ -9,10 +9,11 @@
 #include "ORLM.h"
 
 using std::map;
-namespace Moses 
+namespace Moses
+{
+bool LanguageModelORLM::Load(const std::string &filePath, FactorType factorType,
+                             size_t nGramOrder)
 {
-bool LanguageModelORLM::Load(const std::string &filePath, FactorType factorType, 
-			       size_t nGramOrder) {
   cerr << "Loading LanguageModelORLM..." << endl;
   m_filePath = filePath;
   m_factorType = factorType;
@@ -26,13 +27,14 @@ bool LanguageModelORLM::Load(const std::string &filePath, FactorType factorType,
   CreateFactors();
   return true;
 }
-void LanguageModelORLM::CreateFactors() {
+void LanguageModelORLM::CreateFactors()
+{
   FactorCollection &factorCollection = FactorCollection::Instance();
   size_t maxFactorId = 0; // to create lookup vector later on
   std::map<size_t, wordID_t> m_lmids_map; // map from factor id -> word id
 
   for(std::map<Word, wordID_t>::const_iterator vIter = m_lm->vocab_->VocabStart();
-      vIter != m_lm->vocab_->VocabEnd(); vIter++){
+      vIter != m_lm->vocab_->VocabEnd(); vIter++) {
     // get word from ORLM vocab and associate with (new) factor id
     size_t factorId = factorCollection.AddFactor(Output,m_factorType,vIter->first.ToString())->GetId();
     m_lmids_map[factorId] = vIter->second;
@@ -50,7 +52,7 @@ void LanguageModelORLM::CreateFactors() {
   maxFactorId = (factorId > maxFactorId) ? factorId : maxFactorId;
   m_sentenceEndWord[m_factorType] = m_sentenceEnd;
   // add to lookup vector in object
- lm_ids_vec_.resize(maxFactorId+1);
+  lm_ids_vec_.resize(maxFactorId+1);
   // fill with OOV code
   fill(lm_ids_vec_.begin(), lm_ids_vec_.end(), m_oov_id);
 
@@ -58,15 +60,18 @@ void LanguageModelORLM::CreateFactors() {
        iter != m_lmids_map.end() ; ++iter)
     lm_ids_vec_[iter->first] = iter->second;
 }
-wordID_t LanguageModelORLM::GetLmID(const std::string& str) const {
+wordID_t LanguageModelORLM::GetLmID(const std::string& str) const
+{
   return m_lm->vocab_->GetWordID(str);
 }
-wordID_t LanguageModelORLM::GetLmID(const Factor* factor) const {
+wordID_t LanguageModelORLM::GetLmID(const Factor* factor) const
+{
   size_t factorId = factor->GetId();
   return (factorId >= lm_ids_vec_.size()) ? m_oov_id : lm_ids_vec_[factorId];
 }
-LMResult LanguageModelORLM::GetValue(const std::vector<const Word*> &contextFactor, 
-    State* finalState) const {
+LMResult LanguageModelORLM::GetValue(const std::vector<const Word*> &contextFactor,
+                                     State* finalState) const
+{
   FactorType factorType = GetFactorType();
   // set up context
   //std::vector<long unsigned int> factor(1,0);
@@ -88,13 +93,14 @@ LMResult LanguageModelORLM::GetValue(const std::vector<const Word*> &contextFact
   */
   return ret;
 }
-bool LanguageModelORLM::UpdateORLM(const std::vector<string>& ngram, const int value) {
+bool LanguageModelORLM::UpdateORLM(const std::vector<string>& ngram, const int value)
+{
   /*cerr << "Inserting into ORLM: \"";
   iterate(ngram, nit)
     cerr << *nit << " ";
   cerr << "\"\t" << value << endl; */
   m_lm->vocab_->MakeOpen();
-  bool res = m_lm->update(ngram, value); 
+  bool res = m_lm->update(ngram, value);
   m_lm->vocab_->MakeClosed();
   return res;
 }
diff --git a/moses/LM/ORLM.h b/moses/LM/ORLM.h
index 48909191e..d7a8b5d35 100644
--- a/moses/LM/ORLM.h
+++ b/moses/LM/ORLM.h
@@ -17,7 +17,8 @@ class Phrase;
 
 /** @todo ask ollie
  */
-class LanguageModelORLM : public LanguageModelSingleFactor {
+class LanguageModelORLM : public LanguageModelSingleFactor
+{
 public:
   typedef count_t T;  // type for ORLM filter
   LanguageModelORLM(const std::string &line)
@@ -34,10 +35,12 @@ public:
     fout.close();
     delete m_lm;
   }
-  void CleanUpAfterSentenceProcessing() {m_lm->clearCache();} // clear caches
+  void CleanUpAfterSentenceProcessing() {
+    m_lm->clearCache(); // clear caches
+  }
 
   bool UpdateORLM(const std::vector<string>& ngram, const int value);
- protected:
+protected:
   OnlineRLM<T>* m_lm;
   //MultiOnlineRLM<T>* m_lm;
   wordID_t m_oov_id;
diff --git a/moses/LM/ParallelBackoff.cpp b/moses/LM/ParallelBackoff.cpp
index cf8c1509b..0b996de2b 100644
--- a/moses/LM/ParallelBackoff.cpp
+++ b/moses/LM/ParallelBackoff.cpp
@@ -70,7 +70,7 @@ private:
 
 public:
   LanguageModelParallelBackoff(const std::string &line)
-  :LanguageModelMultiFactor("ParallelBackoffLM", line)
+    :LanguageModelMultiFactor("ParallelBackoffLM", line)
   {}
 
   ~LanguageModelParallelBackoff();
diff --git a/moses/LM/Rand.cpp b/moses/LM/Rand.cpp
index 8e3e37a1f..5e31029d5 100644
--- a/moses/LM/Rand.cpp
+++ b/moses/LM/Rand.cpp
@@ -37,7 +37,7 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 
 namespace Moses
 {
-namespace 
+namespace
 {
 using namespace std;
 
@@ -45,8 +45,8 @@ class LanguageModelRandLM : public LanguageModelSingleFactor
 {
 public:
   LanguageModelRandLM(const std::string &line)
-  :LanguageModelSingleFactor("RandLM", line)
-  , m_lm(0)
+    :LanguageModelSingleFactor("RandLM", line)
+    , m_lm(0)
   {}
   bool Load(const std::string &filePath, FactorType factorType, size_t nGramOrder);
   virtual LMResult GetValue(const std::vector<const Word*> &contextFactor, State* finalState = NULL) const;
@@ -133,7 +133,7 @@ randlm::WordID LanguageModelRandLM::GetLmID( const std::string &str ) const
 }
 
 LMResult LanguageModelRandLM::GetValue(const vector<const Word*> &contextFactor,
-                                    State* finalState) const
+                                       State* finalState) const
 {
   FactorType factorType = GetFactorType();
   // set up context
diff --git a/moses/LM/SRI.cpp b/moses/LM/SRI.cpp
index b6281512c..54e6f93b9 100644
--- a/moses/LM/SRI.cpp
+++ b/moses/LM/SRI.cpp
@@ -39,29 +39,26 @@ using namespace std;
 namespace Moses
 {
 LanguageModelSRI::LanguageModelSRI(const std::string &line)
-:LanguageModelSingleFactor("SRILM", line)
-,m_srilmVocab(0)
-,m_srilmModel(0)
+  :LanguageModelSingleFactor("SRILM", line)
+  ,m_srilmVocab(0)
+  ,m_srilmModel(0)
 {
   FactorType factorType;
   size_t nGramOrder;
   string filePath;
 
   for (size_t i = 0; i < m_args.size(); ++i) {
-	const vector<string> &args = m_args[i];
-
-	if (args[0] == "factor") {
-	  factorType = Scan<FactorType>(args[1]);
-	}
-	else if (args[0] == "order") {
-	  nGramOrder = Scan<size_t>(args[1]);
-	}
-	else if (args[0] == "path") {
-	  filePath = args[1];
-	}
-	else {
-	  throw "Unknown argument " + args[0];
-	}
+    const vector<string> &args = m_args[i];
+
+    if (args[0] == "factor") {
+      factorType = Scan<FactorType>(args[1]);
+    } else if (args[0] == "order") {
+      nGramOrder = Scan<size_t>(args[1]);
+    } else if (args[0] == "path") {
+      filePath = args[1];
+    } else {
+      throw "Unknown argument " + args[0];
+    }
   }
 
   Load(filePath, factorType, nGramOrder);
diff --git a/moses/LM/SingleFactor.cpp b/moses/LM/SingleFactor.cpp
index 031fa38ac..abd8aca51 100644
--- a/moses/LM/SingleFactor.cpp
+++ b/moses/LM/SingleFactor.cpp
@@ -38,7 +38,7 @@ namespace Moses
 {
 
 LanguageModelSingleFactor::LanguageModelSingleFactor(const std::string& description, const std::string &line)
-:LanguageModelImplementation(description, line)
+  :LanguageModelImplementation(description, line)
 {
   m_nullContextState = new PointerState(NULL);
   m_beginSentenceState = new PointerState(NULL);
diff --git a/moses/LM/SingleFactor.h b/moses/LM/SingleFactor.h
index cb51808ac..9a1f30216 100644
--- a/moses/LM/SingleFactor.h
+++ b/moses/LM/SingleFactor.h
@@ -43,31 +43,27 @@ protected:
   FFState *m_nullContextState;
   FFState *m_beginSentenceState;
 
-	LanguageModelSingleFactor(const std::string& description, const std::string &line);
+  LanguageModelSingleFactor(const std::string& description, const std::string &line);
 
 public:
-	virtual ~LanguageModelSingleFactor();
-	virtual bool Load(const std::string &filePath
-					, FactorType factorType
-					, size_t nGramOrder) = 0;
-
-	bool Useable(const Phrase &phrase) const
-	{
-		return (phrase.GetSize()>0 && phrase.GetFactor(0, m_factorType) != NULL);		
-	}
-	
-	const Factor *GetSentenceStart() const
-	{
-		return m_sentenceStart;
-	}
-	const Factor *GetSentenceEnd() const
-	{
-		return m_sentenceEnd;
-	}
-	FactorType GetFactorType() const
-	{
-		return m_factorType;
-	}
+  virtual ~LanguageModelSingleFactor();
+  virtual bool Load(const std::string &filePath
+                    , FactorType factorType
+                    , size_t nGramOrder) = 0;
+
+  bool Useable(const Phrase &phrase) const {
+    return (phrase.GetSize()>0 && phrase.GetFactor(0, m_factorType) != NULL);
+  }
+
+  const Factor *GetSentenceStart() const {
+    return m_sentenceStart;
+  }
+  const Factor *GetSentenceEnd() const {
+    return m_sentenceEnd;
+  }
+  FactorType GetFactorType() const {
+    return m_factorType;
+  }
 
   virtual const FFState *GetNullContextState() const;
   virtual const FFState *GetBeginSentenceState() const;
diff --git a/moses/LexicalReordering.cpp b/moses/LexicalReordering.cpp
index 71c8fb2b8..98dca7b5f 100644
--- a/moses/LexicalReordering.cpp
+++ b/moses/LexicalReordering.cpp
@@ -10,7 +10,7 @@ using namespace std;
 namespace Moses
 {
 LexicalReordering::LexicalReordering(const std::string &line)
-: StatefulFeatureFunction("LexicalReordering", line)
+  : StatefulFeatureFunction("LexicalReordering", line)
 {
   std::cerr << "Initializing LexicalReordering.." << std::endl;
 
@@ -24,41 +24,37 @@ LexicalReordering::LexicalReordering(const std::string &line)
       m_configuration = new LexicalReorderingConfiguration(args[1]);
       m_configuration->SetScoreProducer(this);
       m_modelTypeString = m_configuration->GetModelString();
-    }
-    else if (args[0] == "input-factor") {
+    } else if (args[0] == "input-factor") {
       f_factors =Tokenize<FactorType>(args[1]);
-    }
-    else if (args[0] == "output-factor") {
+    } else if (args[0] == "output-factor") {
       e_factors =Tokenize<FactorType>(args[1]);
-    }
-    else if (args[0] == "path") {
+    } else if (args[0] == "path") {
       filePath = args[1];
-    }
-    else {
+    } else {
       throw "Unknown argument " + args[0];
     }
   }
 
   switch(m_configuration->GetCondition()) {
-    case LexicalReorderingConfiguration::FE:
-    case LexicalReorderingConfiguration::E:
-      m_factorsE = e_factors;
-      if(m_factorsE.empty()) {
-        UserMessage::Add("TL factor mask for lexical reordering is unexpectedly empty");
-        exit(1);
-      }
-      if(m_configuration->GetCondition() == LexicalReorderingConfiguration::E)
-        break; // else fall through
-    case LexicalReorderingConfiguration::F:
-      m_factorsF = f_factors;
-      if(m_factorsF.empty()) {
-        UserMessage::Add("SL factor mask for lexical reordering is unexpectedly empty");
-        exit(1);
-      }
-      break;
-    default:
-      UserMessage::Add("Unknown conditioning option!");
+  case LexicalReorderingConfiguration::FE:
+  case LexicalReorderingConfiguration::E:
+    m_factorsE = e_factors;
+    if(m_factorsE.empty()) {
+      UserMessage::Add("TL factor mask for lexical reordering is unexpectedly empty");
       exit(1);
+    }
+    if(m_configuration->GetCondition() == LexicalReorderingConfiguration::E)
+      break; // else fall through
+  case LexicalReorderingConfiguration::F:
+    m_factorsF = f_factors;
+    if(m_factorsF.empty()) {
+      UserMessage::Add("SL factor mask for lexical reordering is unexpectedly empty");
+      exit(1);
+    }
+    break;
+  default:
+    UserMessage::Add("Unknown conditioning option!");
+    exit(1);
   }
 
   m_table = LexicalReorderingTable::LoadAvailable(filePath, m_factorsF, m_factorsE, std::vector<FactorType>());
diff --git a/moses/LexicalReordering.h b/moses/LexicalReordering.h
index 51cf797f0..abaa31c25 100644
--- a/moses/LexicalReordering.h
+++ b/moses/LexicalReordering.h
@@ -24,15 +24,16 @@ class InputType;
 
 /** implementation of lexical reordering (Tilman ...) for phrase-based decoding
  */
-class LexicalReordering : public StatefulFeatureFunction {
-public:   
+class LexicalReordering : public StatefulFeatureFunction
+{
+public:
   LexicalReordering(const std::string &line);
   virtual ~LexicalReordering();
 
   virtual const FFState* EmptyHypothesisState(const InputType &input) const;
 
-  void InitializeForInput(const InputType& i){
-      m_table->InitializeForInput(i);
+  void InitializeForInput(const InputType& i) {
+    m_table->InitializeForInput(i);
   }
 
   Scores GetProb(const Phrase& f, const Phrase& e) const;
@@ -43,25 +44,25 @@ public:
 
   virtual FFState* EvaluateChart(const ChartHypothesis&,
                                  int /* featureID */,
-																 ScoreComponentCollection*) const {
-		CHECK(0); // not valid for chart decoder
-		return NULL;
-	}
+                                 ScoreComponentCollection*) const {
+    CHECK(0); // not valid for chart decoder
+    return NULL;
+  }
 
 private:
-    bool DecodeCondition(std::string s);
-    bool DecodeDirection(std::string s);
-    bool DecodeNumFeatureFunctions(std::string s);
+  bool DecodeCondition(std::string s);
+  bool DecodeDirection(std::string s);
+  bool DecodeNumFeatureFunctions(std::string s);
 
-    LexicalReorderingConfiguration *m_configuration;
-    std::string m_modelTypeString;
-    std::vector<std::string> m_modelType;
-    LexicalReorderingTable* m_table;
-    //std::vector<Direction> m_direction;
-    std::vector<LexicalReorderingConfiguration::Condition> m_condition;
-    //std::vector<size_t> m_scoreOffset;
-    //bool m_oneScorePerDirection;
-    std::vector<FactorType> m_factorsE, m_factorsF;
+  LexicalReorderingConfiguration *m_configuration;
+  std::string m_modelTypeString;
+  std::vector<std::string> m_modelType;
+  LexicalReorderingTable* m_table;
+  //std::vector<Direction> m_direction;
+  std::vector<LexicalReorderingConfiguration::Condition> m_condition;
+  //std::vector<size_t> m_scoreOffset;
+  //bool m_oneScorePerDirection;
+  std::vector<FactorType> m_factorsE, m_factorsF;
 };
 
 }
diff --git a/moses/LexicalReorderingState.cpp b/moses/LexicalReorderingState.cpp
index ddb089055..3165e447f 100644
--- a/moses/LexicalReorderingState.cpp
+++ b/moses/LexicalReorderingState.cpp
@@ -212,7 +212,7 @@ LexicalReorderingState* PhraseBasedReorderingState::Expand(const TranslationOpti
   if (m_direction == LexicalReorderingConfiguration::Forward && m_first) {
     ClearScores(scores);
   } else {
-    if (!m_first || m_useFirstBackwardScore){
+    if (!m_first || m_useFirstBackwardScore) {
       if (modelType == LexicalReorderingConfiguration::MSD) {
         reoType = GetOrientationTypeMSD(currWordsRange);
       } else if (modelType == LexicalReorderingConfiguration::MSLR) {
diff --git a/moses/LexicalReorderingTable.cpp b/moses/LexicalReorderingTable.cpp
index c0da31402..65ba66047 100644
--- a/moses/LexicalReorderingTable.cpp
+++ b/moses/LexicalReorderingTable.cpp
@@ -9,7 +9,7 @@
 #include "TargetPhraseCollection.h"
 
 #ifndef WIN32
-#include "TranslationModel/CompactPT/LexicalReorderingTableCompact.h"  
+#include "TranslationModel/CompactPT/LexicalReorderingTableCompact.h"
 #endif
 
 namespace Moses
diff --git a/moses/Manager.cpp b/moses/Manager.cpp
index b8e958d04..76809f224 100644
--- a/moses/Manager.cpp
+++ b/moses/Manager.cpp
@@ -80,7 +80,7 @@ void Manager::ProcessSentence()
 {
   // reset statistics
   ResetSentenceStats(m_source);
-  
+
   Timer getOptionsTime;
   getOptionsTime.start();
   m_transOptColl->CreateTranslationOptions();
@@ -262,8 +262,9 @@ struct SGNReverseCompare {
 /**
   * Implements lattice sampling, as in Chatterjee & Cancedda, emnlp 2010
   **/
-void Manager::CalcLatticeSamples(size_t count, TrellisPathList &ret) const {
-  
+void Manager::CalcLatticeSamples(size_t count, TrellisPathList &ret) const
+{
+
   vector<SearchGraphNode> searchGraph;
   GetSearchGraph(searchGraph);
 
@@ -277,15 +278,15 @@ void Manager::CalcLatticeSamples(size_t count, TrellisPathList &ret) const {
   map<int,const Hypothesis*> idToHyp;
   map<int,float> fscores;
 
-  //Iterating through the hypos in reverse order of id gives  a reverse 
-  //topological order. We rely on the fact that hypo ids are given out 
+  //Iterating through the hypos in reverse order of id gives  a reverse
+  //topological order. We rely on the fact that hypo ids are given out
   //sequentially, as the search proceeds.
-  //NB: Could just sort by stack. 
+  //NB: Could just sort by stack.
   sort(searchGraph.begin(), searchGraph.end(), SGNReverseCompare());
 
   //first task is to fill in the outgoing hypos and edge scores.
   for (vector<SearchGraphNode>::const_iterator i = searchGraph.begin();
-    i != searchGraph.end(); ++i) {
+       i != searchGraph.end(); ++i) {
     const Hypothesis* hypo = i->hypo;
     idToHyp[hypo->GetId()] = hypo;
     fscores[hypo->GetId()] = i->fscore;
@@ -293,7 +294,7 @@ void Manager::CalcLatticeSamples(size_t count, TrellisPathList &ret) const {
       //back to  current
       const Hypothesis* prevHypo = i->hypo->GetPrevHypo();
       outgoingHyps[prevHypo].insert(hypo);
-      edgeScores[Edge(prevHypo->GetId(),hypo->GetId())] = 
+      edgeScores[Edge(prevHypo->GetId(),hypo->GetId())] =
         hypo->GetScore() - prevHypo->GetScore();
     }
     //forward from current
@@ -304,7 +305,7 @@ void Manager::CalcLatticeSamples(size_t count, TrellisPathList &ret) const {
       outgoingHyps[hypo].insert(nextHypo);
       map<int,float>::const_iterator fscoreIter = fscores.find(nextHypo->GetId());
       CHECK(fscoreIter != fscores.end());
-      edgeScores[Edge(hypo->GetId(),nextHypo->GetId())] = 
+      edgeScores[Edge(hypo->GetId(),nextHypo->GetId())] =
         i->fscore - fscoreIter->second;
     }
   }
@@ -312,26 +313,26 @@ void Manager::CalcLatticeSamples(size_t count, TrellisPathList &ret) const {
 
   //then run through again to calculate sigmas
   for (vector<SearchGraphNode>::const_iterator i = searchGraph.begin();
-    i != searchGraph.end(); ++i) {
+       i != searchGraph.end(); ++i) {
 
     if (i->forward == -1) {
       sigmas[i->hypo] = 0;
     } else {
-      map<const Hypothesis*, set<const Hypothesis*> >::const_iterator outIter = 
+      map<const Hypothesis*, set<const Hypothesis*> >::const_iterator outIter =
         outgoingHyps.find(i->hypo);
-      
+
       CHECK(outIter != outgoingHyps.end());
       float sigma = 0;
       for (set<const Hypothesis*>::const_iterator j = outIter->second.begin();
-        j != outIter->second.end(); ++j) {
+           j != outIter->second.end(); ++j) {
         map<const Hypothesis*, float>::const_iterator succIter = sigmas.find(*j);
         CHECK(succIter != sigmas.end());
-        map<Edge,float>::const_iterator edgeScoreIter = 
+        map<Edge,float>::const_iterator edgeScoreIter =
           edgeScores.find(Edge(i->hypo->GetId(),(*j)->GetId()));
         CHECK(edgeScoreIter != edgeScores.end());
         float term = edgeScoreIter->second + succIter->second; // Add sigma(*j)
         if (sigma == 0) {
-           sigma = term;
+          sigma = term;
         } else {
           sigma = log_sum(sigma,term);
         }
@@ -347,7 +348,7 @@ void Manager::CalcLatticeSamples(size_t count, TrellisPathList &ret) const {
     vector<const Hypothesis*> path;
     path.push_back(startHypo);
     while(1) {
-      map<const Hypothesis*, set<const Hypothesis*> >::const_iterator outIter = 
+      map<const Hypothesis*, set<const Hypothesis*> >::const_iterator outIter =
         outgoingHyps.find(path.back());
       if (outIter == outgoingHyps.end() || !outIter->second.size()) {
         //end of the path
@@ -358,7 +359,7 @@ void Manager::CalcLatticeSamples(size_t count, TrellisPathList &ret) const {
       vector<float> candidateScores;
       float scoreTotal = 0;
       for (set<const Hypothesis*>::const_iterator j = outIter->second.begin();
-        j != outIter->second.end(); ++j) {
+           j != outIter->second.end(); ++j) {
         candidates.push_back(*j);
         CHECK(sigmas.find(*j) != sigmas.end());
         Edge edge(path.back()->GetId(),(*j)->GetId());
@@ -385,18 +386,18 @@ void Manager::CalcLatticeSamples(size_t count, TrellisPathList &ret) const {
       }
       //cerr << "Random: " << random << " Chose " << position-1 << endl;
       const Hypothesis* chosen =  candidates[position-1];
-      path.push_back(chosen); 
+      path.push_back(chosen);
     }
     //cerr << "Path: " << endl;
     //for (size_t j = 0; j < path.size(); ++j) {
-     // cerr << path[j]->GetId() <<  " " << path[j]->GetScoreBreakdown() << endl;
+    // cerr << path[j]->GetId() <<  " " << path[j]->GetScoreBreakdown() << endl;
     //}
     //cerr << endl;
 
     //Convert the hypos to TrellisPath
     ret.Add(new TrellisPath(path));
     //cerr << ret.at(ret.GetSize()-1).GetScoreBreakdown() << endl;
-  } 
+  }
 
 }
 
@@ -680,7 +681,7 @@ void Manager::OutputFeatureValuesForSLF(const Hypothesis* hypo, bool zeros, std:
 
   // outputSearchGraphStream << endl;
   // outputSearchGraphStream << (*hypo) << endl;
-  // const ScoreComponentCollection& scoreCollection = hypo->GetScoreBreakdown(); 
+  // const ScoreComponentCollection& scoreCollection = hypo->GetScoreBreakdown();
   // outputSearchGraphStream << scoreCollection << endl;
 
   const StaticData& staticData = StaticData::Instance();
@@ -753,10 +754,10 @@ size_t Manager::OutputFeatureWeightsForSLF(size_t index, const FeatureFunction*
   if (numScoreComps != 0) {
     vector<float> values = StaticData::Instance().GetAllWeights().GetScoresForProducer(ff);
     for (size_t i = 0; i < numScoreComps; ++i) {
-      outputSearchGraphStream << "# " << ff->GetScoreProducerDescription() 
-			      << " "  << ff->GetScoreProducerDescription()
-			      << " "  << (i+1) << " of " << numScoreComps << endl
-			      << "x"  << (index+i) << "scale=" << values[i] << endl;
+      outputSearchGraphStream << "# " << ff->GetScoreProducerDescription()
+                              << " "  << ff->GetScoreProducerDescription()
+                              << " "  << (i+1) << " of " << numScoreComps << endl
+                              << "x"  << (index+i) << "scale=" << values[i] << endl;
     }
     return index+numScoreComps;
   } else {
@@ -779,28 +780,28 @@ size_t Manager::OutputFeatureValuesForSLF(size_t index, bool zeros, const Hypoth
   //   // cout << "m_scores.coreSize()==" << m_scores.coreSize() << endl;
   //   // cout << "m_scores.cbegin() ?= m_scores.cend()\t" <<  (m_scores.cbegin() == m_scores.cend()) << endl;
 
-    
+
   //   // for(FVector::FNVmap::const_iterator i = m_scores.cbegin(); i != m_scores.cend(); i++) {
   //   //   std::cout<<prefix << "\t" << (i->first) << "\t" << (i->second) << std::endl;
   //   // }
   //   for(int i=0, n=v.size(); i<n; i+=1) {
   //     //      outputSearchGraphStream << prefix << i << "==" << v[i] << std::endl;
-      
+
   //   }
   // }
 
   // FVector featureValues = scoreCollection.GetVectorForProducer(ff);
   // outputSearchGraphStream << featureValues << endl;
-  const ScoreComponentCollection& scoreCollection = hypo->GetScoreBreakdown(); 
+  const ScoreComponentCollection& scoreCollection = hypo->GetScoreBreakdown();
 
   vector<float> featureValues = scoreCollection.GetScoresForProducer(ff);
   size_t numScoreComps = featureValues.size();//featureValues.coreSize();
   //  if (numScoreComps != ScoreProducer::unlimited) {
-    // vector<float> values = StaticData::Instance().GetAllWeights().GetScoresForProducer(ff);
+  // vector<float> values = StaticData::Instance().GetAllWeights().GetScoresForProducer(ff);
   for (size_t i = 0; i < numScoreComps; ++i) {
     outputSearchGraphStream << "x"  << (index+i) << "=" << ((zeros) ? 0.0 : featureValues[i]) << " ";
-    }
-    return index+numScoreComps;
+  }
+  return index+numScoreComps;
   // } else {
   //   cerr << "Sparse features are not supported when outputting HTK standard lattice format" << endl;
   //   assert(false);
@@ -810,7 +811,7 @@ size_t Manager::OutputFeatureValuesForSLF(size_t index, bool zeros, const Hypoth
 
 size_t Manager::OutputFeatureValuesForHypergraph(size_t index, const Hypothesis* hypo, const FeatureFunction* ff, std::ostream &outputSearchGraphStream) const
 {
-  ScoreComponentCollection scoreCollection = hypo->GetScoreBreakdown(); 
+  ScoreComponentCollection scoreCollection = hypo->GetScoreBreakdown();
   const Hypothesis *prevHypo = hypo->GetPrevHypo();
   if (prevHypo) {
     scoreCollection.MinusEquals( prevHypo->GetScoreBreakdown() );
@@ -851,60 +852,60 @@ void Manager::OutputSearchGraphAsHypergraph(long translationId, std::ostream &ou
   {
     long hypergraphHypothesisID = 0;
     for (size_t arcNumber = 0, size=searchGraph.size(); arcNumber < size; ++arcNumber) {
-    
+
       // Get an id number for the previous hypothesis
       const Hypothesis *prevHypo = searchGraph[arcNumber].hypo->GetPrevHypo();
       if (prevHypo!=NULL) {
-	int mosesPrevHypothesisID = prevHypo->GetId();
-	if (mosesIDToHypergraphID.count(mosesPrevHypothesisID) == 0) {
-	  mosesIDToHypergraphID[mosesPrevHypothesisID] = hypergraphHypothesisID;
-	  //	hypergraphIDToMosesID[hypergraphHypothesisID] = mosesPrevHypothesisID;
-	  hypergraphHypothesisID += 1;
-	}
+        int mosesPrevHypothesisID = prevHypo->GetId();
+        if (mosesIDToHypergraphID.count(mosesPrevHypothesisID) == 0) {
+          mosesIDToHypergraphID[mosesPrevHypothesisID] = hypergraphHypothesisID;
+          //	hypergraphIDToMosesID[hypergraphHypothesisID] = mosesPrevHypothesisID;
+          hypergraphHypothesisID += 1;
+        }
       }
 
       // Get an id number for this hypothesis
       int mosesHypothesisID;
       if (searchGraph[arcNumber].recombinationHypo) {
-	mosesHypothesisID = searchGraph[arcNumber].recombinationHypo->GetId();
+        mosesHypothesisID = searchGraph[arcNumber].recombinationHypo->GetId();
       } else {
-	mosesHypothesisID = searchGraph[arcNumber].hypo->GetId();
+        mosesHypothesisID = searchGraph[arcNumber].hypo->GetId();
       }
 
       if (mosesIDToHypergraphID.count(mosesHypothesisID) == 0) {
-      
-	mosesIDToHypergraphID[mosesHypothesisID] = hypergraphHypothesisID;
-	//      hypergraphIDToMosesID[hypergraphHypothesisID] = mosesHypothesisID;
 
-	bool terminalNode = (searchGraph[arcNumber].forward == -1);
-	if (terminalNode) {
-	  // Final arc to end node, representing the end of the sentence </s>
-	  terminalNodes.insert(hypergraphHypothesisID);
-	}
+        mosesIDToHypergraphID[mosesHypothesisID] = hypergraphHypothesisID;
+        //      hypergraphIDToMosesID[hypergraphHypothesisID] = mosesHypothesisID;
 
-	hypergraphHypothesisID += 1;
+        bool terminalNode = (searchGraph[arcNumber].forward == -1);
+        if (terminalNode) {
+          // Final arc to end node, representing the end of the sentence </s>
+          terminalNodes.insert(hypergraphHypothesisID);
+        }
+
+        hypergraphHypothesisID += 1;
       }
 
       // Record that this arc ends at this node
       hypergraphIDToArcs.insert(pair<int,int>(mosesIDToHypergraphID[mosesHypothesisID],arcNumber));
 
     }
-    
+
     // Unique end node
     endNode = hypergraphHypothesisID;
     //    mosesIDToHypergraphID[hypergraphHypothesisID] = hypergraphHypothesisID;
     numNodes = endNode + 1;
 
   }
-  
+
 
   long numArcs = searchGraph.size() + terminalNodes.size();
 
   // Print number of nodes and arcs
   outputSearchGraphStream << numNodes << " " << numArcs << endl;
 
-  VERBOSE(2,"Search graph to output as hypergraph for sentence " << translationId 
-	  << " contains " << numArcs << " arcs and " << numNodes << " nodes" << std::endl)
+  VERBOSE(2,"Search graph to output as hypergraph for sentence " << translationId
+          << " contains " << numArcs << " arcs and " << numNodes << " nodes" << std::endl)
 
   VERBOSE(2,"Outputting search graph to output as hypergraph for sentence " << translationId << std::endl)
 
@@ -920,51 +921,51 @@ void Manager::OutputSearchGraphAsHypergraph(long translationId, std::ostream &ou
       outputSearchGraphStream << count << "\n";
 
       pair<multimap<int,int>::iterator, multimap<int,int>::iterator> range =
-	hypergraphIDToArcs.equal_range(hypergraphHypothesisID);
+        hypergraphIDToArcs.equal_range(hypergraphHypothesisID);
       for (multimap<int,int>::iterator it=range.first; it!=range.second; ++it) {
-	int lineNumber = (*it).second;
-	const Hypothesis *thisHypo = searchGraph[lineNumber].hypo;
-	int mosesHypothesisID;// = thisHypo->GetId();
-	if (searchGraph[lineNumber].recombinationHypo) {
-	  mosesHypothesisID = searchGraph[lineNumber].recombinationHypo->GetId();
-	} else {
-	  mosesHypothesisID = searchGraph[lineNumber].hypo->GetId();
-	}
-	//	int actualHypergraphHypothesisID = mosesIDToHypergraphID[mosesHypothesisID];
-	UTIL_THROW_IF(
-		      (hypergraphHypothesisID != mosesIDToHypergraphID[mosesHypothesisID]),
-		      util::Exception,
-		      "Error while writing search lattice as hypergraph for sentence " << translationId << ". " <<
-		      "Moses node " << mosesHypothesisID << " was expected to have hypergraph id " << hypergraphHypothesisID <<
-		      ", but actually had hypergraph id " << mosesIDToHypergraphID[mosesHypothesisID] << 
-		      ". There are " << numNodes << " nodes in the search lattice."
-		      );
-
-	const Hypothesis *prevHypo = thisHypo->GetPrevHypo();
-	if (prevHypo==NULL) {
-	  //	VERBOSE(2,"Hypergraph node " << hypergraphHypothesisID << " start of sentence" << std::endl)
-	  outputSearchGraphStream << "<s> ||| \n";
-	} else {
-	  int startNode = mosesIDToHypergraphID[prevHypo->GetId()];
-	  //	  VERBOSE(2,"Hypergraph node " << hypergraphHypothesisID << " has parent node " << startNode << std::endl)
-	  UTIL_THROW_IF(
-			(startNode >= hypergraphHypothesisID),
-			util::Exception,
-			"Error while writing search lattice as hypergraph for sentence" << translationId << ". " <<
-			"The nodes must be output in topological order. The code attempted to violate this restriction."
-			);
-
-	  const TargetPhrase &targetPhrase = thisHypo->GetCurrTargetPhrase();
-	  int targetWordCount = targetPhrase.GetSize();
-
-	  outputSearchGraphStream << "[" << startNode << "]";
-	  for (int targetWordIndex=0; targetWordIndex<targetWordCount; targetWordIndex+=1) {
-	    outputSearchGraphStream << " " << targetPhrase.GetWord(targetWordIndex);
-	  }
-	  outputSearchGraphStream << " ||| ";
-	  OutputFeatureValuesForHypergraph(thisHypo, outputSearchGraphStream);
-	  outputSearchGraphStream << "\n";
-	}
+        int lineNumber = (*it).second;
+        const Hypothesis *thisHypo = searchGraph[lineNumber].hypo;
+        int mosesHypothesisID;// = thisHypo->GetId();
+        if (searchGraph[lineNumber].recombinationHypo) {
+          mosesHypothesisID = searchGraph[lineNumber].recombinationHypo->GetId();
+        } else {
+          mosesHypothesisID = searchGraph[lineNumber].hypo->GetId();
+        }
+        //	int actualHypergraphHypothesisID = mosesIDToHypergraphID[mosesHypothesisID];
+        UTIL_THROW_IF(
+          (hypergraphHypothesisID != mosesIDToHypergraphID[mosesHypothesisID]),
+          util::Exception,
+          "Error while writing search lattice as hypergraph for sentence " << translationId << ". " <<
+          "Moses node " << mosesHypothesisID << " was expected to have hypergraph id " << hypergraphHypothesisID <<
+          ", but actually had hypergraph id " << mosesIDToHypergraphID[mosesHypothesisID] <<
+          ". There are " << numNodes << " nodes in the search lattice."
+        );
+
+        const Hypothesis *prevHypo = thisHypo->GetPrevHypo();
+        if (prevHypo==NULL) {
+          //	VERBOSE(2,"Hypergraph node " << hypergraphHypothesisID << " start of sentence" << std::endl)
+          outputSearchGraphStream << "<s> ||| \n";
+        } else {
+          int startNode = mosesIDToHypergraphID[prevHypo->GetId()];
+          //	  VERBOSE(2,"Hypergraph node " << hypergraphHypothesisID << " has parent node " << startNode << std::endl)
+          UTIL_THROW_IF(
+            (startNode >= hypergraphHypothesisID),
+            util::Exception,
+            "Error while writing search lattice as hypergraph for sentence" << translationId << ". " <<
+            "The nodes must be output in topological order. The code attempted to violate this restriction."
+          );
+
+          const TargetPhrase &targetPhrase = thisHypo->GetCurrTargetPhrase();
+          int targetWordCount = targetPhrase.GetSize();
+
+          outputSearchGraphStream << "[" << startNode << "]";
+          for (int targetWordIndex=0; targetWordIndex<targetWordCount; targetWordIndex+=1) {
+            outputSearchGraphStream << " " << targetPhrase.GetWord(targetWordIndex);
+          }
+          outputSearchGraphStream << " ||| ";
+          OutputFeatureValuesForHypergraph(thisHypo, outputSearchGraphStream);
+          outputSearchGraphStream << "\n";
+        }
       }
     }
   }
@@ -1001,14 +1002,14 @@ void Manager::OutputSearchGraphAsSLF(long translationId, std::ostream &outputSea
 
     int hypothesisID = searchGraph[arcNumber].hypo->GetId();
     if (nodes.count(hypothesisID) == 0) {
-      
+
       numNodes += targetWordCount;
       nodes[hypothesisID] = numNodes;
       //numNodes += 1;
 
       bool terminalNode = (searchGraph[arcNumber].forward == -1);
       if (terminalNode) {
-	numArcs += 1;
+        numArcs += 1;
       }
     }
 
@@ -1038,35 +1039,35 @@ void Manager::OutputSearchGraphAsSLF(long translationId, std::ostream &outputSea
       int targetWordCount = targetPhrase.GetSize();
 
       for (int targetWordIndex=0; targetWordIndex<targetWordCount; targetWordIndex+=1) {
-	int x = (targetWordCount-targetWordIndex);
+        int x = (targetWordCount-targetWordIndex);
 
-	outputSearchGraphStream <<  "J=" << arcNumber;
+        outputSearchGraphStream <<  "J=" << arcNumber;
 
-	if (targetWordIndex==0) {
-	  outputSearchGraphStream << " S=" << startNode;
-	} else {
-	  outputSearchGraphStream << " S=" << endNode - x;
-	}
+        if (targetWordIndex==0) {
+          outputSearchGraphStream << " S=" << startNode;
+        } else {
+          outputSearchGraphStream << " S=" << endNode - x;
+        }
 
-	outputSearchGraphStream << " E=" << endNode - (x-1)
-				<< " W=" << targetPhrase.GetWord(targetWordIndex);
+        outputSearchGraphStream << " E=" << endNode - (x-1)
+                                << " W=" << targetPhrase.GetWord(targetWordIndex);
 
-	OutputFeatureValuesForSLF(thisHypo, (targetWordIndex>0), outputSearchGraphStream);
+        OutputFeatureValuesForSLF(thisHypo, (targetWordIndex>0), outputSearchGraphStream);
 
-	outputSearchGraphStream  << endl;
+        outputSearchGraphStream  << endl;
 
-	arcNumber += 1;
+        arcNumber += 1;
       }
 
       if (terminalNode && terminalNodes.count(endNode) == 0) {
-	terminalNodes.insert(endNode);
-	outputSearchGraphStream <<  "J="   << arcNumber 
-				<< " S="   << endNode
-				<< " E="   << numNodes
-				<< endl;
-	arcNumber += 1;
+        terminalNodes.insert(endNode);
+        outputSearchGraphStream <<  "J="   << arcNumber
+                                << " S="   << endNode
+                                << " E="   << numNodes
+                                << endl;
+        arcNumber += 1;
       }
-    }	    
+    }
   }
 
 }
@@ -1124,17 +1125,17 @@ void OutputSearchNode(long translationId, std::ostream &outputSearchGraphStream,
     outputSearchGraphStream << " recombined=" << searchNode.recombinationHypo->GetId();
 
   outputSearchGraphStream << " forward=" << searchNode.forward	<< " fscore=" << searchNode.fscore
-                            << " covered=" << searchNode.hypo->GetCurrSourceWordsRange().GetStartPos()
-                            << "-" << searchNode.hypo->GetCurrSourceWordsRange().GetEndPos();
+                          << " covered=" << searchNode.hypo->GetCurrSourceWordsRange().GetStartPos()
+                          << "-" << searchNode.hypo->GetCurrSourceWordsRange().GetEndPos();
 
   // Modified so that -osgx is a superset of -osg (GST Oct 2011)
   ScoreComponentCollection scoreBreakdown = searchNode.hypo->GetScoreBreakdown();
   scoreBreakdown.MinusEquals( prevHypo->GetScoreBreakdown() );
   //outputSearchGraphStream << " scores = [ " << StaticData::Instance().GetAllWeights();
-  outputSearchGraphStream << " scores=\"" << scoreBreakdown << "\"";                            
+  outputSearchGraphStream << " scores=\"" << scoreBreakdown << "\"";
 
   outputSearchGraphStream << " out=\"" << searchNode.hypo->GetSourcePhraseStringRep() << "|" <<
-    searchNode.hypo->GetCurrTargetPhrase().GetStringRep(outputFactorOrder) << "\"" << endl;
+                          searchNode.hypo->GetCurrTargetPhrase().GetStringRep(outputFactorOrder) << "\"" << endl;
 //  outputSearchGraphStream << " out=" << searchNode.hypo->GetCurrTargetPhrase().GetStringRep(outputFactorOrder) << endl;
 }
 
diff --git a/moses/Manager.h b/moses/Manager.h
index 687d8dbeb..fd329c309 100644
--- a/moses/Manager.h
+++ b/moses/Manager.h
@@ -56,9 +56,9 @@ struct SearchGraphNode {
     hypo(theHypo), recombinationHypo(theRecombinationHypo),
     forward(theForward), fscore(theFscore) {}
 
-    bool operator<(const SearchGraphNode& sgn) const {
-        return this->hypo->GetId() < sgn.hypo->GetId();
-    }
+  bool operator<(const SearchGraphNode& sgn) const {
+    return this->hypo->GetId() < sgn.hypo->GetId();
+  }
 
 };
 
diff --git a/moses/MockHypothesis.cpp b/moses/MockHypothesis.cpp
index e98794cb7..826104565 100644
--- a/moses/MockHypothesis.cpp
+++ b/moses/MockHypothesis.cpp
@@ -19,7 +19,7 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 
 
 
-#include "MockHypothesis.h" 
+#include "MockHypothesis.h"
 
 #include <boost/test/unit_test.hpp>
 
@@ -28,19 +28,20 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 using namespace Moses;
 using namespace std;
 
-namespace MosesTest {
+namespace MosesTest
+{
 
 
 MockHypothesisGuard::MockHypothesisGuard(
-    const string& sourceSentence,
-    const vector<Alignment>& alignments,
-    const vector<string>& targetSegments) 
-: m_emptyTarget(),
-  m_sentence(),
-  m_wp("WordPenalty"),
-  m_uwp("UnknownWordPenalty"),
-  m_dist("Distortion"),
-  m_manager(0,m_sentence,Normal)
+  const string& sourceSentence,
+  const vector<Alignment>& alignments,
+  const vector<string>& targetSegments)
+  : m_emptyTarget(),
+    m_sentence(),
+    m_wp("WordPenalty"),
+    m_uwp("UnknownWordPenalty"),
+    m_dist("Distortion"),
+    m_manager(0,m_sentence,Normal)
 {
   BOOST_CHECK_EQUAL(alignments.size(), targetSegments.size());
 
@@ -49,7 +50,7 @@ MockHypothesisGuard::MockHypothesisGuard(
 
   stringstream in(sourceSentence + "\n");
   m_sentence.Read(in,factors);
-  
+
 
   //Initial empty hypothesis
   m_manager.ResetSentenceStats(m_sentence);
@@ -58,21 +59,20 @@ MockHypothesisGuard::MockHypothesisGuard(
   //create the chain
   vector<Alignment>::const_iterator ai = alignments.begin();
   vector<string>::const_iterator ti = targetSegments.begin();
-  for (; ti != targetSegments.end() && ai != alignments.end(); ++ti,++ai)
-  {
+  for (; ti != targetSegments.end() && ai != alignments.end(); ++ti,++ai) {
     Hypothesis* prevHypo = m_hypothesis;
     WordsRange wordsRange(ai->first,ai->second);
     m_targetPhrases.push_back(TargetPhrase());
     m_targetPhrases.back().CreateFromString(Input, factors, *ti, "|", NULL);
     m_toptions.push_back(new TranslationOption
-      (wordsRange,m_targetPhrases.back()));
-    m_hypothesis =  Hypothesis::Create(*prevHypo,*m_toptions.back(),NULL); 
+                         (wordsRange,m_targetPhrases.back()));
+    m_hypothesis =  Hypothesis::Create(*prevHypo,*m_toptions.back(),NULL);
   }
 
 
 }
 
-MockHypothesisGuard::~MockHypothesisGuard() 
+MockHypothesisGuard::~MockHypothesisGuard()
 {
   RemoveAllInColl(m_toptions);
   while (m_hypothesis) {
diff --git a/moses/MockHypothesis.h b/moses/MockHypothesis.h
index 2490dd5a6..67182ad56 100644
--- a/moses/MockHypothesis.h
+++ b/moses/MockHypothesis.h
@@ -29,7 +29,8 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 #include "Hypothesis.h"
 #include "Manager.h"
 
-namespace MosesTest {
+namespace MosesTest
+{
 
 //
 // Construct a hypothesis with arbitrary source and target phrase
@@ -38,42 +39,52 @@ namespace MosesTest {
 
 typedef std::pair<size_t,size_t> Alignment; //(first,last) in source
 
-class MockHypothesisGuard {
-  public:
-    /** Creates a phrase-based hypothesis. 
-    */
-    MockHypothesisGuard(
-        const std::string& sourceSentence,
-        const std::vector<Alignment>& alignments,
-        const std::vector<std::string>& targetSegments);
-        Moses::Hypothesis* operator*() const {return m_hypothesis;}
-
-    /** Destroy the hypothesis chain */
-    ~MockHypothesisGuard();
-
-  private:
-    Moses::TargetPhrase m_emptyTarget;
-    Moses::Sentence m_sentence;
-    Moses::WordPenaltyProducer m_wp;
-    Moses::UnknownWordPenaltyProducer m_uwp;
-    Moses::DistortionScoreProducer m_dist;
-    Moses::Manager m_manager;
-    Moses::Hypothesis* m_hypothesis;
-    std::vector<Moses::TargetPhrase> m_targetPhrases;
-    std::vector<Moses::TranslationOption*> m_toptions;
+class MockHypothesisGuard
+{
+public:
+  /** Creates a phrase-based hypothesis.
+  */
+  MockHypothesisGuard(
+    const std::string& sourceSentence,
+    const std::vector<Alignment>& alignments,
+    const std::vector<std::string>& targetSegments);
+  Moses::Hypothesis* operator*() const {
+    return m_hypothesis;
+  }
+
+  /** Destroy the hypothesis chain */
+  ~MockHypothesisGuard();
+
+private:
+  Moses::TargetPhrase m_emptyTarget;
+  Moses::Sentence m_sentence;
+  Moses::WordPenaltyProducer m_wp;
+  Moses::UnknownWordPenaltyProducer m_uwp;
+  Moses::DistortionScoreProducer m_dist;
+  Moses::Manager m_manager;
+  Moses::Hypothesis* m_hypothesis;
+  std::vector<Moses::TargetPhrase> m_targetPhrases;
+  std::vector<Moses::TranslationOption*> m_toptions;
 };
 
-class HypothesisFixture {
-  public:
-    HypothesisFixture();
-    const Moses::Hypothesis* empty() {return **m_empty;}
-    const Moses::Hypothesis* partial() {return **m_partial;}
-    const Moses::Hypothesis* full() {return **m_full;}
- 
-  private:
-    std::auto_ptr<MockHypothesisGuard> m_empty;
-    std::auto_ptr<MockHypothesisGuard> m_partial;
-    std::auto_ptr<MockHypothesisGuard> m_full;
+class HypothesisFixture
+{
+public:
+  HypothesisFixture();
+  const Moses::Hypothesis* empty() {
+    return **m_empty;
+  }
+  const Moses::Hypothesis* partial() {
+    return **m_partial;
+  }
+  const Moses::Hypothesis* full() {
+    return **m_full;
+  }
+
+private:
+  std::auto_ptr<MockHypothesisGuard> m_empty;
+  std::auto_ptr<MockHypothesisGuard> m_partial;
+  std::auto_ptr<MockHypothesisGuard> m_full;
 };
 
 
diff --git a/moses/OutputCollector.h b/moses/OutputCollector.h
index 96353934e..5f72433d8 100644
--- a/moses/OutputCollector.h
+++ b/moses/OutputCollector.h
@@ -45,27 +45,23 @@ public:
   OutputCollector(std::ostream* outStream= &std::cout, std::ostream* debugStream=&std::cerr) :
     m_nextOutput(0),m_outStream(outStream),m_debugStream(debugStream),
     m_isHoldingOutputStream(false), m_isHoldingDebugStream(false) {}
-  
-  ~OutputCollector()
-  {
+
+  ~OutputCollector() {
     if (m_isHoldingOutputStream)
       delete m_outStream;
     if (m_isHoldingDebugStream)
       delete m_debugStream;
   }
-  
-  void HoldOutputStream()
-  {
+
+  void HoldOutputStream() {
     m_isHoldingOutputStream = true;
   }
-  
-  void HoldDebugStream()
-  {
+
+  void HoldDebugStream() {
     m_isHoldingDebugStream = true;
   }
-  
-  bool OutputIsCout() const
-  {
+
+  bool OutputIsCout() const {
     return (m_outStream == std::cout);
   }
 
@@ -87,7 +83,7 @@ public:
         *m_outStream << iter->second << std::flush;
         ++m_nextOutput;
         std::map<int,std::string>::iterator debugIter = m_debugs.find(iter->first);
-		m_outputs.erase(iter);
+        m_outputs.erase(iter);
         if (debugIter != m_debugs.end()) {
           *m_debugStream << debugIter->second << std::flush;
           m_debugs.erase(debugIter);
diff --git a/moses/PCNTools.h b/moses/PCNTools.h
index 8a31e99ad..ea43df838 100644
--- a/moses/PCNTools.h
+++ b/moses/PCNTools.h
@@ -36,7 +36,7 @@ namespace PCN
 typedef std::pair<std::pair<std::string, std::vector<float> >, size_t> CNAlt;
 typedef std::vector<CNAlt> CNCol;
 typedef std::vector<CNCol> CN;
-  
+
 /** Given a string ((('foo',0.1,1),('bar',0.9,2)),...) representation of a
  * word lattice in PCN format, return a CN object representing the lattice
  */
diff --git a/moses/PDTAimp.h b/moses/PDTAimp.h
index 835cd6895..735179217 100644
--- a/moses/PDTAimp.h
+++ b/moses/PDTAimp.h
@@ -38,7 +38,7 @@ protected:
     : m_dict(0),
       m_obj(p),useCache(1),m_numInputScores(nis),totalE(0),distinctE(0) {}
 
- public:
+public:
   std::vector<FactorType> m_input,m_output;
   PhraseDictionaryTree *m_dict;
   typedef std::vector<TargetPhraseCollection const*> vTPC;
@@ -185,7 +185,7 @@ protected:
   void Create(const std::vector<FactorType> &input
               , const std::vector<FactorType> &output
               , const std::string &filePath
-	      , const std::vector<float> &weight
+              , const std::vector<float> &weight
              ) {
 
     // set my members
@@ -267,10 +267,10 @@ protected:
                           StringTgtCand::Tokens const& factorStrings,
                           Scores const& scoreVector,
                           const ScoreComponentCollection& sparseFeatures,
-  		  std::vector<float> &weights,
-  		  float weightWP,
+                          std::vector<float> &weights,
+                          float weightWP,
                           Phrase const* srcPtr) const {
-  FactorCollection &factorCollection = FactorCollection::Instance();
+    FactorCollection &factorCollection = FactorCollection::Instance();
 
     for(size_t k=0; k<factorStrings.size(); ++k) {
       util::TokenIter<util::MultiCharacter, false> word(*factorStrings[k], StaticData::Instance().GetFactorDelimiter());
@@ -438,8 +438,8 @@ protected:
 
               //put in phrase table scores, logging as we insert
               std::transform(tcands[i].scores.begin(),tcands[i].scores.end(),nscores.begin() + m_numInputScores,TransformScore);
-              
-	      CHECK(nscores.size()==weightT.size());
+
+              CHECK(nscores.size()==weightT.size());
 
               //tally up
               float score=std::inner_product(nscores.begin(), nscores.end(), weightT.begin(), 0.0f);
diff --git a/moses/Parameter.cpp b/moses/Parameter.cpp
index 4264010cd..e16b6d08f 100644
--- a/moses/Parameter.cpp
+++ b/moses/Parameter.cpp
@@ -69,30 +69,30 @@ Parameter::Parameter()
   AddParam("report-all-factors", "report all factors in output, not just first");
   AddParam("report-all-factors-in-n-best", "Report all factors in n-best-lists. Default is false");
 #ifdef HAVE_SYNLM
-	AddParam("slmodel-file", "location of the syntactic language model file(s)");
-	AddParam("slmodel-factor", "factor to use with syntactic language model");
-	AddParam("slmodel-beam", "beam width to use with syntactic language model's parser");
+  AddParam("slmodel-file", "location of the syntactic language model file(s)");
+  AddParam("slmodel-factor", "factor to use with syntactic language model");
+  AddParam("slmodel-beam", "beam width to use with syntactic language model's parser");
 #endif
   AddParam("stack", "s", "maximum stack size for histogram pruning");
   AddParam("stack-diversity", "sd", "minimum number of hypothesis of each coverage in stack (default 0)");
   AddParam("threads","th", "number of threads to use in decoding (defaults to single-threaded)");
-	AddParam("translation-details", "T", "for each best hypothesis, report translation details to the given file");
-	AddParam("ttable-file", "location and properties of the translation tables");
-	AddParam("ttable-limit", "ttl", "maximum number of translation table entries per input phrase");
-	AddParam("translation-option-threshold", "tot", "threshold for translation options relative to best for input phrase");
-	AddParam("early-discarding-threshold", "edt", "threshold for constructing hypotheses based on estimate cost");
-	AddParam("verbose", "v", "verbosity level of the logging");
+  AddParam("translation-details", "T", "for each best hypothesis, report translation details to the given file");
+  AddParam("ttable-file", "location and properties of the translation tables");
+  AddParam("ttable-limit", "ttl", "maximum number of translation table entries per input phrase");
+  AddParam("translation-option-threshold", "tot", "threshold for translation options relative to best for input phrase");
+  AddParam("early-discarding-threshold", "edt", "threshold for constructing hypotheses based on estimate cost");
+  AddParam("verbose", "v", "verbosity level of the logging");
   AddParam("references", "Reference file(s) - used for bleu score feature");
-	AddParam("output-factors", "list if factors in the output");
-	AddParam("cache-path", "?");
-	AddParam("distortion-limit", "dl", "distortion (reordering) limit in maximum number of words (0 = monotone, -1 = unlimited)");	
-	AddParam("monotone-at-punctuation", "mp", "do not reorder over punctuation");
-	AddParam("distortion-file", "source factors (0 if table independent of source), target factors, location of the factorized/lexicalized reordering tables");
- 	AddParam("distortion", "configurations for each factorized/lexicalized reordering model.");
- 	AddParam("early-distortion-cost", "edc", "include estimate of distortion cost yet to be incurred in the score [Moore & Quirk 2007]. Default is no");
-	AddParam("xml-input", "xi", "allows markup of input with desired translations and probabilities. values can be 'pass-through' (default), 'inclusive', 'exclusive', 'ignore'");
+  AddParam("output-factors", "list if factors in the output");
+  AddParam("cache-path", "?");
+  AddParam("distortion-limit", "dl", "distortion (reordering) limit in maximum number of words (0 = monotone, -1 = unlimited)");
+  AddParam("monotone-at-punctuation", "mp", "do not reorder over punctuation");
+  AddParam("distortion-file", "source factors (0 if table independent of source), target factors, location of the factorized/lexicalized reordering tables");
+  AddParam("distortion", "configurations for each factorized/lexicalized reordering model.");
+  AddParam("early-distortion-cost", "edc", "include estimate of distortion cost yet to be incurred in the score [Moore & Quirk 2007]. Default is no");
+  AddParam("xml-input", "xi", "allows markup of input with desired translations and probabilities. values can be 'pass-through' (default), 'inclusive', 'exclusive', 'ignore'");
   AddParam("xml-brackets", "xb", "specify strings to be used as xml tags opening and closing, e.g. \"{{ }}\" (default \"< >\"). Avoid square brackets because of configuration file format. Valid only with text input mode" );
- 	AddParam("minimum-bayes-risk", "mbr", "use miminum Bayes risk to determine best translation");
+  AddParam("minimum-bayes-risk", "mbr", "use miminum Bayes risk to determine best translation");
   AddParam("lminimum-bayes-risk", "lmbr", "use lattice miminum Bayes risk to determine best translation");
   AddParam("mira", "do mira training");
   AddParam("consensus-decoding", "con", "use consensus decoding (De Nero et. al. 2009)");
@@ -119,17 +119,17 @@ Parameter::Parameter()
 #ifdef HAVE_PROTOBUF
   AddParam("output-search-graph-pb", "pb", "Write phrase lattice to protocol buffer objects in the specified path.");
 #endif
-	AddParam("cube-pruning-pop-limit", "cbp", "How many hypotheses should be popped for each stack. (default = 1000)");
-	AddParam("cube-pruning-diversity", "cbd", "How many hypotheses should be created for each coverage. (default = 0)");
-	AddParam("search-algorithm", "Which search algorithm to use. 0=normal stack, 1=cube pruning, 2=cube growing. (default = 0)");
-	AddParam("constraint", "Location of the file with target sentences to produce constraining the search");
-	AddParam("description", "Source language, target language, description");
-	AddParam("max-chart-span", "maximum num. of source word chart rules can consume (default 10)");
-	AddParam("non-terminals", "list of non-term symbols, space separated");
-	AddParam("rule-limit", "a little like table limit. But for chart decoding rules. Default is DEFAULT_MAX_TRANS_OPT_SIZE");
-	AddParam("source-label-overlap", "What happens if a span already has a label. 0=add more. 1=replace. 2=discard. Default is 0");
-	AddParam("output-hypo-score", "Output the hypo score to stdout with the output string. For search error analysis. Default is false");
-	AddParam("unknown-lhs", "file containing target lhs of unknown words. 1 per line: LHS prob");
+  AddParam("cube-pruning-pop-limit", "cbp", "How many hypotheses should be popped for each stack. (default = 1000)");
+  AddParam("cube-pruning-diversity", "cbd", "How many hypotheses should be created for each coverage. (default = 0)");
+  AddParam("search-algorithm", "Which search algorithm to use. 0=normal stack, 1=cube pruning, 2=cube growing. (default = 0)");
+  AddParam("constraint", "Location of the file with target sentences to produce constraining the search");
+  AddParam("description", "Source language, target language, description");
+  AddParam("max-chart-span", "maximum num. of source word chart rules can consume (default 10)");
+  AddParam("non-terminals", "list of non-term symbols, space separated");
+  AddParam("rule-limit", "a little like table limit. But for chart decoding rules. Default is DEFAULT_MAX_TRANS_OPT_SIZE");
+  AddParam("source-label-overlap", "What happens if a span already has a label. 0=add more. 1=replace. 2=discard. Default is 0");
+  AddParam("output-hypo-score", "Output the hypo score to stdout with the output string. For search error analysis. Default is false");
+  AddParam("unknown-lhs", "file containing target lhs of unknown words. 1 per line: LHS prob");
   AddParam("phrase-pair-feature", "Source and target factors for phrase pair feature");
   AddParam("phrase-boundary-source-feature", "Source factors for phrase boundary feature");
   AddParam("phrase-boundary-target-feature", "Target factors for phrase boundary feature");
@@ -153,9 +153,9 @@ Parameter::Parameter()
   AddParam("show-weights", "print feature weights and exit");
   AddParam("start-translation-id", "Id of 1st input. Default = 0");
   AddParam("output-unknowns", "Output the unknown (OOV) words to the given file, one line per sentence");
-  
-  // Compact phrase table and reordering table.                                                                                  
-  AddParam("minlexr-memory", "Load lexical reordering table in minlexr format into memory");                                          
+
+  // Compact phrase table and reordering table.
+  AddParam("minlexr-memory", "Load lexical reordering table in minlexr format into memory");
   AddParam("minphr-memory", "Load phrase table in minphr format into memory");
 
   AddParam("print-alignment-info", "Output word-to-word alignment to standard out, separated from translation by |||. Word-to-word alignments are takne from the phrase table if any. Default is false");
@@ -214,7 +214,7 @@ void Parameter::AddParam(const string &paramName, const string &abbrevName, cons
   m_valid[paramName] = true;
   m_valid[abbrevName] = true;
   m_abbreviation[paramName] = abbrevName;
-	m_fullname[abbrevName] = paramName;
+  m_fullname[abbrevName] = paramName;
   m_description[paramName] = description;
 }
 
@@ -263,7 +263,7 @@ bool Parameter::LoadParam(int argc, char* argv[])
     PrintCredit();
     Explain();
 
-    cerr << endl;    
+    cerr << endl;
     UserMessage::Add("No configuration file was specified.  Use -config or -f");
     cerr << endl;
     return false;
@@ -381,11 +381,9 @@ void Parameter::ConvertWeightArgsSingleWeight(const string &oldWeightName, const
   PARAM_MAP::iterator iterMap;
 
   iterMap = m_setting.find(oldWeightName);
-  if (iterMap != m_setting.end())
-  {
+  if (iterMap != m_setting.end()) {
     const PARAM_VEC &weights = iterMap->second;
-    for (size_t i = 0; i < weights.size(); ++i)
-    {
+    for (size_t i = 0; i < weights.size(); ++i) {
       SetWeight(newWeightName, ind, Scan<float>(weights[i]));
     }
 
@@ -403,8 +401,7 @@ void Parameter::ConvertWeightArgsPhraseModel(const string &oldWeightName)
       CHECK(numInputScores.size() == 0);
       numInputScores.push_back("1");
       numInputScores.push_back("0");
-    }
-    else if (inputWeights.size() == 2) {
+    } else if (inputWeights.size() == 2) {
       CHECK(numInputScores.size() == 0);
       numInputScores.push_back("1");
       numInputScores.push_back("1");
@@ -463,8 +460,7 @@ void Parameter::ConvertWeightArgsPhraseModel(const string &oldWeightName)
       PhraseTableImplementation implementation = (PhraseTableImplementation) Scan<int>(token[0]);
 
       string ptType;
-      switch (implementation)
-      {
+      switch (implementation) {
       case Memory:
         ptType = "PhraseDictionaryMemory";
         break;
@@ -488,8 +484,7 @@ void Parameter::ConvertWeightArgsPhraseModel(const string &oldWeightName)
       if (ptIndices.find(ptType) == ptIndices.end()) {
         ptIndices[ptType] = 0;
         ptInd = 0;
-      }
-      else {
+      } else {
         ptInd = ++ptIndices[ptType];
       }
 
@@ -516,7 +511,7 @@ void Parameter::ConvertWeightArgsPhraseModel(const string &oldWeightName)
       //characteristics of the phrase table
 
       vector<FactorType>  input   = Tokenize<FactorType>(token[1], ",")
-                         ,output  = Tokenize<FactorType>(token[2], ",");
+                                    ,output  = Tokenize<FactorType>(token[2], ",");
       size_t numScoreComponent = Scan<size_t>(token[3]);
       string filePath= token[4];
 
@@ -561,14 +556,13 @@ void Parameter::ConvertWeightArgsDistortion()
   // distortion / lex distortion
   const PARAM_VEC &oldWeights = GetParam(oldWeightName);
 
-  if (oldWeights.size() > 0)
-  {
+  if (oldWeights.size() > 0) {
     if (!isParamSpecified("search-algorithm") ||
-         (GetParam("search-algorithm").size() > 0
-           && (Trim(GetParam("search-algorithm")[0]) == "0"
+        (GetParam("search-algorithm").size() > 0
+         && (Trim(GetParam("search-algorithm")[0]) == "0"
              ||Trim(GetParam("search-algorithm")[0]) == "1"
-              )
-         )
+            )
+        )
        ) {
       // phrase-based. Add distance distortion to list of features
       AddFeature("Distortion");
@@ -587,8 +581,7 @@ void Parameter::ConvertWeightArgsDistortion()
       size_t numFF = Scan<size_t>(toks[2]);
 
       vector<float> weights(numFF);
-      for (size_t currFF = 0; currFF < numFF; ++currFF)
-      {
+      for (size_t currFF = 0; currFF < numFF; ++currFF) {
         CHECK(currOldInd < oldWeights.size());
         float weight = Scan<float>(oldWeights[currOldInd]);
         weights[currFF] = weight;
@@ -625,12 +618,12 @@ void Parameter::ConvertWeightArgsLM()
 
   bool isChartDecoding = true;
   if (!isParamSpecified("search-algorithm") ||
-	 (GetParam("search-algorithm").size() > 0
-	   && (Trim(GetParam("search-algorithm")[0]) == "0"
-		 ||Trim(GetParam("search-algorithm")[0]) == "1"
-		  )
-	 )
-   ) {
+      (GetParam("search-algorithm").size() > 0
+       && (Trim(GetParam("search-algorithm")[0]) == "0"
+           ||Trim(GetParam("search-algorithm")[0]) == "1"
+          )
+      )
+     ) {
     isChartDecoding = false;
   }
 
@@ -643,8 +636,7 @@ void Parameter::ConvertWeightArgsLM()
   PARAM_MAP::iterator iterMap;
 
   iterMap = m_setting.find(oldWeightName);
-  if (iterMap != m_setting.end())
-  {
+  if (iterMap != m_setting.end()) {
 
     size_t currOldInd = 0;
     const PARAM_VEC &weights = iterMap->second;
@@ -656,8 +648,7 @@ void Parameter::ConvertWeightArgsLM()
       int lmType = Scan<int>(modelToks[0]);
 
       string newFeatureName;
-      switch (lmType)
-      {
+      switch (lmType) {
       case 0:
         newFeatureName = "SRILM";
         break;
@@ -677,12 +668,11 @@ void Parameter::ConvertWeightArgsLM()
         numFF += oovWeights[lmIndex];
 
       vector<float> weightsLM(numFF);
-      for (size_t currFF = 0; currFF < numFF; ++currFF)
-      {
+      for (size_t currFF = 0; currFF < numFF; ++currFF) {
         CHECK(currOldInd < weights.size());
         weightsLM[currFF] = Scan<float>(weights[currOldInd]);
         if (isChartDecoding) {
-        	weightsLM[currFF] = UntransformLMScore(weightsLM[currFF]);
+          weightsLM[currFF] = UntransformLMScore(weightsLM[currFF]);
         }
 
         ++currOldInd;
@@ -691,12 +681,11 @@ void Parameter::ConvertWeightArgsLM()
       SetWeight(newFeatureName, ind, weightsLM);
 
       string featureLine = newFeatureName + " "
-                        + "factor=" + modelToks[1] + " "  // factor
-                        + "order="  + modelToks[2] + " "; // order
+                           + "factor=" + modelToks[1] + " "  // factor
+                           + "order="  + modelToks[2] + " "; // order
       if (lmType == 9) {
         featureLine += "lazyken=1 ";
-      }
-      else if (lmType == 8) {
+      } else if (lmType == 8) {
         featureLine += "lazyken=0 ";
       }
 
@@ -718,8 +707,7 @@ void Parameter::ConvertWeightArgsGeneration(const std::string &oldWeightName, co
   // distortion / lex distortion
   PARAM_VEC &oldWeights = m_setting[oldWeightName];
 
-  if (oldWeights.size() > 0)
-  {
+  if (oldWeights.size() > 0) {
     size_t currOldInd = 0;
     PARAM_VEC &models = m_setting[oldFeatureName];
 
@@ -730,8 +718,7 @@ void Parameter::ConvertWeightArgsGeneration(const std::string &oldWeightName, co
       size_t numFF = Scan<size_t>(modelToks[2]);
 
       vector<float> weights(numFF);
-      for (size_t currFF = 0; currFF < numFF; ++currFF)
-      {
+      for (size_t currFF = 0; currFF < numFF; ++currFF) {
         CHECK(currOldInd < oldWeights.size());
         float weight = Scan<float>(oldWeights[currOldInd]);
         weights[currFF] = weight;
@@ -742,10 +729,10 @@ void Parameter::ConvertWeightArgsGeneration(const std::string &oldWeightName, co
 
       stringstream strme;
       strme << "Generation "
-                  << "input-factor=" << modelToks[0] << " "
-                  << "output-factor=" << modelToks[1] << " "
-                  << "num-features=" << modelToks[2] << " "
-                  << "path=" << modelToks[3];
+            << "input-factor=" << modelToks[0] << " "
+            << "output-factor=" << modelToks[1] << " "
+            << "num-features=" << modelToks[2] << " "
+            << "path=" << modelToks[3];
       AddFeature(strme.str());
     }
   }
@@ -761,23 +748,21 @@ void Parameter::ConvertWeightArgsWordPenalty()
 
   bool isChartDecoding = true;
   if (!isParamSpecified("search-algorithm") ||
-	 (GetParam("search-algorithm").size() > 0
-	   && (Trim(GetParam("search-algorithm")[0]) == "0"
-		 ||Trim(GetParam("search-algorithm")[0]) == "1"
-		  )
-	 )
-   ) {
+      (GetParam("search-algorithm").size() > 0
+       && (Trim(GetParam("search-algorithm")[0]) == "0"
+           ||Trim(GetParam("search-algorithm")[0]) == "1"
+          )
+      )
+     ) {
     isChartDecoding = false;
   }
 
   PARAM_MAP::iterator iterMap;
 
   iterMap = m_setting.find(oldWeightName);
-  if (iterMap != m_setting.end())
-  {
+  if (iterMap != m_setting.end()) {
     const PARAM_VEC &weights = iterMap->second;
-    for (size_t i = 0; i < weights.size(); ++i)
-    {
+    for (size_t i = 0; i < weights.size(); ++i) {
       float weight = Scan<float>(weights[i]);
       if (isChartDecoding) {
         weight *= 0.434294482;
@@ -800,8 +785,7 @@ void Parameter::ConvertWeightArgs()
       (m_setting.count("weight-i") || m_setting.count("weight-t") || m_setting.count("weight-w") ||
        m_setting.count("weight-l") || m_setting.count("weight-u") || m_setting.count("weight-lex") ||
        m_setting.count("weight-generation") || m_setting.count("weight-lr") || m_setting.count("weight-d")
-       ))
-  {
+      )) {
     cerr << "Do not mix old and new format for specify weights";
   }
 
@@ -833,8 +817,7 @@ void Parameter::ConvertWeightArgs()
 void Parameter::CreateWeightsMap()
 {
   PARAM_VEC &vec = m_setting["weight"];
-  for (size_t i = 0; i < vec.size(); ++i)
-  {
+  for (size_t i = 0; i < vec.size(); ++i) {
     const string &line = vec[i];
     vector<string> toks = Tokenize(line);
     CHECK(toks.size() >= 2);
@@ -865,8 +848,7 @@ void Parameter::WeightOverwrite()
   string name("");
   vector<float> weights;
   vector<string> toks = Tokenize(vec[0]);
-  for (size_t i = 0; i < toks.size(); ++i)
-  {
+  for (size_t i = 0; i < toks.size(); ++i) {
     const string &tok = toks[i];
 
     if (tok.substr(tok.size() - 1, 1) == "=") {
@@ -879,8 +861,7 @@ void Parameter::WeightOverwrite()
       }
 
       name = tok.substr(0, tok.size() - 1);
-    }
-    else {
+    } else {
       // a weight for curr ff
       float weight = Scan<float>(toks[i]);
       weights.push_back(weight);
@@ -899,14 +880,13 @@ bool Parameter::Validate()
   PARAM_MAP::const_iterator iterParams;
   for (iterParams = m_setting.begin(); iterParams != m_setting.end(); ++iterParams) {
     const std::string &key = iterParams->first;
-    
-    if (m_valid.find(key) == m_valid.end())
-    {
+
+    if (m_valid.find(key) == m_valid.end()) {
       UserMessage::Add("Unknown parameter " + key);
       noErrorFlag = false;
     }
   }
-  
+
   if (m_setting["lmodel-dub"].size() > 0) {
     if (m_setting["lmodel-file"].size() != m_setting["lmodel-dub"].size()) {
       stringstream errorMsg("");
@@ -1082,8 +1062,7 @@ bool Parameter::ReadConfigFile(const string &filePath )
 
     if (line.size() == 0) {
       // blank line. do nothing.
-    }
-    else if (line[0]=='[') {
+    } else if (line[0]=='[') {
       // new parameter
       for (size_t currPos = 0 ; currPos < line.size() ; currPos++) {
         if (line[currPos] == ']') {
@@ -1227,23 +1206,23 @@ void Parameter::PrintCredit()
  * \param values inew values for paramName */
 void Parameter::OverwriteParam(const string &paramName, PARAM_VEC values)
 {
-	VERBOSE(2,"Overwriting parameter " << paramName);
-	
-	m_setting[paramName]; // defines the parameter, important for boolean switches
-	if (m_setting[paramName].size() > 1){
-		VERBOSE(2," (the parameter had " << m_setting[paramName].size() << " previous values)");
-		CHECK(m_setting[paramName].size() == values.size());
-	}else{
-		VERBOSE(2," (the parameter does not have previous values)");
-		m_setting[paramName].resize(values.size());
-	}
-	VERBOSE(2," with the following values:");
-	int i=0;
-	for (PARAM_VEC::iterator iter = values.begin(); iter != values.end() ; iter++, i++){
-		m_setting[paramName][i] = *iter;
-		VERBOSE(2, " " << *iter);
-	}
-	VERBOSE(2, std::endl);
+  VERBOSE(2,"Overwriting parameter " << paramName);
+
+  m_setting[paramName]; // defines the parameter, important for boolean switches
+  if (m_setting[paramName].size() > 1) {
+    VERBOSE(2," (the parameter had " << m_setting[paramName].size() << " previous values)");
+    CHECK(m_setting[paramName].size() == values.size());
+  } else {
+    VERBOSE(2," (the parameter does not have previous values)");
+    m_setting[paramName].resize(values.size());
+  }
+  VERBOSE(2," with the following values:");
+  int i=0;
+  for (PARAM_VEC::iterator iter = values.begin(); iter != values.end() ; iter++, i++) {
+    m_setting[paramName][i] = *iter;
+    VERBOSE(2, " " << *iter);
+  }
+  VERBOSE(2, std::endl);
 }
 
 std::set<std::string> Parameter::GetWeightNames() const
@@ -1256,7 +1235,7 @@ std::set<std::string> Parameter::GetWeightNames() const
   }
   return ret;
 }
-	
+
 }
 
 
diff --git a/moses/Parameter.h b/moses/Parameter.h
index a78314692..a0c372a53 100644
--- a/moses/Parameter.h
+++ b/moses/Parameter.h
@@ -38,16 +38,16 @@ typedef std::map<std::string, std::string > PARAM_STRING;
 
 /** Handles parameter values set in config file or on command line.
  * Process raw parameter data (names and values as strings) for StaticData
- * to parse; to get useful values, see StaticData. 
+ * to parse; to get useful values, see StaticData.
  */
 class Parameter
 {
 protected:
-	PARAM_MAP m_setting;
-	PARAM_BOOL m_valid;
-	PARAM_STRING m_abbreviation;
-	PARAM_STRING m_description;
-	PARAM_STRING m_fullname;
+  PARAM_MAP m_setting;
+  PARAM_BOOL m_valid;
+  PARAM_STRING m_abbreviation;
+  PARAM_STRING m_description;
+  PARAM_STRING m_fullname;
 
   std::map<std::string, std::vector<float> >  m_weights;
 
@@ -93,32 +93,30 @@ public:
   bool isParamSpecified(const std::string &paramName) {
     return  m_setting.find( paramName ) != m_setting.end();
   }
-		
-	const std::string GetFullName(std::string abbr)
-	{
-		return m_fullname[abbr];
-	}
-	
-	const std::string GetAbbreviation(std::string full)
-	{
-		return m_abbreviation[full];
-	}
-	const PARAM_VEC &GetParamShortName(const std::string &paramName)
-	{
-		return GetParam(GetFullName(paramName));
-	}
-	
-	void OverwriteParam(const std::string &paramName, PARAM_VEC values);
-
-	void OverwriteParamShortName(const std::string &paramShortName, PARAM_VEC values){
-		OverwriteParam(GetFullName(paramShortName),values);
-	}
-	
+
+  const std::string GetFullName(std::string abbr) {
+    return m_fullname[abbr];
+  }
+
+  const std::string GetAbbreviation(std::string full) {
+    return m_abbreviation[full];
+  }
+  const PARAM_VEC &GetParamShortName(const std::string &paramName) {
+    return GetParam(GetFullName(paramName));
+  }
+
+  void OverwriteParam(const std::string &paramName, PARAM_VEC values);
+
+  void OverwriteParamShortName(const std::string &paramShortName, PARAM_VEC values) {
+    OverwriteParam(GetFullName(paramShortName),values);
+  }
+
   std::vector<float> &GetWeights(const std::string &name);
   std::set<std::string> GetWeightNames() const;
 
-  const PARAM_MAP &GetParams() const
-  { return m_setting; }
+  const PARAM_MAP &GetParams() const {
+    return m_setting;
+  }
 
 };
 
diff --git a/moses/PartialTranslOptColl.h b/moses/PartialTranslOptColl.h
index f4f40d413..5a4e816de 100644
--- a/moses/PartialTranslOptColl.h
+++ b/moses/PartialTranslOptColl.h
@@ -39,7 +39,7 @@ namespace Moses
  *  The expansion process itself may be still explode, so efficient handling
  *  of partial translation options during expansion is required.
  *  This class assists in this tasks by implementing pruning.
- *  This implementation is similar to the one in HypothesisStack. 
+ *  This implementation is similar to the one in HypothesisStack.
  */
 class PartialTranslOptColl
 {
diff --git a/moses/Phrase.cpp b/moses/Phrase.cpp
index ef5d09b23..3fa607fb4 100644
--- a/moses/Phrase.cpp
+++ b/moses/Phrase.cpp
@@ -103,16 +103,15 @@ Phrase Phrase::GetSubString(const WordsRange &wordsRange) const
 
 Phrase Phrase::GetSubString(const WordsRange &wordsRange, FactorType factorType) const
 {
-	Phrase retPhrase(wordsRange.GetNumWordsCovered());
+  Phrase retPhrase(wordsRange.GetNumWordsCovered());
 
-	for (size_t currPos = wordsRange.GetStartPos() ; currPos <= wordsRange.GetEndPos() ; currPos++)
-	{
-		const Factor* f = GetFactor(currPos, factorType);
-		Word &word = retPhrase.AddWord();
-		word.SetFactor(factorType, f);
-	}
+  for (size_t currPos = wordsRange.GetStartPos() ; currPos <= wordsRange.GetEndPos() ; currPos++) {
+    const Factor* f = GetFactor(currPos, factorType);
+    Word &word = retPhrase.AddWord();
+    word.SetFactor(factorType, f);
+  }
 
-	return retPhrase;
+  return retPhrase;
 }
 
 std::string Phrase::GetStringRep(const vector<FactorType> factorsToPrint) const
@@ -153,10 +152,10 @@ void Phrase::PrependWord(const Word &newWord)
 }
 
 void Phrase::CreateFromString(FactorDirection direction
-                            ,const std::vector<FactorType> &factorOrder
-                            ,const StringPiece &phraseString
-                            ,const StringPiece &factorDelimiter
-                            ,Word **lhs)
+                              ,const std::vector<FactorType> &factorOrder
+                              ,const StringPiece &phraseString
+                              ,const StringPiece &factorDelimiter
+                              ,Word **lhs)
 {
   // parse
   vector<StringPiece> annotatedWordVector;
@@ -165,9 +164,9 @@ void Phrase::CreateFromString(FactorDirection direction
   }
 
   if (annotatedWordVector.size() == 0) {
-	if (lhs) {
-	  (*lhs) = NULL;
-	}
+    if (lhs) {
+      (*lhs) = NULL;
+    }
     return;
   }
 
@@ -188,8 +187,7 @@ void Phrase::CreateFromString(FactorDirection direction
     (*lhs) = new Word(true);
     (*lhs)->CreateFromString(direction, factorOrder, annotatedWord.substr(1, annotatedWord.size() - 2), true);
     assert((*lhs)->IsNonTerminal());
-  }
-  else {
+  } else {
     numWords = annotatedWordVector.size();
     //CHECK(lhs == NULL);
     if (lhs) {
diff --git a/moses/Phrase.h b/moses/Phrase.h
index 196e403ac..209f92f9e 100644
--- a/moses/Phrase.h
+++ b/moses/Phrase.h
@@ -69,13 +69,13 @@ public:
   /** Fills phrase with words from format string, typically from phrase table or sentence input
   	* \param factorOrder factor types of each element in 2D string vector
   	* \param phraseString formatted input string to parse
-  	*	\param factorDelimiter delimiter between factors.  
+  	*	\param factorDelimiter delimiter between factors.
   */
   void CreateFromString(FactorDirection direction
                         , const std::vector<FactorType> &factorOrder
-  											, const StringPiece &phraseString
-  											, const StringPiece &factorDelimiter
-  											, Word **lhs);
+                        , const StringPiece &phraseString
+                        , const StringPiece &factorDelimiter
+                        , Word **lhs);
 
   /**	copy factors from the other phrase to this phrase.
   	IsCompatible() must be run beforehand to ensure incompatible factors aren't overwritten
@@ -127,52 +127,49 @@ public:
   void AddWord(const Word &newWord) {
     AddWord() = newWord;
   }
-	
-	/** appends a phrase at the end of current phrase **/
-	void Append(const Phrase &endPhrase);
-	void PrependWord(const Word &newWord);
-	
-	void Clear()
-	{
-		m_words.clear();
-	}
-	
-	void RemoveWord(size_t pos)
-	{
-		CHECK(pos < m_words.size());
-		m_words.erase(m_words.begin() + pos);
-	}
-	
-	//! create new phrase class that is a substring of this phrase
-	Phrase GetSubString(const WordsRange &wordsRange) const;
+
+  /** appends a phrase at the end of current phrase **/
+  void Append(const Phrase &endPhrase);
+  void PrependWord(const Word &newWord);
+
+  void Clear() {
+    m_words.clear();
+  }
+
+  void RemoveWord(size_t pos) {
+    CHECK(pos < m_words.size());
+    m_words.erase(m_words.begin() + pos);
+  }
+
+  //! create new phrase class that is a substring of this phrase
+  Phrase GetSubString(const WordsRange &wordsRange) const;
   Phrase GetSubString(const WordsRange &wordsRange, FactorType factorType) const;
-	
-	//! return a string rep of the phrase. Each factor is separated by the factor delimiter as specified in StaticData class
-	std::string GetStringRep(const std::vector<FactorType> factorsToPrint) const; 
-  
-	TO_STRING();
-
-	
-	int Compare(const Phrase &other) const;
-	
-	/** transitive comparison between 2 phrases
-	 *		used to insert & find phrase in dictionary
-	 */
-	bool operator< (const Phrase &compare) const
-	{
-		return Compare(compare) < 0;
-	}
-	
-	bool operator== (const Phrase &compare) const
-	{
-		return Compare(compare) == 0;
-	}
-
-	void OnlyTheseFactors(const FactorMask &factors);
+
+  //! return a string rep of the phrase. Each factor is separated by the factor delimiter as specified in StaticData class
+  std::string GetStringRep(const std::vector<FactorType> factorsToPrint) const;
+
+  TO_STRING();
+
+
+  int Compare(const Phrase &other) const;
+
+  /** transitive comparison between 2 phrases
+   *		used to insert & find phrase in dictionary
+   */
+  bool operator< (const Phrase &compare) const {
+    return Compare(compare) < 0;
+  }
+
+  bool operator== (const Phrase &compare) const {
+    return Compare(compare) == 0;
+  }
+
+  void OnlyTheseFactors(const FactorMask &factors);
 
 };
 
-inline size_t hash_value(const Phrase& phrase) {
+inline size_t hash_value(const Phrase& phrase)
+{
   size_t  seed = 0;
   for (size_t i = 0; i < phrase.GetSize(); ++i) {
     boost::hash_combine(seed, phrase.GetWord(i));
diff --git a/moses/PrefixTree.h b/moses/PrefixTree.h
index 9cf1360e6..5b81ea175 100644
--- a/moses/PrefixTree.h
+++ b/moses/PrefixTree.h
@@ -63,7 +63,7 @@ public:
       keys.insert(i,*b);
       data.insert(data.begin()+pos,def);
 
-	  Self *self = NULL;
+      Self *self = NULL;
       ptr.insert(ptr.begin()+pos, self);
     }
     if(++b!=e) {
diff --git a/moses/PrefixTreeMap.h b/moses/PrefixTreeMap.h
index fae875bd4..06066878d 100644
--- a/moses/PrefixTreeMap.h
+++ b/moses/PrefixTreeMap.h
@@ -59,7 +59,7 @@ private:
   ScoreList  m_ScoreList;
 };
 
-  
+
 /** @todo How is this used in the pb binary phrase table?
  */
 struct PPimp {
diff --git a/moses/RuleCube.h b/moses/RuleCube.h
index 05f9f1a24..d0c6ea66a 100644
--- a/moses/RuleCube.h
+++ b/moses/RuleCube.h
@@ -44,7 +44,7 @@ class ChartTranslationOptions;
  */
 class RuleCubeItemScoreOrderer
 {
- public:
+public:
   bool operator()(const RuleCubeItem *p, const RuleCubeItem *q) const {
     return p->GetScore() < q->GetScore();
   }
@@ -56,7 +56,7 @@ class RuleCubeItemScoreOrderer
  */
 class RuleCubeItemPositionOrderer
 {
- public:
+public:
   bool operator()(const RuleCubeItem *p, const RuleCubeItem *q) const {
     return *p < *q;
   }
@@ -66,7 +66,7 @@ class RuleCubeItemPositionOrderer
  */
 class RuleCubeItemHasher
 {
- public:
+public:
   size_t operator()(const RuleCubeItem *p) const {
     size_t seed = 0;
     boost::hash_combine(seed, p->GetHypothesisDimensions());
@@ -79,7 +79,7 @@ class RuleCubeItemHasher
  */
 class RuleCubeItemEqualityPred
 {
- public:
+public:
   bool operator()(const RuleCubeItem *p, const RuleCubeItem *q) const {
     return p->GetHypothesisDimensions() == q->GetHypothesisDimensions() &&
            p->GetTranslationDimension() == q->GetTranslationDimension();
@@ -90,7 +90,7 @@ class RuleCubeItemEqualityPred
  */
 class RuleCube
 {
- public:
+public:
   RuleCube(const ChartTranslationOptions &, const ChartCellCollection &,
            ChartManager &);
 
@@ -104,26 +104,28 @@ class RuleCube
 
   RuleCubeItem *Pop(ChartManager &);
 
-  bool IsEmpty() const { return m_queue.empty(); }
+  bool IsEmpty() const {
+    return m_queue.empty();
+  }
 
   const ChartTranslationOptions &GetTranslationOption() const {
     return m_transOpt;
   }
 
- private:
+private:
 #if defined(BOOST_VERSION) && (BOOST_VERSION >= 104200)
   typedef boost::unordered_set<RuleCubeItem*,
-                               RuleCubeItemHasher,
-                               RuleCubeItemEqualityPred
-                              > ItemSet;
+          RuleCubeItemHasher,
+          RuleCubeItemEqualityPred
+          > ItemSet;
 #else
   typedef std::set<RuleCubeItem*, RuleCubeItemPositionOrderer> ItemSet;
 #endif
 
   typedef std::priority_queue<RuleCubeItem*,
-                              std::vector<RuleCubeItem*>,
-                              RuleCubeItemScoreOrderer
-                             > Queue;
+          std::vector<RuleCubeItem*>,
+          RuleCubeItemScoreOrderer
+          > Queue;
 
   RuleCube(const RuleCube &);  // Not implemented
   RuleCube &operator=(const RuleCube &);  // Not implemented
diff --git a/moses/RuleCubeItem.h b/moses/RuleCubeItem.h
index 612079172..75669598b 100644
--- a/moses/RuleCubeItem.h
+++ b/moses/RuleCubeItem.h
@@ -39,14 +39,16 @@ typedef std::vector<const ChartHypothesis*> HypoList;
  */
 class TranslationDimension
 {
- public:
+public:
   TranslationDimension(std::size_t pos,
                        const std::vector<TargetPhrase*> &orderedTargetPhrases)
     : m_pos(pos)
     , m_orderedTargetPhrases(&orderedTargetPhrases)
   {}
 
-  std::size_t IncrementPos() { return m_pos++; }
+  std::size_t IncrementPos() {
+    return m_pos++;
+  }
 
   bool HasMoreTranslations() const {
     return m_pos+1 < m_orderedTargetPhrases->size();
@@ -64,7 +66,7 @@ class TranslationDimension
     return GetTargetPhrase() == compare.GetTargetPhrase();
   }
 
- private:
+private:
   std::size_t m_pos;
   const std::vector<TargetPhrase*> *m_orderedTargetPhrases;
 };
@@ -81,7 +83,9 @@ public:
     , m_orderedHypos(&orderedHypos)
   {}
 
-  std::size_t IncrementPos() { return m_pos++; }
+  std::size_t IncrementPos() {
+    return m_pos++;
+  }
 
   bool HasMoreHypo() const {
     return m_pos+1 < m_orderedHypos->size();
@@ -109,7 +113,7 @@ std::size_t hash_value(const HypothesisDimension &);
 /** @todo How is this used. Split out into separate source file */
 class RuleCubeItem
 {
- public:
+public:
   RuleCubeItem(const ChartTranslationOptions &, const ChartCellCollection &);
   RuleCubeItem(const RuleCubeItem &, int);
   ~RuleCubeItem();
@@ -122,7 +126,9 @@ class RuleCubeItem
     return m_hypothesisDimensions;
   }
 
-  float GetScore() const { return m_score; }
+  float GetScore() const {
+    return m_score;
+  }
 
   void EstimateScore();
 
@@ -132,7 +138,7 @@ class RuleCubeItem
 
   bool operator<(const RuleCubeItem &) const;
 
- private:
+private:
   RuleCubeItem(const RuleCubeItem &);  // Not implemented
   RuleCubeItem &operator=(const RuleCubeItem &);  // Not implemented
 
diff --git a/moses/RuleCubeQueue.h b/moses/RuleCubeQueue.h
index 9763b3877..ae4d20be0 100644
--- a/moses/RuleCubeQueue.h
+++ b/moses/RuleCubeQueue.h
@@ -36,7 +36,7 @@ class ChartManager;
  */
 class RuleCubeOrderer
 {
- public:
+public:
   bool operator()(const RuleCube *p, const RuleCube *q) const {
     return p->GetTopScore() < q->GetTopScore();
   }
@@ -45,17 +45,19 @@ class RuleCubeOrderer
 /** @todo how is this used */
 class RuleCubeQueue
 {
- public:
+public:
   RuleCubeQueue(ChartManager &manager) : m_manager(manager) {}
   ~RuleCubeQueue();
 
   void Add(RuleCube *);
   ChartHypothesis *Pop();
-  bool IsEmpty() const { return m_queue.empty(); }
+  bool IsEmpty() const {
+    return m_queue.empty();
+  }
 
- private:
+private:
   typedef std::priority_queue<RuleCube*, std::vector<RuleCube*>,
-                              RuleCubeOrderer > Queue;
+          RuleCubeOrderer > Queue;
 
   Queue m_queue;
   ChartManager &m_manager;
diff --git a/moses/ScoreComponentCollection.cpp b/moses/ScoreComponentCollection.cpp
index c836ea5b3..44f08b316 100644
--- a/moses/ScoreComponentCollection.cpp
+++ b/moses/ScoreComponentCollection.cpp
@@ -17,7 +17,7 @@ ScoreComponentCollection::ScoreComponentCollection() : m_scores(s_denseVectorSiz
 
 
 void ScoreComponentCollection::RegisterScoreProducer
-  (const FeatureFunction* scoreProducer)
+(const FeatureFunction* scoreProducer)
 {
   size_t start = s_denseVectorSize;
   size_t end = start + scoreProducer->GetNumScoreComponents();
@@ -29,56 +29,58 @@ void ScoreComponentCollection::RegisterScoreProducer
 
 float ScoreComponentCollection::GetWeightedScore() const
 {
-	return m_scores.inner_product(StaticData::Instance().GetAllWeights().m_scores);
+  return m_scores.inner_product(StaticData::Instance().GetAllWeights().m_scores);
 }
 
 void ScoreComponentCollection::MultiplyEquals(float scalar)
 {
-	m_scores *= scalar;
+  m_scores *= scalar;
 }
 
 // Multiply all weights of this sparse producer by a given scalar
-void ScoreComponentCollection::MultiplyEquals(const FeatureFunction* sp, float scalar) {
+void ScoreComponentCollection::MultiplyEquals(const FeatureFunction* sp, float scalar)
+{
   std::string prefix = sp->GetScoreProducerDescription() + FName::SEP;
   for(FVector::FNVmap::const_iterator i = m_scores.cbegin(); i != m_scores.cend(); i++) {
     std::stringstream name;
     name << i->first;
     if (name.str().substr( 0, prefix.length() ).compare( prefix ) == 0)
-    	m_scores[i->first] = i->second * scalar;
+      m_scores[i->first] = i->second * scalar;
   }
 }
 
 // Count weights belonging to this sparse producer
-size_t ScoreComponentCollection::GetNumberWeights(const FeatureFunction* sp) {
+size_t ScoreComponentCollection::GetNumberWeights(const FeatureFunction* sp)
+{
   std::string prefix = sp->GetScoreProducerDescription() + FName::SEP;
   size_t weights = 0;
   for(FVector::FNVmap::const_iterator i = m_scores.cbegin(); i != m_scores.cend(); i++) {
     std::stringstream name;
     name << i->first;
     if (name.str().substr( 0, prefix.length() ).compare( prefix ) == 0)
-    	weights++;
+      weights++;
   }
   return weights;
 }
 
 void ScoreComponentCollection::DivideEquals(float scalar)
 {
-	m_scores /= scalar;
+  m_scores /= scalar;
 }
 
 void ScoreComponentCollection::CoreDivideEquals(float scalar)
 {
-	m_scores.coreDivideEquals(scalar);
+  m_scores.coreDivideEquals(scalar);
 }
 
 void ScoreComponentCollection::DivideEquals(const ScoreComponentCollection& rhs)
 {
-	m_scores.divideEquals(rhs.m_scores);
+  m_scores.divideEquals(rhs.m_scores);
 }
 
 void ScoreComponentCollection::MultiplyEquals(const ScoreComponentCollection& rhs)
 {
-	m_scores *= rhs.m_scores;
+  m_scores *= rhs.m_scores;
 }
 
 void ScoreComponentCollection::MultiplyEqualsBackoff(const ScoreComponentCollection& rhs, float backoff)
@@ -93,42 +95,51 @@ void ScoreComponentCollection::MultiplyEquals(float core_r0, float sparse_r0)
 
 std::ostream& operator<<(std::ostream& os, const ScoreComponentCollection& rhs)
 {
-	os << rhs.m_scores;
-	return os;
+  os << rhs.m_scores;
+  return os;
 }
-void ScoreComponentCollection::L1Normalise() {
+void ScoreComponentCollection::L1Normalise()
+{
   m_scores /= m_scores.l1norm_coreFeatures();
 }
 
-float ScoreComponentCollection::GetL1Norm() const {
+float ScoreComponentCollection::GetL1Norm() const
+{
   return m_scores.l1norm();
 }
 
-float ScoreComponentCollection::GetL2Norm() const {
+float ScoreComponentCollection::GetL2Norm() const
+{
   return m_scores.l2norm();
 }
 
-float ScoreComponentCollection::GetLInfNorm() const {
+float ScoreComponentCollection::GetLInfNorm() const
+{
   return m_scores.linfnorm();
 }
 
-size_t ScoreComponentCollection::L1Regularize(float lambda) {
+size_t ScoreComponentCollection::L1Regularize(float lambda)
+{
   return m_scores.l1regularize(lambda);
 }
 
-void ScoreComponentCollection::L2Regularize(float lambda) {
+void ScoreComponentCollection::L2Regularize(float lambda)
+{
   m_scores.l2regularize(lambda);
 }
 
-size_t ScoreComponentCollection::SparseL1Regularize(float lambda) {
+size_t ScoreComponentCollection::SparseL1Regularize(float lambda)
+{
   return m_scores.sparseL1regularize(lambda);
 }
 
-void ScoreComponentCollection::SparseL2Regularize(float lambda) {
+void ScoreComponentCollection::SparseL2Regularize(float lambda)
+{
   m_scores.sparseL2regularize(lambda);
 }
 
-void ScoreComponentCollection::Save(ostream& out) const {
+void ScoreComponentCollection::Save(ostream& out) const
+{
   ScoreIndexMap::const_iterator iter = s_scoreIndexes.begin();
   for (; iter != s_scoreIndexes.end(); ++iter ) {
     string name = iter->first->GetScoreProducerDescription();
@@ -148,7 +159,8 @@ void ScoreComponentCollection::Save(ostream& out) const {
   m_scores.write(out);
 }
 
-void ScoreComponentCollection::Save(const string& filename) const {
+void ScoreComponentCollection::Save(const string& filename) const
+{
   ofstream out(filename.c_str());
   if (!out) {
     ostringstream msg;
@@ -159,7 +171,8 @@ void ScoreComponentCollection::Save(const string& filename) const {
   out.close();
 }
 
-void ScoreComponentCollection::Assign(const FeatureFunction* sp, const string line) {
+void ScoreComponentCollection::Assign(const FeatureFunction* sp, const string line)
+{
   istringstream istr(line);
   while(istr) {
     string namestring;
diff --git a/moses/ScoreComponentCollection.h b/moses/ScoreComponentCollection.h
index e76c9d06b..70c2a05f1 100644
--- a/moses/ScoreComponentCollection.h
+++ b/moses/ScoreComponentCollection.h
@@ -64,19 +64,18 @@ class ScoreComponentCollection
 {
   friend std::ostream& operator<<(std::ostream& os, const ScoreComponentCollection& rhs);
 private:
-	FVector m_scores;
+  FVector m_scores;
   typedef std::pair<size_t,size_t> IndexPair;
   typedef std::map<const FeatureFunction*,IndexPair> ScoreIndexMap;
   static  ScoreIndexMap s_scoreIndexes;
   static size_t s_denseVectorSize;
-  static IndexPair GetIndexes(const FeatureFunction* sp)
-  {
+  static IndexPair GetIndexes(const FeatureFunction* sp) {
     ScoreIndexMap::const_iterator indexIter = s_scoreIndexes.find(sp);
     if (indexIter == s_scoreIndexes.end()) {
       std::cerr << "ERROR: FeatureFunction: " << sp->GetScoreProducerDescription() <<
-        " not registered with ScoreIndexMap" << std::endl;
+                " not registered with ScoreIndexMap" << std::endl;
       std::cerr << "You must call ScoreComponentCollection.RegisterScoreProducer() " <<
-        " for every FeatureFunction" << std::endl;
+                " for every FeatureFunction" << std::endl;
       abort();
     }
     return indexIter->second;
@@ -91,9 +90,9 @@ public:
   ScoreComponentCollection();
 
   //! Clone a score collection
-	ScoreComponentCollection(const ScoreComponentCollection& rhs)
-	: m_scores(rhs.m_scores)
-	{}
+  ScoreComponentCollection(const ScoreComponentCollection& rhs)
+    : m_scores(rhs.m_scores)
+  {}
 
   ScoreComponentCollection& operator=( const ScoreComponentCollection& rhs ) {
     m_scores = rhs.m_scores;
@@ -101,124 +100,108 @@ public:
   }
 
   /**
-    * Register a ScoreProducer with a fixed number of scores, so that it can 
+    * Register a ScoreProducer with a fixed number of scores, so that it can
     * be allocated space in the dense part of the feature vector.
     **/
   static void RegisterScoreProducer(const FeatureFunction* scoreProducer);
 
   /** Load from file */
-  bool Load(const std::string& filename) 
-  {
-      return m_scores.load(filename);
+  bool Load(const std::string& filename) {
+    return m_scores.load(filename);
   }
 
-  const FVector& GetScoresVector() const
-  {
-	  return m_scores;
+  const FVector& GetScoresVector() const {
+    return m_scores;
   }
 
   const std::valarray<FValue> &getCoreFeatures() const {
     return m_scores.getCoreFeatures();
   }
 
-  size_t Size() const
-  {
-	  return m_scores.size();
+  size_t Size() const {
+    return m_scores.size();
   }
 
-  void Resize() 
-  {
+  void Resize() {
     if (m_scores.coreSize() != s_denseVectorSize) {
       m_scores.resize(s_denseVectorSize);
     }
   }
 
   /** Create and FVector with the right number of core features */
-  static FVector CreateFVector()
-  {
+  static FVector CreateFVector() {
     return FVector(s_denseVectorSize);
   }
 
-  void SetToBinaryOf(const ScoreComponentCollection& rhs)
-  {
-	  m_scores.setToBinaryOf(rhs.m_scores);
+  void SetToBinaryOf(const ScoreComponentCollection& rhs) {
+    m_scores.setToBinaryOf(rhs.m_scores);
   }
 
   //! Set all values to 0.0
-	void ZeroAll()
-	{
-	  m_scores.clear();
-	}
-
-	void MultiplyEquals(float scalar);
-	void DivideEquals(float scalar);
-	void CoreDivideEquals(float scalar);
-	void DivideEquals(const ScoreComponentCollection& rhs);
-	void MultiplyEquals(const ScoreComponentCollection& rhs);	
-	void MultiplyEqualsBackoff(const ScoreComponentCollection& rhs, float backoff);
-	void MultiplyEquals(float core_r0, float sparse_r0);
-	void MultiplyEquals(const FeatureFunction* sp, float scalar);
-
-	size_t GetNumberWeights(const FeatureFunction* sp);
-
-	void CoreAssign(const ScoreComponentCollection& rhs)
-        {
-	  m_scores.coreAssign(rhs.m_scores);
-	}
-
-	//! add the score in rhs
-	void PlusEquals(const ScoreComponentCollection& rhs)
-	{
-	  m_scores += rhs.m_scores;
-	}
-
-	// add only sparse features
-	void SparsePlusEquals(const ScoreComponentCollection& rhs)
-	{
-	  m_scores.sparsePlusEquals(rhs.m_scores);
-	}
-
-	void PlusEquals(const FVector& scores)
-	{
-		m_scores += scores;
-	}
-
-	//! subtract the score in rhs
-	void MinusEquals(const ScoreComponentCollection& rhs)
-	{
-	  m_scores -= rhs.m_scores;
-	}
+  void ZeroAll() {
+    m_scores.clear();
+  }
+
+  void MultiplyEquals(float scalar);
+  void DivideEquals(float scalar);
+  void CoreDivideEquals(float scalar);
+  void DivideEquals(const ScoreComponentCollection& rhs);
+  void MultiplyEquals(const ScoreComponentCollection& rhs);
+  void MultiplyEqualsBackoff(const ScoreComponentCollection& rhs, float backoff);
+  void MultiplyEquals(float core_r0, float sparse_r0);
+  void MultiplyEquals(const FeatureFunction* sp, float scalar);
+
+  size_t GetNumberWeights(const FeatureFunction* sp);
+
+  void CoreAssign(const ScoreComponentCollection& rhs) {
+    m_scores.coreAssign(rhs.m_scores);
+  }
+
+  //! add the score in rhs
+  void PlusEquals(const ScoreComponentCollection& rhs) {
+    m_scores += rhs.m_scores;
+  }
+
+  // add only sparse features
+  void SparsePlusEquals(const ScoreComponentCollection& rhs) {
+    m_scores.sparsePlusEquals(rhs.m_scores);
+  }
+
+  void PlusEquals(const FVector& scores) {
+    m_scores += scores;
+  }
+
+  //! subtract the score in rhs
+  void MinusEquals(const ScoreComponentCollection& rhs) {
+    m_scores -= rhs.m_scores;
+  }
 
   //For features which have an unbounded number of components
-  void MinusEquals(const FeatureFunction*sp, const std::string& name, float score)
-  {
+  void MinusEquals(const FeatureFunction*sp, const std::string& name, float score) {
     FName fname(sp->GetScoreProducerDescription(),name);
     m_scores[fname] -= score;
   }
 
   //For features which have an unbounded number of components
-  void SparseMinusEquals(const std::string& full_name, float score)
-  {
+  void SparseMinusEquals(const std::string& full_name, float score) {
     FName fname(full_name);
     m_scores[fname] -= score;
   }
 
-	//! Add scores from a single ScoreProducer only
-	//! The length of scores must be equal to the number of score components
-	//! produced by sp
-	void PlusEquals(const FeatureFunction* sp, const ScoreComponentCollection& scores)
-	{
+  //! Add scores from a single ScoreProducer only
+  //! The length of scores must be equal to the number of score components
+  //! produced by sp
+  void PlusEquals(const FeatureFunction* sp, const ScoreComponentCollection& scores) {
     IndexPair indexes = GetIndexes(sp);
     for (size_t i = indexes.first; i < indexes.second; ++i) {
       m_scores[i] += scores.m_scores[i];
     }
-	}
+  }
 
-	//! Add scores from a single FeatureFunction only
-	//! The length of scores must be equal to the number of score components
-	//! produced by sp
-  void PlusEquals(const FeatureFunction* sp, const std::vector<float>& scores)
-  {
+  //! Add scores from a single FeatureFunction only
+  //! The length of scores must be equal to the number of score components
+  //! produced by sp
+  void PlusEquals(const FeatureFunction* sp, const std::vector<float>& scores) {
     IndexPair indexes = GetIndexes(sp);
     CHECK(scores.size() == indexes.second - indexes.first);
     for (size_t i = 0; i < scores.size(); ++i) {
@@ -226,56 +209,50 @@ public:
     }
   }
 
-	//! Special version PlusEquals(ScoreProducer, vector<float>)
-	//! to add the score from a single ScoreProducer that produces
-	//! a single value
-	void PlusEquals(const FeatureFunction* sp, float score)
-	{
+  //! Special version PlusEquals(ScoreProducer, vector<float>)
+  //! to add the score from a single ScoreProducer that produces
+  //! a single value
+  void PlusEquals(const FeatureFunction* sp, float score) {
     IndexPair indexes = GetIndexes(sp);
     CHECK(1 == indexes.second - indexes.first);
     m_scores[indexes.first] += score;
-	}
+  }
 
   //For features which have an unbounded number of components
-  void PlusEquals(const FeatureFunction*sp, const StringPiece& name, float score)
-  {
+  void PlusEquals(const FeatureFunction*sp, const StringPiece& name, float score) {
     FName fname(sp->GetScoreProducerDescription(),name);
     m_scores[fname] += score;
   }
 
   //For features which have an unbounded number of components
-  void SparsePlusEquals(const std::string& full_name, float score)
-  {
-  	FName fname(full_name);
+  void SparsePlusEquals(const std::string& full_name, float score) {
+    FName fname(full_name);
     m_scores[fname] += score;
   }
 
-  void Assign(const FeatureFunction* sp, const std::vector<float>& scores)
-  {
+  void Assign(const FeatureFunction* sp, const std::vector<float>& scores) {
     IndexPair indexes = GetIndexes(sp);
     CHECK(scores.size() == indexes.second - indexes.first);
     for (size_t i = 0; i < scores.size(); ++i) {
       m_scores[i + indexes.first] = scores[i];
     }
   }
-  
+
   //! Special version Assign(ScoreProducer, vector<float>)
   //! to add the score from a single ScoreProducer that produces
   //! a single value
-  void Assign(const FeatureFunction* sp, float score)
-  {
+  void Assign(const FeatureFunction* sp, float score) {
     IndexPair indexes = GetIndexes(sp);
     CHECK(1 == indexes.second - indexes.first);
     m_scores[indexes.first] = score;
   }
-  
+
   // Assign core weight by index
   void Assign(size_t index, float score) {
     m_scores[index] = score;
   }
 
-  void Assign(const FeatureFunction*sp, const StringPiece &name, float score)
-  {
+  void Assign(const FeatureFunction*sp, const StringPiece &name, float score) {
     FName fname(sp->GetScoreProducerDescription(),name);
     m_scores[fname] = score;
   }
@@ -285,27 +262,23 @@ public:
   void Assign(const FeatureFunction* sp, const std::string line);
 
   // shortcut: setting the value directly using the feature name
-  void Assign(const std::string name, float score)
-  {
-  	FName fname(name);
-  	m_scores[fname] = score;
-  }
-
-	float InnerProduct(const ScoreComponentCollection& rhs) const
-	{
-		return m_scores.inner_product(rhs.m_scores);
-	}
-	
-	float PartialInnerProduct(const FeatureFunction* sp, const std::vector<float>& rhs) const
-	{
-		std::vector<float> lhs = GetScoresForProducer(sp);
-		CHECK(lhs.size() == rhs.size());
-		return std::inner_product(lhs.begin(), lhs.end(), rhs.begin(), 0.0f);
-	}
-
-	//! return a vector of all the scores associated with a certain FeatureFunction
-	std::vector<float> GetScoresForProducer(const FeatureFunction* sp) const
-	{
+  void Assign(const std::string name, float score) {
+    FName fname(name);
+    m_scores[fname] = score;
+  }
+
+  float InnerProduct(const ScoreComponentCollection& rhs) const {
+    return m_scores.inner_product(rhs.m_scores);
+  }
+
+  float PartialInnerProduct(const FeatureFunction* sp, const std::vector<float>& rhs) const {
+    std::vector<float> lhs = GetScoresForProducer(sp);
+    CHECK(lhs.size() == rhs.size());
+    return std::inner_product(lhs.begin(), lhs.end(), rhs.begin(), 0.0f);
+  }
+
+  //! return a vector of all the scores associated with a certain FeatureFunction
+  std::vector<float> GetScoresForProducer(const FeatureFunction* sp) const {
     size_t components = sp->GetNumScoreComponents();
 
     std::vector<float> res(components);
@@ -314,58 +287,52 @@ public:
       res[i] = m_scores[i + indexes.first];
     }
     return res;
-	}
+  }
 
   //! get subset of scores that belong to a certain sparse ScoreProducer
   FVector GetVectorForProducer(const FeatureFunction* sp) const;
 
-  float GetSparseWeight(const FName& featureName) const
-  {
+  float GetSparseWeight(const FName& featureName) const {
     return m_scores[featureName];
   }
-  
+
   void PrintCoreFeatures() {
     m_scores.printCoreFeatures();
   }
 
-	void ThresholdScaling(float maxValue)
-	{
-		// find (smallest) factor for which all weights are <= maxValue
-		// 0.1 / 0.14 = 0.714285714
-		// 0.1 / 0.17 = 0.588235294
+  void ThresholdScaling(float maxValue) {
+    // find (smallest) factor for which all weights are <= maxValue
+    // 0.1 / 0.14 = 0.714285714
+    // 0.1 / 0.17 = 0.588235294
     m_scores.thresholdScale(maxValue);
-	}
-
-	void CapMax(float maxValue)
-	{
-		// cap all sparse features to maxValue
-		m_scores.capMax(maxValue);
-	}
-
-	void CapMin(float minValue)
-	{
-		// cap all sparse features to minValue
-		m_scores.capMin(minValue);
-	}
-
-	//! if a FeatureFunction produces a single score (for example, a language model score)
-	//! this will return it.  If not, this method will throw
-	float GetScoreForProducer(const FeatureFunction* sp) const
-	{
+  }
+
+  void CapMax(float maxValue) {
+    // cap all sparse features to maxValue
+    m_scores.capMax(maxValue);
+  }
+
+  void CapMin(float minValue) {
+    // cap all sparse features to minValue
+    m_scores.capMin(minValue);
+  }
+
+  //! if a FeatureFunction produces a single score (for example, a language model score)
+  //! this will return it.  If not, this method will throw
+  float GetScoreForProducer(const FeatureFunction* sp) const {
     IndexPair indexes = GetIndexes(sp);
     CHECK(indexes.second - indexes.first == 1);
     return m_scores[indexes.first];
-	}
+  }
 
   //For features which have an unbounded number of components
   float GetScoreForProducer
-    (const FeatureFunction* sp, const std::string& name) const
-  {
+  (const FeatureFunction* sp, const std::string& name) const {
     FName fname(sp->GetScoreProducerDescription(),name);
     return m_scores[fname];
   }
 
-	float GetWeightedScore() const;
+  float GetWeightedScore() const;
 
   void ZeroDenseFeatures(const FeatureFunction* sp);
   void L1Normalise();
@@ -378,45 +345,65 @@ public:
   void SparseL2Regularize(float lambda);
   void Save(const std::string& filename) const;
   void Save(std::ostream&) const;
-  
-  void IncrementSparseHopeFeatures() { m_scores.incrementSparseHopeFeatures(); }
-  void IncrementSparseFearFeatures() { m_scores.incrementSparseFearFeatures(); }
-  void PrintSparseHopeFeatureCounts(std::ofstream& out) { m_scores.printSparseHopeFeatureCounts(out); }
-  void PrintSparseFearFeatureCounts(std::ofstream& out) { m_scores.printSparseFearFeatureCounts(out); }
-  void PrintSparseHopeFeatureCounts() { m_scores.printSparseHopeFeatureCounts(); }
-  void PrintSparseFearFeatureCounts() { m_scores.printSparseFearFeatureCounts(); }
-  size_t PruneSparseFeatures(size_t threshold) { return m_scores.pruneSparseFeatures(threshold); }
-  size_t PruneZeroWeightFeatures() { return m_scores.pruneZeroWeightFeatures(); }
-  void UpdateConfidenceCounts(ScoreComponentCollection &weightUpdate, bool signedCounts) { m_scores.updateConfidenceCounts(weightUpdate.m_scores, signedCounts); }
-  void UpdateLearningRates(float decay_core, float decay_sparse, ScoreComponentCollection &confidenceCounts, float core_r0, float sparse_r0) { m_scores.updateLearningRates(decay_core, decay_sparse, confidenceCounts.m_scores, core_r0, sparse_r0); }
+
+  void IncrementSparseHopeFeatures() {
+    m_scores.incrementSparseHopeFeatures();
+  }
+  void IncrementSparseFearFeatures() {
+    m_scores.incrementSparseFearFeatures();
+  }
+  void PrintSparseHopeFeatureCounts(std::ofstream& out) {
+    m_scores.printSparseHopeFeatureCounts(out);
+  }
+  void PrintSparseFearFeatureCounts(std::ofstream& out) {
+    m_scores.printSparseFearFeatureCounts(out);
+  }
+  void PrintSparseHopeFeatureCounts() {
+    m_scores.printSparseHopeFeatureCounts();
+  }
+  void PrintSparseFearFeatureCounts() {
+    m_scores.printSparseFearFeatureCounts();
+  }
+  size_t PruneSparseFeatures(size_t threshold) {
+    return m_scores.pruneSparseFeatures(threshold);
+  }
+  size_t PruneZeroWeightFeatures() {
+    return m_scores.pruneZeroWeightFeatures();
+  }
+  void UpdateConfidenceCounts(ScoreComponentCollection &weightUpdate, bool signedCounts) {
+    m_scores.updateConfidenceCounts(weightUpdate.m_scores, signedCounts);
+  }
+  void UpdateLearningRates(float decay_core, float decay_sparse, ScoreComponentCollection &confidenceCounts, float core_r0, float sparse_r0) {
+    m_scores.updateLearningRates(decay_core, decay_sparse, confidenceCounts.m_scores, core_r0, sparse_r0);
+  }
 
 #ifdef MPI_ENABLE
-  public:
-    friend class boost::serialization::access;
-		
-  private:
-    //serialization
-    template<class Archive>
-    void save(Archive &ar, const unsigned int version) const {
-			ar << m_scores;
-    }
-		
-    template<class Archive>
-    void load(Archive &ar, const unsigned int version) {
-			ar >> m_scores;
+public:
+  friend class boost::serialization::access;
 
-    }
+private:
+  //serialization
+  template<class Archive>
+  void save(Archive &ar, const unsigned int version) const {
+    ar << m_scores;
+  }
+
+  template<class Archive>
+  void load(Archive &ar, const unsigned int version) {
+    ar >> m_scores;
+
+  }
+
+  BOOST_SERIALIZATION_SPLIT_MEMBER()
 
-    BOOST_SERIALIZATION_SPLIT_MEMBER()
-		
 #endif
 
 };
 
 struct SCCPlus {
   ScoreComponentCollection operator()
-                    (const ScoreComponentCollection& lhs,
-                     const ScoreComponentCollection& rhs) {
+  (const ScoreComponentCollection& lhs,
+   const ScoreComponentCollection& rhs) {
     ScoreComponentCollection sum(lhs);
     sum.PlusEquals(rhs);
     return sum;
diff --git a/moses/ScoreComponentCollectionTest.cpp b/moses/ScoreComponentCollectionTest.cpp
index f0813f4e8..41fa6562f 100644
--- a/moses/ScoreComponentCollectionTest.cpp
+++ b/moses/ScoreComponentCollectionTest.cpp
@@ -29,31 +29,35 @@ using namespace std;
 
 BOOST_AUTO_TEST_SUITE(scc)
 
-class MockStatelessFeatureFunction : public StatelessFeatureFunction {
-  public:
-    MockStatelessFeatureFunction(const string& desc, size_t n, const string &line) :
-      StatelessFeatureFunction(desc,n, line) {}
-    virtual void Evaluate(const PhraseBasedFeatureContext&, ScoreComponentCollection*) const {}
-    virtual void EvaluateChart(const ChartBasedFeatureContext&, ScoreComponentCollection*) const {}
-    virtual void Evaluate(const TargetPhrase &targetPhrase
+class MockStatelessFeatureFunction : public StatelessFeatureFunction
+{
+public:
+  MockStatelessFeatureFunction(const string& desc, size_t n, const string &line) :
+    StatelessFeatureFunction(desc,n, line) {}
+  virtual void Evaluate(const PhraseBasedFeatureContext&, ScoreComponentCollection*) const {}
+  virtual void EvaluateChart(const ChartBasedFeatureContext&, ScoreComponentCollection*) const {}
+  virtual void Evaluate(const TargetPhrase &targetPhrase
                         , ScoreComponentCollection &scoreBreakdown
                         , ScoreComponentCollection &estimatedFutureScore) const
-    { }
+  { }
 };
 
-class MockSingleFeature : public MockStatelessFeatureFunction {
-  public:
-    MockSingleFeature(): MockStatelessFeatureFunction("MockSingle",1, "MockSingle") {}
+class MockSingleFeature : public MockStatelessFeatureFunction
+{
+public:
+  MockSingleFeature(): MockStatelessFeatureFunction("MockSingle",1, "MockSingle") {}
 };
 
-class MockMultiFeature : public MockStatelessFeatureFunction {
-  public:
-    MockMultiFeature(): MockStatelessFeatureFunction("MockMulti", 5, "MockMulti") {}
+class MockMultiFeature : public MockStatelessFeatureFunction
+{
+public:
+  MockMultiFeature(): MockStatelessFeatureFunction("MockMulti", 5, "MockMulti") {}
 };
 
-class MockSparseFeature : public MockStatelessFeatureFunction {
-  public:
-    MockSparseFeature(): MockStatelessFeatureFunction("MockSparse", 0, "MockSparse") {}
+class MockSparseFeature : public MockStatelessFeatureFunction
+{
+public:
+  MockSparseFeature(): MockStatelessFeatureFunction("MockSparse", 0, "MockSparse") {}
 };
 
 
@@ -66,7 +70,7 @@ struct MockProducers {
   MockSparseFeature sparse;
 };
 
-BOOST_FIXTURE_TEST_CASE(ctor, MockProducers) 
+BOOST_FIXTURE_TEST_CASE(ctor, MockProducers)
 {
   ScoreComponentCollection scc;
   BOOST_CHECK_EQUAL(scc.GetScoreForProducer(&single),0);
@@ -88,11 +92,11 @@ BOOST_FIXTURE_TEST_CASE(plusequals, MockProducers)
   scc.PlusEquals(&multi,vec1);
   std::vector<float> actual = scc.GetScoresForProducer(&multi);
   BOOST_CHECK_EQUAL_COLLECTIONS(vec1.begin(),vec1.end()
-        ,actual.begin(), actual.end());
+                                ,actual.begin(), actual.end());
   scc.PlusEquals(&multi,vec1);
   actual = scc.GetScoresForProducer(&multi);
   BOOST_CHECK_EQUAL_COLLECTIONS(vec2.begin(),vec2.end(),
-         actual.begin(), actual.end());
+                                actual.begin(), actual.end());
 
   BOOST_CHECK_EQUAL(scc.GetScoreForProducer(&single), 3.4f);
 }
diff --git a/moses/SearchNormalBatch.cpp b/moses/SearchNormalBatch.cpp
index ca72b3973..aa3aeb0a3 100644
--- a/moses/SearchNormalBatch.cpp
+++ b/moses/SearchNormalBatch.cpp
@@ -18,21 +18,21 @@ SearchNormalBatch::SearchNormalBatch(Manager& manager, const InputType &source,
   // Split the feature functions into sets of stateless, stateful
   // distributed lm, and stateful non-distributed.
   const vector<const StatefulFeatureFunction*>& ffs =
-      StatefulFeatureFunction::GetStatefulFeatureFunctions();
+    StatefulFeatureFunction::GetStatefulFeatureFunctions();
   for (unsigned i = 0; i < ffs.size(); ++i) {
-      if (ffs[i]->GetScoreProducerDescription() == "DLM_5gram") { // TODO WFT
-          m_dlm_ffs[i] = const_cast<LanguageModel*>(static_cast<const LanguageModel* const>(ffs[i]));
-          m_dlm_ffs[i]->SetFFStateIdx(i);
-      }
-      else {
-          m_stateful_ffs[i] = const_cast<StatefulFeatureFunction*>(ffs[i]);
-      }
+    if (ffs[i]->GetScoreProducerDescription() == "DLM_5gram") { // TODO WFT
+      m_dlm_ffs[i] = const_cast<LanguageModel*>(static_cast<const LanguageModel* const>(ffs[i]));
+      m_dlm_ffs[i]->SetFFStateIdx(i);
+    } else {
+      m_stateful_ffs[i] = const_cast<StatefulFeatureFunction*>(ffs[i]);
+    }
   }
   m_stateless_ffs = StatelessFeatureFunction::GetStatelessFeatureFunctions();
- 
+
 }
 
-SearchNormalBatch::~SearchNormalBatch() {
+SearchNormalBatch::~SearchNormalBatch()
+{
 }
 
 /**
@@ -138,79 +138,79 @@ void SearchNormalBatch::ExpandHypothesis(const Hypothesis &hypothesis, const Tra
     for (dlm_iter = m_dlm_ffs.begin();
          dlm_iter != m_dlm_ffs.end();
          ++dlm_iter) {
-        const FFState* input_state = newHypo->GetPrevHypo() ? newHypo->GetPrevHypo()->GetFFState((*dlm_iter).first) : NULL;
-        (*dlm_iter).second->IssueRequestsFor(*newHypo, input_state);
+      const FFState* input_state = newHypo->GetPrevHypo() ? newHypo->GetPrevHypo()->GetFFState((*dlm_iter).first) : NULL;
+      (*dlm_iter).second->IssueRequestsFor(*newHypo, input_state);
     }
     m_partial_hypos.push_back(newHypo);
-  }
-  else {
+  } else {
     std::cerr << "can't use early discarding with batch decoding!" << std::endl;
     abort();
   }
 }
 
-void SearchNormalBatch::EvalAndMergePartialHypos() {
-    std::vector<Hypothesis*>::iterator partial_hypo_iter;
-    for (partial_hypo_iter = m_partial_hypos.begin();
-         partial_hypo_iter != m_partial_hypos.end();
-         ++partial_hypo_iter) {
-        Hypothesis* hypo = *partial_hypo_iter;
-
-        // Evaluate with other ffs.
-        std::map<int, StatefulFeatureFunction*>::iterator sfff_iter;
-        for (sfff_iter = m_stateful_ffs.begin();
-             sfff_iter != m_stateful_ffs.end();
-             ++sfff_iter) {
-          const StatefulFeatureFunction &ff = *(sfff_iter->second);
-          int state_idx = sfff_iter->first;
-          hypo->EvaluateWith(ff, state_idx);
-        }
-        std::vector<const StatelessFeatureFunction*>::iterator slff_iter;
-        for (slff_iter = m_stateless_ffs.begin();
-             slff_iter != m_stateless_ffs.end();
-             ++slff_iter) {
-            hypo->EvaluateWith(**slff_iter);
-        }
+void SearchNormalBatch::EvalAndMergePartialHypos()
+{
+  std::vector<Hypothesis*>::iterator partial_hypo_iter;
+  for (partial_hypo_iter = m_partial_hypos.begin();
+       partial_hypo_iter != m_partial_hypos.end();
+       ++partial_hypo_iter) {
+    Hypothesis* hypo = *partial_hypo_iter;
+
+    // Evaluate with other ffs.
+    std::map<int, StatefulFeatureFunction*>::iterator sfff_iter;
+    for (sfff_iter = m_stateful_ffs.begin();
+         sfff_iter != m_stateful_ffs.end();
+         ++sfff_iter) {
+      const StatefulFeatureFunction &ff = *(sfff_iter->second);
+      int state_idx = sfff_iter->first;
+      hypo->EvaluateWith(ff, state_idx);
+    }
+    std::vector<const StatelessFeatureFunction*>::iterator slff_iter;
+    for (slff_iter = m_stateless_ffs.begin();
+         slff_iter != m_stateless_ffs.end();
+         ++slff_iter) {
+      hypo->EvaluateWith(**slff_iter);
     }
+  }
 
-    // Wait for all requests from the distributed LM to come back.
+  // Wait for all requests from the distributed LM to come back.
+  std::map<int, LanguageModel*>::iterator dlm_iter;
+  for (dlm_iter = m_dlm_ffs.begin();
+       dlm_iter != m_dlm_ffs.end();
+       ++dlm_iter) {
+    (*dlm_iter).second->sync();
+  }
+
+  // Incorporate the DLM scores into all hypotheses and put into their
+  // stacks.
+  for (partial_hypo_iter = m_partial_hypos.begin();
+       partial_hypo_iter != m_partial_hypos.end();
+       ++partial_hypo_iter) {
+    Hypothesis* hypo = *partial_hypo_iter;
+
+    // Calculate DLM scores.
     std::map<int, LanguageModel*>::iterator dlm_iter;
     for (dlm_iter = m_dlm_ffs.begin();
          dlm_iter != m_dlm_ffs.end();
          ++dlm_iter) {
-        (*dlm_iter).second->sync();
+      LanguageModel &lm = *(dlm_iter->second);
+      hypo->EvaluateWith(lm, (*dlm_iter).first);
     }
 
-    // Incorporate the DLM scores into all hypotheses and put into their
-    // stacks.
-    for (partial_hypo_iter = m_partial_hypos.begin();
-         partial_hypo_iter != m_partial_hypos.end();
-         ++partial_hypo_iter) {
-        Hypothesis* hypo = *partial_hypo_iter;
-
-        // Calculate DLM scores.
-        std::map<int, LanguageModel*>::iterator dlm_iter;
-        for (dlm_iter = m_dlm_ffs.begin();
-             dlm_iter != m_dlm_ffs.end();
-             ++dlm_iter) {
-          LanguageModel &lm = *(dlm_iter->second);
-          hypo->EvaluateWith(lm, (*dlm_iter).first);
-        }
-
-        // Put completed hypothesis onto its stack.
-        size_t wordsTranslated = hypo->GetWordsBitmap().GetNumWordsCovered();
-        m_hypoStackColl[wordsTranslated]->AddPrune(hypo);
-    }
-    m_partial_hypos.clear();
-
-    std::vector < HypothesisStack* >::iterator stack_iter;
-    HypothesisStackNormal* stack;
-    for (stack_iter = m_hypoStackColl.begin();
-         stack_iter != m_hypoStackColl.end();
-         ++stack_iter) {
-        stack = static_cast<HypothesisStackNormal*>(*stack_iter);
-        stack->PruneToSize(m_max_stack_size);
-    }
+    // Put completed hypothesis onto its stack.
+    size_t wordsTranslated = hypo->GetWordsBitmap().GetNumWordsCovered();
+    m_hypoStackColl[wordsTranslated]->AddPrune(hypo);
+  }
+  m_partial_hypos.clear();
+
+  std::vector < HypothesisStack* >::iterator stack_iter;
+  HypothesisStackNormal* stack;
+  for (stack_iter = m_hypoStackColl.begin();
+       stack_iter != m_hypoStackColl.end();
+       ++stack_iter) {
+    stack = static_cast<HypothesisStackNormal*>(*stack_iter);
+    stack->PruneToSize(m_max_stack_size);
+  }
 }
 
 }
diff --git a/moses/SearchNormalBatch.h b/moses/SearchNormalBatch.h
index fcfda7054..7f6764635 100644
--- a/moses/SearchNormalBatch.h
+++ b/moses/SearchNormalBatch.h
@@ -13,7 +13,7 @@ class TranslationOptionCollection;
 /** Implements the phrase-based stack decoding algorithm (no cube pruning) with a twist...
  *  Language model requests are batched together, duplicate requests are removed, and requests are sent together.
  *  Useful for distributed LM where network latency is an issue.
- */  
+ */
 class SearchNormalBatch: public SearchNormal
 {
 protected:
@@ -21,7 +21,7 @@ protected:
   // Added for asynclm decoding.
   std::vector<const StatelessFeatureFunction*> m_stateless_ffs;
   std::map<int, LanguageModel*> m_dlm_ffs;
-  std::map<int, StatefulFeatureFunction*> m_stateful_ffs;  
+  std::map<int, StatefulFeatureFunction*> m_stateful_ffs;
   std::vector<Hypothesis*> m_partial_hypos;
   int m_batch_size;
   int m_max_stack_size;
diff --git a/moses/Sentence.cpp b/moses/Sentence.cpp
index b2e5a6633..8e76b0f03 100644
--- a/moses/Sentence.cpp
+++ b/moses/Sentence.cpp
@@ -104,8 +104,7 @@ int Sentence::Read(std::istream& in,const std::vector<FactorType>& factorOrder)
       this->SetTopicId(atol(topic_params[0].c_str()));
       this->SetUseTopicId(true);
       this->SetUseTopicIdAndProb(false);
-    }
-    else {
+    } else {
       this->SetTopicIdAndProb(topic_params);
       this->SetUseTopicId(false);
       this->SetUseTopicIdAndProb(true);
diff --git a/moses/StaticData.cpp b/moses/StaticData.cpp
index df4c14cde..f822e4e13 100644
--- a/moses/StaticData.cpp
+++ b/moses/StaticData.cpp
@@ -109,15 +109,15 @@ StaticData::~StaticData()
   typedef std::map<std::pair<size_t, Phrase>, std::pair<TranslationOptionList*,clock_t> > Coll;
   Coll::iterator iter;
   for (iter = m_transOptCache.begin(); iter != m_transOptCache.end(); ++iter) {
-	std::pair<TranslationOptionList*,clock_t> &valuePair =iter->second;
-	TranslationOptionList *transOptList = valuePair.first;
-	delete transOptList;
+    std::pair<TranslationOptionList*,clock_t> &valuePair =iter->second;
+    TranslationOptionList *transOptList = valuePair.first;
+    delete transOptList;
   }
 
   /*
   const std::vector<FeatureFunction*> &producers = FeatureFunction::GetFeatureFunctions();
   for(size_t i=0;i<producers.size();++i) {
-	FeatureFunction *ff = producers[i];
+  FeatureFunction *ff = producers[i];
     delete ff;
   }
   */
@@ -126,7 +126,8 @@ StaticData::~StaticData()
   Phrase::FinalizeMemPool();
 }
 
-bool StaticData::LoadDataStatic(Parameter *parameter, const std::string &execPath) {
+bool StaticData::LoadDataStatic(Parameter *parameter, const std::string &execPath)
+{
   s_instance.SetExecPath(execPath);
   return s_instance.LoadData(parameter);
 }
@@ -143,7 +144,7 @@ bool StaticData::LoadData(Parameter *parameter)
   }
 
   m_parsingAlgorithm = (m_parameter->GetParam("parsing-algorithm").size() > 0) ?
-                      (ParsingAlgorithm) Scan<size_t>(m_parameter->GetParam("parsing-algorithm")[0]) : ParseCYKPlus;
+                       (ParsingAlgorithm) Scan<size_t>(m_parameter->GetParam("parsing-algorithm")[0]) : ParseCYKPlus;
 
   // to cube or not to cube
   m_searchAlgorithm = (m_parameter->GetParam("search-algorithm").size() > 0) ?
@@ -217,7 +218,7 @@ bool StaticData::LoadData(Parameter *parameter)
   } else {
     m_nBestFactor = 20;
   }
-  
+
   //lattice samples
   if (m_parameter->GetParam("lattice-samples").size() ==2 ) {
     m_latticeSamplesFilePath = m_parameter->GetParam("lattice-samples")[0];
@@ -276,11 +277,11 @@ bool StaticData::LoadData(Parameter *parameter)
 #endif
   SetBooleanParameter( &m_unprunedSearchGraph, "unpruned-search-graph", false );
   SetBooleanParameter( &m_includeLHSInSearchGraph, "include-lhs-in-search-graph", false );
-  
+
   if (m_parameter->isParamSpecified("output-unknowns")) {
 
     if (m_parameter->GetParam("output-unknowns").size() == 1) {
-      m_outputUnknownsFile =Scan<string>(m_parameter->GetParam("output-unknowns")[0]); 
+      m_outputUnknownsFile =Scan<string>(m_parameter->GetParam("output-unknowns")[0]);
     } else {
       UserMessage::Add(string("need to specify exactly one file name for unknowns"));
       return false;
@@ -422,7 +423,7 @@ bool StaticData::LoadData(Parameter *parameter)
     cerr << "Errror: Cannot use both n-best mbr and lattice mbr together" << endl;
     exit(1);
   }
-  
+
   //mira training
   SetBooleanParameter( &m_mira, "mira", false );
 
@@ -446,7 +447,7 @@ bool StaticData::LoadData(Parameter *parameter)
     exit(1);
   }
   if (m_useConsensusDecoding) m_mbr=true;
-  
+
   // Compact phrase table and reordering model
   SetBooleanParameter( &m_minphrMemory, "minphr-memory", false );
   SetBooleanParameter( &m_minlexrMemory, "minlexr-memory", false );
@@ -489,7 +490,7 @@ bool StaticData::LoadData(Parameter *parameter)
   }
 
   m_startTranslationId = (m_parameter->GetParam("start-translation-id").size() > 0) ?
-          Scan<long>(m_parameter->GetParam("start-translation-id")[0]) : 0;
+                         Scan<long>(m_parameter->GetParam("start-translation-id")[0]) : 0;
 
   // Read in constraint decoding file, if provided
   if(m_parameter->GetParam("constraint").size()) {
@@ -503,7 +504,7 @@ bool StaticData::LoadData(Parameter *parameter)
     InputFileStream constraintFile(m_constraintFileName);
 
     std::string line;
-    
+
     long sentenceID = GetStartTranslationId() - 1;
     while (getline(constraintFile, line)) {
       vector<string> vecStr = Tokenize(line, "\t");
@@ -546,14 +547,14 @@ bool StaticData::LoadData(Parameter *parameter)
 
   // specify XML tags opening and closing brackets for XML option
   if (m_parameter->GetParam("xml-brackets").size() > 0) {
-     std::vector<std::string> brackets = Tokenize(m_parameter->GetParam("xml-brackets")[0]);
-     if(brackets.size()!=2) {
-          cerr << "invalid xml-brackets value, must specify exactly 2 blank-delimited strings for XML tags opening and closing brackets" << endl;
-          exit(1);
-     }
-     m_xmlBrackets.first= brackets[0];
-     m_xmlBrackets.second=brackets[1];
-     cerr << "XML tags opening and closing brackets for XML input are: " << m_xmlBrackets.first << " and " << m_xmlBrackets.second << endl;
+    std::vector<std::string> brackets = Tokenize(m_parameter->GetParam("xml-brackets")[0]);
+    if(brackets.size()!=2) {
+      cerr << "invalid xml-brackets value, must specify exactly 2 blank-delimited strings for XML tags opening and closing brackets" << endl;
+      exit(1);
+    }
+    m_xmlBrackets.first= brackets[0];
+    m_xmlBrackets.second=brackets[1];
+    cerr << "XML tags opening and closing brackets for XML input are: " << m_xmlBrackets.first << " and " << m_xmlBrackets.second << endl;
   }
 
   // all features
@@ -574,58 +575,47 @@ bool StaticData::LoadData(Parameter *parameter)
       GlobalLexicalModel *model = new GlobalLexicalModel(line);
       vector<float> weights = m_parameter->GetWeights(model->GetScoreProducerDescription());
       SetWeights(model, weights);
-    }
-    else if (feature == "GlobalLexicalModelUnlimited") {
+    } else if (feature == "GlobalLexicalModelUnlimited") {
       GlobalLexicalModelUnlimited *model = NULL; //new GlobalLexicalModelUnlimited(line);
       vector<float> weights = m_parameter->GetWeights(model->GetScoreProducerDescription());
       SetWeights(model, weights);
-    }
-    else if (feature == "SourceWordDeletionFeature") {
+    } else if (feature == "SourceWordDeletionFeature") {
       SourceWordDeletionFeature *model = new SourceWordDeletionFeature(line);
       vector<float> weights = m_parameter->GetWeights(model->GetScoreProducerDescription());
       //SetWeights(model, weights);
-    }
-    else if (feature == "TargetWordInsertionFeature") {
+    } else if (feature == "TargetWordInsertionFeature") {
       TargetWordInsertionFeature *model = new TargetWordInsertionFeature(line);
       vector<float> weights = m_parameter->GetWeights(model->GetScoreProducerDescription());
       //SetWeights(model, weights);
-    }
-    else if (feature == "PhraseBoundaryFeature") {
+    } else if (feature == "PhraseBoundaryFeature") {
       PhraseBoundaryFeature *model = new PhraseBoundaryFeature(line);
       vector<float> weights = m_parameter->GetWeights(model->GetScoreProducerDescription());
       //SetWeights(model, weights);
-    }
-    else if (feature == "PhraseLengthFeature") {
+    } else if (feature == "PhraseLengthFeature") {
       PhraseLengthFeature *model = new PhraseLengthFeature(line);
       vector<float> weights = m_parameter->GetWeights(model->GetScoreProducerDescription());
       //SetWeights(model, weights);
-    }
-    else if (feature == "WordTranslationFeature") {
+    } else if (feature == "WordTranslationFeature") {
       WordTranslationFeature *model = new WordTranslationFeature(line);
       vector<float> weights = m_parameter->GetWeights(model->GetScoreProducerDescription());
       //SetWeights(model, weights);
-    }
-    else if (feature == "TargetBigramFeature") {
+    } else if (feature == "TargetBigramFeature") {
       TargetBigramFeature *model = new TargetBigramFeature(line);
       vector<float> weights = m_parameter->GetWeights(model->GetScoreProducerDescription());
       //SetWeights(model, weights);
-    }
-    else if (feature == "TargetNgramFeature") {
+    } else if (feature == "TargetNgramFeature") {
       TargetNgramFeature *model = new TargetNgramFeature(line);
       vector<float> weights = m_parameter->GetWeights(model->GetScoreProducerDescription());
       //SetWeights(model, weights);
-    }
-    else if (feature == "PhrasePairFeature") {
+    } else if (feature == "PhrasePairFeature") {
       PhrasePairFeature *model = new PhrasePairFeature(line);
       vector<float> weights = m_parameter->GetWeights(model->GetScoreProducerDescription());
       //SetWeights(model, weights);
-    }
-    else if (feature == "LexicalReordering") {
+    } else if (feature == "LexicalReordering") {
       LexicalReordering *model = new LexicalReordering(line);
       vector<float> weights = m_parameter->GetWeights(model->GetScoreProducerDescription());
       SetWeights(model, weights);
-    }
-    else if (feature == "KENLM") {
+    } else if (feature == "KENLM") {
       LanguageModel *model = ConstructKenLM(feature, line);
       vector<float> weights = m_parameter->GetWeights(model->GetScoreProducerDescription());
       SetWeights(model, weights);
@@ -648,69 +638,58 @@ bool StaticData::LoadData(Parameter *parameter)
       GenerationDictionary *model = new GenerationDictionary(line);
       vector<float> weights = m_parameter->GetWeights(model->GetScoreProducerDescription());
       SetWeights(model, weights);
-    }
-    else if (feature == "BleuScoreFeature") {
+    } else if (feature == "BleuScoreFeature") {
       BleuScoreFeature *model = new BleuScoreFeature(line);
       vector<float> weights = m_parameter->GetWeights(model->GetScoreProducerDescription());
       SetWeights(model, weights);
-    }
-    else if (feature == "Distortion") {
+    } else if (feature == "Distortion") {
       DistortionScoreProducer *model = new DistortionScoreProducer(line);
       vector<float> weights = m_parameter->GetWeights(model->GetScoreProducerDescription());
       SetWeights(model, weights);
-    }
-    else if (feature == "WordPenalty") {
+    } else if (feature == "WordPenalty") {
       WordPenaltyProducer *model = new WordPenaltyProducer(line);
       vector<float> weights = m_parameter->GetWeights(model->GetScoreProducerDescription());
       SetWeights(model, weights);
       m_wpProducer = model;
-    }
-    else if (feature == "UnknownWordPenalty") {
+    } else if (feature == "UnknownWordPenalty") {
       UnknownWordPenaltyProducer *model = new UnknownWordPenaltyProducer(line);
       vector<float> weights = m_parameter->GetWeights(model->GetScoreProducerDescription());
       if (weights.size() == 0)
         weights.push_back(1.0f);
       SetWeights(model, weights);
       m_unknownWordPenaltyProducer = model;
-    }
-    else if (feature == "PhraseDictionaryBinary") {
+    } else if (feature == "PhraseDictionaryBinary") {
       PhraseDictionaryTreeAdaptor* model = new PhraseDictionaryTreeAdaptor(line);
       vector<float> weights = m_parameter->GetWeights(model->GetScoreProducerDescription());
       SetWeights(model, weights);
       m_phraseDictionary.push_back(model);
-    }
-    else if (feature == "PhraseDictionaryOnDisk") {
+    } else if (feature == "PhraseDictionaryOnDisk") {
       PhraseDictionaryOnDisk* model = new PhraseDictionaryOnDisk(line);
       vector<float> weights = m_parameter->GetWeights(model->GetScoreProducerDescription());
       SetWeights(model, weights);
       m_phraseDictionary.push_back(model);
-    }
-    else if (feature == "PhraseDictionaryMemory") {
+    } else if (feature == "PhraseDictionaryMemory") {
       PhraseDictionaryMemory* model = new PhraseDictionaryMemory(line);
       vector<float> weights = m_parameter->GetWeights(model->GetScoreProducerDescription());
       SetWeights(model, weights);
       m_phraseDictionary.push_back(model);
-    }
-    else if (feature == "PhraseDictionaryCompact") {
+    } else if (feature == "PhraseDictionaryCompact") {
       PhraseDictionaryCompact* model = new PhraseDictionaryCompact(line);
       vector<float> weights = m_parameter->GetWeights(model->GetScoreProducerDescription());
       SetWeights(model, weights);
       m_phraseDictionary.push_back(model);
-    }
-    else if (feature == "PhraseDictionaryMultiModel") {
+    } else if (feature == "PhraseDictionaryMultiModel") {
       PhraseDictionaryMultiModel* model = new PhraseDictionaryMultiModel(line);
       vector<float> weights = m_parameter->GetWeights(model->GetScoreProducerDescription());
       SetWeights(model, weights);
       m_phraseDictionary.push_back(model);
-    }
-    else if (feature == "PhraseDictionaryMultiModelCounts") {
+    } else if (feature == "PhraseDictionaryMultiModelCounts") {
       PhraseDictionaryMultiModelCounts* model = new PhraseDictionaryMultiModelCounts(line);
       vector<float> weights = m_parameter->GetWeights(model->GetScoreProducerDescription());
       SetWeights(model, weights);
       m_phraseDictionary.push_back(model);
-    }
-    else if (feature == "PhraseDictionaryALSuffixArray") {
-    	PhraseDictionaryALSuffixArray* model = new PhraseDictionaryALSuffixArray(line);
+    } else if (feature == "PhraseDictionaryALSuffixArray") {
+      PhraseDictionaryALSuffixArray* model = new PhraseDictionaryALSuffixArray(line);
       vector<float> weights = m_parameter->GetWeights(model->GetScoreProducerDescription());
       SetWeights(model, weights);
       m_phraseDictionary.push_back(model);
@@ -912,7 +891,7 @@ bool StaticData::LoadDecodeGraphs()
       DecodeGraph *decodeGraph;
       if (IsChart()) {
         size_t maxChartSpan = (decodeGraphInd < maxChartSpans.size()) ? maxChartSpans[decodeGraphInd] : DEFAULT_MAX_CHART_SPAN;
-	cerr << "max-chart-span: " << maxChartSpans[decodeGraphInd] << endl;
+        cerr << "max-chart-span: " << maxChartSpans[decodeGraphInd] << endl;
         decodeGraph = new DecodeGraph(m_decodeGraphs.size(), maxChartSpan);
       } else {
         decodeGraph = new DecodeGraph(m_decodeGraphs.size());
@@ -947,7 +926,7 @@ const TranslationOptionList* StaticData::FindTransOptListInCache(const DecodeGra
   boost::mutex::scoped_lock lock(m_transOptCacheMutex);
 #endif
   std::map<std::pair<size_t, Phrase>, std::pair<TranslationOptionList*,clock_t> >::iterator iter
-    = m_transOptCache.find(key);
+  = m_transOptCache.find(key);
   if (iter == m_transOptCache.end())
     return NULL;
   iter->second.second = clock(); // update last used time
@@ -994,7 +973,8 @@ void StaticData::AddTransOptListToCache(const DecodeGraph &decodeGraph, const Ph
   m_transOptCache[key] = make_pair( storedTransOptList, clock() );
   ReduceTransOptCache();
 }
-void StaticData::ClearTransOptionCache() const {
+void StaticData::ClearTransOptionCache() const
+{
   map<std::pair<size_t, Phrase>, std::pair< TranslationOptionList*, clock_t > >::iterator iterCache;
   for (iterCache = m_transOptCache.begin() ; iterCache != m_transOptCache.end() ; ++iterCache) {
     TranslationOptionList *transOptList = iterCache->second.first;
@@ -1091,20 +1071,19 @@ void StaticData::SetExecPath(const std::string &path)
 {
   /*
    namespace fs = boost::filesystem;
-   
+
    fs::path full_path( fs::initial_path<fs::path>() );
-   
+
    full_path = fs::system_complete( fs::path( path ) );
-   
+
    //Without file name
    m_binPath = full_path.parent_path().string();
    */
-  
+
   // NOT TESTED
   size_t pos = path.rfind("/");
-  if (pos !=  string::npos)
-  {
-    m_binPath = path.substr(0, pos); 
+  if (pos !=  string::npos) {
+    m_binPath = path.substr(0, pos);
   }
   cerr << m_binPath << endl;
 }
@@ -1114,27 +1093,31 @@ const string &StaticData::GetBinDirectory() const
   return m_binPath;
 }
 
-float StaticData::GetWeightWordPenalty() const {
+float StaticData::GetWeightWordPenalty() const
+{
   float weightWP = GetWeight(m_wpProducer);
   //VERBOSE(1, "Read weightWP from translation sytem: " << weightWP << std::endl);
   return weightWP;
 }
 
-float StaticData::GetWeightUnknownWordPenalty() const {
+float StaticData::GetWeightUnknownWordPenalty() const
+{
   return GetWeight(m_unknownWordPenaltyProducer);
 }
 
-void StaticData::InitializeForInput(const InputType& source) const {
+void StaticData::InitializeForInput(const InputType& source) const
+{
   const std::vector<FeatureFunction*> &producers = FeatureFunction::GetFeatureFunctions();
-  for(size_t i=0;i<producers.size();++i) {
+  for(size_t i=0; i<producers.size(); ++i) {
     FeatureFunction &ff = *producers[i];
     ff.InitializeForInput(source);
   }
 }
 
-void StaticData::CleanUpAfterSentenceProcessing(const InputType& source) const {
+void StaticData::CleanUpAfterSentenceProcessing(const InputType& source) const
+{
   const std::vector<FeatureFunction*> &producers = FeatureFunction::GetFeatureFunctions();
-  for(size_t i=0;i<producers.size();++i) {
+  for(size_t i=0; i<producers.size(); ++i) {
     FeatureFunction &ff = *producers[i];
     ff.CleanUpAfterSentenceProcessing(source);
   }
@@ -1172,8 +1155,7 @@ bool StaticData::CheckWeights() const
     set<string>::iterator iter = weightNames.find(descr);
     if (iter == weightNames.end()) {
       cerr << "Can't find weights for feature function " << descr << endl;
-    }
-    else {
+    } else {
       weightNames.erase(iter);
     }
   }
diff --git a/moses/StaticData.h b/moses/StaticData.h
index 01a0a19df..5a1cec213 100644
--- a/moses/StaticData.h
+++ b/moses/StaticData.h
@@ -87,7 +87,7 @@ protected:
   m_translationOptionThreshold,
   m_wordDeletionWeight;
 
-  
+
   // PhraseTrans, Generation & LanguageModelScore has multiple weights.
   int				m_maxDistortion;
   // do it differently from old pharaoh
@@ -206,7 +206,7 @@ protected:
 
   int m_threadCount;
   long m_startTranslationId;
-  
+
   StaticData();
 
 
@@ -223,7 +223,7 @@ protected:
   bool m_continuePartialTranslation;
 
   std::string m_binPath;
-  
+
 public:
 
   bool IsAlwaysCreateDirectTranslationOption() const {
@@ -363,15 +363,15 @@ public:
   bool IsLabeledNBestList() const {
     return m_labeledNBestList;
   }
-  
+
   bool UseMinphrInMemory() const {
-     return m_minphrMemory;
+    return m_minphrMemory;
   }
 
   bool UseMinlexrInMemory() const {
-     return m_minlexrMemory;
+    return m_minlexrMemory;
   }
-  
+
   size_t GetNumRealWordsInInput() const {
     return m_numRealWordsInInput;
   }
@@ -421,13 +421,16 @@ public:
   bool IsChart() const {
     return m_searchAlgorithm == ChartDecoding || m_searchAlgorithm == ChartIncremental;
   }
-  const WordPenaltyProducer *GetWordPenaltyProducer() const
-  { return m_wpProducer; }
-  WordPenaltyProducer *GetWordPenaltyProducer() // for mira
-  { return m_wpProducer; }
+  const WordPenaltyProducer *GetWordPenaltyProducer() const {
+    return m_wpProducer;
+  }
+  WordPenaltyProducer *GetWordPenaltyProducer() { // for mira
+    return m_wpProducer;
+  }
 
-  const UnknownWordPenaltyProducer *GetUnknownWordPenaltyProducer() const
-  { return m_unknownWordPenaltyProducer; }
+  const UnknownWordPenaltyProducer *GetUnknownWordPenaltyProducer() const {
+    return m_unknownWordPenaltyProducer;
+  }
 
   size_t GetNumInputScores() const {
     return m_numInputScores;
@@ -458,7 +461,7 @@ public:
   float GetSparseWeight(const FName& featureName) const {
     return m_allWeights.GetSparseWeight(featureName);
   }
-  
+
   //Weights for feature with fixed number of values
   void SetWeights(const FeatureFunction* sp, const std::vector<float>& weights);
 
@@ -627,15 +630,17 @@ public:
   int ThreadCount() const {
     return m_threadCount;
   }
-  
-  long GetStartTranslationId() const
-  { return m_startTranslationId; }
-  
+
+  long GetStartTranslationId() const {
+    return m_startTranslationId;
+  }
+
   void SetExecPath(const std::string &path);
   const std::string &GetBinDirectory() const;
 
   bool NeedAlignmentInfo() const {
-    return m_needAlignmentInfo; }
+    return m_needAlignmentInfo;
+  }
   const std::string &GetAlignmentOutputFile() const {
     return m_alignmentOutputFile;
   }
@@ -656,19 +661,26 @@ public:
   float GetWeightWordPenalty() const;
   float GetWeightUnknownWordPenalty() const;
 
-  const std::vector<PhraseDictionary*>& GetPhraseDictionaries() const
-  { return m_phraseDictionary;}
-  const std::vector<const GenerationDictionary*>& GetGenerationDictionaries() const
-  { return m_generationDictionary;}
-  const PhraseDictionary*GetTranslationScoreProducer(size_t index) const
-  { return GetPhraseDictionaries().at(index); }
+  const std::vector<PhraseDictionary*>& GetPhraseDictionaries() const {
+    return m_phraseDictionary;
+  }
+  const std::vector<const GenerationDictionary*>& GetGenerationDictionaries() const {
+    return m_generationDictionary;
+  }
+  const PhraseDictionary*GetTranslationScoreProducer(size_t index) const {
+    return GetPhraseDictionaries().at(index);
+  }
   std::vector<float> GetTranslationWeights(size_t index) const {
     std::vector<float> weights = GetWeights(GetTranslationScoreProducer(index));
     return weights;
   }
 
-  const std::vector<DecodeGraph*>& GetDecodeGraphs() const {return m_decodeGraphs;}
-  const std::vector<size_t>& GetDecodeGraphBackoff() const {return m_decodeGraphBackoff;}
+  const std::vector<DecodeGraph*>& GetDecodeGraphs() const {
+    return m_decodeGraphs;
+  }
+  const std::vector<size_t>& GetDecodeGraphBackoff() const {
+    return m_decodeGraphBackoff;
+  }
 
   //sentence (and thread) specific initialisationn and cleanup
   void InitializeForInput(const InputType& source) const;
@@ -697,8 +709,7 @@ public:
 #ifdef WITH_THREADS
     if (m_multimodelweights_tmp.find(boost::this_thread::get_id()) != m_multimodelweights_tmp.end()) {
       return &m_multimodelweights_tmp.find(boost::this_thread::get_id())->second;
-    }
-    else {
+    } else {
       return NULL;
     }
 #else
diff --git a/moses/SyntacticLanguageModel.cpp b/moses/SyntacticLanguageModel.cpp
index 4a3b26ff1..cde041fe7 100644
--- a/moses/SyntacticLanguageModel.cpp
+++ b/moses/SyntacticLanguageModel.cpp
@@ -10,154 +10,159 @@
 
 namespace Moses
 {
-  SyntacticLanguageModel::SyntacticLanguageModel(const std::string &line)
-  // Initialize member variables
-  /*
-  : m_NumScoreComponents(weights.size())
-  , m_files(new SyntacticLanguageModelFiles<YModel,XModel>(filePath))
-  , m_factorType(factorType)
-  , m_beamWidth(beamWidth) {
-  */
-  {
-    /* taken from StaticData::LoadSyntacticLanguageModel()
-          cerr << "Loading syntactic language models..." << std::endl;
-
-    const vector<float> weights = Scan<float>(m_parameter->GetParam("weight-slm"));
-    const vector<string> files = m_parameter->GetParam("slmodel-file");
-
-    const FactorType factorType = (m_parameter->GetParam("slmodel-factor").size() > 0) ?
-      TransformScore(Scan<int>(m_parameter->GetParam("slmodel-factor")[0]))
-      : 0;
-
-    const size_t beamWidth = (m_parameter->GetParam("slmodel-beam").size() > 0) ?
-      TransformScore(Scan<int>(m_parameter->GetParam("slmodel-beam")[0]))
-      : 500;
-
-    if (files.size() < 1) {
-      cerr << "No syntactic language model files specified!" << std::endl;
-      return false;
-    }
+SyntacticLanguageModel::SyntacticLanguageModel(const std::string &line)
+// Initialize member variables
+/*
+: m_NumScoreComponents(weights.size())
+, m_files(new SyntacticLanguageModelFiles<YModel,XModel>(filePath))
+, m_factorType(factorType)
+, m_beamWidth(beamWidth) {
+*/
+{
+  /* taken from StaticData::LoadSyntacticLanguageModel()
+        cerr << "Loading syntactic language models..." << std::endl;
 
-    // check if feature is used
-    if (weights.size() >= 1) {
+  const vector<float> weights = Scan<float>(m_parameter->GetParam("weight-slm"));
+  const vector<string> files = m_parameter->GetParam("slmodel-file");
 
-      //cout.setf(ios::scientific,ios::floatfield);
-      //cerr.setf(ios::scientific,ios::floatfield);
+  const FactorType factorType = (m_parameter->GetParam("slmodel-factor").size() > 0) ?
+    TransformScore(Scan<int>(m_parameter->GetParam("slmodel-factor")[0]))
+    : 0;
 
-      // create the feature
-      m_syntacticLanguageModel = new SyntacticLanguageModel(files,weights,factorType,beamWidth);
+  const size_t beamWidth = (m_parameter->GetParam("slmodel-beam").size() > 0) ?
+    TransformScore(Scan<int>(m_parameter->GetParam("slmodel-beam")[0]))
+    : 500;
 
+  if (files.size() < 1) {
+    cerr << "No syntactic language model files specified!" << std::endl;
+    return false;
+  }
 
-      /////////////////////////////////////////
-      // BEGIN LANE's UNSTABLE EXPERIMENT :)
-      //
+  // check if feature is used
+  if (weights.size() >= 1) {
 
-      //double ppl = m_syntacticLanguageModel->perplexity();
-      //cerr << "Probability is " << ppl << endl;
+    //cout.setf(ios::scientific,ios::floatfield);
+    //cerr.setf(ios::scientific,ios::floatfield);
 
+    // create the feature
+    m_syntacticLanguageModel = new SyntacticLanguageModel(files,weights,factorType,beamWidth);
 
-      //
-      // END LANE's UNSTABLE EXPERIMENT
-      /////////////////////////////////////////
 
+    /////////////////////////////////////////
+    // BEGIN LANE's UNSTABLE EXPERIMENT :)
+    //
 
+    //double ppl = m_syntacticLanguageModel->perplexity();
+    //cerr << "Probability is " << ppl << endl;
 
-      if (m_syntacticLanguageModel==NULL) {
-        return false;
-      }
 
-    }
+    //
+    // END LANE's UNSTABLE EXPERIMENT
+    /////////////////////////////////////////
 
-    return true;
 
-     */
-  }
 
-  SyntacticLanguageModel::~SyntacticLanguageModel() {
-    VERBOSE(3,"Destructing SyntacticLanguageModel" << std::endl);
-    delete m_files;
-  }
+    if (m_syntacticLanguageModel==NULL) {
+      return false;
+    }
 
-  size_t SyntacticLanguageModel::GetNumScoreComponents() const {
-    return m_NumScoreComponents;
   }
 
-  std::string SyntacticLanguageModel::GetScoreProducerDescription() const {
-    return "SyntacticLM";
-  }
+  return true;
 
-  const FFState* SyntacticLanguageModel::EmptyHypothesisState(const InputType &input) const {
+   */
+}
 
-    return new SyntacticLanguageModelState<YModel,XModel,S,R>(m_files,m_beamWidth);
+SyntacticLanguageModel::~SyntacticLanguageModel()
+{
+  VERBOSE(3,"Destructing SyntacticLanguageModel" << std::endl);
+  delete m_files;
+}
 
-  }
+size_t SyntacticLanguageModel::GetNumScoreComponents() const
+{
+  return m_NumScoreComponents;
+}
 
-  /*
-  double SyntacticLanguageModel::perplexity() {
+std::string SyntacticLanguageModel::GetScoreProducerDescription() const
+{
+  return "SyntacticLM";
+}
+
+const FFState* SyntacticLanguageModel::EmptyHypothesisState(const InputType &input) const
+{
 
-    SyntacticLanguageModelState<YModel,XModel,S,R> *prev = 
-      new SyntacticLanguageModelState<YModel,XModel,S,R>(m_files,m_beamWidth);
+  return new SyntacticLanguageModelState<YModel,XModel,S,R>(m_files,m_beamWidth);
 
-    std::cerr << "Initial prob:" << "\t" << prev->getProb() <<std::endl;
+}
 
+/*
+double SyntacticLanguageModel::perplexity() {
 
-    std::vector<std::string> words(3);
-    words[0] = "no";
-    words[1] = ",";
-    words[2] = "zxvth";
+  SyntacticLanguageModelState<YModel,XModel,S,R> *prev =
+    new SyntacticLanguageModelState<YModel,XModel,S,R>(m_files,m_beamWidth);
 
+  std::cerr << "Initial prob:" << "\t" << prev->getProb() <<std::endl;
 
-    for (std::vector<std::string>::iterator i=words.begin();
-	 i != words.end();
-	 i++) {
 
-      prev = new SyntacticLanguageModelState<YModel,XModel,S,R>(prev, *i);
-      std::cerr << *i << "\t" << prev->getProb() <<std::endl;
+  std::vector<std::string> words(3);
+  words[0] = "no";
+  words[1] = ",";
+  words[2] = "zxvth";
 
-    }
 
-    if (true) exit(-1);
+  for (std::vector<std::string>::iterator i=words.begin();
+ i != words.end();
+ i++) {
 
-    return prev->getProb();
+    prev = new SyntacticLanguageModelState<YModel,XModel,S,R>(prev, *i);
+    std::cerr << *i << "\t" << prev->getProb() <<std::endl;
 
   }
-  */
-  FFState* SyntacticLanguageModel::Evaluate(const Hypothesis& cur_hypo,
-		    const FFState* prev_state,
-		    ScoreComponentCollection* accumulator) const {
-
-    VERBOSE(3,"Evaluating SyntacticLanguageModel for a hypothesis" << endl);
-
-    SyntacticLanguageModelState<YModel,XModel,S,R>*  tmpState = NULL;
-    SyntacticLanguageModelState<YModel,XModel,S,R>* nextState = NULL;
-  
-
-    const TargetPhrase& targetPhrase = cur_hypo.GetCurrTargetPhrase();
-
-    for (size_t i=0, n=targetPhrase.GetSize(); i<n; i++) {
-      
-      const Word& word = targetPhrase.GetWord(i);
-      const Factor* factor = word.GetFactor(m_factorType);
-      
-      const std::string& string = factor->GetString();
-      
-      if (i==0) {
-	nextState = new SyntacticLanguageModelState<YModel,XModel,S,R>((const SyntacticLanguageModelState<YModel,XModel,S,R>*)prev_state, string);
-      } else {
-	tmpState = nextState;
-	nextState = new SyntacticLanguageModelState<YModel,XModel,S,R>(tmpState, string);
-	delete tmpState;
-      }
-      
-      double score = nextState->getScore();
-      VERBOSE(3,"SynLM evaluated a score of " << score << endl);
-      accumulator->Assign( this, score );
-    }
 
-  
+  if (true) exit(-1);
+
+  return prev->getProb();
+
+}
+*/
+FFState* SyntacticLanguageModel::Evaluate(const Hypothesis& cur_hypo,
+    const FFState* prev_state,
+    ScoreComponentCollection* accumulator) const
+{
+
+  VERBOSE(3,"Evaluating SyntacticLanguageModel for a hypothesis" << endl);
+
+  SyntacticLanguageModelState<YModel,XModel,S,R>*  tmpState = NULL;
+  SyntacticLanguageModelState<YModel,XModel,S,R>* nextState = NULL;
+
 
-    return nextState;
+  const TargetPhrase& targetPhrase = cur_hypo.GetCurrTargetPhrase();
 
+  for (size_t i=0, n=targetPhrase.GetSize(); i<n; i++) {
+
+    const Word& word = targetPhrase.GetWord(i);
+    const Factor* factor = word.GetFactor(m_factorType);
+
+    const std::string& string = factor->GetString();
+
+    if (i==0) {
+      nextState = new SyntacticLanguageModelState<YModel,XModel,S,R>((const SyntacticLanguageModelState<YModel,XModel,S,R>*)prev_state, string);
+    } else {
+      tmpState = nextState;
+      nextState = new SyntacticLanguageModelState<YModel,XModel,S,R>(tmpState, string);
+      delete tmpState;
+    }
+
+    double score = nextState->getScore();
+    VERBOSE(3,"SynLM evaluated a score of " << score << endl);
+    accumulator->Assign( this, score );
   }
 
+
+
+  return nextState;
+
+}
+
 }
diff --git a/moses/SyntacticLanguageModel.h b/moses/SyntacticLanguageModel.h
index 3cd4c58e9..6e88d85c1 100644
--- a/moses/SyntacticLanguageModel.h
+++ b/moses/SyntacticLanguageModel.h
@@ -12,40 +12,41 @@ class XModel; // observed model
 namespace Moses
 {
 
-  template <class MH, class MO> class SyntacticLanguageModelFiles;
-  
-  class SyntacticLanguageModel : public StatefulFeatureFunction {
+template <class MH, class MO> class SyntacticLanguageModelFiles;
 
-  public:
-    SyntacticLanguageModel(const std::string &line);
+class SyntacticLanguageModel : public StatefulFeatureFunction
+{
+
+public:
+  SyntacticLanguageModel(const std::string &line);
 
-    ~SyntacticLanguageModel();
+  ~SyntacticLanguageModel();
 
-    size_t GetNumScoreComponents() const;
+  size_t GetNumScoreComponents() const;
 
-    const FFState* EmptyHypothesisState(const InputType &input) const;
+  const FFState* EmptyHypothesisState(const InputType &input) const;
 
-    FFState* Evaluate(const Hypothesis& cur_hypo,
-		      const FFState* prev_state,
-		      ScoreComponentCollection* accumulator) const;
+  FFState* Evaluate(const Hypothesis& cur_hypo,
+                    const FFState* prev_state,
+                    ScoreComponentCollection* accumulator) const;
 
-    FFState* EvaluateChart(const ChartHypothesis& cur_hypo,
-                           int featureID,
-                           ScoreComponentCollection* accumulator) const {
-      throw std::runtime_error("Syntactic LM can only be used with phrase-based decoder.");
-    }
+  FFState* EvaluateChart(const ChartHypothesis& cur_hypo,
+                         int featureID,
+                         ScoreComponentCollection* accumulator) const {
+    throw std::runtime_error("Syntactic LM can only be used with phrase-based decoder.");
+  }
 
 
-    //    double perplexity();
+  //    double perplexity();
 
-  private:
+private:
 
-    const size_t m_NumScoreComponents;
-    SyntacticLanguageModelFiles<YModel,XModel>* m_files;
-    const FactorType m_factorType;
-    const size_t m_beamWidth;
+  const size_t m_NumScoreComponents;
+  SyntacticLanguageModelFiles<YModel,XModel>* m_files;
+  const FactorType m_factorType;
+  const size_t m_beamWidth;
 
-  };
+};
 
 
 }
diff --git a/moses/SyntacticLanguageModelFiles.h b/moses/SyntacticLanguageModelFiles.h
index 2e12e88c6..b91c0abfe 100644
--- a/moses/SyntacticLanguageModelFiles.h
+++ b/moses/SyntacticLanguageModelFiles.h
@@ -9,50 +9,55 @@
 namespace Moses
 {
 
-template <class MH, class MO> 
-class SyntacticLanguageModelFiles {
+template <class MH, class MO>
+class SyntacticLanguageModelFiles
+{
 
- public:
+public:
 
   SyntacticLanguageModelFiles(const std::vector<std::string>& filePaths);
   ~SyntacticLanguageModelFiles();
-  
+
   MH* getHiddenModel();
   MO* getObservedModel();
 
- private:
+private:
   MH* hiddenModel;
   MO* observedModel;
-  
+
 };
 
 
 template <class MH, class MO>
-  SyntacticLanguageModelFiles<MH,MO>::SyntacticLanguageModelFiles(const std::vector<std::string>& filePaths) {
+SyntacticLanguageModelFiles<MH,MO>::SyntacticLanguageModelFiles(const std::vector<std::string>& filePaths)
+{
 
   this->hiddenModel = new MH();
   this->observedModel = new MO();
-  
+
   //// I. LOAD MODELS...
   std::cerr << "Reading syntactic language model files...\n";
   // For each model file...
   for ( int a=0, n=filePaths.size(); a<n; a++ ) {                                           // read models
     FILE* pf = fopen(filePaths[a].c_str(),"r"); //CHECK(pf);                                   // Read model file
-    if(!pf){
+    if(!pf) {
       std::cerr << "Error loading model file " << filePaths[a] << std::endl;
       return;
     }
     std::cerr << "Loading model \'" << filePaths[a] << "\'...\n";
-    int c=' '; int i=0; int line=1; String sBuff(1000);                          // Lookahead/ctrs/buffers
+    int c=' ';
+    int i=0;
+    int line=1;
+    String sBuff(1000);                          // Lookahead/ctrs/buffers
     CONSUME_ALL ( pf, c, WHITESPACE(c), line);                                   // Get to first record
     while ( c!=-1 && c!='\0' && c!='\5' ) {                                      // For each record
       CONSUME_STR ( pf, c, (c!='\n' && c!='\0' && c!='\5'), sBuff, i, line );    //   Consume line
       StringInput si(sBuff.c_array());
       if ( !( sBuff[0]=='#'                                                   //   Accept comments/fields
-			  ||  si>>*(this->hiddenModel)>>"\0"!=NULL 
-			  ||  si>>*(this->observedModel)>>"\0"!=NULL
-			  ))								   
-	std::cerr<<"\nERROR: can't parse \'"<<sBuff<<"\' in line "<<line<<"\n\n";
+              ||  si>>*(this->hiddenModel)>>"\0"!=NULL
+              ||  si>>*(this->observedModel)>>"\0"!=NULL
+            ))
+        std::cerr<<"\nERROR: can't parse \'"<<sBuff<<"\' in line "<<line<<"\n\n";
       CONSUME_ALL ( pf, c, WHITESPACE(c), line);                                 //   Consume whitespace
       if ( line%100000==0 ) std::cerr<<"  "<<line<<" lines read...\n";                //   Progress for big models
     }
@@ -66,7 +71,8 @@ template <class MH, class MO>
 
 
 template <class MH, class MO>
-  SyntacticLanguageModelFiles<MH,MO>::~SyntacticLanguageModelFiles() {
+SyntacticLanguageModelFiles<MH,MO>::~SyntacticLanguageModelFiles()
+{
 
   VERBOSE(3,"Destructing syntactic language model files" << std::endl);
   delete hiddenModel;
@@ -76,15 +82,17 @@ template <class MH, class MO>
 
 
 template <class MH, class MO>
-  MH* SyntacticLanguageModelFiles<MH,MO>::getHiddenModel() {
- 
+MH* SyntacticLanguageModelFiles<MH,MO>::getHiddenModel()
+{
+
   return this->hiddenModel;
 
 }
 
 template <class MH, class MO>
-  MO* SyntacticLanguageModelFiles<MH,MO>::getObservedModel() {
- 
+MO* SyntacticLanguageModelFiles<MH,MO>::getObservedModel()
+{
+
   return this->observedModel;
 
 }
diff --git a/moses/SyntacticLanguageModelState.h b/moses/SyntacticLanguageModelState.h
index 15828eedc..bf35616d9 100644
--- a/moses/SyntacticLanguageModelState.h
+++ b/moses/SyntacticLanguageModelState.h
@@ -15,8 +15,9 @@ namespace Moses
 {
 
 template <class MY, class MX, class YS=typename MY::RandVarType, class B=NullBackDat<typename MY::RandVarType> >
-  class SyntacticLanguageModelState : public FFState {
- public:
+class SyntacticLanguageModelState : public FFState
+{
+public:
 
   // Initialize an empty LM state
   SyntacticLanguageModelState( SyntacticLanguageModelFiles<MY,MX>* modelData, int beamSize );
@@ -25,52 +26,53 @@ template <class MY, class MX, class YS=typename MY::RandVarType, class B=NullBac
   SyntacticLanguageModelState( const SyntacticLanguageModelState* prev, std::string word );
 
 
- ~SyntacticLanguageModelState() {
-   VERBOSE(3,"Destructing SyntacticLanguageModelState" << std::endl);
-   delete randomVariableStore;
- }
+  ~SyntacticLanguageModelState() {
+    VERBOSE(3,"Destructing SyntacticLanguageModelState" << std::endl);
+    delete randomVariableStore;
+  }
 
- virtual int Compare(const FFState& other) const;
+  virtual int Compare(const FFState& other) const;
 
   // Get the LM score from this LM state
   double getScore() const;
 
- double getProb() const;
+  double getProb() const;
 
- private:
+private:
 
- void setScore(double score);
- void printRV();
+  void setScore(double score);
+  void printRV();
 
- SafeArray1D<Id<int>,pair<YS,LogProb> >* randomVariableStore;
- double prob;
- double score;
- int beamSize;
- SyntacticLanguageModelFiles<MY,MX>* modelData;
- bool sentenceStart;
+  SafeArray1D<Id<int>,pair<YS,LogProb> >* randomVariableStore;
+  double prob;
+  double score;
+  int beamSize;
+  SyntacticLanguageModelFiles<MY,MX>* modelData;
+  bool sentenceStart;
 };
 
 
 ////////////////////////////////////////////////////////////////////////////////
 
- 
- template <class MY, class MX, class YS, class B>
-   void SyntacticLanguageModelState<MY,MX,YS,B>::printRV() {
 
-   cerr << "*********** BEGIN printRV() ******************" << endl;
-   int size=randomVariableStore->getSize();
-   cerr << "randomVariableStore->getSize() == " << size << endl;
+template <class MY, class MX, class YS, class B>
+void SyntacticLanguageModelState<MY,MX,YS,B>::printRV()
+{
+
+  cerr << "*********** BEGIN printRV() ******************" << endl;
+  int size=randomVariableStore->getSize();
+  cerr << "randomVariableStore->getSize() == " << size << endl;
+
+  for (int depth=0; depth<size; depth+=1) {
 
-   for (int depth=0; depth<size; depth+=1) {
 
-     
-     const pair<YS,LogProb> *data = &(randomVariableStore->get(depth));
-     std::cerr << "randomVariableStore[" << depth << "]\t" << data->first << "\tprob = " << data->second.toProb() << "\tlogProb = " << double(data->second.toInt())/100 << std::endl;
+    const pair<YS,LogProb> *data = &(randomVariableStore->get(depth));
+    std::cerr << "randomVariableStore[" << depth << "]\t" << data->first << "\tprob = " << data->second.toProb() << "\tlogProb = " << double(data->second.toInt())/100 << std::endl;
 
-   }
-   cerr << "*********** END printRV() ******************" << endl;
+  }
+  cerr << "*********** END printRV() ******************" << endl;
 
- }
+}
 
 // Initialize an empty LM state from grammar files
 //
@@ -78,7 +80,8 @@ template <class MY, class MX, class YS=typename MY::RandVarType, class B=NullBac
 //    argv is the list of model file names
 //
 template <class MY, class MX, class YS, class B>
-  SyntacticLanguageModelState<MY,MX,YS,B>::SyntacticLanguageModelState( SyntacticLanguageModelFiles<MY,MX>* modelData, int beamSize ) {
+SyntacticLanguageModelState<MY,MX,YS,B>::SyntacticLanguageModelState( SyntacticLanguageModelFiles<MY,MX>* modelData, int beamSize )
+{
 
   this->randomVariableStore = new SafeArray1D<Id<int>,pair<YS,LogProb> >();
   this->modelData = modelData;
@@ -89,7 +92,7 @@ template <class MY, class MX, class YS, class B>
   StringInput(String(BEG_STATE).c_array())>>xBEG>>"\0";
   cerr<<xBEG<<"\n";
 
-  //  cout << "Examining RV store just before RV init" << endl;   
+  //  cout << "Examining RV store just before RV init" << endl;
   //printRV();
 
   // Initialize the random variable store
@@ -107,16 +110,17 @@ template <class MY, class MX, class YS, class B>
   //score = l.toDouble();
   setScore(l.toDouble());
   //  MY::F_ROOT_OBS = true;
- // this->modelData->getHiddenModel()->setRootObs(true);
-  
-  
+// this->modelData->getHiddenModel()->setRootObs(true);
+
+
 }
 
 
 template <class MY, class MX, class YS, class B>
-  int SyntacticLanguageModelState<MY,MX,YS,B>::Compare(const FFState& other) const {
+int SyntacticLanguageModelState<MY,MX,YS,B>::Compare(const FFState& other) const
+{
   /*
-  const SyntacticLanguageModelState<MY,MX,YS,B>& o = 
+  const SyntacticLanguageModelState<MY,MX,YS,B>& o =
     static_cast<const SyntacticLanguageModelState<MY,MX,YS,B>&>(other);
 
   if (o.score > score) return 1;
@@ -124,13 +128,14 @@ template <class MY, class MX, class YS, class B>
   else return 0;
   */
   return 0;
- }
+}
 
 
 template <class MY, class MX, class YS, class B>
-  SyntacticLanguageModelState<MY,MX,YS,B>::SyntacticLanguageModelState( const SyntacticLanguageModelState* prev, std::string word ) {
+SyntacticLanguageModelState<MY,MX,YS,B>::SyntacticLanguageModelState( const SyntacticLanguageModelState* prev, std::string word )
+{
 
-  // Initialize member variables 
+  // Initialize member variables
   this->randomVariableStore = new SafeArray1D<Id<int>,pair<YS,LogProb> >();
   this->modelData = prev->modelData;
   this->beamSize = prev->beamSize;
@@ -143,13 +148,13 @@ template <class MY, class MX, class YS, class B>
   // Get HHMM model files
   MY& mH = *(modelData->getHiddenModel());
   MX& mO = *(modelData->getObservedModel());
-  
+
   // Initialize HHMM
-  HMM<MY,MX,YS,B> hmm(mH,mO);  
+  HMM<MY,MX,YS,B> hmm(mH,mO);
   int MAX_WORDS  = 2;
   hmm.init(MAX_WORDS,this->beamSize,prev->randomVariableStore);
-  typename MX::RandVarType x(word.c_str()); 
-  //  cout << "Examining HHMM just after hmm.init" << endl;   
+  typename MX::RandVarType x(word.c_str());
+  //  cout << "Examining HHMM just after hmm.init" << endl;
   //  hmm.debugPrint();
 
 
@@ -158,21 +163,21 @@ template <class MY, class MX, class YS, class B>
   hmm.writeCurr(cout,1);
   cerr << "*********** END writeCurr() ******************" << endl;
   */
-/*
-  {
-    
-  int wnum=1;
-  list<TrellNode<YS,B> > lys = hmm.getMLSnodes(ysEND);                                           // get mls list
-      for ( typename list<TrellNode<YS,B> >::iterator i=lys.begin(); i!=lys.end(); i++, wnum++ ) {   // for each frame
-        cout << "HYPOTH " << wnum
-             << " " << i->getBackData()
-             << " " << x
-             << " " << i->getId() 
-             << " (" << i->getLogProb() << ")"
-             << endl;                                                                             //   print RV val
-      }
-  }
-  */
+  /*
+    {
+
+    int wnum=1;
+    list<TrellNode<YS,B> > lys = hmm.getMLSnodes(ysEND);                                           // get mls list
+        for ( typename list<TrellNode<YS,B> >::iterator i=lys.begin(); i!=lys.end(); i++, wnum++ ) {   // for each frame
+          cout << "HYPOTH " << wnum
+               << " " << i->getBackData()
+               << " " << x
+               << " " << i->getId()
+               << " (" << i->getLogProb() << ")"
+               << endl;                                                                             //   print RV val
+        }
+    }
+    */
 
 
   /*
@@ -189,7 +194,7 @@ template <class MY, class MX, class YS, class B>
   //  typename MX::RandVarType ov;
   //  ov.set(word.c_str(),mO);
   //  MY::WORD = ov.getW();
-  //bool endOfSentence = prev->sentenceStart;//true; 
+  //bool endOfSentence = prev->sentenceStart;//true;
 
   //  std::cerr << "About to give HHMM a word of input:\t" << word << std::endl;
 
@@ -197,27 +202,27 @@ template <class MY, class MX, class YS, class B>
 
   //  cout << "Examining HHMM just after hmm.updateRanked(" << x << "," << prev->sentenceStart << ")" << endl;
   //  hmm.debugPrint();
-/*
-  cerr << "*********** BEGIN writeCurr() ******************" << endl;
-  hmm.writeCurr(cout,0);
-  hmm.writeCurr(cout,1);
-  cerr << "*********** END writeCurr() ******************" << endl;
-  */
-/*
-{
+  /*
+    cerr << "*********** BEGIN writeCurr() ******************" << endl;
+    hmm.writeCurr(cout,0);
+    hmm.writeCurr(cout,1);
+    cerr << "*********** END writeCurr() ******************" << endl;
+    */
+  /*
+  {
 
-  int wnum=1;
-  list<TrellNode<YS,B> > lys = hmm.getMLSnodes(ysEND);                                           // get mls list
-      for ( typename list<TrellNode<YS,B> >::iterator i=lys.begin(); i!=lys.end(); i++, wnum++ ) {   // for each frame
-        cout << "HYPOTH " << wnum
-             << " " << i->getBackData()
-             << " " << x
-             << " " << i->getId() 
-             << " (" << i->getLogProb() << ")"
-             << endl;                                                                             //   print RV val
-      }
-  }
-  */
+    int wnum=1;
+    list<TrellNode<YS,B> > lys = hmm.getMLSnodes(ysEND);                                           // get mls list
+        for ( typename list<TrellNode<YS,B> >::iterator i=lys.begin(); i!=lys.end(); i++, wnum++ ) {   // for each frame
+          cout << "HYPOTH " << wnum
+               << " " << i->getBackData()
+               << " " << x
+               << " " << i->getId()
+               << " (" << i->getLogProb() << ")"
+               << endl;                                                                             //   print RV val
+        }
+    }
+    */
 //  X ov(word.c_str());
   //mH.setWord(ov);
   // MY::WORD = ov;//ov.getW();
@@ -226,17 +231,17 @@ template <class MY, class MX, class YS, class B>
   //hmm.updateRanked(ov);
   //mH.setRootObs(true);
   //MY::F_ROOT_OBS = false;
-  
+
   // Get the current score
-   double currSum = hmm.getCurrSum();
-   //VERBOSE(3,"Setting score using currSum for " << scientific << x << " = " << currSum << endl);
+  double currSum = hmm.getCurrSum();
+  //VERBOSE(3,"Setting score using currSum for " << scientific << x << " = " << currSum << endl);
   setScore(currSum);
-  //  cout << "Examining RV store just before RV init via gatherElementsInBeam" << endl;   
+  //  cout << "Examining RV store just before RV init via gatherElementsInBeam" << endl;
   //  printRV();
 
   // Get new hidden random variable store from HHMM
   hmm.gatherElementsInBeam(randomVariableStore);
-  //  cout << "Examining RV store just after RV init via gatherElementsInBeam" << endl;   
+  //  cout << "Examining RV store just after RV init via gatherElementsInBeam" << endl;
   //  printRV();
   /*
   cerr << "Writing hmm.writeCurr..." << endl;
@@ -248,22 +253,25 @@ template <class MY, class MX, class YS, class B>
 
 
 template <class MY, class MX, class YS, class B>
-double SyntacticLanguageModelState<MY,MX,YS,B>::getProb() const {
-  
+double SyntacticLanguageModelState<MY,MX,YS,B>::getProb() const
+{
+
   return prob;
 }
 
 template <class MY, class MX, class YS, class B>
-double SyntacticLanguageModelState<MY,MX,YS,B>::getScore() const {
-  
+double SyntacticLanguageModelState<MY,MX,YS,B>::getScore() const
+{
+
   return score;
 }
 
 
 template <class MY, class MX, class YS, class B>
-  void SyntacticLanguageModelState<MY,MX,YS,B>::setScore(double score) {
+void SyntacticLanguageModelState<MY,MX,YS,B>::setScore(double score)
+{
+
 
-  
 
 
   this->prob = score;
diff --git a/moses/TargetPhrase.cpp b/moses/TargetPhrase.cpp
index 81b7adf44..f3cf9d1e1 100644
--- a/moses/TargetPhrase.cpp
+++ b/moses/TargetPhrase.cpp
@@ -38,10 +38,10 @@ using namespace std;
 namespace Moses
 {
 TargetPhrase::TargetPhrase( std::string out_string)
-:Phrase(0), m_fullScore(0.0), m_sourcePhrase(0)
-, m_alignTerm(&AlignmentInfoCollection::Instance().GetEmptyAlignmentInfo())
-, m_alignNonTerm(&AlignmentInfoCollection::Instance().GetEmptyAlignmentInfo())
-, m_lhsTarget(NULL)
+  :Phrase(0), m_fullScore(0.0), m_sourcePhrase(0)
+  , m_alignTerm(&AlignmentInfoCollection::Instance().GetEmptyAlignmentInfo())
+  , m_alignNonTerm(&AlignmentInfoCollection::Instance().GetEmptyAlignmentInfo())
+  , m_lhsTarget(NULL)
 {
 
   //ACAT
@@ -50,37 +50,36 @@ TargetPhrase::TargetPhrase( std::string out_string)
 }
 
 TargetPhrase::TargetPhrase()
-:Phrase()
-, m_fullScore(0.0)
-,m_sourcePhrase()
-, m_alignTerm(&AlignmentInfoCollection::Instance().GetEmptyAlignmentInfo())
-, m_alignNonTerm(&AlignmentInfoCollection::Instance().GetEmptyAlignmentInfo())
-, m_lhsTarget(NULL)
+  :Phrase()
+  , m_fullScore(0.0)
+  ,m_sourcePhrase()
+  , m_alignTerm(&AlignmentInfoCollection::Instance().GetEmptyAlignmentInfo())
+  , m_alignNonTerm(&AlignmentInfoCollection::Instance().GetEmptyAlignmentInfo())
+  , m_lhsTarget(NULL)
 {
 }
 
 TargetPhrase::TargetPhrase(const Phrase &phrase)
-: Phrase(phrase)
-, m_fullScore(0.0)
-, m_sourcePhrase()
-, m_alignTerm(&AlignmentInfoCollection::Instance().GetEmptyAlignmentInfo())
-, m_alignNonTerm(&AlignmentInfoCollection::Instance().GetEmptyAlignmentInfo())
-, m_lhsTarget(NULL)
+  : Phrase(phrase)
+  , m_fullScore(0.0)
+  , m_sourcePhrase()
+  , m_alignTerm(&AlignmentInfoCollection::Instance().GetEmptyAlignmentInfo())
+  , m_alignNonTerm(&AlignmentInfoCollection::Instance().GetEmptyAlignmentInfo())
+  , m_lhsTarget(NULL)
 {
 }
 
 TargetPhrase::TargetPhrase(const TargetPhrase &copy)
-: Phrase(copy)
-, m_fullScore(copy.m_fullScore)
-, m_sourcePhrase(copy.m_sourcePhrase)
-, m_alignTerm(copy.m_alignTerm)
-, m_alignNonTerm(copy.m_alignNonTerm)
-, m_scoreBreakdown(copy.m_scoreBreakdown)
+  : Phrase(copy)
+  , m_fullScore(copy.m_fullScore)
+  , m_sourcePhrase(copy.m_sourcePhrase)
+  , m_alignTerm(copy.m_alignTerm)
+  , m_alignNonTerm(copy.m_alignNonTerm)
+  , m_scoreBreakdown(copy.m_scoreBreakdown)
 {
   if (copy.m_lhsTarget) {
     m_lhsTarget = new Word(copy.m_lhsTarget);
-  }
-  else {
+  } else {
     m_lhsTarget = NULL;
   }
 
@@ -125,8 +124,8 @@ void TargetPhrase::Evaluate(const InputType &input)
   const std::vector<FeatureFunction*> &ffs = FeatureFunction::GetFeatureFunctions();
 
   for (size_t i = 0; i < ffs.size(); ++i) {
-	const FeatureFunction &ff = *ffs[i];
-	ff.Evaluate(input, m_scoreBreakdown);
+    const FeatureFunction &ff = *ffs[i];
+    ff.Evaluate(input, m_scoreBreakdown);
   }
 }
 
@@ -180,7 +179,7 @@ TargetPhrase *TargetPhrase::MergeNext(const TargetPhrase &inputPhrase) const
 
 void TargetPhrase::SetAlignmentInfo(const StringPiece &alignString)
 {
-	AlignmentInfo::CollType alignTerm, alignNonTerm;
+  AlignmentInfo::CollType alignTerm, alignNonTerm;
   for (util::TokenIter<util::AnyCharacter, true> token(alignString, util::AnyCharacter(" \t")); token; ++token) {
     util::TokenIter<util::SingleCharacter, false> dash(*token, util::SingleCharacter('-'));
 
@@ -194,11 +193,10 @@ void TargetPhrase::SetAlignmentInfo(const StringPiece &alignString)
 
 
     if (GetWord(targetPos).IsNonTerminal()) {
-    	alignNonTerm.insert(std::pair<size_t,size_t>(sourcePos, targetPos));
+      alignNonTerm.insert(std::pair<size_t,size_t>(sourcePos, targetPos));
+    } else {
+      alignTerm.insert(std::pair<size_t,size_t>(sourcePos, targetPos));
     }
-  	else {
-  		alignTerm.insert(std::pair<size_t,size_t>(sourcePos, targetPos));
-  	}
   }
   SetAlignTerm(alignTerm);
   SetAlignNonTerm(alignNonTerm);
@@ -207,15 +205,15 @@ void TargetPhrase::SetAlignmentInfo(const StringPiece &alignString)
 
 void TargetPhrase::SetAlignTerm(const AlignmentInfo::CollType &coll)
 {
-	const AlignmentInfo *alignmentInfo = AlignmentInfoCollection::Instance().Add(coll);
-	m_alignTerm = alignmentInfo;
+  const AlignmentInfo *alignmentInfo = AlignmentInfoCollection::Instance().Add(coll);
+  m_alignTerm = alignmentInfo;
 
 }
 
 void TargetPhrase::SetAlignNonTerm(const AlignmentInfo::CollType &coll)
 {
-	const AlignmentInfo *alignmentInfo = AlignmentInfoCollection::Instance().Add(coll);
-	m_alignNonTerm = alignmentInfo;
+  const AlignmentInfo *alignmentInfo = AlignmentInfoCollection::Instance().Add(coll);
+  m_alignNonTerm = alignmentInfo;
 }
 
 void TargetPhrase::SetSparseScore(const FeatureFunction* translationScoreProducer, const StringPiece &sparseString)
diff --git a/moses/TargetPhrase.h b/moses/TargetPhrase.h
index df876a00a..bb1c7c5a7 100644
--- a/moses/TargetPhrase.h
+++ b/moses/TargetPhrase.h
@@ -48,10 +48,10 @@ protected:
   float m_fullScore;
   ScoreComponentCollection m_scoreBreakdown;
 
-	// in case of confusion net, ptr to source phrase
-	Phrase m_sourcePhrase; 
-	const AlignmentInfo* m_alignTerm, *m_alignNonTerm;
-	const Word *m_lhsTarget;
+  // in case of confusion net, ptr to source phrase
+  Phrase m_sourcePhrase;
+  const AlignmentInfo* m_alignTerm, *m_alignNonTerm;
+  const Word *m_lhsTarget;
 
 public:
   TargetPhrase();
@@ -86,26 +86,28 @@ public:
     return m_fullScore;
   }
 
-	inline const ScoreComponentCollection &GetScoreBreakdown() const
-	{ return m_scoreBreakdown;	}
-  inline ScoreComponentCollection &GetScoreBreakdown()
-  { return m_scoreBreakdown;  }
+  inline const ScoreComponentCollection &GetScoreBreakdown() const {
+    return m_scoreBreakdown;
+  }
+  inline ScoreComponentCollection &GetScoreBreakdown() {
+    return m_scoreBreakdown;
+  }
 
   //TODO: Probably shouldn't copy this, but otherwise ownership is unclear
-	void SetSourcePhrase(const Phrase&  p) 
-	{
-		m_sourcePhrase=p;
-	}
-	const Phrase& GetSourcePhrase() const
-	{
-		return m_sourcePhrase;
-	}
-	
-	void SetTargetLHS(const Word *lhs)
-	{ 	m_lhsTarget = lhs; }
-	const Word &GetTargetLHS() const
-	{ return *m_lhsTarget; }
-	
+  void SetSourcePhrase(const Phrase&  p) {
+    m_sourcePhrase=p;
+  }
+  const Phrase& GetSourcePhrase() const {
+    return m_sourcePhrase;
+  }
+
+  void SetTargetLHS(const Word *lhs) {
+    m_lhsTarget = lhs;
+  }
+  const Word &GetTargetLHS() const {
+    return *m_lhsTarget;
+  }
+
   void SetAlignmentInfo(const StringPiece &alignString);
   void SetAlignTerm(const AlignmentInfo *alignTerm) {
     m_alignTerm = alignTerm;
@@ -117,11 +119,13 @@ public:
   void SetAlignTerm(const AlignmentInfo::CollType &coll);
   void SetAlignNonTerm(const AlignmentInfo::CollType &coll);
 
-  const AlignmentInfo &GetAlignTerm() const
-	{ return *m_alignTerm; }
-  const AlignmentInfo &GetAlignNonTerm() const
-	{ return *m_alignNonTerm; }
-	
+  const AlignmentInfo &GetAlignTerm() const {
+    return *m_alignTerm;
+  }
+  const AlignmentInfo &GetAlignNonTerm() const {
+    return *m_alignNonTerm;
+  }
+
 
   TO_STRING();
 };
@@ -131,10 +135,8 @@ std::ostream& operator<<(std::ostream&, const TargetPhrase&);
 /**
  * Hasher that looks at source and target phrase.
  **/
-struct TargetPhraseHasher 
-{
-  inline size_t operator()(const TargetPhrase& targetPhrase) const
-  {
+struct TargetPhraseHasher {
+  inline size_t operator()(const TargetPhrase& targetPhrase) const {
     size_t seed = 0;
     boost::hash_combine(seed, targetPhrase);
     boost::hash_combine(seed, targetPhrase.GetSourcePhrase());
@@ -145,14 +147,12 @@ struct TargetPhraseHasher
   }
 };
 
-struct TargetPhraseComparator
-{
-  inline bool operator()(const TargetPhrase& lhs, const TargetPhrase& rhs) const
-  {
+struct TargetPhraseComparator {
+  inline bool operator()(const TargetPhrase& lhs, const TargetPhrase& rhs) const {
     return lhs.Compare(rhs) == 0 &&
-      lhs.GetSourcePhrase().Compare(rhs.GetSourcePhrase()) == 0 &&
-      lhs.GetAlignTerm() == rhs.GetAlignTerm() &&
-      lhs.GetAlignNonTerm() == rhs.GetAlignNonTerm();
+           lhs.GetSourcePhrase().Compare(rhs.GetSourcePhrase()) == 0 &&
+           lhs.GetAlignTerm() == rhs.GetAlignTerm() &&
+           lhs.GetAlignNonTerm() == rhs.GetAlignNonTerm();
   }
 
 };
diff --git a/moses/TargetPhraseCollection.cpp b/moses/TargetPhraseCollection.cpp
index 78b63d852..88ce28eb6 100644
--- a/moses/TargetPhraseCollection.cpp
+++ b/moses/TargetPhraseCollection.cpp
@@ -59,8 +59,8 @@ void TargetPhraseCollection::Sort(bool adhereTableLimit, size_t tableLimit)
 {
   std::vector<TargetPhrase*>::iterator iterMiddle;
   iterMiddle = (tableLimit == 0 || m_collection.size() < tableLimit)
-             ? m_collection.end()
-             : m_collection.begin()+tableLimit;
+               ? m_collection.end()
+               : m_collection.begin()+tableLimit;
 
   std::partial_sort(m_collection.begin(), iterMiddle, m_collection.end(),
                     CompareTargetPhrase());
diff --git a/moses/TargetPhraseCollection.h b/moses/TargetPhraseCollection.h
index 4efb911fb..4207bccef 100644
--- a/moses/TargetPhraseCollection.h
+++ b/moses/TargetPhraseCollection.h
@@ -60,7 +60,9 @@ public:
     RemoveAllInColl(m_collection);
   }
 
-  const std::vector<TargetPhrase*> &GetCollection() const { return m_collection; }
+  const std::vector<TargetPhrase*> &GetCollection() const {
+    return m_collection;
+  }
 
   //! divide collection into 2 buckets using std::nth_element, the top & bottom according to table limit
   void NthElement(size_t tableLimit);
diff --git a/moses/Terminal.h b/moses/Terminal.h
index 6247d0b6c..e7d18676e 100644
--- a/moses/Terminal.h
+++ b/moses/Terminal.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2012 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -29,7 +29,7 @@ namespace Moses
 
 class TerminalHasher
 {
- public:
+public:
   // Generate a hash value for a word representing a terminal.  It's
   // assumed that the same subset of factors will be active for all words
   // that are hashed.
@@ -47,7 +47,7 @@ class TerminalHasher
 
 class TerminalEqualityPred
 {
- public:
+public:
   // Equality predicate for comparing words representing terminals.  As
   // with the hasher, it's assumed that all words will have the same
   // subset of active factors.
diff --git a/moses/ThreadPool.h b/moses/ThreadPool.h
index fad236a98..bf981a2da 100644
--- a/moses/ThreadPool.h
+++ b/moses/ThreadPool.h
@@ -42,7 +42,8 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 /**
   * Classes to implement a ThreadPool.
 **/
-namespace Moses {
+namespace Moses
+{
 
 /** A task to be executed by the ThreadPool
  */
@@ -50,7 +51,9 @@ class Task
 {
 public:
   virtual void Run() = 0;
-  virtual bool DeleteAfterExecution() { return true; }
+  virtual bool DeleteAfterExecution() {
+    return true;
+  }
   virtual ~Task() {}
 };
 
@@ -58,7 +61,7 @@ public:
 
 class ThreadPool
 {
- public:
+public:
   /**
    * Construct a thread pool of a fixed size.
    **/
@@ -82,7 +85,9 @@ class ThreadPool
   /**
    * Set maximum number of queued threads (otherwise Submit blocks)
    **/
-  void SetQueueLimit( size_t limit ) { m_queueLimit = limit; }
+  void SetQueueLimit( size_t limit ) {
+    m_queueLimit = limit;
+  }
 
 private:
   /**
@@ -109,7 +114,7 @@ public:
 #ifdef BOOST_HAS_PTHREADS
     pthread_t tid = pthread_self();
 #else
-	typedef void * pthread_t;
+    typedef void * pthread_t;
     pthread_t tid = 0;
 #endif
     std::cerr << "Executing " << m_id << " in thread id " << tid << std::endl;
diff --git a/moses/Timer.h b/moses/Timer.h
index deefa4a71..a6bd0e91a 100644
--- a/moses/Timer.h
+++ b/moses/Timer.h
@@ -33,7 +33,7 @@ public:
    * using 'start' or 'restart'
    */
   Timer() : running(false) {
-  start_time = 0;
+    start_time = 0;
   }
 
   void start(const char* msg = 0);
diff --git a/moses/TranslationModel/BilingualDynSuffixArray.cpp b/moses/TranslationModel/BilingualDynSuffixArray.cpp
index 824529b91..a47473de5 100644
--- a/moses/TranslationModel/BilingualDynSuffixArray.cpp
+++ b/moses/TranslationModel/BilingualDynSuffixArray.cpp
@@ -7,495 +7,494 @@
 
 using namespace std;
 
-namespace Moses {
+namespace Moses
+{
 
 BilingualDynSuffixArray::BilingualDynSuffixArray():
-	m_maxPhraseLength(StaticData::Instance().GetMaxPhraseLength()), 
-	m_maxSampleSize(20)
-{ 
-	m_srcSA = 0; 
-	m_trgSA = 0;
-	m_srcCorpus = new std::vector<wordID_t>();
-	m_trgCorpus = new std::vector<wordID_t>();
-	m_srcVocab = new Vocab(false);
-	m_trgVocab = new Vocab(false);
-	m_scoreCmp = 0;
+  m_maxPhraseLength(StaticData::Instance().GetMaxPhraseLength()),
+  m_maxSampleSize(20)
+{
+  m_srcSA = 0;
+  m_trgSA = 0;
+  m_srcCorpus = new std::vector<wordID_t>();
+  m_trgCorpus = new std::vector<wordID_t>();
+  m_srcVocab = new Vocab(false);
+  m_trgVocab = new Vocab(false);
+  m_scoreCmp = 0;
 }
 
-BilingualDynSuffixArray::~BilingualDynSuffixArray() 
+BilingualDynSuffixArray::~BilingualDynSuffixArray()
 {
-	if(m_srcSA) delete m_srcSA;
-	if(m_trgSA) delete m_trgSA;
-	if(m_srcVocab) delete m_srcVocab;
-	if(m_trgVocab) delete m_trgVocab;
-	if(m_srcCorpus) delete m_srcCorpus;
-	if(m_trgCorpus) delete m_trgCorpus;
-	if(m_scoreCmp) delete m_scoreCmp;
+  if(m_srcSA) delete m_srcSA;
+  if(m_trgSA) delete m_trgSA;
+  if(m_srcVocab) delete m_srcVocab;
+  if(m_trgVocab) delete m_trgVocab;
+  if(m_srcCorpus) delete m_srcCorpus;
+  if(m_trgCorpus) delete m_trgCorpus;
+  if(m_scoreCmp) delete m_scoreCmp;
 }
 
 bool BilingualDynSuffixArray::Load(
-	const std::vector<FactorType>& inputFactors,
-	const std::vector<FactorType>& outputFactors,
-	std::string source, std::string target, std::string alignments, 
-	const std::vector<float> &weight)
+  const std::vector<FactorType>& inputFactors,
+  const std::vector<FactorType>& outputFactors,
+  std::string source, std::string target, std::string alignments,
+  const std::vector<float> &weight)
 {
   m_inputFactors = inputFactors;
   m_outputFactors = outputFactors;
 
-	m_scoreCmp = new ScoresComp(weight);
-	InputFileStream sourceStrme(source);
-	InputFileStream targetStrme(target);
-	cerr << "Loading source corpus...\n";	
-	LoadCorpus(Input, sourceStrme, m_inputFactors, *m_srcCorpus, m_srcSntBreaks, m_srcVocab);
-	cerr << "Loading target corpus...\n";	
-	LoadCorpus(Output, targetStrme, m_outputFactors,*m_trgCorpus, m_trgSntBreaks, m_trgVocab);
-	CHECK(m_srcSntBreaks.size() == m_trgSntBreaks.size());
-
-	// build suffix arrays and auxilliary arrays
-	cerr << "Building Source Suffix Array...\n"; 
-	m_srcSA = new DynSuffixArray(m_srcCorpus); 
-	if(!m_srcSA) return false;
-	cerr << "Building Target Suffix Array...\n"; 
-	//m_trgSA = new DynSuffixArray(m_trgCorpus); 
-	//if(!m_trgSA) return false;
+  m_scoreCmp = new ScoresComp(weight);
+  InputFileStream sourceStrme(source);
+  InputFileStream targetStrme(target);
+  cerr << "Loading source corpus...\n";
+  LoadCorpus(Input, sourceStrme, m_inputFactors, *m_srcCorpus, m_srcSntBreaks, m_srcVocab);
+  cerr << "Loading target corpus...\n";
+  LoadCorpus(Output, targetStrme, m_outputFactors,*m_trgCorpus, m_trgSntBreaks, m_trgVocab);
+  CHECK(m_srcSntBreaks.size() == m_trgSntBreaks.size());
+
+  // build suffix arrays and auxilliary arrays
+  cerr << "Building Source Suffix Array...\n";
+  m_srcSA = new DynSuffixArray(m_srcCorpus);
+  if(!m_srcSA) return false;
+  cerr << "Building Target Suffix Array...\n";
+  //m_trgSA = new DynSuffixArray(m_trgCorpus);
+  //if(!m_trgSA) return false;
   cerr << "\t(Skipped. Not used)\n";
-	
-	InputFileStream alignStrme(alignments);
-	cerr << "Loading Alignment File...\n"; 
-	LoadRawAlignments(alignStrme);
-	//LoadAlignments(alignStrme);
+
+  InputFileStream alignStrme(alignments);
+  cerr << "Loading Alignment File...\n";
+  LoadRawAlignments(alignStrme);
+  //LoadAlignments(alignStrme);
   cerr << "Building frequent word cache...\n";
   CacheFreqWords();
-	return true;
+  return true;
 }
-  
+
 bool BilingualDynSuffixArray::LoadTM(
-                                   const std::vector<FactorType>& inputFactors,
-                                   const std::vector<FactorType>& outputFactors,
-                                   std::string source, std::string target, std::string alignments, 
-                                   const std::vector<float> &weight)
+  const std::vector<FactorType>& inputFactors,
+  const std::vector<FactorType>& outputFactors,
+  std::string source, std::string target, std::string alignments,
+  const std::vector<float> &weight)
 {
   m_inputFactors = inputFactors;
   m_outputFactors = outputFactors;
-  
+
   m_scoreCmp = new ScoresComp(weight);
   InputFileStream sourceStrme(source);
   InputFileStream targetStrme(target);
 
-  cerr << "Loading target corpus...\n";	
+  cerr << "Loading target corpus...\n";
   LoadCorpus(Output, targetStrme, m_outputFactors,*m_trgCorpus, m_trgSntBreaks, m_trgVocab);
-  
-  cerr << "Loading source corpus...\n";	
+
+  cerr << "Loading source corpus...\n";
   LoadCorpus(Input, sourceStrme, m_inputFactors, *m_srcCorpus, m_srcSntBreaks, m_srcVocab);
-  
+
   CHECK(m_srcSntBreaks.size() == m_trgSntBreaks.size());
-  
+
   // build suffix arrays and auxilliary arrays
-  cerr << "Building Source Suffix Array...\n"; 
-  m_srcSA = new DynSuffixArray(m_srcCorpus); 
+  cerr << "Building Source Suffix Array...\n";
+  m_srcSA = new DynSuffixArray(m_srcCorpus);
   if(!m_srcSA) return false;
-  cerr << "Building Target Suffix Array...\n"; 
-  //m_trgSA = new DynSuffixArray(m_trgCorpus); 
+  cerr << "Building Target Suffix Array...\n";
+  //m_trgSA = new DynSuffixArray(m_trgCorpus);
   //if(!m_trgSA) return false;
   cerr << "\t(Skipped. Not used)\n";
-  
+
   InputFileStream alignStrme(alignments);
-  cerr << "Loading Alignment File...\n"; 
+  cerr << "Loading Alignment File...\n";
   LoadRawAlignments(alignStrme);
   //LoadAlignments(alignStrme);
   cerr << "Building frequent word cache...\n";
   CacheFreqWords();
   return true;
-  
+
 }
 
-int BilingualDynSuffixArray::LoadRawAlignments(InputFileStream& align) 
+int BilingualDynSuffixArray::LoadRawAlignments(InputFileStream& align)
 {
-	// stores the alignments in the raw file format 
-	std::string line;
-	std::vector<int> vtmp;
+  // stores the alignments in the raw file format
+  std::string line;
+  std::vector<int> vtmp;
   int lineNum = 1;
-	while(getline(align, line)) {
+  while(getline(align, line)) {
     if (lineNum % 10000 == 0)
       cerr << lineNum;
-		Utils::splitToInt(line, vtmp, "- ");
-		CHECK(vtmp.size() % 2 == 0);
-		std::vector<short> vAlgn;	// store as short ints for memory
-        for (std::vector<int>::const_iterator itr = vtmp.begin();
-            itr != vtmp.end(); ++itr) {
-            vAlgn.push_back(short(*itr));
-        }
-		m_rawAlignments.push_back(vAlgn);
+    Utils::splitToInt(line, vtmp, "- ");
+    CHECK(vtmp.size() % 2 == 0);
+    std::vector<short> vAlgn;	// store as short ints for memory
+    for (std::vector<int>::const_iterator itr = vtmp.begin();
+         itr != vtmp.end(); ++itr) {
+      vAlgn.push_back(short(*itr));
+    }
+    m_rawAlignments.push_back(vAlgn);
     ++lineNum;
-	}
-	return m_rawAlignments.size();
+  }
+  return m_rawAlignments.size();
 }
-int BilingualDynSuffixArray::LoadRawAlignments(string& align) {
-  // stores the alignments in the raw file format 
+int BilingualDynSuffixArray::LoadRawAlignments(string& align)
+{
+  // stores the alignments in the raw file format
   vector<int> vtmp;
   Utils::splitToInt(align, vtmp, "- ");
   CHECK(vtmp.size() % 2 == 0);
   vector<short> vAlgn;  // store as short ints for memory
   for (std::vector<int>::const_iterator itr = vtmp.begin();
-      itr != vtmp.end(); ++itr) {
-      vAlgn.push_back(short(*itr));
+       itr != vtmp.end(); ++itr) {
+    vAlgn.push_back(short(*itr));
   }
   m_rawAlignments.push_back(vAlgn);
   return m_rawAlignments.size();
 }
 
-int BilingualDynSuffixArray::LoadAlignments(InputFileStream& align) 
+int BilingualDynSuffixArray::LoadAlignments(InputFileStream& align)
 {
-	std::string line;
-	std::vector<int> vtmp;
-	int sntIndex(0);
-	
-	while(getline(align, line)) {
-		Utils::splitToInt(line, vtmp, "- ");
-		CHECK(vtmp.size() % 2 == 0);
-	
-		int sourceSize = GetSourceSentenceSize(sntIndex);
-		int targetSize = GetTargetSentenceSize(sntIndex);
-
-		SentenceAlignment curSnt(sntIndex, sourceSize, targetSize); // initialize empty sentence 
-		for(int i=0; i < (int)vtmp.size(); i+=2) {
-		int sourcePos = vtmp[i];
-		int targetPos = vtmp[i+1];
-		CHECK(sourcePos < sourceSize);
-		CHECK(targetPos < targetSize);
-		
-			curSnt.alignedList[sourcePos].push_back(targetPos);	// list of target nodes for each source word 
-			curSnt.numberAligned[targetPos]++; // cnt of how many source words connect to this target word 
-		}
-		curSnt.srcSnt = m_srcCorpus + sntIndex;	// point source and target sentence
-		curSnt.trgSnt = m_trgCorpus + sntIndex; 
-		m_alignments.push_back(curSnt);
-	
-	sntIndex++;
-	}
-	return m_alignments.size();
+  std::string line;
+  std::vector<int> vtmp;
+  int sntIndex(0);
+
+  while(getline(align, line)) {
+    Utils::splitToInt(line, vtmp, "- ");
+    CHECK(vtmp.size() % 2 == 0);
+
+    int sourceSize = GetSourceSentenceSize(sntIndex);
+    int targetSize = GetTargetSentenceSize(sntIndex);
+
+    SentenceAlignment curSnt(sntIndex, sourceSize, targetSize); // initialize empty sentence
+    for(int i=0; i < (int)vtmp.size(); i+=2) {
+      int sourcePos = vtmp[i];
+      int targetPos = vtmp[i+1];
+      CHECK(sourcePos < sourceSize);
+      CHECK(targetPos < targetSize);
+
+      curSnt.alignedList[sourcePos].push_back(targetPos);	// list of target nodes for each source word
+      curSnt.numberAligned[targetPos]++; // cnt of how many source words connect to this target word
+    }
+    curSnt.srcSnt = m_srcCorpus + sntIndex;	// point source and target sentence
+    curSnt.trgSnt = m_trgCorpus + sntIndex;
+    m_alignments.push_back(curSnt);
+
+    sntIndex++;
+  }
+  return m_alignments.size();
 }
 
-SentenceAlignment BilingualDynSuffixArray::GetSentenceAlignment(const int sntIndex, bool trg2Src) const 
+SentenceAlignment BilingualDynSuffixArray::GetSentenceAlignment(const int sntIndex, bool trg2Src) const
 {
-	// retrieves the alignments in the format used by SentenceAlignment.Extract()
-	int sntGiven = trg2Src ? GetTargetSentenceSize(sntIndex) : GetSourceSentenceSize(sntIndex);
-	int sntExtract = trg2Src ? GetSourceSentenceSize(sntIndex) : GetTargetSentenceSize(sntIndex);
-	std::vector<short> alignment = m_rawAlignments.at(sntIndex);
-	SentenceAlignment curSnt(sntIndex, sntGiven, sntExtract); // initialize empty sentence 
-	for(size_t i=0; i < alignment.size(); i+=2) {
-		int sourcePos = alignment[i];
-		int targetPos = alignment[i+1];
-		if(trg2Src) {
-			curSnt.alignedList[targetPos].push_back(sourcePos);	// list of target nodes for each source word 
-			curSnt.numberAligned[sourcePos]++; // cnt of how many source words connect to this target word 
-		}
-		else {
-			curSnt.alignedList[sourcePos].push_back(targetPos);	// list of target nodes for each source word 
-			curSnt.numberAligned[targetPos]++; // cnt of how many source words connect to this target word 
-		}
-	}
-	curSnt.srcSnt = m_srcCorpus + sntIndex;	// point source and target sentence
-	curSnt.trgSnt = m_trgCorpus + sntIndex; 
-	
-	return curSnt;
+  // retrieves the alignments in the format used by SentenceAlignment.Extract()
+  int sntGiven = trg2Src ? GetTargetSentenceSize(sntIndex) : GetSourceSentenceSize(sntIndex);
+  int sntExtract = trg2Src ? GetSourceSentenceSize(sntIndex) : GetTargetSentenceSize(sntIndex);
+  std::vector<short> alignment = m_rawAlignments.at(sntIndex);
+  SentenceAlignment curSnt(sntIndex, sntGiven, sntExtract); // initialize empty sentence
+  for(size_t i=0; i < alignment.size(); i+=2) {
+    int sourcePos = alignment[i];
+    int targetPos = alignment[i+1];
+    if(trg2Src) {
+      curSnt.alignedList[targetPos].push_back(sourcePos);	// list of target nodes for each source word
+      curSnt.numberAligned[sourcePos]++; // cnt of how many source words connect to this target word
+    } else {
+      curSnt.alignedList[sourcePos].push_back(targetPos);	// list of target nodes for each source word
+      curSnt.numberAligned[targetPos]++; // cnt of how many source words connect to this target word
+    }
+  }
+  curSnt.srcSnt = m_srcCorpus + sntIndex;	// point source and target sentence
+  curSnt.trgSnt = m_trgCorpus + sntIndex;
+
+  return curSnt;
 }
 
-bool BilingualDynSuffixArray::ExtractPhrases(const int& sntIndex, const int& wordIndex,	
-	const int& sourceSize, std::vector<PhrasePair*>& phrasePairs, bool trg2Src) const 
+bool BilingualDynSuffixArray::ExtractPhrases(const int& sntIndex, const int& wordIndex,
+    const int& sourceSize, std::vector<PhrasePair*>& phrasePairs, bool trg2Src) const
 {
-	/* ExtractPhrases() can extract the matching phrases for both directions by using the trg2Src 
-	 * parameter */
-	SentenceAlignment curSnt = GetSentenceAlignment(sntIndex, trg2Src);
-	// get span of phrase in source sentence 
-	int beginSentence = m_srcSntBreaks[sntIndex];
-	int rightIdx = wordIndex - beginSentence
-			,leftIdx = rightIdx - sourceSize + 1;
-	return curSnt.Extract(m_maxPhraseLength, phrasePairs, leftIdx, rightIdx); // extract all phrase Alignments in sentence
+  /* ExtractPhrases() can extract the matching phrases for both directions by using the trg2Src
+   * parameter */
+  SentenceAlignment curSnt = GetSentenceAlignment(sntIndex, trg2Src);
+  // get span of phrase in source sentence
+  int beginSentence = m_srcSntBreaks[sntIndex];
+  int rightIdx = wordIndex - beginSentence
+                 ,leftIdx = rightIdx - sourceSize + 1;
+  return curSnt.Extract(m_maxPhraseLength, phrasePairs, leftIdx, rightIdx); // extract all phrase Alignments in sentence
 }
 
 int BilingualDynSuffixArray::LoadCorpus(FactorDirection direction, InputFileStream& corpus, const FactorList& factors,
-	std::vector<wordID_t>& cArray, std::vector<wordID_t>& sntArray,
-  Vocab* vocab) 
+                                        std::vector<wordID_t>& cArray, std::vector<wordID_t>& sntArray,
+                                        Vocab* vocab)
 {
-	std::string line, word;
-	int sntIdx(0);
+  std::string line, word;
+  int sntIdx(0);
 //	corpus.seekg(0); Seems needless -> commented out to allow loading of gzipped corpora (gzfilebuf doesn't support seeking).
-	const std::string& factorDelimiter = StaticData::Instance().GetFactorDelimiter();
-	while(getline(corpus, line)) {
-		sntArray.push_back(sntIdx);
-		Phrase phrase(ARRAY_SIZE_INCR);
-		// parse phrase
-		phrase.CreateFromString(direction, factors, line, factorDelimiter, NULL);
-		// store words in vocabulary and corpus
-		for( size_t i = 0; i < phrase.GetSize(); ++i) {
-			cArray.push_back( vocab->GetWordID(phrase.GetWord(i)) );
-		}
-		sntIdx += phrase.GetSize();					
-	}
-	//cArray.push_back(vocab->GetkOOVWordID);	// signify end of corpus 
+  const std::string& factorDelimiter = StaticData::Instance().GetFactorDelimiter();
+  while(getline(corpus, line)) {
+    sntArray.push_back(sntIdx);
+    Phrase phrase(ARRAY_SIZE_INCR);
+    // parse phrase
+    phrase.CreateFromString(direction, factors, line, factorDelimiter, NULL);
+    // store words in vocabulary and corpus
+    for( size_t i = 0; i < phrase.GetSize(); ++i) {
+      cArray.push_back( vocab->GetWordID(phrase.GetWord(i)) );
+    }
+    sntIdx += phrase.GetSize();
+  }
+  //cArray.push_back(vocab->GetkOOVWordID);	// signify end of corpus
   vocab->MakeClosed(); // avoid adding words
-	return cArray.size();
+  return cArray.size();
 }
 
-bool BilingualDynSuffixArray::GetLocalVocabIDs(const Phrase& src, SAPhrase &output) const 
+bool BilingualDynSuffixArray::GetLocalVocabIDs(const Phrase& src, SAPhrase &output) const
 {
-	// looks up the SA vocab ids for the current src phrase
-	size_t phraseSize = src.GetSize();
-	for (size_t pos = 0; pos < phraseSize; ++pos) {
-		const Word &word = src.GetWord(pos);
-		wordID_t arrayId = m_srcVocab->GetWordID(word);
-		if (arrayId == m_srcVocab->GetkOOVWordID())
-		{ // oov
-				return false;
-		}
-		else
-		{
-			output.SetId(pos, arrayId);
-			//cerr << arrayId << " ";
-		}
-	}
-	return true;
+  // looks up the SA vocab ids for the current src phrase
+  size_t phraseSize = src.GetSize();
+  for (size_t pos = 0; pos < phraseSize; ++pos) {
+    const Word &word = src.GetWord(pos);
+    wordID_t arrayId = m_srcVocab->GetWordID(word);
+    if (arrayId == m_srcVocab->GetkOOVWordID()) {
+      // oov
+      return false;
+    } else {
+      output.SetId(pos, arrayId);
+      //cerr << arrayId << " ";
+    }
+  }
+  return true;
 }
 
-pair<float, float> BilingualDynSuffixArray::GetLexicalWeight(const PhrasePair& phrasepair) const 
+pair<float, float> BilingualDynSuffixArray::GetLexicalWeight(const PhrasePair& phrasepair) const
 {
-	//return pair<float, float>(1, 1);
-	float srcLexWeight(1.0), trgLexWeight(1.0);
-	std::map<pair<wordID_t, wordID_t>, float> targetProbs; // collect sum of target probs given source words
-	//const SentenceAlignment& alignment = m_alignments[phrasepair.m_sntIndex];
-	const SentenceAlignment& alignment = GetSentenceAlignment(phrasepair.m_sntIndex);
-	std::map<pair<wordID_t, wordID_t>, pair<float, float> >::const_iterator itrCache; 
-	// for each source word
-	for(int srcIdx = phrasepair.m_startSource; srcIdx <= phrasepair.m_endSource; ++srcIdx) {
-		float srcSumPairProbs(0);
-		wordID_t srcWord = m_srcCorpus->at(srcIdx + m_srcSntBreaks[phrasepair.m_sntIndex]);	// localIDs
-		const std::vector<int>& srcWordAlignments = alignment.alignedList.at(srcIdx);
+  //return pair<float, float>(1, 1);
+  float srcLexWeight(1.0), trgLexWeight(1.0);
+  std::map<pair<wordID_t, wordID_t>, float> targetProbs; // collect sum of target probs given source words
+  //const SentenceAlignment& alignment = m_alignments[phrasepair.m_sntIndex];
+  const SentenceAlignment& alignment = GetSentenceAlignment(phrasepair.m_sntIndex);
+  std::map<pair<wordID_t, wordID_t>, pair<float, float> >::const_iterator itrCache;
+  // for each source word
+  for(int srcIdx = phrasepair.m_startSource; srcIdx <= phrasepair.m_endSource; ++srcIdx) {
+    float srcSumPairProbs(0);
+    wordID_t srcWord = m_srcCorpus->at(srcIdx + m_srcSntBreaks[phrasepair.m_sntIndex]);	// localIDs
+    const std::vector<int>& srcWordAlignments = alignment.alignedList.at(srcIdx);
     // for each target word aligned to this source word in this alignment
-		if(srcWordAlignments.size() == 0) { // get p(NULL|src)
-			pair<wordID_t, wordID_t> wordpair = make_pair(srcWord, m_srcVocab->GetkOOVWordID());
-			itrCache = m_wordPairCache.find(wordpair);
-			if(itrCache == m_wordPairCache.end()) { // if not in cache
-				CacheWordProbs(srcWord);
-				itrCache = m_wordPairCache.find(wordpair); // search cache again
-			}
-			CHECK(itrCache != m_wordPairCache.end());
-			srcSumPairProbs += itrCache->second.first;
-			targetProbs[wordpair] = itrCache->second.second;
-		}
-		else { // extract p(trg|src) 
-			for(size_t i = 0; i < srcWordAlignments.size(); ++i) { // for each aligned word
-				int trgIdx = srcWordAlignments[i];
-				wordID_t trgWord = m_trgCorpus->at(trgIdx + m_trgSntBreaks[phrasepair.m_sntIndex]);
-				// get probability of this source->target word pair
-				pair<wordID_t, wordID_t> wordpair = make_pair(srcWord, trgWord);
-				itrCache = m_wordPairCache.find(wordpair);
-				if(itrCache == m_wordPairCache.end()) { // if not in cache
+    if(srcWordAlignments.size() == 0) { // get p(NULL|src)
+      pair<wordID_t, wordID_t> wordpair = make_pair(srcWord, m_srcVocab->GetkOOVWordID());
+      itrCache = m_wordPairCache.find(wordpair);
+      if(itrCache == m_wordPairCache.end()) { // if not in cache
+        CacheWordProbs(srcWord);
+        itrCache = m_wordPairCache.find(wordpair); // search cache again
+      }
+      CHECK(itrCache != m_wordPairCache.end());
+      srcSumPairProbs += itrCache->second.first;
+      targetProbs[wordpair] = itrCache->second.second;
+    } else { // extract p(trg|src)
+      for(size_t i = 0; i < srcWordAlignments.size(); ++i) { // for each aligned word
+        int trgIdx = srcWordAlignments[i];
+        wordID_t trgWord = m_trgCorpus->at(trgIdx + m_trgSntBreaks[phrasepair.m_sntIndex]);
+        // get probability of this source->target word pair
+        pair<wordID_t, wordID_t> wordpair = make_pair(srcWord, trgWord);
+        itrCache = m_wordPairCache.find(wordpair);
+        if(itrCache == m_wordPairCache.end()) { // if not in cache
           CacheWordProbs(srcWord);
-					itrCache = m_wordPairCache.find(wordpair); // search cache again
-				}
-				CHECK(itrCache != m_wordPairCache.end());
-				srcSumPairProbs += itrCache->second.first;
-				targetProbs[wordpair] = itrCache->second.second;	
-			} 
-		}
-		float srcNormalizer = srcWordAlignments.size() < 2 ? 1.0 : 1.0 / float(srcWordAlignments.size());
-		srcLexWeight *= (srcNormalizer * srcSumPairProbs);	
-	}	// end for each source word
-	for(int trgIdx = phrasepair.m_startTarget; trgIdx <= phrasepair.m_endTarget; ++trgIdx) {
-		float trgSumPairProbs(0);
-		wordID_t trgWord = m_trgCorpus->at(trgIdx + m_trgSntBreaks[phrasepair.m_sntIndex]);
-        for (std::map<pair<wordID_t, wordID_t>, float>::const_iterator trgItr
-                = targetProbs.begin(); trgItr != targetProbs.end(); ++trgItr) {
-			if(trgItr->first.second == trgWord) 
-				trgSumPairProbs += trgItr->second;
+          itrCache = m_wordPairCache.find(wordpair); // search cache again
         }
-		if(trgSumPairProbs == 0) continue;	// currently don't store target-side SA
-		int noAligned = alignment.numberAligned.at(trgIdx);
-		float trgNormalizer = noAligned < 2 ? 1.0 : 1.0 / float(noAligned);
-		trgLexWeight *= (trgNormalizer * trgSumPairProbs);
-	}
-	// TODO::Need to get p(NULL|trg)
-	return pair<float, float>(srcLexWeight, trgLexWeight);
+        CHECK(itrCache != m_wordPairCache.end());
+        srcSumPairProbs += itrCache->second.first;
+        targetProbs[wordpair] = itrCache->second.second;
+      }
+    }
+    float srcNormalizer = srcWordAlignments.size() < 2 ? 1.0 : 1.0 / float(srcWordAlignments.size());
+    srcLexWeight *= (srcNormalizer * srcSumPairProbs);
+  }	// end for each source word
+  for(int trgIdx = phrasepair.m_startTarget; trgIdx <= phrasepair.m_endTarget; ++trgIdx) {
+    float trgSumPairProbs(0);
+    wordID_t trgWord = m_trgCorpus->at(trgIdx + m_trgSntBreaks[phrasepair.m_sntIndex]);
+    for (std::map<pair<wordID_t, wordID_t>, float>::const_iterator trgItr
+         = targetProbs.begin(); trgItr != targetProbs.end(); ++trgItr) {
+      if(trgItr->first.second == trgWord)
+        trgSumPairProbs += trgItr->second;
+    }
+    if(trgSumPairProbs == 0) continue;	// currently don't store target-side SA
+    int noAligned = alignment.numberAligned.at(trgIdx);
+    float trgNormalizer = noAligned < 2 ? 1.0 : 1.0 / float(noAligned);
+    trgLexWeight *= (trgNormalizer * trgSumPairProbs);
+  }
+  // TODO::Need to get p(NULL|trg)
+  return pair<float, float>(srcLexWeight, trgLexWeight);
 }
-void BilingualDynSuffixArray::CacheFreqWords() const {
+void BilingualDynSuffixArray::CacheFreqWords() const
+{
   std::multimap<int, wordID_t> wordCnts;
   // for each source word in vocab
-  Vocab::Word2Id::const_iterator it;  
+  Vocab::Word2Id::const_iterator it;
   for(it = m_srcVocab->VocabStart(); it != m_srcVocab->VocabEnd(); ++it) {
     // get its frequency
     wordID_t srcWord = it->second;
     std::vector<wordID_t> sword(1, srcWord), wrdIndices;
     m_srcSA->GetCorpusIndex(&sword, &wrdIndices);
-    if(wrdIndices.size() >= 1000) { // min count 
+    if(wrdIndices.size() >= 1000) { // min count
       wordCnts.insert(make_pair(wrdIndices.size(), srcWord));
     }
   }
   int numSoFar(0);
-	std::multimap<int, wordID_t>::reverse_iterator ritr;
-  for(ritr = wordCnts.rbegin(); ritr != wordCnts.rend(); ++ritr) { 
+  std::multimap<int, wordID_t>::reverse_iterator ritr;
+  for(ritr = wordCnts.rbegin(); ritr != wordCnts.rend(); ++ritr) {
     m_freqWordsCached.insert(ritr->second);
     CacheWordProbs(ritr->second);
     if(++numSoFar == 50) break; // get top counts
   }
   cerr << "\tCached " << m_freqWordsCached.size() << " source words\n";
 }
-void BilingualDynSuffixArray::CacheWordProbs(wordID_t srcWord) const 
+void BilingualDynSuffixArray::CacheWordProbs(wordID_t srcWord) const
 {
-	std::map<wordID_t, int> counts;
-	std::vector<wordID_t> sword(1, srcWord), wrdIndices;
-	bool ret = m_srcSA->GetCorpusIndex(&sword, &wrdIndices);
-	CHECK(ret);
-	std::vector<int> sntIndexes = GetSntIndexes(wrdIndices, 1, m_srcSntBreaks);	
-	float denom(0);
-	// for each occurrence of this word 
-	for(size_t snt = 0; snt < sntIndexes.size(); ++snt) {
-		int sntIdx = sntIndexes.at(snt); // get corpus index for sentence
-		CHECK(sntIdx != -1); 
-		int srcWrdSntIdx = wrdIndices.at(snt) - m_srcSntBreaks.at(sntIdx); // get word index in sentence
-		const std::vector<int> srcAlg = GetSentenceAlignment(sntIdx).alignedList.at(srcWrdSntIdx); // list of target words for this source word
-		if(srcAlg.size() == 0) {
-			++counts[m_srcVocab->GetkOOVWordID()]; // if not alligned then align to NULL word
-			++denom;
-		}
-		else { //get target words aligned to srcword in this sentence
-			for(size_t i=0; i < srcAlg.size(); ++i) {
-				wordID_t trgWord = m_trgCorpus->at(srcAlg[i] + m_trgSntBreaks[sntIdx]);
-				++counts[trgWord];
-				++denom;
-			}
-		}
-	}
-	// now we've gotten counts of all target words aligned to this source word
-	// get probs and cache all pairs
-	for(std::map<wordID_t, int>::const_iterator itrCnt = counts.begin();
-			itrCnt != counts.end(); ++itrCnt) {
-		pair<wordID_t, wordID_t> wordPair = make_pair(srcWord, itrCnt->first);
-		float srcTrgPrb = float(itrCnt->second) / float(denom);	// gives p(src->trg)
-		float trgSrcPrb = float(itrCnt->second) / float(counts.size()); // gives p(trg->src) 
-		m_wordPairCache[wordPair] = pair<float, float>(srcTrgPrb, trgSrcPrb);
-	}
+  std::map<wordID_t, int> counts;
+  std::vector<wordID_t> sword(1, srcWord), wrdIndices;
+  bool ret = m_srcSA->GetCorpusIndex(&sword, &wrdIndices);
+  CHECK(ret);
+  std::vector<int> sntIndexes = GetSntIndexes(wrdIndices, 1, m_srcSntBreaks);
+  float denom(0);
+  // for each occurrence of this word
+  for(size_t snt = 0; snt < sntIndexes.size(); ++snt) {
+    int sntIdx = sntIndexes.at(snt); // get corpus index for sentence
+    CHECK(sntIdx != -1);
+    int srcWrdSntIdx = wrdIndices.at(snt) - m_srcSntBreaks.at(sntIdx); // get word index in sentence
+    const std::vector<int> srcAlg = GetSentenceAlignment(sntIdx).alignedList.at(srcWrdSntIdx); // list of target words for this source word
+    if(srcAlg.size() == 0) {
+      ++counts[m_srcVocab->GetkOOVWordID()]; // if not alligned then align to NULL word
+      ++denom;
+    } else { //get target words aligned to srcword in this sentence
+      for(size_t i=0; i < srcAlg.size(); ++i) {
+        wordID_t trgWord = m_trgCorpus->at(srcAlg[i] + m_trgSntBreaks[sntIdx]);
+        ++counts[trgWord];
+        ++denom;
+      }
+    }
+  }
+  // now we've gotten counts of all target words aligned to this source word
+  // get probs and cache all pairs
+  for(std::map<wordID_t, int>::const_iterator itrCnt = counts.begin();
+      itrCnt != counts.end(); ++itrCnt) {
+    pair<wordID_t, wordID_t> wordPair = make_pair(srcWord, itrCnt->first);
+    float srcTrgPrb = float(itrCnt->second) / float(denom);	// gives p(src->trg)
+    float trgSrcPrb = float(itrCnt->second) / float(counts.size()); // gives p(trg->src)
+    m_wordPairCache[wordPair] = pair<float, float>(srcTrgPrb, trgSrcPrb);
+  }
 }
 
-SAPhrase BilingualDynSuffixArray::TrgPhraseFromSntIdx(const PhrasePair& phrasepair) const 
+SAPhrase BilingualDynSuffixArray::TrgPhraseFromSntIdx(const PhrasePair& phrasepair) const
 {
-	// takes sentence indexes and looks up vocab IDs
-	SAPhrase phraseIds(phrasepair.GetTargetSize());
-	int sntIndex = phrasepair.m_sntIndex;
-	int id(-1), pos(0);
-	for(int i=phrasepair.m_startTarget; i <= phrasepair.m_endTarget; ++i) { // look up trg words
-		id = m_trgCorpus->at(m_trgSntBreaks[sntIndex] + i);
-		phraseIds.SetId(pos++, id);
-	}
-	return phraseIds;
+  // takes sentence indexes and looks up vocab IDs
+  SAPhrase phraseIds(phrasepair.GetTargetSize());
+  int sntIndex = phrasepair.m_sntIndex;
+  int id(-1), pos(0);
+  for(int i=phrasepair.m_startTarget; i <= phrasepair.m_endTarget; ++i) { // look up trg words
+    id = m_trgCorpus->at(m_trgSntBreaks[sntIndex] + i);
+    phraseIds.SetId(pos++, id);
+  }
+  return phraseIds;
 }
-	
+
 TargetPhrase* BilingualDynSuffixArray::GetMosesFactorIDs(const SAPhrase& phrase, const Phrase& sourcePhrase) const
 {
-	TargetPhrase* targetPhrase = new TargetPhrase();
-	for(size_t i=0; i < phrase.words.size(); ++i) { // look up trg words
-		Word& word = m_trgVocab->GetWord( phrase.words[i]);
-		CHECK(word != m_trgVocab->GetkOOVWord());
-		targetPhrase->AddWord(word);
-	}
-	targetPhrase->SetSourcePhrase(sourcePhrase);
-	// scoring
-	return targetPhrase;
+  TargetPhrase* targetPhrase = new TargetPhrase();
+  for(size_t i=0; i < phrase.words.size(); ++i) { // look up trg words
+    Word& word = m_trgVocab->GetWord( phrase.words[i]);
+    CHECK(word != m_trgVocab->GetkOOVWord());
+    targetPhrase->AddWord(word);
+  }
+  targetPhrase->SetSourcePhrase(sourcePhrase);
+  // scoring
+  return targetPhrase;
 }
 
-void BilingualDynSuffixArray::GetTargetPhrasesByLexicalWeight(const Phrase& src, std::vector< std::pair<Scores, TargetPhrase*> > & target) const 
+void BilingualDynSuffixArray::GetTargetPhrasesByLexicalWeight(const Phrase& src, std::vector< std::pair<Scores, TargetPhrase*> > & target) const
 {
   //cerr << "phrase is \"" << src << endl;
-	size_t sourceSize = src.GetSize();
-	SAPhrase localIDs(sourceSize);
-	if(!GetLocalVocabIDs(src, localIDs)) return; 
-	float totalTrgPhrases(0); 
-	std::map<SAPhrase, int> phraseCounts;
-  //std::map<SAPhrase, PhrasePair> phraseColl; // (one of) the word indexes this phrase was taken from 
-	std::map<SAPhrase, pair<float, float> > lexicalWeights;
-	std::map<SAPhrase, pair<float, float> >::iterator itrLexW;
-	std::vector<unsigned> wrdIndices;	
-	// extract sentence IDs from SA and return rightmost index of phrases
-	if(!m_srcSA->GetCorpusIndex(&(localIDs.words), &wrdIndices)) return;
+  size_t sourceSize = src.GetSize();
+  SAPhrase localIDs(sourceSize);
+  if(!GetLocalVocabIDs(src, localIDs)) return;
+  float totalTrgPhrases(0);
+  std::map<SAPhrase, int> phraseCounts;
+  //std::map<SAPhrase, PhrasePair> phraseColl; // (one of) the word indexes this phrase was taken from
+  std::map<SAPhrase, pair<float, float> > lexicalWeights;
+  std::map<SAPhrase, pair<float, float> >::iterator itrLexW;
+  std::vector<unsigned> wrdIndices;
+  // extract sentence IDs from SA and return rightmost index of phrases
+  if(!m_srcSA->GetCorpusIndex(&(localIDs.words), &wrdIndices)) return;
   SampleSelection(wrdIndices);
-	std::vector<int> sntIndexes = GetSntIndexes(wrdIndices, sourceSize, m_srcSntBreaks);	
-	// for each sentence with this phrase
-	for(size_t snt = 0; snt < sntIndexes.size(); ++snt) {
-		std::vector<PhrasePair*> phrasePairs; // to store all phrases possible from current sentence
-		int sntIndex = sntIndexes.at(snt); // get corpus index for sentence
-		if(sntIndex == -1) continue;	// bad flag set by GetSntIndexes()
-		ExtractPhrases(sntIndex, wrdIndices[snt], sourceSize, phrasePairs); 
-		//cerr << "extracted " << phrasePairs.size() << endl;
-		totalTrgPhrases += phrasePairs.size(); // keep track of count of each extracted phrase pair		
-		std::vector<PhrasePair*>::iterator iterPhrasePair;
-		for (iterPhrasePair = phrasePairs.begin(); iterPhrasePair != phrasePairs.end(); ++iterPhrasePair) {
-			SAPhrase phrase = TrgPhraseFromSntIdx(**iterPhrasePair);
-			phraseCounts[phrase]++;	// count each unique phrase
-      // NOTE::Correct but slow to extract lexical weight here. could do 
+  std::vector<int> sntIndexes = GetSntIndexes(wrdIndices, sourceSize, m_srcSntBreaks);
+  // for each sentence with this phrase
+  for(size_t snt = 0; snt < sntIndexes.size(); ++snt) {
+    std::vector<PhrasePair*> phrasePairs; // to store all phrases possible from current sentence
+    int sntIndex = sntIndexes.at(snt); // get corpus index for sentence
+    if(sntIndex == -1) continue;	// bad flag set by GetSntIndexes()
+    ExtractPhrases(sntIndex, wrdIndices[snt], sourceSize, phrasePairs);
+    //cerr << "extracted " << phrasePairs.size() << endl;
+    totalTrgPhrases += phrasePairs.size(); // keep track of count of each extracted phrase pair
+    std::vector<PhrasePair*>::iterator iterPhrasePair;
+    for (iterPhrasePair = phrasePairs.begin(); iterPhrasePair != phrasePairs.end(); ++iterPhrasePair) {
+      SAPhrase phrase = TrgPhraseFromSntIdx(**iterPhrasePair);
+      phraseCounts[phrase]++;	// count each unique phrase
+      // NOTE::Correct but slow to extract lexical weight here. could do
       // it later for only the top phrases chosen by phrase prob p(e|f)
-			pair<float, float> lexWeight = GetLexicalWeight(**iterPhrasePair);	// get lexical weighting for this phrase pair 
-			itrLexW = lexicalWeights.find(phrase); // check if phrase already has lexical weight attached
-			if((itrLexW != lexicalWeights.end()) && (itrLexW->second.first < lexWeight.first)) 
-				itrLexW->second = lexWeight;	// if this lex weight is greater save it
-			else lexicalWeights[phrase] = lexWeight; // else save 
-		}
-		// done with sentence. delete SA phrase pairs
-		RemoveAllInColl(phrasePairs);
-	} // done with all sentences
-	// convert to moses phrase pairs
-	std::map<SAPhrase, int>::const_iterator iterPhrases; 
-	std::multimap<Scores, const SAPhrase*, ScoresComp> phraseScores (*m_scoreCmp);
-	// get scores of all phrases
-	for(iterPhrases = phraseCounts.begin(); iterPhrases != phraseCounts.end(); ++iterPhrases) {
-		float trg2SrcMLE = float(iterPhrases->second) / totalTrgPhrases;
-		itrLexW = lexicalWeights.find(iterPhrases->first);
-		CHECK(itrLexW != lexicalWeights.end());
-		Scores scoreVector(3);
-		scoreVector[0] = trg2SrcMLE; 
-		scoreVector[1] = itrLexW->second.first;
-		scoreVector[2] = 2.718; // exp(1); 
-		phraseScores.insert(make_pair(scoreVector, &iterPhrases->first));
-	}
-	// return top scoring phrases
-	std::multimap<Scores, const SAPhrase*, ScoresComp>::reverse_iterator ritr;
-	for(ritr = phraseScores.rbegin(); ritr != phraseScores.rend(); ++ritr) {
-		Scores scoreVector = ritr->first;
-		TargetPhrase *targetPhrase = GetMosesFactorIDs(*ritr->second, src);
-		target.push_back(make_pair( scoreVector, targetPhrase));
-		if(target.size() == m_maxSampleSize) break;
-	}
+      pair<float, float> lexWeight = GetLexicalWeight(**iterPhrasePair);	// get lexical weighting for this phrase pair
+      itrLexW = lexicalWeights.find(phrase); // check if phrase already has lexical weight attached
+      if((itrLexW != lexicalWeights.end()) && (itrLexW->second.first < lexWeight.first))
+        itrLexW->second = lexWeight;	// if this lex weight is greater save it
+      else lexicalWeights[phrase] = lexWeight; // else save
+    }
+    // done with sentence. delete SA phrase pairs
+    RemoveAllInColl(phrasePairs);
+  } // done with all sentences
+  // convert to moses phrase pairs
+  std::map<SAPhrase, int>::const_iterator iterPhrases;
+  std::multimap<Scores, const SAPhrase*, ScoresComp> phraseScores (*m_scoreCmp);
+  // get scores of all phrases
+  for(iterPhrases = phraseCounts.begin(); iterPhrases != phraseCounts.end(); ++iterPhrases) {
+    float trg2SrcMLE = float(iterPhrases->second) / totalTrgPhrases;
+    itrLexW = lexicalWeights.find(iterPhrases->first);
+    CHECK(itrLexW != lexicalWeights.end());
+    Scores scoreVector(3);
+    scoreVector[0] = trg2SrcMLE;
+    scoreVector[1] = itrLexW->second.first;
+    scoreVector[2] = 2.718; // exp(1);
+    phraseScores.insert(make_pair(scoreVector, &iterPhrases->first));
+  }
+  // return top scoring phrases
+  std::multimap<Scores, const SAPhrase*, ScoresComp>::reverse_iterator ritr;
+  for(ritr = phraseScores.rbegin(); ritr != phraseScores.rend(); ++ritr) {
+    Scores scoreVector = ritr->first;
+    TargetPhrase *targetPhrase = GetMosesFactorIDs(*ritr->second, src);
+    target.push_back(make_pair( scoreVector, targetPhrase));
+    if(target.size() == m_maxSampleSize) break;
+  }
 }
 
-std::vector<int> BilingualDynSuffixArray::GetSntIndexes(std::vector<unsigned>& wrdIndices, 
-	const int sourceSize, const std::vector<unsigned>& sntBreaks) const 
+std::vector<int> BilingualDynSuffixArray::GetSntIndexes(std::vector<unsigned>& wrdIndices,
+    const int sourceSize, const std::vector<unsigned>& sntBreaks) const
 {
-	std::vector<unsigned>::const_iterator vit;
-	std::vector<int> sntIndexes; 
-	for(size_t i=0; i < wrdIndices.size(); ++i) {
-		vit = std::upper_bound(sntBreaks.begin(), sntBreaks.end(), wrdIndices[i]);
-		int index = int(vit - sntBreaks.begin()) - 1;
-		// check for phrases that cross sentence boundaries
-		if(wrdIndices[i] - sourceSize + 1 < sntBreaks.at(index)) 
-			sntIndexes.push_back(-1);	// set bad flag
-		else
-			sntIndexes.push_back(index);	// store the index of the sentence in the corpus
-	}
-	return sntIndexes;
+  std::vector<unsigned>::const_iterator vit;
+  std::vector<int> sntIndexes;
+  for(size_t i=0; i < wrdIndices.size(); ++i) {
+    vit = std::upper_bound(sntBreaks.begin(), sntBreaks.end(), wrdIndices[i]);
+    int index = int(vit - sntBreaks.begin()) - 1;
+    // check for phrases that cross sentence boundaries
+    if(wrdIndices[i] - sourceSize + 1 < sntBreaks.at(index))
+      sntIndexes.push_back(-1);	// set bad flag
+    else
+      sntIndexes.push_back(index);	// store the index of the sentence in the corpus
+  }
+  return sntIndexes;
 }
 
 int BilingualDynSuffixArray::SampleSelection(std::vector<unsigned>& sample,
-  int sampleSize) const 
+    int sampleSize) const
 {
   // only use top 'sampleSize' number of samples
-   if(sample.size() > (size_t)sampleSize)
-     sample.erase(sample.begin()+sampleSize, sample.end());
-   return sample.size(); 
+  if(sample.size() > (size_t)sampleSize)
+    sample.erase(sample.begin()+sampleSize, sample.end());
+  return sample.size();
 }
 
-void BilingualDynSuffixArray::addSntPair(string& source, string& target, string& alignment) {
+void BilingualDynSuffixArray::addSntPair(string& source, string& target, string& alignment)
+{
   vuint_t srcFactor, trgFactor;
   cerr << "source, target, alignment = " << source << ", " << target << ", " << alignment << endl;
-	const std::string& factorDelimiter = StaticData::Instance().GetFactorDelimiter();
+  const std::string& factorDelimiter = StaticData::Instance().GetFactorDelimiter();
   const unsigned oldSrcCrpSize = m_srcCorpus->size(), oldTrgCrpSize = m_trgCorpus->size();
   cerr << "old source corpus size = " << oldSrcCrpSize << "\told target size = " << oldTrgCrpSize << endl;
   Phrase sphrase(ARRAY_SIZE_INCR);
@@ -511,7 +510,7 @@ void BilingualDynSuffixArray::addSntPair(string& source, string& target, string&
     cerr << "srcFactor[" << (srcFactor.size() - 1) << "] = " << srcFactor.back() << endl;
     m_srcCorpus->push_back(srcFactor.back()); // add word to corpus
   }
-  m_srcSntBreaks.push_back(oldSrcCrpSize); // former end of corpus is index of new sentence 
+  m_srcSntBreaks.push_back(oldSrcCrpSize); // former end of corpus is index of new sentence
   m_srcVocab->MakeClosed();
   Phrase tphrase(ARRAY_SIZE_INCR);
   tphrase.CreateFromString(Output, m_outputFactors, target, factorDelimiter, NULL);
@@ -534,16 +533,17 @@ void BilingualDynSuffixArray::addSntPair(string& source, string& target, string&
   LoadRawAlignments(alignment);
   m_trgVocab->MakeClosed();
   //for(size_t i=0; i < sphrase.GetSize(); ++i)
-    //ClearWordInCache(sIDs[i]);
-  
+  //ClearWordInCache(sIDs[i]);
+
 }
-void BilingualDynSuffixArray::ClearWordInCache(wordID_t srcWord) {
+void BilingualDynSuffixArray::ClearWordInCache(wordID_t srcWord)
+{
   if(m_freqWordsCached.find(srcWord) != m_freqWordsCached.end())
     return;
-	std::map<std::pair<wordID_t, wordID_t>, std::pair<float, float> >::iterator it,
-    first, last;
+  std::map<std::pair<wordID_t, wordID_t>, std::pair<float, float> >::iterator it,
+      first, last;
   for(it = m_wordPairCache.begin(); it != m_wordPairCache.end(); ++it) {
-    if(it->first.first == srcWord) {  // all source words grouped 
+    if(it->first.first == srcWord) {  // all source words grouped
       first = it; // copy first entry of srcWord
       last = it++;
       while(it != m_wordPairCache.end() && (it->first.first == srcWord)) {
@@ -553,80 +553,77 @@ void BilingualDynSuffixArray::ClearWordInCache(wordID_t srcWord) {
     m_wordPairCache.erase(first, last);
   }
 }
-SentenceAlignment::SentenceAlignment(int sntIndex, int sourceSize, int targetSize) 
-	:m_sntIndex(sntIndex)
-	,numberAligned(targetSize, 0)
-	,alignedList(sourceSize)
+SentenceAlignment::SentenceAlignment(int sntIndex, int sourceSize, int targetSize)
+  :m_sntIndex(sntIndex)
+  ,numberAligned(targetSize, 0)
+  ,alignedList(sourceSize)
 {
-	for(int i=0; i < sourceSize; ++i) {
-	std::vector<int> trgWrd;
-	alignedList[i] = trgWrd;
-	}
+  for(int i=0; i < sourceSize; ++i) {
+    std::vector<int> trgWrd;
+    alignedList[i] = trgWrd;
+  }
 }
 
 bool SentenceAlignment::Extract(int maxPhraseLength, std::vector<PhrasePair*> &ret, int startSource, int endSource) const
 {
-	// foreign = target, F=T
-	// english = source, E=S
-	int countTarget = numberAligned.size();
-	
-	int minTarget = 9999;
-	int maxTarget = -1;
-	std::vector< int > usedTarget = numberAligned;
-	for(int sourcePos = startSource; sourcePos <= endSource; sourcePos++) 
-	{
-	for(int ind=0; ind < (int)alignedList[sourcePos].size();ind++) 
-	{
-		int targetPos = alignedList[sourcePos][ind];
-		// cout << "point (" << targetPos << ", " << sourcePos << ")\n";
-		if (targetPos<minTarget) { minTarget = targetPos; }
-		if (targetPos>maxTarget) { maxTarget = targetPos; }
-		usedTarget[ targetPos ]--;
-	} // for(int ind=0;ind<sentence
-	} // for(int sourcePos=startSource
-	
-	// cout << "f projected ( " << minTarget << "-" << maxTarget << ", " << startSource << "," << endSource << ")\n"; 
-	
-	if (maxTarget >= 0 && // aligned to any foreign words at all
-		maxTarget-minTarget < maxPhraseLength) 
-	{ // foreign phrase within limits
-	
-	// check if foreign words are aligned to out of bound english words
-	bool out_of_bounds = false;
-	for(int targetPos=minTarget; targetPos <= maxTarget && !out_of_bounds; targetPos++)
-	{
-		if (usedTarget[targetPos]>0) 
-		{
-		// cout << "ouf of bounds: " << targetPos << "\n";
-		out_of_bounds = true;
-		}
-	}
-	
-	// cout << "doing if for ( " << minTarget << "-" << maxTarget << ", " << startSource << "," << endSource << ")\n"; 
-	if (!out_of_bounds)
-	{
-		// start point of foreign phrase may retreat over unaligned
-		for(int startTarget = minTarget;
-			(startTarget >= 0 &&
-			startTarget > maxTarget-maxPhraseLength && // within length limit
-			(startTarget==minTarget || numberAligned[startTarget]==0)); // unaligned
-			startTarget--)
-		{
-		// end point of foreign phrase may advance over unaligned
-		for (int endTarget=maxTarget;
-			 (endTarget<countTarget && 
-				endTarget<startTarget+maxPhraseLength && // within length limit
-				(endTarget==maxTarget || numberAligned[endTarget]==0)); // unaligned
-			 endTarget++)
-		{
-			PhrasePair *phrasePair = new PhrasePair(startTarget,endTarget,startSource,endSource, m_sntIndex);
-			ret.push_back(phrasePair);
-		} // for (int endTarget=maxTarget;
-		}	// for(int startTarget=minTarget;
-	} // if (!out_of_bounds)
-	} // if (maxTarget >= 0 &&
-	return (ret.size() > 0);
-	
+  // foreign = target, F=T
+  // english = source, E=S
+  int countTarget = numberAligned.size();
+
+  int minTarget = 9999;
+  int maxTarget = -1;
+  std::vector< int > usedTarget = numberAligned;
+  for(int sourcePos = startSource; sourcePos <= endSource; sourcePos++) {
+    for(int ind=0; ind < (int)alignedList[sourcePos].size(); ind++) {
+      int targetPos = alignedList[sourcePos][ind];
+      // cout << "point (" << targetPos << ", " << sourcePos << ")\n";
+      if (targetPos<minTarget) {
+        minTarget = targetPos;
+      }
+      if (targetPos>maxTarget) {
+        maxTarget = targetPos;
+      }
+      usedTarget[ targetPos ]--;
+    } // for(int ind=0;ind<sentence
+  } // for(int sourcePos=startSource
+
+  // cout << "f projected ( " << minTarget << "-" << maxTarget << ", " << startSource << "," << endSource << ")\n";
+
+  if (maxTarget >= 0 && // aligned to any foreign words at all
+      maxTarget-minTarget < maxPhraseLength) {
+    // foreign phrase within limits
+
+    // check if foreign words are aligned to out of bound english words
+    bool out_of_bounds = false;
+    for(int targetPos=minTarget; targetPos <= maxTarget && !out_of_bounds; targetPos++) {
+      if (usedTarget[targetPos]>0) {
+        // cout << "ouf of bounds: " << targetPos << "\n";
+        out_of_bounds = true;
+      }
+    }
+
+    // cout << "doing if for ( " << minTarget << "-" << maxTarget << ", " << startSource << "," << endSource << ")\n";
+    if (!out_of_bounds) {
+      // start point of foreign phrase may retreat over unaligned
+      for(int startTarget = minTarget;
+          (startTarget >= 0 &&
+           startTarget > maxTarget-maxPhraseLength && // within length limit
+           (startTarget==minTarget || numberAligned[startTarget]==0)); // unaligned
+          startTarget--) {
+        // end point of foreign phrase may advance over unaligned
+        for (int endTarget=maxTarget;
+             (endTarget<countTarget &&
+              endTarget<startTarget+maxPhraseLength && // within length limit
+              (endTarget==maxTarget || numberAligned[endTarget]==0)); // unaligned
+             endTarget++) {
+          PhrasePair *phrasePair = new PhrasePair(startTarget,endTarget,startSource,endSource, m_sntIndex);
+          ret.push_back(phrasePair);
+        } // for (int endTarget=maxTarget;
+      }	// for(int startTarget=minTarget;
+    } // if (!out_of_bounds)
+  } // if (maxTarget >= 0 &&
+  return (ret.size() > 0);
+
 }
 
 }// end namepsace
diff --git a/moses/TranslationModel/BilingualDynSuffixArray.h b/moses/TranslationModel/BilingualDynSuffixArray.h
index 5dda1e274..08637d095 100644
--- a/moses/TranslationModel/BilingualDynSuffixArray.h
+++ b/moses/TranslationModel/BilingualDynSuffixArray.h
@@ -1,7 +1,7 @@
 #ifndef moses_BilingualDynSuffixArray_h
 #define moses_BilingualDynSuffixArray_h
 
-#include "DynSuffixArray.h" 
+#include "DynSuffixArray.h"
 #include "moses/TranslationModel/DynSAInclude/vocab.h"
 #include "moses/TranslationModel/DynSAInclude/types.h"
 #include "moses/TranslationModel/DynSAInclude/utils.h"
@@ -9,26 +9,27 @@
 #include "moses/FactorTypeSet.h"
 #include "moses/TargetPhrase.h"
 
-namespace Moses {
+namespace Moses
+{
 
 /** @todo ask Abbey Levenberg
  */
 class SAPhrase
 {
 public:
-	std::vector<wordID_t> words;		
-	
-	SAPhrase(size_t phraseSize)
-	:words(phraseSize)
-	{}
-	
-	void SetId(size_t pos, wordID_t id)
-	{
+  std::vector<wordID_t> words;
+
+  SAPhrase(size_t phraseSize)
+    :words(phraseSize)
+  {}
+
+  void SetId(size_t pos, wordID_t id) {
     CHECK(pos < words.size());
-		words[pos] = id;
-	}
-	bool operator<(const SAPhrase& phr2) const
-  { return words < phr2.words; }
+    words[pos] = id;
+  }
+  bool operator<(const SAPhrase& phr2) const {
+    return words < phr2.words;
+  }
 };
 
 /** @todo ask Abbey Levenberg
@@ -36,42 +37,44 @@ public:
 class PhrasePair
 {
 public:
-	int m_startTarget, m_endTarget, m_startSource, m_endSource, m_sntIndex;
-	PhrasePair(int startTarget, int endTarget, int startSource, int endSource, int sntIndex)
-	: m_startTarget(startTarget)
-	, m_endTarget(endTarget)
-	, m_startSource(startSource)
-	, m_endSource(endSource)
-	, m_sntIndex(sntIndex)
-	{}
-
-	size_t GetTargetSize() const
-	{ return m_endTarget - m_startTarget + 1; }
+  int m_startTarget, m_endTarget, m_startSource, m_endSource, m_sntIndex;
+  PhrasePair(int startTarget, int endTarget, int startSource, int endSource, int sntIndex)
+    : m_startTarget(startTarget)
+    , m_endTarget(endTarget)
+    , m_startSource(startSource)
+    , m_endSource(endSource)
+    , m_sntIndex(sntIndex)
+  {}
+
+  size_t GetTargetSize() const {
+    return m_endTarget - m_startTarget + 1;
+  }
 };
-	
+
 /** @todo ask Abbey Levenberg
  */
-class SentenceAlignment 
+class SentenceAlignment
 {
 public:
-	SentenceAlignment(int sntIndex, int sourceSize, int targetSize);
-	int m_sntIndex;
-	std::vector<wordID_t>* trgSnt;
-	std::vector<wordID_t>* srcSnt;
-	std::vector<int> numberAligned; 
-	std::vector< std::vector<int> > alignedList; 
-	bool Extract(int maxPhraseLength, std::vector<PhrasePair*> &ret, int startSource, int endSource) const;
+  SentenceAlignment(int sntIndex, int sourceSize, int targetSize);
+  int m_sntIndex;
+  std::vector<wordID_t>* trgSnt;
+  std::vector<wordID_t>* srcSnt;
+  std::vector<int> numberAligned;
+  std::vector< std::vector<int> > alignedList;
+  bool Extract(int maxPhraseLength, std::vector<PhrasePair*> &ret, int startSource, int endSource) const;
 };
-class ScoresComp {
-public: 
+class ScoresComp
+{
+public:
   ScoresComp(const std::vector<float>& weights): m_weights(weights) {}
-  bool operator()(const Scores& s1, const Scores& s2) const { 
+  bool operator()(const Scores& s1, const Scores& s2) const {
     return s1[0] < s2[0]; // just p(e|f) as approximation
     /*float score1(0), score2(0);
     int idx1(0), idx2(0);
-    for (Scores::const_iterator itr = s1.begin(); 
+    for (Scores::const_iterator itr = s1.begin();
             itr != s1.end(); ++itr) {
-        score1 += log(*itr * m_weights.at(idx1++)); 
+        score1 += log(*itr * m_weights.at(idx1++));
     }
     for (Scores::const_iterator itr = s2.begin();
         itr != s2.end(); ++itr) {
@@ -79,78 +82,77 @@ public:
     }
     return score1 < score2;*/
   }
-private: 
+private:
   const std::vector<float>& m_weights;
 };
-	
+
 /** @todo ask Abbey Levenberg
  */
-class BilingualDynSuffixArray {
-public: 
-	BilingualDynSuffixArray();
-	~BilingualDynSuffixArray();
-	bool Load( const std::vector<FactorType>& inputFactors,
-		const std::vector<FactorType>& outputTactors,
-		std::string source, std::string target, std::string alignments, 
-		const std::vector<float> &weight);
-	bool LoadTM( const std::vector<FactorType>& inputFactors,
-            const std::vector<FactorType>& outputTactors,
-            std::string source, std::string target, std::string alignments, 
-            const std::vector<float> &weight);
-	void GetTargetPhrasesByLexicalWeight(const Phrase& src, std::vector< std::pair<Scores, TargetPhrase*> >& target) const;
+class BilingualDynSuffixArray
+{
+public:
+  BilingualDynSuffixArray();
+  ~BilingualDynSuffixArray();
+  bool Load( const std::vector<FactorType>& inputFactors,
+             const std::vector<FactorType>& outputTactors,
+             std::string source, std::string target, std::string alignments,
+             const std::vector<float> &weight);
+  bool LoadTM( const std::vector<FactorType>& inputFactors,
+               const std::vector<FactorType>& outputTactors,
+               std::string source, std::string target, std::string alignments,
+               const std::vector<float> &weight);
+  void GetTargetPhrasesByLexicalWeight(const Phrase& src, std::vector< std::pair<Scores, TargetPhrase*> >& target) const;
   void addSntPair(string& source, string& target, string& alignment);
 private:
-	DynSuffixArray* m_srcSA;
-	DynSuffixArray* m_trgSA;
-	std::vector<wordID_t>* m_srcCorpus;
-	std::vector<wordID_t>* m_trgCorpus;
+  DynSuffixArray* m_srcSA;
+  DynSuffixArray* m_trgSA;
+  std::vector<wordID_t>* m_srcCorpus;
+  std::vector<wordID_t>* m_trgCorpus;
   std::vector<FactorType> m_inputFactors;
   std::vector<FactorType> m_outputFactors;
 
-	std::vector<unsigned> m_srcSntBreaks, m_trgSntBreaks;
+  std::vector<unsigned> m_srcSntBreaks, m_trgSntBreaks;
 
-	Vocab* m_srcVocab, *m_trgVocab;
-	ScoresComp* m_scoreCmp;
+  Vocab* m_srcVocab, *m_trgVocab;
+  ScoresComp* m_scoreCmp;
 
-	std::vector<SentenceAlignment> m_alignments;
-	std::vector<std::vector<short> > m_rawAlignments;
+  std::vector<SentenceAlignment> m_alignments;
+  std::vector<std::vector<short> > m_rawAlignments;
 
-	mutable std::map<std::pair<wordID_t, wordID_t>, std::pair<float, float> > m_wordPairCache; 
+  mutable std::map<std::pair<wordID_t, wordID_t>, std::pair<float, float> > m_wordPairCache;
   mutable std::set<wordID_t> m_freqWordsCached;
-	const size_t m_maxPhraseLength, m_maxSampleSize;
-
-	int LoadCorpus(FactorDirection direction, InputFileStream&, const std::vector<FactorType>& factors,
-		std::vector<wordID_t>&, std::vector<wordID_t>&,
-    Vocab*);
-	int LoadAlignments(InputFileStream& aligs);
-	int LoadRawAlignments(InputFileStream& aligs);
-	int LoadRawAlignments(string& aligs);
-
-	bool ExtractPhrases(const int&, const int&, const int&, std::vector<PhrasePair*>&, bool=false) const;
-	SentenceAlignment GetSentenceAlignment(const int, bool=false) const; 
-	int SampleSelection(std::vector<unsigned>&, int = 300) const;
-
-	std::vector<int> GetSntIndexes(std::vector<unsigned>&, int, const std::vector<unsigned>&) const;	
-	TargetPhrase* GetMosesFactorIDs(const SAPhrase&, const Phrase& sourcePhrase) const;
-	SAPhrase TrgPhraseFromSntIdx(const PhrasePair&) const;
-	bool GetLocalVocabIDs(const Phrase&, SAPhrase &) const;
-	void CacheWordProbs(wordID_t) const;
+  const size_t m_maxPhraseLength, m_maxSampleSize;
+
+  int LoadCorpus(FactorDirection direction, InputFileStream&, const std::vector<FactorType>& factors,
+                 std::vector<wordID_t>&, std::vector<wordID_t>&,
+                 Vocab*);
+  int LoadAlignments(InputFileStream& aligs);
+  int LoadRawAlignments(InputFileStream& aligs);
+  int LoadRawAlignments(string& aligs);
+
+  bool ExtractPhrases(const int&, const int&, const int&, std::vector<PhrasePair*>&, bool=false) const;
+  SentenceAlignment GetSentenceAlignment(const int, bool=false) const;
+  int SampleSelection(std::vector<unsigned>&, int = 300) const;
+
+  std::vector<int> GetSntIndexes(std::vector<unsigned>&, int, const std::vector<unsigned>&) const;
+  TargetPhrase* GetMosesFactorIDs(const SAPhrase&, const Phrase& sourcePhrase) const;
+  SAPhrase TrgPhraseFromSntIdx(const PhrasePair&) const;
+  bool GetLocalVocabIDs(const Phrase&, SAPhrase &) const;
+  void CacheWordProbs(wordID_t) const;
   void CacheFreqWords() const;
   void ClearWordInCache(wordID_t);
-	std::pair<float, float> GetLexicalWeight(const PhrasePair&) const;
-
-	int GetSourceSentenceSize(size_t sentenceId) const
-	{ 
-		return (sentenceId==m_srcSntBreaks.size()-1) ? 
-			m_srcCorpus->size() - m_srcSntBreaks.at(sentenceId) : 
-			m_srcSntBreaks.at(sentenceId+1) - m_srcSntBreaks.at(sentenceId); 
-	}
-	int GetTargetSentenceSize(size_t sentenceId) const
-	{ 
-		return (sentenceId==m_trgSntBreaks.size()-1) ?
-			m_trgCorpus->size() - m_trgSntBreaks.at(sentenceId) : 
-			m_trgSntBreaks.at(sentenceId+1) - m_trgSntBreaks.at(sentenceId); 
-	}
+  std::pair<float, float> GetLexicalWeight(const PhrasePair&) const;
+
+  int GetSourceSentenceSize(size_t sentenceId) const {
+    return (sentenceId==m_srcSntBreaks.size()-1) ?
+           m_srcCorpus->size() - m_srcSntBreaks.at(sentenceId) :
+           m_srcSntBreaks.at(sentenceId+1) - m_srcSntBreaks.at(sentenceId);
+  }
+  int GetTargetSentenceSize(size_t sentenceId) const {
+    return (sentenceId==m_trgSntBreaks.size()-1) ?
+           m_trgCorpus->size() - m_trgSntBreaks.at(sentenceId) :
+           m_trgSntBreaks.at(sentenceId+1) - m_trgSntBreaks.at(sentenceId);
+  }
 };
 } // end namespace
 #endif
diff --git a/moses/TranslationModel/CYKPlusParser/ChartRuleLookupManagerCYKPlus.cpp b/moses/TranslationModel/CYKPlusParser/ChartRuleLookupManagerCYKPlus.cpp
index 4f0f6c2cd..e8d2f734a 100644
--- a/moses/TranslationModel/CYKPlusParser/ChartRuleLookupManagerCYKPlus.cpp
+++ b/moses/TranslationModel/CYKPlusParser/ChartRuleLookupManagerCYKPlus.cpp
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2012 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
diff --git a/moses/TranslationModel/CYKPlusParser/ChartRuleLookupManagerCYKPlus.h b/moses/TranslationModel/CYKPlusParser/ChartRuleLookupManagerCYKPlus.h
index 61982299f..3c3f468c2 100644
--- a/moses/TranslationModel/CYKPlusParser/ChartRuleLookupManagerCYKPlus.h
+++ b/moses/TranslationModel/CYKPlusParser/ChartRuleLookupManagerCYKPlus.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2012 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -35,12 +35,12 @@ class WordsRange;
  */
 class ChartRuleLookupManagerCYKPlus : public ChartRuleLookupManager
 {
- public:
+public:
   ChartRuleLookupManagerCYKPlus(const InputType &sentence,
                                 const ChartCellCollectionBase &cellColl)
     : ChartRuleLookupManager(sentence, cellColl) {}
 
- protected:
+protected:
   void AddCompletedRule(
     const DottedRule &dottedRule,
     const TargetPhraseCollection &tpc,
diff --git a/moses/TranslationModel/CYKPlusParser/ChartRuleLookupManagerMemory.cpp b/moses/TranslationModel/CYKPlusParser/ChartRuleLookupManagerMemory.cpp
index ce6a1d30d..c0c1986f4 100644
--- a/moses/TranslationModel/CYKPlusParser/ChartRuleLookupManagerMemory.cpp
+++ b/moses/TranslationModel/CYKPlusParser/ChartRuleLookupManagerMemory.cpp
@@ -75,19 +75,19 @@ void ChartRuleLookupManagerMemory::GetChartRuleCollection(
   // get list of all rules that apply to spans at same starting position
   DottedRuleColl &dottedRuleCol = *m_dottedRuleColls[range.GetStartPos()];
   const DottedRuleList &expandableDottedRuleList = dottedRuleCol.GetExpandableDottedRuleList();
-  
+
   const ChartCellLabel &sourceWordLabel = GetSourceAt(absEndPos);
 
   // loop through the rules
-  // (note that expandableDottedRuleList can be expanded as the loop runs 
+  // (note that expandableDottedRuleList can be expanded as the loop runs
   //  through calls to ExtendPartialRuleApplication())
   for (size_t ind = 0; ind < expandableDottedRuleList.size(); ++ind) {
     // rule we are about to extend
     const DottedRuleInMemory &prevDottedRule = *expandableDottedRuleList[ind];
     // we will now try to extend it, starting after where it ended
     size_t startPos = prevDottedRule.IsRoot()
-                    ? range.GetStartPos()
-                    : prevDottedRule.GetWordsRange().GetEndPos() + 1;
+                      ? range.GetStartPos()
+                      : prevDottedRule.GetWordsRange().GetEndPos() + 1;
 
     // search for terminal symbol
     // (if only one more word position needs to be covered)
@@ -100,15 +100,15 @@ void ChartRuleLookupManagerMemory::GetChartRuleCollection(
 
       // if we found a new rule -> create it and add it to the list
       if (node != NULL) {
-				// create the rule
+        // create the rule
 #ifdef USE_BOOST_POOL
         DottedRuleInMemory *dottedRule = m_dottedRulePool.malloc();
         new (dottedRule) DottedRuleInMemory(*node, sourceWordLabel,
                                             prevDottedRule);
 #else
         DottedRuleInMemory *dottedRule = new DottedRuleInMemory(*node,
-                                                                sourceWordLabel,
-                                                                prevDottedRule);
+            sourceWordLabel,
+            prevDottedRule);
 #endif
         dottedRuleCol.Add(relEndPos+1, dottedRule);
       }
@@ -134,9 +134,7 @@ void ChartRuleLookupManagerMemory::GetChartRuleCollection(
       // word.
       endPos = absEndPos - 1;
       stackInd = relEndPos;
-    }
-    else 
-    {
+    } else {
       endPos = absEndPos;
       stackInd = relEndPos + 1;
     }
@@ -208,7 +206,7 @@ void ChartRuleLookupManagerMemory::ExtendPartialRuleApplication(
   // We'll do whichever minimises the number of lookups:
   if (numCombinations <= numChildren*2) {
 
-		// loop over possible source non-terminal labels (as found in input tree)
+    // loop over possible source non-terminal labels (as found in input tree)
     NonTerminalSet::const_iterator p = sourceNonTerms.begin();
     NonTerminalSet::const_iterator sEnd = sourceNonTerms.end();
     for (; p != sEnd; ++p) {
@@ -235,14 +233,12 @@ void ChartRuleLookupManagerMemory::ExtendPartialRuleApplication(
         new (rule) DottedRuleInMemory(*child, cellLabel, prevDottedRule);
 #else
         DottedRuleInMemory *rule = new DottedRuleInMemory(*child, cellLabel,
-                                                          prevDottedRule);
+            prevDottedRule);
 #endif
         dottedRuleColl.Add(stackInd, rule);
       }
     }
-  } 
-  else 
-  {
+  } else {
     // loop over possible expansions of the rule
     PhraseDictionaryNodeMemory::NonTerminalMap::const_iterator p;
     PhraseDictionaryNodeMemory::NonTerminalMap::const_iterator end =
@@ -267,7 +263,7 @@ void ChartRuleLookupManagerMemory::ExtendPartialRuleApplication(
       new (rule) DottedRuleInMemory(child, *cellLabel, prevDottedRule);
 #else
       DottedRuleInMemory *rule = new DottedRuleInMemory(child, *cellLabel,
-                                                        prevDottedRule);
+          prevDottedRule);
 #endif
       dottedRuleColl.Add(stackInd, rule);
     }
diff --git a/moses/TranslationModel/CYKPlusParser/ChartRuleLookupManagerMemory.h b/moses/TranslationModel/CYKPlusParser/ChartRuleLookupManagerMemory.h
index 784e1c70d..74bc7d253 100644
--- a/moses/TranslationModel/CYKPlusParser/ChartRuleLookupManagerMemory.h
+++ b/moses/TranslationModel/CYKPlusParser/ChartRuleLookupManagerMemory.h
@@ -44,7 +44,7 @@ class WordsRange;
 //! Implementation of ChartRuleLookupManager for in-memory rule tables.
 class ChartRuleLookupManagerMemory : public ChartRuleLookupManagerCYKPlus
 {
- public:
+public:
   ChartRuleLookupManagerMemory(const InputType &sentence,
                                const ChartCellCollectionBase &cellColl,
                                const PhraseDictionaryMemory &ruleTable);
@@ -55,7 +55,7 @@ class ChartRuleLookupManagerMemory : public ChartRuleLookupManagerCYKPlus
     const WordsRange &range,
     ChartParserCallback &outColl);
 
- private:
+private:
   void ExtendPartialRuleApplication(
     const DottedRuleInMemory &prevDottedRule,
     size_t startPos,
diff --git a/moses/TranslationModel/CYKPlusParser/ChartRuleLookupManagerMemoryPerSentence.cpp b/moses/TranslationModel/CYKPlusParser/ChartRuleLookupManagerMemoryPerSentence.cpp
index 4ad60eb43..412840782 100644
--- a/moses/TranslationModel/CYKPlusParser/ChartRuleLookupManagerMemoryPerSentence.cpp
+++ b/moses/TranslationModel/CYKPlusParser/ChartRuleLookupManagerMemoryPerSentence.cpp
@@ -75,17 +75,17 @@ void ChartRuleLookupManagerMemoryPerSentence::GetChartRuleCollection(
   // get list of all rules that apply to spans at same starting position
   DottedRuleColl &dottedRuleCol = *m_dottedRuleColls[range.GetStartPos()];
   const DottedRuleList &expandableDottedRuleList = dottedRuleCol.GetExpandableDottedRuleList();
-  
+
   // loop through the rules
-  // (note that expandableDottedRuleList can be expanded as the loop runs 
+  // (note that expandableDottedRuleList can be expanded as the loop runs
   //  through calls to ExtendPartialRuleApplication())
   for (size_t ind = 0; ind < expandableDottedRuleList.size(); ++ind) {
     // rule we are about to extend
     const DottedRuleInMemory &prevDottedRule = *expandableDottedRuleList[ind];
     // we will now try to extend it, starting after where it ended
     size_t startPos = prevDottedRule.IsRoot()
-                    ? range.GetStartPos()
-                    : prevDottedRule.GetWordsRange().GetEndPos() + 1;
+                      ? range.GetStartPos()
+                      : prevDottedRule.GetWordsRange().GetEndPos() + 1;
 
     // search for terminal symbol
     // (if only one more word position needs to be covered)
@@ -99,15 +99,15 @@ void ChartRuleLookupManagerMemoryPerSentence::GetChartRuleCollection(
 
       // if we found a new rule -> create it and add it to the list
       if (node != NULL) {
-				// create the rule
+        // create the rule
 #ifdef USE_BOOST_POOL
         DottedRuleInMemory *dottedRule = m_dottedRulePool.malloc();
         new (dottedRule) DottedRuleInMemory(*node, sourceWordLabel,
                                             prevDottedRule);
 #else
         DottedRuleInMemory *dottedRule = new DottedRuleInMemory(*node,
-                                                                sourceWordLabel,
-                                                                prevDottedRule);
+            sourceWordLabel,
+            prevDottedRule);
 #endif
         dottedRuleCol.Add(relEndPos+1, dottedRule);
       }
@@ -133,9 +133,7 @@ void ChartRuleLookupManagerMemoryPerSentence::GetChartRuleCollection(
       // word.
       endPos = absEndPos - 1;
       stackInd = relEndPos;
-    }
-    else 
-    {
+    } else {
       endPos = absEndPos;
       stackInd = relEndPos + 1;
     }
@@ -207,7 +205,7 @@ void ChartRuleLookupManagerMemoryPerSentence::ExtendPartialRuleApplication(
   // We'll do whichever minimises the number of lookups:
   if (numCombinations <= numChildren*2) {
 
-		// loop over possible source non-terminal labels (as found in input tree)
+    // loop over possible source non-terminal labels (as found in input tree)
     NonTerminalSet::const_iterator p = sourceNonTerms.begin();
     NonTerminalSet::const_iterator sEnd = sourceNonTerms.end();
     for (; p != sEnd; ++p) {
@@ -234,14 +232,12 @@ void ChartRuleLookupManagerMemoryPerSentence::ExtendPartialRuleApplication(
         new (rule) DottedRuleInMemory(*child, cellLabel, prevDottedRule);
 #else
         DottedRuleInMemory *rule = new DottedRuleInMemory(*child, cellLabel,
-                                                          prevDottedRule);
+            prevDottedRule);
 #endif
         dottedRuleColl.Add(stackInd, rule);
       }
     }
-  } 
-  else 
-  {
+  } else {
     // loop over possible expansions of the rule
     PhraseDictionaryNodeMemory::NonTerminalMap::const_iterator p;
     PhraseDictionaryNodeMemory::NonTerminalMap::const_iterator end =
@@ -266,7 +262,7 @@ void ChartRuleLookupManagerMemoryPerSentence::ExtendPartialRuleApplication(
       new (rule) DottedRuleInMemory(child, *cellLabel, prevDottedRule);
 #else
       DottedRuleInMemory *rule = new DottedRuleInMemory(child, *cellLabel,
-                                                        prevDottedRule);
+          prevDottedRule);
 #endif
       dottedRuleColl.Add(stackInd, rule);
     }
diff --git a/moses/TranslationModel/CYKPlusParser/ChartRuleLookupManagerMemoryPerSentence.h b/moses/TranslationModel/CYKPlusParser/ChartRuleLookupManagerMemoryPerSentence.h
index 6f2b209a7..ebb8cdd7c 100644
--- a/moses/TranslationModel/CYKPlusParser/ChartRuleLookupManagerMemoryPerSentence.h
+++ b/moses/TranslationModel/CYKPlusParser/ChartRuleLookupManagerMemoryPerSentence.h
@@ -44,10 +44,10 @@ class WordsRange;
 //! Implementation of ChartRuleLookupManager for in-memory rule tables.
 class ChartRuleLookupManagerMemoryPerSentence : public ChartRuleLookupManagerCYKPlus
 {
- public:
+public:
   ChartRuleLookupManagerMemoryPerSentence(const InputType &sentence,
-                               const ChartCellCollectionBase &cellColl,
-                               const PhraseDictionaryFuzzyMatch &ruleTable);
+                                          const ChartCellCollectionBase &cellColl,
+                                          const PhraseDictionaryFuzzyMatch &ruleTable);
 
   ~ChartRuleLookupManagerMemoryPerSentence();
 
@@ -55,7 +55,7 @@ class ChartRuleLookupManagerMemoryPerSentence : public ChartRuleLookupManagerCYK
     const WordsRange &range,
     ChartParserCallback &outColl);
 
- private:
+private:
   void ExtendPartialRuleApplication(
     const DottedRuleInMemory &prevDottedRule,
     size_t startPos,
diff --git a/moses/TranslationModel/CYKPlusParser/ChartRuleLookupManagerOnDisk.h b/moses/TranslationModel/CYKPlusParser/ChartRuleLookupManagerOnDisk.h
index 23f83623d..24d06270b 100644
--- a/moses/TranslationModel/CYKPlusParser/ChartRuleLookupManagerOnDisk.h
+++ b/moses/TranslationModel/CYKPlusParser/ChartRuleLookupManagerOnDisk.h
@@ -35,7 +35,7 @@ namespace Moses
 //! Implementation of ChartRuleLookupManager for on-disk rule tables.
 class ChartRuleLookupManagerOnDisk : public ChartRuleLookupManagerCYKPlus
 {
- public:
+public:
   ChartRuleLookupManagerOnDisk(const InputType &sentence,
                                const ChartCellCollectionBase &cellColl,
                                const PhraseDictionaryOnDisk &dictionary,
@@ -49,7 +49,7 @@ class ChartRuleLookupManagerOnDisk : public ChartRuleLookupManagerCYKPlus
   virtual void GetChartRuleCollection(const WordsRange &range,
                                       ChartParserCallback &outColl);
 
- private:
+private:
   const PhraseDictionaryOnDisk &m_dictionary;
   OnDiskPt::OnDiskWrapper &m_dbWrapper;
   const std::vector<FactorType> &m_inputFactorsVec;
diff --git a/moses/TranslationModel/CYKPlusParser/DotChart.h b/moses/TranslationModel/CYKPlusParser/DotChart.h
index 9dd34593f..946f36ff2 100644
--- a/moses/TranslationModel/CYKPlusParser/DotChart.h
+++ b/moses/TranslationModel/CYKPlusParser/DotChart.h
@@ -28,26 +28,38 @@ namespace Moses
  */
 class DottedRule
 {
- public:
+public:
   // used only to init dot stack.
   DottedRule()
-      : m_cellLabel(NULL)
-      , m_prev(NULL) {}
+    : m_cellLabel(NULL)
+    , m_prev(NULL) {}
 
   DottedRule(const ChartCellLabel &ccl, const DottedRule &prev)
-      : m_cellLabel(&ccl)
-      , m_prev(&prev) {}
+    : m_cellLabel(&ccl)
+    , m_prev(&prev) {}
 
-  const WordsRange &GetWordsRange() const { return m_cellLabel->GetCoverage(); }
-  const Word &GetSourceWord() const { return m_cellLabel->GetLabel(); }
-  bool IsNonTerminal() const { return m_cellLabel->GetLabel().IsNonTerminal(); }
-  const DottedRule *GetPrev() const { return m_prev; }
-  bool IsRoot() const { return m_prev == NULL; }
-  const ChartCellLabel &GetChartCellLabel() const { return *m_cellLabel; }
+  const WordsRange &GetWordsRange() const {
+    return m_cellLabel->GetCoverage();
+  }
+  const Word &GetSourceWord() const {
+    return m_cellLabel->GetLabel();
+  }
+  bool IsNonTerminal() const {
+    return m_cellLabel->GetLabel().IsNonTerminal();
+  }
+  const DottedRule *GetPrev() const {
+    return m_prev;
+  }
+  bool IsRoot() const {
+    return m_prev == NULL;
+  }
+  const ChartCellLabel &GetChartCellLabel() const {
+    return *m_cellLabel;
+  }
 
- private:
+private:
   const ChartCellLabel *m_cellLabel; // usually contains something, unless
-                                     // it's the init processed rule
+  // it's the init processed rule
   const DottedRule *m_prev;
 };
 
diff --git a/moses/TranslationModel/CYKPlusParser/DotChartInMemory.cpp b/moses/TranslationModel/CYKPlusParser/DotChartInMemory.cpp
index a28387027..616a2907c 100644
--- a/moses/TranslationModel/CYKPlusParser/DotChartInMemory.cpp
+++ b/moses/TranslationModel/CYKPlusParser/DotChartInMemory.cpp
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
diff --git a/moses/TranslationModel/CYKPlusParser/DotChartInMemory.h b/moses/TranslationModel/CYKPlusParser/DotChartInMemory.h
index f0753a8f1..cfd986d7a 100644
--- a/moses/TranslationModel/CYKPlusParser/DotChartInMemory.h
+++ b/moses/TranslationModel/CYKPlusParser/DotChartInMemory.h
@@ -32,21 +32,23 @@ namespace Moses
  */
 class DottedRuleInMemory : public DottedRule
 {
- public:
+public:
   // used only to init dot stack.
   explicit DottedRuleInMemory(const PhraseDictionaryNodeMemory &node)
-      : DottedRule()
-      , m_node(node) {}
+    : DottedRule()
+    , m_node(node) {}
 
   DottedRuleInMemory(const PhraseDictionaryNodeMemory &node,
                      const ChartCellLabel &cellLabel,
                      const DottedRuleInMemory &prev)
-      : DottedRule(cellLabel, prev)
-      , m_node(node) {}
-             
-  const PhraseDictionaryNodeMemory &GetLastNode() const { return m_node; }
+    : DottedRule(cellLabel, prev)
+    , m_node(node) {}
+
+  const PhraseDictionaryNodeMemory &GetLastNode() const {
+    return m_node;
+  }
 
- private:
+private:
   const PhraseDictionaryNodeMemory &m_node;
 };
 
diff --git a/moses/TranslationModel/CYKPlusParser/DotChartOnDisk.h b/moses/TranslationModel/CYKPlusParser/DotChartOnDisk.h
index 5b756ba8d..edd9f3a62 100644
--- a/moses/TranslationModel/CYKPlusParser/DotChartOnDisk.h
+++ b/moses/TranslationModel/CYKPlusParser/DotChartOnDisk.h
@@ -36,26 +36,32 @@ namespace Moses
  */
 class DottedRuleOnDisk : public DottedRule
 {
- public:
+public:
   // used only to init dot stack.
   explicit DottedRuleOnDisk(const OnDiskPt::PhraseNode &lastNode)
-      : DottedRule()
-      , m_lastNode(lastNode)
-      , m_done(false) {}
+    : DottedRule()
+    , m_lastNode(lastNode)
+    , m_done(false) {}
 
   DottedRuleOnDisk(const OnDiskPt::PhraseNode &lastNode,
                    const ChartCellLabel &cellLabel,
                    const DottedRuleOnDisk &prev)
-      : DottedRule(cellLabel, prev)
-      , m_lastNode(lastNode)
-      , m_done(false) {}
+    : DottedRule(cellLabel, prev)
+    , m_lastNode(lastNode)
+    , m_done(false) {}
 
-  const OnDiskPt::PhraseNode &GetLastNode() const { return m_lastNode; }
+  const OnDiskPt::PhraseNode &GetLastNode() const {
+    return m_lastNode;
+  }
 
-  bool Done() const { return m_done; }
-  void Done(bool value) const { m_done = value; }
+  bool Done() const {
+    return m_done;
+  }
+  void Done(bool value) const {
+    m_done = value;
+  }
 
- private:
+private:
   const OnDiskPt::PhraseNode &m_lastNode;
   mutable bool m_done;
 };
diff --git a/moses/TranslationModel/CompactPT/BlockHashIndex.cpp b/moses/TranslationModel/CompactPT/BlockHashIndex.cpp
index 705493ab7..9afe474f7 100644
--- a/moses/TranslationModel/CompactPT/BlockHashIndex.cpp
+++ b/moses/TranslationModel/CompactPT/BlockHashIndex.cpp
@@ -1,23 +1,23 @@
-// $Id$                                                                                                                               
-// vim:tabstop=2                                                                                                                      
-/***********************************************************************                                                              
-Moses - factored phrase-based language decoder                                                                                        
-Copyright (C) 2006 University of Edinburgh                                                                                            
-                                                                                                                                      
-This library is free software; you can redistribute it and/or                                                                         
-modify it under the terms of the GNU Lesser General Public                                                                            
-License as published by the Free Software Foundation; either                                                                          
-version 2.1 of the License, or (at your option) any later version.                                                                    
-                                                                                                                                      
-This library is distributed in the hope that it will be useful,                                                                       
-but WITHOUT ANY WARRANTY; without even the implied warranty of                                                                        
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU                                                                     
-Lesser General Public License for more details.                                                                                       
-                                                                                                                                      
-You should have received a copy of the GNU Lesser General Public                                                                      
-License along with this library; if not, write to the Free Software                                                                   
-Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA                                                        
-***********************************************************************/  
+// $Id$
+// vim:tabstop=2
+/***********************************************************************
+Moses - factored phrase-based language decoder
+Copyright (C) 2006 University of Edinburgh
+
+This library is free software; you can redistribute it and/or
+modify it under the terms of the GNU Lesser General Public
+License as published by the Free Software Foundation; either
+version 2.1 of the License, or (at your option) any later version.
+
+This library is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public
+License along with this library; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+***********************************************************************/
 
 #include "ThrowingFwrite.h"
 #include "BlockHashIndex.h"
@@ -32,25 +32,27 @@ namespace Moses
 #ifdef WITH_THREADS
 BlockHashIndex::BlockHashIndex(size_t orderBits, size_t fingerPrintBits,
                                size_t threadsNum)
-: m_orderBits(orderBits), m_fingerPrintBits(fingerPrintBits),
-  m_fileHandle(0), m_fileHandleStart(0), m_size(0),
-  m_lastSaved(-1), m_lastDropped(-1), m_numLoadedRanges(0),
-  m_threadPool(threadsNum) {
+  : m_orderBits(orderBits), m_fingerPrintBits(fingerPrintBits),
+    m_fileHandle(0), m_fileHandleStart(0), m_size(0),
+    m_lastSaved(-1), m_lastDropped(-1), m_numLoadedRanges(0),
+    m_threadPool(threadsNum)
+{
 #ifndef HAVE_CMPH
-    std::cerr << "minphr: CMPH support not compiled in." << std::endl;
-    exit(1);
-#endif    
-  }
+  std::cerr << "minphr: CMPH support not compiled in." << std::endl;
+  exit(1);
+#endif
+}
 #else
 BlockHashIndex::BlockHashIndex(size_t orderBits, size_t fingerPrintBits)
-: m_orderBits(orderBits), m_fingerPrintBits(fingerPrintBits),
-  m_fileHandle(0), m_fileHandleStart(0), m_size(0),
-  m_lastSaved(-1), m_lastDropped(-1), m_numLoadedRanges(0) {
+  : m_orderBits(orderBits), m_fingerPrintBits(fingerPrintBits),
+    m_fileHandle(0), m_fileHandleStart(0), m_size(0),
+    m_lastSaved(-1), m_lastDropped(-1), m_numLoadedRanges(0)
+{
 #ifndef HAVE_CMPH
-    std::cerr << "minphr: CMPH support not compiled in." << std::endl;
-    exit(1);
-#endif        
-  }
+  std::cerr << "minphr: CMPH support not compiled in." << std::endl;
+  exit(1);
+#endif
+}
 #endif
 
 BlockHashIndex::~BlockHashIndex()
@@ -60,7 +62,7 @@ BlockHashIndex::~BlockHashIndex()
       it != m_hashes.end(); it++)
     if(*it != 0)
       cmph_destroy((cmph_t*)*it);
-      
+
   for(std::vector<PairedPackedArray<>*>::iterator it = m_arrays.begin();
       it != m_arrays.end(); it++)
     if(*it != 0)
@@ -72,15 +74,15 @@ size_t BlockHashIndex::GetHash(const char* key)
 {
   std::string keyStr(key);
   size_t i = std::distance(m_landmarks.begin(),
-      std::upper_bound(m_landmarks.begin(),
-      m_landmarks.end(), keyStr)) - 1;
-  
+                           std::upper_bound(m_landmarks.begin(),
+                               m_landmarks.end(), keyStr)) - 1;
+
   if(i == 0ul-1)
     return GetSize();
-    
+
   size_t pos = GetHash(i, key);
   if(pos != GetSize())
-    return (1ul << m_orderBits) * i + pos; 
+    return (1ul << m_orderBits) * i + pos;
   else
     return GetSize();
 }
@@ -100,7 +102,7 @@ size_t BlockHashIndex::GetHash(size_t i, const char* key)
 #endif
   if(m_hashes[i] == 0)
     LoadRange(i);
-#ifdef HAVE_CMPH    
+#ifdef HAVE_CMPH
   size_t idx = cmph_search((cmph_t*)m_hashes[i], key, (cmph_uint32) strlen(key));
 #else
   assert(0);
@@ -109,11 +111,11 @@ size_t BlockHashIndex::GetHash(size_t i, const char* key)
 
   std::pair<size_t, size_t> orderPrint = m_arrays[i]->Get(idx, m_orderBits, m_fingerPrintBits);
   m_clocks[i] = clock();
-  
+
   if(GetFprint(key) == orderPrint.second)
-      return orderPrint.first;
+    return orderPrint.first;
   else
-      return GetSize();
+    return GetSize();
 }
 
 size_t BlockHashIndex::GetHash(std::string key)
@@ -144,11 +146,11 @@ void BlockHashIndex::BeginSave(std::FILE * mphf)
   m_fileHandle = mphf;
   ThrowingFwrite(&m_orderBits, sizeof(size_t), 1, m_fileHandle);
   ThrowingFwrite(&m_fingerPrintBits, sizeof(size_t), 1, m_fileHandle);
-  
+
   m_fileHandleStart = std::ftell(m_fileHandle);
-  
+
   size_t relIndexPos = 0;
-  ThrowingFwrite(&relIndexPos, sizeof(size_t), 1, m_fileHandle);    
+  ThrowingFwrite(&relIndexPos, sizeof(size_t), 1, m_fileHandle);
 }
 
 void BlockHashIndex::SaveRange(size_t i)
@@ -168,25 +170,22 @@ void BlockHashIndex::SaveLastRange()
   boost::mutex::scoped_lock lock(m_mutex);
 #endif
 
-  while(!m_queue.empty() && m_lastSaved + 1 == -m_queue.top())
-  {
+  while(!m_queue.empty() && m_lastSaved + 1 == -m_queue.top()) {
     size_t current = -m_queue.top();
     m_queue.pop();
     SaveRange(current);
     m_lastSaved = current;
-  }   
+  }
 }
 
 void BlockHashIndex::DropRange(size_t i)
 {
 #ifdef HAVE_CMPH
-  if(m_hashes[i] != 0)
-  {
+  if(m_hashes[i] != 0) {
     cmph_destroy((cmph_t*)m_hashes[i]);
     m_hashes[i] = 0;
   }
-  if(m_arrays[i] != 0)
-  {
+  if(m_arrays[i] != 0) {
     delete m_arrays[i];
     m_arrays[i] = 0;
     m_clocks[i] = 0;
@@ -201,7 +200,7 @@ void BlockHashIndex::DropLastRange()
   boost::mutex::scoped_lock lock(m_mutex);
 #endif
 
-  while(m_lastDropped != m_lastSaved) 
+  while(m_lastDropped != m_lastSaved)
     DropRange(++m_lastDropped);
 }
 
@@ -219,24 +218,24 @@ size_t BlockHashIndex::FinalizeSave()
 #endif
 
   SaveLastRange();
-  
+
   size_t relIndexPos = std::ftell(m_fileHandle) - m_fileHandleStart;
-  
+
   std::fseek(m_fileHandle, m_fileHandleStart, SEEK_SET);
   ThrowingFwrite(&relIndexPos, sizeof(size_t), 1, m_fileHandle);
-  
+
   std::fseek(m_fileHandle, m_fileHandleStart + relIndexPos, SEEK_SET);
   m_landmarks.save(m_fileHandle);
-  
+
   size_t seekIndexSize = m_seekIndex.size();
   ThrowingFwrite(&seekIndexSize, sizeof(size_t), 1, m_fileHandle);
   ThrowingFwrite(&m_seekIndex[0], sizeof(size_t), seekIndexSize, m_fileHandle);
-  
+
   ThrowingFwrite(&m_size, sizeof(size_t), 1, m_fileHandle);
-  
+
   size_t fileHandleStop = std::ftell(m_fileHandle);
   return fileHandleStop - m_fileHandleStart + sizeof(m_orderBits)
-    + sizeof(m_fingerPrintBits);
+         + sizeof(m_fingerPrintBits);
 }
 
 size_t BlockHashIndex::Save(std::FILE * mphf)
@@ -251,14 +250,14 @@ size_t BlockHashIndex::Save(std::FILE * mphf)
 size_t BlockHashIndex::LoadIndex(std::FILE* mphf)
 {
   m_fileHandle = mphf;
-  
+
   size_t beginning = std::ftell(mphf);
 
   size_t read = 0;
   read += std::fread(&m_orderBits, sizeof(size_t), 1, mphf);
   read += std::fread(&m_fingerPrintBits, sizeof(size_t), 1, mphf);
   m_fileHandleStart = std::ftell(m_fileHandle);
-  
+
   size_t relIndexPos;
   read += std::fread(&relIndexPos, sizeof(size_t), 1, mphf);
   std::fseek(m_fileHandle, m_fileHandleStart + relIndexPos, SEEK_SET);
@@ -272,12 +271,12 @@ size_t BlockHashIndex::LoadIndex(std::FILE* mphf)
   m_hashes.resize(seekIndexSize, 0);
   m_clocks.resize(seekIndexSize, 0);
   m_arrays.resize(seekIndexSize, 0);
-  
+
   read += std::fread(&m_size, sizeof(size_t), 1, m_fileHandle);
 
   size_t end = std::ftell(mphf);
 
-  return end - beginning;  
+  return end - beginning;
 }
 
 void BlockHashIndex::LoadRange(size_t i)
@@ -288,10 +287,10 @@ void BlockHashIndex::LoadRange(size_t i)
   m_arrays[i] = new PairedPackedArray<>(0, m_orderBits,
                                         m_fingerPrintBits);
   m_arrays[i]->Load(m_fileHandle);
-  
+
   m_hashes[i] = (void*)hash;
   m_clocks[i] = clock();
-  
+
   m_numLoadedRanges++;
 #endif
 }
@@ -308,9 +307,9 @@ size_t BlockHashIndex::Load(std::FILE * mphf)
 {
   size_t byteSize = LoadIndex(mphf);
   size_t end = std::ftell(mphf);
-  
+
   for(size_t i = 0; i < m_seekIndex.size(); i++)
-      LoadRange(i);
+    LoadRange(i);
   std::fseek(m_fileHandle, end, SEEK_SET);
   return byteSize;
 }
@@ -327,14 +326,13 @@ void BlockHashIndex::KeepNLastRanges(float ratio, float tolerance)
 #endif
   size_t n = m_hashes.size() * ratio;
   size_t max = n * (1 + tolerance);
-  if(m_numLoadedRanges > max)
-  {
+  if(m_numLoadedRanges > max) {
     typedef std::vector<std::pair<clock_t, size_t> > LastLoaded;
     LastLoaded lastLoaded;
     for(size_t i = 0; i < m_hashes.size(); i++)
       if(m_hashes[i] != 0)
         lastLoaded.push_back(std::make_pair(m_clocks[i], i));
-      
+
     std::sort(lastLoaded.begin(), lastLoaded.end());
     for(LastLoaded::reverse_iterator it = lastLoaded.rbegin() + size_t(n * (1 - tolerance));
         it != lastLoaded.rend(); it++)
@@ -348,24 +346,23 @@ void BlockHashIndex::CalcHash(size_t current, void* source_void)
   cmph_io_adapter_t* source = (cmph_io_adapter_t*) source_void;
   cmph_config_t *config = cmph_config_new(source);
   cmph_config_set_algo(config, CMPH_CHD);
-            
+
   cmph_t* hash = cmph_new(config);
   PairedPackedArray<> *pv =
     new PairedPackedArray<>(source->nkeys, m_orderBits, m_fingerPrintBits);
 
   size_t i = 0;
-  
+
   source->rewind(source->data);
-  
+
   std::string lastKey = "";
-  while(i < source->nkeys)
-  {
+  while(i < source->nkeys) {
     unsigned keylen;
     char* key;
     source->read(source->data, &key, &keylen);
     std::string temp(key, keylen);
     source->dispose(source->data, key, keylen);
-  
+
     if(lastKey > temp) {
       if(source->nkeys != 2 || temp != "###DUMMY_KEY###") {
         std::cerr << "ERROR: Input file does not appear to be sorted with  LC_ALL=C sort" << std::endl;
@@ -375,41 +372,40 @@ void BlockHashIndex::CalcHash(size_t current, void* source_void)
       }
     }
     lastKey = temp;
-    
+
     size_t fprint = GetFprint(temp.c_str());
     size_t idx = cmph_search(hash, temp.c_str(),
                              (cmph_uint32) temp.size());
-  
+
     pv->Set(idx, i, fprint, m_orderBits, m_fingerPrintBits);
     i++;
   }
-  
+
   cmph_config_destroy(config);
-  
+
 #ifdef WITH_THREADS
   boost::mutex::scoped_lock lock(m_mutex);
 #endif
 
-  if(m_hashes.size() <= current)
-  {
-    m_hashes.resize(current + 1, 0);    
+  if(m_hashes.size() <= current) {
+    m_hashes.resize(current + 1, 0);
     m_arrays.resize(current + 1, 0);
     m_clocks.resize(current + 1, 0);
   }
-  
+
   m_hashes[current] = (void*)hash;
   m_arrays[current] = pv;
   m_clocks[current] = clock();
-  m_queue.push(-current);  
+  m_queue.push(-current);
 #endif
 }
 
-#ifdef HAVE_CMPH 
+#ifdef HAVE_CMPH
 void* BlockHashIndex::vectorAdapter(std::vector<std::string>& v)
 {
   return (void*)CmphVectorAdapter(v);
 }
-      
+
 void* BlockHashIndex::vectorAdapter(StringVector<unsigned, size_t, std::allocator>& sv)
 {
   return (void*)CmphStringVectorAdapter(sv);
diff --git a/moses/TranslationModel/CompactPT/BlockHashIndex.h b/moses/TranslationModel/CompactPT/BlockHashIndex.h
index 8541a2a19..c245d2d66 100644
--- a/moses/TranslationModel/CompactPT/BlockHashIndex.h
+++ b/moses/TranslationModel/CompactPT/BlockHashIndex.h
@@ -1,23 +1,23 @@
-// $Id$                                                                                                                               
-// vim:tabstop=2                                                                                                                      
-/***********************************************************************                                                              
-Moses - factored phrase-based language decoder                                                                                        
-Copyright (C) 2006 University of Edinburgh                                                                                            
-                                                                                                                                      
-This library is free software; you can redistribute it and/or                                                                         
-modify it under the terms of the GNU Lesser General Public                                                                            
-License as published by the Free Software Foundation; either                                                                          
-version 2.1 of the License, or (at your option) any later version.                                                                    
-                                                                                                                                      
-This library is distributed in the hope that it will be useful,                                                                       
-but WITHOUT ANY WARRANTY; without even the implied warranty of                                                                        
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU                                                                     
-Lesser General Public License for more details.                                                                                       
-                                                                                                                                      
-You should have received a copy of the GNU Lesser General Public                                                                      
-License along with this library; if not, write to the Free Software                                                                   
-Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA                                                        
-***********************************************************************/  
+// $Id$
+// vim:tabstop=2
+/***********************************************************************
+Moses - factored phrase-based language decoder
+Copyright (C) 2006 University of Edinburgh
+
+This library is free software; you can redistribute it and/or
+modify it under the terms of the GNU Lesser General Public
+License as published by the Free Software Foundation; either
+version 2.1 of the License, or (at your option) any later version.
+
+This library is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public
+License along with this library; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+***********************************************************************/
 
 #ifndef moses_BlockHashIndex_h
 #define moses_BlockHashIndex_h
@@ -25,7 +25,7 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 #include <iostream>
 #include <string>
 #include <vector>
-#include <queue> 
+#include <queue>
 #include <cstring>
 #include <cstdio>
 
@@ -42,144 +42,139 @@ namespace Moses
 
 class BlockHashIndex
 {
-  private:
-    std::priority_queue<int> m_queue;
-    
-    size_t m_orderBits;
-    size_t m_fingerPrintBits;
-
-    std::FILE* m_fileHandle;
-    size_t m_fileHandleStart;
-        
-    StringVector<unsigned char, unsigned long> m_landmarks;
-    
-    std::vector<void*> m_hashes;
-    std::vector<clock_t> m_clocks;
-    std::vector<PairedPackedArray<>*> m_arrays;
-    
-    std::vector<size_t> m_seekIndex;
-    
-    size_t m_size;
-    int m_lastSaved;
-    int m_lastDropped;
-    size_t m_numLoadedRanges;
-    
+private:
+  std::priority_queue<int> m_queue;
+
+  size_t m_orderBits;
+  size_t m_fingerPrintBits;
+
+  std::FILE* m_fileHandle;
+  size_t m_fileHandleStart;
+
+  StringVector<unsigned char, unsigned long> m_landmarks;
+
+  std::vector<void*> m_hashes;
+  std::vector<clock_t> m_clocks;
+  std::vector<PairedPackedArray<>*> m_arrays;
+
+  std::vector<size_t> m_seekIndex;
+
+  size_t m_size;
+  int m_lastSaved;
+  int m_lastDropped;
+  size_t m_numLoadedRanges;
+
 #ifdef WITH_THREADS
-    ThreadPool m_threadPool;
-    boost::mutex m_mutex;
- 
-    template <typename Keys>
-    class HashTask : public Task
-    {
-      public:
-        HashTask(int id, BlockHashIndex& hash, Keys& keys)
-        : m_id(id), m_hash(hash), m_keys(new Keys(keys)) {}
-        
-        virtual void Run()
-        {
-          m_hash.CalcHash(m_id, *m_keys);
-        }
-    
-        virtual ~HashTask()
-        {
-            delete m_keys;
-        }
-    
-      private:
-        int m_id;
-        BlockHashIndex& m_hash;
-        Keys* m_keys;
-    };
-#endif
-    
-    size_t GetFprint(const char* key) const;
-    size_t GetHash(size_t i, const char* key);
-        
+  ThreadPool m_threadPool;
+  boost::mutex m_mutex;
+
+  template <typename Keys>
+  class HashTask : public Task
+  {
   public:
+    HashTask(int id, BlockHashIndex& hash, Keys& keys)
+      : m_id(id), m_hash(hash), m_keys(new Keys(keys)) {}
+
+    virtual void Run() {
+      m_hash.CalcHash(m_id, *m_keys);
+    }
+
+    virtual ~HashTask() {
+      delete m_keys;
+    }
+
+  private:
+    int m_id;
+    BlockHashIndex& m_hash;
+    Keys* m_keys;
+  };
+#endif
+
+  size_t GetFprint(const char* key) const;
+  size_t GetHash(size_t i, const char* key);
+
+public:
 #ifdef WITH_THREADS
-    BlockHashIndex(size_t orderBits, size_t fingerPrintBits,
-                   size_t threadsNum = 2);
+  BlockHashIndex(size_t orderBits, size_t fingerPrintBits,
+                 size_t threadsNum = 2);
 #else
-    BlockHashIndex(size_t orderBits, size_t fingerPrintBits);
+  BlockHashIndex(size_t orderBits, size_t fingerPrintBits);
 #endif
 
-    ~BlockHashIndex();
-        
-    size_t GetHash(const char* key);
-    size_t GetHash(std::string key);
-    
-    size_t operator[](std::string key);
-    size_t operator[](char* key);
-    
-    void BeginSave(std::FILE* mphf);
-    void SaveRange(size_t i);
-    void SaveLastRange();
-    size_t FinalizeSave();
+  ~BlockHashIndex();
+
+  size_t GetHash(const char* key);
+  size_t GetHash(std::string key);
+
+  size_t operator[](std::string key);
+  size_t operator[](char* key);
+
+  void BeginSave(std::FILE* mphf);
+  void SaveRange(size_t i);
+  void SaveLastRange();
+  size_t FinalizeSave();
 
 #ifdef WITH_THREADS
-    void WaitAll();
+  void WaitAll();
 #endif
- 
-    void DropRange(size_t i);
-    void DropLastRange();
-    
-    size_t LoadIndex(std::FILE* mphf);
-    void LoadRange(size_t i);
-    
-    size_t Save(std::string filename);
-    size_t Save(std::FILE * mphf);
-    
-    size_t Load(std::string filename);
-    size_t Load(std::FILE * mphf);
-    
-    size_t GetSize() const;
-    
-    void KeepNLastRanges(float ratio = 0.1, float tolerance = 0.1);
-    
-    template <typename Keys>
-    void AddRange(Keys &keys)
-    {
-      size_t current = m_landmarks.size();
-      
-      if(m_landmarks.size() && m_landmarks.back().str() >= keys[0])
-      {
-        std::cerr << "ERROR: Input file does not appear to be sorted with  LC_ALL=C sort" << std::endl;
-        std::cerr << "1: " << m_landmarks.back().str() << std::endl;
-        std::cerr << "2: " << keys[0] << std::endl;
-        abort();
-      }
-      
-      m_landmarks.push_back(keys[0]);
-      m_size += keys.size();
-      
-      if(keys.size() == 1) {
-        // add dummy key to avoid null hash
-        keys.push_back("###DUMMY_KEY###");
-      }
-      
+
+  void DropRange(size_t i);
+  void DropLastRange();
+
+  size_t LoadIndex(std::FILE* mphf);
+  void LoadRange(size_t i);
+
+  size_t Save(std::string filename);
+  size_t Save(std::FILE * mphf);
+
+  size_t Load(std::string filename);
+  size_t Load(std::FILE * mphf);
+
+  size_t GetSize() const;
+
+  void KeepNLastRanges(float ratio = 0.1, float tolerance = 0.1);
+
+  template <typename Keys>
+  void AddRange(Keys &keys) {
+    size_t current = m_landmarks.size();
+
+    if(m_landmarks.size() && m_landmarks.back().str() >= keys[0]) {
+      std::cerr << "ERROR: Input file does not appear to be sorted with  LC_ALL=C sort" << std::endl;
+      std::cerr << "1: " << m_landmarks.back().str() << std::endl;
+      std::cerr << "2: " << keys[0] << std::endl;
+      abort();
+    }
+
+    m_landmarks.push_back(keys[0]);
+    m_size += keys.size();
+
+    if(keys.size() == 1) {
+      // add dummy key to avoid null hash
+      keys.push_back("###DUMMY_KEY###");
+    }
+
 #ifdef WITH_THREADS
-      HashTask<Keys>* ht = new HashTask<Keys>(current, *this, keys);
-      m_threadPool.Submit(ht);
+    HashTask<Keys>* ht = new HashTask<Keys>(current, *this, keys);
+    m_threadPool.Submit(ht);
 #else
-      CalcHash(current, keys);
+    CalcHash(current, keys);
 #endif
-    }
-    
-    template <typename Keys>
-    void CalcHash(size_t current, Keys &keys)
-    {
-#ifdef HAVE_CMPH 
-      void* source = vectorAdapter(keys);
-      CalcHash(current, source);    
+  }
+
+  template <typename Keys>
+  void CalcHash(size_t current, Keys &keys) {
+#ifdef HAVE_CMPH
+    void* source = vectorAdapter(keys);
+    CalcHash(current, source);
 #endif
-    }
+  }
+
+  void CalcHash(size_t current, void* source);
 
-    void CalcHash(size_t current, void* source);
-    
-#ifdef HAVE_CMPH 
-    void* vectorAdapter(std::vector<std::string>& v);
-    void* vectorAdapter(StringVector<unsigned, size_t, std::allocator>& sv);
-    void* vectorAdapter(StringVector<unsigned, size_t, MmapAllocator>& sv);
+#ifdef HAVE_CMPH
+  void* vectorAdapter(std::vector<std::string>& v);
+  void* vectorAdapter(StringVector<unsigned, size_t, std::allocator>& sv);
+  void* vectorAdapter(StringVector<unsigned, size_t, MmapAllocator>& sv);
 #endif
 };
 
diff --git a/moses/TranslationModel/CompactPT/CanonicalHuffman.h b/moses/TranslationModel/CompactPT/CanonicalHuffman.h
index faf7ce411..8d6e1cbb1 100644
--- a/moses/TranslationModel/CompactPT/CanonicalHuffman.h
+++ b/moses/TranslationModel/CompactPT/CanonicalHuffman.h
@@ -1,23 +1,23 @@
-// $Id$                                                                                                                               
-// vim:tabstop=2                                                                                                                      
-/***********************************************************************                                                              
-Moses - factored phrase-based language decoder                                                                                        
-Copyright (C) 2006 University of Edinburgh                                                                                            
-
-This library is free software; you can redistribute it and/or                                                                         
-modify it under the terms of the GNU Lesser General Public                                                                            
-License as published by the Free Software Foundation; either                                                                          
-version 2.1 of the License, or (at your option) any later version.                                                                    
-
-This library is distributed in the hope that it will be useful,                                                                       
-but WITHOUT ANY WARRANTY; without even the implied warranty of                                                                        
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU                                                                     
-Lesser General Public License for more details.                                                                                       
-
-You should have received a copy of the GNU Lesser General Public                                                                      
-License along with this library; if not, write to the Free Software                                                                   
-Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA                                                        
-***********************************************************************/  
+// $Id$
+// vim:tabstop=2
+/***********************************************************************
+Moses - factored phrase-based language decoder
+Copyright (C) 2006 University of Edinburgh
+
+This library is free software; you can redistribute it and/or
+modify it under the terms of the GNU Lesser General Public
+License as published by the Free Software Foundation; either
+version 2.1 of the License, or (at your option) any later version.
+
+This library is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public
+License along with this library; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+***********************************************************************/
 
 #ifndef moses_CanonicalHuffman_h
 #define moses_CanonicalHuffman_h
@@ -29,320 +29,293 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 
 #include "ThrowingFwrite.h"
 
-namespace Moses {
+namespace Moses
+{
 
 template <typename Data>
 class CanonicalHuffman
 {
-  private:
-    std::vector<Data> m_symbols;    
-    std::vector<size_t> m_firstCodes;
-    std::vector<size_t> m_lengthIndex;
-    
-    typedef boost::unordered_map<Data, boost::dynamic_bitset<> > EncodeMap;
-    EncodeMap m_encodeMap;
-    
-    struct MinHeapSorter {
-      std::vector<size_t>& m_vec;
-      
-      MinHeapSorter(std::vector<size_t>& vec) : m_vec(vec) { }
-      
-      bool operator()(size_t a, size_t b)
-      {
-        return m_vec[a] > m_vec[b];
-      }
-    };
-    
-    template <class Iterator>
-    void CalcLengths(Iterator begin, Iterator end, std::vector<size_t>& lengths)
-    {
-      size_t n = std::distance(begin, end);
-      std::vector<size_t> A(2 * n, 0);
-      
-      m_symbols.resize(n);
-      size_t i = 0;
-      for(Iterator it = begin; it != end; it++)
-      {
-        m_symbols[i] = it->first;
-        
-        A[i] = n + i;
-        A[n + i] = it->second;
-        i++;
-      }
-      
-      if(n == 1)
-      {
-        lengths.push_back(1);
-        return;
-      }
-      
-      MinHeapSorter hs(A);
-      std::make_heap(A.begin(), A.begin() + n, hs);
-      
-      size_t h = n;
-      size_t m1, m2;
-      while(h > 1)
-      {
-        m1 = A[0];
-        std::pop_heap(A.begin(), A.begin() + h, hs);
-        
-        h--;
-         
-        m2 = A[0];
-        std::pop_heap(A.begin(), A.begin() + h, hs);
-      
-        A[h] = A[m1] + A[m2];
-        A[h-1] = h;
-        A[m1] = A[m2] = h;
-        
-        std::push_heap(A.begin(), A.begin() + h, hs);
-      }
-      
-      A[1] = 0;
-      for(size_t i = 2; i < 2*n; i++)
-        A[i] = A[A[i]] + 1;
-        
-      lengths.resize(n);
-      for(size_t i = 0; i < n; i++)
-        lengths[i] = A[i + n];
-    }
+private:
+  std::vector<Data> m_symbols;
+  std::vector<size_t> m_firstCodes;
+  std::vector<size_t> m_lengthIndex;
 
-    void CalcCodes(std::vector<size_t>& lengths)
-    {
-      std::vector<size_t> numLength;
-      for(std::vector<size_t>::iterator it = lengths.begin();
-          it != lengths.end(); it++) {
-        size_t length = *it;
-        if(numLength.size() <= length)
-          numLength.resize(length + 1, 0);
-        numLength[length]++;
-      }
-      
-      m_lengthIndex.resize(numLength.size());
-      m_lengthIndex[0] = 0; 
-      for(size_t l = 1; l < numLength.size(); l++)
-        m_lengthIndex[l] = m_lengthIndex[l - 1] + numLength[l - 1];
-      
-      size_t maxLength = numLength.size() - 1;
-      
-      m_firstCodes.resize(maxLength + 1, 0);
-      for(size_t l = maxLength - 1; l > 0; l--)
-        m_firstCodes[l] = (m_firstCodes[l + 1] + numLength[l + 1]) / 2;
-      
-      std::vector<Data> t_symbols;
-      t_symbols.resize(lengths.size());
-      
-      std::vector<size_t> nextCode = m_firstCodes;
-      for(size_t i = 0; i < lengths.size(); i++)
-      {    
-        Data data = m_symbols[i];
-        size_t length = lengths[i];
-        
-        size_t pos = m_lengthIndex[length]
-                     + (nextCode[length] - m_firstCodes[length]);
-        t_symbols[pos] = data;
-
-        nextCode[length] = nextCode[length] + 1;
-      }
-      
-      m_symbols.swap(t_symbols);
-    }
-    
-    void CreateCodeMap()
-    {
-      for(size_t l = 1; l < m_lengthIndex.size(); l++)
-      {
-        size_t intCode = m_firstCodes[l];
-        size_t num = ((l+1 < m_lengthIndex.size()) ? m_lengthIndex[l+1]
-                      : m_symbols.size()) - m_lengthIndex[l];
-        
-        for(size_t i = 0; i < num; i++)
-        {
-          Data data = m_symbols[m_lengthIndex[l] + i];  
-          boost::dynamic_bitset<> bitCode(l, intCode);
-          m_encodeMap[data] = bitCode;  
-          intCode++;
-        }
-      }
-    }
-    
-    boost::dynamic_bitset<>& Encode(Data data)
-    {
-      return m_encodeMap[data];
+  typedef boost::unordered_map<Data, boost::dynamic_bitset<> > EncodeMap;
+  EncodeMap m_encodeMap;
+
+  struct MinHeapSorter {
+    std::vector<size_t>& m_vec;
+
+    MinHeapSorter(std::vector<size_t>& vec) : m_vec(vec) { }
+
+    bool operator()(size_t a, size_t b) {
+      return m_vec[a] > m_vec[b];
     }
-    
-    template <class BitWrapper>
-    void PutCode(BitWrapper& bitWrapper, boost::dynamic_bitset<>& code)
-    {
-      for(int j = code.size()-1; j >= 0; j--)
-        bitWrapper.Put(code[j]);
+  };
+
+  template <class Iterator>
+  void CalcLengths(Iterator begin, Iterator end, std::vector<size_t>& lengths) {
+    size_t n = std::distance(begin, end);
+    std::vector<size_t> A(2 * n, 0);
+
+    m_symbols.resize(n);
+    size_t i = 0;
+    for(Iterator it = begin; it != end; it++) {
+      m_symbols[i] = it->first;
+
+      A[i] = n + i;
+      A[n + i] = it->second;
+      i++;
     }
-    
-  public:
-
-    template <class Iterator>
-    CanonicalHuffman(Iterator begin, Iterator end, bool forEncoding = true)
-    {
-      std::vector<size_t> lengths;
-      CalcLengths(begin, end, lengths);
-      CalcCodes(lengths);
-
-      if(forEncoding)
-        CreateCodeMap();
+
+    if(n == 1) {
+      lengths.push_back(1);
+      return;
     }
-    
-    CanonicalHuffman(std::FILE* pFile, bool forEncoding = false)
-    {
-      Load(pFile);
-      
-      if(forEncoding)
-        CreateCodeMap();
+
+    MinHeapSorter hs(A);
+    std::make_heap(A.begin(), A.begin() + n, hs);
+
+    size_t h = n;
+    size_t m1, m2;
+    while(h > 1) {
+      m1 = A[0];
+      std::pop_heap(A.begin(), A.begin() + h, hs);
+
+      h--;
+
+      m2 = A[0];
+      std::pop_heap(A.begin(), A.begin() + h, hs);
+
+      A[h] = A[m1] + A[m2];
+      A[h-1] = h;
+      A[m1] = A[m2] = h;
+
+      std::push_heap(A.begin(), A.begin() + h, hs);
     }
-        
-    template <class BitWrapper>
-    void Put(BitWrapper& bitWrapper, Data data)
-    {
-      PutCode(bitWrapper, Encode(data));
+
+    A[1] = 0;
+    for(size_t i = 2; i < 2*n; i++)
+      A[i] = A[A[i]] + 1;
+
+    lengths.resize(n);
+    for(size_t i = 0; i < n; i++)
+      lengths[i] = A[i + n];
+  }
+
+  void CalcCodes(std::vector<size_t>& lengths) {
+    std::vector<size_t> numLength;
+    for(std::vector<size_t>::iterator it = lengths.begin();
+        it != lengths.end(); it++) {
+      size_t length = *it;
+      if(numLength.size() <= length)
+        numLength.resize(length + 1, 0);
+      numLength[length]++;
     }
-    
-    template <class BitWrapper>
-    Data Read(BitWrapper& bitWrapper)
-    {
-      if(bitWrapper.TellFromEnd())
-      {
-        size_t intCode = bitWrapper.Read();
-        size_t len = 1;
-        while(intCode < m_firstCodes[len]) {
-          intCode = 2 * intCode + bitWrapper.Read();
-          len++;
-        }
-        return m_symbols[m_lengthIndex[len] + (intCode - m_firstCodes[len])];
-      }   
-      return Data();
+
+    m_lengthIndex.resize(numLength.size());
+    m_lengthIndex[0] = 0;
+    for(size_t l = 1; l < numLength.size(); l++)
+      m_lengthIndex[l] = m_lengthIndex[l - 1] + numLength[l - 1];
+
+    size_t maxLength = numLength.size() - 1;
+
+    m_firstCodes.resize(maxLength + 1, 0);
+    for(size_t l = maxLength - 1; l > 0; l--)
+      m_firstCodes[l] = (m_firstCodes[l + 1] + numLength[l + 1]) / 2;
+
+    std::vector<Data> t_symbols;
+    t_symbols.resize(lengths.size());
+
+    std::vector<size_t> nextCode = m_firstCodes;
+    for(size_t i = 0; i < lengths.size(); i++) {
+      Data data = m_symbols[i];
+      size_t length = lengths[i];
+
+      size_t pos = m_lengthIndex[length]
+                   + (nextCode[length] - m_firstCodes[length]);
+      t_symbols[pos] = data;
+
+      nextCode[length] = nextCode[length] + 1;
     }
-    
-    size_t Load(std::FILE* pFile)
-    {
-      size_t start = std::ftell(pFile);
-      size_t read = 0;
-      
-      size_t size;
-      read += std::fread(&size, sizeof(size_t), 1, pFile);
-      m_symbols.resize(size);
-      read += std::fread(&m_symbols[0], sizeof(Data), size, pFile);
-      
-      read += std::fread(&size, sizeof(size_t), 1, pFile);
-      m_firstCodes.resize(size);
-      read += std::fread(&m_firstCodes[0], sizeof(size_t), size, pFile);
-      
-      read += std::fread(&size, sizeof(size_t), 1, pFile);
-      m_lengthIndex.resize(size);
-      read += std::fread(&m_lengthIndex[0], sizeof(size_t), size, pFile);
-      
-      return std::ftell(pFile) - start;
+
+    m_symbols.swap(t_symbols);
+  }
+
+  void CreateCodeMap() {
+    for(size_t l = 1; l < m_lengthIndex.size(); l++) {
+      size_t intCode = m_firstCodes[l];
+      size_t num = ((l+1 < m_lengthIndex.size()) ? m_lengthIndex[l+1]
+                    : m_symbols.size()) - m_lengthIndex[l];
+
+      for(size_t i = 0; i < num; i++) {
+        Data data = m_symbols[m_lengthIndex[l] + i];
+        boost::dynamic_bitset<> bitCode(l, intCode);
+        m_encodeMap[data] = bitCode;
+        intCode++;
+      }
     }
-    
-    size_t Save(std::FILE* pFile)
-    {
-      size_t start = std::ftell(pFile);
-      
-      size_t size = m_symbols.size();
-      ThrowingFwrite(&size, sizeof(size_t), 1, pFile);
-      ThrowingFwrite(&m_symbols[0], sizeof(Data), size, pFile);
-      
-      size = m_firstCodes.size();
-      ThrowingFwrite(&size, sizeof(size_t), 1, pFile);
-      ThrowingFwrite(&m_firstCodes[0], sizeof(size_t), size, pFile);
-      
-      size = m_lengthIndex.size();
-      ThrowingFwrite(&size, sizeof(size_t), 1, pFile);
-      ThrowingFwrite(&m_lengthIndex[0], sizeof(size_t), size, pFile);
-      
-      return std::ftell(pFile) - start;
+  }
+
+  boost::dynamic_bitset<>& Encode(Data data) {
+    return m_encodeMap[data];
+  }
+
+  template <class BitWrapper>
+  void PutCode(BitWrapper& bitWrapper, boost::dynamic_bitset<>& code) {
+    for(int j = code.size()-1; j >= 0; j--)
+      bitWrapper.Put(code[j]);
+  }
+
+public:
+
+  template <class Iterator>
+  CanonicalHuffman(Iterator begin, Iterator end, bool forEncoding = true) {
+    std::vector<size_t> lengths;
+    CalcLengths(begin, end, lengths);
+    CalcCodes(lengths);
+
+    if(forEncoding)
+      CreateCodeMap();
+  }
+
+  CanonicalHuffman(std::FILE* pFile, bool forEncoding = false) {
+    Load(pFile);
+
+    if(forEncoding)
+      CreateCodeMap();
+  }
+
+  template <class BitWrapper>
+  void Put(BitWrapper& bitWrapper, Data data) {
+    PutCode(bitWrapper, Encode(data));
+  }
+
+  template <class BitWrapper>
+  Data Read(BitWrapper& bitWrapper) {
+    if(bitWrapper.TellFromEnd()) {
+      size_t intCode = bitWrapper.Read();
+      size_t len = 1;
+      while(intCode < m_firstCodes[len]) {
+        intCode = 2 * intCode + bitWrapper.Read();
+        len++;
+      }
+      return m_symbols[m_lengthIndex[len] + (intCode - m_firstCodes[len])];
     }
+    return Data();
+  }
+
+  size_t Load(std::FILE* pFile) {
+    size_t start = std::ftell(pFile);
+    size_t read = 0;
+
+    size_t size;
+    read += std::fread(&size, sizeof(size_t), 1, pFile);
+    m_symbols.resize(size);
+    read += std::fread(&m_symbols[0], sizeof(Data), size, pFile);
+
+    read += std::fread(&size, sizeof(size_t), 1, pFile);
+    m_firstCodes.resize(size);
+    read += std::fread(&m_firstCodes[0], sizeof(size_t), size, pFile);
+
+    read += std::fread(&size, sizeof(size_t), 1, pFile);
+    m_lengthIndex.resize(size);
+    read += std::fread(&m_lengthIndex[0], sizeof(size_t), size, pFile);
+
+    return std::ftell(pFile) - start;
+  }
+
+  size_t Save(std::FILE* pFile) {
+    size_t start = std::ftell(pFile);
+
+    size_t size = m_symbols.size();
+    ThrowingFwrite(&size, sizeof(size_t), 1, pFile);
+    ThrowingFwrite(&m_symbols[0], sizeof(Data), size, pFile);
+
+    size = m_firstCodes.size();
+    ThrowingFwrite(&size, sizeof(size_t), 1, pFile);
+    ThrowingFwrite(&m_firstCodes[0], sizeof(size_t), size, pFile);
+
+    size = m_lengthIndex.size();
+    ThrowingFwrite(&size, sizeof(size_t), 1, pFile);
+    ThrowingFwrite(&m_lengthIndex[0], sizeof(size_t), size, pFile);
+
+    return std::ftell(pFile) - start;
+  }
 };
 
 template <class Container = std::string>
 class BitWrapper
 {
-  private:
-    Container& m_data;
-    
-    typename Container::iterator m_iterator;
-    typename Container::value_type m_currentValue;
-    
-    size_t m_valueBits;
-    typename Container::value_type m_mask;
-    size_t m_bitPos;
-    
-  public:
-    
-    BitWrapper(Container &data)
+private:
+  Container& m_data;
+
+  typename Container::iterator m_iterator;
+  typename Container::value_type m_currentValue;
+
+  size_t m_valueBits;
+  typename Container::value_type m_mask;
+  size_t m_bitPos;
+
+public:
+
+  BitWrapper(Container &data)
     : m_data(data), m_iterator(m_data.begin()), m_currentValue(0),
       m_valueBits(sizeof(typename Container::value_type) * 8),
       m_mask(1), m_bitPos(0) { }
-    
-    bool Read()
-    {
-      if(m_bitPos % m_valueBits == 0)
-      {
-        if(m_iterator != m_data.end())
-          m_currentValue = *m_iterator++;
-      }
-      else
-        m_currentValue = m_currentValue >> 1;
-      
-      m_bitPos++;
-      return (m_currentValue & m_mask);
-    }
-    
-    void Put(bool bit) {
-      if(m_bitPos % m_valueBits == 0)
-         m_data.push_back(0);
-        
-      if(bit)
-        m_data[m_data.size()-1] |= m_mask << (m_bitPos % m_valueBits);
-    
-      m_bitPos++;
-    }
-    
-    size_t Tell()
-    {
-      return m_bitPos;
-    }
-    
-    size_t TellFromEnd()
-    {
-      if(m_data.size() * m_valueBits < m_bitPos)
-        return 0;
-      return m_data.size() * m_valueBits - m_bitPos;
-    }
-    
-    void Seek(size_t bitPos)
-    {
-      m_bitPos = bitPos;
-      m_iterator = m_data.begin() + int((m_bitPos-1)/m_valueBits);
-      m_currentValue = (*m_iterator) >> ((m_bitPos-1) % m_valueBits);
-      m_iterator++;
-    }
-    
-    void SeekFromEnd(size_t bitPosFromEnd)
-    {
-      size_t bitPos = m_data.size() * m_valueBits - bitPosFromEnd;
-      Seek(bitPos);
-    }
-    
-    void Reset()
-    {
-      m_iterator = m_data.begin();
-      m_currentValue = 0;
-      m_bitPos = 0;
-    }
-    
-    Container& GetContainer()
-    {
-      return m_data;
-    }
+
+  bool Read() {
+    if(m_bitPos % m_valueBits == 0) {
+      if(m_iterator != m_data.end())
+        m_currentValue = *m_iterator++;
+    } else
+      m_currentValue = m_currentValue >> 1;
+
+    m_bitPos++;
+    return (m_currentValue & m_mask);
+  }
+
+  void Put(bool bit) {
+    if(m_bitPos % m_valueBits == 0)
+      m_data.push_back(0);
+
+    if(bit)
+      m_data[m_data.size()-1] |= m_mask << (m_bitPos % m_valueBits);
+
+    m_bitPos++;
+  }
+
+  size_t Tell() {
+    return m_bitPos;
+  }
+
+  size_t TellFromEnd() {
+    if(m_data.size() * m_valueBits < m_bitPos)
+      return 0;
+    return m_data.size() * m_valueBits - m_bitPos;
+  }
+
+  void Seek(size_t bitPos) {
+    m_bitPos = bitPos;
+    m_iterator = m_data.begin() + int((m_bitPos-1)/m_valueBits);
+    m_currentValue = (*m_iterator) >> ((m_bitPos-1) % m_valueBits);
+    m_iterator++;
+  }
+
+  void SeekFromEnd(size_t bitPosFromEnd) {
+    size_t bitPos = m_data.size() * m_valueBits - bitPosFromEnd;
+    Seek(bitPos);
+  }
+
+  void Reset() {
+    m_iterator = m_data.begin();
+    m_currentValue = 0;
+    m_bitPos = 0;
+  }
+
+  Container& GetContainer() {
+    return m_data;
+  }
 };
 
 }
diff --git a/moses/TranslationModel/CompactPT/CmphStringVectorAdapter.cpp b/moses/TranslationModel/CompactPT/CmphStringVectorAdapter.cpp
index 40fff6690..8e4d1641f 100644
--- a/moses/TranslationModel/CompactPT/CmphStringVectorAdapter.cpp
+++ b/moses/TranslationModel/CompactPT/CmphStringVectorAdapter.cpp
@@ -1,23 +1,23 @@
-// $Id$                                                                                                                               
-// vim:tabstop=2                                                                                                                      
-/***********************************************************************                                                              
-Moses - factored phrase-based language decoder                                                                                        
-Copyright (C) 2006 University of Edinburgh                                                                                            
-                                                                                                                                      
-This library is free software; you can redistribute it and/or                                                                         
-modify it under the terms of the GNU Lesser General Public                                                                            
-License as published by the Free Software Foundation; either                                                                          
-version 2.1 of the License, or (at your option) any later version.                                                                    
-                                                                                                                                      
-This library is distributed in the hope that it will be useful,                                                                       
-but WITHOUT ANY WARRANTY; without even the implied warranty of                                                                        
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU                                                                     
-Lesser General Public License for more details.                                                                                       
-                                                                                                                                      
-You should have received a copy of the GNU Lesser General Public                                                                      
-License along with this library; if not, write to the Free Software                                                                   
-Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA                                                        
-***********************************************************************/  
+// $Id$
+// vim:tabstop=2
+/***********************************************************************
+Moses - factored phrase-based language decoder
+Copyright (C) 2006 University of Edinburgh
+
+This library is free software; you can redistribute it and/or
+modify it under the terms of the GNU Lesser General Public
+License as published by the Free Software Foundation; either
+version 2.1 of the License, or (at your option) any later version.
+
+This library is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public
+License along with this library; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+***********************************************************************/
 
 #ifdef HAVE_CMPH
 
@@ -25,70 +25,70 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 
 namespace Moses
 {
-    
-    void CmphStringVectorAdapterDispose(void *data, char *key, cmph_uint32 keylen)
-    {
-        delete[] key;
-    }
-
-    void CmphStringVectorAdapterRewind(void *data)
-    {
-        cmph_vector_t *cmph_vector = (cmph_vector_t *)data;
-        cmph_vector->position = 0;
-    }
-    
-    //************************************************************************//
-    
-    cmph_io_adapter_t *CmphVectorAdapterNew(std::vector<std::string>& v)
-    {
-        cmph_io_adapter_t * key_source = (cmph_io_adapter_t *)malloc(sizeof(cmph_io_adapter_t));
-        cmph_vector_t * cmph_vector = (cmph_vector_t *)malloc(sizeof(cmph_vector_t));
-        assert(key_source);
-        assert(cmph_vector);
-        
-        cmph_vector->vector = (void *)&v;
-        cmph_vector->position = 0;
-        key_source->data = (void *)cmph_vector;
-        key_source->nkeys = v.size();
-        
-        return key_source;
-    }
-
-    int CmphVectorAdapterRead(void *data, char **key, cmph_uint32 *keylen)
-    {
-        cmph_vector_t *cmph_vector = (cmph_vector_t *)data;
-        std::vector<std::string>* v = (std::vector<std::string>*)cmph_vector->vector;
-        size_t size;
-        *keylen = (*v)[cmph_vector->position].size();
-        size = *keylen;
-        *key = new char[size + 1];
-        std::string temp = (*v)[cmph_vector->position];
-        strcpy(*key, temp.c_str());
-        cmph_vector->position = cmph_vector->position + 1;
-        return (int)(*keylen);
-    }
-    
-    void CmphVectorAdapterDispose(void *data, char *key, cmph_uint32 keylen)
-    {
-        delete[] key;
-    }
-
-    void CmphVectorAdapterRewind(void *data)
-    {
-        cmph_vector_t *cmph_vector = (cmph_vector_t *)data;
-        cmph_vector->position = 0;
-    }
-
-    cmph_io_adapter_t* CmphVectorAdapter(std::vector<std::string>& v)
-    {
-        cmph_io_adapter_t * key_source = CmphVectorAdapterNew(v);
-        
-        key_source->read = CmphVectorAdapterRead;
-        key_source->dispose = CmphVectorAdapterDispose;
-        key_source->rewind = CmphVectorAdapterRewind;
-        return key_source;
-    }
-    
+
+void CmphStringVectorAdapterDispose(void *data, char *key, cmph_uint32 keylen)
+{
+  delete[] key;
+}
+
+void CmphStringVectorAdapterRewind(void *data)
+{
+  cmph_vector_t *cmph_vector = (cmph_vector_t *)data;
+  cmph_vector->position = 0;
+}
+
+//************************************************************************//
+
+cmph_io_adapter_t *CmphVectorAdapterNew(std::vector<std::string>& v)
+{
+  cmph_io_adapter_t * key_source = (cmph_io_adapter_t *)malloc(sizeof(cmph_io_adapter_t));
+  cmph_vector_t * cmph_vector = (cmph_vector_t *)malloc(sizeof(cmph_vector_t));
+  assert(key_source);
+  assert(cmph_vector);
+
+  cmph_vector->vector = (void *)&v;
+  cmph_vector->position = 0;
+  key_source->data = (void *)cmph_vector;
+  key_source->nkeys = v.size();
+
+  return key_source;
+}
+
+int CmphVectorAdapterRead(void *data, char **key, cmph_uint32 *keylen)
+{
+  cmph_vector_t *cmph_vector = (cmph_vector_t *)data;
+  std::vector<std::string>* v = (std::vector<std::string>*)cmph_vector->vector;
+  size_t size;
+  *keylen = (*v)[cmph_vector->position].size();
+  size = *keylen;
+  *key = new char[size + 1];
+  std::string temp = (*v)[cmph_vector->position];
+  strcpy(*key, temp.c_str());
+  cmph_vector->position = cmph_vector->position + 1;
+  return (int)(*keylen);
+}
+
+void CmphVectorAdapterDispose(void *data, char *key, cmph_uint32 keylen)
+{
+  delete[] key;
+}
+
+void CmphVectorAdapterRewind(void *data)
+{
+  cmph_vector_t *cmph_vector = (cmph_vector_t *)data;
+  cmph_vector->position = 0;
+}
+
+cmph_io_adapter_t* CmphVectorAdapter(std::vector<std::string>& v)
+{
+  cmph_io_adapter_t * key_source = CmphVectorAdapterNew(v);
+
+  key_source->read = CmphVectorAdapterRead;
+  key_source->dispose = CmphVectorAdapterDispose;
+  key_source->rewind = CmphVectorAdapterRewind;
+  return key_source;
+}
+
 }
 
 #endif
diff --git a/moses/TranslationModel/CompactPT/CmphStringVectorAdapter.h b/moses/TranslationModel/CompactPT/CmphStringVectorAdapter.h
index 5516d4f4d..4a532c289 100644
--- a/moses/TranslationModel/CompactPT/CmphStringVectorAdapter.h
+++ b/moses/TranslationModel/CompactPT/CmphStringVectorAdapter.h
@@ -1,23 +1,23 @@
-// $Id$                                                                                                                               
-// vim:tabstop=2                                                                                                                      
-/***********************************************************************                                                              
-Moses - factored phrase-based language decoder                                                                                        
-Copyright (C) 2006 University of Edinburgh                                                                                            
-                                                                                                                                      
-This library is free software; you can redistribute it and/or                                                                         
-modify it under the terms of the GNU Lesser General Public                                                                            
-License as published by the Free Software Foundation; either                                                                          
-version 2.1 of the License, or (at your option) any later version.                                                                    
-                                                                                                                                      
-This library is distributed in the hope that it will be useful,                                                                       
-but WITHOUT ANY WARRANTY; without even the implied warranty of                                                                        
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU                                                                     
-Lesser General Public License for more details.                                                                                       
-                                                                                                                                      
-You should have received a copy of the GNU Lesser General Public                                                                      
-License along with this library; if not, write to the Free Software                                                                   
-Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA                                                        
-***********************************************************************/  
+// $Id$
+// vim:tabstop=2
+/***********************************************************************
+Moses - factored phrase-based language decoder
+Copyright (C) 2006 University of Edinburgh
+
+This library is free software; you can redistribute it and/or
+modify it under the terms of the GNU Lesser General Public
+License as published by the Free Software Foundation; either
+version 2.1 of the License, or (at your option) any later version.
+
+This library is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public
+License along with this library; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+***********************************************************************/
 
 #ifndef moses_CmphStringVectorAdapterNew_h
 #define moses_CmphStringVectorAdapterNew_h
@@ -33,72 +33,71 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 namespace Moses
 {
 
-    typedef struct
-    {
-        void *vector;
-        cmph_uint32 position; 
-    }
-    cmph_vector_t;
-   
-      
-    template <typename ValueT, typename PosT, template <typename> class Allocator>
-    cmph_io_adapter_t *CmphStringVectorAdapterNew(StringVector<ValueT, PosT, Allocator>& sv)
-    {
-        cmph_io_adapter_t * key_source = (cmph_io_adapter_t *)malloc(sizeof(cmph_io_adapter_t));
-        cmph_vector_t * cmph_vector = (cmph_vector_t *)malloc(sizeof(cmph_vector_t));
-        assert(key_source);
-        assert(cmph_vector);
-        
-        cmph_vector->vector = (void *)&sv;
-        cmph_vector->position = 0;
-        key_source->data = (void *)cmph_vector;
-        key_source->nkeys = sv.size();
-        
-        return key_source;
-    }
-
-    template <typename ValueT, typename PosT, template <typename> class Allocator>
-    int CmphStringVectorAdapterRead(void *data, char **key, cmph_uint32 *keylen)
-    {
-        cmph_vector_t *cmph_vector = (cmph_vector_t *)data;
-        StringVector<ValueT, PosT, Allocator>* sv = (StringVector<ValueT, PosT, Allocator>*)cmph_vector->vector;
-        size_t size;
-        *keylen = (*sv)[cmph_vector->position].size();
-        size = *keylen;
-        *key = new char[size + 1];
-        std::string temp = (*sv)[cmph_vector->position];
-        std::strcpy(*key, temp.c_str());
-        cmph_vector->position = cmph_vector->position + 1;
-        return (int)(*keylen);
-    }
-    
-    void CmphStringVectorAdapterDispose(void *data, char *key, cmph_uint32 keylen);
-
-    void CmphStringVectorAdapterRewind(void *data);
-
-    template <typename ValueT, typename PosT, template <typename> class Allocator>
-    cmph_io_adapter_t* CmphStringVectorAdapter(StringVector<ValueT, PosT, Allocator>& sv)
-    {
-        cmph_io_adapter_t * key_source = CmphStringVectorAdapterNew(sv);
-        
-        key_source->read = CmphStringVectorAdapterRead<ValueT, PosT, Allocator>;
-        key_source->dispose = CmphStringVectorAdapterDispose;
-        key_source->rewind = CmphStringVectorAdapterRewind;
-        return key_source;
-    }
-    
-    //************************************************************************//
-    
-    cmph_io_adapter_t *CmphVectorAdapterNew(std::vector<std::string>& v);
-
-    int CmphVectorAdapterRead(void *data, char **key, cmph_uint32 *keylen);
-    
-    void CmphVectorAdapterDispose(void *data, char *key, cmph_uint32 keylen);
-
-    void CmphVectorAdapterRewind(void *data);
-
-    cmph_io_adapter_t* CmphVectorAdapter(std::vector<std::string>& v);
-    
+typedef struct {
+  void *vector;
+  cmph_uint32 position;
+}
+cmph_vector_t;
+
+
+template <typename ValueT, typename PosT, template <typename> class Allocator>
+cmph_io_adapter_t *CmphStringVectorAdapterNew(StringVector<ValueT, PosT, Allocator>& sv)
+{
+  cmph_io_adapter_t * key_source = (cmph_io_adapter_t *)malloc(sizeof(cmph_io_adapter_t));
+  cmph_vector_t * cmph_vector = (cmph_vector_t *)malloc(sizeof(cmph_vector_t));
+  assert(key_source);
+  assert(cmph_vector);
+
+  cmph_vector->vector = (void *)&sv;
+  cmph_vector->position = 0;
+  key_source->data = (void *)cmph_vector;
+  key_source->nkeys = sv.size();
+
+  return key_source;
+}
+
+template <typename ValueT, typename PosT, template <typename> class Allocator>
+int CmphStringVectorAdapterRead(void *data, char **key, cmph_uint32 *keylen)
+{
+  cmph_vector_t *cmph_vector = (cmph_vector_t *)data;
+  StringVector<ValueT, PosT, Allocator>* sv = (StringVector<ValueT, PosT, Allocator>*)cmph_vector->vector;
+  size_t size;
+  *keylen = (*sv)[cmph_vector->position].size();
+  size = *keylen;
+  *key = new char[size + 1];
+  std::string temp = (*sv)[cmph_vector->position];
+  std::strcpy(*key, temp.c_str());
+  cmph_vector->position = cmph_vector->position + 1;
+  return (int)(*keylen);
+}
+
+void CmphStringVectorAdapterDispose(void *data, char *key, cmph_uint32 keylen);
+
+void CmphStringVectorAdapterRewind(void *data);
+
+template <typename ValueT, typename PosT, template <typename> class Allocator>
+cmph_io_adapter_t* CmphStringVectorAdapter(StringVector<ValueT, PosT, Allocator>& sv)
+{
+  cmph_io_adapter_t * key_source = CmphStringVectorAdapterNew(sv);
+
+  key_source->read = CmphStringVectorAdapterRead<ValueT, PosT, Allocator>;
+  key_source->dispose = CmphStringVectorAdapterDispose;
+  key_source->rewind = CmphStringVectorAdapterRewind;
+  return key_source;
+}
+
+//************************************************************************//
+
+cmph_io_adapter_t *CmphVectorAdapterNew(std::vector<std::string>& v);
+
+int CmphVectorAdapterRead(void *data, char **key, cmph_uint32 *keylen);
+
+void CmphVectorAdapterDispose(void *data, char *key, cmph_uint32 keylen);
+
+void CmphVectorAdapterRewind(void *data);
+
+cmph_io_adapter_t* CmphVectorAdapter(std::vector<std::string>& v);
+
 }
 
 #endif
diff --git a/moses/TranslationModel/CompactPT/ConsistentPhrases.h b/moses/TranslationModel/CompactPT/ConsistentPhrases.h
index 0ec86e1ac..c7b7c733b 100644
--- a/moses/TranslationModel/CompactPT/ConsistentPhrases.h
+++ b/moses/TranslationModel/CompactPT/ConsistentPhrases.h
@@ -1,23 +1,23 @@
-// $Id$                                                                                                                               
-// vim:tabstop=2                                                                                                                      
-/***********************************************************************                                                              
-Moses - factored phrase-based language decoder                                                                                        
-Copyright (C) 2006 University of Edinburgh                                                                                            
-                                                                                                                                      
-This library is free software; you can redistribute it and/or                                                                         
-modify it under the terms of the GNU Lesser General Public                                                                            
-License as published by the Free Software Foundation; either                                                                          
-version 2.1 of the License, or (at your option) any later version.                                                                    
-                                                                                                                                      
-This library is distributed in the hope that it will be useful,                                                                       
-but WITHOUT ANY WARRANTY; without even the implied warranty of                                                                        
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU                                                                     
-Lesser General Public License for more details.                                                                                       
-                                                                                                                                      
-You should have received a copy of the GNU Lesser General Public                                                                      
-License along with this library; if not, write to the Free Software                                                                   
-Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA                                                        
-***********************************************************************/  
+// $Id$
+// vim:tabstop=2
+/***********************************************************************
+Moses - factored phrase-based language decoder
+Copyright (C) 2006 University of Edinburgh
+
+This library is free software; you can redistribute it and/or
+modify it under the terms of the GNU Lesser General Public
+License as published by the Free Software Foundation; either
+version 2.1 of the License, or (at your option) any later version.
+
+This library is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public
+License along with this library; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+***********************************************************************/
 
 #ifndef moses_ConsistentPhrases_h
 #define moses_ConsistentPhrases_h
@@ -29,97 +29,82 @@ namespace Moses
 
 class ConsistentPhrases
 {
-  public:
-    struct Phrase
-    {
-      int i, j, m, n;
-      Phrase(int i_, int m_, int j_, int n_) : i(i_), j(j_), m(m_), n(n_) { }
-    };
-    
-    struct PhraseSorter
-    {
-      bool operator()(Phrase a, Phrase b)
-      {
-        if(a.n > b.n)
-          return true;
-        if(a.n == b.n && a.j < b.j)
-          return true;
-        if(a.n == b.n && a.j == b.j && a.m > b.m)
-          return true;
-        if(a.n == b.n && a.j == b.j && a.m == b.m && a.i < b.i)
-          return true;
-        return false;
-      }
-    };
-    
-  private:
-    typedef std::set<Phrase, PhraseSorter> PhraseQueue;
-    PhraseQueue m_phraseQueue;
-    
-    typedef std::pair<unsigned char, unsigned char> AlignPoint;
-    typedef std::set<AlignPoint> Alignment;
-    
-  public:
-    
-    ConsistentPhrases(int mmax, int nmax, Alignment& a)
-    {
-      for(int i = 0; i < mmax; i++)
-      {
-        for(int m = 1; m <= mmax-i; m++)
-        {
-          for(int j = 0; j < nmax; j++)
-          {
-            for(int n = 1; n <= nmax-j; n++)
-            {
-              bool consistant = true;
-              for(Alignment::iterator it = a.begin(); it != a.end(); it++)
-              {
-                int ip = it->first;
-                int jp = it->second;
-                if((i <= ip && ip < i+m) != (j <= jp && jp < j+n))
-                {
-                  consistant = false;
-                  break;
-                }
+public:
+  struct Phrase {
+    int i, j, m, n;
+    Phrase(int i_, int m_, int j_, int n_) : i(i_), j(j_), m(m_), n(n_) { }
+  };
+
+  struct PhraseSorter {
+    bool operator()(Phrase a, Phrase b) {
+      if(a.n > b.n)
+        return true;
+      if(a.n == b.n && a.j < b.j)
+        return true;
+      if(a.n == b.n && a.j == b.j && a.m > b.m)
+        return true;
+      if(a.n == b.n && a.j == b.j && a.m == b.m && a.i < b.i)
+        return true;
+      return false;
+    }
+  };
+
+private:
+  typedef std::set<Phrase, PhraseSorter> PhraseQueue;
+  PhraseQueue m_phraseQueue;
+
+  typedef std::pair<unsigned char, unsigned char> AlignPoint;
+  typedef std::set<AlignPoint> Alignment;
+
+public:
+
+  ConsistentPhrases(int mmax, int nmax, Alignment& a) {
+    for(int i = 0; i < mmax; i++) {
+      for(int m = 1; m <= mmax-i; m++) {
+        for(int j = 0; j < nmax; j++) {
+          for(int n = 1; n <= nmax-j; n++) {
+            bool consistant = true;
+            for(Alignment::iterator it = a.begin(); it != a.end(); it++) {
+              int ip = it->first;
+              int jp = it->second;
+              if((i <= ip && ip < i+m) != (j <= jp && jp < j+n)) {
+                consistant = false;
+                break;
               }
-              if(consistant)
-                m_phraseQueue.insert(Phrase(i, m, j, n));
-            } 
-          }  
-        } 
+            }
+            if(consistant)
+              m_phraseQueue.insert(Phrase(i, m, j, n));
+          }
+        }
       }
-      m_phraseQueue.erase(Phrase(0, mmax, 0, nmax));
-    }
-    
-    size_t Empty()
-    {
-      return !m_phraseQueue.size();
     }
-    
-    Phrase Pop()
-    {
-      if(m_phraseQueue.size())
-      {
-        Phrase p = *m_phraseQueue.begin();
-        m_phraseQueue.erase(m_phraseQueue.begin());
-        return p;
-      }
-      return Phrase(0,0,0,0);
+    m_phraseQueue.erase(Phrase(0, mmax, 0, nmax));
+  }
+
+  size_t Empty() {
+    return !m_phraseQueue.size();
+  }
+
+  Phrase Pop() {
+    if(m_phraseQueue.size()) {
+      Phrase p = *m_phraseQueue.begin();
+      m_phraseQueue.erase(m_phraseQueue.begin());
+      return p;
     }
-    
-    void RemoveOverlap(Phrase p)
-    {
-      PhraseQueue ok;
-      for(PhraseQueue::iterator it = m_phraseQueue.begin(); it != m_phraseQueue.end(); it++)
-      {
-        Phrase pp = *it;
-        if(!((p.i <= pp.i && pp.i < p.i + p.m) || (pp.i <= p.i && p.i < pp.i + pp.m) ||
-          (p.j <= pp.j && pp.j < p.j + p.n) || (pp.j <= p.j && p.j < pp.j + pp.n)))
-          ok.insert(pp);
-      }
-      m_phraseQueue = ok;
+    return Phrase(0,0,0,0);
+  }
+
+  void RemoveOverlap(Phrase p) {
+    PhraseQueue ok;
+    for(PhraseQueue::iterator it = m_phraseQueue.begin(); it != m_phraseQueue.end(); it++) {
+      Phrase pp = *it;
+      if(!((p.i <= pp.i && pp.i < p.i + p.m) || (pp.i <= p.i && p.i < pp.i + pp.m) ||
+           (p.j <= pp.j && pp.j < p.j + p.n) || (pp.j <= p.j && p.j < pp.j + pp.n)))
+        ok.insert(pp);
     }
-  
+    m_phraseQueue = ok;
+  }
+
 };
 
 }
diff --git a/moses/TranslationModel/CompactPT/LexicalReorderingTableCompact.cpp b/moses/TranslationModel/CompactPT/LexicalReorderingTableCompact.cpp
index ff1c663c9..ad7591a7b 100644
--- a/moses/TranslationModel/CompactPT/LexicalReorderingTableCompact.cpp
+++ b/moses/TranslationModel/CompactPT/LexicalReorderingTableCompact.cpp
@@ -1,27 +1,28 @@
-// $Id$                                                                                                                               
-// vim:tabstop=2                                                                                                                      
-/***********************************************************************                                                              
-Moses - factored phrase-based language decoder                                                                                        
-Copyright (C) 2006 University of Edinburgh                                                                                            
-                                                                                                                                      
-This library is free software; you can redistribute it and/or                                                                         
-modify it under the terms of the GNU Lesser General Public                                                                            
-License as published by the Free Software Foundation; either                                                                          
-version 2.1 of the License, or (at your option) any later version.                                                                    
-                                                                                                                                      
-This library is distributed in the hope that it will be useful,                                                                       
-but WITHOUT ANY WARRANTY; without even the implied warranty of                                                                        
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU                                                                     
-Lesser General Public License for more details.                                                                                       
-                                                                                                                                      
-You should have received a copy of the GNU Lesser General Public                                                                      
-License along with this library; if not, write to the Free Software                                                                   
-Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA                                                        
-***********************************************************************/  
+// $Id$
+// vim:tabstop=2
+/***********************************************************************
+Moses - factored phrase-based language decoder
+Copyright (C) 2006 University of Edinburgh
+
+This library is free software; you can redistribute it and/or
+modify it under the terms of the GNU Lesser General Public
+License as published by the Free Software Foundation; either
+version 2.1 of the License, or (at your option) any later version.
+
+This library is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public
+License along with this library; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+***********************************************************************/
 
 #include "LexicalReorderingTableCompact.h"
 
-namespace Moses {
+namespace Moses
+{
 
 LexicalReorderingTableCompact::LexicalReorderingTableCompact(
   const std::string& filePath,
@@ -29,9 +30,9 @@ LexicalReorderingTableCompact::LexicalReorderingTableCompact(
   const std::vector<FactorType>& e_factors,
   const std::vector<FactorType>& c_factors)
   : LexicalReorderingTable(f_factors, e_factors, c_factors),
-  m_inMemory(StaticData::Instance().UseMinlexrInMemory()),
-  m_numScoreComponent(6), m_multipleScoreTrees(true),
-  m_hash(10, 16), m_scoreTrees(1)
+    m_inMemory(StaticData::Instance().UseMinlexrInMemory()),
+    m_numScoreComponent(6), m_multipleScoreTrees(true),
+    m_hash(10, 16), m_scoreTrees(1)
 {
   Load(filePath);
 }
@@ -41,12 +42,13 @@ LexicalReorderingTableCompact::LexicalReorderingTableCompact(
   const std::vector<FactorType>& e_factors,
   const std::vector<FactorType>& c_factors)
   : LexicalReorderingTable(f_factors, e_factors, c_factors),
-  m_inMemory(StaticData::Instance().UseMinlexrInMemory()),
-  m_numScoreComponent(6), m_multipleScoreTrees(true),
-  m_hash(10, 16), m_scoreTrees(1)
+    m_inMemory(StaticData::Instance().UseMinlexrInMemory()),
+    m_numScoreComponent(6), m_multipleScoreTrees(true),
+    m_hash(10, 16), m_scoreTrees(1)
 { }
 
-LexicalReorderingTableCompact::~LexicalReorderingTableCompact() {
+LexicalReorderingTableCompact::~LexicalReorderingTableCompact()
+{
   for(size_t i = 0; i < m_scoreTrees.size(); i++)
     delete m_scoreTrees[i];
 }
@@ -57,25 +59,23 @@ std::vector<float> LexicalReorderingTableCompact::GetScore(const Phrase& f,
 {
   std::string key;
   Scores scores;
-  
+
   if(0 == c.GetSize())
     key = MakeKey(f, e, c);
   else
-    for(size_t i = 0; i <= c.GetSize(); ++i)
-    {
+    for(size_t i = 0; i <= c.GetSize(); ++i) {
       Phrase sub_c(c.GetSubString(WordsRange(i,c.GetSize()-1)));
       key = MakeKey(f,e,sub_c);
     }
-    
+
   size_t index = m_hash[key];
-  if(m_hash.GetSize() != index)
-  {
+  if(m_hash.GetSize() != index) {
     std::string scoresString;
     if(m_inMemory)
       scoresString = m_scoresMemory[index];
     else
       scoresString = m_scoresMapped[index];
-      
+
     BitWrapper<> bitStream(scoresString);
     for(size_t i = 0; i < m_numScoreComponent; i++)
       scores.push_back(m_scoreTrees[m_multipleScoreTrees ? i : 0]->Read(bitStream));
@@ -100,22 +100,17 @@ std::string  LexicalReorderingTableCompact::MakeKey(const std::string& f,
     const std::string& c) const
 {
   std::string key;
-  if(!f.empty())
-  {
+  if(!f.empty()) {
     key += f;
   }
-  if(!m_FactorsE.empty())
-  {
-    if(!key.empty())
-    {
+  if(!m_FactorsE.empty()) {
+    if(!key.empty()) {
       key += " ||| ";
     }
     key += e;
   }
-  if(!m_FactorsC.empty())
-  {
-    if(!key.empty())
-    {
+  if(!m_FactorsC.empty()) {
+    if(!key.empty()) {
       key += " ||| ";
     }
     key += c;
@@ -133,48 +128,43 @@ LexicalReorderingTable* LexicalReorderingTableCompact::CheckAndLoad(
 #ifdef HAVE_CMPH
   std::string minlexr = ".minlexr";
   // file name is specified without suffix
-  if(FileExists(filePath + minlexr))
-  {                                                                                                                                   
+  if(FileExists(filePath + minlexr)) {
     //there exists a compact binary version use that
-    VERBOSE(2,"Using compact lexical reordering table" << std::endl);  
-    return new LexicalReorderingTableCompact(filePath + minlexr, f_factors, e_factors, c_factors);                                              
+    VERBOSE(2,"Using compact lexical reordering table" << std::endl);
+    return new LexicalReorderingTableCompact(filePath + minlexr, f_factors, e_factors, c_factors);
   }
   // file name is specified with suffix
   if(filePath.substr(filePath.length() - minlexr.length(), minlexr.length()) == minlexr
-     && FileExists(filePath))
-  {
+      && FileExists(filePath)) {
     //there exists a compact binary version use that
-    VERBOSE(2,"Using compact lexical reordering table" << std::endl);  
-    return new LexicalReorderingTableCompact(filePath, f_factors, e_factors, c_factors);                                              
+    VERBOSE(2,"Using compact lexical reordering table" << std::endl);
+    return new LexicalReorderingTableCompact(filePath, f_factors, e_factors, c_factors);
   }
 #endif
   return 0;
 }
 
 void LexicalReorderingTableCompact::Load(std::string filePath)
-{  
+{
   std::FILE* pFile = std::fopen(filePath.c_str(), "r");
   if(m_inMemory)
     m_hash.Load(pFile);
   else
     m_hash.LoadIndex(pFile);
-  
+
   size_t read = 0;
   read += std::fread(&m_numScoreComponent, sizeof(m_numScoreComponent), 1, pFile);
   read += std::fread(&m_multipleScoreTrees, sizeof(m_multipleScoreTrees), 1, pFile);
-  
-  if(m_multipleScoreTrees)
-  {
+
+  if(m_multipleScoreTrees) {
     m_scoreTrees.resize(m_numScoreComponent);
     for(size_t i = 0; i < m_numScoreComponent; i++)
       m_scoreTrees[i] = new CanonicalHuffman<float>(pFile);
-  }
-  else
-  {
+  } else {
     m_scoreTrees.resize(1);
     m_scoreTrees[0] = new CanonicalHuffman<float>(pFile);
   }
-  
+
   if(m_inMemory)
     m_scoresMemory.load(pFile, false);
   else
diff --git a/moses/TranslationModel/CompactPT/LexicalReorderingTableCompact.h b/moses/TranslationModel/CompactPT/LexicalReorderingTableCompact.h
index 849c61c08..46f2228c9 100644
--- a/moses/TranslationModel/CompactPT/LexicalReorderingTableCompact.h
+++ b/moses/TranslationModel/CompactPT/LexicalReorderingTableCompact.h
@@ -1,23 +1,23 @@
-// $Id$                                                                                                                               
-// vim:tabstop=2                                                                                                                      
-/***********************************************************************                                                              
-Moses - factored phrase-based language decoder                                                                                        
-Copyright (C) 2006 University of Edinburgh                                                                                            
-                                                                                                                                      
-This library is free software; you can redistribute it and/or                                                                         
-modify it under the terms of the GNU Lesser General Public                                                                            
-License as published by the Free Software Foundation; either                                                                          
-version 2.1 of the License, or (at your option) any later version.                                                                    
-                                                                                                                                      
-This library is distributed in the hope that it will be useful,                                                                       
-but WITHOUT ANY WARRANTY; without even the implied warranty of                                                                        
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU                                                                     
-Lesser General Public License for more details.                                                                                       
-                                                                                                                                      
-You should have received a copy of the GNU Lesser General Public                                                                      
-License along with this library; if not, write to the Free Software                                                                   
-Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA                                                        
-***********************************************************************/  
+// $Id$
+// vim:tabstop=2
+/***********************************************************************
+Moses - factored phrase-based language decoder
+Copyright (C) 2006 University of Edinburgh
+
+This library is free software; you can redistribute it and/or
+modify it under the terms of the GNU Lesser General Public
+License as published by the Free Software Foundation; either
+version 2.1 of the License, or (at your option) any later version.
+
+This library is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public
+License along with this library; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+***********************************************************************/
 
 #ifndef moses_LexicalReorderingTableCompact_h
 #define moses_LexicalReorderingTableCompact_h
@@ -33,50 +33,51 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 #include "CanonicalHuffman.h"
 #include "StringVector.h"
 
-namespace Moses {
+namespace Moses
+{
 
 class LexicalReorderingTableCompact: public LexicalReorderingTable
 {
-  private:
-    bool m_inMemory;
-    
-    size_t m_numScoreComponent;
-    bool m_multipleScoreTrees;
-    
-    BlockHashIndex m_hash;
-    
-    typedef CanonicalHuffman<float> ScoreTree;  
-    std::vector<ScoreTree*> m_scoreTrees;
-    
-    StringVector<unsigned char, unsigned long, MmapAllocator>  m_scoresMapped;
-    StringVector<unsigned char, unsigned long, std::allocator> m_scoresMemory;
-
-    std::string MakeKey(const Phrase& f, const Phrase& e, const Phrase& c) const;
-    std::string MakeKey(const std::string& f, const std::string& e, const std::string& c) const;
-    
-  public:
-    LexicalReorderingTableCompact(
-                                const std::string& filePath,
-                                const std::vector<FactorType>& f_factors,
-                                const std::vector<FactorType>& e_factors,
-                                const std::vector<FactorType>& c_factors);
-  
-    LexicalReorderingTableCompact(
-                                const std::vector<FactorType>& f_factors,
-                                const std::vector<FactorType>& e_factors,
-                                const std::vector<FactorType>& c_factors);
-  
-    virtual ~LexicalReorderingTableCompact();
-
-    virtual std::vector<float> GetScore(const Phrase& f, const Phrase& e, const Phrase& c);
-    
-    static LexicalReorderingTable* CheckAndLoad(
-                                const std::string& filePath,
-                                const std::vector<FactorType>& f_factors,
-                                const std::vector<FactorType>& e_factors,
-                                const std::vector<FactorType>& c_factors);
-    
-    void Load(std::string filePath);
+private:
+  bool m_inMemory;
+
+  size_t m_numScoreComponent;
+  bool m_multipleScoreTrees;
+
+  BlockHashIndex m_hash;
+
+  typedef CanonicalHuffman<float> ScoreTree;
+  std::vector<ScoreTree*> m_scoreTrees;
+
+  StringVector<unsigned char, unsigned long, MmapAllocator>  m_scoresMapped;
+  StringVector<unsigned char, unsigned long, std::allocator> m_scoresMemory;
+
+  std::string MakeKey(const Phrase& f, const Phrase& e, const Phrase& c) const;
+  std::string MakeKey(const std::string& f, const std::string& e, const std::string& c) const;
+
+public:
+  LexicalReorderingTableCompact(
+    const std::string& filePath,
+    const std::vector<FactorType>& f_factors,
+    const std::vector<FactorType>& e_factors,
+    const std::vector<FactorType>& c_factors);
+
+  LexicalReorderingTableCompact(
+    const std::vector<FactorType>& f_factors,
+    const std::vector<FactorType>& e_factors,
+    const std::vector<FactorType>& c_factors);
+
+  virtual ~LexicalReorderingTableCompact();
+
+  virtual std::vector<float> GetScore(const Phrase& f, const Phrase& e, const Phrase& c);
+
+  static LexicalReorderingTable* CheckAndLoad(
+    const std::string& filePath,
+    const std::vector<FactorType>& f_factors,
+    const std::vector<FactorType>& e_factors,
+    const std::vector<FactorType>& c_factors);
+
+  void Load(std::string filePath);
 };
 
 }
diff --git a/moses/TranslationModel/CompactPT/LexicalReorderingTableCreator.cpp b/moses/TranslationModel/CompactPT/LexicalReorderingTableCreator.cpp
index a3eee1694..655ed01ca 100644
--- a/moses/TranslationModel/CompactPT/LexicalReorderingTableCreator.cpp
+++ b/moses/TranslationModel/CompactPT/LexicalReorderingTableCreator.cpp
@@ -1,23 +1,23 @@
-// $Id$                                                                                                                               
-// vim:tabstop=2                                                                                                                      
-/***********************************************************************                                                              
-Moses - factored phrase-based language decoder                                                                                        
-Copyright (C) 2006 University of Edinburgh                                                                                            
-                                                                                                                                      
-This library is free software; you can redistribute it and/or                                                                         
-modify it under the terms of the GNU Lesser General Public                                                                            
-License as published by the Free Software Foundation; either                                                                          
-version 2.1 of the License, or (at your option) any later version.                                                                    
-                                                                                                                                      
-This library is distributed in the hope that it will be useful,                                                                       
-but WITHOUT ANY WARRANTY; without even the implied warranty of                                                                        
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU                                                                     
-Lesser General Public License for more details.                                                                                       
-                                                                                                                                      
-You should have received a copy of the GNU Lesser General Public                                                                      
-License along with this library; if not, write to the Free Software                                                                   
-Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA                                                        
-***********************************************************************/  
+// $Id$
+// vim:tabstop=2
+/***********************************************************************
+Moses - factored phrase-based language decoder
+Copyright (C) 2006 University of Edinburgh
+
+This library is free software; you can redistribute it and/or
+modify it under the terms of the GNU Lesser General Public
+License as published by the Free Software Foundation; either
+version 2.1 of the License, or (at your option) any later version.
+
+This library is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public
+License along with this library; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+***********************************************************************/
 
 #include "LexicalReorderingTableCreator.h"
 #include "ThrowingFwrite.h"
@@ -25,7 +25,8 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 
 #include "util/file.hh"
 
-namespace Moses {
+namespace Moses
+{
 
 LexicalReorderingTableCreator::LexicalReorderingTableCreator(
   std::string inPath, std::string outPath, std::string tempfilePath,
@@ -34,49 +35,47 @@ LexicalReorderingTableCreator::LexicalReorderingTableCreator(
 #ifdef WITH_THREADS
   , size_t threads
 #endif
-  )
+)
   : m_inPath(inPath), m_outPath(outPath), m_tempfilePath(tempfilePath),
-  m_orderBits(orderBits), m_fingerPrintBits(fingerPrintBits),
-  m_numScoreComponent(0), m_multipleScoreTrees(multipleScoreTrees),
-  m_quantize(quantize), m_separator(" ||| "),
-  m_hash(m_orderBits, m_fingerPrintBits), m_lastFlushedLine(-1)
-#ifdef WITH_THREADS  
-  , m_threads(threads)
+    m_orderBits(orderBits), m_fingerPrintBits(fingerPrintBits),
+    m_numScoreComponent(0), m_multipleScoreTrees(multipleScoreTrees),
+    m_quantize(quantize), m_separator(" ||| "),
+    m_hash(m_orderBits, m_fingerPrintBits), m_lastFlushedLine(-1)
+#ifdef WITH_THREADS
+    , m_threads(threads)
 #endif
-{  
+{
   PrintInfo();
-    
+
   m_outFile = std::fopen(m_outPath.c_str(), "w");
-  
+
   std::cerr << "Pass 1/2: Creating phrase index + Counting scores" << std::endl;
-  m_hash.BeginSave(m_outFile); 
+  m_hash.BeginSave(m_outFile);
 
 
   if(tempfilePath.size()) {
     MmapAllocator<unsigned char> allocEncoded(util::FMakeTemp(tempfilePath));
     m_encodedScores = new StringVector<unsigned char, unsigned long, MmapAllocator>(allocEncoded);
-  }
-  else {
+  } else {
     m_encodedScores = new StringVector<unsigned char, unsigned long, MmapAllocator>();
   }
-  
+
   EncodeScores();
-  
+
   std::cerr << "Intermezzo: Calculating Huffman code sets" << std::endl;
   CalcHuffmanCodes();
-  
+
   std::cerr << "Pass 2/2: Compressing scores" << std::endl;
-  
-  
-    if(tempfilePath.size()) {
+
+
+  if(tempfilePath.size()) {
     MmapAllocator<unsigned char> allocCompressed(util::FMakeTemp(tempfilePath));
     m_compressedScores = new StringVector<unsigned char, unsigned long, MmapAllocator>(allocCompressed);
-  }
-  else {
+  } else {
     m_compressedScores = new StringVector<unsigned char, unsigned long, MmapAllocator>();
   }
   CompressScores();
-  
+
   std::cerr << "Saving to " << m_outPath << std::endl;
   Save();
   std::cerr << "Done" << std::endl;
@@ -84,20 +83,20 @@ LexicalReorderingTableCreator::LexicalReorderingTableCreator(
 }
 
 void LexicalReorderingTableCreator::PrintInfo()
-{  
+{
   std::cerr << "Used options:" << std::endl;
   std::cerr << "\tText reordering table will be read from: " << m_inPath << std::endl;
   std::cerr << "\tOutput reordering table will be written to: " << m_outPath << std::endl;
   std::cerr << "\tStep size for source landmark phrases: 2^" << m_orderBits << "=" << (1ul << m_orderBits) << std::endl;
   std::cerr << "\tPhrase fingerprint size: " << m_fingerPrintBits << " bits / P(fp)=" << (float(1)/(1ul << m_fingerPrintBits)) << std::endl;
-  std::cerr << "\tSingle Huffman code set for score components: " << (m_multipleScoreTrees ? "no" : "yes") << std::endl;    
+  std::cerr << "\tSingle Huffman code set for score components: " << (m_multipleScoreTrees ? "no" : "yes") << std::endl;
   std::cerr << "\tUsing score quantization: ";
   if(m_quantize)
     std::cerr << m_quantize << " best" << std::endl;
   else
     std::cerr << "no" << std::endl;
-  
-#ifdef WITH_THREADS    
+
+#ifdef WITH_THREADS
   std::cerr << "\tRunning with " << m_threads << " threads" << std::endl;
 #endif
   std::cerr << std::endl;
@@ -109,7 +108,7 @@ LexicalReorderingTableCreator::~LexicalReorderingTableCreator()
     delete m_scoreTrees[i];
     delete m_scoreCounters[i];
   }
-  
+
   delete m_encodedScores;
   delete m_compressedScores;
 }
@@ -121,9 +120,8 @@ void LexicalReorderingTableCreator::EncodeScores()
 
 #ifdef WITH_THREADS
   boost::thread_group threads;
-  for (size_t i = 0; i < m_threads; ++i)
-  {
-    EncodingTaskReordering* et = new EncodingTaskReordering(inFile, *this);    
+  for (size_t i = 0; i < m_threads; ++i) {
+    EncodingTaskReordering* et = new EncodingTaskReordering(inFile, *this);
     threads.create_thread(*et);
   }
   threads.join_all();
@@ -136,17 +134,16 @@ void LexicalReorderingTableCreator::EncodeScores()
 }
 
 void LexicalReorderingTableCreator::CalcHuffmanCodes()
-{   
+{
   std::vector<ScoreTree*>::iterator treeIt = m_scoreTrees.begin();
   for(std::vector<ScoreCounter*>::iterator it = m_scoreCounters.begin();
-    it != m_scoreCounters.end(); it++)
-  {
+      it != m_scoreCounters.end(); it++) {
     if(m_quantize)
-        (*it)->Quantize(m_quantize);
-    
+      (*it)->Quantize(m_quantize);
+
     std::cerr << "\tCreating Huffman codes for " << (*it)->Size()
-        << " scores" << std::endl;
-    
+              << " scores" << std::endl;
+
     *treeIt = new ScoreTree((*it)->Begin(), (*it)->End());
     treeIt++;
   }
@@ -158,7 +155,7 @@ void LexicalReorderingTableCreator::CompressScores()
 #ifdef WITH_THREADS
   boost::thread_group threads;
   for (size_t i = 0; i < m_threads; ++i) {
-    CompressionTaskReordering* ct = new CompressionTaskReordering(*m_encodedScores, *this);    
+    CompressionTaskReordering* ct = new CompressionTaskReordering(*m_encodedScores, *this);
     threads.create_thread(*ct);
   }
   threads.join_all();
@@ -171,12 +168,12 @@ void LexicalReorderingTableCreator::CompressScores()
 }
 
 void LexicalReorderingTableCreator::Save()
-{  
+{
   ThrowingFwrite(&m_numScoreComponent, sizeof(m_numScoreComponent), 1, m_outFile);
   ThrowingFwrite(&m_multipleScoreTrees, sizeof(m_multipleScoreTrees), 1, m_outFile);
   for(size_t i = 0; i < m_scoreTrees.size(); i++)
     m_scoreTrees[i]->Save(m_outFile);
-  
+
   m_compressedScores->save(m_outFile);
 }
 
@@ -192,38 +189,37 @@ std::string LexicalReorderingTableCreator::EncodeLine(std::vector<std::string>&
 {
   std::string scoresString = tokens.back();
   std::stringstream scoresStream;
-  
+
   std::vector<float> scores;
   Tokenize<float>(scores, scoresString);
-  
+
   if(!m_numScoreComponent) {
     m_numScoreComponent = scores.size();
     m_scoreCounters.resize(m_multipleScoreTrees ? m_numScoreComponent : 1);
     for(std::vector<ScoreCounter*>::iterator it = m_scoreCounters.begin();
         it != m_scoreCounters.end(); it++)
-        *it = new ScoreCounter();
+      *it = new ScoreCounter();
     m_scoreTrees.resize(m_multipleScoreTrees ? m_numScoreComponent : 1);
   }
-  
+
   if(m_numScoreComponent != scores.size()) {
     std::cerr << "Error: Wrong number of scores detected ("
-      << scores.size() << " != " << m_numScoreComponent << ") :" << std::endl;
+              << scores.size() << " != " << m_numScoreComponent << ") :" << std::endl;
     std::cerr << "Line: " << tokens[0] << " ||| ... ||| " << scoresString << std::endl;
-    abort();  
+    abort();
   }
-  
+
   size_t c = 0;
   float score;
-  while(c < m_numScoreComponent)
-  {
+  while(c < m_numScoreComponent) {
     score = scores[c];
     score = FloorScore(TransformScore(score));
     scoresStream.write((char*)&score, sizeof(score));
-    
+
     m_scoreCounters[m_multipleScoreTrees ? c : 0]->Increase(score);
     c++;
   }
-  
+
   return scoresStream.str();
 }
 
@@ -232,25 +228,23 @@ void LexicalReorderingTableCreator::AddEncodedLine(PackedItem& pi)
   m_queue.push(pi);
 }
 
-void LexicalReorderingTableCreator::FlushEncodedQueue(bool force) {
-  if(force || m_queue.size() > 10000)
-  {
-    while(!m_queue.empty() && m_lastFlushedLine + 1 == m_queue.top().GetLine())
-    {
+void LexicalReorderingTableCreator::FlushEncodedQueue(bool force)
+{
+  if(force || m_queue.size() > 10000) {
+    while(!m_queue.empty() && m_lastFlushedLine + 1 == m_queue.top().GetLine()) {
       PackedItem pi = m_queue.top();
       m_queue.pop();
       m_lastFlushedLine++;
-      
-      m_lastRange.push_back(pi.GetSrc());    
+
+      m_lastRange.push_back(pi.GetSrc());
       m_encodedScores->push_back(pi.GetTrg());
-      
+
       if((pi.GetLine()+1) % 100000 == 0)
-          std::cerr << ".";
+        std::cerr << ".";
       if((pi.GetLine()+1) % 5000000 == 0)
-          std::cerr << "[" << (pi.GetLine()+1) << "]" << std::endl;
-          
-      if(m_lastRange.size() == (1ul << m_orderBits))
-      {
+        std::cerr << "[" << (pi.GetLine()+1) << "]" << std::endl;
+
+      if(m_lastRange.size() == (1ul << m_orderBits)) {
         m_hash.AddRange(m_lastRange);
         m_hash.SaveLastRange();
         m_hash.DropLastRange();
@@ -258,14 +252,13 @@ void LexicalReorderingTableCreator::FlushEncodedQueue(bool force) {
       }
     }
   }
-  
-  if(force)
-  {
+
+  if(force) {
     m_lastFlushedLine = -1;
 
     m_hash.AddRange(m_lastRange);
     m_lastRange.clear();
-    
+
 #ifdef WITH_THREADS
     m_hash.WaitAll();
 #endif
@@ -278,56 +271,55 @@ void LexicalReorderingTableCreator::FlushEncodedQueue(bool force) {
   }
 }
 
-std::string LexicalReorderingTableCreator::CompressEncodedScores(std::string &encodedScores) {
+std::string LexicalReorderingTableCreator::CompressEncodedScores(std::string &encodedScores)
+{
   std::stringstream encodedScoresStream(encodedScores);
   encodedScoresStream.unsetf(std::ios::skipws);
-  
+
   std::string compressedScores;
   BitWrapper<> compressedScoresStream(compressedScores);
-  
+
   size_t currScore = 0;
   float score;
   encodedScoresStream.read((char*) &score, sizeof(score));
-  
+
   while(encodedScoresStream) {
     size_t index = currScore % m_scoreTrees.size();
-    
+
     if(m_quantize)
       score = m_scoreCounters[index]->LowerBound(score);
-    
+
     m_scoreTrees[index]->Put(compressedScoresStream, score);
     encodedScoresStream.read((char*) &score, sizeof(score));
     currScore++;
   }
-  
+
   return compressedScores;
 }
 
-void LexicalReorderingTableCreator::AddCompressedScores(PackedItem& pi) {
-  m_queue.push(pi); 
+void LexicalReorderingTableCreator::AddCompressedScores(PackedItem& pi)
+{
+  m_queue.push(pi);
 }
 
 void LexicalReorderingTableCreator::FlushCompressedQueue(bool force)
-{  
-  if(force || m_queue.size() > 10000)
-  {
-    while(!m_queue.empty() && m_lastFlushedLine + 1 == m_queue.top().GetLine())
-    {
+{
+  if(force || m_queue.size() > 10000) {
+    while(!m_queue.empty() && m_lastFlushedLine + 1 == m_queue.top().GetLine()) {
       PackedItem pi = m_queue.top();
       m_queue.pop();
       m_lastFlushedLine++;
-          
+
       m_compressedScores->push_back(pi.GetTrg());
-      
+
       if((pi.GetLine()+1) % 100000 == 0)
-          std::cerr << ".";
+        std::cerr << ".";
       if((pi.GetLine()+1) % 5000000 == 0)
-          std::cerr << "[" << (pi.GetLine()+1) << "]" << std::endl;
+        std::cerr << "[" << (pi.GetLine()+1) << "]" << std::endl;
     }
   }
-  
-  if(force)
-  {
+
+  if(force) {
     m_lastFlushedLine = -1;
     std::cerr << std::endl << std::endl;
   }
@@ -343,63 +335,61 @@ boost::mutex EncodingTaskReordering::m_fileMutex;
 
 EncodingTaskReordering::EncodingTaskReordering(InputFileStream& inFile, LexicalReorderingTableCreator& creator)
   : m_inFile(inFile), m_creator(creator) {}
-  
+
 void EncodingTaskReordering::operator()()
 {
   size_t lineNum = 0;
-  
+
   std::vector<std::string> lines;
   size_t max_lines = 1000;
   lines.reserve(max_lines);
-  
+
   {
 #ifdef WITH_THREADS
     boost::mutex::scoped_lock lock(m_fileMutex);
 #endif
     std::string line;
     while(lines.size() < max_lines && std::getline(m_inFile, line))
-        lines.push_back(line);
+      lines.push_back(line);
     lineNum = m_lineNum;
     m_lineNum += lines.size();
   }
-  
+
   std::vector<PackedItem> result;
   result.reserve(max_lines);
-  
-  while(lines.size())
-  {
-    for(size_t i = 0; i < lines.size(); i++)
-    {
+
+  while(lines.size()) {
+    for(size_t i = 0; i < lines.size(); i++) {
       std::vector<std::string> tokens;
       Moses::TokenizeMultiCharSeparator(tokens, lines[i], m_creator.m_separator);
-      
+
       std::string encodedLine = m_creator.EncodeLine(tokens);
-      
+
       std::string f = tokens[0];
-      
+
       std::string e;
       if(tokens.size() > 2)
         e = tokens[1];
-      
+
       PackedItem packedItem(lineNum + i, m_creator.MakeSourceTargetKey(f, e),
                             encodedLine, i);
       result.push_back(packedItem);
     }
     lines.clear();
-    
+
     {
 #ifdef WITH_THREADS
       boost::mutex::scoped_lock lock(m_mutex);
 #endif
-      for(size_t i = 0; i < result.size(); i++) 
+      for(size_t i = 0; i < result.size(); i++)
         m_creator.AddEncodedLine(result[i]);
-      m_creator.FlushEncodedQueue();  
+      m_creator.FlushEncodedQueue();
     }
-    
+
     result.clear();
     lines.reserve(max_lines);
     result.reserve(max_lines);
-    
+
 #ifdef WITH_THREADS
     boost::mutex::scoped_lock lock(m_fileMutex);
 #endif
@@ -419,11 +409,11 @@ boost::mutex CompressionTaskReordering::m_mutex;
 #endif
 
 CompressionTaskReordering::CompressionTaskReordering(StringVector<unsigned char, unsigned long,
-                              MmapAllocator>& encodedScores,
-                              LexicalReorderingTableCreator& creator)
+    MmapAllocator>& encodedScores,
+    LexicalReorderingTableCreator& creator)
   : m_encodedScores(encodedScores), m_creator(creator)
 { }
-  
+
 void CompressionTaskReordering::operator()()
 {
   size_t scoresNum;
@@ -434,12 +424,11 @@ void CompressionTaskReordering::operator()()
     scoresNum = m_scoresNum;
     m_scoresNum++;
   }
-  
-  while(scoresNum < m_encodedScores.size())
-  {
+
+  while(scoresNum < m_encodedScores.size()) {
     std::string scores = m_encodedScores[scoresNum];
     std::string compressedScores
-        = m_creator.CompressEncodedScores(scores);
+    = m_creator.CompressEncodedScores(scores);
 
     std::string dummy;
     PackedItem packedItem(scoresNum, dummy, compressedScores, 0);
@@ -449,9 +438,9 @@ void CompressionTaskReordering::operator()()
 #endif
     m_creator.AddCompressedScores(packedItem);
     m_creator.FlushCompressedQueue();
-    
-    scoresNum = m_scoresNum;  
-    m_scoresNum++;    
+
+    scoresNum = m_scoresNum;
+    m_scoresNum++;
   }
 }
 
diff --git a/moses/TranslationModel/CompactPT/LexicalReorderingTableCreator.h b/moses/TranslationModel/CompactPT/LexicalReorderingTableCreator.h
index 2e202ce9b..1bf8444fe 100644
--- a/moses/TranslationModel/CompactPT/LexicalReorderingTableCreator.h
+++ b/moses/TranslationModel/CompactPT/LexicalReorderingTableCreator.h
@@ -1,139 +1,141 @@
-// $Id$                                                                                                                               
-// vim:tabstop=2                                                                                                                      
-/***********************************************************************                                                              
-Moses - factored phrase-based language decoder                                                                                        
-Copyright (C) 2006 University of Edinburgh                                                                                            
-                                                                                                                                      
-This library is free software; you can redistribute it and/or                                                                         
-modify it under the terms of the GNU Lesser General Public                                                                            
-License as published by the Free Software Foundation; either                                                                          
-version 2.1 of the License, or (at your option) any later version.                                                                    
-                                                                                                                                      
-This library is distributed in the hope that it will be useful,                                                                       
-but WITHOUT ANY WARRANTY; without even the implied warranty of                                                                        
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU                                                                     
-Lesser General Public License for more details.                                                                                       
-                                                                                                                                      
-You should have received a copy of the GNU Lesser General Public                                                                      
-License along with this library; if not, write to the Free Software                                                                   
-Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA                                                        
-***********************************************************************/  
+// $Id$
+// vim:tabstop=2
+/***********************************************************************
+Moses - factored phrase-based language decoder
+Copyright (C) 2006 University of Edinburgh
+
+This library is free software; you can redistribute it and/or
+modify it under the terms of the GNU Lesser General Public
+License as published by the Free Software Foundation; either
+version 2.1 of the License, or (at your option) any later version.
+
+This library is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public
+License along with this library; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+***********************************************************************/
 
 #ifndef moses_LexicalReorderingTableCreator_h
 #define moses_LexicalReorderingTableCreator_h
 
 #include "PhraseTableCreator.h"
 
-namespace Moses {
-
-class LexicalReorderingTableCreator {
-  private:
-    std::string m_inPath;
-    std::string m_outPath;
-    std::string m_tempfilePath;
-    
-    std::FILE* m_outFile;
-    
-    size_t m_orderBits;
-    size_t m_fingerPrintBits;
-    
-    size_t m_numScoreComponent;
-    
-    bool m_multipleScoreTrees;
-    bool m_quantize;
-    
-    std::string m_separator;
-    
-    BlockHashIndex m_hash;
-    
-    typedef Counter<float> ScoreCounter;
-    typedef CanonicalHuffman<float> ScoreTree;  
-  
-    std::vector<ScoreCounter*> m_scoreCounters;
-    std::vector<ScoreTree*> m_scoreTrees;
-    
-    StringVector<unsigned char, unsigned long, MmapAllocator>* m_encodedScores;
-    StringVector<unsigned char, unsigned long, MmapAllocator>* m_compressedScores;
-    
-    std::priority_queue<PackedItem> m_queue;
-    long m_lastFlushedLine;
-    long m_lastFlushedSourceNum;
-    std::string m_lastFlushedSourcePhrase;
-    std::vector<std::string> m_lastRange;
-    
-#ifdef WITH_THREADS    
-    size_t m_threads;
+namespace Moses
+{
+
+class LexicalReorderingTableCreator
+{
+private:
+  std::string m_inPath;
+  std::string m_outPath;
+  std::string m_tempfilePath;
+
+  std::FILE* m_outFile;
+
+  size_t m_orderBits;
+  size_t m_fingerPrintBits;
+
+  size_t m_numScoreComponent;
+
+  bool m_multipleScoreTrees;
+  bool m_quantize;
+
+  std::string m_separator;
+
+  BlockHashIndex m_hash;
+
+  typedef Counter<float> ScoreCounter;
+  typedef CanonicalHuffman<float> ScoreTree;
+
+  std::vector<ScoreCounter*> m_scoreCounters;
+  std::vector<ScoreTree*> m_scoreTrees;
+
+  StringVector<unsigned char, unsigned long, MmapAllocator>* m_encodedScores;
+  StringVector<unsigned char, unsigned long, MmapAllocator>* m_compressedScores;
+
+  std::priority_queue<PackedItem> m_queue;
+  long m_lastFlushedLine;
+  long m_lastFlushedSourceNum;
+  std::string m_lastFlushedSourcePhrase;
+  std::vector<std::string> m_lastRange;
+
+#ifdef WITH_THREADS
+  size_t m_threads;
 #endif
-    
-    void PrintInfo();
-    
-    void EncodeScores();
-    void CalcHuffmanCodes();
-    void CompressScores();
-    void Save();
-    
-    std::string MakeSourceTargetKey(std::string&, std::string&);
-    
-    std::string EncodeLine(std::vector<std::string>& tokens);
-    void AddEncodedLine(PackedItem& pi);
-    void FlushEncodedQueue(bool force = false);
-    
-    std::string CompressEncodedScores(std::string &encodedScores);
-    void AddCompressedScores(PackedItem& pi);
-    void FlushCompressedQueue(bool force = false);
-    
-  public:
-    LexicalReorderingTableCreator(std::string inPath,
-                                  std::string outPath,
-                                  std::string tempfilePath,
-                                  size_t orderBits = 10,
-                                  size_t fingerPrintBits = 16,
-                                  bool multipleScoreTrees = true,
-                                  size_t quantize = 0
+
+  void PrintInfo();
+
+  void EncodeScores();
+  void CalcHuffmanCodes();
+  void CompressScores();
+  void Save();
+
+  std::string MakeSourceTargetKey(std::string&, std::string&);
+
+  std::string EncodeLine(std::vector<std::string>& tokens);
+  void AddEncodedLine(PackedItem& pi);
+  void FlushEncodedQueue(bool force = false);
+
+  std::string CompressEncodedScores(std::string &encodedScores);
+  void AddCompressedScores(PackedItem& pi);
+  void FlushCompressedQueue(bool force = false);
+
+public:
+  LexicalReorderingTableCreator(std::string inPath,
+                                std::string outPath,
+                                std::string tempfilePath,
+                                size_t orderBits = 10,
+                                size_t fingerPrintBits = 16,
+                                bool multipleScoreTrees = true,
+                                size_t quantize = 0
 #ifdef WITH_THREADS
-                                  , size_t threads = 2
-#endif   
-                                  );
-    
-    ~LexicalReorderingTableCreator();
-    
+                                    , size_t threads = 2
+#endif
+                               );
+
+  ~LexicalReorderingTableCreator();
+
   friend class EncodingTaskReordering;
   friend class CompressionTaskReordering;
 };
 
 class EncodingTaskReordering
 {
-  private:
+private:
 #ifdef WITH_THREADS
-    static boost::mutex m_mutex;
-    static boost::mutex m_fileMutex;
+  static boost::mutex m_mutex;
+  static boost::mutex m_fileMutex;
 #endif
-    static size_t m_lineNum;
-    static size_t m_sourcePhraseNum;
-    static std::string m_lastSourcePhrase;
-    
-    InputFileStream& m_inFile;
-    LexicalReorderingTableCreator& m_creator;
-    
-  public:
-    EncodingTaskReordering(InputFileStream& inFile, LexicalReorderingTableCreator& creator);
-    void operator()();
+  static size_t m_lineNum;
+  static size_t m_sourcePhraseNum;
+  static std::string m_lastSourcePhrase;
+
+  InputFileStream& m_inFile;
+  LexicalReorderingTableCreator& m_creator;
+
+public:
+  EncodingTaskReordering(InputFileStream& inFile, LexicalReorderingTableCreator& creator);
+  void operator()();
 };
 
 class CompressionTaskReordering
 {
-  private:
+private:
 #ifdef WITH_THREADS
-    static boost::mutex m_mutex;
+  static boost::mutex m_mutex;
 #endif
-    static size_t m_scoresNum;
-    StringVector<unsigned char, unsigned long, MmapAllocator> &m_encodedScores;
-    LexicalReorderingTableCreator &m_creator;
-    
-  public:
-    CompressionTaskReordering(StringVector<unsigned char, unsigned long, MmapAllocator>&
-                    m_encodedScores, LexicalReorderingTableCreator& creator);
-    void operator()();
+  static size_t m_scoresNum;
+  StringVector<unsigned char, unsigned long, MmapAllocator> &m_encodedScores;
+  LexicalReorderingTableCreator &m_creator;
+
+public:
+  CompressionTaskReordering(StringVector<unsigned char, unsigned long, MmapAllocator>&
+                            m_encodedScores, LexicalReorderingTableCreator& creator);
+  void operator()();
 };
 
 }
diff --git a/moses/TranslationModel/CompactPT/ListCoders.h b/moses/TranslationModel/CompactPT/ListCoders.h
index 329e1297a..b41e183ce 100644
--- a/moses/TranslationModel/CompactPT/ListCoders.h
+++ b/moses/TranslationModel/CompactPT/ListCoders.h
@@ -1,23 +1,23 @@
-// $Id$                                                                                                                               
-// vim:tabstop=2                                                                                                                      
-/***********************************************************************                                                              
-Moses - factored phrase-based language decoder                                                                                        
-Copyright (C) 2006 University of Edinburgh                                                                                            
-                                                                                                                                      
-This library is free software; you can redistribute it and/or                                                                         
-modify it under the terms of the GNU Lesser General Public                                                                            
-License as published by the Free Software Foundation; either                                                                          
-version 2.1 of the License, or (at your option) any later version.                                                                    
-                                                                                                                                      
-This library is distributed in the hope that it will be useful,                                                                       
-but WITHOUT ANY WARRANTY; without even the implied warranty of                                                                        
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU                                                                     
-Lesser General Public License for more details.                                                                                       
-                                                                                                                                      
-You should have received a copy of the GNU Lesser General Public                                                                      
-License along with this library; if not, write to the Free Software                                                                   
-Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA                                                        
-***********************************************************************/  
+// $Id$
+// vim:tabstop=2
+/***********************************************************************
+Moses - factored phrase-based language decoder
+Copyright (C) 2006 University of Edinburgh
+
+This library is free software; you can redistribute it and/or
+modify it under the terms of the GNU Lesser General Public
+License as published by the Free Software Foundation; either
+version 2.1 of the License, or (at your option) any later version.
+
+This library is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public
+License along with this library; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+***********************************************************************/
 
 #ifndef moses_ListCoders_h
 #define moses_ListCoders_h
@@ -31,94 +31,86 @@ namespace Moses
 template <typename T = unsigned int>
 class VarIntType
 {
-  private:
-    template <typename IntType, typename OutIt>
-    static void EncodeSymbol(IntType input, OutIt output)
-    {
-      if(input == 0)
-      {
-        *output = 0;
-        output++;
-        return;
-      }
-    
-      T msb = 1 << (sizeof(T)*8-1);
-      IntType mask  = ~msb;
-      IntType shift = (sizeof(T)*8-1);
-      
-      while(input)
-      {
-        T res = input & mask;
-        input >>= shift;
-        if(input)
-            res |= msb;
-        *output = res;
-        output++;
-      }
-    };
-    
-    template <typename InIt, typename IntType>
-    static void DecodeSymbol(InIt &it, InIt end, IntType &output)
-    {
-      T msb = 1 << (sizeof(T)*8-1);
-      IntType shift = (sizeof(T)*8-1);
-      
-      output = 0;
-      size_t i = 0;
-      while(it != end && *it & msb) {
-        IntType temp = *it & ~msb;
-        temp <<= shift*i;
-        output |= temp;
-        it++; i++;
-      }
-      assert(it != end);
-      
-      IntType temp = *it;
+private:
+  template <typename IntType, typename OutIt>
+  static void EncodeSymbol(IntType input, OutIt output) {
+    if(input == 0) {
+      *output = 0;
+      output++;
+      return;
+    }
+
+    T msb = 1 << (sizeof(T)*8-1);
+    IntType mask  = ~msb;
+    IntType shift = (sizeof(T)*8-1);
+
+    while(input) {
+      T res = input & mask;
+      input >>= shift;
+      if(input)
+        res |= msb;
+      *output = res;
+      output++;
+    }
+  };
+
+  template <typename InIt, typename IntType>
+  static void DecodeSymbol(InIt &it, InIt end, IntType &output) {
+    T msb = 1 << (sizeof(T)*8-1);
+    IntType shift = (sizeof(T)*8-1);
+
+    output = 0;
+    size_t i = 0;
+    while(it != end && *it & msb) {
+      IntType temp = *it & ~msb;
       temp <<= shift*i;
       output |= temp;
       it++;
+      i++;
     }
+    assert(it != end);
 
-  public:
-        
-    template <typename InIt, typename OutIt>
-    static void Encode(InIt it, InIt end, OutIt outIt)
-    {
-      while(it != end)
-      {
-        EncodeSymbol(*it, outIt);
-        it++;
-      }
+    IntType temp = *it;
+    temp <<= shift*i;
+    output |= temp;
+    it++;
+  }
+
+public:
+
+  template <typename InIt, typename OutIt>
+  static void Encode(InIt it, InIt end, OutIt outIt) {
+    while(it != end) {
+      EncodeSymbol(*it, outIt);
+      it++;
     }
-        
-    template <typename InIt, typename OutIt>
-    static void Decode(InIt &it, InIt end, OutIt outIt)
-    {
-      while(it != end)
-      {
-        size_t output;
-        DecodeSymbol(it, end, output);
-        *outIt = output;
-        outIt++;
-      }
+  }
+
+  template <typename InIt, typename OutIt>
+  static void Decode(InIt &it, InIt end, OutIt outIt) {
+    while(it != end) {
+      size_t output;
+      DecodeSymbol(it, end, output);
+      *outIt = output;
+      outIt++;
     }
-    
-    template <typename InIt>
-    static size_t DecodeAndSum(InIt &it, InIt end, size_t num)
-    {
-      size_t sum = 0;
-      size_t curr = 0;
-      
-      while(it != end && curr < num)
-      {
-        size_t output;
-        DecodeSymbol(it, end, output);
-        sum += output; curr++;
-      }
-      
-      return sum;
+  }
+
+  template <typename InIt>
+  static size_t DecodeAndSum(InIt &it, InIt end, size_t num) {
+    size_t sum = 0;
+    size_t curr = 0;
+
+    while(it != end && curr < num) {
+      size_t output;
+      DecodeSymbol(it, end, output);
+      sum += output;
+      curr++;
     }
 
+    return sum;
+  }
+
 };
 
 typedef VarIntType<unsigned char> VarByte;
@@ -129,179 +121,262 @@ typedef VarIntType<unsigned int>   VarInt32;
 
 class Simple9
 {
-  private:
-    typedef unsigned int uint;
-        
-    template <typename InIt>
-    inline static void EncodeSymbol(uint &output, InIt it, InIt end)
-    {
-      uint length = end - it;
-    
-      uint type = 0;
-      uint bitlength = 0;
-      
-      switch(length)
-      {
-        case 1:  type = 1; bitlength = 28; break;
-        case 2:  type = 2; bitlength = 14; break;
-        case 3:  type = 3; bitlength = 9;  break;
-        case 4:  type = 4; bitlength = 7;  break;
-        case 5:  type = 5; bitlength = 5;  break;
-        case 7:  type = 6; bitlength = 4;  break;
-        case 9:  type = 7; bitlength = 3;  break;
-        case 14: type = 8; bitlength = 2;  break;
-        case 28: type = 9; bitlength = 1;  break;
-      }
-    
-      output = 0;
-      output |= (type << 28);
-
-      uint i = 0;
-      while(it != end)
-      {
-          uint l = bitlength * (length-i-1);
-          output |= *it << l;
-          it++;
-          i++;
-      }
+private:
+  typedef unsigned int uint;
+
+  template <typename InIt>
+  inline static void EncodeSymbol(uint &output, InIt it, InIt end) {
+    uint length = end - it;
+
+    uint type = 0;
+    uint bitlength = 0;
+
+    switch(length) {
+    case 1:
+      type = 1;
+      bitlength = 28;
+      break;
+    case 2:
+      type = 2;
+      bitlength = 14;
+      break;
+    case 3:
+      type = 3;
+      bitlength = 9;
+      break;
+    case 4:
+      type = 4;
+      bitlength = 7;
+      break;
+    case 5:
+      type = 5;
+      bitlength = 5;
+      break;
+    case 7:
+      type = 6;
+      bitlength = 4;
+      break;
+    case 9:
+      type = 7;
+      bitlength = 3;
+      break;
+    case 14:
+      type = 8;
+      bitlength = 2;
+      break;
+    case 28:
+      type = 9;
+      bitlength = 1;
+      break;
     }
-    
-    template <typename OutIt>
-    static inline void DecodeSymbol(uint input, OutIt outIt)
-    {
-      uint type = (input >> 28);
-      
-      uint bitlen = 0;
-      uint shift = 0;
-      uint mask = 0;
-      
-      switch(type)
-      {
-        case 1: bitlen = 28; shift = 0;  mask = 268435455; break;
-        case 2: bitlen = 14; shift = 14; mask = 16383; break;
-        case 3: bitlen = 9;  shift = 18; mask = 511; break;
-        case 4: bitlen = 7;  shift = 21; mask = 127; break;
-        case 5: bitlen = 5;  shift = 20; mask = 31; break;
-        case 6: bitlen = 4;  shift = 24; mask = 15; break;
-        case 7: bitlen = 3;  shift = 24; mask = 7; break;
-        case 8: bitlen = 2;  shift = 26; mask = 3; break;
-        case 9: bitlen = 1;  shift = 27; mask = 1; break;
-      }
-    
-      while(shift > 0)
-      {
-        *outIt = (input >> shift) & mask;
-        shift -= bitlen;  
-        outIt++;
-      }
-      *outIt = input & mask;
-      outIt++;  
+
+    output = 0;
+    output |= (type << 28);
+
+    uint i = 0;
+    while(it != end) {
+      uint l = bitlength * (length-i-1);
+      output |= *it << l;
+      it++;
+      i++;
     }
-    
-    static inline size_t DecodeAndSumSymbol(uint input, size_t num, size_t &curr)
-    {
-      uint type = (input >> 28);
-      
-      uint bitlen = 0;
-      uint shift = 0;
-      uint mask = 0;
-      
-      switch(type)
-      {
-        case 1: bitlen = 28; shift = 0;  mask = 268435455; break;
-        case 2: bitlen = 14; shift = 14; mask = 16383; break;
-        case 3: bitlen = 9;  shift = 18; mask = 511; break;
-        case 4: bitlen = 7;  shift = 21; mask = 127; break;
-        case 5: bitlen = 5;  shift = 20; mask = 31; break;
-        case 6: bitlen = 4;  shift = 24; mask = 15; break;
-        case 7: bitlen = 3;  shift = 24; mask = 7; break;
-        case 8: bitlen = 2;  shift = 26; mask = 3; break;
-        case 9: bitlen = 1;  shift = 27; mask = 1; break;
-      }
+  }
 
-      size_t sum = 0;
-      while(shift > 0)
-      {
-        sum += (input >> shift) & mask;
-        shift -= bitlen;
-        if(++curr == num)
-          return sum;
-      }
-      sum += input & mask;
-      curr++;
-      return sum;
+  template <typename OutIt>
+  static inline void DecodeSymbol(uint input, OutIt outIt) {
+    uint type = (input >> 28);
+
+    uint bitlen = 0;
+    uint shift = 0;
+    uint mask = 0;
+
+    switch(type) {
+    case 1:
+      bitlen = 28;
+      shift = 0;
+      mask = 268435455;
+      break;
+    case 2:
+      bitlen = 14;
+      shift = 14;
+      mask = 16383;
+      break;
+    case 3:
+      bitlen = 9;
+      shift = 18;
+      mask = 511;
+      break;
+    case 4:
+      bitlen = 7;
+      shift = 21;
+      mask = 127;
+      break;
+    case 5:
+      bitlen = 5;
+      shift = 20;
+      mask = 31;
+      break;
+    case 6:
+      bitlen = 4;
+      shift = 24;
+      mask = 15;
+      break;
+    case 7:
+      bitlen = 3;
+      shift = 24;
+      mask = 7;
+      break;
+    case 8:
+      bitlen = 2;
+      shift = 26;
+      mask = 3;
+      break;
+    case 9:
+      bitlen = 1;
+      shift = 27;
+      mask = 1;
+      break;
     }
-    
-  public:
-    template <typename InIt, typename OutIt>
-    static void Encode(InIt it, InIt end, OutIt outIt)
-    {        
-      uint parts[] = { 1, 2, 3, 4, 5, 7, 9, 14, 28 };
-
-      uint buffer[28];
-      for(InIt i = it; i < end; i++)
-      {
-        uint lastbit = 1;
-        uint lastpos = 0;
-        uint lastyes = 0;
-        uint j = 0;
-        
-        double log2 = log(2);
-        while(j < 9 && lastpos < 28 && (i+lastpos) < end)
-        {
-          if(lastpos >= parts[j]) 
-              j++;
-          
-          buffer[lastpos] = *(i + lastpos);
-          
-          uint reqbit = ceil(log(buffer[lastpos]+1)/log2);
-          assert(reqbit <= 28);
-          
-          uint bit = 28/floor(28/reqbit);
-          if(lastbit < bit)
-              lastbit = bit;
-              
-          if(parts[j] > 28/lastbit)
-              break;
-          else if(lastpos == parts[j]-1)
-              lastyes = lastpos;
-              
-          lastpos++;
-        }
-        i += lastyes;       
-        
-        uint length = lastyes + 1;
-        uint output;
-        EncodeSymbol(output, buffer, buffer + length);
-        
-        *outIt = output;
-        outIt++;
-      }
+
+    while(shift > 0) {
+      *outIt = (input >> shift) & mask;
+      shift -= bitlen;
+      outIt++;
     }
-    
-    template <typename InIt, typename OutIt>
-    static void Decode(InIt &it, InIt end, OutIt outIt)
-    {
-      while(it != end)
-      {
-        DecodeSymbol(*it, outIt);
-        it++;
-      }
+    *outIt = input & mask;
+    outIt++;
+  }
+
+  static inline size_t DecodeAndSumSymbol(uint input, size_t num, size_t &curr) {
+    uint type = (input >> 28);
+
+    uint bitlen = 0;
+    uint shift = 0;
+    uint mask = 0;
+
+    switch(type) {
+    case 1:
+      bitlen = 28;
+      shift = 0;
+      mask = 268435455;
+      break;
+    case 2:
+      bitlen = 14;
+      shift = 14;
+      mask = 16383;
+      break;
+    case 3:
+      bitlen = 9;
+      shift = 18;
+      mask = 511;
+      break;
+    case 4:
+      bitlen = 7;
+      shift = 21;
+      mask = 127;
+      break;
+    case 5:
+      bitlen = 5;
+      shift = 20;
+      mask = 31;
+      break;
+    case 6:
+      bitlen = 4;
+      shift = 24;
+      mask = 15;
+      break;
+    case 7:
+      bitlen = 3;
+      shift = 24;
+      mask = 7;
+      break;
+    case 8:
+      bitlen = 2;
+      shift = 26;
+      mask = 3;
+      break;
+    case 9:
+      bitlen = 1;
+      shift = 27;
+      mask = 1;
+      break;
+    }
+
+    size_t sum = 0;
+    while(shift > 0) {
+      sum += (input >> shift) & mask;
+      shift -= bitlen;
+      if(++curr == num)
+        return sum;
     }
-    
-    template <typename InIt>
-    static size_t DecodeAndSum(InIt &it, InIt end, size_t num)
-    {
-      size_t sum = 0;
-      size_t curr = 0;
-      while(it != end && curr < num)
-      {
-        sum += DecodeAndSumSymbol(*it, num, curr);
-        it++;
+    sum += input & mask;
+    curr++;
+    return sum;
+  }
+
+public:
+  template <typename InIt, typename OutIt>
+  static void Encode(InIt it, InIt end, OutIt outIt) {
+    uint parts[] = { 1, 2, 3, 4, 5, 7, 9, 14, 28 };
+
+    uint buffer[28];
+    for(InIt i = it; i < end; i++) {
+      uint lastbit = 1;
+      uint lastpos = 0;
+      uint lastyes = 0;
+      uint j = 0;
+
+      double log2 = log(2);
+      while(j < 9 && lastpos < 28 && (i+lastpos) < end) {
+        if(lastpos >= parts[j])
+          j++;
+
+        buffer[lastpos] = *(i + lastpos);
+
+        uint reqbit = ceil(log(buffer[lastpos]+1)/log2);
+        assert(reqbit <= 28);
+
+        uint bit = 28/floor(28/reqbit);
+        if(lastbit < bit)
+          lastbit = bit;
+
+        if(parts[j] > 28/lastbit)
+          break;
+        else if(lastpos == parts[j]-1)
+          lastyes = lastpos;
+
+        lastpos++;
       }
-      assert(curr == num);
-      return sum;
+      i += lastyes;
+
+      uint length = lastyes + 1;
+      uint output;
+      EncodeSymbol(output, buffer, buffer + length);
+
+      *outIt = output;
+      outIt++;
+    }
+  }
+
+  template <typename InIt, typename OutIt>
+  static void Decode(InIt &it, InIt end, OutIt outIt) {
+    while(it != end) {
+      DecodeSymbol(*it, outIt);
+      it++;
+    }
+  }
+
+  template <typename InIt>
+  static size_t DecodeAndSum(InIt &it, InIt end, size_t num) {
+    size_t sum = 0;
+    size_t curr = 0;
+    while(it != end && curr < num) {
+      sum += DecodeAndSumSymbol(*it, num, curr);
+      it++;
     }
+    assert(curr == num);
+    return sum;
+  }
 };
 
 }
diff --git a/moses/TranslationModel/CompactPT/MmapAllocator.h b/moses/TranslationModel/CompactPT/MmapAllocator.h
index 049c0149d..7cd6dd49e 100644
--- a/moses/TranslationModel/CompactPT/MmapAllocator.h
+++ b/moses/TranslationModel/CompactPT/MmapAllocator.h
@@ -1,23 +1,23 @@
-// $Id$                                                                                                                               
-// vim:tabstop=2                                                                                                                      
-/***********************************************************************                                                              
-Moses - factored phrase-based language decoder                                                                                        
-Copyright (C) 2006 University of Edinburgh                                                                                            
-                                                                                                                                      
-This library is free software; you can redistribute it and/or                                                                         
-modify it under the terms of the GNU Lesser General Public                                                                            
-License as published by the Free Software Foundation; either                                                                          
-version 2.1 of the License, or (at your option) any later version.                                                                    
-                                                                                                                                      
-This library is distributed in the hope that it will be useful,                                                                       
-but WITHOUT ANY WARRANTY; without even the implied warranty of                                                                        
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU                                                                     
-Lesser General Public License for more details.                                                                                       
-                                                                                                                                      
-You should have received a copy of the GNU Lesser General Public                                                                      
-License along with this library; if not, write to the Free Software                                                                   
-Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA                                                        
-***********************************************************************/  
+// $Id$
+// vim:tabstop=2
+/***********************************************************************
+Moses - factored phrase-based language decoder
+Copyright (C) 2006 University of Edinburgh
+
+This library is free software; you can redistribute it and/or
+modify it under the terms of the GNU Lesser General Public
+License as published by the Free Software Foundation; either
+version 2.1 of the License, or (at your option) any later version.
+
+This library is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public
+License along with this library; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+***********************************************************************/
 
 #ifndef moses_MmapAllocator_h
 #define moses_MmapAllocator_h
@@ -30,175 +30,161 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 
 namespace Moses
 {
-    template <class T>
-    class MmapAllocator
-    {
-      protected:    
-        std::FILE* m_file_ptr;
-        size_t m_file_desc;
-        
-        size_t m_page_size;
-        size_t m_map_size;
-        
-        char* m_data_ptr;
-        size_t m_data_offset;
-        bool m_fixed;
-        size_t* m_count;
-        
-      public:
-        typedef T        value_type;
-        typedef T*       pointer;
-        typedef const T* const_pointer;
-        typedef T&       reference;
-        typedef const T& const_reference;
-        typedef std::size_t    size_type;
-        typedef std::ptrdiff_t difference_type;
-    
-        MmapAllocator() throw()
-         : m_file_ptr(std::tmpfile()), m_file_desc(fileno(m_file_ptr)),
-           m_page_size(sysconf(_SC_PAGE_SIZE)), m_map_size(0), m_data_ptr(0),
-           m_data_offset(0), m_fixed(false), m_count(new size_t(0))
-        { }
-        
-        MmapAllocator(std::FILE* f_ptr) throw()
-         : m_file_ptr(f_ptr), m_file_desc(fileno(m_file_ptr)),
-           m_page_size(sysconf(_SC_PAGE_SIZE)), m_map_size(0), m_data_ptr(0),
-           m_data_offset(0), m_fixed(false), m_count(new size_t(0))
-        { }
-        
-        MmapAllocator(std::FILE* f_ptr, size_t data_offset) throw()
-         : m_file_ptr(f_ptr), m_file_desc(fileno(m_file_ptr)),
-           m_page_size(sysconf(_SC_PAGE_SIZE)), m_map_size(0), m_data_ptr(0),
-           m_data_offset(data_offset), m_fixed(true), m_count(new size_t(0))
-        { }
-        
-        MmapAllocator(std::string fileName) throw()
-         : m_file_ptr(std::fopen(fileName.c_str(), "wb+")), m_file_desc(fileno(m_file_ptr)),
-           m_page_size(sysconf(_SC_PAGE_SIZE)), m_map_size(0), m_data_ptr(0),
-           m_data_offset(0), m_fixed(false), m_count(new size_t(0))
-        { }
-            
-        MmapAllocator(const MmapAllocator& c) throw()
-         : m_file_ptr(c.m_file_ptr), m_file_desc(c.m_file_desc),
-           m_page_size(c.m_page_size), m_map_size(c.m_map_size),
-           m_data_ptr(c.m_data_ptr), m_data_offset(c.m_data_offset),
-           m_fixed(c.m_fixed), m_count(c.m_count)
-        { 
-          (*m_count)++;
-        }
-        
-        ~MmapAllocator() throw()
-        {
-            if(m_data_ptr && *m_count == 0)
-            {
-                munmap(m_data_ptr, m_map_size);
-                if(!m_fixed && std::ftell(m_file_ptr) != -1)
-                    std::fclose(m_file_ptr);
-            }
-            (*m_count)--;
-        }
-     
-        template <class U>
-        struct rebind {
-            typedef MmapAllocator<U> other;
-        };
-     
-        pointer address (reference value) const
-        {
-            return &value;
-        }
-     
-        const_pointer address (const_reference value) const
-        {
-            return &value;
-        }
-     
-        size_type max_size () const throw()
-        {
-            return std::numeric_limits<size_t>::max() / sizeof(value_type);
-        }
-     
-        pointer allocate (size_type num, const void* = 0)
-        {
-            m_map_size = num * sizeof(T);
-            
-            if(!m_fixed)
-            {
-                size_t read = 0;
-                read += ftruncate(m_file_desc, m_map_size);
-                m_data_ptr = (char*)mmap(0, m_map_size, PROT_READ|PROT_WRITE, MAP_SHARED,
-                                       m_file_desc, 0);
-                if(m_data_ptr == MAP_FAILED)
-                  std::cerr << "Error: mmapping" << std::endl;
-                return (pointer)m_data_ptr;
-            }
-            else
-            {
-                size_t map_offset = (m_data_offset / m_page_size) * m_page_size;
-                size_t relative_offset = m_data_offset - map_offset;
-                
-                size_t map_size = m_map_size + relative_offset;
-            
-                m_data_ptr = (char*)mmap(0, map_size, PROT_READ, MAP_SHARED,
-                                       m_file_desc, map_offset);
-
-                return (pointer)(m_data_ptr + relative_offset);
-            }
-        }
-     
-        void deallocate (pointer p, size_type num)
-        {
-            if(!m_fixed) {
-                munmap(p, num * sizeof(T));
-            }
-            else {
-                size_t map_offset = (m_data_offset / m_page_size) * m_page_size;
-                size_t relative_offset = m_data_offset - map_offset;
-                munmap((pointer)((char*)p - relative_offset), num * sizeof(T));    
-            }
-            
-        }
-    
-        void construct (pointer p, const T& value)
-        {
-            if(!m_fixed)
-                new(p) value_type(value);
-        }
-        void destroy (pointer p)
-        {
-            if(!m_fixed)
-                p->~T();
-        }
-         
-        template <class T1, class T2>
-        friend bool operator== (const MmapAllocator<T1>&, const MmapAllocator<T2>&) throw();
-    
-        template <class T1, class T2>
-        friend bool operator!= (const MmapAllocator<T1>&, const MmapAllocator<T2>&) throw();
-    };
-    
-    template <class T1, class T2>
-    bool operator== (const MmapAllocator<T1>& a1,
-                     const MmapAllocator<T2>& a2) throw()
-    {    
-        bool equal = true;
-        equal &= a1.m_file_ptr == a2.m_file_ptr;
-        equal &= a1.m_file_desc == a2.m_file_desc;
-        equal &= a1.m_page_size == a2.m_page_size;
-        equal &= a1.m_map_size == a2.m_map_size;
-        equal &= a1.m_data_ptr == a2.m_data_ptr;
-        equal &= a1.m_data_offset == a2.m_data_offset;
-        equal &= a1.m_fixed == a2.m_fixed;
-        return equal;
+template <class T>
+class MmapAllocator
+{
+protected:
+  std::FILE* m_file_ptr;
+  size_t m_file_desc;
+
+  size_t m_page_size;
+  size_t m_map_size;
+
+  char* m_data_ptr;
+  size_t m_data_offset;
+  bool m_fixed;
+  size_t* m_count;
+
+public:
+  typedef T        value_type;
+  typedef T*       pointer;
+  typedef const T* const_pointer;
+  typedef T&       reference;
+  typedef const T& const_reference;
+  typedef std::size_t    size_type;
+  typedef std::ptrdiff_t difference_type;
+
+  MmapAllocator() throw()
+    : m_file_ptr(std::tmpfile()), m_file_desc(fileno(m_file_ptr)),
+      m_page_size(sysconf(_SC_PAGE_SIZE)), m_map_size(0), m_data_ptr(0),
+      m_data_offset(0), m_fixed(false), m_count(new size_t(0))
+  { }
+
+  MmapAllocator(std::FILE* f_ptr) throw()
+    : m_file_ptr(f_ptr), m_file_desc(fileno(m_file_ptr)),
+      m_page_size(sysconf(_SC_PAGE_SIZE)), m_map_size(0), m_data_ptr(0),
+      m_data_offset(0), m_fixed(false), m_count(new size_t(0))
+  { }
+
+  MmapAllocator(std::FILE* f_ptr, size_t data_offset) throw()
+    : m_file_ptr(f_ptr), m_file_desc(fileno(m_file_ptr)),
+      m_page_size(sysconf(_SC_PAGE_SIZE)), m_map_size(0), m_data_ptr(0),
+      m_data_offset(data_offset), m_fixed(true), m_count(new size_t(0))
+  { }
+
+  MmapAllocator(std::string fileName) throw()
+    : m_file_ptr(std::fopen(fileName.c_str(), "wb+")), m_file_desc(fileno(m_file_ptr)),
+      m_page_size(sysconf(_SC_PAGE_SIZE)), m_map_size(0), m_data_ptr(0),
+      m_data_offset(0), m_fixed(false), m_count(new size_t(0))
+  { }
+
+  MmapAllocator(const MmapAllocator& c) throw()
+    : m_file_ptr(c.m_file_ptr), m_file_desc(c.m_file_desc),
+      m_page_size(c.m_page_size), m_map_size(c.m_map_size),
+      m_data_ptr(c.m_data_ptr), m_data_offset(c.m_data_offset),
+      m_fixed(c.m_fixed), m_count(c.m_count) {
+    (*m_count)++;
+  }
+
+  ~MmapAllocator() throw() {
+    if(m_data_ptr && *m_count == 0) {
+      munmap(m_data_ptr, m_map_size);
+      if(!m_fixed && std::ftell(m_file_ptr) != -1)
+        std::fclose(m_file_ptr);
+    }
+    (*m_count)--;
+  }
+
+  template <class U>
+  struct rebind {
+    typedef MmapAllocator<U> other;
+  };
+
+  pointer address (reference value) const {
+    return &value;
+  }
+
+  const_pointer address (const_reference value) const {
+    return &value;
+  }
+
+  size_type max_size () const throw() {
+    return std::numeric_limits<size_t>::max() / sizeof(value_type);
+  }
+
+  pointer allocate (size_type num, const void* = 0) {
+    m_map_size = num * sizeof(T);
+
+    if(!m_fixed) {
+      size_t read = 0;
+      read += ftruncate(m_file_desc, m_map_size);
+      m_data_ptr = (char*)mmap(0, m_map_size, PROT_READ|PROT_WRITE, MAP_SHARED,
+                               m_file_desc, 0);
+      if(m_data_ptr == MAP_FAILED)
+        std::cerr << "Error: mmapping" << std::endl;
+      return (pointer)m_data_ptr;
+    } else {
+      size_t map_offset = (m_data_offset / m_page_size) * m_page_size;
+      size_t relative_offset = m_data_offset - map_offset;
+
+      size_t map_size = m_map_size + relative_offset;
+
+      m_data_ptr = (char*)mmap(0, map_size, PROT_READ, MAP_SHARED,
+                               m_file_desc, map_offset);
+
+      return (pointer)(m_data_ptr + relative_offset);
     }
-    
-    template <class T1, class T2>
-    bool operator!=(const MmapAllocator<T1>& a1,
-                     const MmapAllocator<T2>& a2) throw()
-    {
-        return !(a1 == a2);    
+  }
+
+  void deallocate (pointer p, size_type num) {
+    if(!m_fixed) {
+      munmap(p, num * sizeof(T));
+    } else {
+      size_t map_offset = (m_data_offset / m_page_size) * m_page_size;
+      size_t relative_offset = m_data_offset - map_offset;
+      munmap((pointer)((char*)p - relative_offset), num * sizeof(T));
     }
 
+  }
+
+  void construct (pointer p, const T& value) {
+    if(!m_fixed)
+      new(p) value_type(value);
+  }
+  void destroy (pointer p) {
+    if(!m_fixed)
+      p->~T();
+  }
+
+  template <class T1, class T2>
+  friend bool operator== (const MmapAllocator<T1>&, const MmapAllocator<T2>&) throw();
+
+  template <class T1, class T2>
+  friend bool operator!= (const MmapAllocator<T1>&, const MmapAllocator<T2>&) throw();
+};
+
+template <class T1, class T2>
+bool operator== (const MmapAllocator<T1>& a1,
+                 const MmapAllocator<T2>& a2) throw()
+{
+  bool equal = true;
+  equal &= a1.m_file_ptr == a2.m_file_ptr;
+  equal &= a1.m_file_desc == a2.m_file_desc;
+  equal &= a1.m_page_size == a2.m_page_size;
+  equal &= a1.m_map_size == a2.m_map_size;
+  equal &= a1.m_data_ptr == a2.m_data_ptr;
+  equal &= a1.m_data_offset == a2.m_data_offset;
+  equal &= a1.m_fixed == a2.m_fixed;
+  return equal;
+}
+
+template <class T1, class T2>
+bool operator!=(const MmapAllocator<T1>& a1,
+                const MmapAllocator<T2>& a2) throw()
+{
+  return !(a1 == a2);
+}
+
 }
 
 #endif
diff --git a/moses/TranslationModel/CompactPT/MonotonicVector.h b/moses/TranslationModel/CompactPT/MonotonicVector.h
index a4423c369..5e965d3e5 100644
--- a/moses/TranslationModel/CompactPT/MonotonicVector.h
+++ b/moses/TranslationModel/CompactPT/MonotonicVector.h
@@ -1,23 +1,23 @@
-// $Id$                                                                                                                               
-// vim:tabstop=2                                                                                                                      
-/***********************************************************************                                                              
-Moses - factored phrase-based language decoder                                                                                        
-Copyright (C) 2006 University of Edinburgh                                                                                            
-                                                                                                                                      
-This library is free software; you can redistribute it and/or                                                                         
-modify it under the terms of the GNU Lesser General Public                                                                            
-License as published by the Free Software Foundation; either                                                                          
-version 2.1 of the License, or (at your option) any later version.                                                                    
-                                                                                                                                      
-This library is distributed in the hope that it will be useful,                                                                       
-but WITHOUT ANY WARRANTY; without even the implied warranty of                                                                        
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU                                                                     
-Lesser General Public License for more details.                                                                                       
-                                                                                                                                      
-You should have received a copy of the GNU Lesser General Public                                                                      
-License along with this library; if not, write to the Free Software                                                                   
-Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA                                                        
-***********************************************************************/  
+// $Id$
+// vim:tabstop=2
+/***********************************************************************
+Moses - factored phrase-based language decoder
+Copyright (C) 2006 University of Edinburgh
+
+This library is free software; you can redistribute it and/or
+modify it under the terms of the GNU Lesser General Public
+License as published by the Free Software Foundation; either
+version 2.1 of the License, or (at your option) any later version.
+
+This library is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public
+License along with this library; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+***********************************************************************/
 
 #ifndef moses_MonotonicVector_h
 #define moses_MonotonicVector_h
@@ -43,206 +43,187 @@ namespace Moses
 {
 
 template<typename PosT = size_t, typename NumT = size_t, PosT stepSize = 32,
-template <typename> class Allocator = std::allocator>
+         template <typename> class Allocator = std::allocator>
 class MonotonicVector
 {
-  private:
-    typedef std::vector<NumT, Allocator<NumT> > Anchors;
-    typedef std::vector<unsigned int, Allocator<unsigned int> > Diffs;
-    
-    Anchors m_anchors;
-    Diffs m_diffs;
-    std::vector<unsigned int> m_tempDiffs;
-    
-    size_t m_size;
-    PosT m_last;
-    bool m_final;
-    
-  public:
-    typedef PosT value_type;
-    
-    MonotonicVector() : m_size(0), m_last(0), m_final(false) {}
-    
-    size_t size() const
-    {
-      return m_size + m_tempDiffs.size();
-    }
-    
-    PosT at(size_t i) const
-    {
-      PosT s = stepSize;
-      PosT j = m_anchors[i / s];
-      PosT r = i % s;
-          
-      typename Diffs::const_iterator it = m_diffs.begin() + j;
-      
-      PosT k = 0;
-      k += VarInt32::DecodeAndSum(it, m_diffs.end(), 1);
-      if(i < m_size)
-        k += Simple9::DecodeAndSum(it, m_diffs.end(), r);
-      else if(i < m_size + m_tempDiffs.size())
-        for(size_t l = 0; l < r; l++)
-          k += m_tempDiffs[l];
-      
-      return k;
-    }
-    
-    PosT operator[](PosT i) const
-    {
-      return at(i);
-    }
-    
-    PosT back() const
-    {
-      return at(size()-1);
-    }
-    
-    void push_back(PosT i)
-    {
-      assert(m_final != true);
-    
-      if(m_anchors.size() == 0 && m_tempDiffs.size() == 0)
-      {
-        m_anchors.push_back(0);
-        VarInt32::Encode(&i, &i+1, std::back_inserter(m_diffs));
-        m_last = i;
-        m_size++;
-            
-        return;
-      }
-      
-      if(m_tempDiffs.size() == stepSize-1)
-      {
-        Simple9::Encode(m_tempDiffs.begin(), m_tempDiffs.end(),
-                        std::back_inserter(m_diffs));
-        m_anchors.push_back(m_diffs.size());
-        VarInt32::Encode(&i, &i+1, std::back_inserter(m_diffs));
-        
-        m_size += m_tempDiffs.size() + 1;
-        m_tempDiffs.clear();
-      }
-      else
-      {
-        PosT last = m_last;
-        PosT diff = i - last;
-        m_tempDiffs.push_back(diff);
-      }
+private:
+  typedef std::vector<NumT, Allocator<NumT> > Anchors;
+  typedef std::vector<unsigned int, Allocator<unsigned int> > Diffs;
+
+  Anchors m_anchors;
+  Diffs m_diffs;
+  std::vector<unsigned int> m_tempDiffs;
+
+  size_t m_size;
+  PosT m_last;
+  bool m_final;
+
+public:
+  typedef PosT value_type;
+
+  MonotonicVector() : m_size(0), m_last(0), m_final(false) {}
+
+  size_t size() const {
+    return m_size + m_tempDiffs.size();
+  }
+
+  PosT at(size_t i) const {
+    PosT s = stepSize;
+    PosT j = m_anchors[i / s];
+    PosT r = i % s;
+
+    typename Diffs::const_iterator it = m_diffs.begin() + j;
+
+    PosT k = 0;
+    k += VarInt32::DecodeAndSum(it, m_diffs.end(), 1);
+    if(i < m_size)
+      k += Simple9::DecodeAndSum(it, m_diffs.end(), r);
+    else if(i < m_size + m_tempDiffs.size())
+      for(size_t l = 0; l < r; l++)
+        k += m_tempDiffs[l];
+
+    return k;
+  }
+
+  PosT operator[](PosT i) const {
+    return at(i);
+  }
+
+  PosT back() const {
+    return at(size()-1);
+  }
+
+  void push_back(PosT i) {
+    assert(m_final != true);
+
+    if(m_anchors.size() == 0 && m_tempDiffs.size() == 0) {
+      m_anchors.push_back(0);
+      VarInt32::Encode(&i, &i+1, std::back_inserter(m_diffs));
       m_last = i;
+      m_size++;
+
+      return;
     }
-    
-    void commit()
-    {
-      assert(m_final != true);
+
+    if(m_tempDiffs.size() == stepSize-1) {
       Simple9::Encode(m_tempDiffs.begin(), m_tempDiffs.end(),
                       std::back_inserter(m_diffs));
-      m_size += m_tempDiffs.size();
+      m_anchors.push_back(m_diffs.size());
+      VarInt32::Encode(&i, &i+1, std::back_inserter(m_diffs));
+
+      m_size += m_tempDiffs.size() + 1;
       m_tempDiffs.clear();
-      m_final = true;
-    }
-    
-    size_t usage()
-    {      
-      return m_diffs.size() * sizeof(unsigned int)
-        + m_anchors.size() * sizeof(NumT);
+    } else {
+      PosT last = m_last;
+      PosT diff = i - last;
+      m_tempDiffs.push_back(diff);
     }
-    
-    size_t load(std::FILE* in, bool map = false)
-    {
-      size_t byteSize = 0;
-      
-      byteSize += fread(&m_final, sizeof(bool), 1, in) * sizeof(bool);
-      byteSize += fread(&m_size, sizeof(size_t), 1, in) * sizeof(size_t);
-      byteSize += fread(&m_last, sizeof(PosT), 1, in) * sizeof(PosT);
-      
-      byteSize += loadVector(m_diffs, in, map);
-      byteSize += loadVector(m_anchors, in, map);
-      
-      return byteSize;
-    }
-    
-    template <typename ValueT>
-    size_t loadVector(std::vector<ValueT, std::allocator<ValueT> >& v,
-                       std::FILE* in, bool map = false)
-    {
-      // Can only be read into memory. Mapping not possible with std:allocator.
-      assert(map == false);
-      
-      size_t byteSize = 0;
-      
-      size_t valSize;
-      byteSize += std::fread(&valSize, sizeof(size_t), 1, in) * sizeof(size_t);
-      
+    m_last = i;
+  }
+
+  void commit() {
+    assert(m_final != true);
+    Simple9::Encode(m_tempDiffs.begin(), m_tempDiffs.end(),
+                    std::back_inserter(m_diffs));
+    m_size += m_tempDiffs.size();
+    m_tempDiffs.clear();
+    m_final = true;
+  }
+
+  size_t usage() {
+    return m_diffs.size() * sizeof(unsigned int)
+           + m_anchors.size() * sizeof(NumT);
+  }
+
+  size_t load(std::FILE* in, bool map = false) {
+    size_t byteSize = 0;
+
+    byteSize += fread(&m_final, sizeof(bool), 1, in) * sizeof(bool);
+    byteSize += fread(&m_size, sizeof(size_t), 1, in) * sizeof(size_t);
+    byteSize += fread(&m_last, sizeof(PosT), 1, in) * sizeof(PosT);
+
+    byteSize += loadVector(m_diffs, in, map);
+    byteSize += loadVector(m_anchors, in, map);
+
+    return byteSize;
+  }
+
+  template <typename ValueT>
+  size_t loadVector(std::vector<ValueT, std::allocator<ValueT> >& v,
+                    std::FILE* in, bool map = false) {
+    // Can only be read into memory. Mapping not possible with std:allocator.
+    assert(map == false);
+
+    size_t byteSize = 0;
+
+    size_t valSize;
+    byteSize += std::fread(&valSize, sizeof(size_t), 1, in) * sizeof(size_t);
+
+    v.resize(valSize, 0);
+    byteSize += std::fread(&v[0], sizeof(ValueT), valSize, in) * sizeof(ValueT);
+
+    return byteSize;
+  }
+
+  template <typename ValueT>
+  size_t loadVector(std::vector<ValueT, MmapAllocator<ValueT> >& v,
+                    std::FILE* in, bool map = false) {
+    size_t byteSize = 0;
+
+    size_t valSize;
+    byteSize += std::fread(&valSize, sizeof(size_t), 1, in) * sizeof(size_t);
+
+    if(map == false) {
+      // Read data into temporary file (default constructor of MmapAllocator)
+      // and map memory onto temporary file. Can be resized.
+
       v.resize(valSize, 0);
       byteSize += std::fread(&v[0], sizeof(ValueT), valSize, in) * sizeof(ValueT);
-    
-      return byteSize;
-    }
-    
-    template <typename ValueT>
-    size_t loadVector(std::vector<ValueT, MmapAllocator<ValueT> >& v,
-                       std::FILE* in, bool map = false)
-    {
-      size_t byteSize = 0;
-
-      size_t valSize;
-      byteSize += std::fread(&valSize, sizeof(size_t), 1, in) * sizeof(size_t);
-
-      if(map == false)
-      {
-        // Read data into temporary file (default constructor of MmapAllocator)
-        // and map memory onto temporary file. Can be resized.
-        
-        v.resize(valSize, 0);
-        byteSize += std::fread(&v[0], sizeof(ValueT), valSize, in) * sizeof(ValueT);
-      }
-      else
-      {
-        // Map it directly on specified region of file "in" starting at valPos
-        // with length valSize * sizeof(ValueT). Mapped region cannot be resized.
-        
-        size_t valPos = std::ftell(in);
-        
-        Allocator<ValueT> alloc(in, valPos);
-        std::vector<ValueT, Allocator<ValueT> > vTemp(alloc);
-        vTemp.resize(valSize);
-        v.swap(vTemp);
-        
-        std::fseek(in, valSize * sizeof(ValueT), SEEK_CUR);
-        byteSize += valSize * sizeof(ValueT);
-      }
-      
-      return byteSize;
-    }
-    
-    size_t save(std::FILE* out)
-    {
-      if(!m_final)
-        commit();
-      
-      bool byteSize = 0;
-      byteSize += ThrowingFwrite(&m_final, sizeof(bool), 1, out) * sizeof(bool);
-      byteSize += ThrowingFwrite(&m_size, sizeof(size_t), 1, out) * sizeof(size_t);
-      byteSize += ThrowingFwrite(&m_last, sizeof(PosT), 1, out) * sizeof(PosT);
-      
-      size_t size = m_diffs.size();
-      byteSize += ThrowingFwrite(&size, sizeof(size_t), 1, out) * sizeof(size_t);
-      byteSize += ThrowingFwrite(&m_diffs[0], sizeof(unsigned int), size, out) * sizeof(unsigned int);
-      
-      size = m_anchors.size();
-      byteSize += ThrowingFwrite(&size, sizeof(size_t), 1, out) * sizeof(size_t);
-      byteSize += ThrowingFwrite(&m_anchors[0], sizeof(NumT), size, out) * sizeof(NumT);
-      
-      return byteSize;
-    }
-    
-    void swap(MonotonicVector<PosT, NumT, stepSize, Allocator> &mv)
-    {
-      if(!m_final)
-        commit();
-        
-      m_diffs.swap(mv.m_diffs);
-      m_anchors.swap(mv.m_anchors);
+    } else {
+      // Map it directly on specified region of file "in" starting at valPos
+      // with length valSize * sizeof(ValueT). Mapped region cannot be resized.
+
+      size_t valPos = std::ftell(in);
+
+      Allocator<ValueT> alloc(in, valPos);
+      std::vector<ValueT, Allocator<ValueT> > vTemp(alloc);
+      vTemp.resize(valSize);
+      v.swap(vTemp);
+
+      std::fseek(in, valSize * sizeof(ValueT), SEEK_CUR);
+      byteSize += valSize * sizeof(ValueT);
     }
+
+    return byteSize;
+  }
+
+  size_t save(std::FILE* out) {
+    if(!m_final)
+      commit();
+
+    bool byteSize = 0;
+    byteSize += ThrowingFwrite(&m_final, sizeof(bool), 1, out) * sizeof(bool);
+    byteSize += ThrowingFwrite(&m_size, sizeof(size_t), 1, out) * sizeof(size_t);
+    byteSize += ThrowingFwrite(&m_last, sizeof(PosT), 1, out) * sizeof(PosT);
+
+    size_t size = m_diffs.size();
+    byteSize += ThrowingFwrite(&size, sizeof(size_t), 1, out) * sizeof(size_t);
+    byteSize += ThrowingFwrite(&m_diffs[0], sizeof(unsigned int), size, out) * sizeof(unsigned int);
+
+    size = m_anchors.size();
+    byteSize += ThrowingFwrite(&size, sizeof(size_t), 1, out) * sizeof(size_t);
+    byteSize += ThrowingFwrite(&m_anchors[0], sizeof(NumT), size, out) * sizeof(NumT);
+
+    return byteSize;
+  }
+
+  void swap(MonotonicVector<PosT, NumT, stepSize, Allocator> &mv) {
+    if(!m_final)
+      commit();
+
+    m_diffs.swap(mv.m_diffs);
+    m_anchors.swap(mv.m_anchors);
+  }
 };
 
 }
diff --git a/moses/TranslationModel/CompactPT/MurmurHash3.cpp b/moses/TranslationModel/CompactPT/MurmurHash3.cpp
index 0bf738662..d16cd9502 100644
--- a/moses/TranslationModel/CompactPT/MurmurHash3.cpp
+++ b/moses/TranslationModel/CompactPT/MurmurHash3.cpp
@@ -107,16 +107,15 @@ void MurmurHash3_x86_32 ( const void * key, int len,
 

   const uint32_t * blocks = (const uint32_t *)(data + nblocks*4);

 

-  for(int i = -nblocks; i; i++)

-  {

+  for(int i = -nblocks; i; i++) {

     uint32_t k1 = getblock(blocks,i);

 

     k1 *= c1;

     k1 = ROTL32(k1,15);

     k1 *= c2;

-    

+

     h1 ^= k1;

-    h1 = ROTL32(h1,13); 

+    h1 = ROTL32(h1,13);

     h1 = h1*5+0xe6546b64;

   }

 

@@ -127,12 +126,17 @@ void MurmurHash3_x86_32 ( const void * key, int len,
 

   uint32_t k1 = 0;

 

-  switch(len & 3)

-  {

-  case 3: k1 ^= tail[2] << 16;

-  case 2: k1 ^= tail[1] << 8;

-  case 1: k1 ^= tail[0];

-          k1 *= c1; k1 = ROTL32(k1,15); k1 *= c2; h1 ^= k1;

+  switch(len & 3) {

+  case 3:

+    k1 ^= tail[2] << 16;

+  case 2:

+    k1 ^= tail[1] << 8;

+  case 1:

+    k1 ^= tail[0];

+    k1 *= c1;

+    k1 = ROTL32(k1,15);

+    k1 *= c2;

+    h1 ^= k1;

   };

 

   //----------

@@ -143,7 +147,7 @@ void MurmurHash3_x86_32 ( const void * key, int len,
   h1 = fmix(h1);

 

   *(uint32_t*)out = h1;

-} 

+}

 

 //-----------------------------------------------------------------------------

 

@@ -158,9 +162,9 @@ void MurmurHash3_x86_128 ( const void * key, const int len,
   uint32_t h3 = seed;

   uint32_t h4 = seed;

 

-  uint32_t c1 = 0x239b961b; 

+  uint32_t c1 = 0x239b961b;

   uint32_t c2 = 0xab0e9789;

-  uint32_t c3 = 0x38b34ae5; 

+  uint32_t c3 = 0x38b34ae5;

   uint32_t c4 = 0xa1e38b93;

 

   //----------

@@ -168,28 +172,47 @@ void MurmurHash3_x86_128 ( const void * key, const int len,
 

   const uint32_t * blocks = (const uint32_t *)(data + nblocks*16);

 

-  for(int i = -nblocks; i; i++)

-  {

+  for(int i = -nblocks; i; i++) {

     uint32_t k1 = getblock(blocks,i*4+0);

     uint32_t k2 = getblock(blocks,i*4+1);

     uint32_t k3 = getblock(blocks,i*4+2);

     uint32_t k4 = getblock(blocks,i*4+3);

 

-    k1 *= c1; k1  = ROTL32(k1,15); k1 *= c2; h1 ^= k1;

+    k1 *= c1;

+    k1  = ROTL32(k1,15);

+    k1 *= c2;

+    h1 ^= k1;

 

-    h1 = ROTL32(h1,19); h1 += h2; h1 = h1*5+0x561ccd1b;

+    h1 = ROTL32(h1,19);

+    h1 += h2;

+    h1 = h1*5+0x561ccd1b;

 

-    k2 *= c2; k2  = ROTL32(k2,16); k2 *= c3; h2 ^= k2;

+    k2 *= c2;

+    k2  = ROTL32(k2,16);

+    k2 *= c3;

+    h2 ^= k2;

 

-    h2 = ROTL32(h2,17); h2 += h3; h2 = h2*5+0x0bcaa747;

+    h2 = ROTL32(h2,17);

+    h2 += h3;

+    h2 = h2*5+0x0bcaa747;

 

-    k3 *= c3; k3  = ROTL32(k3,17); k3 *= c4; h3 ^= k3;

+    k3 *= c3;

+    k3  = ROTL32(k3,17);

+    k3 *= c4;

+    h3 ^= k3;

 

-    h3 = ROTL32(h3,15); h3 += h4; h3 = h3*5+0x96cd1c35;

+    h3 = ROTL32(h3,15);

+    h3 += h4;

+    h3 = h3*5+0x96cd1c35;

 

-    k4 *= c4; k4  = ROTL32(k4,18); k4 *= c1; h4 ^= k4;

+    k4 *= c4;

+    k4  = ROTL32(k4,18);

+    k4 *= c1;

+    h4 ^= k4;

 

-    h4 = ROTL32(h4,13); h4 += h1; h4 = h4*5+0x32ac3b17;

+    h4 = ROTL32(h4,13);

+    h4 += h1;

+    h4 = h4*5+0x32ac3b17;

   }

 

   //----------

@@ -202,47 +225,84 @@ void MurmurHash3_x86_128 ( const void * key, const int len,
   uint32_t k3 = 0;

   uint32_t k4 = 0;

 

-  switch(len & 15)

-  {

-  case 15: k4 ^= tail[14] << 16;

-  case 14: k4 ^= tail[13] << 8;

-  case 13: k4 ^= tail[12] << 0;

-           k4 *= c4; k4  = ROTL32(k4,18); k4 *= c1; h4 ^= k4;

-

-  case 12: k3 ^= tail[11] << 24;

-  case 11: k3 ^= tail[10] << 16;

-  case 10: k3 ^= tail[ 9] << 8;

-  case  9: k3 ^= tail[ 8] << 0;

-           k3 *= c3; k3  = ROTL32(k3,17); k3 *= c4; h3 ^= k3;

-

-  case  8: k2 ^= tail[ 7] << 24;

-  case  7: k2 ^= tail[ 6] << 16;

-  case  6: k2 ^= tail[ 5] << 8;

-  case  5: k2 ^= tail[ 4] << 0;

-           k2 *= c2; k2  = ROTL32(k2,16); k2 *= c3; h2 ^= k2;

-

-  case  4: k1 ^= tail[ 3] << 24;

-  case  3: k1 ^= tail[ 2] << 16;

-  case  2: k1 ^= tail[ 1] << 8;

-  case  1: k1 ^= tail[ 0] << 0;

-           k1 *= c1; k1  = ROTL32(k1,15); k1 *= c2; h1 ^= k1;

+  switch(len & 15) {

+  case 15:

+    k4 ^= tail[14] << 16;

+  case 14:

+    k4 ^= tail[13] << 8;

+  case 13:

+    k4 ^= tail[12] << 0;

+    k4 *= c4;

+    k4  = ROTL32(k4,18);

+    k4 *= c1;

+    h4 ^= k4;

+

+  case 12:

+    k3 ^= tail[11] << 24;

+  case 11:

+    k3 ^= tail[10] << 16;

+  case 10:

+    k3 ^= tail[ 9] << 8;

+  case  9:

+    k3 ^= tail[ 8] << 0;

+    k3 *= c3;

+    k3  = ROTL32(k3,17);

+    k3 *= c4;

+    h3 ^= k3;

+

+  case  8:

+    k2 ^= tail[ 7] << 24;

+  case  7:

+    k2 ^= tail[ 6] << 16;

+  case  6:

+    k2 ^= tail[ 5] << 8;

+  case  5:

+    k2 ^= tail[ 4] << 0;

+    k2 *= c2;

+    k2  = ROTL32(k2,16);

+    k2 *= c3;

+    h2 ^= k2;

+

+  case  4:

+    k1 ^= tail[ 3] << 24;

+  case  3:

+    k1 ^= tail[ 2] << 16;

+  case  2:

+    k1 ^= tail[ 1] << 8;

+  case  1:

+    k1 ^= tail[ 0] << 0;

+    k1 *= c1;

+    k1  = ROTL32(k1,15);

+    k1 *= c2;

+    h1 ^= k1;

   };

 

   //----------

   // finalization

 

-  h1 ^= len; h2 ^= len; h3 ^= len; h4 ^= len;

+  h1 ^= len;

+  h2 ^= len;

+  h3 ^= len;

+  h4 ^= len;

 

-  h1 += h2; h1 += h3; h1 += h4;

-  h2 += h1; h3 += h1; h4 += h1;

+  h1 += h2;

+  h1 += h3;

+  h1 += h4;

+  h2 += h1;

+  h3 += h1;

+  h4 += h1;

 

   h1 = fmix(h1);

   h2 = fmix(h2);

   h3 = fmix(h3);

   h4 = fmix(h4);

 

-  h1 += h2; h1 += h3; h1 += h4;

-  h2 += h1; h3 += h1; h4 += h1;

+  h1 += h2;

+  h1 += h3;

+  h1 += h4;

+  h2 += h1;

+  h3 += h1;

+  h4 += h1;

 

   ((uint32_t*)out)[0] = h1;

   ((uint32_t*)out)[1] = h2;

@@ -269,18 +329,27 @@ void MurmurHash3_x64_128 ( const void * key, const int len,
 

   const uint64_t * blocks = (const uint64_t *)(data);

 

-  for(int i = 0; i < nblocks; i++)

-  {

+  for(int i = 0; i < nblocks; i++) {

     uint64_t k1 = getblock(blocks,i*2+0);

     uint64_t k2 = getblock(blocks,i*2+1);

 

-    k1 *= c1; k1  = ROTL64(k1,31); k1 *= c2; h1 ^= k1;

+    k1 *= c1;

+    k1  = ROTL64(k1,31);

+    k1 *= c2;

+    h1 ^= k1;

 

-    h1 = ROTL64(h1,27); h1 += h2; h1 = h1*5+0x52dce729;

+    h1 = ROTL64(h1,27);

+    h1 += h2;

+    h1 = h1*5+0x52dce729;

 

-    k2 *= c2; k2  = ROTL64(k2,33); k2 *= c1; h2 ^= k2;

+    k2 *= c2;

+    k2  = ROTL64(k2,33);

+    k2 *= c1;

+    h2 ^= k2;

 

-    h2 = ROTL64(h2,31); h2 += h1; h2 = h2*5+0x38495ab5;

+    h2 = ROTL64(h2,31);

+    h2 += h1;

+    h2 = h2*5+0x38495ab5;

   }

 

   //----------

@@ -291,32 +360,53 @@ void MurmurHash3_x64_128 ( const void * key, const int len,
   uint64_t k1 = 0;

   uint64_t k2 = 0;

 

-  switch(len & 15)

-  {

-  case 15: k2 ^= uint64_t(tail[14]) << 48;

-  case 14: k2 ^= uint64_t(tail[13]) << 40;

-  case 13: k2 ^= uint64_t(tail[12]) << 32;

-  case 12: k2 ^= uint64_t(tail[11]) << 24;

-  case 11: k2 ^= uint64_t(tail[10]) << 16;

-  case 10: k2 ^= uint64_t(tail[ 9]) << 8;

-  case  9: k2 ^= uint64_t(tail[ 8]) << 0;

-           k2 *= c2; k2  = ROTL64(k2,33); k2 *= c1; h2 ^= k2;

-

-  case  8: k1 ^= uint64_t(tail[ 7]) << 56;

-  case  7: k1 ^= uint64_t(tail[ 6]) << 48;

-  case  6: k1 ^= uint64_t(tail[ 5]) << 40;

-  case  5: k1 ^= uint64_t(tail[ 4]) << 32;

-  case  4: k1 ^= uint64_t(tail[ 3]) << 24;

-  case  3: k1 ^= uint64_t(tail[ 2]) << 16;

-  case  2: k1 ^= uint64_t(tail[ 1]) << 8;

-  case  1: k1 ^= uint64_t(tail[ 0]) << 0;

-           k1 *= c1; k1  = ROTL64(k1,31); k1 *= c2; h1 ^= k1;

+  switch(len & 15) {

+  case 15:

+    k2 ^= uint64_t(tail[14]) << 48;

+  case 14:

+    k2 ^= uint64_t(tail[13]) << 40;

+  case 13:

+    k2 ^= uint64_t(tail[12]) << 32;

+  case 12:

+    k2 ^= uint64_t(tail[11]) << 24;

+  case 11:

+    k2 ^= uint64_t(tail[10]) << 16;

+  case 10:

+    k2 ^= uint64_t(tail[ 9]) << 8;

+  case  9:

+    k2 ^= uint64_t(tail[ 8]) << 0;

+    k2 *= c2;

+    k2  = ROTL64(k2,33);

+    k2 *= c1;

+    h2 ^= k2;

+

+  case  8:

+    k1 ^= uint64_t(tail[ 7]) << 56;

+  case  7:

+    k1 ^= uint64_t(tail[ 6]) << 48;

+  case  6:

+    k1 ^= uint64_t(tail[ 5]) << 40;

+  case  5:

+    k1 ^= uint64_t(tail[ 4]) << 32;

+  case  4:

+    k1 ^= uint64_t(tail[ 3]) << 24;

+  case  3:

+    k1 ^= uint64_t(tail[ 2]) << 16;

+  case  2:

+    k1 ^= uint64_t(tail[ 1]) << 8;

+  case  1:

+    k1 ^= uint64_t(tail[ 0]) << 0;

+    k1 *= c1;

+    k1  = ROTL64(k1,31);

+    k1 *= c2;

+    h1 ^= k1;

   };

 

   //----------

   // finalization

 

-  h1 ^= len; h2 ^= len;

+  h1 ^= len;

+  h2 ^= len;

 

   h1 += h2;

   h2 += h1;

diff --git a/moses/TranslationModel/CompactPT/PackedArray.h b/moses/TranslationModel/CompactPT/PackedArray.h
index ad4596546..479c2cc79 100644
--- a/moses/TranslationModel/CompactPT/PackedArray.h
+++ b/moses/TranslationModel/CompactPT/PackedArray.h
@@ -1,23 +1,23 @@
-// $Id$                                                                                                                               
-// vim:tabstop=2                                                                                                                      
-/***********************************************************************                                                              
-Moses - factored phrase-based language decoder                                                                                        
-Copyright (C) 2006 University of Edinburgh                                                                                            
-                                                                                                                                      
-This library is free software; you can redistribute it and/or                                                                         
-modify it under the terms of the GNU Lesser General Public                                                                            
-License as published by the Free Software Foundation; either                                                                          
-version 2.1 of the License, or (at your option) any later version.                                                                    
-                                                                                                                                      
-This library is distributed in the hope that it will be useful,                                                                       
-but WITHOUT ANY WARRANTY; without even the implied warranty of                                                                        
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU                                                                     
-Lesser General Public License for more details.                                                                                       
-                                                                                                                                      
-You should have received a copy of the GNU Lesser General Public                                                                      
-License along with this library; if not, write to the Free Software                                                                   
-Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA                                                        
-***********************************************************************/  
+// $Id$
+// vim:tabstop=2
+/***********************************************************************
+Moses - factored phrase-based language decoder
+Copyright (C) 2006 University of Edinburgh
+
+This library is free software; you can redistribute it and/or
+modify it under the terms of the GNU Lesser General Public
+License as published by the Free Software Foundation; either
+version 2.1 of the License, or (at your option) any later version.
+
+This library is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public
+License along with this library; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+***********************************************************************/
 
 #ifndef moses_PackedArray_h
 #define moses_PackedArray_h
@@ -35,128 +35,117 @@ namespace Moses
 template <typename T = size_t, typename D = unsigned char>
 class PackedArray
 {
-  protected:
-    static size_t m_dataBits;
-    
-    size_t m_size;
-    size_t m_storageSize;
-    D* m_storage;
-    
-  public:
-    PackedArray()
-    {
-      m_size = 0;
-      m_storageSize = 0;
-      m_storage = new D[0];
-    }
-    
-    PackedArray(size_t size, size_t bits) : m_size(size)
-    {  
-      m_storageSize = ceil(float(bits * size) / float(m_dataBits));
-      m_storage = new D[m_storageSize];
-    }
-    
-    PackedArray(const PackedArray<T, D> &c)
-    {
-      m_size = c.m_size;
-      
-      m_storageSize = c.m_storageSize;
-      m_storage = new D[m_storageSize];
-      
-      std::memcpy(m_storage, c.m_storage, m_storageSize * sizeof(D));
-    }
-    
-    virtual ~PackedArray()
-    {
-      delete [] m_storage;
-      m_size = 0;
-      m_storageSize = 0;
-      m_storage = 0;
-    }
-    
-    T Get(size_t i, size_t bits) const
-    {
-      T out = 0;
-      
-      size_t bitstart = (i * bits);
-      size_t bitpos = bitstart;
-      
-      size_t zero = ((1ul << (bits)) - 1);
-      
-      while(bitpos - bitstart < bits) {
-        size_t pos = bitpos / m_dataBits;
-        size_t off = bitpos % m_dataBits;
-           
-        out |= (T(m_storage[pos]) << (bitpos - bitstart)) >> off;
-
-        bitpos += (m_dataBits - off);
-      }
-      
-      out &= zero;
-      return out;
-    }
-    
-    void Set(size_t i, T v, size_t bits)
-    {
-      size_t bitstart = (i * bits);
-      size_t bitpos = bitstart;
-      
-      while(bitpos - bitstart < bits) {
-        size_t pos = bitpos / m_dataBits;
-        size_t off = bitpos % m_dataBits;
-        
-        size_t rest = bits - (bitpos - bitstart);
-        D zero = ~((1ul << (rest + off)) - 1) | ((1ul << off) - 1);
-        
-        m_storage[pos] &= zero;
-        m_storage[pos] |= v << off;
-        v = v >> (m_dataBits - off);
-        bitpos += (m_dataBits - off);
-      }
-    }
-    
-    virtual D*& GetStorage()
-    {
-      return m_storage;
-    }
-    
-    virtual size_t GetStorageSize() const
-    {
-      return m_storageSize;
-    }
-    
-    virtual size_t Size() const
-    {
-      return m_size;
-    }
-    
-    virtual size_t Load(std::FILE* in)
-    {
-      size_t a1 = std::ftell(in);
-      
-      size_t read = 0;
-      read += std::fread(&m_size, sizeof(m_size), 1, in);
-      read += std::fread(&m_storageSize, sizeof(m_storageSize), 1, in);
-      delete [] m_storage;
-      m_storage = new D[m_storageSize];
-      read += std::fread(m_storage, sizeof(D), m_storageSize, in);
-      
-      size_t a2 = std::ftell(in);
-      return a2 - a1;
+protected:
+  static size_t m_dataBits;
+
+  size_t m_size;
+  size_t m_storageSize;
+  D* m_storage;
+
+public:
+  PackedArray() {
+    m_size = 0;
+    m_storageSize = 0;
+    m_storage = new D[0];
+  }
+
+  PackedArray(size_t size, size_t bits) : m_size(size) {
+    m_storageSize = ceil(float(bits * size) / float(m_dataBits));
+    m_storage = new D[m_storageSize];
+  }
+
+  PackedArray(const PackedArray<T, D> &c) {
+    m_size = c.m_size;
+
+    m_storageSize = c.m_storageSize;
+    m_storage = new D[m_storageSize];
+
+    std::memcpy(m_storage, c.m_storage, m_storageSize * sizeof(D));
+  }
+
+  virtual ~PackedArray() {
+    delete [] m_storage;
+    m_size = 0;
+    m_storageSize = 0;
+    m_storage = 0;
+  }
+
+  T Get(size_t i, size_t bits) const {
+    T out = 0;
+
+    size_t bitstart = (i * bits);
+    size_t bitpos = bitstart;
+
+    size_t zero = ((1ul << (bits)) - 1);
+
+    while(bitpos - bitstart < bits) {
+      size_t pos = bitpos / m_dataBits;
+      size_t off = bitpos % m_dataBits;
+
+      out |= (T(m_storage[pos]) << (bitpos - bitstart)) >> off;
+
+      bitpos += (m_dataBits - off);
     }
-    
-    virtual size_t Save(std::FILE* out)
-    {
-      size_t a1 = std::ftell(out);
-      
-      ThrowingFwrite(&m_size, sizeof(m_size), 1, out);
-      ThrowingFwrite(&m_storageSize, sizeof(m_storageSize), 1, out);
-      ThrowingFwrite(m_storage, sizeof(D), m_storageSize, out);
-      
-      size_t a2 = std::ftell(out);
-      return a2 - a1;
+
+    out &= zero;
+    return out;
+  }
+
+  void Set(size_t i, T v, size_t bits) {
+    size_t bitstart = (i * bits);
+    size_t bitpos = bitstart;
+
+    while(bitpos - bitstart < bits) {
+      size_t pos = bitpos / m_dataBits;
+      size_t off = bitpos % m_dataBits;
+
+      size_t rest = bits - (bitpos - bitstart);
+      D zero = ~((1ul << (rest + off)) - 1) | ((1ul << off) - 1);
+
+      m_storage[pos] &= zero;
+      m_storage[pos] |= v << off;
+      v = v >> (m_dataBits - off);
+      bitpos += (m_dataBits - off);
     }
-    
+  }
+
+  virtual D*& GetStorage() {
+    return m_storage;
+  }
+
+  virtual size_t GetStorageSize() const {
+    return m_storageSize;
+  }
+
+  virtual size_t Size() const {
+    return m_size;
+  }
+
+  virtual size_t Load(std::FILE* in) {
+    size_t a1 = std::ftell(in);
+
+    size_t read = 0;
+    read += std::fread(&m_size, sizeof(m_size), 1, in);
+    read += std::fread(&m_storageSize, sizeof(m_storageSize), 1, in);
+    delete [] m_storage;
+    m_storage = new D[m_storageSize];
+    read += std::fread(m_storage, sizeof(D), m_storageSize, in);
+
+    size_t a2 = std::ftell(in);
+    return a2 - a1;
+  }
+
+  virtual size_t Save(std::FILE* out) {
+    size_t a1 = std::ftell(out);
+
+    ThrowingFwrite(&m_size, sizeof(m_size), 1, out);
+    ThrowingFwrite(&m_storageSize, sizeof(m_storageSize), 1, out);
+    ThrowingFwrite(m_storage, sizeof(D), m_storageSize, out);
+
+    size_t a2 = std::ftell(out);
+    return a2 - a1;
+  }
+
 };
 
 template <typename T, typename D>
@@ -166,34 +155,31 @@ size_t PackedArray<T, D>::m_dataBits = sizeof(D)*8;
 
 template <typename T = size_t, typename D = unsigned char>
 class PairedPackedArray : public PackedArray<T,D>
-{    
-  public:
-    PairedPackedArray() : PackedArray<T,D>() {}
-    
-    PairedPackedArray(size_t size, size_t bits1, size_t bits2)
+{
+public:
+  PairedPackedArray() : PackedArray<T,D>() {}
+
+  PairedPackedArray(size_t size, size_t bits1, size_t bits2)
     : PackedArray<T, D>(size, bits1 + bits2) { }
-    
-    void Set(size_t i, T a, T b, size_t bits1, size_t bits2)
-    {
-      T c = 0;
-      c = a | (b << bits1);
-      PackedArray<T,D>::Set(i, c, bits1 + bits2);
-    }
-    
-    void Set(size_t i, std::pair<T,T> p, size_t bits1, size_t bits2)
-    {
-      T c = 0;
-      c = p.second | (p.first << bits1);
-      PackedArray<T, D>::Set(i, c);
-    }
-    
-    std::pair<T, T> Get(size_t i, size_t bits1, size_t bits2)
-    {
-      T v = PackedArray<T, D>::Get(i, bits1 + bits2);
-      T a = v & ((1 << bits1) - 1);
-      T b = v >> bits1;
-      return std::pair<T, T>(a, b);
-    }
+
+  void Set(size_t i, T a, T b, size_t bits1, size_t bits2) {
+    T c = 0;
+    c = a | (b << bits1);
+    PackedArray<T,D>::Set(i, c, bits1 + bits2);
+  }
+
+  void Set(size_t i, std::pair<T,T> p, size_t bits1, size_t bits2) {
+    T c = 0;
+    c = p.second | (p.first << bits1);
+    PackedArray<T, D>::Set(i, c);
+  }
+
+  std::pair<T, T> Get(size_t i, size_t bits1, size_t bits2) {
+    T v = PackedArray<T, D>::Get(i, bits1 + bits2);
+    T a = v & ((1 << bits1) - 1);
+    T b = v >> bits1;
+    return std::pair<T, T>(a, b);
+  }
 };
 
 }
diff --git a/moses/TranslationModel/CompactPT/PhraseDecoder.cpp b/moses/TranslationModel/CompactPT/PhraseDecoder.cpp
index 03b3f6825..085a7337c 100644
--- a/moses/TranslationModel/CompactPT/PhraseDecoder.cpp
+++ b/moses/TranslationModel/CompactPT/PhraseDecoder.cpp
@@ -1,23 +1,23 @@
-// $Id$                                                                                                                               
-// vim:tabstop=2                                                                                                                      
-/***********************************************************************                                                              
-Moses - factored phrase-based language decoder                                                                                        
-Copyright (C) 2006 University of Edinburgh                                                                                            
-                                                                                                                                      
-This library is free software; you can redistribute it and/or                                                                         
-modify it under the terms of the GNU Lesser General Public                                                                            
-License as published by the Free Software Foundation; either                                                                          
-version 2.1 of the License, or (at your option) any later version.                                                                    
-                                                                                                                                      
-This library is distributed in the hope that it will be useful,                                                                       
-but WITHOUT ANY WARRANTY; without even the implied warranty of                                                                        
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU                                                                     
-Lesser General Public License for more details.                                                                                       
-                                                                                                                                      
-You should have received a copy of the GNU Lesser General Public                                                                      
-License along with this library; if not, write to the Free Software                                                                   
-Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA                                                        
-***********************************************************************/  
+// $Id$
+// vim:tabstop=2
+/***********************************************************************
+Moses - factored phrase-based language decoder
+Copyright (C) 2006 University of Edinburgh
+
+This library is free software; you can redistribute it and/or
+modify it under the terms of the GNU Lesser General Public
+License as published by the Free Software Foundation; either
+version 2.1 of the License, or (at your option) any later version.
+
+This library is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public
+License along with this library; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+***********************************************************************/
 
 #include <deque>
 
@@ -37,23 +37,23 @@ PhraseDecoder::PhraseDecoder(
   const std::vector<float>* weight
 )
   : m_coding(None), m_numScoreComponent(numScoreComponent),
-  m_containsAlignmentInfo(true), m_maxRank(0),
-  m_symbolTree(0), m_multipleScoreTrees(false),
-  m_scoreTrees(1), m_alignTree(0),
-  m_phraseDictionary(phraseDictionary), m_input(input), m_output(output),
-  m_weight(weight),
-  m_separator(" ||| ")
+    m_containsAlignmentInfo(true), m_maxRank(0),
+    m_symbolTree(0), m_multipleScoreTrees(false),
+    m_scoreTrees(1), m_alignTree(0),
+    m_phraseDictionary(phraseDictionary), m_input(input), m_output(output),
+    m_weight(weight),
+    m_separator(" ||| ")
 { }
 
 PhraseDecoder::~PhraseDecoder()
 {
   if(m_symbolTree)
     delete m_symbolTree;
-  
+
   for(size_t i = 0; i < m_scoreTrees.size(); i++)
     if(m_scoreTrees[i])
       delete m_scoreTrees[i];
-  
+
   if(m_alignTree)
     delete m_alignTree;
 }
@@ -61,10 +61,10 @@ PhraseDecoder::~PhraseDecoder()
 inline unsigned PhraseDecoder::GetSourceSymbolId(std::string& symbol)
 {
   boost::unordered_map<std::string, unsigned>::iterator it
-    = m_sourceSymbolsMap.find(symbol);
+  = m_sourceSymbolsMap.find(symbol);
   if(it != m_sourceSymbolsMap.end())
     return it->second;
-    
+
   size_t idx = m_sourceSymbols.find(symbol);
   m_sourceSymbolsMap[symbol] = idx;
   return idx;
@@ -144,76 +144,70 @@ size_t PhraseDecoder::Load(std::FILE* in)
 {
   size_t start = std::ftell(in);
   size_t read = 0;
-  
+
   read += std::fread(&m_coding, sizeof(m_coding), 1, in);
   read += std::fread(&m_numScoreComponent, sizeof(m_numScoreComponent), 1, in);
   read += std::fread(&m_containsAlignmentInfo, sizeof(m_containsAlignmentInfo), 1, in);
   read += std::fread(&m_maxRank, sizeof(m_maxRank), 1, in);
   read += std::fread(&m_maxPhraseLength, sizeof(m_maxPhraseLength), 1, in);
-  
-  if(m_coding == REnc)
-  {
+
+  if(m_coding == REnc) {
     m_sourceSymbols.load(in);
-    
+
     size_t size;
     read += std::fread(&size, sizeof(size_t), 1, in);
     m_lexicalTableIndex.resize(size);
     read += std::fread(&m_lexicalTableIndex[0], sizeof(size_t), size, in);
-    
+
     read += std::fread(&size, sizeof(size_t), 1, in);
     m_lexicalTable.resize(size);
     read += std::fread(&m_lexicalTable[0], sizeof(SrcTrg), size, in);
   }
-  
+
   m_targetSymbols.load(in);
-  
+
   m_symbolTree = new CanonicalHuffman<unsigned>(in);
-  
+
   read += std::fread(&m_multipleScoreTrees, sizeof(m_multipleScoreTrees), 1, in);
-  if(m_multipleScoreTrees)
-  {
+  if(m_multipleScoreTrees) {
     m_scoreTrees.resize(m_numScoreComponent);
     for(size_t i = 0; i < m_numScoreComponent; i++)
       m_scoreTrees[i] = new CanonicalHuffman<float>(in);
-  }
-  else
-  {
+  } else {
     m_scoreTrees.resize(1);
     m_scoreTrees[0] = new CanonicalHuffman<float>(in);
   }
-  
+
   if(m_containsAlignmentInfo)
     m_alignTree = new CanonicalHuffman<AlignPoint>(in);
-  
+
   size_t end = std::ftell(in);
   return end - start;
 }
-  
+
 std::string PhraseDecoder::MakeSourceKey(std::string &source)
 {
-    return source + m_separator;
+  return source + m_separator;
 }
-  
+
 TargetPhraseVectorPtr PhraseDecoder::CreateTargetPhraseCollection(const Phrase &sourcePhrase, bool topLevel)
 {
-    
+
   // Not using TargetPhraseCollection avoiding "new" operator
   // which can introduce heavy locking with multiple threads
   TargetPhraseVectorPtr tpv(new TargetPhraseVector());
   size_t bitsLeft = 0;
-                                
-  if(m_coding == PREnc)
-  {
+
+  if(m_coding == PREnc) {
     std::pair<TargetPhraseVectorPtr, size_t> cachedPhraseColl
-      = m_decodingCache.Retrieve(sourcePhrase);
-    
+    = m_decodingCache.Retrieve(sourcePhrase);
+
     // Has been cached and is complete or does not need to be completed
     if(cachedPhraseColl.first != NULL && (!topLevel || cachedPhraseColl.second == 0))
       return cachedPhraseColl.first;
-  
+
     // Has been cached, but is incomplete
-    else if(cachedPhraseColl.first != NULL)
-    {
+    else if(cachedPhraseColl.first != NULL) {
       bitsLeft = cachedPhraseColl.second;
       tpv->resize(cachedPhraseColl.first->size());
       std::copy(cachedPhraseColl.first->begin(),
@@ -221,220 +215,187 @@ TargetPhraseVectorPtr PhraseDecoder::CreateTargetPhraseCollection(const Phrase &
                 tpv->begin());
     }
   }
-  
+
   // Retrieve source phrase identifier
   std::string sourcePhraseString = sourcePhrase.GetStringRep(*m_input);
   size_t sourcePhraseId = m_phraseDictionary.m_hash[MakeSourceKey(sourcePhraseString)];
-  
-  if(sourcePhraseId != m_phraseDictionary.m_hash.GetSize())
-  {
-    // Retrieve compressed and encoded target phrase collection  
+
+  if(sourcePhraseId != m_phraseDictionary.m_hash.GetSize()) {
+    // Retrieve compressed and encoded target phrase collection
     std::string encodedPhraseCollection;
     if(m_phraseDictionary.m_inMemory)
       encodedPhraseCollection = m_phraseDictionary.m_targetPhrasesMemory[sourcePhraseId];
     else
       encodedPhraseCollection = m_phraseDictionary.m_targetPhrasesMapped[sourcePhraseId];
-    
+
     BitWrapper<> encodedBitStream(encodedPhraseCollection);
     if(m_coding == PREnc && bitsLeft)
       encodedBitStream.SeekFromEnd(bitsLeft);
-    
+
     // Decompress and decode target phrase collection
     TargetPhraseVectorPtr decodedPhraseColl =
       DecodeCollection(tpv, encodedBitStream, sourcePhrase, topLevel);
-    
+
     return decodedPhraseColl;
-  }
-  else
-    return TargetPhraseVectorPtr(); 
+  } else
+    return TargetPhraseVectorPtr();
 }
-  
+
 TargetPhraseVectorPtr PhraseDecoder::DecodeCollection(
   TargetPhraseVectorPtr tpv, BitWrapper<> &encodedBitStream,
   const Phrase &sourcePhrase, bool topLevel)
 {
-  
+
   bool extending = tpv->size();
   size_t bitsLeft = encodedBitStream.TellFromEnd();
-    
+
   typedef std::pair<size_t, size_t> AlignPointSizeT;
-  
+
   std::vector<int> sourceWords;
-  if(m_coding == REnc)
-  {
-    for(size_t i = 0; i < sourcePhrase.GetSize(); i++)
-    {
+  if(m_coding == REnc) {
+    for(size_t i = 0; i < sourcePhrase.GetSize(); i++) {
       std::string sourceWord
-        = sourcePhrase.GetWord(i).GetString(*m_input, false);
+      = sourcePhrase.GetWord(i).GetString(*m_input, false);
       unsigned idx = GetSourceSymbolId(sourceWord);
       sourceWords.push_back(idx);
     }
   }
-  
+
   unsigned phraseStopSymbol = 0;
   AlignPoint alignStopSymbol(-1, -1);
-  
+
   std::vector<float> scores;
   std::set<AlignPointSizeT> alignment;
-  
+
   enum DecodeState { New, Symbol, Score, Alignment, Add } state = New;
-  
+
   size_t srcSize = sourcePhrase.GetSize();
-  
+
   TargetPhrase* targetPhrase = NULL;
-  while(encodedBitStream.TellFromEnd())
-  {
-     
-    if(state == New)
-    {
+  while(encodedBitStream.TellFromEnd()) {
+
+    if(state == New) {
       // Creating new TargetPhrase on the heap
       tpv->push_back(TargetPhrase());
       targetPhrase = &tpv->back();
-      
+
       targetPhrase->SetSourcePhrase(sourcePhrase);
       alignment.clear();
       scores.clear();
-        
+
       state = Symbol;
     }
-    
-    if(state == Symbol)
-    {
-      unsigned symbol = m_symbolTree->Read(encodedBitStream);      
-      if(symbol == phraseStopSymbol)
-      {
+
+    if(state == Symbol) {
+      unsigned symbol = m_symbolTree->Read(encodedBitStream);
+      if(symbol == phraseStopSymbol) {
         state = Score;
-      }
-      else
-      {
-        if(m_coding == REnc)
-        {
+      } else {
+        if(m_coding == REnc) {
           std::string wordString;
           size_t type = GetREncType(symbol);
-          
-          if(type == 1)
-          {
+
+          if(type == 1) {
             unsigned decodedSymbol = DecodeREncSymbol1(symbol);
             wordString = GetTargetSymbol(decodedSymbol);
-          }
-          else if (type == 2)
-          {
+          } else if (type == 2) {
             size_t rank = DecodeREncSymbol2Rank(symbol);
             size_t srcPos = DecodeREncSymbol2Position(symbol);
-            
+
             if(srcPos >= sourceWords.size())
-              return TargetPhraseVectorPtr();  
-            
+              return TargetPhraseVectorPtr();
+
             wordString = GetTargetSymbol(GetTranslation(sourceWords[srcPos], rank));
-            if(m_phraseDictionary.m_useAlignmentInfo)
-            {
+            if(m_phraseDictionary.m_useAlignmentInfo) {
               size_t trgPos = targetPhrase->GetSize();
               alignment.insert(AlignPoint(srcPos, trgPos));
             }
-          }
-          else if(type == 3)
-          {
+          } else if(type == 3) {
             size_t rank = DecodeREncSymbol3(symbol);
             size_t srcPos = targetPhrase->GetSize();
-            
+
             if(srcPos >= sourceWords.size())
-              return TargetPhraseVectorPtr();  
-                            
-            wordString = GetTargetSymbol(GetTranslation(sourceWords[srcPos], rank));   
-            if(m_phraseDictionary.m_useAlignmentInfo)
-            {
+              return TargetPhraseVectorPtr();
+
+            wordString = GetTargetSymbol(GetTranslation(sourceWords[srcPos], rank));
+            if(m_phraseDictionary.m_useAlignmentInfo) {
               size_t trgPos = srcPos;
               alignment.insert(AlignPoint(srcPos, trgPos));
             }
           }
-          
+
           Word word;
           word.CreateFromString(Output, *m_output, wordString, false);
           targetPhrase->AddWord(word);
-        }
-        else if(m_coding == PREnc)
-        {
+        } else if(m_coding == PREnc) {
           // if the symbol is just a word
-          if(GetPREncType(symbol) == 1)
-          {
+          if(GetPREncType(symbol) == 1) {
             unsigned decodedSymbol = DecodePREncSymbol1(symbol);
-     
+
             Word word;
             word.CreateFromString(Output, *m_output,
                                   GetTargetSymbol(decodedSymbol), false);
             targetPhrase->AddWord(word);
           }
           // if the symbol is a subphrase pointer
-          else
-          {
+          else {
             int left = DecodePREncSymbol2Left(symbol);
             int right = DecodePREncSymbol2Right(symbol);
             unsigned rank = DecodePREncSymbol2Rank(symbol);
-            
+
             int srcStart = left + targetPhrase->GetSize();
             int srcEnd   = srcSize - right - 1;
-            
+
             // false positive consistency check
             if(0 > srcStart || srcStart > srcEnd || unsigned(srcEnd) >= srcSize)
               return TargetPhraseVectorPtr();
-            
+
             // false positive consistency check
             if(m_maxRank && rank > m_maxRank)
-                return TargetPhraseVectorPtr();
-            
+              return TargetPhraseVectorPtr();
+
             // set subphrase by default to itself
             TargetPhraseVectorPtr subTpv = tpv;
-            
+
             // if range smaller than source phrase retrieve subphrase
-            if(unsigned(srcEnd - srcStart + 1) != srcSize)
-            {
+            if(unsigned(srcEnd - srcStart + 1) != srcSize) {
               Phrase subPhrase = sourcePhrase.GetSubString(WordsRange(srcStart, srcEnd));
               subTpv = CreateTargetPhraseCollection(subPhrase, false);
-            }
-            else {
+            } else {
               // false positive consistency check
               if(rank >= tpv->size()-1)
                 return TargetPhraseVectorPtr();
             }
-            
+
             // false positive consistency check
-            if(subTpv != NULL && rank < subTpv->size())
-            {
+            if(subTpv != NULL && rank < subTpv->size()) {
               // insert the subphrase into the main target phrase
               TargetPhrase& subTp = subTpv->at(rank);
-              if(m_phraseDictionary.m_useAlignmentInfo)
-              {
+              if(m_phraseDictionary.m_useAlignmentInfo) {
                 // reconstruct the alignment data based on the alignment of the subphrase
                 for(AlignmentInfo::const_iterator it = subTp.GetAlignTerm().begin();
-                    it != subTp.GetAlignTerm().end(); it++)
-                {
+                    it != subTp.GetAlignTerm().end(); it++) {
                   alignment.insert(AlignPointSizeT(srcStart + it->first,
                                                    targetPhrase->GetSize() + it->second));
                 }
               }
               targetPhrase->Append(subTp);
-            }
-            else 
+            } else
               return TargetPhraseVectorPtr();
           }
-        }
-        else
-        {
-            Word word;
-            word.CreateFromString(Output, *m_output,
-                                  GetTargetSymbol(symbol), false);
-            targetPhrase->AddWord(word);
+        } else {
+          Word word;
+          word.CreateFromString(Output, *m_output,
+                                GetTargetSymbol(symbol), false);
+          targetPhrase->AddWord(word);
         }
       }
-    }
-    else if(state == Score)
-    {
+    } else if(state == Score) {
       size_t idx = m_multipleScoreTrees ? scores.size() : 0;
       float score = m_scoreTrees[idx]->Read(encodedBitStream);
       scores.push_back(score);
-      
-      if(scores.size() == m_numScoreComponent)
-      {
+
+      if(scores.size() == m_numScoreComponent) {
         targetPhrase->GetScoreBreakdown().Assign(&m_phraseDictionary, scores);
         targetPhrase->Evaluate(sourcePhrase);
 
@@ -443,49 +404,41 @@ TargetPhraseVectorPtr PhraseDecoder::DecodeCollection(
         else
           state = Add;
       }
-    }
-    else if(state == Alignment)
-    {
+    } else if(state == Alignment) {
       AlignPoint alignPoint = m_alignTree->Read(encodedBitStream);
-      if(alignPoint == alignStopSymbol)
-      {
+      if(alignPoint == alignStopSymbol) {
         state = Add;
-      }
-      else
-      {
-        if(m_phraseDictionary.m_useAlignmentInfo)  
+      } else {
+        if(m_phraseDictionary.m_useAlignmentInfo)
           alignment.insert(AlignPointSizeT(alignPoint));
       }
     }
-    
-    if(state == Add)
-    {
+
+    if(state == Add) {
       if(m_phraseDictionary.m_useAlignmentInfo) {
         targetPhrase->SetAlignTerm(alignment);
       }
-      
-      if(m_coding == PREnc)
-      {
+
+      if(m_coding == PREnc) {
         if(!m_maxRank || tpv->size() <= m_maxRank)
           bitsLeft = encodedBitStream.TellFromEnd();
-        
+
         if(!topLevel && m_maxRank && tpv->size() >= m_maxRank)
           break;
       }
-      
+
       if(encodedBitStream.TellFromEnd() <= 8)
         break;
-      
+
       state = New;
-    }    
+    }
   }
-  
-  if(m_coding == PREnc && !extending)
-  {
+
+  if(m_coding == PREnc && !extending) {
     bitsLeft = bitsLeft > 8 ? bitsLeft : 0;
     m_decodingCache.Cache(sourcePhrase, tpv, bitsLeft, m_maxRank);
   }
-  
+
   return tpv;
 }
 
diff --git a/moses/TranslationModel/CompactPT/PhraseDecoder.h b/moses/TranslationModel/CompactPT/PhraseDecoder.h
index 13c8af300..85e9334da 100644
--- a/moses/TranslationModel/CompactPT/PhraseDecoder.h
+++ b/moses/TranslationModel/CompactPT/PhraseDecoder.h
@@ -1,23 +1,23 @@
-// $Id$                                                                                                                               
-// vim:tabstop=2                                                                                                                      
-/***********************************************************************                                                              
-Moses - factored phrase-based language decoder                                                                                        
-Copyright (C) 2006 University of Edinburgh                                                                                            
-                                                                                                                                      
-This library is free software; you can redistribute it and/or                                                                         
-modify it under the terms of the GNU Lesser General Public                                                                            
-License as published by the Free Software Foundation; either                                                                          
-version 2.1 of the License, or (at your option) any later version.                                                                    
-                                                                                                                                      
-This library is distributed in the hope that it will be useful,                                                                       
-but WITHOUT ANY WARRANTY; without even the implied warranty of                                                                        
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU                                                                     
-Lesser General Public License for more details.                                                                                       
-                                                                                                                                      
-You should have received a copy of the GNU Lesser General Public                                                                      
-License along with this library; if not, write to the Free Software                                                                   
-Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA                                                        
-***********************************************************************/  
+// $Id$
+// vim:tabstop=2
+/***********************************************************************
+Moses - factored phrase-based language decoder
+Copyright (C) 2006 University of Edinburgh
+
+This library is free software; you can redistribute it and/or
+modify it under the terms of the GNU Lesser General Public
+License as published by the Free Software Foundation; either
+version 2.1 of the License, or (at your option) any later version.
+
+This library is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public
+License along with this library; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+***********************************************************************/
 
 #ifndef moses_PhraseDecoder_h
 #define moses_PhraseDecoder_h
@@ -52,93 +52,93 @@ class PhraseDictionaryCompact;
 
 class PhraseDecoder
 {
-  protected:
-    
-    friend class PhraseDictionaryCompact;
-    
-    typedef std::pair<unsigned char, unsigned char> AlignPoint;
-    typedef std::pair<unsigned, unsigned> SrcTrg;
-        
-    enum Coding { None, REnc, PREnc } m_coding;
-    
-    size_t m_numScoreComponent;
-    bool m_containsAlignmentInfo;
-    size_t m_maxRank;
-    size_t m_maxPhraseLength;
-    
-    boost::unordered_map<std::string, unsigned> m_sourceSymbolsMap;
-    StringVector<unsigned char, unsigned, std::allocator> m_sourceSymbols;
-    StringVector<unsigned char, unsigned, std::allocator> m_targetSymbols;
-    
-    std::vector<size_t> m_lexicalTableIndex;
-    std::vector<SrcTrg> m_lexicalTable;
-    
-    CanonicalHuffman<unsigned>* m_symbolTree;
-    
-    bool m_multipleScoreTrees;
-    std::vector<CanonicalHuffman<float>*> m_scoreTrees;
-    
-    CanonicalHuffman<AlignPoint>* m_alignTree;
-    
-    TargetPhraseCollectionCache m_decodingCache;
-    
-    PhraseDictionaryCompact& m_phraseDictionary;   
-    
-    // ***********************************************
-    
-    const std::vector<FactorType>* m_input;
-    const std::vector<FactorType>* m_output;
-    const std::vector<float>* m_weight;
-    
-    std::string m_separator;
-  
-    // ***********************************************
-    
-    unsigned GetSourceSymbolId(std::string& s);
-    std::string GetTargetSymbol(unsigned id) const;
-    
-    size_t GetREncType(unsigned encodedSymbol);
-    size_t GetPREncType(unsigned encodedSymbol);
-    
-    unsigned GetTranslation(unsigned srcIdx, size_t rank);
-    
-    size_t GetMaxSourcePhraseLength();
-    
-    unsigned DecodeREncSymbol1(unsigned encodedSymbol);
-    unsigned DecodeREncSymbol2Rank(unsigned encodedSymbol);
-    unsigned DecodeREncSymbol2Position(unsigned encodedSymbol);
-    unsigned DecodeREncSymbol3(unsigned encodedSymbol);
-    
-    unsigned DecodePREncSymbol1(unsigned encodedSymbol);
-    int DecodePREncSymbol2Left(unsigned encodedSymbol);
-    int DecodePREncSymbol2Right(unsigned encodedSymbol);
-    unsigned DecodePREncSymbol2Rank(unsigned encodedSymbol);
-    
-    std::string MakeSourceKey(std::string &);
-    
-  public:
-    
-    PhraseDecoder(
-      PhraseDictionaryCompact &phraseDictionary,
-      const std::vector<FactorType>* input,
-      const std::vector<FactorType>* output,
-      size_t numScoreComponent,
-      const std::vector<float>* weight
-    );
-    
-    ~PhraseDecoder();
-     
-    size_t Load(std::FILE* in);
-    
-    TargetPhraseVectorPtr CreateTargetPhraseCollection(const Phrase &sourcePhrase,
-                                                       bool topLevel = false);
-    
-    TargetPhraseVectorPtr DecodeCollection(TargetPhraseVectorPtr tpv,
-                                           BitWrapper<> &encodedBitStream,
-                                           const Phrase &sourcePhrase,
-                                           bool topLevel);
-    
-    void PruneCache();
+protected:
+
+  friend class PhraseDictionaryCompact;
+
+  typedef std::pair<unsigned char, unsigned char> AlignPoint;
+  typedef std::pair<unsigned, unsigned> SrcTrg;
+
+  enum Coding { None, REnc, PREnc } m_coding;
+
+  size_t m_numScoreComponent;
+  bool m_containsAlignmentInfo;
+  size_t m_maxRank;
+  size_t m_maxPhraseLength;
+
+  boost::unordered_map<std::string, unsigned> m_sourceSymbolsMap;
+  StringVector<unsigned char, unsigned, std::allocator> m_sourceSymbols;
+  StringVector<unsigned char, unsigned, std::allocator> m_targetSymbols;
+
+  std::vector<size_t> m_lexicalTableIndex;
+  std::vector<SrcTrg> m_lexicalTable;
+
+  CanonicalHuffman<unsigned>* m_symbolTree;
+
+  bool m_multipleScoreTrees;
+  std::vector<CanonicalHuffman<float>*> m_scoreTrees;
+
+  CanonicalHuffman<AlignPoint>* m_alignTree;
+
+  TargetPhraseCollectionCache m_decodingCache;
+
+  PhraseDictionaryCompact& m_phraseDictionary;
+
+  // ***********************************************
+
+  const std::vector<FactorType>* m_input;
+  const std::vector<FactorType>* m_output;
+  const std::vector<float>* m_weight;
+
+  std::string m_separator;
+
+  // ***********************************************
+
+  unsigned GetSourceSymbolId(std::string& s);
+  std::string GetTargetSymbol(unsigned id) const;
+
+  size_t GetREncType(unsigned encodedSymbol);
+  size_t GetPREncType(unsigned encodedSymbol);
+
+  unsigned GetTranslation(unsigned srcIdx, size_t rank);
+
+  size_t GetMaxSourcePhraseLength();
+
+  unsigned DecodeREncSymbol1(unsigned encodedSymbol);
+  unsigned DecodeREncSymbol2Rank(unsigned encodedSymbol);
+  unsigned DecodeREncSymbol2Position(unsigned encodedSymbol);
+  unsigned DecodeREncSymbol3(unsigned encodedSymbol);
+
+  unsigned DecodePREncSymbol1(unsigned encodedSymbol);
+  int DecodePREncSymbol2Left(unsigned encodedSymbol);
+  int DecodePREncSymbol2Right(unsigned encodedSymbol);
+  unsigned DecodePREncSymbol2Rank(unsigned encodedSymbol);
+
+  std::string MakeSourceKey(std::string &);
+
+public:
+
+  PhraseDecoder(
+    PhraseDictionaryCompact &phraseDictionary,
+    const std::vector<FactorType>* input,
+    const std::vector<FactorType>* output,
+    size_t numScoreComponent,
+    const std::vector<float>* weight
+  );
+
+  ~PhraseDecoder();
+
+  size_t Load(std::FILE* in);
+
+  TargetPhraseVectorPtr CreateTargetPhraseCollection(const Phrase &sourcePhrase,
+      bool topLevel = false);
+
+  TargetPhraseVectorPtr DecodeCollection(TargetPhraseVectorPtr tpv,
+                                         BitWrapper<> &encodedBitStream,
+                                         const Phrase &sourcePhrase,
+                                         bool topLevel);
+
+  void PruneCache();
 };
 
 }
diff --git a/moses/TranslationModel/CompactPT/PhraseDictionaryCompact.cpp b/moses/TranslationModel/CompactPT/PhraseDictionaryCompact.cpp
index e863eb812..ff33f10a7 100644
--- a/moses/TranslationModel/CompactPT/PhraseDictionaryCompact.cpp
+++ b/moses/TranslationModel/CompactPT/PhraseDictionaryCompact.cpp
@@ -1,23 +1,23 @@
-// $Id$                                                                                                                               
-// vim:tabstop=2                                                                                                                      
-/***********************************************************************                                                              
-Moses - factored phrase-based language decoder                                                                                        
-Copyright (C) 2006 University of Edinburgh                                                                                            
-                                                                                                                                      
-This library is free software; you can redistribute it and/or                                                                         
-modify it under the terms of the GNU Lesser General Public                                                                            
-License as published by the Free Software Foundation; either                                                                          
-version 2.1 of the License, or (at your option) any later version.                                                                    
-                                                                                                                                      
-This library is distributed in the hope that it will be useful,                                                                       
-but WITHOUT ANY WARRANTY; without even the implied warranty of                                                                        
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU                                                                     
-Lesser General Public License for more details.                                                                                       
-                                                                                                                                      
-You should have received a copy of the GNU Lesser General Public                                                                      
-License along with this library; if not, write to the Free Software                                                                   
-Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA                                                        
-***********************************************************************/  
+// $Id$
+// vim:tabstop=2
+/***********************************************************************
+Moses - factored phrase-based language decoder
+Copyright (C) 2006 University of Edinburgh
+
+This library is free software; you can redistribute it and/or
+modify it under the terms of the GNU Lesser General Public
+License as published by the Free Software Foundation; either
+version 2.1 of the License, or (at your option) any later version.
+
+This library is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public
+License along with this library; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+***********************************************************************/
 
 #include <fstream>
 #include <string>
@@ -40,42 +40,35 @@ using namespace std;
 
 namespace Moses
 {
-  
+
 bool PhraseDictionaryCompact::InitDictionary()
 {
   const StaticData &staticData = StaticData::Instance();
 
   m_weight = staticData.GetWeights(this);
- 
+
   std::string tFilePath = m_filePath;
-  
+
   std::string suffix = ".minphr";
-  if(tFilePath.substr(tFilePath.length() - suffix.length(), suffix.length()) == suffix)
-  {
-    if(!FileExists(tFilePath))
-    {
+  if(tFilePath.substr(tFilePath.length() - suffix.length(), suffix.length()) == suffix) {
+    if(!FileExists(tFilePath)) {
       std::cerr << "Error: File " << tFilePath << " does not exit." << std::endl;
       exit(1);
     }
-  }
-  else 
-  {
-    if(FileExists(tFilePath + suffix))
-    {
+  } else {
+    if(FileExists(tFilePath + suffix)) {
       tFilePath += suffix;
-    }
-    else
-    {
-       std::cerr << "Error: File " << tFilePath << ".minphr does not exit." << std::endl;
-       exit(1);
+    } else {
+      std::cerr << "Error: File " << tFilePath << ".minphr does not exit." << std::endl;
+      exit(1);
     }
   }
 
   m_phraseDecoder = new PhraseDecoder(*this, &m_input, &m_output,
-                                  m_numScoreComponents, &m_weight);
+                                      m_numScoreComponents, &m_weight);
 
   std::FILE* pFile = std::fopen(tFilePath.c_str() , "r");
-  
+
   size_t indexSize;
   if(m_inMemory)
     // Load source phrase index into memory
@@ -85,7 +78,7 @@ bool PhraseDictionaryCompact::InitDictionary()
     indexSize = m_hash.LoadIndex(pFile);
 
   size_t coderSize = m_phraseDecoder->Load(pFile);
-  
+
   size_t phraseSize;
   if(m_inMemory)
     // Load target phrase collections into memory
@@ -93,8 +86,8 @@ bool PhraseDictionaryCompact::InitDictionary()
   else
     // Keep target phrase collections on disk
     phraseSize = m_targetPhrasesMapped.load(pFile, true);
-  
-  return indexSize && coderSize && phraseSize;    
+
+  return indexSize && coderSize && phraseSize;
 }
 
 struct CompareTargetPhrase {
@@ -104,21 +97,22 @@ struct CompareTargetPhrase {
 };
 
 const TargetPhraseCollection*
-PhraseDictionaryCompact::GetTargetPhraseCollection(const Phrase &sourcePhrase) const {
-  
+PhraseDictionaryCompact::GetTargetPhraseCollection(const Phrase &sourcePhrase) const
+{
+
   // There is no souch source phrase if source phrase is longer than longest
-  // observed source phrase during compilation 
+  // observed source phrase during compilation
   if(sourcePhrase.GetSize() > m_phraseDecoder->GetMaxSourcePhraseLength())
     return NULL;
 
   // Retrieve target phrase collection from phrase table
   TargetPhraseVectorPtr decodedPhraseColl
-    = m_phraseDecoder->CreateTargetPhraseCollection(sourcePhrase, true);
-  
+  = m_phraseDecoder->CreateTargetPhraseCollection(sourcePhrase, true);
+
   if(decodedPhraseColl != NULL && decodedPhraseColl->size()) {
     TargetPhraseVectorPtr tpv(new TargetPhraseVector(*decodedPhraseColl));
     TargetPhraseCollection* phraseColl = new TargetPhraseCollection();
-    
+
     // Score phrases and if possible apply ttable_limit
     TargetPhraseVector::iterator nth =
       (m_tableLimit == 0 || tpv->size() < m_tableLimit) ?
@@ -129,21 +123,21 @@ PhraseDictionaryCompact::GetTargetPhraseCollection(const Phrase &sourcePhrase) c
       cerr << *tp << endl;
       phraseColl->Add(tp);
     }
-    
+
     // Cache phrase pair for for clean-up or retrieval with PREnc
     const_cast<PhraseDictionaryCompact*>(this)->CacheForCleanup(phraseColl);
-    
+
     return phraseColl;
-  }
-  else
+  } else
     return NULL;
 }
 
 TargetPhraseVectorPtr
-PhraseDictionaryCompact::GetTargetPhraseCollectionRaw(const Phrase &sourcePhrase) const {
+PhraseDictionaryCompact::GetTargetPhraseCollectionRaw(const Phrase &sourcePhrase) const
+{
 
   // There is no souch source phrase if source phrase is longer than longest
-  // observed source phrase during compilation 
+  // observed source phrase during compilation
   if(sourcePhrase.GetSize() > m_phraseDecoder->GetMaxSourcePhraseLength())
     return TargetPhraseVectorPtr();
 
@@ -151,42 +145,45 @@ PhraseDictionaryCompact::GetTargetPhraseCollectionRaw(const Phrase &sourcePhrase
   return m_phraseDecoder->CreateTargetPhraseCollection(sourcePhrase, true);
 }
 
-PhraseDictionaryCompact::~PhraseDictionaryCompact() {
+PhraseDictionaryCompact::~PhraseDictionaryCompact()
+{
   if(m_phraseDecoder)
     delete m_phraseDecoder;
 }
 
 //TO_STRING_BODY(PhraseDictionaryCompact)
 
-void PhraseDictionaryCompact::CacheForCleanup(TargetPhraseCollection* tpc) {
+void PhraseDictionaryCompact::CacheForCleanup(TargetPhraseCollection* tpc)
+{
 #ifdef WITH_THREADS
   boost::mutex::scoped_lock lock(m_sentenceMutex);
-  PhraseCache &ref = m_sentenceCache[boost::this_thread::get_id()]; 
+  PhraseCache &ref = m_sentenceCache[boost::this_thread::get_id()];
 #else
-  PhraseCache &ref = m_sentenceCache; 
+  PhraseCache &ref = m_sentenceCache;
 #endif
   ref.push_back(tpc);
 }
 
 void PhraseDictionaryCompact::AddEquivPhrase(const Phrase &source,
-                                             const TargetPhrase &targetPhrase) { }
+    const TargetPhrase &targetPhrase) { }
 
-void PhraseDictionaryCompact::CleanUpAfterSentenceProcessing(const InputType &source) {
+void PhraseDictionaryCompact::CleanUpAfterSentenceProcessing(const InputType &source)
+{
   if(!m_inMemory)
     m_hash.KeepNLastRanges(0.01, 0.2);
-    
+
   m_phraseDecoder->PruneCache();
-  
+
 #ifdef WITH_THREADS
   boost::mutex::scoped_lock lock(m_sentenceMutex);
-  PhraseCache &ref = m_sentenceCache[boost::this_thread::get_id()]; 
+  PhraseCache &ref = m_sentenceCache[boost::this_thread::get_id()];
 #else
-  PhraseCache &ref = m_sentenceCache; 
+  PhraseCache &ref = m_sentenceCache;
 #endif
-  
-  for(PhraseCache::iterator it = ref.begin(); it != ref.end(); it++) 
-      delete *it;
-      
+
+  for(PhraseCache::iterator it = ref.begin(); it != ref.end(); it++)
+    delete *it;
+
   PhraseCache temp;
   temp.swap(ref);
 }
diff --git a/moses/TranslationModel/CompactPT/PhraseDictionaryCompact.h b/moses/TranslationModel/CompactPT/PhraseDictionaryCompact.h
index 1eab58894..60969665a 100644
--- a/moses/TranslationModel/CompactPT/PhraseDictionaryCompact.h
+++ b/moses/TranslationModel/CompactPT/PhraseDictionaryCompact.h
@@ -1,23 +1,23 @@
-// $Id$                                                                                                                               
-// vim:tabstop=2                                                                                                                      
-/***********************************************************************                                                              
-Moses - factored phrase-based language decoder                                                                                        
-Copyright (C) 2006 University of Edinburgh                                                                                            
-                                                                                                                                      
-This library is free software; you can redistribute it and/or                                                                         
-modify it under the terms of the GNU Lesser General Public                                                                            
-License as published by the Free Software Foundation; either                                                                          
-version 2.1 of the License, or (at your option) any later version.                                                                    
-                                                                                                                                      
-This library is distributed in the hope that it will be useful,                                                                       
-but WITHOUT ANY WARRANTY; without even the implied warranty of                                                                        
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU                                                                     
-Lesser General Public License for more details.                                                                                       
-                                                                                                                                      
-You should have received a copy of the GNU Lesser General Public                                                                      
-License along with this library; if not, write to the Free Software                                                                   
-Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA                                                        
-***********************************************************************/  
+// $Id$
+// vim:tabstop=2
+/***********************************************************************
+Moses - factored phrase-based language decoder
+Copyright (C) 2006 University of Edinburgh
+
+This library is free software; you can redistribute it and/or
+modify it under the terms of the GNU Lesser General Public
+License as published by the Free Software Foundation; either
+version 2.1 of the License, or (at your option) any later version.
+
+This library is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public
+License along with this library; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+***********************************************************************/
 
 #ifndef moses_PhraseDictionaryCompact_h
 #define moses_PhraseDictionaryCompact_h
@@ -50,7 +50,7 @@ protected:
 
   bool m_inMemory;
   bool m_useAlignmentInfo;
-  
+
   typedef std::vector<TargetPhraseCollection*> PhraseCache;
 #ifdef WITH_THREADS
   boost::mutex m_sentenceMutex;
@@ -59,23 +59,22 @@ protected:
   typedef PhraseCache SentenceCache;
 #endif
   SentenceCache m_sentenceCache;
-  
+
   BlockHashIndex m_hash;
   PhraseDecoder* m_phraseDecoder;
-  
+
   StringVector<unsigned char, size_t, MmapAllocator>  m_targetPhrasesMapped;
   StringVector<unsigned char, size_t, std::allocator> m_targetPhrasesMemory;
 
   std::vector<float> m_weight;
 public:
   PhraseDictionaryCompact(const std::string &line)
-  :PhraseDictionary("PhraseDictionaryCompact", line)
-  ,m_inMemory(true)
-  ,m_useAlignmentInfo(true)
-  ,m_hash(10, 16)
-  ,m_phraseDecoder(0)
-  ,m_weight(0)
-  {
+    :PhraseDictionary("PhraseDictionaryCompact", line)
+    ,m_inMemory(true)
+    ,m_useAlignmentInfo(true)
+    ,m_hash(10, 16)
+    ,m_phraseDecoder(0)
+    ,m_weight(0) {
   }
 
   ~PhraseDictionaryCompact();
@@ -84,16 +83,15 @@ public:
 
   const TargetPhraseCollection* GetTargetPhraseCollection(const Phrase &source) const;
   TargetPhraseVectorPtr GetTargetPhraseCollectionRaw(const Phrase &source) const;
-  
+
   void AddEquivPhrase(const Phrase &source, const TargetPhrase &targetPhrase);
-  
+
   void CacheForCleanup(TargetPhraseCollection* tpc);
   void CleanUpAfterSentenceProcessing(const InputType &source);
 
   virtual ChartRuleLookupManager *CreateRuleLookupManager(
     const InputType &,
-    const ChartCellCollectionBase &)
-  {
+    const ChartCellCollectionBase &) {
     assert(false);
     return 0;
   }
diff --git a/moses/TranslationModel/CompactPT/PhraseTableCreator.cpp b/moses/TranslationModel/CompactPT/PhraseTableCreator.cpp
index c7bd81019..fc3b056c6 100644
--- a/moses/TranslationModel/CompactPT/PhraseTableCreator.cpp
+++ b/moses/TranslationModel/CompactPT/PhraseTableCreator.cpp
@@ -1,23 +1,23 @@
-// $Id$                                                                                                                               
-// vim:tabstop=2                                                                                                                      
-/***********************************************************************                                                              
-Moses - factored phrase-based language decoder                                                                                        
-Copyright (C) 2006 University of Edinburgh                                                                                            
-                                                                                                                                      
-This library is free software; you can redistribute it and/or                                                                         
-modify it under the terms of the GNU Lesser General Public                                                                            
-License as published by the Free Software Foundation; either                                                                          
-version 2.1 of the License, or (at your option) any later version.                                                                    
-                                                                                                                                      
-This library is distributed in the hope that it will be useful,                                                                       
-but WITHOUT ANY WARRANTY; without even the implied warranty of                                                                        
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU                                                                     
-Lesser General Public License for more details.                                                                                       
-                                                                                                                                      
-You should have received a copy of the GNU Lesser General Public                                                                      
-License along with this library; if not, write to the Free Software                                                                   
-Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA                                                        
-***********************************************************************/  
+// $Id$
+// vim:tabstop=2
+/***********************************************************************
+Moses - factored phrase-based language decoder
+Copyright (C) 2006 University of Edinburgh
+
+This library is free software; you can redistribute it and/or
+modify it under the terms of the GNU Lesser General Public
+License as published by the Free Software Foundation; either
+version 2.1 of the License, or (at your option) any later version.
+
+This library is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public
+License along with this library; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+***********************************************************************/
 
 #include <cstdio>
 
@@ -29,17 +29,17 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 
 namespace Moses
 {
-    
+
 bool operator<(const PackedItem &pi1, const PackedItem &pi2)
 {
   if(pi1.GetLine() < pi2.GetLine())
-      return false;
+    return false;
   return true;
 }
-    
+
 std::string PhraseTableCreator::m_phraseStopSymbol = "__SPECIAL_STOP_SYMBOL__";
 std::string PhraseTableCreator::m_separator = " ||| ";
-    
+
 PhraseTableCreator::PhraseTableCreator(std::string inPath,
                                        std::string outPath,
                                        std::string tempfilePath,
@@ -56,7 +56,7 @@ PhraseTableCreator::PhraseTableCreator(std::string inPath,
 #ifdef WITH_THREADS
                                        , size_t threads
 #endif
-                                       )
+                                      )
   : m_inPath(inPath), m_outPath(outPath), m_tempfilePath(tempfilePath),
     m_outFile(std::fopen(m_outPath.c_str(), "w")), m_numScoreComponent(numScoreComponent),
     m_sortScoreIndex(sortScoreIndex), m_warnMe(warnMe),
@@ -64,81 +64,76 @@ PhraseTableCreator::PhraseTableCreator(std::string inPath,
     m_useAlignmentInfo(useAlignmentInfo),
     m_multipleScoreTrees(multipleScoreTrees),
     m_quantize(quantize), m_maxRank(maxRank),
-  #ifdef WITH_THREADS
+#ifdef WITH_THREADS
     m_threads(threads),
     m_srcHash(m_orderBits, m_fingerPrintBits, 1),
     m_rnkHash(10, 24, m_threads),
-  #else
+#else
     m_srcHash(m_orderBits, m_fingerPrintBits),
     m_rnkHash(m_orderBits, m_fingerPrintBits),
-  #endif
+#endif
     m_maxPhraseLength(0),
     m_lastFlushedLine(-1), m_lastFlushedSourceNum(0),
     m_lastFlushedSourcePhrase("")
 {
   PrintInfo();
-  
+
   AddTargetSymbolId(m_phraseStopSymbol);
-  
+
   size_t cur_pass = 1;
   size_t all_passes = 2;
   if(m_coding == PREnc)
     all_passes = 3;
-  
+
   m_scoreCounters.resize(m_multipleScoreTrees ? m_numScoreComponent : 1);
   for(std::vector<ScoreCounter*>::iterator it = m_scoreCounters.begin();
-    it != m_scoreCounters.end(); it++)
+      it != m_scoreCounters.end(); it++)
     *it = new ScoreCounter();
   m_scoreTrees.resize(m_multipleScoreTrees ? m_numScoreComponent : 1);
-  
+
   // 0th pass
-  if(m_coding == REnc)
-  {
+  if(m_coding == REnc) {
     size_t found = inPath.find_last_of("/\\");
     std::string path;
-    if(found != std::string::npos) 
+    if(found != std::string::npos)
       path = inPath.substr(0, found);
     else
       path = ".";
     LoadLexicalTable(path + "/lex.f2e");
-  }
-  else if(m_coding == PREnc)
-  {
+  } else if(m_coding == PREnc) {
     std::cerr << "Pass " << cur_pass << "/" << all_passes << ": Creating hash function for rank assignment" << std::endl;
     cur_pass++;
     CreateRankHash();
   }
-  
+
   // 1st pass
   std::cerr << "Pass " << cur_pass << "/" << all_passes << ": Creating source phrase index + Encoding target phrases" << std::endl;
   m_srcHash.BeginSave(m_outFile);
-  
+
   if(tempfilePath.size()) {
     MmapAllocator<unsigned char> allocEncoded(util::FMakeTemp(tempfilePath));
     m_encodedTargetPhrases = new StringVector<unsigned char, unsigned long, MmapAllocator>(allocEncoded);
-  }
-  else {
-    m_encodedTargetPhrases = new StringVector<unsigned char, unsigned long, MmapAllocator>();    
+  } else {
+    m_encodedTargetPhrases = new StringVector<unsigned char, unsigned long, MmapAllocator>();
   }
   EncodeTargetPhrases();
-  
+
   cur_pass++;
-  
+
   std::cerr << "Intermezzo: Calculating Huffman code sets" << std::endl;
   CalcHuffmanCodes();
-  
+
   // 2nd pass
   std::cerr << "Pass " << cur_pass << "/" << all_passes << ": Compressing target phrases" << std::endl;
-  
+
   if(tempfilePath.size()) {
     MmapAllocator<unsigned char> allocCompressed(util::FMakeTemp(tempfilePath));
     m_compressedTargetPhrases = new StringVector<unsigned char, unsigned long, MmapAllocator>(allocCompressed);
-  }
-  else {
+  } else {
     m_compressedTargetPhrases = new StringVector<unsigned char, unsigned long, MmapAllocator>();
   }
   CompressTargetPhrases();
-  
+
   std::cerr << "Saving to " << m_outPath << std::endl;
   Save();
   std::cerr << "Done" << std::endl;
@@ -149,44 +144,43 @@ PhraseTableCreator::~PhraseTableCreator()
 {
   delete m_symbolTree;
   if(m_useAlignmentInfo)
-    delete m_alignTree; 
+    delete m_alignTree;
   for(size_t i = 0; i < m_scoreTrees.size(); i++) {
     delete m_scoreTrees[i];
     delete m_scoreCounters[i];
   }
-  
+
   delete m_encodedTargetPhrases;
-  delete m_compressedTargetPhrases;  
+  delete m_compressedTargetPhrases;
 }
 
 void PhraseTableCreator::PrintInfo()
 {
   std::string encodings[3] = {"Huffman", "Huffman + REnc", "Huffman + PREnc"};
-  
+
   std::cerr << "Used options:" << std::endl;
   std::cerr << "\tText phrase table will be read from: " << m_inPath << std::endl;
   std::cerr << "\tOutput phrase table will be written to: " << m_outPath << std::endl;
   std::cerr << "\tStep size for source landmark phrases: 2^" << m_orderBits << "=" << (1ul << m_orderBits) << std::endl;
   std::cerr << "\tSource phrase fingerprint size: " << m_fingerPrintBits << " bits / P(fp)=" << (float(1)/(1ul << m_fingerPrintBits)) << std::endl;
   std::cerr << "\tSelected target phrase encoding: " << encodings[m_coding] << std::endl;
-  if(m_coding == PREnc)
-  {
+  if(m_coding == PREnc) {
     std::cerr << "\tMaxiumum allowed rank for PREnc: ";
     if(!m_maxRank)
       std::cerr << "unlimited" << std::endl;
     else
-      std::cerr << m_maxRank << std::endl;    
+      std::cerr << m_maxRank << std::endl;
   }
-  std::cerr << "\tNumber of score components in phrase table: " << m_numScoreComponent << std::endl;    
-  std::cerr << "\tSingle Huffman code set for score components: " << (m_multipleScoreTrees ? "no" : "yes") << std::endl;    
+  std::cerr << "\tNumber of score components in phrase table: " << m_numScoreComponent << std::endl;
+  std::cerr << "\tSingle Huffman code set for score components: " << (m_multipleScoreTrees ? "no" : "yes") << std::endl;
   std::cerr << "\tUsing score quantization: ";
   if(m_quantize)
     std::cerr << m_quantize << " best" << std::endl;
   else
     std::cerr << "no" << std::endl;
-  std::cerr << "\tExplicitly included alignment information: " << (m_useAlignmentInfo ? "yes" : "no") << std::endl;    
-  
-#ifdef WITH_THREADS    
+  std::cerr << "\tExplicitly included alignment information: " << (m_useAlignmentInfo ? "yes" : "no") << std::endl;
+
+#ifdef WITH_THREADS
   std::cerr << "\tRunning with " << m_threads << " threads" << std::endl;
 #endif
   std::cerr << std::endl;
@@ -200,22 +194,21 @@ void PhraseTableCreator::Save()
   ThrowingFwrite(&m_useAlignmentInfo, sizeof(m_useAlignmentInfo), 1, m_outFile);
   ThrowingFwrite(&m_maxRank, sizeof(m_maxRank), 1, m_outFile);
   ThrowingFwrite(&m_maxPhraseLength, sizeof(m_maxPhraseLength), 1, m_outFile);
-    
-  if(m_coding == REnc)
-  {
+
+  if(m_coding == REnc) {
     // Save source language symbols for REnc
     std::vector<std::string> temp1;
     temp1.resize(m_sourceSymbolsMap.size());
     for(boost::unordered_map<std::string, unsigned>::iterator it
         = m_sourceSymbolsMap.begin(); it != m_sourceSymbolsMap.end(); it++)
-        temp1[it->second] = it->first;
+      temp1[it->second] = it->first;
     std::sort(temp1.begin(), temp1.end());
     StringVector<unsigned char, unsigned, std::allocator> sourceSymbols;
     for(std::vector<std::string>::iterator it = temp1.begin();
         it != temp1.end(); it++)
-        sourceSymbols.push_back(*it);
+      sourceSymbols.push_back(*it);
     sourceSymbols.save(m_outFile);
-        
+
     // Save lexical translation table for REnc
     size_t size = m_lexicalTableIndex.size();
     ThrowingFwrite(&size, sizeof(size_t), 1, m_outFile);
@@ -224,95 +217,92 @@ void PhraseTableCreator::Save()
     ThrowingFwrite(&size, sizeof(size_t), 1, m_outFile);
     ThrowingFwrite(&m_lexicalTable[0], sizeof(SrcTrg), size, m_outFile);
   }
-    
+
   // Save target language symbols
   std::vector<std::string> temp2;
   temp2.resize(m_targetSymbolsMap.size());
   for(boost::unordered_map<std::string, unsigned>::iterator it
-    = m_targetSymbolsMap.begin(); it != m_targetSymbolsMap.end(); it++)
+      = m_targetSymbolsMap.begin(); it != m_targetSymbolsMap.end(); it++)
     temp2[it->second] = it->first;
   StringVector<unsigned char, unsigned, std::allocator> targetSymbols;
   for(std::vector<std::string>::iterator it = temp2.begin();
-    it != temp2.end(); it++)
+      it != temp2.end(); it++)
     targetSymbols.push_back(*it);
   targetSymbols.save(m_outFile);
-  
+
   // Save Huffman codes for target language symbols
   m_symbolTree->Save(m_outFile);
-  
+
   // Save number of Huffman code sets for scores and
   // save Huffman code sets
   ThrowingFwrite(&m_multipleScoreTrees, sizeof(m_multipleScoreTrees), 1, m_outFile);
   size_t numScoreTrees = m_scoreTrees.size();
   for(size_t i = 0; i < numScoreTrees; i++)
     m_scoreTrees[i]->Save(m_outFile);
-  
+
   // Save Huffman codes for alignments
   if(m_useAlignmentInfo)
     m_alignTree->Save(m_outFile);
-  
-  // Save compressed target phrase collections 
+
+  // Save compressed target phrase collections
   m_compressedTargetPhrases->save(m_outFile);
 }
-    
+
 void PhraseTableCreator::LoadLexicalTable(std::string filePath)
 {
   std::vector<SrcTrgProb> t_lexTable;
-    
+
   std::cerr << "Reading in lexical table for Rank Encoding" << std::endl;
   std::ifstream lexIn(filePath.c_str(), std::ifstream::in);
   std::string src, trg;
   float prob;
-  
+
   // Reading in the translation probability lexicon
-  
+
   std::cerr << "\tLoading from " << filePath << std::endl;
-  while(lexIn >> trg >> src >> prob)
-  {
+  while(lexIn >> trg >> src >> prob) {
     t_lexTable.push_back(SrcTrgProb(SrcTrgString(src, trg), prob));
     AddSourceSymbolId(src);
     AddTargetSymbolId(trg);
   }
-  
+
   // Sorting lexicon by source words by lexicographical order, corresponding
   // target words by decreasing probability.
-  
+
   std::cerr << "\tSorting according to translation rank" << std::endl;
   std::sort(t_lexTable.begin(), t_lexTable.end(), SrcTrgProbSorter());
-  
+
   // Re-assigning source word ids in lexicographical order
-  
+
   std::vector<std::string> temp1;
   temp1.resize(m_sourceSymbolsMap.size());
   for(boost::unordered_map<std::string, unsigned>::iterator it
-    = m_sourceSymbolsMap.begin(); it != m_sourceSymbolsMap.end(); it++)
+      = m_sourceSymbolsMap.begin(); it != m_sourceSymbolsMap.end(); it++)
     temp1[it->second] = it->first;
-      
+
   std::sort(temp1.begin(), temp1.end());
-  
+
   for(size_t i = 0; i < temp1.size(); i++)
     m_sourceSymbolsMap[temp1[i]] = i;
-  
+
   // Building the lexicon based on source and target word ids
-  
+
   std::string srcWord = "";
   size_t srcIdx = 0;
   for(std::vector<SrcTrgProb>::iterator it = t_lexTable.begin();
-      it != t_lexTable.end(); it++)
-  { 
+      it != t_lexTable.end(); it++) {
     // If we encounter a new source word
-    if(it->first.first != srcWord)
-    {
+    if(it->first.first != srcWord) {
       srcIdx = GetSourceSymbolId(it->first.first);
-      
+
       // Store position of first translation
       if(srcIdx >= m_lexicalTableIndex.size())
         m_lexicalTableIndex.resize(srcIdx + 1);
       m_lexicalTableIndex[srcIdx] = m_lexicalTable.size();
     }
-    
+
     // Store pair of source word and target word
-    size_t trgIdx = GetTargetSymbolId(it->first.second);        
+    size_t trgIdx = GetTargetSymbolId(it->first.second);
     m_lexicalTable.push_back(SrcTrg(srcIdx, trgIdx));
 
     srcWord = it->first.first;
@@ -322,14 +312,13 @@ void PhraseTableCreator::LoadLexicalTable(std::string filePath)
 }
 
 void PhraseTableCreator::CreateRankHash()
-{    
+{
   InputFileStream inFile(m_inPath);
 
 #ifdef WITH_THREADS
   boost::thread_group threads;
-  for (size_t i = 0; i < m_threads; ++i)
-  {
-    RankingTask* rt = new RankingTask(inFile, *this);    
+  for (size_t i = 0; i < m_threads; ++i) {
+    RankingTask* rt = new RankingTask(inFile, *this);
     threads.create_thread(*rt);
   }
   threads.join_all();
@@ -343,7 +332,7 @@ void PhraseTableCreator::CreateRankHash()
 
 inline std::string PhraseTableCreator::MakeSourceKey(std::string &source)
 {
-    return source + m_separator;
+  return source + m_separator;
 }
 
 inline std::string PhraseTableCreator::MakeSourceTargetKey(std::string &source, std::string &target)
@@ -357,9 +346,8 @@ void PhraseTableCreator::EncodeTargetPhrases()
 
 #ifdef WITH_THREADS
   boost::thread_group threads;
-  for (size_t i = 0; i < m_threads; ++i)
-  {
-    EncodingTask* et = new EncodingTask(inFile, *this);    
+  for (size_t i = 0; i < m_threads; ++i) {
+    EncodingTask* et = new EncodingTask(inFile, *this);
     threads.create_thread(*et);
   }
   threads.join_all();
@@ -368,17 +356,17 @@ void PhraseTableCreator::EncodeTargetPhrases()
   (*et)();
   delete et;
 #endif
-    FlushEncodedQueue(true);
+  FlushEncodedQueue(true);
 }
 
 
 void PhraseTableCreator::CompressTargetPhrases()
-{    
+{
 #ifdef WITH_THREADS
   boost::thread_group threads;
   for (size_t i = 0; i < m_threads; ++i) {
-      CompressionTask* ct = new CompressionTask(*m_encodedTargetPhrases, *this);    
-      threads.create_thread(*ct);
+    CompressionTask* ct = new CompressionTask(*m_encodedTargetPhrases, *this);
+    threads.create_thread(*ct);
   }
   threads.join_all();
 #else
@@ -392,29 +380,27 @@ void PhraseTableCreator::CompressTargetPhrases()
 void PhraseTableCreator::CalcHuffmanCodes()
 {
   std::cerr << "\tCreating Huffman codes for " << m_symbolCounter.Size()
-      << " target phrase symbols" << std::endl;
-       
+            << " target phrase symbols" << std::endl;
+
   m_symbolTree = new SymbolTree(m_symbolCounter.Begin(),
-                                m_symbolCounter.End());      
-  
+                                m_symbolCounter.End());
+
   std::vector<ScoreTree*>::iterator treeIt = m_scoreTrees.begin();
   for(std::vector<ScoreCounter*>::iterator it = m_scoreCounters.begin();
-    it != m_scoreCounters.end(); it++)
-  {    
+      it != m_scoreCounters.end(); it++) {
     if(m_quantize)
-        (*it)->Quantize(m_quantize);
-    
+      (*it)->Quantize(m_quantize);
+
     std::cerr << "\tCreating Huffman codes for " << (*it)->Size()
-        << " scores" << std::endl;
-    
+              << " scores" << std::endl;
+
     *treeIt = new ScoreTree((*it)->Begin(), (*it)->End());
     treeIt++;
   }
-  
-  if(m_useAlignmentInfo)
-  {
+
+  if(m_useAlignmentInfo) {
     std::cerr << "\tCreating Huffman codes for " << m_alignCounter.Size()
-        << " alignment points" << std::endl;
+              << " alignment points" << std::endl;
     m_alignTree = new AlignTree(m_alignCounter.Begin(), m_alignCounter.End());
   }
   std::cerr << std::endl;
@@ -440,9 +426,9 @@ void PhraseTableCreator::AddTargetSymbolId(std::string& symbol)
 unsigned PhraseTableCreator::GetSourceSymbolId(std::string& symbol)
 {
   boost::unordered_map<std::string, unsigned>::iterator it
-    = m_sourceSymbolsMap.find(symbol);
-      
-  if(it != m_sourceSymbolsMap.end())   
+  = m_sourceSymbolsMap.find(symbol);
+
+  if(it != m_sourceSymbolsMap.end())
     return it->second;
   else
     return m_sourceSymbolsMap.size();
@@ -451,9 +437,9 @@ unsigned PhraseTableCreator::GetSourceSymbolId(std::string& symbol)
 unsigned PhraseTableCreator::GetTargetSymbolId(std::string& symbol)
 {
   boost::unordered_map<std::string, unsigned>::iterator it
-      = m_targetSymbolsMap.find(symbol);
-      
-  if(it != m_targetSymbolsMap.end())   
+  = m_targetSymbolsMap.find(symbol);
+
+  if(it != m_targetSymbolsMap.end())
     return it->second;
   else
     return m_targetSymbolsMap.size();
@@ -465,12 +451,11 @@ unsigned PhraseTableCreator::GetOrAddTargetSymbolId(std::string& symbol)
   boost::mutex::scoped_lock lock(m_mutex);
 #endif
   boost::unordered_map<std::string, unsigned>::iterator it
-    = m_targetSymbolsMap.find(symbol);
-      
-  if(it != m_targetSymbolsMap.end())   
+  = m_targetSymbolsMap.find(symbol);
+
+  if(it != m_targetSymbolsMap.end())
     return it->second;
-  else
-  {
+  else {
     unsigned value = m_targetSymbolsMap.size();
     m_targetSymbolsMap[symbol] = value;
     return value;
@@ -481,12 +466,12 @@ unsigned PhraseTableCreator::GetRank(unsigned srcIdx, unsigned trgIdx)
 {
   size_t srcTrgIdx = m_lexicalTableIndex[srcIdx];
   while(srcTrgIdx < m_lexicalTable.size()
-    && srcIdx == m_lexicalTable[srcTrgIdx].first
-    && m_lexicalTable[srcTrgIdx].second != trgIdx)
+        && srcIdx == m_lexicalTable[srcTrgIdx].first
+        && m_lexicalTable[srcTrgIdx].second != trgIdx)
     srcTrgIdx++;
-  
+
   if(srcTrgIdx < m_lexicalTable.size()
-     && m_lexicalTable[srcTrgIdx].second == trgIdx)  
+      && m_lexicalTable[srcTrgIdx].second == trgIdx)
     return srcTrgIdx - m_lexicalTableIndex[srcIdx];
   else
     return m_lexicalTable.size();
@@ -522,14 +507,14 @@ unsigned PhraseTableCreator::EncodePREncSymbol1(unsigned trgIdx)
 unsigned PhraseTableCreator::EncodePREncSymbol2(int left, int right, unsigned rank)
 {
   // "left" and "right" must be smaller than 2^5
-  // "rank" must be smaller than 2^19  
+  // "rank" must be smaller than 2^19
   left  = left  + 32;
   right = right + 32;
-  
+
   assert(64 > left);
   assert(64 > right);
   assert(524288 > rank);
-  
+
   unsigned symbol = 0;
   symbol |=    1  << 31;
   symbol |= left  << 25;
@@ -539,151 +524,135 @@ unsigned PhraseTableCreator::EncodePREncSymbol2(int left, int right, unsigned ra
 }
 
 void PhraseTableCreator::EncodeTargetPhraseNone(std::vector<std::string>& t,
-                                                std::ostream& os)
+    std::ostream& os)
 {
   std::stringstream encodedTargetPhrase;
   size_t j = 0;
-  while(j < t.size())
-  {
+  while(j < t.size()) {
     unsigned targetSymbolId = GetOrAddTargetSymbolId(t[j]);
-    
+
     m_symbolCounter.Increase(targetSymbolId);
     os.write((char*)&targetSymbolId, sizeof(targetSymbolId));
     j++;
   }
-  
+
   unsigned stopSymbolId = GetTargetSymbolId(m_phraseStopSymbol);
   os.write((char*)&stopSymbolId, sizeof(stopSymbolId));
   m_symbolCounter.Increase(stopSymbolId);
 }
 
 void PhraseTableCreator::EncodeTargetPhraseREnc(std::vector<std::string>& s,
-                                                std::vector<std::string>& t,
-                                                std::set<AlignPoint>& a,
-                                                std::ostream& os)
-{  
+    std::vector<std::string>& t,
+    std::set<AlignPoint>& a,
+    std::ostream& os)
+{
   std::stringstream encodedTargetPhrase;
 
   std::vector<std::vector<size_t> > a2(t.size());
   for(std::set<AlignPoint>::iterator it = a.begin(); it != a.end(); it++)
     a2[it->second].push_back(it->first);
 
-  for(size_t i = 0; i < t.size(); i++)
-  {
+  for(size_t i = 0; i < t.size(); i++) {
     unsigned idxTarget = GetOrAddTargetSymbolId(t[i]);
     unsigned encodedSymbol = -1;
-    
+
     unsigned bestSrcPos = s.size();
     unsigned bestDiff = s.size();
     unsigned bestRank = m_lexicalTable.size();
     unsigned badRank = m_lexicalTable.size();
-    
-    for(std::vector<size_t>::iterator it = a2[i].begin(); it != a2[i].end(); it++)
-    {
+
+    for(std::vector<size_t>::iterator it = a2[i].begin(); it != a2[i].end(); it++) {
       unsigned idxSource = GetSourceSymbolId(s[*it]);
       size_t r = GetRank(idxSource, idxTarget);
-      if(r != badRank)
-      {
-        if(r < bestRank)
-        {
+      if(r != badRank) {
+        if(r < bestRank) {
           bestRank = r;
           bestSrcPos = *it;
           bestDiff = abs(*it-i);
-        }
-        else if(r == bestRank && unsigned(abs(*it-i)) < bestDiff)
-        {
+        } else if(r == bestRank && unsigned(abs(*it-i)) < bestDiff) {
           bestSrcPos = *it;
           bestDiff = abs(*it-i);
         }
       }
     }
-  
-    if(bestRank != badRank && bestSrcPos < s.size())
-    {
+
+    if(bestRank != badRank && bestSrcPos < s.size()) {
       if(bestSrcPos == i)
         encodedSymbol = EncodeREncSymbol3(bestRank);
       else
-        encodedSymbol = EncodeREncSymbol2(bestSrcPos, bestRank);          
+        encodedSymbol = EncodeREncSymbol2(bestSrcPos, bestRank);
       a.erase(AlignPoint(bestSrcPos, i));
-    }
-    else
-    {
+    } else {
       encodedSymbol = EncodeREncSymbol1(idxTarget);
     }
-  
+
     os.write((char*)&encodedSymbol, sizeof(encodedSymbol));
     m_symbolCounter.Increase(encodedSymbol);
   }
-  
+
   unsigned stopSymbolId = GetTargetSymbolId(m_phraseStopSymbol);
   unsigned encodedSymbol = EncodeREncSymbol1(stopSymbolId);
   os.write((char*)&encodedSymbol, sizeof(encodedSymbol));
-  m_symbolCounter.Increase(encodedSymbol);    
+  m_symbolCounter.Increase(encodedSymbol);
 }
 
 void PhraseTableCreator::EncodeTargetPhrasePREnc(std::vector<std::string>& s,
-                                                 std::vector<std::string>& t,
-                                                 std::set<AlignPoint>& a,
-                                                 size_t ownRank,
-                                                 std::ostream& os)
+    std::vector<std::string>& t,
+    std::set<AlignPoint>& a,
+    size_t ownRank,
+    std::ostream& os)
 {
   std::vector<unsigned> encodedSymbols(t.size());
   std::vector<unsigned> encodedSymbolsLengths(t.size(), 0);
-  
+
   ConsistentPhrases cp(s.size(), t.size(), a);
   while(!cp.Empty()) {
     ConsistentPhrases::Phrase p = cp.Pop();
-    
+
     std::stringstream key1;
     key1 << s[p.i];
     for(int i = p.i+1; i < p.i+p.m; i++)
       key1 << " " << s[i];
-        
+
     std::stringstream key2;
     key2 << t[p.j];
     for(int i = p.j+1; i < p.j+p.n; i++)
       key2 << " " << t[i];
-    
+
     int rank = -1;
     std::string key1Str = key1.str(), key2Str = key2.str();
     size_t idx = m_rnkHash[MakeSourceTargetKey(key1Str, key2Str)];
     if(idx != m_rnkHash.GetSize())
-      rank = m_ranks[idx];        
-    
-    if(rank >= 0 && (m_maxRank == 0 || unsigned(rank) < m_maxRank))
-    {
-      if(unsigned(p.m) != s.size() || unsigned(rank) < ownRank)
-      {   
+      rank = m_ranks[idx];
+
+    if(rank >= 0 && (m_maxRank == 0 || unsigned(rank) < m_maxRank)) {
+      if(unsigned(p.m) != s.size() || unsigned(rank) < ownRank) {
         std::stringstream encodedSymbol;
         encodedSymbols[p.j] = EncodePREncSymbol2(p.i-p.j, s.size()-(p.i+p.m), rank);
         encodedSymbolsLengths[p.j] = p.n;
-       
+
         std::set<AlignPoint> tAlignment;
         for(std::set<AlignPoint>::iterator it = a.begin();
-          it != a.end(); it++)
+            it != a.end(); it++)
           if(it->first < p.i || it->first >= p.i + p.m
-            || it->second < p.j || it->second >= p.j + p.n)
-             tAlignment.insert(*it);
+              || it->second < p.j || it->second >= p.j + p.n)
+            tAlignment.insert(*it);
         a = tAlignment;
-        cp.RemoveOverlap(p);  
+        cp.RemoveOverlap(p);
       }
     }
   }
-  
+
   std::stringstream encodedTargetPhrase;
-  
+
   size_t j = 0;
-  while(j < t.size())
-  {
-    if(encodedSymbolsLengths[j] > 0)
-    {
+  while(j < t.size()) {
+    if(encodedSymbolsLengths[j] > 0) {
       unsigned encodedSymbol = encodedSymbols[j];
       m_symbolCounter.Increase(encodedSymbol);
       os.write((char*)&encodedSymbol, sizeof(encodedSymbol));
       j += encodedSymbolsLengths[j];
-    }
-    else
-    {
+    } else {
       unsigned targetSymbolId = GetOrAddTargetSymbolId(t[j]);
       unsigned encodedSymbol = EncodePREncSymbol1(targetSymbolId);
       m_symbolCounter.Increase(encodedSymbol);
@@ -691,7 +660,7 @@ void PhraseTableCreator::EncodeTargetPhrasePREnc(std::vector<std::string>& s,
       j++;
     }
   }
-  
+
   unsigned stopSymbolId = GetTargetSymbolId(m_phraseStopSymbol);
   unsigned encodedSymbol = EncodePREncSymbol1(stopSymbolId);
   os.write((char*)&encodedSymbol, sizeof(encodedSymbol));
@@ -702,9 +671,8 @@ void PhraseTableCreator::EncodeScores(std::vector<float>& scores, std::ostream&
 {
   size_t c = 0;
   float score;
-  
-  while(c < scores.size())
-  {
+
+  while(c < scores.size()) {
     score = scores[c];
     score = FloorScore(TransformScore(score));
     os.write((char*)&score, sizeof(score));
@@ -714,11 +682,10 @@ void PhraseTableCreator::EncodeScores(std::vector<float>& scores, std::ostream&
 }
 
 void PhraseTableCreator::EncodeAlignment(std::set<AlignPoint>& alignment,
-                                         std::ostream& os)
+    std::ostream& os)
 {
   for(std::set<AlignPoint>::iterator it = alignment.begin();
-    it != alignment.end(); it++)
-  {
+      it != alignment.end(); it++) {
     os.write((char*)&(*it), sizeof(AlignPoint));
     m_alignCounter.Increase(*it);
   }
@@ -728,83 +695,77 @@ void PhraseTableCreator::EncodeAlignment(std::set<AlignPoint>& alignment,
 }
 
 std::string PhraseTableCreator::EncodeLine(std::vector<std::string>& tokens, size_t ownRank)
-{        
+{
   std::string sourcePhraseStr = tokens[0];
   std::string targetPhraseStr = tokens[1];
   std::string scoresStr = tokens[2];
-  
+
   std::string alignmentStr = "";
   if(tokens.size() > 3)
     alignmentStr = tokens[3];
-  
+
   std::vector<std::string> s = Tokenize(sourcePhraseStr);
-  
+
   size_t phraseLength = s.size();
   if(m_maxPhraseLength < phraseLength)
     m_maxPhraseLength = phraseLength;
-  
+
   std::vector<std::string> t = Tokenize(targetPhraseStr);
   std::vector<float> scores = Tokenize<float>(scoresStr);
-  
+
   if(scores.size() != m_numScoreComponent) {
     std::cerr << "Error: Wrong number of scores detected ("
-      << scores.size() << " != " << m_numScoreComponent << ") :" << std::endl;
+              << scores.size() << " != " << m_numScoreComponent << ") :" << std::endl;
     std::cerr << "Line: " << tokens[0] << " ||| " << tokens[1] << " ||| " << tokens[3] << " ..." << std::endl;
-    abort();     
+    abort();
   }
-  
+
   std::set<AlignPoint> a;
-  if(m_coding != None || m_useAlignmentInfo)
-  {
+  if(m_coding != None || m_useAlignmentInfo) {
     std::vector<size_t> positions = Tokenize<size_t>(alignmentStr, " \t-");
-    for(size_t i = 0; i < positions.size(); i += 2)
-    {
+    for(size_t i = 0; i < positions.size(); i += 2) {
       a.insert(AlignPoint(positions[i], positions[i+1]));
     }
   }
-  
+
   std::stringstream encodedTargetPhrase;
-  
-  if(m_coding == PREnc)
-  {
+
+  if(m_coding == PREnc) {
     EncodeTargetPhrasePREnc(s, t, a, ownRank, encodedTargetPhrase);
+  } else if(m_coding == REnc) {
+    EncodeTargetPhraseREnc(s, t, a, encodedTargetPhrase);
+  } else {
+    EncodeTargetPhraseNone(t, encodedTargetPhrase);
   }
-  else if(m_coding == REnc)
-  {
-    EncodeTargetPhraseREnc(s, t, a, encodedTargetPhrase);        
-  }
-  else
-  {
-    EncodeTargetPhraseNone(t, encodedTargetPhrase);      
-  }
-  
+
   EncodeScores(scores, encodedTargetPhrase);
-  
+
   if(m_useAlignmentInfo)
     EncodeAlignment(a, encodedTargetPhrase);
-  
+
   return encodedTargetPhrase.str();
 }
 
 std::string PhraseTableCreator::CompressEncodedCollection(std::string encodedCollection)
-{  
+{
   enum EncodeState {
-      ReadSymbol, ReadScore, ReadAlignment,
-      EncodeSymbol, EncodeScore, EncodeAlignment };
+    ReadSymbol, ReadScore, ReadAlignment,
+    EncodeSymbol, EncodeScore, EncodeAlignment
+  };
   EncodeState state = ReadSymbol;
 
   unsigned phraseStopSymbolId;
   if(m_coding == REnc)
     phraseStopSymbolId = EncodeREncSymbol1(GetTargetSymbolId(m_phraseStopSymbol));
   else if(m_coding == PREnc)
-      phraseStopSymbolId = EncodePREncSymbol1(GetTargetSymbolId(m_phraseStopSymbol));
+    phraseStopSymbolId = EncodePREncSymbol1(GetTargetSymbolId(m_phraseStopSymbol));
   else
     phraseStopSymbolId = GetTargetSymbolId(m_phraseStopSymbol);
   AlignPoint alignStopSymbol(-1, -1);
 
   std::stringstream encodedStream(encodedCollection);
   encodedStream.unsetf(std::ios::skipws);
-  
+
   std::string compressedEncodedCollection;
   BitWrapper<> bitStream(compressedEncodedCollection);
 
@@ -812,56 +773,50 @@ std::string PhraseTableCreator::CompressEncodedCollection(std::string encodedCol
   float score;
   size_t currScore = 0;
   AlignPoint alignPoint;
-                                     
-  while(encodedStream) 
-  {
-    switch(state)
-    {
-      case ReadSymbol:
-        encodedStream.read((char*) &symbol, sizeof(unsigned));
-        state = EncodeSymbol;
-        break;
-      case ReadScore:
-        if(currScore == m_numScoreComponent)
-        {
-          currScore = 0;
-          if(m_useAlignmentInfo)
-            state = ReadAlignment;
-          else
-            state = ReadSymbol;
-        }
+
+  while(encodedStream) {
+    switch(state) {
+    case ReadSymbol:
+      encodedStream.read((char*) &symbol, sizeof(unsigned));
+      state = EncodeSymbol;
+      break;
+    case ReadScore:
+      if(currScore == m_numScoreComponent) {
+        currScore = 0;
+        if(m_useAlignmentInfo)
+          state = ReadAlignment;
         else
-        {
-          encodedStream.read((char*) &score, sizeof(float));
-          currScore++;
-          state = EncodeScore;
-        }
-        break;
-      case ReadAlignment:
-        encodedStream.read((char*) &alignPoint, sizeof(AlignPoint));
-        state = EncodeAlignment;
-        break;
-      
-      case EncodeSymbol:
-        state = (symbol == phraseStopSymbolId) ? ReadScore : ReadSymbol;
-        m_symbolTree->Put(bitStream, symbol);
-        break;
-      case EncodeScore:
-        {
-          state = ReadScore;
-          size_t idx = m_multipleScoreTrees ? currScore-1 : 0;
-          if(m_quantize)
-            score = m_scoreCounters[idx]->LowerBound(score);
-          m_scoreTrees[idx]->Put(bitStream, score);
-        }
-        break;
-      case EncodeAlignment:
-        state = (alignPoint == alignStopSymbol) ? ReadSymbol : ReadAlignment;
-        m_alignTree->Put(bitStream, alignPoint);
-        break;
+          state = ReadSymbol;
+      } else {
+        encodedStream.read((char*) &score, sizeof(float));
+        currScore++;
+        state = EncodeScore;
+      }
+      break;
+    case ReadAlignment:
+      encodedStream.read((char*) &alignPoint, sizeof(AlignPoint));
+      state = EncodeAlignment;
+      break;
+
+    case EncodeSymbol:
+      state = (symbol == phraseStopSymbolId) ? ReadScore : ReadSymbol;
+      m_symbolTree->Put(bitStream, symbol);
+      break;
+    case EncodeScore: {
+      state = ReadScore;
+      size_t idx = m_multipleScoreTrees ? currScore-1 : 0;
+      if(m_quantize)
+        score = m_scoreCounters[idx]->LowerBound(score);
+      m_scoreTrees[idx]->Put(bitStream, score);
+    }
+    break;
+    case EncodeAlignment:
+      state = (alignPoint == alignStopSymbol) ? ReadSymbol : ReadAlignment;
+      m_alignTree->Put(bitStream, alignPoint);
+      break;
     }
   }
-  
+
   return compressedEncodedCollection;
 }
 
@@ -873,32 +828,28 @@ void PhraseTableCreator::AddRankedLine(PackedItem& pi)
 void PhraseTableCreator::FlushRankedQueue(bool force)
 {
   size_t step = 1ul << 10;
-   
-  while(!m_queue.empty() && m_lastFlushedLine + 1 == m_queue.top().GetLine())
-  {
+
+  while(!m_queue.empty() && m_lastFlushedLine + 1 == m_queue.top().GetLine()) {
     m_lastFlushedLine++;
 
     PackedItem pi = m_queue.top();
     m_queue.pop();
-    
-    if(m_lastSourceRange.size() == step)
-    {
+
+    if(m_lastSourceRange.size() == step) {
       m_rnkHash.AddRange(m_lastSourceRange);
       m_lastSourceRange.clear();
     }
-    
-    if(m_lastFlushedSourcePhrase != pi.GetSrc())
-    {
-      if(m_rankQueue.size()) {        
+
+    if(m_lastFlushedSourcePhrase != pi.GetSrc()) {
+      if(m_rankQueue.size()) {
         m_lastFlushedSourceNum++;
         if(m_lastFlushedSourceNum % 100000 == 0) {
           std::cerr << ".";
         }
-        if(m_lastFlushedSourceNum % 5000000 == 0)
-        {
+        if(m_lastFlushedSourceNum % 5000000 == 0) {
           std::cerr << "[" << m_lastFlushedSourceNum << "]" << std::endl;
         }
-            
+
         m_ranks.resize(m_lastFlushedLine + 1);
         int r = 0;
         while(!m_rankQueue.empty()) {
@@ -907,33 +858,31 @@ void PhraseTableCreator::FlushRankedQueue(bool force)
         }
       }
     }
-    
+
     m_lastSourceRange.push_back(pi.GetTrg());
-    
+
     m_rankQueue.push(std::make_pair(pi.GetScore(), pi.GetLine()));
     m_lastFlushedSourcePhrase = pi.GetSrc();
   }
-  
-  if(force)
-  {    
+
+  if(force) {
     m_rnkHash.AddRange(m_lastSourceRange);
     m_lastSourceRange.clear();
 
 #ifdef WITH_THREADS
     m_rnkHash.WaitAll();
 #endif
- 
+
     m_ranks.resize(m_lastFlushedLine + 1);
     int r = 0;
-    while(!m_rankQueue.empty())
-    {
+    while(!m_rankQueue.empty()) {
       m_ranks[m_rankQueue.top().second] = r++;
       m_rankQueue.pop();
     }
 
     m_lastFlushedLine = -1;
     m_lastFlushedSourceNum = 0;
-    
+
     std::cerr << std::endl << std::endl;
   }
 }
@@ -946,74 +895,65 @@ void PhraseTableCreator::AddEncodedLine(PackedItem& pi)
 
 void PhraseTableCreator::FlushEncodedQueue(bool force)
 {
-  while(!m_queue.empty() && m_lastFlushedLine + 1 == m_queue.top().GetLine())
-  {
+  while(!m_queue.empty() && m_lastFlushedLine + 1 == m_queue.top().GetLine()) {
     PackedItem pi = m_queue.top();
     m_queue.pop();
     m_lastFlushedLine++;
-    
-    if(m_lastFlushedSourcePhrase != pi.GetSrc())
-    {
-      if(m_lastCollection.size())
-      {
+
+    if(m_lastFlushedSourcePhrase != pi.GetSrc()) {
+      if(m_lastCollection.size()) {
         std::stringstream targetPhraseCollection;
         for(std::vector<std::string>::iterator it =
-          m_lastCollection.begin(); it != m_lastCollection.end(); it++)
+              m_lastCollection.begin(); it != m_lastCollection.end(); it++)
           targetPhraseCollection << *it;
-        
-        m_lastSourceRange.push_back(MakeSourceKey(m_lastFlushedSourcePhrase));    
+
+        m_lastSourceRange.push_back(MakeSourceKey(m_lastFlushedSourcePhrase));
         m_encodedTargetPhrases->push_back(targetPhraseCollection.str());
-        
+
         m_lastFlushedSourceNum++;
         if(m_lastFlushedSourceNum % 100000 == 0)
           std::cerr << ".";
         if(m_lastFlushedSourceNum % 5000000 == 0)
           std::cerr << "[" << m_lastFlushedSourceNum << "]" << std::endl;
-        
+
         m_lastCollection.clear();
       }
     }
-    
-    if(m_lastSourceRange.size() == (1ul << m_orderBits))
-    {
+
+    if(m_lastSourceRange.size() == (1ul << m_orderBits)) {
       m_srcHash.AddRange(m_lastSourceRange);
       m_srcHash.SaveLastRange();
       m_srcHash.DropLastRange();
       m_lastSourceRange.clear();
     }
-    
+
     m_lastFlushedSourcePhrase = pi.GetSrc();
-    if(m_coding == PREnc)
-    {
+    if(m_coding == PREnc) {
       if(m_lastCollection.size() <= pi.GetRank())
         m_lastCollection.resize(pi.GetRank() + 1);
       m_lastCollection[pi.GetRank()] = pi.GetTrg();
-    }
-    else
-    {
+    } else {
       m_lastCollection.push_back(pi.GetTrg());
     }
   }
-  
-  if(force)
-  {
+
+  if(force) {
     if(!m_lastSourceRange.size() || m_lastSourceRange.back() != m_lastFlushedSourcePhrase)
       m_lastSourceRange.push_back(MakeSourceKey(m_lastFlushedSourcePhrase));
-      
-    if(m_lastCollection.size())
-    {
+
+    if(m_lastCollection.size()) {
       std::stringstream targetPhraseCollection;
       for(std::vector<std::string>::iterator it =
-        m_lastCollection.begin(); it != m_lastCollection.end(); it++)
+            m_lastCollection.begin(); it != m_lastCollection.end(); it++)
         targetPhraseCollection << *it;
-          
+
       m_encodedTargetPhrases->push_back(targetPhraseCollection.str());
       m_lastCollection.clear();
     }
-      
+
     m_srcHash.AddRange(m_lastSourceRange);
     m_lastSourceRange.clear();
-    
+
 #ifdef WITH_THREADS
     m_srcHash.WaitAll();
 #endif
@@ -1021,7 +961,7 @@ void PhraseTableCreator::FlushEncodedQueue(bool force)
     m_srcHash.SaveLastRange();
     m_srcHash.DropLastRange();
     m_srcHash.FinalizeSave();
-     
+
     m_lastFlushedLine = -1;
     m_lastFlushedSourceNum = 0;
 
@@ -1031,30 +971,27 @@ void PhraseTableCreator::FlushEncodedQueue(bool force)
 
 void PhraseTableCreator::AddCompressedCollection(PackedItem& pi)
 {
-    m_queue.push(pi); 
+  m_queue.push(pi);
 }
 
 void PhraseTableCreator::FlushCompressedQueue(bool force)
 {
-  if(force || m_queue.size() > 10000)
-  {
-    while(!m_queue.empty() && m_lastFlushedLine + 1 == m_queue.top().GetLine())
-    {
+  if(force || m_queue.size() > 10000) {
+    while(!m_queue.empty() && m_lastFlushedLine + 1 == m_queue.top().GetLine()) {
       PackedItem pi = m_queue.top();
       m_queue.pop();
       m_lastFlushedLine++;
-          
+
       m_compressedTargetPhrases->push_back(pi.GetTrg());
-      
+
       if((pi.GetLine()+1) % 100000 == 0)
         std::cerr << ".";
       if((pi.GetLine()+1) % 5000000 == 0)
         std::cerr << "[" << (pi.GetLine()+1) << "]" << std::endl;
     }
   }
-  
-  if(force)
-  {
+
+  if(force) {
     m_lastFlushedLine = -1;
     std::cerr << std::endl << std::endl;
   }
@@ -1070,38 +1007,35 @@ boost::mutex RankingTask::m_fileMutex;
 
 RankingTask::RankingTask(InputFileStream& inFile, PhraseTableCreator& creator)
   : m_inFile(inFile), m_creator(creator) {}
-  
+
 void RankingTask::operator()()
 {
   size_t lineNum = 0;
-  
+
   std::vector<std::string> lines;
   size_t max_lines = 1000;
   lines.reserve(max_lines);
-  
+
   {
 #ifdef WITH_THREADS
-      boost::mutex::scoped_lock lock(m_fileMutex);
+    boost::mutex::scoped_lock lock(m_fileMutex);
 #endif
-      std::string line;
-      while(lines.size() < max_lines && std::getline(m_inFile, line))
-          lines.push_back(line);
-      lineNum = m_lineNum;
-      m_lineNum += lines.size();
+    std::string line;
+    while(lines.size() < max_lines && std::getline(m_inFile, line))
+      lines.push_back(line);
+    lineNum = m_lineNum;
+    m_lineNum += lines.size();
   }
-  
+
   std::vector<PackedItem> result;
   result.reserve(max_lines);
-  
-  while(lines.size())
-  {
-    for(size_t i = 0; i < lines.size(); i++)
-    {
+
+  while(lines.size()) {
+    for(size_t i = 0; i < lines.size(); i++) {
       std::vector<std::string> tokens;
       Moses::TokenizeMultiCharSeparator(tokens, lines[i], m_creator.m_separator);
-      
-      if(tokens.size() < 3)
-      {
+
+      if(tokens.size() < 3) {
         std::cerr << "Error: It seems the following line has a wrong format:" << std::endl;
         std::cerr << "Line " << i << ": " << lines[i] << std::endl;
         abort();
@@ -1112,38 +1046,38 @@ void RankingTask::operator()()
         std::cerr << "Better use  -encoding None  or disable this warning with  -no-warnings ." << std::endl;
         std::cerr << "Line " << i << ": " << lines[i] << std::endl;
       }
-      
+
       std::vector<float> scores = Tokenize<float>(tokens[2]);
       if(scores.size() != m_creator.m_numScoreComponent) {
         std::cerr << "Error: It seems the following line has a wrong number of scores ("
-          << scores.size() << " != " << m_creator.m_numScoreComponent << ") :" << std::endl;
+                  << scores.size() << " != " << m_creator.m_numScoreComponent << ") :" << std::endl;
         std::cerr << "Line " << i << ": " << lines[i] << std::endl;
-        abort();     
+        abort();
       }
-      
+
       float sortScore = scores[m_creator.m_sortScoreIndex];
-      
+
       std::string key1 = m_creator.MakeSourceKey(tokens[0]);
       std::string key2 = m_creator.MakeSourceTargetKey(tokens[0], tokens[1]);
-      
+
       PackedItem packedItem(lineNum + i, key1, key2, 0, sortScore);
       result.push_back(packedItem);
     }
     lines.clear();
-    
+
     {
 #ifdef WITH_THREADS
       boost::mutex::scoped_lock lock(m_mutex);
 #endif
-      for(size_t i = 0; i < result.size(); i++) 
+      for(size_t i = 0; i < result.size(); i++)
         m_creator.AddRankedLine(result[i]);
-      m_creator.FlushRankedQueue();  
+      m_creator.FlushRankedQueue();
     }
-    
+
     result.clear();
     lines.reserve(max_lines);
     result.reserve(max_lines);
-    
+
 #ifdef WITH_THREADS
     boost::mutex::scoped_lock lock(m_fileMutex);
 #endif
@@ -1163,15 +1097,15 @@ boost::mutex EncodingTask::m_fileMutex;
 
 EncodingTask::EncodingTask(InputFileStream& inFile, PhraseTableCreator& creator)
   : m_inFile(inFile), m_creator(creator) {}
-  
+
 void EncodingTask::operator()()
 {
   size_t lineNum = 0;
-  
+
   std::vector<std::string> lines;
   size_t max_lines = 1000;
   lines.reserve(max_lines);
-  
+
   {
 #ifdef WITH_THREADS
     boost::mutex::scoped_lock lock(m_fileMutex);
@@ -1182,19 +1116,16 @@ void EncodingTask::operator()()
     lineNum = m_lineNum;
     m_lineNum += lines.size();
   }
-  
+
   std::vector<PackedItem> result;
   result.reserve(max_lines);
-  
-  while(lines.size())
-  {
-    for(size_t i = 0; i < lines.size(); i++)
-    {
+
+  while(lines.size()) {
+    for(size_t i = 0; i < lines.size(); i++) {
       std::vector<std::string> tokens;
       Moses::TokenizeMultiCharSeparator(tokens, lines[i], m_creator.m_separator);
-      
-      if(tokens.size() < 3)
-      {
+
+      if(tokens.size() < 3) {
         std::cerr << "Error: It seems the following line has a wrong format:" << std::endl;
         std::cerr << "Line " << i << ": " << lines[i] << std::endl;
         abort();
@@ -1207,31 +1138,31 @@ void EncodingTask::operator()()
         std::cerr << "Better use -encoding None or disable this warning with -no-warnings." << std::endl;
         std::cerr << "Line " << i << ": " << lines[i] << std::endl;
       }
-  
+
       size_t ownRank = 0;
       if(m_creator.m_coding == PhraseTableCreator::PREnc)
         ownRank = m_creator.m_ranks[lineNum + i];
-      
+
       std::string encodedLine = m_creator.EncodeLine(tokens, ownRank);
-      
+
       PackedItem packedItem(lineNum + i, tokens[0], encodedLine, ownRank);
       result.push_back(packedItem);
     }
     lines.clear();
-    
+
     {
 #ifdef WITH_THREADS
       boost::mutex::scoped_lock lock(m_mutex);
 #endif
-      for(size_t i = 0; i < result.size(); i++) 
+      for(size_t i = 0; i < result.size(); i++)
         m_creator.AddEncodedLine(result[i]);
-      m_creator.FlushEncodedQueue();  
+      m_creator.FlushEncodedQueue();
     }
-    
+
     result.clear();
     lines.reserve(max_lines);
     result.reserve(max_lines);
-    
+
 #ifdef WITH_THREADS
     boost::mutex::scoped_lock lock(m_fileMutex);
 #endif
@@ -1251,10 +1182,10 @@ boost::mutex CompressionTask::m_mutex;
 #endif
 
 CompressionTask::CompressionTask(StringVector<unsigned char, unsigned long,
-                              MmapAllocator>& encodedCollections,
-                              PhraseTableCreator& creator)
+                                 MmapAllocator>& encodedCollections,
+                                 PhraseTableCreator& creator)
   : m_encodedCollections(encodedCollections), m_creator(creator) {}
-  
+
 void CompressionTask::operator()()
 {
   size_t collectionNum;
@@ -1265,12 +1196,11 @@ void CompressionTask::operator()()
     collectionNum = m_collectionNum;
     m_collectionNum++;
   }
-  
-  while(collectionNum < m_encodedCollections.size())
-  {
+
+  while(collectionNum < m_encodedCollections.size()) {
     std::string collection = m_encodedCollections[collectionNum];
     std::string compressedCollection
-      = m_creator.CompressEncodedCollection(collection);
+    = m_creator.CompressEncodedCollection(collection);
 
     std::string dummy;
     PackedItem packedItem(collectionNum, dummy, compressedCollection, 0);
@@ -1280,29 +1210,44 @@ void CompressionTask::operator()()
 #endif
     m_creator.AddCompressedCollection(packedItem);
     m_creator.FlushCompressedQueue();
-    
-    collectionNum = m_collectionNum;  
-    m_collectionNum++;    
+
+    collectionNum = m_collectionNum;
+    m_collectionNum++;
   }
 }
 
 //****************************************************************************//
 
 PackedItem::PackedItem(long line, std::string sourcePhrase,
-           std::string packedTargetPhrase, size_t rank,
-           float score)
+                       std::string packedTargetPhrase, size_t rank,
+                       float score)
   : m_line(line), m_sourcePhrase(sourcePhrase),
     m_packedTargetPhrase(packedTargetPhrase), m_rank(rank),
     m_score(score) {}
 
-long PackedItem::GetLine() const { return m_line; }
+long PackedItem::GetLine() const
+{
+  return m_line;
+}
 
-const std::string& PackedItem::GetSrc() const { return m_sourcePhrase; }
+const std::string& PackedItem::GetSrc() const
+{
+  return m_sourcePhrase;
+}
 
-const std::string& PackedItem::GetTrg() const { return m_packedTargetPhrase; }
+const std::string& PackedItem::GetTrg() const
+{
+  return m_packedTargetPhrase;
+}
 
-size_t PackedItem::GetRank() const { return m_rank; }
+size_t PackedItem::GetRank() const
+{
+  return m_rank;
+}
 
-float PackedItem::GetScore() const { return m_score; }
+float PackedItem::GetScore() const
+{
+  return m_score;
+}
 
 }
diff --git a/moses/TranslationModel/CompactPT/PhraseTableCreator.h b/moses/TranslationModel/CompactPT/PhraseTableCreator.h
index ded3a84eb..fd5fc1581 100644
--- a/moses/TranslationModel/CompactPT/PhraseTableCreator.h
+++ b/moses/TranslationModel/CompactPT/PhraseTableCreator.h
@@ -1,23 +1,23 @@
-// $Id$                                                                                                                               
-// vim:tabstop=2                                                                                                                      
-/***********************************************************************                                                              
-Moses - factored phrase-based language decoder                                                                                        
-Copyright (C) 2006 University of Edinburgh                                                                                            
-                                                                                                                                      
-This library is free software; you can redistribute it and/or                                                                         
-modify it under the terms of the GNU Lesser General Public                                                                            
-License as published by the Free Software Foundation; either                                                                          
-version 2.1 of the License, or (at your option) any later version.                                                                    
-                                                                                                                                      
-This library is distributed in the hope that it will be useful,                                                                       
-but WITHOUT ANY WARRANTY; without even the implied warranty of                                                                        
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU                                                                     
-Lesser General Public License for more details.                                                                                       
-                                                                                                                                      
-You should have received a copy of the GNU Lesser General Public                                                                      
-License along with this library; if not, write to the Free Software                                                                   
-Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA                                                        
-***********************************************************************/  
+// $Id$
+// vim:tabstop=2
+/***********************************************************************
+Moses - factored phrase-based language decoder
+Copyright (C) 2006 University of Edinburgh
+
+This library is free software; you can redistribute it and/or
+modify it under the terms of the GNU Lesser General Public
+License as published by the Free Software Foundation; either
+version 2.1 of the License, or (at your option) any later version.
+
+This library is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public
+License along with this library; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+***********************************************************************/
 
 #ifndef moses_PhraseTableCreator_h
 #define moses_PhraseTableCreator_h
@@ -40,386 +40,371 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 
 namespace Moses
 {
-    
+
 typedef std::pair<unsigned char, unsigned char> AlignPoint;
 
-template <typename DataType> 
+template <typename DataType>
 class Counter
 {
-  public:
-    typedef boost::unordered_map<DataType, size_t> FreqMap;
-    typedef typename FreqMap::iterator iterator;
-    typedef typename FreqMap::mapped_type mapped_type;
-    typedef typename FreqMap::value_type value_type; 
-
-  private:
-#ifdef WITH_THREADS    
-    boost::mutex m_mutex;
+public:
+  typedef boost::unordered_map<DataType, size_t> FreqMap;
+  typedef typename FreqMap::iterator iterator;
+  typedef typename FreqMap::mapped_type mapped_type;
+  typedef typename FreqMap::value_type value_type;
+
+private:
+#ifdef WITH_THREADS
+  boost::mutex m_mutex;
 #endif
-    FreqMap m_freqMap;
-    size_t m_maxSize;
-    std::vector<DataType> m_bestVec;
-    
-    struct FreqSorter
-    {
-      bool operator()(const value_type& a, const value_type& b) const
-      {
-        if(a.second > b.second)
-          return true;
-        // Check impact on translation quality!
-        if(a.second == b.second && a.first > b.first)
-          return true;
-        return false;
-      }
-    };
-  
-  public:
-    Counter() : m_maxSize(0) {}
-    
-    iterator Begin()
-    {
-      return m_freqMap.begin();
-    }
-    
-    iterator End()
-    {
-      return m_freqMap.end();
+  FreqMap m_freqMap;
+  size_t m_maxSize;
+  std::vector<DataType> m_bestVec;
+
+  struct FreqSorter {
+    bool operator()(const value_type& a, const value_type& b) const {
+      if(a.second > b.second)
+        return true;
+      // Check impact on translation quality!
+      if(a.second == b.second && a.first > b.first)
+        return true;
+      return false;
     }
-    
-    void Increase(DataType data)
-    {
+  };
+
+public:
+  Counter() : m_maxSize(0) {}
+
+  iterator Begin() {
+    return m_freqMap.begin();
+  }
+
+  iterator End() {
+    return m_freqMap.end();
+  }
+
+  void Increase(DataType data) {
 #ifdef WITH_THREADS
-      boost::mutex::scoped_lock lock(m_mutex);
+    boost::mutex::scoped_lock lock(m_mutex);
 #endif
-      m_freqMap[data]++;
-    }
-  
-    void IncreaseBy(DataType data, size_t num)
-    {
+    m_freqMap[data]++;
+  }
+
+  void IncreaseBy(DataType data, size_t num) {
 #ifdef WITH_THREADS
-      boost::mutex::scoped_lock lock(m_mutex);
+    boost::mutex::scoped_lock lock(m_mutex);
 #endif
-      m_freqMap[data] += num;
-    }
-    
-    mapped_type& operator[](DataType data)
-    {
-      return m_freqMap[data];
-    }
-    
-    size_t Size()
-    {
+    m_freqMap[data] += num;
+  }
+
+  mapped_type& operator[](DataType data) {
+    return m_freqMap[data];
+  }
+
+  size_t Size() {
 #ifdef WITH_THREADS
-      boost::mutex::scoped_lock lock(m_mutex);
+    boost::mutex::scoped_lock lock(m_mutex);
 #endif
-      return m_freqMap.size();
-    }
-    
-    void Quantize(size_t maxSize)
-    {
+    return m_freqMap.size();
+  }
+
+  void Quantize(size_t maxSize) {
 #ifdef WITH_THREADS
-      boost::mutex::scoped_lock lock(m_mutex);
+    boost::mutex::scoped_lock lock(m_mutex);
 #endif
-      m_maxSize = maxSize;
-      std::vector<std::pair<DataType, mapped_type> > freqVec;
-      freqVec.insert(freqVec.begin(), m_freqMap.begin(), m_freqMap.end());
-      std::sort(freqVec.begin(), freqVec.end(), FreqSorter());
-      
-      for(size_t i = 0; i < freqVec.size() && i < m_maxSize; i++)
-        m_bestVec.push_back(freqVec[i].first);
-        
-      std::sort(m_bestVec.begin(), m_bestVec.end());
-      
-      FreqMap t_freqMap;
-      for(typename std::vector<std::pair<DataType, mapped_type> >::iterator it
-          = freqVec.begin(); it != freqVec.end(); it++)
-      {
-        DataType closest = LowerBound(it->first);
-        t_freqMap[closest] += it->second;
-      }
-      
-      m_freqMap.swap(t_freqMap);   
+    m_maxSize = maxSize;
+    std::vector<std::pair<DataType, mapped_type> > freqVec;
+    freqVec.insert(freqVec.begin(), m_freqMap.begin(), m_freqMap.end());
+    std::sort(freqVec.begin(), freqVec.end(), FreqSorter());
+
+    for(size_t i = 0; i < freqVec.size() && i < m_maxSize; i++)
+      m_bestVec.push_back(freqVec[i].first);
+
+    std::sort(m_bestVec.begin(), m_bestVec.end());
+
+    FreqMap t_freqMap;
+    for(typename std::vector<std::pair<DataType, mapped_type> >::iterator it
+        = freqVec.begin(); it != freqVec.end(); it++) {
+      DataType closest = LowerBound(it->first);
+      t_freqMap[closest] += it->second;
     }
-    
-    void Clear()
-    {
+
+    m_freqMap.swap(t_freqMap);
+  }
+
+  void Clear() {
 #ifdef WITH_THREADS
-      boost::mutex::scoped_lock lock(m_mutex);
+    boost::mutex::scoped_lock lock(m_mutex);
 #endif
-      m_freqMap.clear();
-    }
-    
-    DataType LowerBound(DataType data)
-    {
-      if(m_maxSize == 0 || m_bestVec.size() == 0)
-        return data;
+    m_freqMap.clear();
+  }
+
+  DataType LowerBound(DataType data) {
+    if(m_maxSize == 0 || m_bestVec.size() == 0)
+      return data;
+    else {
+      typename std::vector<DataType>::iterator it
+      = std::lower_bound(m_bestVec.begin(), m_bestVec.end(), data);
+      if(it != m_bestVec.end())
+        return *it;
       else
-      {
-        typename std::vector<DataType>::iterator it
-          = std::lower_bound(m_bestVec.begin(), m_bestVec.end(), data);
-        if(it != m_bestVec.end())
-          return *it;
-        else
-          return m_bestVec.back();
-      }
+        return m_bestVec.back();
     }
+  }
 };
- 
+
 class PackedItem
 {
-  private:
-    long m_line;
-    std::string m_sourcePhrase;
-    std::string m_packedTargetPhrase;
-    size_t m_rank;
-    float m_score;
-    
-  public:
-    PackedItem(long line, std::string sourcePhrase,
-               std::string packedTargetPhrase, size_t rank,
-               float m_score = 0);
-    
-    long GetLine() const;
-    const std::string& GetSrc() const;
-    const std::string& GetTrg() const;
-    size_t GetRank() const;
-    float GetScore() const;
+private:
+  long m_line;
+  std::string m_sourcePhrase;
+  std::string m_packedTargetPhrase;
+  size_t m_rank;
+  float m_score;
+
+public:
+  PackedItem(long line, std::string sourcePhrase,
+             std::string packedTargetPhrase, size_t rank,
+             float m_score = 0);
+
+  long GetLine() const;
+  const std::string& GetSrc() const;
+  const std::string& GetTrg() const;
+  size_t GetRank() const;
+  float GetScore() const;
 };
 
 bool operator<(const PackedItem &pi1, const PackedItem &pi2);
 
 class PhraseTableCreator
 {
-  public:
-    enum Coding { None, REnc, PREnc };
-    
-  private:
-    std::string m_inPath;
-    std::string m_outPath;
-    std::string m_tempfilePath;
-    
-    std::FILE* m_outFile;
-    
-    size_t m_numScoreComponent;
-    size_t m_sortScoreIndex;
-    size_t m_warnMe;
-    
-    Coding m_coding;
-    size_t m_orderBits;
-    size_t m_fingerPrintBits;
-    bool m_useAlignmentInfo;
-    bool m_multipleScoreTrees;
-    size_t m_quantize;
-    size_t m_maxRank;
-        
-    static std::string m_phraseStopSymbol;
-    static std::string m_separator;
-    
+public:
+  enum Coding { None, REnc, PREnc };
+
+private:
+  std::string m_inPath;
+  std::string m_outPath;
+  std::string m_tempfilePath;
+
+  std::FILE* m_outFile;
+
+  size_t m_numScoreComponent;
+  size_t m_sortScoreIndex;
+  size_t m_warnMe;
+
+  Coding m_coding;
+  size_t m_orderBits;
+  size_t m_fingerPrintBits;
+  bool m_useAlignmentInfo;
+  bool m_multipleScoreTrees;
+  size_t m_quantize;
+  size_t m_maxRank;
+
+  static std::string m_phraseStopSymbol;
+  static std::string m_separator;
+
 #ifdef WITH_THREADS
-    size_t m_threads;
-    boost::mutex m_mutex;
+  size_t m_threads;
+  boost::mutex m_mutex;
 #endif
-    
-    BlockHashIndex m_srcHash;
-    BlockHashIndex m_rnkHash;
-    
-    size_t m_maxPhraseLength;
-    
-    std::vector<unsigned> m_ranks;
-    
-    typedef std::pair<unsigned, unsigned> SrcTrg;
-    typedef std::pair<std::string, std::string> SrcTrgString;
-    typedef std::pair<SrcTrgString, float> SrcTrgProb;
-        
-    struct SrcTrgProbSorter
-    {
-      bool operator()(const SrcTrgProb& a, const SrcTrgProb& b) const
-      {
-        if(a.first.first < b.first.first)
-          return true;
-
-        if(a.first.first == b.first.first && a.second > b.second)
-          return true;
-        
-        if(a.first.first == b.first.first
-           && a.second == b.second
-           && a.first.second < b.first.second)
-          return true;
-        
-        return false;
-      }
-    };
-    
-    std::vector<size_t> m_lexicalTableIndex;
-    std::vector<SrcTrg> m_lexicalTable;
-    
-    StringVector<unsigned char, unsigned long, MmapAllocator>*
-    m_encodedTargetPhrases;
-        
-    StringVector<unsigned char, unsigned long, MmapAllocator>*
-    m_compressedTargetPhrases;
-    
-    boost::unordered_map<std::string, unsigned> m_targetSymbolsMap;
-    boost::unordered_map<std::string, unsigned> m_sourceSymbolsMap;
-    
-    typedef Counter<unsigned> SymbolCounter;
-    typedef Counter<float> ScoreCounter;
-    typedef Counter<AlignPoint> AlignCounter;
-    
-    typedef CanonicalHuffman<unsigned> SymbolTree;
-    typedef CanonicalHuffman<float> ScoreTree;
-    typedef CanonicalHuffman<AlignPoint> AlignTree;
-    
-    SymbolCounter m_symbolCounter;
-    SymbolTree* m_symbolTree;
-    
-    AlignCounter m_alignCounter;
-    AlignTree* m_alignTree; 
-    
-    std::vector<ScoreCounter*> m_scoreCounters;
-    std::vector<ScoreTree*> m_scoreTrees;
-    
-    std::priority_queue<PackedItem> m_queue;
-    long m_lastFlushedLine;
-    long m_lastFlushedSourceNum;
-    std::string m_lastFlushedSourcePhrase;
-    std::vector<std::string> m_lastSourceRange;
-    std::priority_queue<std::pair<float, size_t> > m_rankQueue;
-    std::vector<std::string> m_lastCollection;
-    
-    void Save();
-    void PrintInfo();
-    
-    void AddSourceSymbolId(std::string& symbol);
-    unsigned GetSourceSymbolId(std::string& symbol);
-    
-    void AddTargetSymbolId(std::string& symbol);
-    unsigned GetTargetSymbolId(std::string& symbol);
-    unsigned GetOrAddTargetSymbolId(std::string& symbol);
-    
-    unsigned GetRank(unsigned srcIdx, unsigned trgIdx);
-    
-    unsigned EncodeREncSymbol1(unsigned symbol);
-    unsigned EncodeREncSymbol2(unsigned position, unsigned rank);
-    unsigned EncodeREncSymbol3(unsigned rank);
-    
-    unsigned EncodePREncSymbol1(unsigned symbol);
-    unsigned EncodePREncSymbol2(int lOff, int rOff, unsigned rank);
-    
-    void EncodeTargetPhraseNone(std::vector<std::string>& t,
-                                std::ostream& os);
-    
-    void EncodeTargetPhraseREnc(std::vector<std::string>& s,
-                                std::vector<std::string>& t,
-                                std::set<AlignPoint>& a,
-                                std::ostream& os);
-    
-    void EncodeTargetPhrasePREnc(std::vector<std::string>& s,
-                                 std::vector<std::string>& t,
-                                 std::set<AlignPoint>& a, size_t ownRank,
-                                 std::ostream& os);
-    
-    void EncodeScores(std::vector<float>& scores, std::ostream& os);
-    void EncodeAlignment(std::set<AlignPoint>& alignment, std::ostream& os);
-    
-    std::string MakeSourceKey(std::string&);
-    std::string MakeSourceTargetKey(std::string&, std::string&);
-    
-    void LoadLexicalTable(std::string filePath);
-    
-    void CreateRankHash();
-    void EncodeTargetPhrases();
-    void CalcHuffmanCodes();
-    void CompressTargetPhrases();
-    
-    void AddRankedLine(PackedItem& pi);
-    void FlushRankedQueue(bool force = false);
-    
-    std::string EncodeLine(std::vector<std::string>& tokens, size_t ownRank);
-    void AddEncodedLine(PackedItem& pi);
-    void FlushEncodedQueue(bool force = false);
-    
-    std::string CompressEncodedCollection(std::string encodedCollection);
-    void AddCompressedCollection(PackedItem& pi);
-    void FlushCompressedQueue(bool force = false);
-    
-  public:
-    
-    PhraseTableCreator(std::string inPath,
-                       std::string outPath,
-                       std::string tempfilePath,
-                       size_t numScoreComponent = 5,
-                       size_t sortScoreIndex = 2,
-                       Coding coding = PREnc,
-                       size_t orderBits = 10,
-                       size_t fingerPrintBits = 16,
-                       bool useAlignmentInfo = false,
-                       bool multipleScoreTrees = true,
-                       size_t quantize = 0,
-                       size_t maxRank = 100,
-                       bool warnMe = true
+
+  BlockHashIndex m_srcHash;
+  BlockHashIndex m_rnkHash;
+
+  size_t m_maxPhraseLength;
+
+  std::vector<unsigned> m_ranks;
+
+  typedef std::pair<unsigned, unsigned> SrcTrg;
+  typedef std::pair<std::string, std::string> SrcTrgString;
+  typedef std::pair<SrcTrgString, float> SrcTrgProb;
+
+  struct SrcTrgProbSorter {
+    bool operator()(const SrcTrgProb& a, const SrcTrgProb& b) const {
+      if(a.first.first < b.first.first)
+        return true;
+
+      if(a.first.first == b.first.first && a.second > b.second)
+        return true;
+
+      if(a.first.first == b.first.first
+          && a.second == b.second
+          && a.first.second < b.first.second)
+        return true;
+
+      return false;
+    }
+  };
+
+  std::vector<size_t> m_lexicalTableIndex;
+  std::vector<SrcTrg> m_lexicalTable;
+
+  StringVector<unsigned char, unsigned long, MmapAllocator>*
+  m_encodedTargetPhrases;
+
+  StringVector<unsigned char, unsigned long, MmapAllocator>*
+  m_compressedTargetPhrases;
+
+  boost::unordered_map<std::string, unsigned> m_targetSymbolsMap;
+  boost::unordered_map<std::string, unsigned> m_sourceSymbolsMap;
+
+  typedef Counter<unsigned> SymbolCounter;
+  typedef Counter<float> ScoreCounter;
+  typedef Counter<AlignPoint> AlignCounter;
+
+  typedef CanonicalHuffman<unsigned> SymbolTree;
+  typedef CanonicalHuffman<float> ScoreTree;
+  typedef CanonicalHuffman<AlignPoint> AlignTree;
+
+  SymbolCounter m_symbolCounter;
+  SymbolTree* m_symbolTree;
+
+  AlignCounter m_alignCounter;
+  AlignTree* m_alignTree;
+
+  std::vector<ScoreCounter*> m_scoreCounters;
+  std::vector<ScoreTree*> m_scoreTrees;
+
+  std::priority_queue<PackedItem> m_queue;
+  long m_lastFlushedLine;
+  long m_lastFlushedSourceNum;
+  std::string m_lastFlushedSourcePhrase;
+  std::vector<std::string> m_lastSourceRange;
+  std::priority_queue<std::pair<float, size_t> > m_rankQueue;
+  std::vector<std::string> m_lastCollection;
+
+  void Save();
+  void PrintInfo();
+
+  void AddSourceSymbolId(std::string& symbol);
+  unsigned GetSourceSymbolId(std::string& symbol);
+
+  void AddTargetSymbolId(std::string& symbol);
+  unsigned GetTargetSymbolId(std::string& symbol);
+  unsigned GetOrAddTargetSymbolId(std::string& symbol);
+
+  unsigned GetRank(unsigned srcIdx, unsigned trgIdx);
+
+  unsigned EncodeREncSymbol1(unsigned symbol);
+  unsigned EncodeREncSymbol2(unsigned position, unsigned rank);
+  unsigned EncodeREncSymbol3(unsigned rank);
+
+  unsigned EncodePREncSymbol1(unsigned symbol);
+  unsigned EncodePREncSymbol2(int lOff, int rOff, unsigned rank);
+
+  void EncodeTargetPhraseNone(std::vector<std::string>& t,
+                              std::ostream& os);
+
+  void EncodeTargetPhraseREnc(std::vector<std::string>& s,
+                              std::vector<std::string>& t,
+                              std::set<AlignPoint>& a,
+                              std::ostream& os);
+
+  void EncodeTargetPhrasePREnc(std::vector<std::string>& s,
+                               std::vector<std::string>& t,
+                               std::set<AlignPoint>& a, size_t ownRank,
+                               std::ostream& os);
+
+  void EncodeScores(std::vector<float>& scores, std::ostream& os);
+  void EncodeAlignment(std::set<AlignPoint>& alignment, std::ostream& os);
+
+  std::string MakeSourceKey(std::string&);
+  std::string MakeSourceTargetKey(std::string&, std::string&);
+
+  void LoadLexicalTable(std::string filePath);
+
+  void CreateRankHash();
+  void EncodeTargetPhrases();
+  void CalcHuffmanCodes();
+  void CompressTargetPhrases();
+
+  void AddRankedLine(PackedItem& pi);
+  void FlushRankedQueue(bool force = false);
+
+  std::string EncodeLine(std::vector<std::string>& tokens, size_t ownRank);
+  void AddEncodedLine(PackedItem& pi);
+  void FlushEncodedQueue(bool force = false);
+
+  std::string CompressEncodedCollection(std::string encodedCollection);
+  void AddCompressedCollection(PackedItem& pi);
+  void FlushCompressedQueue(bool force = false);
+
+public:
+
+  PhraseTableCreator(std::string inPath,
+                     std::string outPath,
+                     std::string tempfilePath,
+                     size_t numScoreComponent = 5,
+                     size_t sortScoreIndex = 2,
+                     Coding coding = PREnc,
+                     size_t orderBits = 10,
+                     size_t fingerPrintBits = 16,
+                     bool useAlignmentInfo = false,
+                     bool multipleScoreTrees = true,
+                     size_t quantize = 0,
+                     size_t maxRank = 100,
+                     bool warnMe = true
 #ifdef WITH_THREADS
-                       , size_t threads = 2
+                                   , size_t threads = 2
 #endif
-                      );
-    
-    ~PhraseTableCreator();
-    
-    friend class RankingTask;
-    friend class EncodingTask;
-    friend class CompressionTask;
+                    );
+
+  ~PhraseTableCreator();
+
+  friend class RankingTask;
+  friend class EncodingTask;
+  friend class CompressionTask;
 };
 
 class RankingTask
 {
-  private:
+private:
 #ifdef WITH_THREADS
-    static boost::mutex m_mutex;
-    static boost::mutex m_fileMutex;
+  static boost::mutex m_mutex;
+  static boost::mutex m_fileMutex;
 #endif
-    static size_t m_lineNum;
-    InputFileStream& m_inFile;
-    PhraseTableCreator& m_creator;
-    
-  public:
-    RankingTask(InputFileStream& inFile, PhraseTableCreator& creator);
-    void operator()();
+  static size_t m_lineNum;
+  InputFileStream& m_inFile;
+  PhraseTableCreator& m_creator;
+
+public:
+  RankingTask(InputFileStream& inFile, PhraseTableCreator& creator);
+  void operator()();
 };
 
 class EncodingTask
 {
-  private:
+private:
 #ifdef WITH_THREADS
-    static boost::mutex m_mutex;
-    static boost::mutex m_fileMutex;
+  static boost::mutex m_mutex;
+  static boost::mutex m_fileMutex;
 #endif
-    static size_t m_lineNum;
-    static size_t m_sourcePhraseNum;
-    static std::string m_lastSourcePhrase;
-    
-    InputFileStream& m_inFile;
-    PhraseTableCreator& m_creator;
-    
-  public:
-    EncodingTask(InputFileStream& inFile, PhraseTableCreator& creator);
-    void operator()();
+  static size_t m_lineNum;
+  static size_t m_sourcePhraseNum;
+  static std::string m_lastSourcePhrase;
+
+  InputFileStream& m_inFile;
+  PhraseTableCreator& m_creator;
+
+public:
+  EncodingTask(InputFileStream& inFile, PhraseTableCreator& creator);
+  void operator()();
 };
 
 class CompressionTask
 {
-  private:
+private:
 #ifdef WITH_THREADS
-    static boost::mutex m_mutex;
+  static boost::mutex m_mutex;
 #endif
-    static size_t m_collectionNum;
-    StringVector<unsigned char, unsigned long, MmapAllocator>&
-    m_encodedCollections;
-    PhraseTableCreator& m_creator;
-    
-  public:
-    CompressionTask(StringVector<unsigned char, unsigned long, MmapAllocator>&
-                    encodedCollections, PhraseTableCreator& creator);
-    void operator()();
+  static size_t m_collectionNum;
+  StringVector<unsigned char, unsigned long, MmapAllocator>&
+  m_encodedCollections;
+  PhraseTableCreator& m_creator;
+
+public:
+  CompressionTask(StringVector<unsigned char, unsigned long, MmapAllocator>&
+                  encodedCollections, PhraseTableCreator& creator);
+  void operator()();
 };
 
 }
diff --git a/moses/TranslationModel/CompactPT/StringVector.h b/moses/TranslationModel/CompactPT/StringVector.h
index fcc545a19..4545d61c6 100644
--- a/moses/TranslationModel/CompactPT/StringVector.h
+++ b/moses/TranslationModel/CompactPT/StringVector.h
@@ -1,23 +1,23 @@
-// $Id$                                                                                                                               
-// vim:tabstop=2                                                                                                                      
-/***********************************************************************                                                              
-Moses - factored phrase-based language decoder                                                                                        
-Copyright (C) 2006 University of Edinburgh                                                                                            
-                                                                                                                                      
-This library is free software; you can redistribute it and/or                                                                         
-modify it under the terms of the GNU Lesser General Public                                                                            
-License as published by the Free Software Foundation; either                                                                          
-version 2.1 of the License, or (at your option) any later version.                                                                    
-                                                                                                                                      
-This library is distributed in the hope that it will be useful,                                                                       
-but WITHOUT ANY WARRANTY; without even the implied warranty of                                                                        
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU                                                                     
-Lesser General Public License for more details.                                                                                       
-                                                                                                                                      
-You should have received a copy of the GNU Lesser General Public                                                                      
-License along with this library; if not, write to the Free Software                                                                   
-Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA                                                        
-***********************************************************************/  
+// $Id$
+// vim:tabstop=2
+/***********************************************************************
+Moses - factored phrase-based language decoder
+Copyright (C) 2006 University of Edinburgh
+
+This library is free software; you can redistribute it and/or
+modify it under the terms of the GNU Lesser General Public
+License as published by the Free Software Foundation; either
+version 2.1 of the License, or (at your option) any later version.
+
+This library is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public
+License along with this library; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+***********************************************************************/
 
 #ifndef moses_StringVector_h
 #define moses_StringVector_h
@@ -43,255 +43,241 @@ namespace Moses
 template <typename ValueIteratorT>
 class ValueIteratorRange
 {
-  private:
-    ValueIteratorT m_begin;
-    ValueIteratorT m_end;
-    
-  public:
-    ValueIteratorRange(ValueIteratorT begin, ValueIteratorT end);
-    
-    const ValueIteratorT& begin() const;
-    const ValueIteratorT& end() const;
-    const std::string str() const;
-    operator const std::string()
-    {
-      return str();
-    }
-    
-    size_t size()
-    {
-      return std::distance(m_begin, m_end);
-    }
-    
-    template <typename StringT>
-    bool operator==(const StringT& o) const;
-    bool operator==(const char* c) const;
-
-    template <typename StringT>
-    bool operator<(const StringT& o) const;
-    bool operator<(const char* c) const;
+private:
+  ValueIteratorT m_begin;
+  ValueIteratorT m_end;
+
+public:
+  ValueIteratorRange(ValueIteratorT begin, ValueIteratorT end);
+
+  const ValueIteratorT& begin() const;
+  const ValueIteratorT& end() const;
+  const std::string str() const;
+  operator const std::string() {
+    return str();
+  }
+
+  size_t size() {
+    return std::distance(m_begin, m_end);
+  }
+
+  template <typename StringT>
+  bool operator==(const StringT& o) const;
+  bool operator==(const char* c) const;
+
+  template <typename StringT>
+  bool operator<(const StringT& o) const;
+  bool operator<(const char* c) const;
 };
 
 // ********** StringVector **********
 
 template <typename ValueT = unsigned char, typename PosT = unsigned int,
-          template <typename> class Allocator = std::allocator>
+         template <typename> class Allocator = std::allocator>
 class StringVector
-{    
-  protected:
-    bool m_sorted;
-    bool m_memoryMapped;
-    
-    std::vector<ValueT, Allocator<ValueT> >* m_charArray;
-    MonotonicVector<PosT, unsigned int, 32> m_positions; 
-    
-    virtual const ValueT* value_ptr(PosT i) const;
-    
+{
+protected:
+  bool m_sorted;
+  bool m_memoryMapped;
+
+  std::vector<ValueT, Allocator<ValueT> >* m_charArray;
+  MonotonicVector<PosT, unsigned int, 32> m_positions;
+
+  virtual const ValueT* value_ptr(PosT i) const;
+
+public:
+  typedef ValueIteratorRange<typename std::vector<ValueT, Allocator<ValueT> >::const_iterator> range;
+
+  // ********** RangeIterator **********
+
+  class RangeIterator : public boost::iterator_facade<RangeIterator,
+    range, std::random_access_iterator_tag, range, PosT>
+  {
+
+  private:
+    PosT m_index;
+    StringVector<ValueT, PosT, Allocator>* m_container;
+
   public:
-    typedef ValueIteratorRange<typename std::vector<ValueT, Allocator<ValueT> >::const_iterator> range;
-    
-    // ********** RangeIterator **********
-    
-    class RangeIterator : public boost::iterator_facade<RangeIterator,
-        range, std::random_access_iterator_tag, range, PosT>
-    {
-      
-      private:
-        PosT m_index;
-        StringVector<ValueT, PosT, Allocator>* m_container;
-    
-      public:
-        RangeIterator();
-        RangeIterator(StringVector<ValueT, PosT, Allocator> &sv, PosT index=0);
-        
-        PosT get_index();
-  
-      private:
-        friend class boost::iterator_core_access;
-        
-        range dereference() const;
-        bool equal(RangeIterator const& other) const;
-        void increment();
-        void decrement();
-        void advance(PosT n);
-        
-        PosT distance_to(RangeIterator const& other) const;
-    };
-    
-    // ********** StringIterator **********
-    
-    class StringIterator : public boost::iterator_facade<StringIterator,
-        std::string, std::random_access_iterator_tag, const std::string, PosT>
-    {
-    
-      private:
-        PosT m_index;
-        StringVector<ValueT, PosT, Allocator>* m_container;
-    
-      public:
-        StringIterator();
-        StringIterator(StringVector<ValueT, PosT, Allocator> &sv, PosT index=0);
-            
-        PosT get_index();
-        
-      private:
-        friend class boost::iterator_core_access;
-        
-        const std::string dereference() const;
-        bool equal(StringIterator const& other) const;
-        void increment();
-        void decrement();
-        void advance(PosT n);
-        PosT distance_to(StringIterator const& other) const;
-    };
-
-    typedef RangeIterator iterator;
-    typedef StringIterator string_iterator;
-    
-    StringVector();
-    StringVector(Allocator<ValueT> alloc);
-    
-    virtual ~StringVector()
-    {
-      delete m_charArray;
-    }
-    
-    void swap(StringVector<ValueT, PosT, Allocator> &c)
-    {
-      m_positions.commit();
-      m_positions.swap(c.m_positions);
-      m_charArray->swap(*c.m_charArray);
-      
-      bool temp = m_sorted;
-      m_sorted = c.m_sorted;
-      c.m_sorted = temp;
-    }
-    
-    bool is_sorted() const;
-    PosT size() const;
-    virtual PosT size2() const;
-    
-    template<class Iterator> Iterator begin() const; 
-    template<class Iterator> Iterator end() const;
-    
-    iterator begin() const;  
-    iterator end() const;  
-    
-    PosT length(PosT i) const;
-    typename std::vector<ValueT, Allocator<ValueT> >::const_iterator begin(PosT i) const;
-    typename std::vector<ValueT, Allocator<ValueT> >::const_iterator end(PosT i) const;
-    
-    void clear()
-    {
-      m_charArray->clear();
-      m_sorted = true;
-      m_positions = MonotonicVector<PosT, unsigned int, 32>();
-    }
-    
-    range at(PosT i) const;
-    range operator[](PosT i) const;
-    range back() const;
-    
-    template <typename StringT>
-    void push_back(StringT s);
-    void push_back(const char* c);
-        
-    template <typename StringT>
-    PosT find(StringT &s) const;
-    PosT find(const char* c) const;
-    
-    virtual size_t load(std::FILE* in, bool memoryMapped = false)
-    {
-      size_t size = 0;
-      m_memoryMapped = memoryMapped;
-      
-      size += std::fread(&m_sorted, sizeof(bool), 1, in) * sizeof(bool);
-      size += m_positions.load(in, m_memoryMapped);
-      
-      size += loadCharArray(*m_charArray, in, m_memoryMapped);       
-      return size;
-    }
-    
-    size_t loadCharArray(std::vector<ValueT, std::allocator<ValueT> >& c,
-                       std::FILE* in, bool map = false)
-    {
-      // Can only be read into memory. Mapping not possible with std:allocator.
-      assert(map == false);
-      
-      size_t byteSize = 0;
-      
-      size_t valSize;
-      byteSize += std::fread(&valSize, sizeof(size_t), 1, in) * sizeof(size_t);
-      
+    RangeIterator();
+    RangeIterator(StringVector<ValueT, PosT, Allocator> &sv, PosT index=0);
+
+    PosT get_index();
+
+  private:
+    friend class boost::iterator_core_access;
+
+    range dereference() const;
+    bool equal(RangeIterator const& other) const;
+    void increment();
+    void decrement();
+    void advance(PosT n);
+
+    PosT distance_to(RangeIterator const& other) const;
+  };
+
+  // ********** StringIterator **********
+
+  class StringIterator : public boost::iterator_facade<StringIterator,
+    std::string, std::random_access_iterator_tag, const std::string, PosT>
+  {
+
+  private:
+    PosT m_index;
+    StringVector<ValueT, PosT, Allocator>* m_container;
+
+  public:
+    StringIterator();
+    StringIterator(StringVector<ValueT, PosT, Allocator> &sv, PosT index=0);
+
+    PosT get_index();
+
+  private:
+    friend class boost::iterator_core_access;
+
+    const std::string dereference() const;
+    bool equal(StringIterator const& other) const;
+    void increment();
+    void decrement();
+    void advance(PosT n);
+    PosT distance_to(StringIterator const& other) const;
+  };
+
+  typedef RangeIterator iterator;
+  typedef StringIterator string_iterator;
+
+  StringVector();
+  StringVector(Allocator<ValueT> alloc);
+
+  virtual ~StringVector() {
+    delete m_charArray;
+  }
+
+  void swap(StringVector<ValueT, PosT, Allocator> &c) {
+    m_positions.commit();
+    m_positions.swap(c.m_positions);
+    m_charArray->swap(*c.m_charArray);
+
+    bool temp = m_sorted;
+    m_sorted = c.m_sorted;
+    c.m_sorted = temp;
+  }
+
+  bool is_sorted() const;
+  PosT size() const;
+  virtual PosT size2() const;
+
+  template<class Iterator> Iterator begin() const;
+  template<class Iterator> Iterator end() const;
+
+  iterator begin() const;
+  iterator end() const;
+
+  PosT length(PosT i) const;
+  typename std::vector<ValueT, Allocator<ValueT> >::const_iterator begin(PosT i) const;
+  typename std::vector<ValueT, Allocator<ValueT> >::const_iterator end(PosT i) const;
+
+  void clear() {
+    m_charArray->clear();
+    m_sorted = true;
+    m_positions = MonotonicVector<PosT, unsigned int, 32>();
+  }
+
+  range at(PosT i) const;
+  range operator[](PosT i) const;
+  range back() const;
+
+  template <typename StringT>
+  void push_back(StringT s);
+  void push_back(const char* c);
+
+  template <typename StringT>
+  PosT find(StringT &s) const;
+  PosT find(const char* c) const;
+
+  virtual size_t load(std::FILE* in, bool memoryMapped = false) {
+    size_t size = 0;
+    m_memoryMapped = memoryMapped;
+
+    size += std::fread(&m_sorted, sizeof(bool), 1, in) * sizeof(bool);
+    size += m_positions.load(in, m_memoryMapped);
+
+    size += loadCharArray(*m_charArray, in, m_memoryMapped);
+    return size;
+  }
+
+  size_t loadCharArray(std::vector<ValueT, std::allocator<ValueT> >& c,
+                       std::FILE* in, bool map = false) {
+    // Can only be read into memory. Mapping not possible with std:allocator.
+    assert(map == false);
+
+    size_t byteSize = 0;
+
+    size_t valSize;
+    byteSize += std::fread(&valSize, sizeof(size_t), 1, in) * sizeof(size_t);
+
+    c.resize(valSize, 0);
+    byteSize += std::fread(&c[0], sizeof(ValueT), valSize, in) * sizeof(ValueT);
+
+    return byteSize;
+  }
+
+  size_t loadCharArray(std::vector<ValueT, MmapAllocator<ValueT> >& c,
+                       std::FILE* in, bool map = false) {
+    size_t byteSize = 0;
+
+    size_t valSize;
+    byteSize += std::fread(&valSize, sizeof(size_t), 1, in) * sizeof(size_t);
+
+    if(map == false) {
+      // Read data into temporary file (default constructor of MmapAllocator)
+      // and map memory onto temporary file. Can be resized.
+
       c.resize(valSize, 0);
       byteSize += std::fread(&c[0], sizeof(ValueT), valSize, in) * sizeof(ValueT);
-    
-      return byteSize;
-    }
-    
-    size_t loadCharArray(std::vector<ValueT, MmapAllocator<ValueT> >& c,
-                       std::FILE* in, bool map = false)
-    {
-      size_t byteSize = 0;
-
-      size_t valSize;
-      byteSize += std::fread(&valSize, sizeof(size_t), 1, in) * sizeof(size_t);
-
-      if(map == false)
-      {
-        // Read data into temporary file (default constructor of MmapAllocator)
-        // and map memory onto temporary file. Can be resized.
-        
-        c.resize(valSize, 0);
-        byteSize += std::fread(&c[0], sizeof(ValueT), valSize, in) * sizeof(ValueT);    
-      }
-      else
-      {
-        // Map it directly on specified region of file "in" starting at valPos
-        // with length valSize * sizeof(ValueT). Mapped region cannot be resized.
-        
-        size_t valPos = std::ftell(in);
-        Allocator<ValueT> alloc(in, valPos);
-        std::vector<ValueT, Allocator<ValueT> > charArrayTemp(alloc);
-        charArrayTemp.resize(valSize);
-        c.swap(charArrayTemp);
-        
-        byteSize += valSize * sizeof(ValueT);
-      }
-      
-      return byteSize;
-    }
-    
-    size_t load(std::string filename, bool memoryMapped = false)
-    {
-      std::FILE* pFile = fopen(filename.c_str(), "r");
-      size_t byteSize = load(pFile, memoryMapped);
-      fclose(pFile);
-      return byteSize;
-    }
+    } else {
+      // Map it directly on specified region of file "in" starting at valPos
+      // with length valSize * sizeof(ValueT). Mapped region cannot be resized.
 
-    size_t save(std::FILE* out)
-    {
-      size_t byteSize = 0;
-      byteSize += ThrowingFwrite(&m_sorted, sizeof(bool), 1, out) * sizeof(bool);
-      
-      byteSize += m_positions.save(out);
-    
-      size_t valSize = size2();
-      byteSize += ThrowingFwrite(&valSize, sizeof(size_t), 1, out) * sizeof(size_t);
-      byteSize += ThrowingFwrite(&(*m_charArray)[0], sizeof(ValueT), valSize, out) * sizeof(ValueT);
-
-      return byteSize;
-    }
-    
-    size_t save(std::string filename)
-    { 
-      std::FILE* pFile = fopen(filename.c_str(), "w");
-      size_t byteSize = save(pFile);
-      fclose(pFile);
-      return byteSize;
+      size_t valPos = std::ftell(in);
+      Allocator<ValueT> alloc(in, valPos);
+      std::vector<ValueT, Allocator<ValueT> > charArrayTemp(alloc);
+      charArrayTemp.resize(valSize);
+      c.swap(charArrayTemp);
+
+      byteSize += valSize * sizeof(ValueT);
     }
-    
+
+    return byteSize;
+  }
+
+  size_t load(std::string filename, bool memoryMapped = false) {
+    std::FILE* pFile = fopen(filename.c_str(), "r");
+    size_t byteSize = load(pFile, memoryMapped);
+    fclose(pFile);
+    return byteSize;
+  }
+
+  size_t save(std::FILE* out) {
+    size_t byteSize = 0;
+    byteSize += ThrowingFwrite(&m_sorted, sizeof(bool), 1, out) * sizeof(bool);
+
+    byteSize += m_positions.save(out);
+
+    size_t valSize = size2();
+    byteSize += ThrowingFwrite(&valSize, sizeof(size_t), 1, out) * sizeof(size_t);
+    byteSize += ThrowingFwrite(&(*m_charArray)[0], sizeof(ValueT), valSize, out) * sizeof(ValueT);
+
+    return byteSize;
+  }
+
+  size_t save(std::string filename) {
+    std::FILE* pFile = fopen(filename.c_str(), "w");
+    size_t byteSize = save(pFile);
+    fclose(pFile);
+    return byteSize;
+  }
+
 };
 
 // ********** Implementation **********
@@ -300,214 +286,214 @@ class StringVector
 
 template <typename ValueIteratorT>
 ValueIteratorRange<ValueIteratorT>::ValueIteratorRange(ValueIteratorT begin,
-  ValueIteratorT end) : m_begin(begin), m_end(end) { }
-    
+    ValueIteratorT end) : m_begin(begin), m_end(end) { }
+
 template <typename ValueIteratorT>
 const ValueIteratorT& ValueIteratorRange<ValueIteratorT>::begin() const
 {
-    return m_begin;
+  return m_begin;
 }
 
 template <typename ValueIteratorT>
 const ValueIteratorT& ValueIteratorRange<ValueIteratorT>::end() const
 {
-    return m_end;
+  return m_end;
 }
 
 template <typename ValueIteratorT>
 const std::string ValueIteratorRange<ValueIteratorT>::str() const
 {
-    std::string dummy;
-    for(ValueIteratorT it = m_begin; it != m_end; it++)
-        dummy.push_back(*it);
-    return dummy;
+  std::string dummy;
+  for(ValueIteratorT it = m_begin; it != m_end; it++)
+    dummy.push_back(*it);
+  return dummy;
 }
 
 template <typename ValueIteratorT>
 template <typename StringT>
 bool ValueIteratorRange<ValueIteratorT>::operator==(const StringT& o) const
 {
-    if(std::distance(m_begin, m_end) == std::distance(o.begin(), o.end()))
-        return std::equal(m_begin, m_end, o.begin());
-    else
-        return false;
+  if(std::distance(m_begin, m_end) == std::distance(o.begin(), o.end()))
+    return std::equal(m_begin, m_end, o.begin());
+  else
+    return false;
 }
-    
+
 template <typename ValueIteratorT>
 bool ValueIteratorRange<ValueIteratorT>::operator==(const char* c) const
 {
-    return *this == std::string(c);
+  return *this == std::string(c);
 }
 
 template <typename ValueIteratorT>
 template <typename StringT>
 bool ValueIteratorRange<ValueIteratorT>::operator<(const StringT &s2) const
 {
-    return std::lexicographical_compare(m_begin, m_end, s2.begin(), s2.end(),
-      std::less<typename std::iterator_traits<ValueIteratorT>::value_type>());  
+  return std::lexicographical_compare(m_begin, m_end, s2.begin(), s2.end(),
+                                      std::less<typename std::iterator_traits<ValueIteratorT>::value_type>());
 }
 
 template <typename ValueIteratorT>
 bool ValueIteratorRange<ValueIteratorT>::operator<(const char* c) const
 {
-    return *this < std::string(c);  
+  return *this < std::string(c);
 }
 
 template <typename StringT, typename ValueIteratorT>
 bool operator<(const StringT &s1, const ValueIteratorRange<ValueIteratorT> &s2)
 {
-    return std::lexicographical_compare(s1.begin(), s1.end(), s2.begin(), s2.end(),
-      std::less<typename std::iterator_traits<ValueIteratorT>::value_type>());  
+  return std::lexicographical_compare(s1.begin(), s1.end(), s2.begin(), s2.end(),
+                                      std::less<typename std::iterator_traits<ValueIteratorT>::value_type>());
 }
 
 template <typename ValueIteratorT>
 bool operator<(const char* c, const ValueIteratorRange<ValueIteratorT> &s2)
 {
-    size_t len = std::char_traits<char>::length(c);
-    return std::lexicographical_compare(c, c + len, s2.begin(), s2.end(),
-        std::less<typename std::iterator_traits<ValueIteratorT>::value_type>());  
+  size_t len = std::char_traits<char>::length(c);
+  return std::lexicographical_compare(c, c + len, s2.begin(), s2.end(),
+                                      std::less<typename std::iterator_traits<ValueIteratorT>::value_type>());
 }
 
 template <typename OStream, typename ValueIteratorT>
 OStream& operator<<(OStream &os, ValueIteratorRange<ValueIteratorT> cr)
 {
   ValueIteratorT it = cr.begin();
-    while(it != cr.end())
-        os << *(it++);
-    return os;
+  while(it != cr.end())
+    os << *(it++);
+  return os;
 }
 
 // StringVector
 
 template<typename ValueT, typename PosT, template <typename> class Allocator>
 StringVector<ValueT, PosT, Allocator>::StringVector()
- : m_sorted(true), m_memoryMapped(false), m_charArray(new std::vector<ValueT, Allocator<ValueT> >()) { }
+  : m_sorted(true), m_memoryMapped(false), m_charArray(new std::vector<ValueT, Allocator<ValueT> >()) { }
 
 template<typename ValueT, typename PosT, template <typename> class Allocator>
 StringVector<ValueT, PosT, Allocator>::StringVector(Allocator<ValueT> alloc)
- : m_sorted(true), m_memoryMapped(false), m_charArray(new std::vector<ValueT, Allocator<ValueT> >(alloc)) { }
+  : m_sorted(true), m_memoryMapped(false), m_charArray(new std::vector<ValueT, Allocator<ValueT> >(alloc)) { }
 
-template<typename ValueT, typename PosT, template <typename> class Allocator> 
+template<typename ValueT, typename PosT, template <typename> class Allocator>
 template <typename StringT>
 void StringVector<ValueT, PosT, Allocator>::push_back(StringT s)
 {
-    if(is_sorted() && size() && !(back() < s))
-        m_sorted = false;
+  if(is_sorted() && size() && !(back() < s))
+    m_sorted = false;
 
-    m_positions.push_back(size2());
-    std::copy(s.begin(), s.end(), std::back_inserter(*m_charArray));
+  m_positions.push_back(size2());
+  std::copy(s.begin(), s.end(), std::back_inserter(*m_charArray));
 }
 
-template<typename ValueT, typename PosT, template <typename> class Allocator> 
+template<typename ValueT, typename PosT, template <typename> class Allocator>
 void StringVector<ValueT, PosT, Allocator>::push_back(const char* c)
 {
-    std::string dummy(c);
-    push_back(dummy);
+  std::string dummy(c);
+  push_back(dummy);
 }
 
-template<typename ValueT, typename PosT, template <typename> class Allocator> 
+template<typename ValueT, typename PosT, template <typename> class Allocator>
 template <typename Iterator>
 Iterator StringVector<ValueT, PosT, Allocator>::begin() const
 {
-    return Iterator(const_cast<StringVector<ValueT, PosT, Allocator>&>(*this), 0);
+  return Iterator(const_cast<StringVector<ValueT, PosT, Allocator>&>(*this), 0);
 }
-    
-template<typename ValueT, typename PosT, template <typename> class Allocator> 
+
+template<typename ValueT, typename PosT, template <typename> class Allocator>
 template <typename Iterator>
 Iterator StringVector<ValueT, PosT, Allocator>::end() const
 {
-    return Iterator(const_cast<StringVector<ValueT, PosT, Allocator>&>(*this), size());
+  return Iterator(const_cast<StringVector<ValueT, PosT, Allocator>&>(*this), size());
 }
 
 template<typename ValueT, typename PosT, template <typename> class Allocator>
 typename StringVector<ValueT, PosT, Allocator>::iterator StringVector<ValueT, PosT, Allocator>::begin() const
 {
-    return begin<iterator>();
-};  
+  return begin<iterator>();
+};
 
 template<typename ValueT, typename PosT, template <typename> class Allocator>
 typename StringVector<ValueT, PosT, Allocator>::iterator StringVector<ValueT, PosT, Allocator>::end() const
 {
-    return end<iterator>();
-};  
+  return end<iterator>();
+};
 
 template<typename ValueT, typename PosT, template <typename> class Allocator>
 bool StringVector<ValueT, PosT, Allocator>::is_sorted() const
 {
-    return m_sorted;
+  return m_sorted;
 }
 
 template<typename ValueT, typename PosT, template <typename> class Allocator>
 PosT StringVector<ValueT, PosT, Allocator>::size() const
 {
-    return m_positions.size();
+  return m_positions.size();
 }
 
 template<typename ValueT, typename PosT, template <typename> class Allocator>
 PosT StringVector<ValueT, PosT, Allocator>::size2() const
 {
-    return m_charArray->size();
+  return m_charArray->size();
 }
-    
+
 template<typename ValueT, typename PosT, template <typename> class Allocator>
 typename StringVector<ValueT, PosT, Allocator>::range StringVector<ValueT, PosT, Allocator>::at(PosT i) const
 {
-    return range(begin(i), end(i));
+  return range(begin(i), end(i));
 }
-    
+
 template<typename ValueT, typename PosT, template <typename> class Allocator>
 typename StringVector<ValueT, PosT, Allocator>::range StringVector<ValueT, PosT, Allocator>::operator[](PosT i) const
 {
-    return at(i);
+  return at(i);
 }
 
 template<typename ValueT, typename PosT, template <typename> class Allocator>
 typename StringVector<ValueT, PosT, Allocator>::range StringVector<ValueT, PosT, Allocator>::back() const
 {
-    return at(size()-1);
+  return at(size()-1);
 }
 
 template<typename ValueT, typename PosT, template <typename> class Allocator>
 PosT StringVector<ValueT, PosT, Allocator>::length(PosT i) const
 {
-    if(i+1 < size())
-        return m_positions[i+1] - m_positions[i];
-    else
-        return size2() - m_positions[i];
+  if(i+1 < size())
+    return m_positions[i+1] - m_positions[i];
+  else
+    return size2() - m_positions[i];
 }
 
 template<typename ValueT, typename PosT, template <typename> class Allocator>
 const ValueT* StringVector<ValueT, PosT, Allocator>::value_ptr(PosT i) const
 {
-    return &(*m_charArray)[m_positions[i]];
+  return &(*m_charArray)[m_positions[i]];
 }
 
 template<typename ValueT, typename PosT, template <typename> class Allocator>
 typename std::vector<ValueT, Allocator<ValueT> >::const_iterator StringVector<ValueT, PosT, Allocator>::begin(PosT i) const
 {
-    return typename std::vector<ValueT, Allocator<ValueT> >::const_iterator(value_ptr(i));
-}    
+  return typename std::vector<ValueT, Allocator<ValueT> >::const_iterator(value_ptr(i));
+}
 
 template<typename ValueT, typename PosT, template <typename> class Allocator>
 typename std::vector<ValueT, Allocator<ValueT> >::const_iterator StringVector<ValueT, PosT, Allocator>::end(PosT i) const
 {
-    return typename std::vector<ValueT, Allocator<ValueT> >::const_iterator(value_ptr(i) + length(i));
-}    
+  return typename std::vector<ValueT, Allocator<ValueT> >::const_iterator(value_ptr(i) + length(i));
+}
 
 template<typename ValueT, typename PosT, template <typename> class Allocator>
 template <typename StringT>
 PosT StringVector<ValueT, PosT, Allocator>::find(StringT &s) const
 {
-    if(m_sorted)
-        return std::distance(begin(), std::lower_bound(begin(), end(), s));
-    return std::distance(begin(), std::find(begin(), end(), s));
+  if(m_sorted)
+    return std::distance(begin(), std::lower_bound(begin(), end(), s));
+  return std::distance(begin(), std::find(begin(), end(), s));
 }
 
 template<typename ValueT, typename PosT, template <typename> class Allocator>
 PosT StringVector<ValueT, PosT, Allocator>::find(const char* c) const
 {
-    std::string s(c);
-    return find(s);
+  std::string s(c);
+  return find(s);
 }
 
 // RangeIterator
@@ -518,21 +504,21 @@ StringVector<ValueT, PosT, Allocator>::RangeIterator::RangeIterator() : m_index(
 template<typename ValueT, typename PosT, template <typename> class Allocator>
 StringVector<ValueT, PosT, Allocator>::RangeIterator::RangeIterator(StringVector<ValueT, PosT, Allocator> &sv, PosT index)
   : m_index(index), m_container(&sv) { }
-    
+
 template<typename ValueT, typename PosT, template <typename> class Allocator>
 PosT StringVector<ValueT, PosT, Allocator>::RangeIterator::get_index()
 {
   return m_index;
 }
-    
+
 template<typename ValueT, typename PosT, template <typename> class Allocator>
 typename StringVector<ValueT, PosT, Allocator>::range
-  StringVector<ValueT, PosT, Allocator>::RangeIterator::dereference() const
+StringVector<ValueT, PosT, Allocator>::RangeIterator::dereference() const
 {
   return typename StringVector<ValueT, PosT, Allocator>::range(
-    m_container->begin(m_index),
-    m_container->end(m_index)
-  );
+           m_container->begin(m_index),
+           m_container->end(m_index)
+         );
 }
 
 template<typename ValueT, typename PosT, template <typename> class Allocator>
@@ -577,18 +563,18 @@ template<typename ValueT, typename PosT, template <typename> class Allocator>
 StringVector<ValueT, PosT, Allocator>::StringIterator::StringIterator(
   StringVector<ValueT, PosT, Allocator> &sv, PosT index) : m_index(index),
   m_container(&sv) { }
-    
+
 template<typename ValueT, typename PosT, template <typename> class Allocator>
 PosT StringVector<ValueT, PosT, Allocator>::StringIterator::get_index()
 {
   return m_index;
 }
-    
+
 template<typename ValueT, typename PosT, template <typename> class Allocator>
 const std::string StringVector<ValueT, PosT, Allocator>::StringIterator::dereference() const
 {
   return StringVector<ValueT, PosT, Allocator>::range(m_container->begin(m_index),
-    m_container->end(m_index)).str();    
+         m_container->end(m_index)).str();
 }
 
 template<typename ValueT, typename PosT, template <typename> class Allocator>
@@ -620,7 +606,7 @@ template<typename ValueT, typename PosT, template <typename> class Allocator>
 PosT StringVector<ValueT, PosT, Allocator>::StringIterator::distance_to(
   StringVector<ValueT, PosT, Allocator>::StringIterator const& other) const
 {
-  return other.m_index - m_index;    
+  return other.m_index - m_index;
 }
 
 // ********** Some typedefs **********
diff --git a/moses/TranslationModel/CompactPT/TargetPhraseCollectionCache.h b/moses/TranslationModel/CompactPT/TargetPhraseCollectionCache.h
index 7687d1498..3eac0226a 100644
--- a/moses/TranslationModel/CompactPT/TargetPhraseCollectionCache.h
+++ b/moses/TranslationModel/CompactPT/TargetPhraseCollectionCache.h
@@ -1,23 +1,23 @@
-// $Id$                                                                                                                               
-// vim:tabstop=2                                                                                                                      
-/***********************************************************************                                                              
-Moses - factored phrase-based language decoder                                                                                        
-Copyright (C) 2006 University of Edinburgh                                                                                            
-                                                                                                                                      
-This library is free software; you can redistribute it and/or                                                                         
-modify it under the terms of the GNU Lesser General Public                                                                            
-License as published by the Free Software Foundation; either                                                                          
-version 2.1 of the License, or (at your option) any later version.                                                                    
-                                                                                                                                      
-This library is distributed in the hope that it will be useful,                                                                       
-but WITHOUT ANY WARRANTY; without even the implied warranty of                                                                        
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU                                                                     
-Lesser General Public License for more details.                                                                                       
-                                                                                                                                      
-You should have received a copy of the GNU Lesser General Public                                                                      
-License along with this library; if not, write to the Free Software                                                                   
-Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA                                                        
-***********************************************************************/  
+// $Id$
+// vim:tabstop=2
+/***********************************************************************
+Moses - factored phrase-based language decoder
+Copyright (C) 2006 University of Edinburgh
+
+This library is free software; you can redistribute it and/or
+modify it under the terms of the GNU Lesser General Public
+License as published by the Free Software Foundation; either
+version 2.1 of the License, or (at your option) any later version.
+
+This library is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public
+License along with this library; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+***********************************************************************/
 
 #ifndef moses_TargetPhraseCollectionCache_h
 #define moses_TargetPhraseCollectionCache_h
@@ -46,135 +46,119 @@ typedef boost::shared_ptr<TargetPhraseVector> TargetPhraseVectorPtr;
 
 class TargetPhraseCollectionCache
 {
-  private:
-    size_t m_max;
-    float m_tolerance;
-    
-    struct LastUsed {
-      clock_t m_clock;
-      TargetPhraseVectorPtr m_tpv;
-      size_t m_bitsLeft;
-      
-      LastUsed() : m_clock(0), m_bitsLeft(0) {}
-      
-      LastUsed(clock_t clock, TargetPhraseVectorPtr tpv, size_t bitsLeft = 0)
+private:
+  size_t m_max;
+  float m_tolerance;
+
+  struct LastUsed {
+    clock_t m_clock;
+    TargetPhraseVectorPtr m_tpv;
+    size_t m_bitsLeft;
+
+    LastUsed() : m_clock(0), m_bitsLeft(0) {}
+
+    LastUsed(clock_t clock, TargetPhraseVectorPtr tpv, size_t bitsLeft = 0)
       : m_clock(clock), m_tpv(tpv), m_bitsLeft(bitsLeft) {}
-    };
-    
-    typedef std::map<Phrase, LastUsed> CacheMap;
-    
-    CacheMap m_phraseCache;
-    
+  };
+
+  typedef std::map<Phrase, LastUsed> CacheMap;
+
+  CacheMap m_phraseCache;
+
 #ifdef WITH_THREADS
-    boost::mutex m_mutex;
+  boost::mutex m_mutex;
 #endif
 
-  public:
-    
-    typedef CacheMap::iterator iterator;
-    typedef CacheMap::const_iterator const_iterator;
-        
-    TargetPhraseCollectionCache(size_t max = 5000, float tolerance = 0.2)
+public:
+
+  typedef CacheMap::iterator iterator;
+  typedef CacheMap::const_iterator const_iterator;
+
+  TargetPhraseCollectionCache(size_t max = 5000, float tolerance = 0.2)
     : m_max(max), m_tolerance(tolerance)
-    {}
-    
-    iterator Begin()
-    {
-      return m_phraseCache.begin();
-    }
-    
-    const_iterator Begin() const
-    {
-      return m_phraseCache.begin();
-    }
-    
-    iterator End()
-    {
-      return m_phraseCache.end();
-    }
-    
-    const_iterator End() const
-    {
-      return m_phraseCache.end();
-    }
-    
-    void Cache(const Phrase &sourcePhrase, TargetPhraseVectorPtr tpv,
-               size_t bitsLeft = 0, size_t maxRank = 0)
-    {
+  {}
+
+  iterator Begin() {
+    return m_phraseCache.begin();
+  }
+
+  const_iterator Begin() const {
+    return m_phraseCache.begin();
+  }
+
+  iterator End() {
+    return m_phraseCache.end();
+  }
+
+  const_iterator End() const {
+    return m_phraseCache.end();
+  }
+
+  void Cache(const Phrase &sourcePhrase, TargetPhraseVectorPtr tpv,
+             size_t bitsLeft = 0, size_t maxRank = 0) {
 #ifdef WITH_THREADS
-      boost::mutex::scoped_lock lock(m_mutex);
+    boost::mutex::scoped_lock lock(m_mutex);
 #endif
 
-      iterator it = m_phraseCache.find(sourcePhrase);
-      if(it != m_phraseCache.end())
-        it->second.m_clock = clock();
-      else
-      {
-        if(maxRank && tpv->size() > maxRank)
-        {
-          TargetPhraseVectorPtr tpv_temp(new TargetPhraseVector());
-          tpv_temp->resize(maxRank);
-          std::copy(tpv->begin(), tpv->begin() + maxRank, tpv_temp->begin());
-          m_phraseCache[sourcePhrase] = LastUsed(clock(), tpv_temp, bitsLeft);
-        }
-        else
-          m_phraseCache[sourcePhrase] = LastUsed(clock(), tpv, bitsLeft);
-      }
+    iterator it = m_phraseCache.find(sourcePhrase);
+    if(it != m_phraseCache.end())
+      it->second.m_clock = clock();
+    else {
+      if(maxRank && tpv->size() > maxRank) {
+        TargetPhraseVectorPtr tpv_temp(new TargetPhraseVector());
+        tpv_temp->resize(maxRank);
+        std::copy(tpv->begin(), tpv->begin() + maxRank, tpv_temp->begin());
+        m_phraseCache[sourcePhrase] = LastUsed(clock(), tpv_temp, bitsLeft);
+      } else
+        m_phraseCache[sourcePhrase] = LastUsed(clock(), tpv, bitsLeft);
     }
+  }
 
-    std::pair<TargetPhraseVectorPtr, size_t> Retrieve(const Phrase &sourcePhrase)
-    {
+  std::pair<TargetPhraseVectorPtr, size_t> Retrieve(const Phrase &sourcePhrase) {
 #ifdef WITH_THREADS
-      boost::mutex::scoped_lock lock(m_mutex);
+    boost::mutex::scoped_lock lock(m_mutex);
 #endif
 
-      iterator it = m_phraseCache.find(sourcePhrase);
-      if(it != m_phraseCache.end())
-      {
-        LastUsed &lu = it->second;
-        lu.m_clock = clock();
-        return std::make_pair(lu.m_tpv, lu.m_bitsLeft);
-      }
-      else
-        return std::make_pair(TargetPhraseVectorPtr(), 0);
-    }
+    iterator it = m_phraseCache.find(sourcePhrase);
+    if(it != m_phraseCache.end()) {
+      LastUsed &lu = it->second;
+      lu.m_clock = clock();
+      return std::make_pair(lu.m_tpv, lu.m_bitsLeft);
+    } else
+      return std::make_pair(TargetPhraseVectorPtr(), 0);
+  }
 
-    void Prune()
-    {
+  void Prune() {
 #ifdef WITH_THREADS
-      boost::mutex::scoped_lock lock(m_mutex);
+    boost::mutex::scoped_lock lock(m_mutex);
 #endif
 
-      if(m_phraseCache.size() > m_max * (1 + m_tolerance))
-      {
-        typedef std::set<std::pair<clock_t, Phrase> > Cands;
-        Cands cands; 
-        for(CacheMap::iterator it = m_phraseCache.begin();
-            it != m_phraseCache.end(); it++)
-        {
-          LastUsed &lu = it->second;
-          cands.insert(std::make_pair(lu.m_clock, it->first));
-        }
-         
-        for(Cands::iterator it = cands.begin(); it != cands.end(); it++)
-        {
-          const Phrase& p = it->second;
-          m_phraseCache.erase(p);
-          
-          if(m_phraseCache.size() < (m_max * (1 - m_tolerance)))
-            break;
-        }
+    if(m_phraseCache.size() > m_max * (1 + m_tolerance)) {
+      typedef std::set<std::pair<clock_t, Phrase> > Cands;
+      Cands cands;
+      for(CacheMap::iterator it = m_phraseCache.begin();
+          it != m_phraseCache.end(); it++) {
+        LastUsed &lu = it->second;
+        cands.insert(std::make_pair(lu.m_clock, it->first));
+      }
+
+      for(Cands::iterator it = cands.begin(); it != cands.end(); it++) {
+        const Phrase& p = it->second;
+        m_phraseCache.erase(p);
+
+        if(m_phraseCache.size() < (m_max * (1 - m_tolerance)))
+          break;
       }
     }
+  }
 
-    void CleanUp()
-    {
+  void CleanUp() {
 #ifdef WITH_THREADS
-      boost::mutex::scoped_lock lock(m_mutex);
+    boost::mutex::scoped_lock lock(m_mutex);
 #endif
-      m_phraseCache.clear();
-    }
-    
+    m_phraseCache.clear();
+  }
+
 };
 
 }
diff --git a/moses/TranslationModel/CompactPT/ThrowingFwrite.cpp b/moses/TranslationModel/CompactPT/ThrowingFwrite.cpp
index 35e8e3122..b231836f5 100644
--- a/moses/TranslationModel/CompactPT/ThrowingFwrite.cpp
+++ b/moses/TranslationModel/CompactPT/ThrowingFwrite.cpp
@@ -1,27 +1,28 @@
-// $Id$                                                                                                                               
-// vim:tabstop=2                                                                                                                      
-/***********************************************************************                                                              
-Moses - factored phrase-based language decoder                                                                                        
-Copyright (C) 2006 University of Edinburgh                                                                                            
-                                                                                                                                      
-This library is free software; you can redistribute it and/or                                                                         
-modify it under the terms of the GNU Lesser General Public                                                                            
-License as published by the Free Software Foundation; either                                                                          
-version 2.1 of the License, or (at your option) any later version.                                                                    
-                                                                                                                                      
-This library is distributed in the hope that it will be useful,                                                                       
-but WITHOUT ANY WARRANTY; without even the implied warranty of                                                                        
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU                                                                     
-Lesser General Public License for more details.                                                                                       
-                                                                                                                                      
-You should have received a copy of the GNU Lesser General Public                                                                      
-License along with this library; if not, write to the Free Software                                                                   
-Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA                                                        
-***********************************************************************/  
+// $Id$
+// vim:tabstop=2
+/***********************************************************************
+Moses - factored phrase-based language decoder
+Copyright (C) 2006 University of Edinburgh
 
-#include "ThrowingFwrite.h" 
+This library is free software; you can redistribute it and/or
+modify it under the terms of the GNU Lesser General Public
+License as published by the Free Software Foundation; either
+version 2.1 of the License, or (at your option) any later version.
 
-size_t ThrowingFwrite(const void *ptr, size_t size, size_t count, FILE* stream) {
+This library is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public
+License along with this library; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+***********************************************************************/
+
+#include "ThrowingFwrite.h"
+
+size_t ThrowingFwrite(const void *ptr, size_t size, size_t count, FILE* stream)
+{
   assert(size);
   size_t returnValue = std::fwrite(ptr, size, count, stream);
   UTIL_THROW_IF(count != returnValue, util::ErrnoException, "Short fwrite; requested size " << size);
diff --git a/moses/TranslationModel/CompactPT/ThrowingFwrite.h b/moses/TranslationModel/CompactPT/ThrowingFwrite.h
index 4f45ae8f5..466d3973b 100644
--- a/moses/TranslationModel/CompactPT/ThrowingFwrite.h
+++ b/moses/TranslationModel/CompactPT/ThrowingFwrite.h
@@ -1,30 +1,30 @@
-// $Id$                                                                                                                               
-// vim:tabstop=2                                                                                                                      
-/***********************************************************************                                                              
-Moses - factored phrase-based language decoder                                                                                        
-Copyright (C) 2006 University of Edinburgh                                                                                            
-                                                                                                                                      
-This library is free software; you can redistribute it and/or                                                                         
-modify it under the terms of the GNU Lesser General Public                                                                            
-License as published by the Free Software Foundation; either                                                                          
-version 2.1 of the License, or (at your option) any later version.                                                                    
-                                                                                                                                      
-This library is distributed in the hope that it will be useful,                                                                       
-but WITHOUT ANY WARRANTY; without even the implied warranty of                                                                        
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU                                                                     
-Lesser General Public License for more details.                                                                                       
-                                                                                                                                      
-You should have received a copy of the GNU Lesser General Public                                                                      
-License along with this library; if not, write to the Free Software                                                                   
-Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA                                                        
-***********************************************************************/  
+// $Id$
+// vim:tabstop=2
+/***********************************************************************
+Moses - factored phrase-based language decoder
+Copyright (C) 2006 University of Edinburgh
+
+This library is free software; you can redistribute it and/or
+modify it under the terms of the GNU Lesser General Public
+License as published by the Free Software Foundation; either
+version 2.1 of the License, or (at your option) any later version.
+
+This library is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+Lesser General Public License for more details.
+
+You should have received a copy of the GNU Lesser General Public
+License along with this library; if not, write to the Free Software
+Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+***********************************************************************/
 
 #ifndef moses_ThrowingFwrite_h
 #define moses_ThrowingFwrite_h
 
 #include <cassert>
 #include <cstdio>
-#include "util/exception.hh" 
+#include "util/exception.hh"
 
 size_t ThrowingFwrite(const void *ptr, size_t size, size_t count, FILE* stream);
 
diff --git a/moses/TranslationModel/DynSAInclude/RandLMCache.h b/moses/TranslationModel/DynSAInclude/RandLMCache.h
index b92a2a164..06ce240a1 100644
--- a/moses/TranslationModel/DynSAInclude/RandLMCache.h
+++ b/moses/TranslationModel/DynSAInclude/RandLMCache.h
@@ -22,177 +22,180 @@
 #include <ctime>
 #include <iostream>
 
-namespace randlm {
-    
-  //! @todo ask abby2
-  template<typename T>
-  class CacheNode {
-  public:
-    typedef std::map<wordID_t, CacheNode<T>* > childMap;
-    // initialise value to 'unknown' (i.e. not yet queried or cached).
-    CacheNode(T unknown_value) : value_(unknown_value) {}
-    childMap childs_;  // child pointers
-    T value_;  // value stored
-    const void* state_;  // state pointer
-  };
-  
-  template<typename T>
-  class Cache {
-  public:
-    typedef typename std::map<wordID_t, CacheNode<T>* >::iterator childPtr;
-    // unknown_value is used to indicate the ngram was not queried (yet)
-    // null_value_ indicates it was queried but not found in model
-    // space usage is handled by client.
-    Cache(T unknown_value, T null_value)  : 
-      cur_nodes_(0), unknown_value_(unknown_value), null_value_(null_value) {
-      root_ = newNode();
+namespace randlm
+{
+
+//! @todo ask abby2
+template<typename T>
+class CacheNode
+{
+public:
+  typedef std::map<wordID_t, CacheNode<T>* > childMap;
+  // initialise value to 'unknown' (i.e. not yet queried or cached).
+  CacheNode(T unknown_value) : value_(unknown_value) {}
+  childMap childs_;  // child pointers
+  T value_;  // value stored
+  const void* state_;  // state pointer
+};
+
+template<typename T>
+class Cache
+{
+public:
+  typedef typename std::map<wordID_t, CacheNode<T>* >::iterator childPtr;
+  // unknown_value is used to indicate the ngram was not queried (yet)
+  // null_value_ indicates it was queried but not found in model
+  // space usage is handled by client.
+  Cache(T unknown_value, T null_value)  :
+    cur_nodes_(0), unknown_value_(unknown_value), null_value_(null_value) {
+    root_ = newNode();
+  }
+  ~Cache() {
+    if(clear()) {
+      delete root_;
+      root_ = NULL;
+    }  else {
+      std::cerr << "Error freeing cache memory.\n";
     }
-    ~Cache() {
-      if(clear()) {
-	delete root_;
-	root_ = NULL;
+  }
+  bool setCacheNgram(const wordID_t* ngram, int len, T value, const void* state) {
+    // inserts full ngram into cache
+    CacheNode<T>* node = root_;
+    for (int i = len - 1; i > -1; --i) {
+      childPtr child = node->childs_.find(ngram[i]);
+      if( child != node->childs_.end() ) {
+        // current node is already prefix. Go to child node
+        node = node->childs_[ngram[i]];
       }  else {
-	std::cerr << "Error freeing cache memory.\n";
-      }
-    }
-    bool setCacheNgram(const wordID_t* ngram, int len, T value, const void* state) {
-      // inserts full ngram into cache 
-      CacheNode<T>* node = root_;
-      for (int i = len - 1; i > -1; --i) {
-	childPtr child = node->childs_.find(ngram[i]);
-	if( child != node->childs_.end() ) {
-	  // current node is already prefix. Go to child node
-	  node = node->childs_[ngram[i]]; 
-	}  else {
-	  // no child for prefix. set new child link in current node
-	  CacheNode<T> * newChild = newNode(node);
-	  node->childs_[ngram[i]] = newChild;
-	  // go to new node
-	  node = newChild;
-	}
+        // no child for prefix. set new child link in current node
+        CacheNode<T> * newChild = newNode(node);
+        node->childs_[ngram[i]] = newChild;
+        // go to new node
+        node = newChild;
       }
-      node->value_ = value;
-      node->state_ = state;
-      return true; 
     }
-    bool checkCacheNgram(const wordID_t* ngram, int len, T* value, const void** state) {
-      // finds value for this full ngram only (returns false if full ngram not in cache)
-      CacheNode<T> * node = root_;      
-      for(int i = len - 1; i > -1; --i) {
-	// go to deepest level node of ngram in cache 
-	childPtr child = node->childs_.find(ngram[i]);
-	if( child != node->childs_.end() ) {
-	  // switch to child node
-	  node = node->childs_[ngram[i]]; 
-	} else {
-	  // not cached
-	  return false;
-	}
+    node->value_ = value;
+    node->state_ = state;
+    return true;
+  }
+  bool checkCacheNgram(const wordID_t* ngram, int len, T* value, const void** state) {
+    // finds value for this full ngram only (returns false if full ngram not in cache)
+    CacheNode<T> * node = root_;
+    for(int i = len - 1; i > -1; --i) {
+      // go to deepest level node of ngram in cache
+      childPtr child = node->childs_.find(ngram[i]);
+      if( child != node->childs_.end() ) {
+        // switch to child node
+        node = node->childs_[ngram[i]];
+      } else {
+        // not cached
+        return false;
       }
-      *value = node->value_;
-      if(state) *state = node->state_;
-      return *value != null_value_ && *value != unknown_value_;
     }
-    int getCache2(const wordID_t* ngram, int len, T** values, int* found) {
-      // set values array to point to cache value nodes
-      CacheNode<T> * node = root_;
-      *found = 0;
-      //values[0] = &node->value_; // pointer to root node's value
-      bool all_found = true;
-      for(int i = len - 1; i > -1; --i) {
-	// go to deepest level node of ngram in cache 
-	childPtr child = node->childs_.find(ngram[i]);
-	if( child != node->childs_.end() ) {
-	  // switch to child node
-	  node = node->childs_[ngram[i]]; 
-	  // get pointer to value (index by length - 1) 
-	  values[i] = &node->value_;
-	  // if null_value then assume all extensions impossible
-	  if (node->value_ == null_value_) {
-	    return len - 1 - i; // max length posible
-          }
-	  all_found = all_found && (node->value_ != unknown_value_);
-	  if (all_found)
-	    ++(*found);
-	} else {
-	  // initialise uncached values
-	  CacheNode<T> * newChild = newNode(node);
-	  node->childs_[ngram[i]] = newChild;
-	  // go to new node
-	  node = newChild;
-	  values[i] = &node->value_;
-	}
+    *value = node->value_;
+    if(state) *state = node->state_;
+    return *value != null_value_ && *value != unknown_value_;
+  }
+  int getCache2(const wordID_t* ngram, int len, T** values, int* found) {
+    // set values array to point to cache value nodes
+    CacheNode<T> * node = root_;
+    *found = 0;
+    //values[0] = &node->value_; // pointer to root node's value
+    bool all_found = true;
+    for(int i = len - 1; i > -1; --i) {
+      // go to deepest level node of ngram in cache
+      childPtr child = node->childs_.find(ngram[i]);
+      if( child != node->childs_.end() ) {
+        // switch to child node
+        node = node->childs_[ngram[i]];
+        // get pointer to value (index by length - 1)
+        values[i] = &node->value_;
+        // if null_value then assume all extensions impossible
+        if (node->value_ == null_value_) {
+          return len - 1 - i; // max length posible
+        }
+        all_found = all_found && (node->value_ != unknown_value_);
+        if (all_found)
+          ++(*found);
+      } else {
+        // initialise uncached values
+        CacheNode<T> * newChild = newNode(node);
+        node->childs_[ngram[i]] = newChild;
+        // go to new node
+        node = newChild;
+        values[i] = &node->value_;
       }
-      return len; // all possible
     }
-    int getCache(const wordID_t* ngram, int len, T** values, int* found) {
-      // get pointers to values for ngram and constituents.
-      // returns upper bound on longest subngram in model.
-      // 'found' stores longest non-null and known value found.
-      CacheNode<T> * node = root_;
-      *found = 0;
-      values[0] = &node->value_; // pointer to root node's value
-      bool all_found = true;
-      for(int i = len - 1; i > -1; --i) {
-	// go to deepest level node of ngram in cache 
-	childPtr child = node->childs_.find(ngram[i]);
-	if( child != node->childs_.end() ) {
-	  // switch to child node
-	  node = node->childs_[ngram[i]]; 
-	  // get pointer to value (index by length - 1) 
-	  values[len - i] = &node->value_;
-	  // if null_value then assume all extensions impossible
-	  if (node->value_ == null_value_)
-	    return len - 1 - i; // max length posible
-	  all_found = all_found && (node->value_ != unknown_value_);
-	  if (all_found)
-	    ++(*found);
-	} else {
-	  // initialise uncached values
-	  CacheNode<T> * newChild = newNode(node);
-	  node->childs_[ngram[i]] = newChild;
-	  // go to new node
-	  node = newChild;
-	  values[len - i] = &node->value_;
-	}
+    return len; // all possible
+  }
+  int getCache(const wordID_t* ngram, int len, T** values, int* found) {
+    // get pointers to values for ngram and constituents.
+    // returns upper bound on longest subngram in model.
+    // 'found' stores longest non-null and known value found.
+    CacheNode<T> * node = root_;
+    *found = 0;
+    values[0] = &node->value_; // pointer to root node's value
+    bool all_found = true;
+    for(int i = len - 1; i > -1; --i) {
+      // go to deepest level node of ngram in cache
+      childPtr child = node->childs_.find(ngram[i]);
+      if( child != node->childs_.end() ) {
+        // switch to child node
+        node = node->childs_[ngram[i]];
+        // get pointer to value (index by length - 1)
+        values[len - i] = &node->value_;
+        // if null_value then assume all extensions impossible
+        if (node->value_ == null_value_)
+          return len - 1 - i; // max length posible
+        all_found = all_found && (node->value_ != unknown_value_);
+        if (all_found)
+          ++(*found);
+      } else {
+        // initialise uncached values
+        CacheNode<T> * newChild = newNode(node);
+        node->childs_[ngram[i]] = newChild;
+        // go to new node
+        node = newChild;
+        values[len - i] = &node->value_;
       }
-      return len; // all possible
-    }
-    bool clear() {
-      std::cerr << "Clearing cache with " << static_cast<float>(cur_nodes_ * nodeSize()) 
-	 / static_cast<float>(1ull << 20) << "MB" << std::endl;
-      return clearNodes(root_);
-    }
-    int nodes() {
-      // returns number of nodes
-      return cur_nodes_;
-    }
-    int nodeSize() {
-      return sizeof(CacheNode<T>) + sizeof(root_->childs_);
-    }
-    private:
-    CacheNode<T> * root_;
-    count_t cur_nodes_; 
-    T unknown_value_; // Used to initialise data at each node
-    T null_value_; // Indicates cached something not in model
-    CacheNode<T>* newNode(CacheNode<T> * node = 0) {
-      ++cur_nodes_;
-      return new CacheNode<T>(unknown_value_);
     }
-    bool clearNodes(CacheNode<T> * node) {
-      //delete children from this node
-      if(!node->childs_.empty()) {
-	iterate(node->childs_, itr) {
-	  if(!clearNodes(itr->second)) 
-	    std::cerr << "Error emptying cache\n";
-	  delete itr->second;
-	  --cur_nodes_;
-	}
-	node->childs_.clear();
+    return len; // all possible
+  }
+  bool clear() {
+    std::cerr << "Clearing cache with " << static_cast<float>(cur_nodes_ * nodeSize())
+              / static_cast<float>(1ull << 20) << "MB" << std::endl;
+    return clearNodes(root_);
+  }
+  int nodes() {
+    // returns number of nodes
+    return cur_nodes_;
+  }
+  int nodeSize() {
+    return sizeof(CacheNode<T>) + sizeof(root_->childs_);
+  }
+private:
+  CacheNode<T> * root_;
+  count_t cur_nodes_;
+  T unknown_value_; // Used to initialise data at each node
+  T null_value_; // Indicates cached something not in model
+  CacheNode<T>* newNode(CacheNode<T> * node = 0) {
+    ++cur_nodes_;
+    return new CacheNode<T>(unknown_value_);
+  }
+  bool clearNodes(CacheNode<T> * node) {
+    //delete children from this node
+    if(!node->childs_.empty()) {
+      iterate(node->childs_, itr) {
+        if(!clearNodes(itr->second))
+          std::cerr << "Error emptying cache\n";
+        delete itr->second;
+        --cur_nodes_;
       }
-      return true;
+      node->childs_.clear();
     }
+    return true;
+  }
 
-  };
+};
 } //end namespace
 #endif //INC_RANDLM_CACHE_H
diff --git a/moses/TranslationModel/DynSAInclude/RandLMFilter.h b/moses/TranslationModel/DynSAInclude/RandLMFilter.h
index 298464693..0923f52af 100644
--- a/moses/TranslationModel/DynSAInclude/RandLMFilter.h
+++ b/moses/TranslationModel/DynSAInclude/RandLMFilter.h
@@ -24,296 +24,307 @@
 #define log2(X) (log((double)X)/log((double)2))
 #endif
 
-namespace randlm {
-  
-  /* Class Filter wraps a contiguous array of data. Filter and its subclasses
-    * implement read/write/increment functionality on arrays with arbitrary sized addresses
-    * (i.e. an address may not use a full number of bytes). When converting to byte-based 
-    * representation we assume "unused" bits are to left. 
-    * E.g. if the underlying data is stored in units T = uint16 and the 'width' = 11
-    * to read 'address' = 3 we extract bits at indices [33,42] (i.e. [11*3, 11*4 - 1])
-    * and store in a uint16 in positions 0000 0001 111111 where the first 7 bits have 
-    * been masked out.
-   */
-  template<typename T>
-  class Filter {
-  public:
-    Filter(uint64_t addresses, int width) : addresses_(addresses), width_(width), data_(NULL) {
-      // number of bits in T
-      cell_width_ = sizeof(T) << 3;  
-      // current implementation has following constraints
-      CHECK(cell_width_ > 0 && cell_width_ <= 64 && cell_width_ >= width);
-      // used for >> division
-      log_cell_width_ = static_cast<int>(floor(log((double)cell_width_)/log((double)2) + 0.000001)); 
-      // size of underlying data in Ts
-      cells_ = ((addresses * width) + cell_width_ - 1) >> log_cell_width_; 
-      // instantiate underlying data
-      data_ = new T[cells_];
-      CHECK(data_ != NULL);
-      CHECK(reset());
-      // 'first_bit' marks the first bit used by 'address' (left padded with zeros).
-      first_bit_ = (width % cell_width_ == 0) ? 0 : cell_width_ - (width % cell_width_);
-      // mask for full cell
-      full_mask_ = static_cast<T>(0xffffffffffffffffull);
-      // mask for bits that make up the address
-      address_mask_ = full_mask_ >> first_bit_;
-    }
-    Filter(FileHandler* fin, bool loaddata = true) : data_(NULL) {
-      CHECK(loadHeader(fin));
-      if (loaddata)
-	CHECK(loadData(fin));
-    }
-    virtual ~Filter() {
-      delete[] data_;
-    }
-    bool reset() {
-      for (uint64_t i = 0; i < cells_; ++i)
-	data_[i] = 0;
+namespace randlm
+{
+
+/* Class Filter wraps a contiguous array of data. Filter and its subclasses
+  * implement read/write/increment functionality on arrays with arbitrary sized addresses
+  * (i.e. an address may not use a full number of bytes). When converting to byte-based
+  * representation we assume "unused" bits are to left.
+  * E.g. if the underlying data is stored in units T = uint16 and the 'width' = 11
+  * to read 'address' = 3 we extract bits at indices [33,42] (i.e. [11*3, 11*4 - 1])
+  * and store in a uint16 in positions 0000 0001 111111 where the first 7 bits have
+  * been masked out.
+ */
+template<typename T>
+class Filter
+{
+public:
+  Filter(uint64_t addresses, int width) : addresses_(addresses), width_(width), data_(NULL) {
+    // number of bits in T
+    cell_width_ = sizeof(T) << 3;
+    // current implementation has following constraints
+    CHECK(cell_width_ > 0 && cell_width_ <= 64 && cell_width_ >= width);
+    // used for >> division
+    log_cell_width_ = static_cast<int>(floor(log((double)cell_width_)/log((double)2) + 0.000001));
+    // size of underlying data in Ts
+    cells_ = ((addresses * width) + cell_width_ - 1) >> log_cell_width_;
+    // instantiate underlying data
+    data_ = new T[cells_];
+    CHECK(data_ != NULL);
+    CHECK(reset());
+    // 'first_bit' marks the first bit used by 'address' (left padded with zeros).
+    first_bit_ = (width % cell_width_ == 0) ? 0 : cell_width_ - (width % cell_width_);
+    // mask for full cell
+    full_mask_ = static_cast<T>(0xffffffffffffffffull);
+    // mask for bits that make up the address
+    address_mask_ = full_mask_ >> first_bit_;
+  }
+  Filter(FileHandler* fin, bool loaddata = true) : data_(NULL) {
+    CHECK(loadHeader(fin));
+    if (loaddata)
+      CHECK(loadData(fin));
+  }
+  virtual ~Filter() {
+    delete[] data_;
+  }
+  bool reset() {
+    for (uint64_t i = 0; i < cells_; ++i)
+      data_[i] = 0;
+    return true;
+  }
+  count_t size() {
+    // return approx size of filter in MBs
+    return cells_ * sizeof(T) >> 20;
+  }
+  // read / write functions
+  inline bool read(uint64_t address, T* value) {
+    CHECK(address <= addresses_);
+    // copy address to 'value'
+    uint64_t data_bit = address * width_;
+    uint32_t data_cell = (data_bit >> log_cell_width_); // % cells_;
+    // 'offset' shows how address in 'data' and 'value' align
+    int offset = (data_bit % cell_width_) - first_bit_;
+    // they align so just copy across masking unneeded leading bits
+    if (offset == 0) {
+      *value = data_[data_cell] & address_mask_;
       return true;
     }
-    count_t size() {
-      // return approx size of filter in MBs
-      return cells_ * sizeof(T) >> 20;
-    }
-    // read / write functions
-    inline bool read(uint64_t address, T* value) {
-      CHECK(address <= addresses_);
-      // copy address to 'value' 
-      uint64_t data_bit = address * width_; 
-      uint32_t data_cell = (data_bit >> log_cell_width_); // % cells_;
-      // 'offset' shows how address in 'data' and 'value' align
-      int offset = (data_bit % cell_width_) - first_bit_;
-      // they align so just copy across masking unneeded leading bits
-      if (offset == 0) {
-	*value = data_[data_cell] & address_mask_;
-	return true;
-      }
-      // data address starts to left so shift it right
-      if (offset < 0) {
-	*value = (data_[data_cell] >> -offset) & address_mask_;
-	return true;
-      }
-      // data address is to right so shift it left and look at one more cell to right
-      *value = ((data_[data_cell] << offset) 
-		| (data_[data_cell + 1] >> (cell_width_ - offset))) & address_mask_ ;
+    // data address starts to left so shift it right
+    if (offset < 0) {
+      *value = (data_[data_cell] >> -offset) & address_mask_;
       return true;
     }
-    inline T read(uint64_t address) {
-      CHECK(address <= addresses_);
-      // return value at address 
-      T value = 0;
-      uint64_t data_bit = address * width_; 
-      uint32_t data_cell = (data_bit >> log_cell_width_); // % cells_;
-      // 'offset' shows how address in 'data' and 'value' align
-      int offset = (data_bit % cell_width_) - first_bit_;
-      // they align so just copy across masking unneeded leading bits
-      if (offset == 0) {
-	value = data_[data_cell] & address_mask_;
-      }
-      // data address starts to left so shift it right
-      else if (offset < 0) {
-	value = (data_[data_cell] >> -offset) & address_mask_;
-      }
-      // data address is to right so shift it left and look at one more cell to right
-      else
-        value = ((data_[data_cell] << offset) 
-	   	  | (data_[data_cell + 1] >> (cell_width_ - offset))) & address_mask_ ;
-      return value;
-    }
-    inline bool write(uint64_t address, T value) {
-      CHECK(address <= addresses_);
-      CHECK(log2(value) <= width_);
-      // write 'value' to address
-      uint64_t data_bit = address * width_; 
-      uint32_t data_cell = (data_bit >> log_cell_width_); // % cells_;
-      // 'offset' shows how address in 'data' and 'value' align
-      int offset = (data_bit % cell_width_) - first_bit_;
-      // they align so just copy across masking unneeded leading zeros of value
-      if (offset == 0) {
-	data_[data_cell] = value | (data_[data_cell] & ~address_mask_); 
-	return true;
-      } 
-      // address in data is to left so shift value left by -offset
-      if (offset < 0) {
-	data_[data_cell] = (value << -offset) 
-	  | (data_[data_cell] & ~(address_mask_ << -offset));
-	return true;
-      }
-      // address in data is to right so shift value right by offset
-      data_[data_cell] = (value >> offset) | 
-	(data_[data_cell] & ~(address_mask_ >> offset));
-      data_[data_cell + 1] = (value << (cell_width_ - offset)) |
-	(data_[data_cell + 1] & (full_mask_ >> offset));
-      return true;
-    }
-    inline bool readWithFingerprint(uint64_t address, T finger, T* value) {
-      // copy 'address' ^ 'finger' to 'value' 
-      uint64_t data_bit = address * width_; 
-      uint32_t data_cell = (data_bit >> log_cell_width_); // % cells_;
-      // 'offset' shows how address in 'data' and 'value' align
-      int offset = (data_bit % cell_width_) - first_bit_;
-      // they align so just copy across masking unneeded leading bits
-      if (offset == 0) {
-	*value = (finger ^ data_[data_cell]) & address_mask_;
-	return true;
-      }
-      // data address starts to left so shift it right
-      if (offset < 0) {
-	*value = ((data_[data_cell] >> -offset) ^ finger) & address_mask_;
-	return true;
-      }
-      // data address is to right so shift it left and look at one more cell to right
-      *value = (((data_[data_cell] << offset) 
-		 | (data_[data_cell + 1] >> (cell_width_ - offset))) ^ finger) 
-	& address_mask_ ;
-      return true;
+    // data address is to right so shift it left and look at one more cell to right
+    *value = ((data_[data_cell] << offset)
+              | (data_[data_cell + 1] >> (cell_width_ - offset))) & address_mask_ ;
+    return true;
+  }
+  inline T read(uint64_t address) {
+    CHECK(address <= addresses_);
+    // return value at address
+    T value = 0;
+    uint64_t data_bit = address * width_;
+    uint32_t data_cell = (data_bit >> log_cell_width_); // % cells_;
+    // 'offset' shows how address in 'data' and 'value' align
+    int offset = (data_bit % cell_width_) - first_bit_;
+    // they align so just copy across masking unneeded leading bits
+    if (offset == 0) {
+      value = data_[data_cell] & address_mask_;
     }
-    inline bool writeWithFingerprint(uint64_t address, T finger, T value) {
-      // write 'value' ^ 'finger' to address
-      finger &= address_mask_; // make sure fingerprint is correct size
-      uint64_t data_bit = address * width_; 
-      uint32_t data_cell = (data_bit >> log_cell_width_); // % cells_;
-      // 'offset' shows how address in 'data' and 'value' align
-      int offset = (data_bit % cell_width_) - first_bit_;
-      // they align so just copy across masking unneeded leading zeros of value
-      if (offset == 0) {
-	data_[data_cell] = (finger ^ value) | (data_[data_cell] & ~address_mask_); 
-	return true;
-      } 
-      // address in data is to left so shift value left by -offset
-      if (offset < 0) {
-	data_[data_cell] = ((finger ^ value) << -offset) 
-	  | (data_[data_cell] & ~(address_mask_ << -offset));
-	return true;
-      }
-      // address in data is to right so shift value right by offset
-      data_[data_cell] = ((finger ^ value) >> offset) | 
-	(data_[data_cell] & ~(address_mask_ >> offset));
-      data_[data_cell + 1] = ((finger ^ value) << (cell_width_ - offset)) |
-	(data_[data_cell + 1] & (full_mask_ >> offset));
-      return true;
-    }    
-    // debugging
-    void printFilter(const std::string & prefix = "", uint32_t truncate = 64){
-      std::cout << prefix;
-      for (uint32_t i = 0; i < cells_ && i < truncate; ++i) {
-	for (int j = cell_width_ - 1; j >= 0; --j)
-	  if (data_[i] & (1ull << j))
-	    std::cout << 1;
-	  else
-	    std::cout << 0;
-	std::cout << "\n";
-      }
-      std::cout << std::endl;
+    // data address starts to left so shift it right
+    else if (offset < 0) {
+      value = (data_[data_cell] >> -offset) & address_mask_;
     }
-    // i/o
-    uint64_t getAddresses() { return addresses_; }
-    int getWidth() { return width_; }
-    int getCellWidth() { return cell_width_; }
-    uint32_t getCells() { return cells_; }
-    virtual bool save(FileHandler* out) {
-      CHECK(out != NULL);
-      CHECK(out->write((char*)&cells_, sizeof(cells_)));
-      CHECK(out->write((char*)&cell_width_, sizeof(cell_width_)));
-      CHECK(out->write((char*)&log_cell_width_, sizeof(log_cell_width_)));
-      CHECK(out->write((char*)&addresses_, sizeof(addresses_)));
-      CHECK(out->write((char*)&width_, sizeof(width_)));
-      CHECK(out->write((char*)&first_bit_, sizeof(first_bit_)));
-      CHECK(out->write((char*)&full_mask_, sizeof(full_mask_)));
-      CHECK(out->write((char*)&address_mask_, sizeof(address_mask_)));
-      //CHECK(out->write((char*)data_, cells_ * sizeof(T)));
-      const uint64_t jump  =  524288032ul; //(uint64_t)pow(2, 29);
-      if((width_ == 1) || cells_ < jump)
-        CHECK(out->write((char*)data_, cells_ * sizeof(T)));
-      else {
-        uint64_t idx(0);
-        while(idx + jump < cells_) {
-          CHECK(out->write((char*)&data_[idx], jump * sizeof(T)));
-          idx += jump;
-        }
-        CHECK(out->write((char*)&data_[idx], (cells_ - idx) * sizeof(T)));
-      }
+    // data address is to right so shift it left and look at one more cell to right
+    else
+      value = ((data_[data_cell] << offset)
+               | (data_[data_cell + 1] >> (cell_width_ - offset))) & address_mask_ ;
+    return value;
+  }
+  inline bool write(uint64_t address, T value) {
+    CHECK(address <= addresses_);
+    CHECK(log2(value) <= width_);
+    // write 'value' to address
+    uint64_t data_bit = address * width_;
+    uint32_t data_cell = (data_bit >> log_cell_width_); // % cells_;
+    // 'offset' shows how address in 'data' and 'value' align
+    int offset = (data_bit % cell_width_) - first_bit_;
+    // they align so just copy across masking unneeded leading zeros of value
+    if (offset == 0) {
+      data_[data_cell] = value | (data_[data_cell] & ~address_mask_);
       return true;
     }
-  protected:
-    bool loadHeader(FileHandler* fin) {
-      CHECK(fin != NULL);
-      CHECK(fin->read((char*)&cells_, sizeof(cells_)));
-      CHECK(fin->read((char*)&cell_width_, sizeof(cell_width_)));
-      CHECK(cell_width_ == sizeof(T) << 3); // make sure correct underlying data type
-      CHECK(fin->read((char*)&log_cell_width_, sizeof(log_cell_width_)));
-      CHECK(fin->read((char*)&addresses_, sizeof(addresses_)));
-      CHECK(fin->read((char*)&width_, sizeof(width_)));
-      CHECK(fin->read((char*)&first_bit_, sizeof(first_bit_)));
-      CHECK(fin->read((char*)&full_mask_, sizeof(full_mask_)));
-      CHECK(fin->read((char*)&address_mask_, sizeof(address_mask_)));
+    // address in data is to left so shift value left by -offset
+    if (offset < 0) {
+      data_[data_cell] = (value << -offset)
+                         | (data_[data_cell] & ~(address_mask_ << -offset));
       return true;
     }
-    bool loadData(FileHandler* fin) {
-      // instantiate underlying array
-      data_ = new T[cells_];
-      CHECK(data_ != NULL);
-      CHECK(fin->read((char*)data_, cells_ * sizeof(T)));
-      //CHECK(fin->read((char*)&data_[0], ceil(float(cells_) / 2.0) * sizeof(T)));
-      //CHECK(fin->read((char*)&data_[cells_ / 2], (cells_ / 2) * sizeof(T)));
+    // address in data is to right so shift value right by offset
+    data_[data_cell] = (value >> offset) |
+                       (data_[data_cell] & ~(address_mask_ >> offset));
+    data_[data_cell + 1] = (value << (cell_width_ - offset)) |
+                           (data_[data_cell + 1] & (full_mask_ >> offset));
+    return true;
+  }
+  inline bool readWithFingerprint(uint64_t address, T finger, T* value) {
+    // copy 'address' ^ 'finger' to 'value'
+    uint64_t data_bit = address * width_;
+    uint32_t data_cell = (data_bit >> log_cell_width_); // % cells_;
+    // 'offset' shows how address in 'data' and 'value' align
+    int offset = (data_bit % cell_width_) - first_bit_;
+    // they align so just copy across masking unneeded leading bits
+    if (offset == 0) {
+      *value = (finger ^ data_[data_cell]) & address_mask_;
       return true;
     }
-    uint64_t cells_;  // number T making up 'data_'
-    int cell_width_;  // bits per cell (i.e. sizeof(T) << 3)
-    int log_cell_width_;  // log of bits used for >> division
-    uint64_t addresses_;  // number of addresses in the filter
-    int width_;  // width in bits of each address
-    int first_bit_;  // position of first bit in initial byte 
-    T full_mask_;  // all 1s
-    T address_mask_;  // 1s in those positions that are part of address
-    T* data_;  // the raw data as bytes
-  };
-
-  // Extension with bit test/setter methods added 
-  class BitFilter : public Filter<uint8_t> {
-  public:
-    BitFilter(uint64_t bits) : Filter<uint8_t>(bits, 1) {}
-    BitFilter(FileHandler* fin, bool loaddata = true) 
-      : Filter<uint8_t>(fin, loaddata) {
-      if (loaddata)
-	CHECK(load(fin));
-    }
-    // TODO: overload operator[]
-    virtual bool testBit(uint64_t location) {
-      // test bit referenced by location
-      return data_[(location % addresses_) >> 3] & 1 << ((location % addresses_) % 8);
-    }
-    virtual bool setBit(uint64_t location) {
-      // set bit referenced by location
-      data_[(location % addresses_) >> 3] |= 1 << ((location % addresses_) % 8);
+    // data address starts to left so shift it right
+    if (offset < 0) {
+      *value = ((data_[data_cell] >> -offset) ^ finger) & address_mask_;
       return true;
     }
-    virtual bool clearBit(uint64_t location) {
-      // set bit referenced by location
-      data_[(location % addresses_) >> 3] &= 0 << ((location % addresses_) % 8);
+    // data address is to right so shift it left and look at one more cell to right
+    *value = (((data_[data_cell] << offset)
+               | (data_[data_cell + 1] >> (cell_width_ - offset))) ^ finger)
+             & address_mask_ ;
+    return true;
+  }
+  inline bool writeWithFingerprint(uint64_t address, T finger, T value) {
+    // write 'value' ^ 'finger' to address
+    finger &= address_mask_; // make sure fingerprint is correct size
+    uint64_t data_bit = address * width_;
+    uint32_t data_cell = (data_bit >> log_cell_width_); // % cells_;
+    // 'offset' shows how address in 'data' and 'value' align
+    int offset = (data_bit % cell_width_) - first_bit_;
+    // they align so just copy across masking unneeded leading zeros of value
+    if (offset == 0) {
+      data_[data_cell] = (finger ^ value) | (data_[data_cell] & ~address_mask_);
       return true;
     }
-    bool save(FileHandler* fout) {
-      CHECK(Filter<uint8_t>::save(fout));
-      std::cerr << "Saved BitFilter. Rho = " << rho() << "." << std::endl;;
+    // address in data is to left so shift value left by -offset
+    if (offset < 0) {
+      data_[data_cell] = ((finger ^ value) << -offset)
+                         | (data_[data_cell] & ~(address_mask_ << -offset));
       return true;
     }
-    float rho(uint64_t limit = 0) {
-      uint64_t ones = 0;
-      uint64_t range = limit > 0 ? std::min(limit,cells_) : cells_;
-      for (uint64_t i = 0; i < range; ++i)
-	for (int j = 0; j < 8; ++j)
-	  if (data_[i] & (1 << j))
-	    ++ones;
-      return static_cast<float>((range << 3) - ones)/static_cast<float>(range << 3);
+    // address in data is to right so shift value right by offset
+    data_[data_cell] = ((finger ^ value) >> offset) |
+                       (data_[data_cell] & ~(address_mask_ >> offset));
+    data_[data_cell + 1] = ((finger ^ value) << (cell_width_ - offset)) |
+                           (data_[data_cell + 1] & (full_mask_ >> offset));
+    return true;
+  }
+  // debugging
+  void printFilter(const std::string & prefix = "", uint32_t truncate = 64) {
+    std::cout << prefix;
+    for (uint32_t i = 0; i < cells_ && i < truncate; ++i) {
+      for (int j = cell_width_ - 1; j >= 0; --j)
+        if (data_[i] & (1ull << j))
+          std::cout << 1;
+        else
+          std::cout << 0;
+      std::cout << "\n";
     }
-  protected:
-    bool load(FileHandler* fin) {
-      std::cerr << "Loaded BitFilter. Rho = " << rho() << "." << std::endl;;
-      return true;
+    std::cout << std::endl;
+  }
+  // i/o
+  uint64_t getAddresses() {
+    return addresses_;
+  }
+  int getWidth() {
+    return width_;
+  }
+  int getCellWidth() {
+    return cell_width_;
+  }
+  uint32_t getCells() {
+    return cells_;
+  }
+  virtual bool save(FileHandler* out) {
+    CHECK(out != NULL);
+    CHECK(out->write((char*)&cells_, sizeof(cells_)));
+    CHECK(out->write((char*)&cell_width_, sizeof(cell_width_)));
+    CHECK(out->write((char*)&log_cell_width_, sizeof(log_cell_width_)));
+    CHECK(out->write((char*)&addresses_, sizeof(addresses_)));
+    CHECK(out->write((char*)&width_, sizeof(width_)));
+    CHECK(out->write((char*)&first_bit_, sizeof(first_bit_)));
+    CHECK(out->write((char*)&full_mask_, sizeof(full_mask_)));
+    CHECK(out->write((char*)&address_mask_, sizeof(address_mask_)));
+    //CHECK(out->write((char*)data_, cells_ * sizeof(T)));
+    const uint64_t jump  =  524288032ul; //(uint64_t)pow(2, 29);
+    if((width_ == 1) || cells_ < jump)
+      CHECK(out->write((char*)data_, cells_ * sizeof(T)));
+    else {
+      uint64_t idx(0);
+      while(idx + jump < cells_) {
+        CHECK(out->write((char*)&data_[idx], jump * sizeof(T)));
+        idx += jump;
+      }
+      CHECK(out->write((char*)&data_[idx], (cells_ - idx) * sizeof(T)));
     }
-  };
-/* 
+    return true;
+  }
+protected:
+  bool loadHeader(FileHandler* fin) {
+    CHECK(fin != NULL);
+    CHECK(fin->read((char*)&cells_, sizeof(cells_)));
+    CHECK(fin->read((char*)&cell_width_, sizeof(cell_width_)));
+    CHECK(cell_width_ == sizeof(T) << 3); // make sure correct underlying data type
+    CHECK(fin->read((char*)&log_cell_width_, sizeof(log_cell_width_)));
+    CHECK(fin->read((char*)&addresses_, sizeof(addresses_)));
+    CHECK(fin->read((char*)&width_, sizeof(width_)));
+    CHECK(fin->read((char*)&first_bit_, sizeof(first_bit_)));
+    CHECK(fin->read((char*)&full_mask_, sizeof(full_mask_)));
+    CHECK(fin->read((char*)&address_mask_, sizeof(address_mask_)));
+    return true;
+  }
+  bool loadData(FileHandler* fin) {
+    // instantiate underlying array
+    data_ = new T[cells_];
+    CHECK(data_ != NULL);
+    CHECK(fin->read((char*)data_, cells_ * sizeof(T)));
+    //CHECK(fin->read((char*)&data_[0], ceil(float(cells_) / 2.0) * sizeof(T)));
+    //CHECK(fin->read((char*)&data_[cells_ / 2], (cells_ / 2) * sizeof(T)));
+    return true;
+  }
+  uint64_t cells_;  // number T making up 'data_'
+  int cell_width_;  // bits per cell (i.e. sizeof(T) << 3)
+  int log_cell_width_;  // log of bits used for >> division
+  uint64_t addresses_;  // number of addresses in the filter
+  int width_;  // width in bits of each address
+  int first_bit_;  // position of first bit in initial byte
+  T full_mask_;  // all 1s
+  T address_mask_;  // 1s in those positions that are part of address
+  T* data_;  // the raw data as bytes
+};
+
+// Extension with bit test/setter methods added
+class BitFilter : public Filter<uint8_t>
+{
+public:
+  BitFilter(uint64_t bits) : Filter<uint8_t>(bits, 1) {}
+  BitFilter(FileHandler* fin, bool loaddata = true)
+    : Filter<uint8_t>(fin, loaddata) {
+    if (loaddata)
+      CHECK(load(fin));
+  }
+  // TODO: overload operator[]
+  virtual bool testBit(uint64_t location) {
+    // test bit referenced by location
+    return data_[(location % addresses_) >> 3] & 1 << ((location % addresses_) % 8);
+  }
+  virtual bool setBit(uint64_t location) {
+    // set bit referenced by location
+    data_[(location % addresses_) >> 3] |= 1 << ((location % addresses_) % 8);
+    return true;
+  }
+  virtual bool clearBit(uint64_t location) {
+    // set bit referenced by location
+    data_[(location % addresses_) >> 3] &= 0 << ((location % addresses_) % 8);
+    return true;
+  }
+  bool save(FileHandler* fout) {
+    CHECK(Filter<uint8_t>::save(fout));
+    std::cerr << "Saved BitFilter. Rho = " << rho() << "." << std::endl;;
+    return true;
+  }
+  float rho(uint64_t limit = 0) {
+    uint64_t ones = 0;
+    uint64_t range = limit > 0 ? std::min(limit,cells_) : cells_;
+    for (uint64_t i = 0; i < range; ++i)
+      for (int j = 0; j < 8; ++j)
+        if (data_[i] & (1 << j))
+          ++ones;
+    return static_cast<float>((range << 3) - ones)/static_cast<float>(range << 3);
+  }
+protected:
+  bool load(FileHandler* fin) {
+    std::cerr << "Loaded BitFilter. Rho = " << rho() << "." << std::endl;;
+    return true;
+  }
+};
+/*
   // ResizedBitFilter deals with resizing to save memory
   // whereas other filters should expect locations to be within range
   // this filter will need to resize (and possibly rehash) locations
@@ -385,9 +396,9 @@ namespace randlm {
 	carry = incrementSubCell(data_bit, this->width_, &this->data_[data_cell]);
       }
       // last update must not have carried
-      if (!carry) 
+      if (!carry)
 	return true;
-      // wrapped round so check whether need to reset to max count 
+      // wrapped round so check whether need to reset to max count
       if (!wrap_around_)
 	CHECK(this->write(address, this->address_mask_));
       return false; // false to indicate that overflowed
@@ -402,7 +413,7 @@ namespace randlm {
     }
     inline bool incrementSubCell(int bit, int len, T* cell) {
       // increment counter consisting of bits [startbit, startbit + len - 1] rest stays unchanged
-      *cell = ((((*cell >> (this->cell_width_ - bit - len)) + 1) 
+      *cell = ((((*cell >> (this->cell_width_ - bit - len)) + 1)
 		& (this->full_mask_ >> (this->cell_width_ - len))) << (this->cell_width_ - bit - len))
 	| (*cell & ~(((this->full_mask_ >> (this->cell_width_ - len)) << (this->cell_width_ - bit - len))));
       // indicate overflow as true
diff --git a/moses/TranslationModel/DynSAInclude/hash.h b/moses/TranslationModel/DynSAInclude/hash.h
index 03669845e..9e6cfe62a 100644
--- a/moses/TranslationModel/DynSAInclude/hash.h
+++ b/moses/TranslationModel/DynSAInclude/hash.h
@@ -11,60 +11,68 @@ typedef uint64_t P;   // largest input range is 2^64
 
 //! @todo ask abby2
 template <typename T>
-class HashBase {
-  protected:
-    T m_;       // range of hash output
-    count_t H_; // number of hash functions to instantiate
-    virtual void initSeeds()=0;
-    virtual void freeSeeds()=0;
-  public:
-    HashBase(float m, count_t H=1):m_((T)m), H_(H) {
-      //cerr << "range = (0..." << m_ << "]" << endl;
-    }
-    HashBase(FileHandler* fin) {
-      load(fin);
-    }
-    virtual ~HashBase(){}
-    virtual T hash(const char*s, count_t h)=0;  // string hashing
-    virtual T hash(const wordID_t* id, const int len, count_t h)=0;  // vocab mapped hashing
-    count_t size() { return H_;}
-    virtual void save(FileHandler* fout) {
-      CHECK(fout != 0);
-      fout->write((char*)&m_, sizeof(m_));
-      fout->write((char*)&H_, sizeof(H_));
-    }
-    virtual void load(FileHandler* fin) {
-      CHECK(fin != 0);
-      fin->read((char*)&m_, sizeof(m_));
-      fin->read((char*)&H_, sizeof(H_));
-    }
+class HashBase
+{
+protected:
+  T m_;       // range of hash output
+  count_t H_; // number of hash functions to instantiate
+  virtual void initSeeds()=0;
+  virtual void freeSeeds()=0;
+public:
+  HashBase(float m, count_t H=1):m_((T)m), H_(H) {
+    //cerr << "range = (0..." << m_ << "]" << endl;
+  }
+  HashBase(FileHandler* fin) {
+    load(fin);
+  }
+  virtual ~HashBase() {}
+  virtual T hash(const char*s, count_t h)=0;  // string hashing
+  virtual T hash(const wordID_t* id, const int len, count_t h)=0;  // vocab mapped hashing
+  count_t size() {
+    return H_;
+  }
+  virtual void save(FileHandler* fout) {
+    CHECK(fout != 0);
+    fout->write((char*)&m_, sizeof(m_));
+    fout->write((char*)&H_, sizeof(H_));
+  }
+  virtual void load(FileHandler* fin) {
+    CHECK(fin != 0);
+    fin->read((char*)&m_, sizeof(m_));
+    fin->read((char*)&H_, sizeof(H_));
+  }
 };
 
 //! @todo ask abby2
 template <typename T>
-class UnivHash_linear: public HashBase<T> {
-  public:
-    UnivHash_linear(float m, count_t H, P pr):
-      HashBase<T>(m, H), pr_(pr) {
-      //CHECK(isPrime(pr_));
-      initSeeds();
-    }
-    UnivHash_linear(FileHandler* fin):
-      HashBase<T>(fin) {
-      load(fin);
-    }
-    ~UnivHash_linear() {freeSeeds();}
-    T hash(const char* s, count_t h){return 0;}  //not implemented
-    T hash(const wordID_t* id, const int len, count_t h);
-    T hash(const wordID_t id, const count_t pos, 
-           const T prevValue, count_t h);
-    void save(FileHandler* fout);
-    void load(FileHandler* fin);
-  private:
-    T** a_, **b_;
-    P pr_;
-    void initSeeds();
-    void freeSeeds(); 
+class UnivHash_linear: public HashBase<T>
+{
+public:
+  UnivHash_linear(float m, count_t H, P pr):
+    HashBase<T>(m, H), pr_(pr) {
+    //CHECK(isPrime(pr_));
+    initSeeds();
+  }
+  UnivHash_linear(FileHandler* fin):
+    HashBase<T>(fin) {
+    load(fin);
+  }
+  ~UnivHash_linear() {
+    freeSeeds();
+  }
+  T hash(const char* s, count_t h) {
+    return 0; //not implemented
+  }
+  T hash(const wordID_t* id, const int len, count_t h);
+  T hash(const wordID_t id, const count_t pos,
+         const T prevValue, count_t h);
+  void save(FileHandler* fout);
+  void load(FileHandler* fin);
+private:
+  T** a_, **b_;
+  P pr_;
+  void initSeeds();
+  void freeSeeds();
 };
 
 /** UnivHash_noPrimes:
@@ -74,76 +82,91 @@ class UnivHash_linear: public HashBase<T> {
  * # of hash function = 2^(l-1)
  */
 template <typename T>
-class UnivHash_noPrimes: public HashBase<T> {
-  public:
-    UnivHash_noPrimes(float k, float l): 
-      HashBase<T>(k, 100), d_(count_t((l-k))) {
-      if(((int)l >> 3) == sizeof(P)) p_ = (P) pow(2,l) - 1;
-      else p_ = (P) pow(2,l);
-      initSeeds();
-    }
-    UnivHash_noPrimes(FileHandler* fin):
-     HashBase<T>(fin) {
-     load(fin);
-    }
-    ~UnivHash_noPrimes() {freeSeeds();}
-    T hash(const char* s, count_t h);
-    T hash(const wordID_t* id, const int len, count_t h);
-    T hash(const P x, count_t h);
-    void save(FileHandler* fout);
-    void load(FileHandler* fin);
-  private:
-    count_t d_;  // l-k
-    P p_, *a_;   // real-valued input range, storage
-    void initSeeds();
-    void freeSeeds() {delete[] a_;}
+class UnivHash_noPrimes: public HashBase<T>
+{
+public:
+  UnivHash_noPrimes(float k, float l):
+    HashBase<T>(k, 100), d_(count_t((l-k))) {
+    if(((int)l >> 3) == sizeof(P)) p_ = (P) pow(2,l) - 1;
+    else p_ = (P) pow(2,l);
+    initSeeds();
+  }
+  UnivHash_noPrimes(FileHandler* fin):
+    HashBase<T>(fin) {
+    load(fin);
+  }
+  ~UnivHash_noPrimes() {
+    freeSeeds();
+  }
+  T hash(const char* s, count_t h);
+  T hash(const wordID_t* id, const int len, count_t h);
+  T hash(const P x, count_t h);
+  void save(FileHandler* fout);
+  void load(FileHandler* fin);
+private:
+  count_t d_;  // l-k
+  P p_, *a_;   // real-valued input range, storage
+  void initSeeds();
+  void freeSeeds() {
+    delete[] a_;
+  }
 };
 
 //! @todo ask abby2
 template <typename T>
-class Hash_shiftAddXOR: public HashBase<T> {
-  public:
-    Hash_shiftAddXOR(float m, count_t H=5): HashBase<T>(m,H),
-      l_(5), r_(2) {
-      initSeeds();
-    }
-    ~Hash_shiftAddXOR() {freeSeeds();}
-    T hash(const char* s, count_t h);
-    T hash(const wordID_t* id, const int len, count_t h) {} // empty
-  private:
-    T* v_;      // random seed storage
-    const unsigned short l_, r_; // left-shift bits, right-shift bits
-    void initSeeds();
-    void freeSeeds() {delete[] v_;}
+class Hash_shiftAddXOR: public HashBase<T>
+{
+public:
+  Hash_shiftAddXOR(float m, count_t H=5): HashBase<T>(m,H),
+    l_(5), r_(2) {
+    initSeeds();
+  }
+  ~Hash_shiftAddXOR() {
+    freeSeeds();
+  }
+  T hash(const char* s, count_t h);
+  T hash(const wordID_t* id, const int len, count_t h) {} // empty
+private:
+  T* v_;      // random seed storage
+  const unsigned short l_, r_; // left-shift bits, right-shift bits
+  void initSeeds();
+  void freeSeeds() {
+    delete[] v_;
+  }
 };
 
 //! @todo ask abby2
 template <typename T>
-class UnivHash_tableXOR: public HashBase<T> {
-  public:
-    UnivHash_tableXOR(float m, count_t H=5): HashBase<T>(m, H),
-      table_(NULL), tblLen_(255*MAX_STR_LEN) {
-      initSeeds();
-    }
-    ~UnivHash_tableXOR() {freeSeeds();}
-    T hash(const char* s, count_t h);
-    T hash(const wordID_t* id, const int len, count_t h) {}
-  private:
-    T** table_; // storage for random numbers
-    count_t tblLen_;     // length of table
-    void initSeeds();
-    void freeSeeds(); 
+class UnivHash_tableXOR: public HashBase<T>
+{
+public:
+  UnivHash_tableXOR(float m, count_t H=5): HashBase<T>(m, H),
+    table_(NULL), tblLen_(255*MAX_STR_LEN) {
+    initSeeds();
+  }
+  ~UnivHash_tableXOR() {
+    freeSeeds();
+  }
+  T hash(const char* s, count_t h);
+  T hash(const wordID_t* id, const int len, count_t h) {}
+private:
+  T** table_; // storage for random numbers
+  count_t tblLen_;     // length of table
+  void initSeeds();
+  void freeSeeds();
 };
 
 // ShiftAddXor
 template <typename T>
-void Hash_shiftAddXOR<T>::initSeeds() {
+void Hash_shiftAddXOR<T>::initSeeds()
+{
   v_ = new T[this->H_];
   for(count_t i=0; i < this->H_; i++)
-    v_[i] = Utils::rand<T>() + 1; 
+    v_[i] = Utils::rand<T>() + 1;
 }
 template <typename T>
-T Hash_shiftAddXOR<T>::hash(const char* s, count_t h) {
+T Hash_shiftAddXOR<T>::hash(const char* s, count_t h)
+{
   T value = v_[h];
   int pos(0);
   unsigned char c;
@@ -155,40 +178,44 @@ T Hash_shiftAddXOR<T>::hash(const char* s, count_t h) {
 
 // UnivHash_tableXOR
 template <typename T>
-void UnivHash_tableXOR<T>::initSeeds() {
+void UnivHash_tableXOR<T>::initSeeds()
+{
   // delete any values in table
-  if(table_) freeSeeds(); 
+  if(table_) freeSeeds();
   // instance of new table
   table_ = new T* [this->H_];
   // fill with random values
   for(count_t j=0; j < this->H_; j++) {
     table_[j] = new T[tblLen_];
-    for(count_t i=0; i < tblLen_; i++) { 
-      table_[j][i] = Utils::rand<T>(this->m_-1); 
+    for(count_t i=0; i < tblLen_; i++) {
+      table_[j][i] = Utils::rand<T>(this->m_-1);
     }
   }
 }
 template <typename T>
-void UnivHash_tableXOR<T>::freeSeeds() {
+void UnivHash_tableXOR<T>::freeSeeds()
+{
   for(count_t j = 0; j < this->H_; j++)
     delete[] table_[j];
   delete[] table_;
   table_ = NULL;
 }
 template <typename T>
-T UnivHash_tableXOR<T>::hash(const char* s, count_t h) {  
+T UnivHash_tableXOR<T>::hash(const char* s, count_t h)
+{
   T value = 0;
   count_t pos = 0, idx = 0;
   unsigned char c;
   while((c = *s++) && (++pos < MAX_STR_LEN))
     value ^= table_[h][idx += c];
-  CHECK(value < this->m_); 
+  CHECK(value < this->m_);
   return value;
 }
 
 // UnivHash_noPrimes
 template <typename T>
-void UnivHash_noPrimes<T>::initSeeds() {
+void UnivHash_noPrimes<T>::initSeeds()
+{
   a_ = new P[this->H_];
   for(T i=0; i < this->H_; i++) {
     a_[i] = Utils::rand<P>();
@@ -196,14 +223,16 @@ void UnivHash_noPrimes<T>::initSeeds() {
   }
 }
 template <typename T>
-T UnivHash_noPrimes<T>::hash(const P x, count_t h) {
+T UnivHash_noPrimes<T>::hash(const P x, count_t h)
+{
   // h_a(x) = (ax mod 2^l) div 2^(l-k)
   T value = ((a_[h] * x) % p_) >> d_;
   return value % this->m_;
 }
 template <typename T>
-T UnivHash_noPrimes<T>::hash(const wordID_t* id, const int len, 
-  count_t h) {
+T UnivHash_noPrimes<T>::hash(const wordID_t* id, const int len,
+                             count_t h)
+{
   T value = 0;
   int pos(0);
   while(pos < len) {
@@ -213,39 +242,42 @@ T UnivHash_noPrimes<T>::hash(const wordID_t* id, const int len,
   return value % this->m_;
 }
 template <typename T>
-T UnivHash_noPrimes<T>::hash(const char* s, count_t h) {
+T UnivHash_noPrimes<T>::hash(const char* s, count_t h)
+{
   T value = 0;
   int pos(0);
   unsigned char c;
   while((c = *s++) && (++pos < MAX_STR_LEN)) {
-    value ^= hash((P)c, h); 
+    value ^= hash((P)c, h);
   }
   return value % this->m_;
 }
 template <typename T>
-void UnivHash_noPrimes<T>::save(FileHandler* fout) {
+void UnivHash_noPrimes<T>::save(FileHandler* fout)
+{
   HashBase<T>::save(fout);
   fout->write((char*)&p_, sizeof(p_));
   fout->write((char*)&d_, sizeof(d_));
-  for(T i=0; i < this->H_; i++) { 
+  for(T i=0; i < this->H_; i++) {
     fout->write((char*)&a_[i], sizeof(a_[i]));
   }
 }
 template <typename T>
-void UnivHash_noPrimes<T>::load(FileHandler* fin) {
+void UnivHash_noPrimes<T>::load(FileHandler* fin)
+{
   a_ = new P[this->H_];
   // HashBase<T>::load(fin) already done in constructor
   fin->read((char*)&p_, sizeof(p_));
   fin->read((char*)&d_, sizeof(d_));
-  for(T i=0; i < this->H_; i++) 
-  { 
+  for(T i=0; i < this->H_; i++) {
     fin->read((char*)&a_[i], sizeof(a_[i]));
   }
 }
 
 //UnivHash_linear
 template <typename T>
-void UnivHash_linear<T>::initSeeds() {
+void UnivHash_linear<T>::initSeeds()
+{
   a_ = new T*[this->H_];
   b_ = new T*[this->H_];
   for(count_t i=0; i < this->H_; i++) {
@@ -258,7 +290,8 @@ void UnivHash_linear<T>::initSeeds() {
   }
 }
 template <typename T>
-void UnivHash_linear<T>::freeSeeds() {
+void UnivHash_linear<T>::freeSeeds()
+{
   for(count_t i=0; i < this->H_; i++) {
     delete[] a_[i];
     delete[] b_[i];
@@ -268,8 +301,9 @@ void UnivHash_linear<T>::freeSeeds() {
   a_ = b_ = NULL;
 }
 template <typename T>
-inline T UnivHash_linear<T>::hash(const wordID_t* id, const int len, 
-                           count_t h) {
+inline T UnivHash_linear<T>::hash(const wordID_t* id, const int len,
+                                  count_t h)
+{
   CHECK(h < this->H_);
   T value = 0;
   int pos(0);
@@ -281,19 +315,21 @@ inline T UnivHash_linear<T>::hash(const wordID_t* id, const int len,
 }
 template <typename T>
 inline T UnivHash_linear<T>::hash(const wordID_t id, const count_t pos,
-                           const T prevValue, count_t h) {
+                                  const T prevValue, count_t h)
+{
   CHECK(h < this->H_);
   T value = prevValue + ((a_[h][pos] * id) + b_[h][pos]); // % pr_;
   return value % this->m_;
 }
 template <typename T>
-void UnivHash_linear<T>::save(FileHandler* fout) {
+void UnivHash_linear<T>::save(FileHandler* fout)
+{
   // int bytes = sizeof(a_[0][0]);
   HashBase<T>::save(fout);
   fout->write((char*)&pr_, sizeof(pr_));
   for(count_t i=0; i < this->H_; i++) {
     for(count_t j=0; j < MAX_NGRAM_ORDER; j++) {
-      fout->write((char*)&a_[i][j], sizeof(a_[i][j])); 
+      fout->write((char*)&a_[i][j], sizeof(a_[i][j]));
       fout->write((char*)&b_[i][j], sizeof(b_[i][j]));
       //cout << "a[" << i << "][" << j << "]=" << a_[i][j] << endl;
       //cout << "b[" << i << "][" << j << "]=" << b_[i][j] << endl;
@@ -301,7 +337,8 @@ void UnivHash_linear<T>::save(FileHandler* fout) {
   }
 }
 template <typename T>
-void UnivHash_linear<T>::load(FileHandler* fin) {
+void UnivHash_linear<T>::load(FileHandler* fin)
+{
   // HashBase<T>::load(fin) already done in constructor
   fin->read((char*)&pr_, sizeof(pr_));
   a_ = new T*[this->H_];
@@ -310,8 +347,8 @@ void UnivHash_linear<T>::load(FileHandler* fin) {
     a_[i] = new T[MAX_NGRAM_ORDER];
     b_[i] = new T[MAX_NGRAM_ORDER];
     for(count_t j=0; j < MAX_NGRAM_ORDER; j++) {
-      fin->read((char*)&a_[i][j], sizeof(a_[i][j])); 
-      fin->read((char*)&b_[i][j], sizeof(b_[i][j])); 
+      fin->read((char*)&a_[i][j], sizeof(a_[i][j]));
+      fin->read((char*)&b_[i][j], sizeof(b_[i][j]));
       //cout << "a[" << i << "][" << j << "]=" << a_[i][j] << endl;
       //cout << "b[" << i << "][" << j << "]=" << b_[i][j] << endl;
     }
diff --git a/moses/TranslationModel/DynSAInclude/onlineRLM.h b/moses/TranslationModel/DynSAInclude/onlineRLM.h
index b47cfdd0e..527f1e5d9 100644
--- a/moses/TranslationModel/DynSAInclude/onlineRLM.h
+++ b/moses/TranslationModel/DynSAInclude/onlineRLM.h
@@ -18,27 +18,28 @@ const bool strict_checks_ = false;
 
 //! @todo ask abby2
 template<typename T>
-class OnlineRLM: public PerfectHash<T> {
+class OnlineRLM: public PerfectHash<T>
+{
 public:
-  OnlineRLM(uint16_t MBs, int width, int bucketRange, count_t order, 
-    Moses::Vocab* v, float qBase = 8): PerfectHash<T>(MBs, width, bucketRange, qBase), 
+  OnlineRLM(uint16_t MBs, int width, int bucketRange, count_t order,
+            Moses::Vocab* v, float qBase = 8): PerfectHash<T>(MBs, width, bucketRange, qBase),
     vocab_(v), bAdapting_(false), order_(order), corpusSize_(0), alpha_(0) {
     CHECK(vocab_ != 0);
     //instantiate quantizer class here
     cache_ = new Cache<float>(8888.8888, 9999.9999); // unknown_value, null_value
     alpha_ = new float[order_ + 1];
-    for(count_t i = 0; i <= order_; ++i) 
+    for(count_t i = 0; i <= order_; ++i)
       alpha_[i] = i * log10(0.4);
     cerr << "Initialzing auxillary bit filters...\n";
     bPrefix_ = new BitFilter(this->cells_);
     bHit_ = new BitFilter(this->cells_);
   }
-  OnlineRLM(FileHandler* fin, count_t order): 
+  OnlineRLM(FileHandler* fin, count_t order):
     PerfectHash<T>(fin), bAdapting_(true), order_(order), corpusSize_(0) {
     load(fin);
     cache_ = new Cache<float>(8888.8888, 9999.9999); // unknown_value, null_value
     alpha_ = new float[order_ + 1];
-    for(count_t i = 0; i <= order_; ++i) 
+    for(count_t i = 0; i <= order_; ++i)
       alpha_[i] = i * log10(0.4);
   }
   ~OnlineRLM() {
@@ -54,14 +55,18 @@ public:
   bool insert(const std::vector<string>& ngram, const int value);
   bool update(const std::vector<string>& ngram, const int value);
   int query(const wordID_t* IDs, const int len);
-  int sbsqQuery(const std::vector<string>& ngram, int* len, 
-    bool bStrict = false);
-  int sbsqQuery(const wordID_t* IDs, const int len, int* codes, 
-    bool bStrict = false);
+  int sbsqQuery(const std::vector<string>& ngram, int* len,
+                bool bStrict = false);
+  int sbsqQuery(const wordID_t* IDs, const int len, int* codes,
+                bool bStrict = false);
   void remove(const std::vector<string>& ngram);
   count_t heurDelete(count_t num2del, count_t order = 5);
-  uint64_t corpusSize() {return corpusSize_;}
-  void corpusSize(uint64_t c) {corpusSize_ = c;}
+  uint64_t corpusSize() {
+    return corpusSize_;
+  }
+  void corpusSize(uint64_t c) {
+    corpusSize_ = c;
+  }
   void clearCache() {
     if(cache_) cache_->clear();
   }
@@ -79,7 +84,7 @@ protected:
   void markQueried(hpdEntry_t& value);
   bool markPrefix(const wordID_t* IDs, const int len, bool bSet);
 private:
-  const void* getContext(const wordID_t* ngram, int len); 
+  const void* getContext(const wordID_t* ngram, int len);
   const bool bAdapting_; // used to signal adaptation of model
   const count_t order_; // LM order
   uint64_t corpusSize_; // total training corpus size
@@ -90,48 +95,50 @@ private:
 };
 
 template<typename T>
-bool OnlineRLM<T>::insert(const std::vector<string>& ngram, const int value) {
+bool OnlineRLM<T>::insert(const std::vector<string>& ngram, const int value)
+{
   int len = ngram.size();
   wordID_t wrdIDs[len];
   uint64_t index(this->cells_ + 1);
-  for(int i = 0; i < len; ++i) 
+  for(int i = 0; i < len; ++i)
     wrdIDs[i] = vocab_->GetWordID(ngram[i]);
   index = PerfectHash<T>::insert(wrdIDs, len, value);
   if(value > 1 && len < order_)
     markPrefix(wrdIDs, ngram.size(), true); // mark context
   // keep track of total items from training data minus "<s>"
-  if(ngram.size() == 1 && (!bAdapting_)) // hack to not change corpusSize when adapting 
+  if(ngram.size() == 1 && (!bAdapting_)) // hack to not change corpusSize when adapting
     corpusSize_ += (wrdIDs[0] != vocab_->GetBOSWordID()) ? value : 0;
-  if(bAdapting_ && (index < this->cells_)) // mark to keep while adapting  
+  if(bAdapting_ && (index < this->cells_)) // mark to keep while adapting
     markQueried(index);
   return true;
 }
 
 template<typename T>
-bool OnlineRLM<T>::update(const std::vector<string>& ngram, const int value) {
+bool OnlineRLM<T>::update(const std::vector<string>& ngram, const int value)
+{
   int len = ngram.size();
   std::vector<wordID_t> wrdIDs(len);
   uint64_t index(this->cells_ + 1);
   hpdEntry_t hpdItr;
   vocab_->MakeOpen();
-  for(int i = 0; i < len; ++i) 
+  for(int i = 0; i < len; ++i)
     wrdIDs[i] = vocab_->GetWordID(ngram[i]);
-  // if updating, minimize false positives by pre-checking if context already in model 
-  bool bIncluded(true); 
+  // if updating, minimize false positives by pre-checking if context already in model
+  bool bIncluded(true);
   if(value > 1 && len < (int)order_)
     bIncluded = markPrefix(&wrdIDs[0], ngram.size(), true); // mark context
-  if(bIncluded) { // if context found 
+  if(bIncluded) { // if context found
     bIncluded = PerfectHash<T>::update2(&wrdIDs[0], len, value, hpdItr, index);
     if(index < this->cells_) {
       markQueried(index);
-    }
-    else if(hpdItr != this->dict_.end()) markQueried(hpdItr);
+    } else if(hpdItr != this->dict_.end()) markQueried(hpdItr);
   }
 
   return bIncluded;
 }
 template<typename T>
-int OnlineRLM<T>::query(const wordID_t* IDs, int len) {
+int OnlineRLM<T>::query(const wordID_t* IDs, int len)
+{
   uint64_t filterIdx = 0;
   hpdEntry_t hpdItr;
   int value(0);
@@ -140,8 +147,7 @@ int OnlineRLM<T>::query(const wordID_t* IDs, int len) {
     if(hpdItr != this->dict_.end()) {
       //markQueried(hpdItr);  // mark this event as "hit"
       value -= ((value & this->hitMask_) != 0) ? this->hitMask_ : 0; // check for previous hit marks
-    }
-    else {
+    } else {
       CHECK(filterIdx < this->cells_);
       //markQueried(filterIdx);
     }
@@ -150,15 +156,16 @@ int OnlineRLM<T>::query(const wordID_t* IDs, int len) {
 }
 
 template<typename T>
-bool OnlineRLM<T>::markPrefix(const wordID_t* IDs, const int len, bool bSet) {
-  if(len <= 1) return true; // only do this for for ngrams with context 
-  static Cache<int> pfCache(-1, -1); // local prefix cache 
+bool OnlineRLM<T>::markPrefix(const wordID_t* IDs, const int len, bool bSet)
+{
+  if(len <= 1) return true; // only do this for for ngrams with context
+  static Cache<int> pfCache(-1, -1); // local prefix cache
   int code(0);
-  if(!pfCache.checkCacheNgram(IDs, len - 1, &code, NULL)) { 
-    hpdEntry_t hpdItr; 
+  if(!pfCache.checkCacheNgram(IDs, len - 1, &code, NULL)) {
+    hpdEntry_t hpdItr;
     uint64_t filterIndex(0);
     code = PerfectHash<T>::query(IDs, len - 1, hpdItr, filterIndex); // hash IDs[0..len-1]
-    if(code == -1) { // encountered false positive in pipeline  
+    if(code == -1) { // encountered false positive in pipeline
       cerr << "WARNING: markPrefix(). The O-RLM is *not* well-formed.\n";
       // add all prefixes or return false;
       return false;
@@ -167,10 +174,9 @@ bool OnlineRLM<T>::markPrefix(const wordID_t* IDs, const int len, bool bSet) {
       CHECK(hpdItr == this->dict_.end());
       if(bSet) bPrefix_->setBit(filterIndex); // mark index
       else bPrefix_->clearBit(filterIndex);   // unset index
-    }
-    else {
+    } else {
       CHECK(filterIndex == this->cells_ + 1);
-      //how to handle hpd prefixes? 
+      //how to handle hpd prefixes?
     }
     if(pfCache.nodes() > 10000) pfCache.clear();
     pfCache.setCacheNgram(IDs, len - 1, code, NULL);
@@ -179,39 +185,43 @@ bool OnlineRLM<T>::markPrefix(const wordID_t* IDs, const int len, bool bSet) {
 }
 
 template<typename T>
-void OnlineRLM<T>::markQueried(const uint64_t& index) {
+void OnlineRLM<T>::markQueried(const uint64_t& index)
+{
   bHit_->setBit(index);
   //cerr << "filter[" << index << "] = " << this->filter_->read(index) << endl;
 }
 
 template<typename T>
-void OnlineRLM<T>::markQueried(hpdEntry_t& value) {
-  // set high bit of counter to indicate "hit" status 
+void OnlineRLM<T>::markQueried(hpdEntry_t& value)
+{
+  // set high bit of counter to indicate "hit" status
   value->second |= this->hitMask_;
 }
 
 template<typename T>
-void OnlineRLM<T>::remove(const std::vector<string>& ngram) {
+void OnlineRLM<T>::remove(const std::vector<string>& ngram)
+{
   wordID_t IDs[ngram.size()];
-  for(count_t i = 0; i < ngram.size(); ++i) 
+  for(count_t i = 0; i < ngram.size(); ++i)
     IDs[i] = vocab_->GetWordID(ngram[i]);
   PerfectHash<T>::remove(IDs, ngram.size());
 }
 
 template<typename T>
-count_t OnlineRLM<T>::heurDelete(count_t num2del, count_t order) {
+count_t OnlineRLM<T>::heurDelete(count_t num2del, count_t order)
+{
   count_t deleted = 0;
   cout << "Deleting " << num2del << " of order "<< order << endl;
   // delete from filter first
-  int full = *std::max_element(this->idxTracker_, this->idxTracker_ 
-      + this->totBuckets_);
+  int full = *std::max_element(this->idxTracker_, this->idxTracker_
+                               + this->totBuckets_);
   for(; full > 0; --full) // delete from fullest buckets first
-    for(int bk = 0; bk < this->totBuckets_; ++bk) {       
+    for(int bk = 0; bk < this->totBuckets_; ++bk) {
       if(deleted >= num2del) break;
       if(this->idxTracker_[bk] == full) {        // if full
         uint64_t first = bk * this->bucketRange_,
-          last = first + this->bucketRange_;
-        for(uint64_t row = first; row < last; ++row) {  // check each row 
+                 last = first + this->bucketRange_;
+        for(uint64_t row = first; row < last; ++row) {  // check each row
           if(!(bHit_->testBit(row) || bPrefix_->testBit(row) )) {
             if(this->filter_->read(row) != 0) {
               PerfectHash<T>::remove(row);  // remove from filter
@@ -231,16 +241,18 @@ count_t OnlineRLM<T>::heurDelete(count_t num2del, count_t order) {
 
 template<typename T>
 int OnlineRLM<T>::sbsqQuery(const std::vector<string>& ngram, int* codes,
-  bool bStrict) {
+                            bool bStrict)
+{
   wordID_t IDs[ngram.size()];
-  for(count_t i = 0; i < ngram.size(); ++i) 
+  for(count_t i = 0; i < ngram.size(); ++i)
     IDs[i] = vocab_->GetWordID(ngram[i]);
   return sbsqQuery(IDs, ngram.size(), codes, bStrict);
 }
 
 template<typename T>
-int OnlineRLM<T>::sbsqQuery(const wordID_t* IDs, const int len, int* codes, 
-  bool bStrict) {
+int OnlineRLM<T>::sbsqQuery(const wordID_t* IDs, const int len, int* codes,
+                            bool bStrict)
+{
   uint64_t filterIdx = 0;
   int val(0), fnd(0);
   hpdEntry_t hpdItr;
@@ -252,14 +264,13 @@ int OnlineRLM<T>::sbsqQuery(const wordID_t* IDs, const int len, int* codes,
       if(hpdItr != this->dict_.end()) {
         val -= ((val & this->hitMask_) != 0) ? this->hitMask_ : 0; // account for previous hit marks
       }
-    }
-    else if(bStrict) {
-      break; 
+    } else if(bStrict) {
+      break;
     }
     // add to value array
     codes[i] = val > 0 ? val : 0;
   }
-  while(bStrict && (fnd > 1)) { // do checks the other way 
+  while(bStrict && (fnd > 1)) { // do checks the other way
     val = PerfectHash<T>::query(&IDs[len - fnd], fnd - 1, hpdItr, filterIdx);
     if(val != -1) break; // if anything found
     else --fnd; // else decrement found
@@ -269,8 +280,9 @@ int OnlineRLM<T>::sbsqQuery(const wordID_t* IDs, const int len, int* codes,
 }
 
 template<typename T>
-float OnlineRLM<T>::getProb(const wordID_t* ngram, int len, 
-  const void** state) {
+float OnlineRLM<T>::getProb(const wordID_t* ngram, int len,
+                            const void** state)
+{
   static const float oovprob = log10(1.0 / (static_cast<float>(vocab_->Size()) - 1));
   float logprob(0);
   const void* context = (state) ? *state : 0;
@@ -278,66 +290,66 @@ float OnlineRLM<T>::getProb(const wordID_t* ngram, int len,
   if(!cache_->checkCacheNgram(ngram, len, &logprob, &context)) {
     // get full prob and put in cache
     int num_fnd(0), den_val(0);
-    int *in = new int[len]; // in[] keeps counts of increasing order numerator 
+    int *in = new int[len]; // in[] keeps counts of increasing order numerator
     for(int i = 0; i < len; ++i) in[i] = 0;
     for(int i = len - 1; i >= 0; --i) {
       if(ngram[i] == vocab_->GetkOOVWordID()) break;  // no need to query if OOV
       in[i] = query(&ngram[i], len - i);
       if(in[i] > 0) {
         num_fnd = len - i;
-      }
-      else if(strict_checks_) break;
+      } else if(strict_checks_) break;
     }
     while(num_fnd > 1) { // get lower order count
-      //get sub-context of size one less than length found (exluding target) 
+      //get sub-context of size one less than length found (exluding target)
       if(((den_val = query(&ngram[len - num_fnd], num_fnd - 1)) > 0) &&
           (den_val >= in[len - num_fnd]) && (in[len - num_fnd] > 0)) {
         break;
-      }
-      else --num_fnd; // else backoff to lower ngram order 
+      } else --num_fnd; // else backoff to lower ngram order
     }
-    if(num_fnd == 1 && (in[len - 1] < 1)) // sanity check for unigrams 
+    if(num_fnd == 1 && (in[len - 1] < 1)) // sanity check for unigrams
       num_fnd = 0;
     switch(num_fnd) { // find prob (need to refactor into precomputation)
-      case 0: // OOV
-        logprob = alpha_[len] + oovprob;
-        break;
-      case 1: // unigram found only
-        CHECK(in[len - 1] > 0);
-        logprob = alpha_[len - 1] + (corpusSize_ > 0 ?  
-          log10(static_cast<float>(in[len - 1]) / static_cast<float>(corpusSize_)) : 0);
-        //logprob = alpha_[len - 1] + 
-          //log10(static_cast<float>(in[len - 1]) / static_cast<float>(corpusSize_));
-        break;
-      default:
-        CHECK(den_val > 0);
-        //if(subgram == in[len - found]) ++subgram; // avoid returning zero probs????
-        logprob = alpha_[len - num_fnd] + 
-          log10(static_cast<float>(in[len - num_fnd]) / static_cast<float>(den_val));
-        break;
+    case 0: // OOV
+      logprob = alpha_[len] + oovprob;
+      break;
+    case 1: // unigram found only
+      CHECK(in[len - 1] > 0);
+      logprob = alpha_[len - 1] + (corpusSize_ > 0 ?
+                                   log10(static_cast<float>(in[len - 1]) / static_cast<float>(corpusSize_)) : 0);
+      //logprob = alpha_[len - 1] +
+      //log10(static_cast<float>(in[len - 1]) / static_cast<float>(corpusSize_));
+      break;
+    default:
+      CHECK(den_val > 0);
+      //if(subgram == in[len - found]) ++subgram; // avoid returning zero probs????
+      logprob = alpha_[len - num_fnd] +
+                log10(static_cast<float>(in[len - num_fnd]) / static_cast<float>(den_val));
+      break;
     }
     // need unique context
     context = getContext(&ngram[len - num_fnd], num_fnd);
     // put whatever was found in cache
     cache_->setCacheNgram(ngram, len, logprob, context);
   } // end checkCache
-  return logprob; 
+  return logprob;
 }
 
 template<typename T>
-const void* OnlineRLM<T>::getContext(const wordID_t* ngram, int len) {
+const void* OnlineRLM<T>::getContext(const wordID_t* ngram, int len)
+{
   int dummy(0);
   float* *addresses = new float*[len];  // only interested in addresses of cache
   CHECK(cache_->getCache2(ngram, len, &addresses[0], &dummy) == len);
   // return address of cache node
-  
+
   float *addr0 = addresses[0];
   free( addresses );
   return (const void*)addr0;
 }
 
 template<typename T>
-void OnlineRLM<T>::randDelete(int num2del) {
+void OnlineRLM<T>::randDelete(int num2del)
+{
   int deleted = 0;
   for(uint64_t i = 0; i < this->cells_; i++) {
     if(this->filter_->read(i) != 0) {
@@ -349,19 +361,21 @@ void OnlineRLM<T>::randDelete(int num2del) {
 }
 
 template<typename T>
-int OnlineRLM<T>::countHits() {
+int OnlineRLM<T>::countHits()
+{
   int hit(0);
   for(uint64_t i = 0; i < this->cells_; ++i)
     if(bHit_->testBit(i)) ++hit;
   iterate(this->dict_, itr)
-    if((itr->second & this->hitMask_) != 0)
-      ++hit;
+  if((itr->second & this->hitMask_) != 0)
+    ++hit;
   cerr << "Hit count = " << hit << endl;
   return hit;
 }
 
 template<typename T>
-int OnlineRLM<T>::countPrefixes() {
+int OnlineRLM<T>::countPrefixes()
+{
   int pfx(0);
   for(uint64_t i = 0; i < this->cells_; ++i)
     if(bPrefix_->testBit(i)) ++pfx;
@@ -371,23 +385,25 @@ int OnlineRLM<T>::countPrefixes() {
 }
 
 template<typename T>
-int OnlineRLM<T>::cleanUpHPD() {
+int OnlineRLM<T>::cleanUpHPD()
+{
   cerr << "HPD size before = " << this->dict_.size() << endl;
   std::vector<string> vDel, vtmp;
   iterate(this->dict_, itr) {
     if(((itr->second & this->hitMask_) == 0) &&  // if not hit during testing
-      (Utils::splitToStr(itr->first, vtmp, "¬") >= 3)) {  // and higher order ngram
+        (Utils::splitToStr(itr->first, vtmp, "¬") >= 3)) {  // and higher order ngram
       vDel.push_back(itr->first);
     }
   }
-  iterate(vDel, vitr) 
-    this->dict_.erase(*vitr);
+  iterate(vDel, vitr)
+  this->dict_.erase(*vitr);
   cerr << "HPD size after = " << this->dict_.size() << endl;
   return vDel.size();
 }
 
 template<typename T>
-void OnlineRLM<T>::clearMarkings() {
+void OnlineRLM<T>::clearMarkings()
+{
   cerr << "clearing all event hits\n";
   bHit_->reset();
   count_t* value(0);
@@ -398,7 +414,8 @@ void OnlineRLM<T>::clearMarkings() {
 }
 
 template<typename T>
-void OnlineRLM<T>::save(FileHandler* fout) {
+void OnlineRLM<T>::save(FileHandler* fout)
+{
   cerr << "Saving ORLM...\n";
   // save vocab
   vocab_->Save(fout);
@@ -412,7 +429,8 @@ void OnlineRLM<T>::save(FileHandler* fout) {
 }
 
 template<typename T>
-void OnlineRLM<T>::load(FileHandler* fin) {
+void OnlineRLM<T>::load(FileHandler* fin)
+{
   cerr << "Loading ORLM...\n";
   // load vocab first
   vocab_ = new Moses::Vocab(fin);
@@ -428,12 +446,13 @@ void OnlineRLM<T>::load(FileHandler* fin) {
 }
 
 template<typename T>
-void OnlineRLM<T>::removeNonMarked() {
+void OnlineRLM<T>::removeNonMarked()
+{
   cerr << "deleting all unused events\n";
   int deleted(0);
   for(uint64_t i = 0; i < this->cells_; ++i) {
-    if(!(bHit_->testBit(i) || bPrefix_->testBit(i)) 
-      && (this->filter_->read(i) != 0)) {
+    if(!(bHit_->testBit(i) || bPrefix_->testBit(i))
+        && (this->filter_->read(i) != 0)) {
       PerfectHash<T>::remove(i);
       ++deleted;
     }
@@ -456,36 +475,36 @@ float OnlineRLM<T>::getProb2(const wordID_t* ngram, int len, const void** state)
   // constrain cache queries using model assumptions
   int denom_len = cache_->getCache(ngram, len - 1, &denom_codes[0], &denom_found);
   cerr << "denom_len = " << denom_len << endl;
-  int num_len = cache_->getCache(&ngram[len - denom_len - 1], denom_len + 1, 
+  int num_len = cache_->getCache(&ngram[len - denom_len - 1], denom_len + 1,
                                           &num_codes[0], &found);
   cerr << "num_len= " << num_len << endl;
   // keed reducing ngram size until both denominator and numerator are found
   // allowed to leave kUnknownCode in cache because we check for this.
   found = num_len; // guaranteed to be <= denom_len + 1
   // still check for OOV
-  for (int i = len - found; i < len; ++i) 
-    if (ngram[i] == Vocab::kOOVWordID) {   
+  for (int i = len - found; i < len; ++i)
+    if (ngram[i] == Vocab::kOOVWordID) {
         found = len - i - 1;
     }
   // check for relative estimator
   while(found > 1) {
-    if(*denom_codes[found-1] == cache_unk_ && 
-      ((*denom_codes[found-1] = query(&ngram[len-found], found-1)) == 0)) { 
+    if(*denom_codes[found-1] == cache_unk_ &&
+      ((*denom_codes[found-1] = query(&ngram[len-found], found-1)) == 0)) {
         //!struct_->query(&ngram[len-*found], *found-1, kMainEventIdx, denom_codes[*found-1])) {
       *num_codes[found] = cache_unk_;
     } else {
       if(*num_codes[found] != cache_unk_ ||
         ((*num_codes[found] = query(&ngram[len-found], found)) <= *denom_codes[found-1]))
-        //  struct_->query(&ngram[len-*found], *found, kMainEventIdx, 
+        //  struct_->query(&ngram[len-*found], *found, kMainEventIdx,
         //                 num_codes[*found], *denom_codes[*found-1]))
         break;
-    }	
+    }
     --found;
   }
-  // didn't find bigram numerator or unigram denominator 
+  // didn't find bigram numerator or unigram denominator
   if (found == 1)
-    found = *num_codes[1] != cache_unk_ 
-      || ((*num_codes[1] = query(&ngram[len - 1], 1)) != 0); 
+    found = *num_codes[1] != cache_unk_
+      || ((*num_codes[1] = query(&ngram[len - 1], 1)) != 0);
       //struct_->query(&ngram[len - 1], 1, kMainEventIdx, num_codes[1]);
   // ....
   // return estimate applying correct backoff score (precomputed)
@@ -496,20 +515,20 @@ float OnlineRLM<T>::getProb2(const wordID_t* ngram, int len, const void** state)
     //log_prob = stupid_backoff_log10_[len] + uniform_log10prob_;
     break;
   case 1: // unigram over whole corpus
-    log_prob = alpha_[len - 1] + 
+    log_prob = alpha_[len - 1] +
       log10(static_cast<float>(*num_codes[1]) / static_cast<float>(corpusSize_));
-    //log_prob = log_quantiser_->getLog10Value(*num_codes[1]) - corpus_size_log10_ 
+    //log_prob = log_quantiser_->getLog10Value(*num_codes[1]) - corpus_size_log10_
     //  + stupid_backoff_log10_[len - 1];  // precomputed
     break;
   default: // otherwise use both statistics and (possibly zero) backoff weight
-    log_prob = alpha_[len - found] + 
+    log_prob = alpha_[len - found] +
       log10(static_cast<float>(*num_codes[found]) / static_cast<float>(*denom_codes[found-1]));
-    //log_prob = log_quantiser_->getLog10Value(*num_codes[*found ]) 
-    //  - log_quantiser_->getLog10Value(*denom_codes[*found - 1]) 
+    //log_prob = log_quantiser_->getLog10Value(*num_codes[*found ])
+    //  - log_quantiser_->getLog10Value(*denom_codes[*found - 1])
     //  + stupid_backoff_log10_[len - *found];
   }
   context_state = (const void*)num_codes[found == len ? found - 1 : found];;
-  //probCache_->store(len, log_prob, context_state); 
+  //probCache_->store(len, log_prob, context_state);
   if (state)
     *state = context_state;
   return log_prob;
diff --git a/moses/TranslationModel/DynSAInclude/params.cpp b/moses/TranslationModel/DynSAInclude/params.cpp
index 4be3a1676..a4d51d5b2 100644
--- a/moses/TranslationModel/DynSAInclude/params.cpp
+++ b/moses/TranslationModel/DynSAInclude/params.cpp
@@ -1,10 +1,11 @@
 #include "params.h"
 
-namespace Moses {
+namespace Moses
+{
 // parameter constants
 const std::string Parameters::kNotSetValue = "__NOT_SET__";
 
-const int Parameters::kBoolValue = 0; 
+const int Parameters::kBoolValue = 0;
 const int Parameters::kIntValue = 1;
 const int Parameters::kFloatValue = 2;
 const int Parameters::kStringValue = 3;
@@ -13,26 +14,30 @@ const int Parameters::kUndefinedValue = -1;
 const std::string Parameters::kTrueValue = "1";
 const std::string Parameters::kFalseValue = "0";
 
-Parameters::Parameters(const ParamDefs * paramdefs, const count_t paramNum) {
+Parameters::Parameters(const ParamDefs * paramdefs, const count_t paramNum)
+{
   initialize(paramdefs, paramNum);
 }
 
-Parameters::Parameters(int argc, char ** argv, const ParamDefs * paramdefs, 
-    const count_t paramNum) {
+Parameters::Parameters(int argc, char ** argv, const ParamDefs * paramdefs,
+                       const count_t paramNum)
+{
   initialize(paramdefs, paramNum);
   loadParams(argc, argv);
 }
 
-void Parameters::initialize(const ParamDefs * paramdefs, const count_t paramNum) {
+void Parameters::initialize(const ParamDefs * paramdefs, const count_t paramNum)
+{
   for( count_t i = 0; i < paramNum; i++ ) {
     params_[paramdefs[i].name] = paramdefs[i]; // assign name
   }
   cerr << "Default parameter values:\n";
-  iterate(params_, itr) 
-    cerr << "\t" << itr->first << " --> " << itr->second.value << endl;
+  iterate(params_, itr)
+  cerr << "\t" << itr->first << " --> " << itr->second.value << endl;
 }
 
-bool Parameters::loadParams(int argc, char ** argv) {
+bool Parameters::loadParams(int argc, char ** argv)
+{
   // load params from commandline args
   //if( argc < 3 ) {
   //  fprintf(stderr, "ERROR: No parameters. Use \"-config\" or \"-f\" to specify configuration file.\n");
@@ -66,7 +71,7 @@ bool Parameters::loadParams(int argc, char ** argv) {
       std::string val = argv[i+1];
       Utils::trim(val);
       if( param == "config" )
-        load_from_file = true;      
+        load_from_file = true;
       if(!setParamValue(param, val)) {
         std::cerr << "Invalid Param name->value " << param << "->" << val << std::endl;
         return false;
@@ -80,35 +85,40 @@ bool Parameters::loadParams(int argc, char ** argv) {
   return success;
 }
 
-std::string Parameters::normaliseParamName(const std::string & name) {
+std::string Parameters::normaliseParamName(const std::string & name)
+{
   // Map valid abbreviations to long names. Retain other names.
   if( params_.find(name) == params_.end() )
-    iterate(params_, i) 
-      if( i->second.abbrev == name ) 
-        return i->first;
+    iterate(params_, i)
+    if( i->second.abbrev == name )
+      return i->first;
   return name;
 }
 
-int Parameters::getValueType(const std::string& name) {
+int Parameters::getValueType(const std::string& name)
+{
   if(params_.find(name) != params_.end())
     return params_[name].type;
   return Parameters::kUndefinedValue;
 }
 
-bool Parameters::isValidParamName(const std::string & name) {
-  return params_.find(name) != params_.end(); 
+bool Parameters::isValidParamName(const std::string & name)
+{
+  return params_.find(name) != params_.end();
 }
 
-bool Parameters::setParamValue(const std::string& name, const std::string& val) {
-  // TODO: Add basic type checking w verifyValueType() 
-  bool set = isValidParamName(name); 
-  if(set) { 
-    params_[name].value = val;  
+bool Parameters::setParamValue(const std::string& name, const std::string& val)
+{
+  // TODO: Add basic type checking w verifyValueType()
+  bool set = isValidParamName(name);
+  if(set) {
+    params_[name].value = val;
     std::cerr << "PARAM SET: "<< name << "=" << val << std::endl;
   }
   return( set );
 }
-std::string Parameters::getParamValue(const std::string& name) {
+std::string Parameters::getParamValue(const std::string& name)
+{
   std::string value = Parameters::kNotSetValue;
   if(isValidParamName(name))
     if(params_.find(name) != params_.end())
@@ -117,43 +127,46 @@ std::string Parameters::getParamValue(const std::string& name) {
       value = kFalseValue;
   return value;
 }
-std::string Parameters::getParam(const std::string& name) {
+std::string Parameters::getParam(const std::string& name)
+{
   return getParamValue(name);
-/*void* Parameters::getParam(const std::string& name) {
-  void* paramVal = 0;
-  int type = getValueType(name);
-  const char* sval = getParamValue(name).c_str();
-  switch(type) {
-    case kIntValue: {
-      int ival = atoi(sval);
-      paramVal = (void*)&ival;
-      break;
-    }
-    case kFloatValue: {
-      float fval = atof(sval);
-      paramVal = (void*)&fval;
-      break;
-    }
-    case kStringValue: {
-      paramVal = (void*)sval;
-      break;
-    }
-    case kBoolValue: {
-      bool bval = sval == Parameters::kTrueValue ? true : false;
-      paramVal = (void*)&bval;
-      break;
+  /*void* Parameters::getParam(const std::string& name) {
+    void* paramVal = 0;
+    int type = getValueType(name);
+    const char* sval = getParamValue(name).c_str();
+    switch(type) {
+      case kIntValue: {
+        int ival = atoi(sval);
+        paramVal = (void*)&ival;
+        break;
+      }
+      case kFloatValue: {
+        float fval = atof(sval);
+        paramVal = (void*)&fval;
+        break;
+      }
+      case kStringValue: {
+        paramVal = (void*)sval;
+        break;
+      }
+      case kBoolValue: {
+        bool bval = sval == Parameters::kTrueValue ? true : false;
+        paramVal = (void*)&bval;
+        break;
+      }
+      default: // --> Parameters::kUndefinedValue
+        paramVal = (void*)sval; // will set to Parameters::kNotSetValue
     }
-    default: // --> Parameters::kUndefinedValue 
-      paramVal = (void*)sval; // will set to Parameters::kNotSetValue
-  }
-  return paramVal;*/
+    return paramVal;*/
 }
-bool Parameters::verifyValueType(const std::string& name, const std::string& val) {
+bool Parameters::verifyValueType(const std::string& name, const std::string& val)
+{
   // Implement basic type checking
   return true;
 }
 
-int Parameters::getParamCount() const {
+int Parameters::getParamCount() const
+{
   return params_.size();
 }
 
@@ -161,7 +174,8 @@ int Parameters::getParamCount() const {
  * HAVE TO CHANGE loadParams() from file to not overwrite command lines but
  * override default if different*/
 bool Parameters::loadParams(const std::string & file_path,
-    std::set<std::string>& setParams) {
+                            std::set<std::string>& setParams)
+{
   // parameters loaded from file don't override cmd line paramters
   /*std::set<std::string>::iterator end = setParams.end();
   FileHandler file(file_path.c_str(), std::ios::in);
diff --git a/moses/TranslationModel/DynSAInclude/params.h b/moses/TranslationModel/DynSAInclude/params.h
index d5af6331d..efc0a6ba3 100644
--- a/moses/TranslationModel/DynSAInclude/params.h
+++ b/moses/TranslationModel/DynSAInclude/params.h
@@ -10,21 +10,23 @@
 #include "utils.h"
 #include "types.h"
 
-#define NumOfParams(paramArray) (sizeof(paramArray)/sizeof((paramArray)[0])) 
+#define NumOfParams(paramArray) (sizeof(paramArray)/sizeof((paramArray)[0]))
 
-namespace Moses {
+namespace Moses
+{
 typedef struct ParamDefs {
   std::string name;
-  std::string value; 
+  std::string value;
   std::string abbrev;
   int type;
   std::string description;
 } ParamDefs;
 
-  //! @todo ask abby2
-class Parameters {
+//! @todo ask abby2
+class Parameters
+{
 public:
-  static const std::string kNotSetValue; 
+  static const std::string kNotSetValue;
   static const int kBoolValue;
   static const int kIntValue;
   static const int kFloatValue;
@@ -32,15 +34,15 @@ public:
   static const int kUndefinedValue;
   static const std::string kFalseValue;
   static const std::string kTrueValue;
-  
+
   Parameters(const ParamDefs * paramdefs, const count_t paramNum);
   Parameters(int argc, char** argv, const ParamDefs * paramdefs, const count_t paramNum);
   ~Parameters() {}
   bool loadParams(int argc, char ** argv);
   bool loadParams(const std::string& param_file, std::set<std::string>&);
   int getValueType(const std::string & name);
-  bool setParamValue(const std::string& name, const std::string& value); 
-  bool verifyValueType(const std::string& name, const std::string& value); 
+  bool setParamValue(const std::string& name, const std::string& value);
+  bool verifyValueType(const std::string& name, const std::string& value);
   bool isValidParamName(const std::string & name);
   std::string getParamValue(const std::string& name);
   //void* getParam(const std::string& name);
diff --git a/moses/TranslationModel/DynSAInclude/perfectHash.h b/moses/TranslationModel/DynSAInclude/perfectHash.h
index f445e063a..8ea20fa06 100644
--- a/moses/TranslationModel/DynSAInclude/perfectHash.h
+++ b/moses/TranslationModel/DynSAInclude/perfectHash.h
@@ -9,18 +9,19 @@
 #include "quantizer.h"
 
 /**
- * PerfectHash handles setting up hash functions and storage 
- * for LM data. 
- */ 
+ * PerfectHash handles setting up hash functions and storage
+ * for LM data.
+ */
 using randlm::Filter;
 using randlm::BitFilter;
 typedef std::map<string, count_t> hpDict_t;
 typedef hpDict_t::iterator hpdEntry_t;
 static count_t collisions_ = 0;
 
-/* Based on Mortenson et. al. 2006 */ 
+/* Based on Mortenson et. al. 2006 */
 template<typename T>
-class PerfectHash {
+class PerfectHash
+{
 public:
   PerfectHash(uint16_t MBs, int width, int bucketRange, float qBase);
   PerfectHash(FileHandler* fin) {
@@ -41,11 +42,11 @@ protected:
   uint8_t* idxTracker_;
   uint64_t insert(const wordID_t* IDs, const int len, const count_t value);
   bool update(const wordID_t* IDs, const int len, const count_t value,
-    hpdEntry_t& hpdAddr, uint64_t& filterIdx);
+              hpdEntry_t& hpdAddr, uint64_t& filterIdx);
   bool update2(const wordID_t* IDs, const int len, const count_t value,
-    hpdEntry_t& hpdAddr, uint64_t& filterIdx);
-  int query(const wordID_t* IDs, const int len, 
-    hpdEntry_t& hpdAddr, uint64_t& filterIdx);
+               hpdEntry_t& hpdAddr, uint64_t& filterIdx);
+  int query(const wordID_t* IDs, const int len,
+            hpdEntry_t& hpdAddr, uint64_t& filterIdx);
   virtual void remove(const wordID_t* IDs, const int len);
   void remove(uint64_t index);
   void save(FileHandler* fout);
@@ -54,33 +55,34 @@ protected:
   //pointer to a specific entry in a hpDict_t
   virtual void markQueried(hpdEntry_t&)=0;
 private:
-  T nonZeroSignature(const wordID_t* IDs, const int len, count_t bucket); 
+  T nonZeroSignature(const wordID_t* IDs, const int len, count_t bucket);
   string hpDictKeyValue(const wordID_t* IDs, const int len);
   uint64_t memBound_; // total memory bound in bytes
   uint16_t cellWidth_; // in bits
-  UnivHash_linear<count_t>* bucketHash_; 
+  UnivHash_linear<count_t>* bucketHash_;
   UnivHash_linear<T>* fingerHash_;
   LogQtizer* qtizer_;
 };
 
 template<typename T>
-PerfectHash<T>::PerfectHash(uint16_t MBs, int width, int bucketRange, 
-  float qBase): hitMask_(1 << 31), memBound_(MBs * (1ULL << 20)), 
-  cellWidth_(width) {
+PerfectHash<T>::PerfectHash(uint16_t MBs, int width, int bucketRange,
+                            float qBase): hitMask_(1 << 31), memBound_(MBs * (1ULL << 20)),
+  cellWidth_(width)
+{
   bucketRange_ = static_cast<uint8_t>(bucketRange);
   if(bucketRange > 255) {
-    cerr << "ERROR: Max bucket range is > 2^8\n"; 
+    cerr << "ERROR: Max bucket range is > 2^8\n";
     exit(1);
   }
   qtizer_ = new LogQtizer(qBase);
   int valBits = (int)ceil(log2((float)qtizer_->maxcode()));
   cerr << "BITS FOR VALUES ARRAY = " << valBits << endl;
   uint64_t totalBits = memBound_ << 3;
-  cells_ = (uint64_t) ceil((float)totalBits / (float)(cellWidth_ + valBits)); // upper bound on cells  
+  cells_ = (uint64_t) ceil((float)totalBits / (float)(cellWidth_ + valBits)); // upper bound on cells
   cells_ += (cells_ % bucketRange_); // make cells multiple of bucket range
   totBuckets_ = (cells_ / bucketRange_) - 1; // minus 1 so totBuckets * bucksize + bucksize = cells
   filter_ = new Filter<T>(cells_, cellWidth_);
-  values_ = new Filter<T>(cells_, valBits); 
+  values_ = new Filter<T>(cells_, valBits);
   idxTracker_ = new uint8_t[totBuckets_];
   for(int i=0; i < totBuckets_; ++i) idxTracker_[i] = 0;
   // initialize ranges for each hash function
@@ -89,7 +91,8 @@ PerfectHash<T>::PerfectHash(uint16_t MBs, int width, int bucketRange,
 }
 
 template<typename T>
-PerfectHash<T>::~PerfectHash() {
+PerfectHash<T>::~PerfectHash()
+{
   delete[] idxTracker_;
   delete filter_;
   filter_ = NULL;
@@ -99,22 +102,22 @@ PerfectHash<T>::~PerfectHash() {
   delete values_;
 }
 
-template<typename T>  
-uint64_t PerfectHash<T>::insert(const wordID_t* IDs, const int len, 
-                            const count_t value) {
+template<typename T>
+uint64_t PerfectHash<T>::insert(const wordID_t* IDs, const int len,
+                                const count_t value)
+{
   count_t bucket = (bucketHash_->size() > 1 ? bucketHash_->hash(IDs, len, len) : bucketHash_->hash(IDs, len, 0));
-  if(idxTracker_[bucket] < (int)bucketRange_) {  // if empty rows 
+  if(idxTracker_[bucket] < (int)bucketRange_) {  // if empty rows
     // restriction on fprint value is non-zero
     T fp = nonZeroSignature(IDs, len, (bucket % MAX_HASH_FUNCS));
     uint64_t emptyidx = cells_ + 1;
     uint64_t index = bucket * bucketRange_,  // starting bucket row
-            lastrow = index + bucketRange_;  // ending row 
-    while(index < lastrow) { // unique so check each row for "matching" signature 
+             lastrow = index + bucketRange_;  // ending row
+    while(index < lastrow) { // unique so check each row for "matching" signature
       T filterVal = filter_->read(index);
-      if((filterVal == 0) && (emptyidx == cells_ + 1)) {  // record first empty row 
+      if((filterVal == 0) && (emptyidx == cells_ + 1)) {  // record first empty row
         emptyidx = index;
-      }
-      else if(filterVal == fp) { 
+      } else if(filterVal == fp) {
         ++collisions_;
         dict_[hpDictKeyValue(IDs, len)] = value; // store exact in hpd
         return cells_ + 1;  // finished
@@ -127,21 +130,21 @@ uint64_t PerfectHash<T>::insert(const wordID_t* IDs, const int len,
     values_->write(emptyidx, code);
     ++idxTracker_[bucket]; // keep track of bucket size
     return emptyidx;
-  }
-  else { // bucket is full
+  } else { // bucket is full
     dict_[hpDictKeyValue(IDs, len)] = value; // add to hpd
     return cells_ + 1;
   }
 }
 
-template<typename T>  
-bool PerfectHash<T>::update(const wordID_t* IDs, const int len, 
-  const count_t value, hpdEntry_t& hpdAddr, uint64_t& filterIdx) {
+template<typename T>
+bool PerfectHash<T>::update(const wordID_t* IDs, const int len,
+                            const count_t value, hpdEntry_t& hpdAddr, uint64_t& filterIdx)
+{
   // check if key is in high perf. dictionary
   filterIdx = cells_ + 1;
   string skey = hpDictKeyValue(IDs, len);
   if((hpdAddr = dict_.find(skey)) != dict_.end()) {
-    hpdAddr->second = value;  
+    hpdAddr->second = value;
     return true;
   }
   // else hash ngram
@@ -150,45 +153,45 @@ bool PerfectHash<T>::update(const wordID_t* IDs, const int len,
   // restriction on fprint value is non-zero
   T fp = nonZeroSignature(IDs, len, (bucket % MAX_HASH_FUNCS));
   uint64_t index = bucket * bucketRange_,  // starting bucket row
-          lastrow = index + bucketRange_; 
+           lastrow = index + bucketRange_;
   while(index < lastrow) { // must check each row for matching fp event
     T filterVal = filter_->read(index);
     if(filterVal == fp) { // found event w.h.p.
-      values_->write(index, (T)qtizer_->code(value)); 
+      values_->write(index, (T)qtizer_->code(value));
       filterIdx = index;
       return true;
     }
     ++index;
   }
-  // could add if it gets here. 
+  // could add if it gets here.
   return false;
 }
 
-template<typename T>   
-int PerfectHash<T>::query(const wordID_t* IDs, const int len, 
-  hpdEntry_t& hpdAddr, uint64_t& filterIdx) {
+template<typename T>
+int PerfectHash<T>::query(const wordID_t* IDs, const int len,
+                          hpdEntry_t& hpdAddr, uint64_t& filterIdx)
+{
   // check if key is in high perf. dictionary
   string skey = hpDictKeyValue(IDs, len);
   if((hpdAddr = dict_.find(skey)) != dict_.end()) {
     filterIdx = cells_ + 1;
     return(hpdAddr->second);  // returns copy of value
-  }
-  else {  // check if key is in filter
-    // get bucket 
+  } else { // check if key is in filter
+    // get bucket
     //count_t bucket = bucketHash_->hash(IDs, len);
     count_t bucket = (bucketHash_->size() > 1 ? bucketHash_->hash(IDs, len, len) : bucketHash_->hash(IDs, len, 0));
     // restriction on fprint value is non-zero
     T fp = nonZeroSignature(IDs, len, (bucket % MAX_HASH_FUNCS));
     // return value if ngram is in filter
     uint64_t index = bucket * bucketRange_,
-            lastrow = index + bucketRange_;
+             lastrow = index + bucketRange_;
     for(; index < lastrow; ++index) {
       if(filter_->read(index) == fp) {
-        //cout << "fp = " << fp << "\tbucket = " << bucket << "\tfilter =" << 
-          //filter_->read(index) << "\tcode = " << code << endl;
+        //cout << "fp = " << fp << "\tbucket = " << bucket << "\tfilter =" <<
+        //filter_->read(index) << "\tcode = " << code << endl;
         filterIdx = index;
         hpdAddr = dict_.end();
-        return (int)qtizer_->value(values_->read(index)); 
+        return (int)qtizer_->value(values_->read(index));
       }
     }
   }
@@ -196,22 +199,23 @@ int PerfectHash<T>::query(const wordID_t* IDs, const int len,
 }
 
 template<typename T>
-void PerfectHash<T>::remove(const wordID_t* IDs, const int len) {
+void PerfectHash<T>::remove(const wordID_t* IDs, const int len)
+{
   // delete key if in high perf. dictionary
   string skey = hpDictKeyValue(IDs, len);
   if(dict_.find(skey) != dict_.end())
     dict_.erase(skey);
   else {  // check if key is in filter
-    // get small representation for ngrams 
+    // get small representation for ngrams
     //count_t bucket = bucketHash_->hash(IDs, len);
     count_t bucket = (bucketHash_->size() > 1? bucketHash_->hash(IDs, len, len) : bucketHash_->hash(IDs, len, 0));
     // retrieve non zero fingerprint for ngram
-    T fp = nonZeroSignature(IDs, len, (bucket % MAX_HASH_FUNCS)); 
+    T fp = nonZeroSignature(IDs, len, (bucket % MAX_HASH_FUNCS));
     // return value if ngram is in filter
     uint64_t index = bucket * bucketRange_,
-            lastrow = index + bucketRange_; 
+             lastrow = index + bucketRange_;
     for(; index < lastrow; ++index) {
-      if(filter_->read(index) == fp) { 
+      if(filter_->read(index) == fp) {
         filter_->write(index, 0);
         values_->write(index, 0);
         --idxTracker_[bucket]; // track bucket size reduction
@@ -222,7 +226,8 @@ void PerfectHash<T>::remove(const wordID_t* IDs, const int len) {
 }
 
 template<typename T> // clear filter index
-void PerfectHash<T>::remove(uint64_t index) {
+void PerfectHash<T>::remove(uint64_t index)
+{
   CHECK(index < cells_);
   CHECK(filter_->read(index) != 0); // slow
   filter_->write(index, 0);
@@ -234,20 +239,22 @@ void PerfectHash<T>::remove(uint64_t index) {
 
 template<typename T>
 T PerfectHash<T>::nonZeroSignature(const wordID_t* IDs, const int len,
-  count_t bucket) {
+                                   count_t bucket)
+{
   count_t h = bucket;
   T fingerprint(0);
   do {
     fingerprint = fingerHash_->hash(IDs, len, h);
-    h += (h < fingerHash_->size() - 1 ? 1 : -h); // wrap around 
+    h += (h < fingerHash_->size() - 1 ? 1 : -h); // wrap around
   } while((fingerprint == 0) && (h != bucket));
-  if(fingerprint == 0) 
+  if(fingerprint == 0)
     cerr << "WARNING: Unable to find non-zero signature for ngram\n" << endl;
   return fingerprint;
 }
 
 template<typename T>
-string PerfectHash<T>::hpDictKeyValue(const wordID_t* IDs, const int len) {
+string PerfectHash<T>::hpDictKeyValue(const wordID_t* IDs, const int len)
+{
   string skey(" ");
   for(int i = 0; i < len; ++i)
     skey += Utils::IntToStr(IDs[i]) + "¬";
@@ -256,19 +263,22 @@ string PerfectHash<T>::hpDictKeyValue(const wordID_t* IDs, const int len) {
 }
 
 template<typename T>
-count_t PerfectHash<T>::hpDictMemUse() {
+count_t PerfectHash<T>::hpDictMemUse()
+{
   // return hpDict memory usage in MBs
   return (count_t) sizeof(hpDict_t::value_type)* dict_.size() >> 20;
 }
 
 template<typename T>
-count_t PerfectHash<T>::bucketsMemUse() {
+count_t PerfectHash<T>::bucketsMemUse()
+{
   // return bucket memory usage in MBs
-  return (count_t) (filter_->size() + values_->size()); 
+  return (count_t) (filter_->size() + values_->size());
 }
 
 template<typename T>
-void PerfectHash<T>::save(FileHandler* fout) {
+void PerfectHash<T>::save(FileHandler* fout)
+{
   CHECK(fout != 0);
   cerr << "\tSaving perfect hash parameters...\n";
   fout->write((char*)&hitMask_, sizeof(hitMask_));
@@ -289,12 +299,13 @@ void PerfectHash<T>::save(FileHandler* fout) {
   count_t size = dict_.size();
   fout->write((char*)&size, sizeof(count_t));
   *fout << endl;
-  iterate(dict_, t) 
-    *fout << t->first << "\t" << t->second << "\n";
+  iterate(dict_, t)
+  *fout << t->first << "\t" << t->second << "\n";
 }
 
 template<typename T>
-void PerfectHash<T>::load(FileHandler* fin) {
+void PerfectHash<T>::load(FileHandler* fin)
+{
   CHECK(fin != 0);
   cerr << "\tLoading perfect hash parameters...\n";
   fin->read((char*)&hitMask_, sizeof(hitMask_));
@@ -331,12 +342,13 @@ void PerfectHash<T>::load(FileHandler* fin) {
 }
 
 template<typename T>
-void PerfectHash<T>::analyze() {
+void PerfectHash<T>::analyze()
+{
   cerr << "Analyzing Dynamic Bloomier Filter...\n";
   // see how many items in each bucket
   uint8_t* bucketCnt = new uint8_t[totBuckets_];
-  unsigned largestBucket = 0, totalCellsSet = 0, 
-    smallestBucket = bucketRange_, totalZeroes = 0;
+  unsigned largestBucket = 0, totalCellsSet = 0,
+           smallestBucket = bucketRange_, totalZeroes = 0;
   int curBucket = -1, fullBuckets(0);
   for(int i = 0; i < totBuckets_; ++i) bucketCnt[i] = 0;
   for(uint64_t i =0; i < cells_; ++i) {
@@ -344,16 +356,14 @@ void PerfectHash<T>::analyze() {
     if(filter_->read(i) != 0) {
       ++bucketCnt[curBucket];
       ++totalCellsSet;
-    }
-    else ++totalZeroes;
+    } else ++totalZeroes;
   }
   count_t bi = 0, si = 0;
   for(int i = 0; i < totBuckets_; ++i) {
     if(bucketCnt[i] > largestBucket) {
       largestBucket = bucketCnt[i];
       bi = i;
-    }
-    else if(bucketCnt[i] < smallestBucket) {
+    } else if(bucketCnt[i] < smallestBucket) {
       smallestBucket = bucketCnt[i];
       si = i;
     }
@@ -366,8 +376,8 @@ void PerfectHash<T>::analyze() {
   }
   for(int i = 0; i < totBuckets_; ++i) {
     if(bucketCnt[i] != idxTracker_[i])
-      cerr << "bucketCnt[" << i << "] = " << (int)bucketCnt[i] << 
-        "\tidxTracker_[" << i << "] = " << (int)idxTracker_[i] << endl;
+      cerr << "bucketCnt[" << i << "] = " << (int)bucketCnt[i] <<
+           "\tidxTracker_[" << i << "] = " << (int)idxTracker_[i] << endl;
   }
   cerr << "total cells= " << cells_ << endl;
   cerr << "total buckets= " << totBuckets_ << endl;
@@ -380,7 +390,7 @@ void PerfectHash<T>::analyze() {
   cerr << "largest bucket (" << bi << ") size= " << largestBucket << endl;
   cerr << "smallest bucket (" << si << ") size= " << smallestBucket << endl;
   cerr << "last bucket size= " << (int)bucketCnt[totBuckets_ - 1] <<
-    " (idxTracker last bucket size = " << (int)idxTracker_[totBuckets_ - 1] << ")" << endl;
+       " (idxTracker last bucket size = " << (int)idxTracker_[totBuckets_ - 1] << ")" << endl;
   cerr << "total buckets full = " << fullBuckets << endl;
   cerr << "total collision errors= " << collisions_ << endl;
   cerr << "high performance dictionary size= " << dict_.size() << endl;
@@ -390,14 +400,15 @@ void PerfectHash<T>::analyze() {
   delete[] bucketCnt;
 }
 
-template<typename T>  
-bool PerfectHash<T>::update2(const wordID_t* IDs, const int len, 
-  const count_t value, hpdEntry_t& hpdAddr, uint64_t& filterIdx) {
+template<typename T>
+bool PerfectHash<T>::update2(const wordID_t* IDs, const int len,
+                             const count_t value, hpdEntry_t& hpdAddr, uint64_t& filterIdx)
+{
   // check if key is in high perf. dictionary
   filterIdx = cells_ + 1;
   string skey = hpDictKeyValue(IDs, len);
   if((hpdAddr = dict_.find(skey)) != dict_.end()) {
-    hpdAddr->second += value;  
+    hpdAddr->second += value;
     return true;
   }
   // else hash ngram
@@ -406,18 +417,18 @@ bool PerfectHash<T>::update2(const wordID_t* IDs, const int len,
   // restriction on fprint value is non-zero
   T fp = nonZeroSignature(IDs, len, (bucket % MAX_HASH_FUNCS));
   uint64_t index = bucket * bucketRange_,  // starting bucket row
-          lastrow = index + bucketRange_; 
+           lastrow = index + bucketRange_;
   while(index < lastrow) { // must check each row for matching fp event
     T filterVal = filter_->read(index);
     if(filterVal == fp) { // found event w.h.p.
-      int oldval = (int)qtizer_->value(values_->read(index)); 
-      values_->write(index, (T)qtizer_->code(oldval + value)); 
+      int oldval = (int)qtizer_->value(values_->read(index));
+      values_->write(index, (T)qtizer_->code(oldval + value));
       filterIdx = index;
       return true;
     }
     ++index;
   }
-  // add if it gets here. 
+  // add if it gets here.
   insert(IDs, len, value);
   return false;
 }
diff --git a/moses/TranslationModel/DynSAInclude/quantizer.h b/moses/TranslationModel/DynSAInclude/quantizer.h
index 6c6850fa6..68d6a55a3 100644
--- a/moses/TranslationModel/DynSAInclude/quantizer.h
+++ b/moses/TranslationModel/DynSAInclude/quantizer.h
@@ -14,7 +14,8 @@ static const float kFloatErr = 0.00001f;
 #endif
 
 //! @todo ask abby2
-class LogQtizer {
+class LogQtizer
+{
 public:
   LogQtizer(float i): base_(pow(2, 1 / i)) {
     CHECK(base_ > 1);
@@ -22,8 +23,8 @@ public:
     float value = 1; // code = 1 -> value = 1 for any base
     std::vector<float> code_to_value_vec;
     while (log2(value) < 30) { // assume 2^30 is largest count
-      code_to_value_vec.push_back(value);  
-      value = pow(base_, ++max_code_);      
+      code_to_value_vec.push_back(value);
+      value = pow(base_, ++max_code_);
     }
     code_to_value_vec.push_back(value);  // store max_code_ so in total [0, max_code_]
     // get valid range
@@ -46,22 +47,22 @@ public:
   int code(float value) {
     // should just be: return log_b(value)
     CHECK(!(value < min_value_ || value > max_value_));
-    // but binary search removes errors due to floor operator above 
-    int code =  static_cast<int>(std::lower_bound(code_to_value_, code_to_value_+ max_code_, 
-						  value) - code_to_value_);
-    // make sure not overestimating 
+    // but binary search removes errors due to floor operator above
+    int code =  static_cast<int>(std::lower_bound(code_to_value_, code_to_value_+ max_code_,
+                                 value) - code_to_value_);
+    // make sure not overestimating
     code = code_to_value_[code] > value ? code - 1 : code;
     return code;
   }
   inline float value(int code) {
-    // table look up for values 
+    // table look up for values
     return code_to_value_[code];
   }
   inline int maxcode() {
     return max_code_;
   }
   inline float logValue(int code) {
-    // table look up for log of values 
+    // table look up for log of values
     return code_to_log_value_[code];
   }
   ~LogQtizer() {
@@ -75,15 +76,15 @@ public:
     fout->write((char*)&min_value_, sizeof(min_value_));
     for (int j = 0; j <= max_code_; ++j)
       fout->write((char*)&code_to_value_[j], sizeof(code_to_value_[j]));
-    for (int j = 0; j <= max_code_; ++j) 
+    for (int j = 0; j <= max_code_; ++j)
       fout->write((char*)&code_to_log_value_[j], sizeof(code_to_log_value_[j]));
     std::cerr << "Saved log codebook with " << max_code_ + 1 << " codes." <<std::endl;
   }
 private:
   float base_;
-  float* code_to_value_; 
+  float* code_to_value_;
   float* code_to_log_value_;
-  int max_code_; 
+  int max_code_;
   float max_value_;
   float min_value_;
   void load(FileHandler* fin) {
diff --git a/moses/TranslationModel/DynSAInclude/vocab.cpp b/moses/TranslationModel/DynSAInclude/vocab.cpp
index 27e052260..da1443f66 100644
--- a/moses/TranslationModel/DynSAInclude/vocab.cpp
+++ b/moses/TranslationModel/DynSAInclude/vocab.cpp
@@ -103,10 +103,11 @@ bool Vocab::Load(const std::string & vocab_path, const FactorDirection& directio
   std::cerr << "Loading vocab from " << vocab_path << std::endl;
   return Load(&vcbin, direction, factors, closed);
 }
-bool Vocab::Load(FileHandler* vcbin) {
+bool Vocab::Load(FileHandler* vcbin)
+{
   FactorList factors;
   factors.push_back(0);
-  return Load(vcbin, Input, factors);  
+  return Load(vcbin, Input, factors);
 }
 bool Vocab::Load(FileHandler* vcbin, const FactorDirection& direction,
                  const FactorList& factors, bool closed)
diff --git a/moses/TranslationModel/DynSAInclude/vocab.h b/moses/TranslationModel/DynSAInclude/vocab.h
index 0c0d50a07..18ff96c8d 100644
--- a/moses/TranslationModel/DynSAInclude/vocab.h
+++ b/moses/TranslationModel/DynSAInclude/vocab.h
@@ -11,7 +11,7 @@
 
 namespace Moses
 {
-  
+
 //! Vocab maps between strings and uint32 ids.
 class Vocab
 {
diff --git a/moses/TranslationModel/DynSuffixArray.cpp b/moses/TranslationModel/DynSuffixArray.cpp
index 7d5847cc6..c5fddf3f0 100644
--- a/moses/TranslationModel/DynSuffixArray.cpp
+++ b/moses/TranslationModel/DynSuffixArray.cpp
@@ -74,12 +74,12 @@ int DynSuffixArray::F_firstIdx(unsigned word)
   // return index of first row where word is found in m_F
   /*for(int i=0; i < m_F->size(); ++i) {
     if(m_F->at(i) == word) {
-      return i; 
+      return i;
     }
   }
   return -1;*/
-  //NOTE: lower_bound  is faster than linear search above but may cause issues 
-  //      if ordering of vocab is not consecutive (ie..after deletions) 
+  //NOTE: lower_bound  is faster than linear search above but may cause issues
+  //      if ordering of vocab is not consecutive (ie..after deletions)
   int low = std::lower_bound(m_F->begin(), m_F->end(), word) - m_F->begin();
   //cerr << "in F_firstIdx with word = " << word << " and low = " << low <<  " and F->size() =" << m_F->size() << endl;
   if((size_t)low >= m_F->size())
@@ -146,8 +146,8 @@ void DynSuffixArray::Reorder(unsigned j, unsigned jprime)
 {
   set<pair<unsigned, unsigned> > seen;
   while(j != jprime) {
-    // this 'seenit' check added for data with many loops. will remove after double 
-    // checking.  
+    // this 'seenit' check added for data with many loops. will remove after double
+    // checking.
     bool seenit = seen.insert(std::make_pair(j, jprime)).second;
     if(seenit) {
       for(size_t i=1; i < m_SA->size(); ++i) {
@@ -163,9 +163,9 @@ void DynSuffixArray::Reorder(unsigned j, unsigned jprime)
     int new_j = LastFirstFunc(j);
     CHECK(j <= jprime);
     // for SA and L, the element at pos j is moved to pos j'
-    m_L->insert(m_L->begin() + jprime + 1, m_L->at(j)); 
+    m_L->insert(m_L->begin() + jprime + 1, m_L->at(j));
     m_L->erase(m_L->begin() + j);
-    m_SA->insert(m_SA->begin() + jprime + 1, m_SA->at(j)); 
+    m_SA->insert(m_SA->begin() + jprime + 1, m_SA->at(j));
     m_SA->erase(m_SA->begin() + j);
     // all ISA values between (j...j'] decremented
     for(size_t i = 0; i < m_ISA->size(); ++i) {
diff --git a/moses/TranslationModel/PhraseDictionary.cpp b/moses/TranslationModel/PhraseDictionary.cpp
index 808f7ce81..a0c94ccdc 100644
--- a/moses/TranslationModel/PhraseDictionary.cpp
+++ b/moses/TranslationModel/PhraseDictionary.cpp
@@ -31,7 +31,7 @@ namespace Moses
 {
 
 PhraseDictionary::PhraseDictionary(const std::string &description, const std::string &line)
-:DecodeFeature(description, line)
+  :DecodeFeature(description, line)
 {
   m_tableLimit= 20; // TODO default?
 
@@ -40,20 +40,15 @@ PhraseDictionary::PhraseDictionary(const std::string &description, const std::st
 
     if (args[0] == "num-input-features") {
       m_numInputScores = Scan<unsigned>(args[1]);
-    }
-    else if (args[0] == "path") {
+    } else if (args[0] == "path") {
       m_filePath = args[1];
-    }
-    else if (args[0] == "table-limit") {
+    } else if (args[0] == "table-limit") {
       m_tableLimit = Scan<size_t>(args[1]);
-    }
-    else if (args[0] == "target-path") {
+    } else if (args[0] == "target-path") {
       m_targetFile = args[1];
-    }
-    else if (args[0] == "alignment-path") {
+    } else if (args[0] == "alignment-path") {
       m_alignmentsFile = args[1];
-    }
-    else {
+    } else {
       //throw "Unknown argument " + args[0];
     }
   } // for (size_t i = 0; i < toks.size(); ++i) {
diff --git a/moses/TranslationModel/PhraseDictionary.h b/moses/TranslationModel/PhraseDictionary.h
index 4c10c2e6b..1b1197eb1 100644
--- a/moses/TranslationModel/PhraseDictionary.h
+++ b/moses/TranslationModel/PhraseDictionary.h
@@ -88,7 +88,9 @@ public:
   const PhraseDictionary* GetDictionary() const;
   PhraseDictionary* GetDictionary();
 
-  const std::string &GetFilePath() const { return m_filePath; }
+  const std::string &GetFilePath() const {
+    return m_filePath;
+  }
 
 protected:
   size_t m_tableLimit;
diff --git a/moses/TranslationModel/PhraseDictionaryDynSuffixArray.cpp b/moses/TranslationModel/PhraseDictionaryDynSuffixArray.cpp
index 126dd3365..afa1c4abc 100644
--- a/moses/TranslationModel/PhraseDictionaryDynSuffixArray.cpp
+++ b/moses/TranslationModel/PhraseDictionaryDynSuffixArray.cpp
@@ -9,7 +9,7 @@ using namespace std;
 namespace Moses
 {
 PhraseDictionaryDynSuffixArray::PhraseDictionaryDynSuffixArray(const std::string &line)
-:PhraseDictionary("PhraseDictionaryDynSuffixArray", line)
+  :PhraseDictionary("PhraseDictionaryDynSuffixArray", line)
 {
   m_biSA = new BilingualDynSuffixArray();
 }
@@ -63,7 +63,7 @@ const TargetPhraseCollection *PhraseDictionaryDynSuffixArray::GetTargetPhraseCol
 void PhraseDictionaryDynSuffixArray::insertSnt(string& source, string& target, string& alignment)
 {
   m_biSA->addSntPair(source, target, alignment); // insert sentence pair into suffix arrays
-  //StaticData::Instance().ClearTransOptionCache(); // clear translation option cache 
+  //StaticData::Instance().ClearTransOptionCache(); // clear translation option cache
 }
 void PhraseDictionaryDynSuffixArray::deleteSnt(unsigned /* idx */, unsigned /* num2Del */)
 {
diff --git a/moses/TranslationModel/PhraseDictionaryMemory.cpp b/moses/TranslationModel/PhraseDictionaryMemory.cpp
index 27cac9f5f..c43b919a4 100644
--- a/moses/TranslationModel/PhraseDictionaryMemory.cpp
+++ b/moses/TranslationModel/PhraseDictionaryMemory.cpp
@@ -41,9 +41,9 @@ namespace Moses
 {
 
 TargetPhraseCollection &PhraseDictionaryMemory::GetOrCreateTargetPhraseCollection(
-                                                                                const Phrase &source
-                                                                                , const TargetPhrase &target
-                                                                                , const Word *sourceLHS)
+  const Phrase &source
+  , const TargetPhrase &target
+  , const Word *sourceLHS)
 {
   PhraseDictionaryNodeMemory &currNode = GetOrCreateNode(source, target, sourceLHS);
   return currNode.GetOrCreateTargetPhraseCollection();
@@ -73,8 +73,8 @@ const TargetPhraseCollection *PhraseDictionaryMemory::GetTargetPhraseCollection(
 }
 
 PhraseDictionaryNodeMemory &PhraseDictionaryMemory::GetOrCreateNode(const Phrase &source
-                                                                , const TargetPhrase &target
-                                                                , const Word *sourceLHS)
+    , const TargetPhrase &target
+    , const Word *sourceLHS)
 {
   const size_t size = source.GetSize();
 
@@ -102,12 +102,12 @@ PhraseDictionaryNodeMemory &PhraseDictionaryMemory::GetOrCreateNode(const Phrase
 
     CHECK(currNode != NULL);
   }
-  
+
   // finally, the source LHS
   //currNode = currNode->GetOrCreateChild(sourceLHS);
   //CHECK(currNode != NULL);
 
-  
+
   return *currNode;
 }
 
@@ -120,8 +120,7 @@ ChartRuleLookupManager *PhraseDictionaryMemory::CreateRuleLookupManager(
 
 void PhraseDictionaryMemory::SortAndPrune()
 {
-  if (GetTableLimit())
-  {
+  if (GetTableLimit()) {
     m_collection.Sort(GetTableLimit());
   }
 }
diff --git a/moses/TranslationModel/PhraseDictionaryMemory.h b/moses/TranslationModel/PhraseDictionaryMemory.h
index dad8b3bbd..d2a8d0ad3 100644
--- a/moses/TranslationModel/PhraseDictionaryMemory.h
+++ b/moses/TranslationModel/PhraseDictionaryMemory.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -38,15 +38,17 @@ class PhraseDictionaryMemory : public RuleTableTrie
 
 protected:
   PhraseDictionaryMemory(const std::string &description, const std::string &line)
-      : RuleTableTrie(description, line)
+    : RuleTableTrie(description, line)
   {}
 
 public:
   PhraseDictionaryMemory(const std::string &line)
-      : RuleTableTrie("PhraseDictionaryMemory", line)
+    : RuleTableTrie("PhraseDictionaryMemory", line)
   {}
 
-  const PhraseDictionaryNodeMemory &GetRootNode() const { return m_collection; }
+  const PhraseDictionaryNodeMemory &GetRootNode() const {
+    return m_collection;
+  }
 
   ChartRuleLookupManager *CreateRuleLookupManager(
     const InputType &,
@@ -54,14 +56,14 @@ public:
 
   TO_STRING();
 
- protected:
+protected:
   TargetPhraseCollection &GetOrCreateTargetPhraseCollection(
-      const Phrase &source, const TargetPhrase &target, const Word *sourceLHS);
+    const Phrase &source, const TargetPhrase &target, const Word *sourceLHS);
   const TargetPhraseCollection *GetTargetPhraseCollection(const Phrase& source) const;
 
   PhraseDictionaryNodeMemory &GetOrCreateNode(const Phrase &source
-                                            , const TargetPhrase &target
-                                            , const Word *sourceLHS);
+      , const TargetPhrase &target
+      , const Word *sourceLHS);
 
   void SortAndPrune();
 
diff --git a/moses/TranslationModel/PhraseDictionaryMultiModel.cpp b/moses/TranslationModel/PhraseDictionaryMultiModel.cpp
index bf3f01a1e..e395cb5a3 100644
--- a/moses/TranslationModel/PhraseDictionaryMultiModel.cpp
+++ b/moses/TranslationModel/PhraseDictionaryMultiModel.cpp
@@ -26,7 +26,7 @@ namespace Moses
 
 {
 PhraseDictionaryMultiModel::PhraseDictionaryMultiModel(const std::string &line)
-:PhraseDictionary("PhraseDictionaryMultiModel", line)
+  :PhraseDictionary("PhraseDictionaryMultiModel", line)
 {
   for (size_t i = 0; i < m_args.size(); ++i) {
     const vector<string> &args = m_args[i];
@@ -37,12 +37,10 @@ PhraseDictionaryMultiModel::PhraseDictionaryMultiModel(const std::string &line)
         msg << "combination mode unknown: " << m_mode;
         throw runtime_error(msg.str());
       }
-    }
-    else if (args[0] == "components") {
+    } else if (args[0] == "components") {
       m_pdStr = Tokenize(args[1], ",");
       m_numModels = m_pdStr.size();
-    }
-    else if (args[0] == "lambda") {
+    } else if (args[0] == "lambda") {
       m_multimodelweights = Tokenize<float>(args[1], ",");
     }
   } // for
@@ -55,15 +53,14 @@ PhraseDictionaryMultiModel::PhraseDictionaryMultiModel(const std::string &line)
 }
 
 PhraseDictionaryMultiModel::PhraseDictionaryMultiModel(const std::string &description, const std::string &line)
-:PhraseDictionary(description, line)
+  :PhraseDictionary(description, line)
 {
   for (size_t i = 0; i < m_args.size(); ++i) {
     const vector<string> &args = m_args[i];
     if (args[0] == "components") {
       m_pdStr = Tokenize(args[1], ",");
       m_numModels = m_pdStr.size();
-    }
-    else if (args[0] == "lambda") {
+    } else if (args[0] == "lambda") {
       m_multimodelweights = Tokenize<float>(args[1], ",");
     }
   } // for
@@ -83,7 +80,7 @@ bool PhraseDictionaryMultiModel::InitDictionary()
   // one could choose a higher value than tableLimit (or 0) here for maximal precision, at a cost of speed.
 
 
-  for(size_t i = 0; i < m_numModels; ++i){
+  for(size_t i = 0; i < m_numModels; ++i) {
     const string &ptName = m_pdStr[i];
 
     PhraseDictionary *pt = FindPhraseDictionary(ptName);
@@ -144,7 +141,7 @@ const TargetPhraseCollection *PhraseDictionaryMultiModel::GetTargetPhraseCollect
 
 void PhraseDictionaryMultiModel::CollectSufficientStatistics(const Phrase& src, std::map<std::string,multiModelStatistics*>* allStats) const
 {
-  for(size_t i = 0; i < m_numModels; ++i){
+  for(size_t i = 0; i < m_numModels; ++i) {
     const PhraseDictionary &pd = *m_pd[i];
 
     TargetPhraseCollection *ret_raw = (TargetPhraseCollection*)  pd.GetTargetPhraseCollection( src);
@@ -152,10 +149,9 @@ void PhraseDictionaryMultiModel::CollectSufficientStatistics(const Phrase& src,
 
       TargetPhraseCollection::iterator iterTargetPhrase, iterLast;
       if (m_tableLimit != 0 && ret_raw->GetSize() > m_tableLimit) {
-          iterLast = ret_raw->begin() + m_tableLimit;
-      }
-      else {
-          iterLast = ret_raw->end();
+        iterLast = ret_raw->begin() + m_tableLimit;
+      } else {
+        iterLast = ret_raw->end();
       }
 
       for (iterTargetPhrase = ret_raw->begin(); iterTargetPhrase != iterLast;  ++iterTargetPhrase) {
@@ -173,9 +169,9 @@ void PhraseDictionaryMultiModel::CollectSufficientStatistics(const Phrase& src,
 
           Scores scoreVector(m_numScoreComponents);
           statistics->p.resize(m_numScoreComponents);
-          for(size_t j = 0; j < m_numScoreComponents; ++j){
-              statistics->p[j].resize(m_numModels);
-              scoreVector[j] = -raw_scores[j];
+          for(size_t j = 0; j < m_numScoreComponents; ++j) {
+            statistics->p[j].resize(m_numModels);
+            scoreVector[j] = -raw_scores[j];
           }
 
           statistics->targetPhrase->GetScoreBreakdown().Assign(this, scoreVector); // set scores to 0
@@ -186,8 +182,8 @@ void PhraseDictionaryMultiModel::CollectSufficientStatistics(const Phrase& src,
         }
         multiModelStatistics * statistics = (*allStats)[targetString];
 
-        for(size_t j = 0; j < m_numScoreComponents; ++j){
-            statistics->p[j][i] = UntransformScore(raw_scores[j]);
+        for(size_t j = 0; j < m_numScoreComponents; ++j) {
+          statistics->p[j][i] = UntransformScore(raw_scores[j]);
         }
 
         (*allStats)[targetString] = statistics;
@@ -199,26 +195,26 @@ void PhraseDictionaryMultiModel::CollectSufficientStatistics(const Phrase& src,
 
 TargetPhraseCollection* PhraseDictionaryMultiModel::CreateTargetPhraseCollectionLinearInterpolation(const Phrase& src, std::map<std::string,multiModelStatistics*>* allStats, std::vector<std::vector<float> > &multimodelweights) const
 {
-    TargetPhraseCollection *ret = new TargetPhraseCollection();
-    for ( std::map< std::string, multiModelStatistics*>::const_iterator iter = allStats->begin(); iter != allStats->end(); ++iter ) {
+  TargetPhraseCollection *ret = new TargetPhraseCollection();
+  for ( std::map< std::string, multiModelStatistics*>::const_iterator iter = allStats->begin(); iter != allStats->end(); ++iter ) {
 
-        multiModelStatistics * statistics = iter->second;
+    multiModelStatistics * statistics = iter->second;
 
-        Scores scoreVector(m_numScoreComponents);
+    Scores scoreVector(m_numScoreComponents);
 
-        for(size_t i = 0; i < m_numScoreComponents-1; ++i){
-            scoreVector[i] = TransformScore(std::inner_product(statistics->p[i].begin(), statistics->p[i].end(), multimodelweights[i].begin(), 0.0));
-        }
+    for(size_t i = 0; i < m_numScoreComponents-1; ++i) {
+      scoreVector[i] = TransformScore(std::inner_product(statistics->p[i].begin(), statistics->p[i].end(), multimodelweights[i].begin(), 0.0));
+    }
 
-        //assuming that last value is phrase penalty
-        scoreVector[m_numScoreComponents-1] = 1.0;
+    //assuming that last value is phrase penalty
+    scoreVector[m_numScoreComponents-1] = 1.0;
 
-        statistics->targetPhrase->GetScoreBreakdown().Assign(this, scoreVector);
-        statistics->targetPhrase->Evaluate(src);
+    statistics->targetPhrase->GetScoreBreakdown().Assign(this, scoreVector);
+    statistics->targetPhrase->Evaluate(src);
 
-        ret->Add(new TargetPhrase(*statistics->targetPhrase));
-    }
-    return ret;
+    ret->Add(new TargetPhrase(*statistics->targetPhrase));
+  }
+  return ret;
 }
 
 
@@ -235,8 +231,7 @@ std::vector<std::vector<float> > PhraseDictionaryMultiModel::getWeights(size_t n
   //checking weights passed to mosesserver; only valid for this sentence; *don't* raise exception if client weights are malformed
   if (weights_ptr == NULL || weights_ptr->size() == 0) {
     weights_ptr = &m_multimodelweights; //fall back to weights defined in config
-  }
-  else if(weights_ptr->size() != m_numModels && weights_ptr->size() != m_numModels * numWeights) {
+  } else if(weights_ptr->size() != m_numModels && weights_ptr->size() != m_numModels * numWeights) {
     //TODO: can we pass error message to client if weights are malformed?
     std::stringstream strme;
     strme << "Must have either one multimodel weight per model (" << m_numModels << "), or one per weighted feature and model (" << numWeights << "*" << m_numModels << "). You have " << weights_ptr->size() << ". Reverting to weights in config";
@@ -246,34 +241,30 @@ std::vector<std::vector<float> > PhraseDictionaryMultiModel::getWeights(size_t n
 
   //checking weights defined in config; only valid for this sentence; raise exception if config weights are malformed
   if (weights_ptr == NULL || weights_ptr->size() == 0) {
-    for (size_t i=0;i < m_numModels;i++) {
+    for (size_t i=0; i < m_numModels; i++) {
       raw_weights.push_back(1.0/m_numModels); //uniform weights created online
     }
-  }
-  else if(weights_ptr->size() != m_numModels && weights_ptr->size() != m_numModels * numWeights) {
+  } else if(weights_ptr->size() != m_numModels && weights_ptr->size() != m_numModels * numWeights) {
     std::stringstream strme;
     strme << "Must have either one multimodel weight per model (" << m_numModels << "), or one per weighted feature and model (" << numWeights << "*" << m_numModels << "). You have " << weights_ptr->size() << ".";
     UTIL_THROW(util::Exception, strme.str());
-  }
-  else {
-      raw_weights = *weights_ptr;
+  } else {
+    raw_weights = *weights_ptr;
   }
 
   std::vector<std::vector<float> > multimodelweights (numWeights);
 
-  for (size_t i=0;i < numWeights;i++) {
+  for (size_t i=0; i < numWeights; i++) {
     std::vector<float> weights_onefeature (m_numModels);
     if(raw_weights.size() == m_numModels) {
-        weights_onefeature = raw_weights;
-    }
-    else {
-        copy ( raw_weights.begin()+i*m_numModels, raw_weights.begin()+(i+1)*m_numModels, weights_onefeature.begin() );
+      weights_onefeature = raw_weights;
+    } else {
+      copy ( raw_weights.begin()+i*m_numModels, raw_weights.begin()+(i+1)*m_numModels, weights_onefeature.begin() );
     }
     if(normalize) {
-         multimodelweights[i] = normalizeWeights(weights_onefeature);
-    }
-    else {
-        multimodelweights[i] = weights_onefeature;
+      multimodelweights[i] = normalizeWeights(weights_onefeature);
+    } else {
+      multimodelweights[i] = weights_onefeature;
     }
   }
 
@@ -282,12 +273,12 @@ std::vector<std::vector<float> > PhraseDictionaryMultiModel::getWeights(size_t n
 
 std::vector<float> PhraseDictionaryMultiModel::normalizeWeights(std::vector<float> &weights) const
 {
-    std::vector<float> ret (m_numModels);
-    float total = std::accumulate(weights.begin(),weights.end(),0.0);
-    for (size_t i=0;i < weights.size();i++) {
-        ret[i] = weights[i]/total;
-    }
-    return ret;
+  std::vector<float> ret (m_numModels);
+  float total = std::accumulate(weights.begin(),weights.end(),0.0);
+  for (size_t i=0; i < weights.size(); i++) {
+    ret[i] = weights[i]/total;
+  }
+  return ret;
 }
 
 
@@ -298,7 +289,8 @@ ChartRuleLookupManager *PhraseDictionaryMultiModel::CreateRuleLookupManager(cons
 
 
 //copied from PhraseDictionaryCompact; free memory allocated to TargetPhraseCollection (and each TargetPhrase) at end of sentence
-void PhraseDictionaryMultiModel::CacheForCleanup(TargetPhraseCollection* tpc) {
+void PhraseDictionaryMultiModel::CacheForCleanup(TargetPhraseCollection* tpc)
+{
 #ifdef WITH_THREADS
   boost::mutex::scoped_lock lock(m_sentenceMutex);
   PhraseCache &ref = m_sentenceCache[boost::this_thread::get_id()];
@@ -309,7 +301,8 @@ void PhraseDictionaryMultiModel::CacheForCleanup(TargetPhraseCollection* tpc) {
 }
 
 
-void PhraseDictionaryMultiModel::CleanUpAfterSentenceProcessing(const InputType &source) {
+void PhraseDictionaryMultiModel::CleanUpAfterSentenceProcessing(const InputType &source)
+{
 #ifdef WITH_THREADS
   boost::mutex::scoped_lock lock(m_sentenceMutex);
   PhraseCache &ref = m_sentenceCache[boost::this_thread::get_id()];
@@ -317,7 +310,7 @@ void PhraseDictionaryMultiModel::CleanUpAfterSentenceProcessing(const InputType
   PhraseCache &ref = m_sentenceCache;
 #endif
   for(PhraseCache::iterator it = ref.begin(); it != ref.end(); it++) {
-      delete *it;
+    delete *it;
   }
 
   PhraseCache temp;
@@ -331,149 +324,150 @@ void PhraseDictionaryMultiModel::CleanUpAfterSentenceProcessing(const InputType
 }
 
 
-void  PhraseDictionaryMultiModel::CleanUpComponentModels(const InputType &source) {
-  for(size_t i = 0; i < m_numModels; ++i){
+void  PhraseDictionaryMultiModel::CleanUpComponentModels(const InputType &source)
+{
+  for(size_t i = 0; i < m_numModels; ++i) {
     m_pd[i]->CleanUpAfterSentenceProcessing(source);
   }
 }
 
 
 #ifdef WITH_DLIB
-vector<float> PhraseDictionaryMultiModel::MinimizePerplexity(vector<pair<string, string> > &phrase_pair_vector) {
+vector<float> PhraseDictionaryMultiModel::MinimizePerplexity(vector<pair<string, string> > &phrase_pair_vector)
+{
 
-    const StaticData &staticData = StaticData::Instance();
-    const string& factorDelimiter = staticData.GetFactorDelimiter();
+  const StaticData &staticData = StaticData::Instance();
+  const string& factorDelimiter = staticData.GetFactorDelimiter();
 
-    map<pair<string, string>, size_t> phrase_pair_map;
+  map<pair<string, string>, size_t> phrase_pair_map;
 
-    for ( vector<pair<string, string> >::const_iterator iter = phrase_pair_vector.begin(); iter != phrase_pair_vector.end(); ++iter ) {
-        phrase_pair_map[*iter] += 1;
-    }
+  for ( vector<pair<string, string> >::const_iterator iter = phrase_pair_vector.begin(); iter != phrase_pair_vector.end(); ++iter ) {
+    phrase_pair_map[*iter] += 1;
+  }
 
-    vector<multiModelStatisticsOptimization*> optimizerStats;
+  vector<multiModelStatisticsOptimization*> optimizerStats;
 
-    for ( map<pair<string, string>, size_t>::iterator iter = phrase_pair_map.begin(); iter != phrase_pair_map.end(); ++iter ) {
+  for ( map<pair<string, string>, size_t>::iterator iter = phrase_pair_map.begin(); iter != phrase_pair_map.end(); ++iter ) {
 
-        pair<string, string> phrase_pair = iter->first;
-        string source_string = phrase_pair.first;
-        string target_string = phrase_pair.second;
+    pair<string, string> phrase_pair = iter->first;
+    string source_string = phrase_pair.first;
+    string target_string = phrase_pair.second;
 
-        vector<float> fs(m_numModels);
-        map<string,multiModelStatistics*>* allStats = new(map<string,multiModelStatistics*>);
+    vector<float> fs(m_numModels);
+    map<string,multiModelStatistics*>* allStats = new(map<string,multiModelStatistics*>);
 
-        Phrase sourcePhrase(0);
-        sourcePhrase.CreateFromString(Input, m_input, source_string, factorDelimiter, NULL);
+    Phrase sourcePhrase(0);
+    sourcePhrase.CreateFromString(Input, m_input, source_string, factorDelimiter, NULL);
 
-        CollectSufficientStatistics(sourcePhrase, allStats); //optimization potential: only call this once per source phrase
+    CollectSufficientStatistics(sourcePhrase, allStats); //optimization potential: only call this once per source phrase
 
-        //phrase pair not found; leave cache empty
-        if (allStats->find(target_string) == allStats->end()) {
-            RemoveAllInMap(*allStats);
-            delete allStats;
-            continue;
-        }
+    //phrase pair not found; leave cache empty
+    if (allStats->find(target_string) == allStats->end()) {
+      RemoveAllInMap(*allStats);
+      delete allStats;
+      continue;
+    }
 
-        multiModelStatisticsOptimization* targetStatistics = new multiModelStatisticsOptimization();
-        targetStatistics->targetPhrase = new TargetPhrase(*(*allStats)[target_string]->targetPhrase);
-        targetStatistics->p = (*allStats)[target_string]->p;
-        targetStatistics->f = iter->second;
-        optimizerStats.push_back(targetStatistics);
+    multiModelStatisticsOptimization* targetStatistics = new multiModelStatisticsOptimization();
+    targetStatistics->targetPhrase = new TargetPhrase(*(*allStats)[target_string]->targetPhrase);
+    targetStatistics->p = (*allStats)[target_string]->p;
+    targetStatistics->f = iter->second;
+    optimizerStats.push_back(targetStatistics);
 
-        RemoveAllInMap(*allStats);
-        delete allStats;
-        }
+    RemoveAllInMap(*allStats);
+    delete allStats;
+  }
 
-    Sentence sentence;
-    CleanUpAfterSentenceProcessing(sentence); // free memory used by compact phrase tables
+  Sentence sentence;
+  CleanUpAfterSentenceProcessing(sentence); // free memory used by compact phrase tables
 
-    size_t numWeights = m_numScoreComponents;
-    if (m_mode == "interpolate") {
-        //interpolation of phrase penalty is skipped, and fixed-value (2.718) is used instead. results will be screwed up if phrase penalty is not last feature
-        numWeights = m_numScoreComponents-1;
-    }
+  size_t numWeights = m_numScoreComponents;
+  if (m_mode == "interpolate") {
+    //interpolation of phrase penalty is skipped, and fixed-value (2.718) is used instead. results will be screwed up if phrase penalty is not last feature
+    numWeights = m_numScoreComponents-1;
+  }
 
-    vector<float> ret (m_numModels*numWeights);
-    for (size_t iFeature=0; iFeature < numWeights; iFeature++) {
+  vector<float> ret (m_numModels*numWeights);
+  for (size_t iFeature=0; iFeature < numWeights; iFeature++) {
 
-        CrossEntropy * ObjectiveFunction = new CrossEntropy(optimizerStats, this, iFeature);
+    CrossEntropy * ObjectiveFunction = new CrossEntropy(optimizerStats, this, iFeature);
 
-        vector<float> weight_vector = Optimize(ObjectiveFunction, m_numModels);
+    vector<float> weight_vector = Optimize(ObjectiveFunction, m_numModels);
 
-        if (m_mode == "interpolate") {
-            weight_vector = normalizeWeights(weight_vector);
-        }
+    if (m_mode == "interpolate") {
+      weight_vector = normalizeWeights(weight_vector);
+    }
 
-        cerr << "Weight vector for feature " << iFeature << ": ";
-        for (size_t i=0; i < m_numModels; i++) {
-            ret[(iFeature*m_numModels)+i] = weight_vector[i];
-            cerr << weight_vector[i] << " ";
-        }
-        cerr << endl;
-        delete ObjectiveFunction;
+    cerr << "Weight vector for feature " << iFeature << ": ";
+    for (size_t i=0; i < m_numModels; i++) {
+      ret[(iFeature*m_numModels)+i] = weight_vector[i];
+      cerr << weight_vector[i] << " ";
     }
+    cerr << endl;
+    delete ObjectiveFunction;
+  }
 
-    RemoveAllInColl(optimizerStats);
-    return ret;
+  RemoveAllInColl(optimizerStats);
+  return ret;
 
 }
 
-vector<float> PhraseDictionaryMultiModel::Optimize(OptimizationObjective *ObjectiveFunction, size_t numModels) {
-
-        dlib::matrix<double,0,1> starting_point;
-        starting_point.set_size(numModels);
-        starting_point = 1.0;
-
-        try {
-            dlib::find_min_bobyqa(*ObjectiveFunction,
-                            starting_point,
-                            2*numModels+1,    // number of interpolation points
-                            dlib::uniform_matrix<double>(numModels,1, 1e-09),  // lower bound constraint
-                            dlib::uniform_matrix<double>(numModels,1, 1e100),   // upper bound constraint
-                            1.0,    // initial trust region radius
-                            1e-5,  // stopping trust region radius
-                            10000    // max number of objective function evaluations
-            );
-        }
-        catch (dlib::bobyqa_failure& e)
-        {
-            cerr << e.what() << endl;
-        }
+vector<float> PhraseDictionaryMultiModel::Optimize(OptimizationObjective *ObjectiveFunction, size_t numModels)
+{
 
-        vector<float> weight_vector (numModels);
+  dlib::matrix<double,0,1> starting_point;
+  starting_point.set_size(numModels);
+  starting_point = 1.0;
+
+  try {
+    dlib::find_min_bobyqa(*ObjectiveFunction,
+                          starting_point,
+                          2*numModels+1,    // number of interpolation points
+                          dlib::uniform_matrix<double>(numModels,1, 1e-09),  // lower bound constraint
+                          dlib::uniform_matrix<double>(numModels,1, 1e100),   // upper bound constraint
+                          1.0,    // initial trust region radius
+                          1e-5,  // stopping trust region radius
+                          10000    // max number of objective function evaluations
+                         );
+  } catch (dlib::bobyqa_failure& e) {
+    cerr << e.what() << endl;
+  }
 
-        for (int i=0; i < starting_point.nr(); i++) {
-            weight_vector[i] = starting_point(i);
-        }
+  vector<float> weight_vector (numModels);
+
+  for (int i=0; i < starting_point.nr(); i++) {
+    weight_vector[i] = starting_point(i);
+  }
 
-        cerr << "Cross-entropy: " << (*ObjectiveFunction)(starting_point) << endl;
-        return weight_vector;
+  cerr << "Cross-entropy: " << (*ObjectiveFunction)(starting_point) << endl;
+  return weight_vector;
 }
 
 
 double CrossEntropy::operator() ( const dlib::matrix<double,0,1>& arg) const
 {
-    double total = 0.0;
-    double n = 0.0;
-    std::vector<float> weight_vector (m_model->m_numModels);
+  double total = 0.0;
+  double n = 0.0;
+  std::vector<float> weight_vector (m_model->m_numModels);
 
-    for (int i=0; i < arg.nr(); i++) {
-        weight_vector[i] = arg(i);
-    }
-    if (m_model->m_mode == "interpolate") {
-        weight_vector = m_model->normalizeWeights(weight_vector);
-    }
+  for (int i=0; i < arg.nr(); i++) {
+    weight_vector[i] = arg(i);
+  }
+  if (m_model->m_mode == "interpolate") {
+    weight_vector = m_model->normalizeWeights(weight_vector);
+  }
 
-    for ( std::vector<multiModelStatisticsOptimization*>::const_iterator iter = m_optimizerStats.begin(); iter != m_optimizerStats.end(); ++iter ) {
-        multiModelStatisticsOptimization* statistics = *iter;
-        size_t f = statistics->f;
+  for ( std::vector<multiModelStatisticsOptimization*>::const_iterator iter = m_optimizerStats.begin(); iter != m_optimizerStats.end(); ++iter ) {
+    multiModelStatisticsOptimization* statistics = *iter;
+    size_t f = statistics->f;
 
-        double score;
-        score = std::inner_product(statistics->p[m_iFeature].begin(), statistics->p[m_iFeature].end(), weight_vector.begin(), 0.0);
+    double score;
+    score = std::inner_product(statistics->p[m_iFeature].begin(), statistics->p[m_iFeature].end(), weight_vector.begin(), 0.0);
 
-        total -= (FloorScore(TransformScore(score))/TransformScore(2))*f;
-        n += f;
-    }
-    return total/n;
+    total -= (FloorScore(TransformScore(score))/TransformScore(2))*f;
+    n += f;
+  }
+  return total/n;
 }
 
 #endif
diff --git a/moses/TranslationModel/PhraseDictionaryMultiModel.h b/moses/TranslationModel/PhraseDictionaryMultiModel.h
index 467333b0a..5feb4f373 100644
--- a/moses/TranslationModel/PhraseDictionaryMultiModel.h
+++ b/moses/TranslationModel/PhraseDictionaryMultiModel.h
@@ -36,15 +36,17 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 namespace Moses
 {
 
-  struct multiModelStatistics {
-    TargetPhrase *targetPhrase;
-    std::vector<std::vector<float> > p;
-    ~multiModelStatistics() {delete targetPhrase;};
+struct multiModelStatistics {
+  TargetPhrase *targetPhrase;
+  std::vector<std::vector<float> > p;
+  ~multiModelStatistics() {
+    delete targetPhrase;
   };
+};
 
-  struct multiModelStatisticsOptimization: multiModelStatistics {
-    size_t f;
-  };
+struct multiModelStatisticsOptimization: multiModelStatistics {
+  size_t f;
+};
 
 class OptimizationObjective;
 
@@ -53,7 +55,7 @@ class OptimizationObjective;
 class PhraseDictionaryMultiModel: public PhraseDictionary
 {
 #ifdef WITH_DLIB
-friend class CrossEntropy;
+  friend class CrossEntropy;
 #endif
 
 public:
@@ -100,34 +102,33 @@ protected:
 };
 
 #ifdef WITH_DLIB
-class OptimizationObjective 
+class OptimizationObjective
 {
 public:
 
-    virtual double operator() ( const dlib::matrix<double,0,1>& arg) const = 0;
+  virtual double operator() ( const dlib::matrix<double,0,1>& arg) const = 0;
 };
 
 class CrossEntropy: public OptimizationObjective
 {
 public:
 
-    CrossEntropy (
-        std::vector<multiModelStatisticsOptimization*> &optimizerStats,
-        PhraseDictionaryMultiModel * model,
-        size_t iFeature
-    )
-    {
-        m_optimizerStats = optimizerStats;
-        m_model = model;
-        m_iFeature = iFeature;
-    }
+  CrossEntropy (
+    std::vector<multiModelStatisticsOptimization*> &optimizerStats,
+    PhraseDictionaryMultiModel * model,
+    size_t iFeature
+  ) {
+    m_optimizerStats = optimizerStats;
+    m_model = model;
+    m_iFeature = iFeature;
+  }
 
-    double operator() ( const dlib::matrix<double,0,1>& arg) const;
+  double operator() ( const dlib::matrix<double,0,1>& arg) const;
 
 protected:
-    std::vector<multiModelStatisticsOptimization*> m_optimizerStats;
-    PhraseDictionaryMultiModel * m_model;
-    size_t m_iFeature;
+  std::vector<multiModelStatisticsOptimization*> m_optimizerStats;
+  PhraseDictionaryMultiModel * m_model;
+  size_t m_iFeature;
 };
 #endif
 
diff --git a/moses/TranslationModel/PhraseDictionaryMultiModelCounts.cpp b/moses/TranslationModel/PhraseDictionaryMultiModelCounts.cpp
index 4c61fba91..298e23a9b 100644
--- a/moses/TranslationModel/PhraseDictionaryMultiModelCounts.cpp
+++ b/moses/TranslationModel/PhraseDictionaryMultiModelCounts.cpp
@@ -61,59 +61,56 @@ namespace Moses
 {
 
 PhraseDictionaryMultiModelCounts::PhraseDictionaryMultiModelCounts(const std::string &line)
-:PhraseDictionaryMultiModel("PhraseDictionaryMultiModelCounts", line)
+  :PhraseDictionaryMultiModel("PhraseDictionaryMultiModelCounts", line)
 {
-    m_mode = "instance_weighting"; //TODO: set this in config; use m_mode to switch between interpolation and instance weighting
-    m_combineFunction = InstanceWeighting;
-    //m_mode = "interpolate";
-    //m_combineFunction = LinearInterpolationFromCounts;
-
-    for (size_t i = 0; i < m_args.size(); ++i) {
-      const vector<string> &args = m_args[i];
-      if (args[0] == "mode") {
-        m_mode = args[1];
-        if (m_mode == "instance_weighting")
-          m_combineFunction = InstanceWeighting;
-        else if (m_mode == "interpolate") {
-          m_combineFunction = LinearInterpolationFromCounts;
-        }
-        else {
-          ostringstream msg;
-          msg << "combination mode unknown: " << m_mode;
-          throw runtime_error(msg.str());
-        }
-
-      }
-      else if (args[0] == "lex-e2f") {
-        m_lexE2FStr = Tokenize(args[1], ",");
-        CHECK(m_lexE2FStr.size() == m_pdStr.size());
-      }
-      else if (args[0] == "lex-f2e") {
-        m_lexF2EStr = Tokenize(args[1], ",");
-        CHECK(m_lexF2EStr.size() == m_pdStr.size());
+  m_mode = "instance_weighting"; //TODO: set this in config; use m_mode to switch between interpolation and instance weighting
+  m_combineFunction = InstanceWeighting;
+  //m_mode = "interpolate";
+  //m_combineFunction = LinearInterpolationFromCounts;
+
+  for (size_t i = 0; i < m_args.size(); ++i) {
+    const vector<string> &args = m_args[i];
+    if (args[0] == "mode") {
+      m_mode = args[1];
+      if (m_mode == "instance_weighting")
+        m_combineFunction = InstanceWeighting;
+      else if (m_mode == "interpolate") {
+        m_combineFunction = LinearInterpolationFromCounts;
+      } else {
+        ostringstream msg;
+        msg << "combination mode unknown: " << m_mode;
+        throw runtime_error(msg.str());
       }
 
-      else if (args[0] == "target-table") {
-        m_targetTable = Tokenize(args[1], ",");
-        CHECK(m_targetTable.size() == m_pdStr.size());
-      }
+    } else if (args[0] == "lex-e2f") {
+      m_lexE2FStr = Tokenize(args[1], ",");
+      CHECK(m_lexE2FStr.size() == m_pdStr.size());
+    } else if (args[0] == "lex-f2e") {
+      m_lexF2EStr = Tokenize(args[1], ",");
+      CHECK(m_lexF2EStr.size() == m_pdStr.size());
+    }
 
+    else if (args[0] == "target-table") {
+      m_targetTable = Tokenize(args[1], ",");
+      CHECK(m_targetTable.size() == m_pdStr.size());
+    }
 
 
-    } // for
+
+  } // for
 
 }
 
 PhraseDictionaryMultiModelCounts::~PhraseDictionaryMultiModelCounts()
 {
-    RemoveAllInColl(m_lexTable_e2f);
-    RemoveAllInColl(m_lexTable_f2e);
+  RemoveAllInColl(m_lexTable_e2f);
+  RemoveAllInColl(m_lexTable_f2e);
 }
 
 
 bool PhraseDictionaryMultiModelCounts::InitDictionary()
 {
-  for(size_t i = 0; i < m_numModels; ++i){
+  for(size_t i = 0; i < m_numModels; ++i) {
 
     // phrase table
     const string &ptName = m_pdStr[i];
@@ -189,8 +186,8 @@ bool PhraseDictionaryMultiModelCounts::InitDictionary()
             pdta_inverse->SetNumScoreComponentMultiModel(m_numScoreComponent);
             pdta_inverse->Load(input, output, target_table, m_weight, m_componentTableLimit, languageModels, m_weightWP);
             m_inverse_pd.push_back(pdta_inverse);
-      } else if (implementation == Compact) { 
-#ifndef WIN32
+      } else if (implementation == Compact) {
+  #ifndef WIN32
             PhraseDictionaryCompact* pdc = new PhraseDictionaryCompact(m_numScoreComponent, implementation, m_feature_load);
             pdc->SetNumScoreComponentMultiModel(m_numScoreComponent); //for compact models, we need to pass number of log-linear components to correctly resize the score vector
             pdc->Load( input, output, main_table, m_weight, componentTableLimit, languageModels, m_weightWP);
@@ -200,9 +197,9 @@ bool PhraseDictionaryMultiModelCounts::InitDictionary()
             pdc_inverse->SetNumScoreComponentMultiModel(m_numScoreComponent);
             pdc_inverse->Load( input, output, target_table, m_weight, componentTableLimit, languageModels, m_weightWP);
             m_inverse_pd.push_back(pdc_inverse);
-#else
-            UTIL_THROW(util::Exception, "Compact phrase table not supported in windows"); 
-#endif
+  #else
+            UTIL_THROW(util::Exception, "Compact phrase table not supported in windows");
+  #endif
       }
       else {
         UTIL_THROW(util::Exception,"PhraseDictionaryMultiModel does not support phrase table type " << implementation);
@@ -218,7 +215,7 @@ bool PhraseDictionaryMultiModelCounts::InitDictionary()
 
   }
 
-*/
+  */
 
   return true;
 }
@@ -250,7 +247,7 @@ const TargetPhraseCollection *PhraseDictionaryMultiModelCounts::GetTargetPhraseC
 void PhraseDictionaryMultiModelCounts::CollectSufficientStatistics(const Phrase& src, vector<float> &fs, map<string,multiModelCountsStatistics*>* allStats) const
 //fill fs and allStats with statistics from models
 {
-  for(size_t i = 0; i < m_numModels; ++i){
+  for(size_t i = 0; i < m_numModels; ++i) {
     const PhraseDictionary &pd = *m_pd[i];
 
     TargetPhraseCollection *ret_raw = (TargetPhraseCollection*)  pd.GetTargetPhraseCollection( src);
@@ -298,9 +295,9 @@ void PhraseDictionaryMultiModelCounts::CollectSufficientStatistics(const Phrase&
     multiModelCountsStatistics * statistics = iter->second;
 
     for (size_t i = 0; i < m_numModels; ++i) {
-        if (!statistics->ft[i]) {
-            statistics->ft[i] = GetTargetCount(static_cast<const Phrase&>(*statistics->targetPhrase), i);
-        }
+      if (!statistics->ft[i]) {
+        statistics->ft[i] = GetTargetCount(static_cast<const Phrase&>(*statistics->targetPhrase), i);
+      }
     }
   }
 }
@@ -313,28 +310,27 @@ TargetPhraseCollection* PhraseDictionaryMultiModelCounts::CreateTargetPhraseColl
     multiModelCountsStatistics * statistics = iter->second;
 
     if (statistics->targetPhrase->GetAlignTerm().GetSize() == 0) {
-        UTIL_THROW(util::Exception, " alignment information empty\ncount-tables need to include alignment information for computation of lexical weights.\nUse --phrase-word-alignment during training; for on-disk tables, also set -alignment-info when creating on-disk tables."); 
+      UTIL_THROW(util::Exception, " alignment information empty\ncount-tables need to include alignment information for computation of lexical weights.\nUse --phrase-word-alignment during training; for on-disk tables, also set -alignment-info when creating on-disk tables.");
     }
 
     try {
-        pair<vector< set<size_t> >, vector< set<size_t> > > alignment = GetAlignmentsForLexWeights(src, static_cast<const Phrase&>(*statistics->targetPhrase), statistics->targetPhrase->GetAlignTerm());
-        vector< set<size_t> > alignedToT = alignment.first;
-        vector< set<size_t> > alignedToS = alignment.second;
-        double lexst = ComputeWeightedLexicalTranslation(static_cast<const Phrase&>(*statistics->targetPhrase), src, alignedToS, m_lexTable_e2f, multimodelweights[1], m_output, m_input );
-        double lexts = ComputeWeightedLexicalTranslation(src, static_cast<const Phrase&>(*statistics->targetPhrase), alignedToT, m_lexTable_f2e, multimodelweights[3], m_input, m_output );
-
-        Scores scoreVector(5);
-        scoreVector[0] = FloorScore(TransformScore(m_combineFunction(statistics->fst, statistics->ft, multimodelweights[0])));
-        scoreVector[1] = FloorScore(TransformScore(lexst));
-        scoreVector[2] = FloorScore(TransformScore(m_combineFunction(statistics->fst, fs, multimodelweights[2])));
-        scoreVector[3] = FloorScore(TransformScore(lexts));
-        scoreVector[4] = FloorScore(TransformScore(2.718));
-
-        statistics->targetPhrase->GetScoreBreakdown().Assign(this, scoreVector);
-        statistics->targetPhrase->Evaluate(src);
-    }
-    catch (AlignmentException& e) {
-        continue;
+      pair<vector< set<size_t> >, vector< set<size_t> > > alignment = GetAlignmentsForLexWeights(src, static_cast<const Phrase&>(*statistics->targetPhrase), statistics->targetPhrase->GetAlignTerm());
+      vector< set<size_t> > alignedToT = alignment.first;
+      vector< set<size_t> > alignedToS = alignment.second;
+      double lexst = ComputeWeightedLexicalTranslation(static_cast<const Phrase&>(*statistics->targetPhrase), src, alignedToS, m_lexTable_e2f, multimodelweights[1], m_output, m_input );
+      double lexts = ComputeWeightedLexicalTranslation(src, static_cast<const Phrase&>(*statistics->targetPhrase), alignedToT, m_lexTable_f2e, multimodelweights[3], m_input, m_output );
+
+      Scores scoreVector(5);
+      scoreVector[0] = FloorScore(TransformScore(m_combineFunction(statistics->fst, statistics->ft, multimodelweights[0])));
+      scoreVector[1] = FloorScore(TransformScore(lexst));
+      scoreVector[2] = FloorScore(TransformScore(m_combineFunction(statistics->fst, fs, multimodelweights[2])));
+      scoreVector[3] = FloorScore(TransformScore(lexts));
+      scoreVector[4] = FloorScore(TransformScore(2.718));
+
+      statistics->targetPhrase->GetScoreBreakdown().Assign(this, scoreVector);
+      statistics->targetPhrase->Evaluate(src);
+    } catch (AlignmentException& e) {
+      continue;
     }
 
     ret->Add(new TargetPhrase(*statistics->targetPhrase));
@@ -346,47 +342,50 @@ TargetPhraseCollection* PhraseDictionaryMultiModelCounts::CreateTargetPhraseColl
 }
 
 
-float PhraseDictionaryMultiModelCounts::GetTargetCount(const Phrase &target, size_t modelIndex) const {
+float PhraseDictionaryMultiModelCounts::GetTargetCount(const Phrase &target, size_t modelIndex) const
+{
 
-    const PhraseDictionary &pd = *m_inverse_pd[modelIndex];
-    TargetPhraseCollection *ret_raw = (TargetPhraseCollection*)  pd.GetTargetPhraseCollection(target);
+  const PhraseDictionary &pd = *m_inverse_pd[modelIndex];
+  TargetPhraseCollection *ret_raw = (TargetPhraseCollection*)  pd.GetTargetPhraseCollection(target);
 
-    // in inverse mode, we want the first score of the first phrase pair (note: if we were to work with truly symmetric models, it would be the third score)
-    if (ret_raw != NULL) {
-        TargetPhrase * targetPhrase = *(ret_raw->begin());
-        return UntransformScore(targetPhrase->GetScoreBreakdown().GetScoresForProducer(&pd)[0]);
-    }
+  // in inverse mode, we want the first score of the first phrase pair (note: if we were to work with truly symmetric models, it would be the third score)
+  if (ret_raw != NULL) {
+    TargetPhrase * targetPhrase = *(ret_raw->begin());
+    return UntransformScore(targetPhrase->GetScoreBreakdown().GetScoresForProducer(&pd)[0]);
+  }
 
-    // target phrase unknown
-    else return 0;
+  // target phrase unknown
+  else return 0;
 }
 
 
-pair<PhraseDictionaryMultiModelCounts::AlignVector,PhraseDictionaryMultiModelCounts::AlignVector> PhraseDictionaryMultiModelCounts::GetAlignmentsForLexWeights(const Phrase &phraseS, const Phrase &phraseT, const AlignmentInfo &alignment) const {
+pair<PhraseDictionaryMultiModelCounts::AlignVector,PhraseDictionaryMultiModelCounts::AlignVector> PhraseDictionaryMultiModelCounts::GetAlignmentsForLexWeights(const Phrase &phraseS, const Phrase &phraseT, const AlignmentInfo &alignment) const
+{
 
-    size_t tsize = phraseT.GetSize();
-    size_t ssize = phraseS.GetSize();
-    AlignVector alignedToT (tsize);
-    AlignVector alignedToS (ssize);
-    AlignmentInfo::const_iterator iter;
+  size_t tsize = phraseT.GetSize();
+  size_t ssize = phraseS.GetSize();
+  AlignVector alignedToT (tsize);
+  AlignVector alignedToS (ssize);
+  AlignmentInfo::const_iterator iter;
 
-    for (iter = alignment.begin(); iter != alignment.end(); ++iter) {
+  for (iter = alignment.begin(); iter != alignment.end(); ++iter) {
     const pair<size_t,size_t> &alignPair = *iter;
-        size_t s = alignPair.first;
-        size_t t = alignPair.second;
-        if (s >= ssize || t >= tsize) {
-            cerr << "Error: inconsistent alignment for phrase pair: " << phraseS << " - " << phraseT << endl;
-            cerr << "phrase pair will be discarded" << endl;
-            throw AlignmentException();
-        }
-        alignedToT[t].insert( s );
-        alignedToS[s].insert( t );
+    size_t s = alignPair.first;
+    size_t t = alignPair.second;
+    if (s >= ssize || t >= tsize) {
+      cerr << "Error: inconsistent alignment for phrase pair: " << phraseS << " - " << phraseT << endl;
+      cerr << "phrase pair will be discarded" << endl;
+      throw AlignmentException();
+    }
+    alignedToT[t].insert( s );
+    alignedToS[s].insert( t );
   }
   return make_pair(alignedToT,alignedToS);
 }
 
 
-double PhraseDictionaryMultiModelCounts::ComputeWeightedLexicalTranslation( const Phrase &phraseS, const Phrase &phraseT, AlignVector &alignment, const vector<lexicalTable*> &tables, vector<float> &multimodelweights, const vector<FactorType> &input_factors, const vector<FactorType> &output_factors ) const {
+double PhraseDictionaryMultiModelCounts::ComputeWeightedLexicalTranslation( const Phrase &phraseS, const Phrase &phraseT, AlignVector &alignment, const vector<lexicalTable*> &tables, vector<float> &multimodelweights, const vector<FactorType> &input_factors, const vector<FactorType> &output_factors ) const
+{
   // lexical translation probability
 
   double lexScore = 1.0;
@@ -414,7 +413,8 @@ double PhraseDictionaryMultiModelCounts::ComputeWeightedLexicalTranslation( cons
 }
 
 
-lexicalCache PhraseDictionaryMultiModelCounts::CacheLexicalStatistics( const Phrase &phraseS, const Phrase &phraseT, AlignVector &alignment, const vector<lexicalTable*> &tables, const vector<FactorType> &input_factors, const vector<FactorType> &output_factors ) {
+lexicalCache PhraseDictionaryMultiModelCounts::CacheLexicalStatistics( const Phrase &phraseS, const Phrase &phraseT, AlignVector &alignment, const vector<lexicalTable*> &tables, const vector<FactorType> &input_factors, const vector<FactorType> &output_factors )
+{
 //do all the necessary lexical table lookups and get counts, but don't apply weights yet
 
   string null = "NULL";
@@ -455,60 +455,65 @@ lexicalCache PhraseDictionaryMultiModelCounts::CacheLexicalStatistics( const Phr
 }
 
 
-double PhraseDictionaryMultiModelCounts::ComputeWeightedLexicalTranslationFromCache( lexicalCache &cache, vector<float> &weights ) const {
+double PhraseDictionaryMultiModelCounts::ComputeWeightedLexicalTranslationFromCache( lexicalCache &cache, vector<float> &weights ) const
+{
   // lexical translation probability
 
   double lexScore = 1.0;
 
   for (lexicalCache::const_iterator iter = cache.begin();  iter != cache.end(); ++iter) {
-      vector<lexicalPair> t_vector = *iter;
-      double thisWordScore = 0;
-      for ( vector<lexicalPair>::const_iterator iter2 = t_vector.begin();  iter2 != t_vector.end(); ++iter2) {
-          vector<float> joint_count = iter2->first;
-          vector<float> marginal = iter2->second;
-          thisWordScore += m_combineFunction(joint_count, marginal, weights);
-      }
-      lexScore *= thisWordScore / t_vector.size();
+    vector<lexicalPair> t_vector = *iter;
+    double thisWordScore = 0;
+    for ( vector<lexicalPair>::const_iterator iter2 = t_vector.begin();  iter2 != t_vector.end(); ++iter2) {
+      vector<float> joint_count = iter2->first;
+      vector<float> marginal = iter2->second;
+      thisWordScore += m_combineFunction(joint_count, marginal, weights);
+    }
+    lexScore *= thisWordScore / t_vector.size();
   }
   return lexScore;
 }
 
 // get lexical probability for single word alignment pair
-double PhraseDictionaryMultiModelCounts::GetLexicalProbability( string &wordS, string &wordT, const vector<lexicalTable*> &tables, vector<float> &multimodelweights ) const {
-    vector<float> joint_count (m_numModels);
-    vector<float> marginals (m_numModels);
+double PhraseDictionaryMultiModelCounts::GetLexicalProbability( string &wordS, string &wordT, const vector<lexicalTable*> &tables, vector<float> &multimodelweights ) const
+{
+  vector<float> joint_count (m_numModels);
+  vector<float> marginals (m_numModels);
 
-    FillLexicalCountsJoint(wordS, wordT, joint_count, tables);
-    FillLexicalCountsMarginal(wordS, marginals, tables);
+  FillLexicalCountsJoint(wordS, wordT, joint_count, tables);
+  FillLexicalCountsMarginal(wordS, marginals, tables);
 
-    double lexProb = m_combineFunction(joint_count, marginals, multimodelweights);
+  double lexProb = m_combineFunction(joint_count, marginals, multimodelweights);
 
   return lexProb;
 }
 
 
-void PhraseDictionaryMultiModelCounts::FillLexicalCountsJoint(string &wordS, string &wordT, vector<float> &count, const vector<lexicalTable*> &tables) const {
-    for (size_t i=0;i < m_numModels;i++) {
-        lexicalMapJoint::iterator joint_s = tables[i]->joint.find( wordS );
-        if (joint_s == tables[i]->joint.end()) count[i] = 0.0;
-        else {
-            lexicalMap::iterator joint_t = joint_s->second.find( wordT );
-            if (joint_t == joint_s->second.end()) count[i] = 0.0;
-            else count[i] = joint_t->second;
-        }
+void PhraseDictionaryMultiModelCounts::FillLexicalCountsJoint(string &wordS, string &wordT, vector<float> &count, const vector<lexicalTable*> &tables) const
+{
+  for (size_t i=0; i < m_numModels; i++) {
+    lexicalMapJoint::iterator joint_s = tables[i]->joint.find( wordS );
+    if (joint_s == tables[i]->joint.end()) count[i] = 0.0;
+    else {
+      lexicalMap::iterator joint_t = joint_s->second.find( wordT );
+      if (joint_t == joint_s->second.end()) count[i] = 0.0;
+      else count[i] = joint_t->second;
     }
+  }
 }
 
-void PhraseDictionaryMultiModelCounts::FillLexicalCountsMarginal(string &wordS, vector<float> &count, const vector<lexicalTable*> &tables) const {
-    for (size_t i=0;i < m_numModels;i++) {
-        lexicalMap::iterator marginal_s = tables[i]->marginal.find( wordS );
-        if (marginal_s == tables[i]->marginal.end()) count[i] = 0.0;
-        else count[i] = marginal_s->second;
-    }
+void PhraseDictionaryMultiModelCounts::FillLexicalCountsMarginal(string &wordS, vector<float> &count, const vector<lexicalTable*> &tables) const
+{
+  for (size_t i=0; i < m_numModels; i++) {
+    lexicalMap::iterator marginal_s = tables[i]->marginal.find( wordS );
+    if (marginal_s == tables[i]->marginal.end()) count[i] = 0.0;
+    else count[i] = marginal_s->second;
+  }
 }
 
 
-void PhraseDictionaryMultiModelCounts::LoadLexicalTable( string &fileName, lexicalTable* ltable) {
+void PhraseDictionaryMultiModelCounts::LoadLexicalTable( string &fileName, lexicalTable* ltable)
+{
 
   cerr << "Loading lexical translation table from " << fileName;
   ifstream inFile;
@@ -549,165 +554,161 @@ void PhraseDictionaryMultiModelCounts::LoadLexicalTable( string &fileName, lexic
 
 
 #ifdef WITH_DLIB
-vector<float> PhraseDictionaryMultiModelCounts::MinimizePerplexity(vector<pair<string, string> > &phrase_pair_vector) {
+vector<float> PhraseDictionaryMultiModelCounts::MinimizePerplexity(vector<pair<string, string> > &phrase_pair_vector)
+{
 
-    const StaticData &staticData = StaticData::Instance();
-    const string& factorDelimiter = staticData.GetFactorDelimiter();
+  const StaticData &staticData = StaticData::Instance();
+  const string& factorDelimiter = staticData.GetFactorDelimiter();
 
-    map<pair<string, string>, size_t> phrase_pair_map;
+  map<pair<string, string>, size_t> phrase_pair_map;
 
-    for ( vector<pair<string, string> >::const_iterator iter = phrase_pair_vector.begin(); iter != phrase_pair_vector.end(); ++iter ) {
-        phrase_pair_map[*iter] += 1;
-    }
+  for ( vector<pair<string, string> >::const_iterator iter = phrase_pair_vector.begin(); iter != phrase_pair_vector.end(); ++iter ) {
+    phrase_pair_map[*iter] += 1;
+  }
 
-    vector<multiModelCountsStatisticsOptimization*> optimizerStats;
+  vector<multiModelCountsStatisticsOptimization*> optimizerStats;
 
-    for ( map<pair<string, string>, size_t>::iterator iter = phrase_pair_map.begin(); iter != phrase_pair_map.end(); ++iter ) {
+  for ( map<pair<string, string>, size_t>::iterator iter = phrase_pair_map.begin(); iter != phrase_pair_map.end(); ++iter ) {
 
-        pair<string, string> phrase_pair = iter->first;
-        string source_string = phrase_pair.first;
-        string target_string = phrase_pair.second;
+    pair<string, string> phrase_pair = iter->first;
+    string source_string = phrase_pair.first;
+    string target_string = phrase_pair.second;
 
-        vector<float> fs(m_numModels);
-        map<string,multiModelCountsStatistics*>* allStats = new(map<string,multiModelCountsStatistics*>);
+    vector<float> fs(m_numModels);
+    map<string,multiModelCountsStatistics*>* allStats = new(map<string,multiModelCountsStatistics*>);
 
-        Phrase sourcePhrase(0);
-        sourcePhrase.CreateFromString(Input, m_input, source_string, factorDelimiter, NULL);
+    Phrase sourcePhrase(0);
+    sourcePhrase.CreateFromString(Input, m_input, source_string, factorDelimiter, NULL);
 
-        CollectSufficientStatistics(sourcePhrase, fs, allStats); //optimization potential: only call this once per source phrase
+    CollectSufficientStatistics(sourcePhrase, fs, allStats); //optimization potential: only call this once per source phrase
 
-        //phrase pair not found; leave cache empty
-        if (allStats->find(target_string) == allStats->end()) {
-            RemoveAllInMap(*allStats);
-            delete allStats;
-            continue;
-        }
+    //phrase pair not found; leave cache empty
+    if (allStats->find(target_string) == allStats->end()) {
+      RemoveAllInMap(*allStats);
+      delete allStats;
+      continue;
+    }
 
-        multiModelCountsStatisticsOptimization * targetStatistics = new multiModelCountsStatisticsOptimization();
-        targetStatistics->targetPhrase = new TargetPhrase(*(*allStats)[target_string]->targetPhrase);
-        targetStatistics->fs = fs;
-        targetStatistics->fst = (*allStats)[target_string]->fst;
-        targetStatistics->ft = (*allStats)[target_string]->ft;
-        targetStatistics->f = iter->second;
+    multiModelCountsStatisticsOptimization * targetStatistics = new multiModelCountsStatisticsOptimization();
+    targetStatistics->targetPhrase = new TargetPhrase(*(*allStats)[target_string]->targetPhrase);
+    targetStatistics->fs = fs;
+    targetStatistics->fst = (*allStats)[target_string]->fst;
+    targetStatistics->ft = (*allStats)[target_string]->ft;
+    targetStatistics->f = iter->second;
 
-        try {
-            pair<vector< set<size_t> >, vector< set<size_t> > > alignment = GetAlignmentsForLexWeights(sourcePhrase, static_cast<const Phrase&>(*targetStatistics->targetPhrase), targetStatistics->targetPhrase->GetAlignTerm());
-            targetStatistics->lexCachee2f = CacheLexicalStatistics(static_cast<const Phrase&>(*targetStatistics->targetPhrase), sourcePhrase, alignment.second, m_lexTable_e2f, m_output, m_input );
-            targetStatistics->lexCachef2e = CacheLexicalStatistics(sourcePhrase, static_cast<const Phrase&>(*targetStatistics->targetPhrase), alignment.first, m_lexTable_f2e, m_input, m_output );
+    try {
+      pair<vector< set<size_t> >, vector< set<size_t> > > alignment = GetAlignmentsForLexWeights(sourcePhrase, static_cast<const Phrase&>(*targetStatistics->targetPhrase), targetStatistics->targetPhrase->GetAlignTerm());
+      targetStatistics->lexCachee2f = CacheLexicalStatistics(static_cast<const Phrase&>(*targetStatistics->targetPhrase), sourcePhrase, alignment.second, m_lexTable_e2f, m_output, m_input );
+      targetStatistics->lexCachef2e = CacheLexicalStatistics(sourcePhrase, static_cast<const Phrase&>(*targetStatistics->targetPhrase), alignment.first, m_lexTable_f2e, m_input, m_output );
 
-            optimizerStats.push_back(targetStatistics);
-        }
-        catch (AlignmentException& e) {}
+      optimizerStats.push_back(targetStatistics);
+    } catch (AlignmentException& e) {}
 
-        RemoveAllInMap(*allStats);
-        delete allStats;
-    }
+    RemoveAllInMap(*allStats);
+    delete allStats;
+  }
 
-    Sentence sentence;
-    CleanUpAfterSentenceProcessing(sentence); // free memory used by compact phrase tables
+  Sentence sentence;
+  CleanUpAfterSentenceProcessing(sentence); // free memory used by compact phrase tables
 
-    vector<float> ret (m_numModels*4);
-    for (size_t iFeature=0; iFeature < 4; iFeature++) {
+  vector<float> ret (m_numModels*4);
+  for (size_t iFeature=0; iFeature < 4; iFeature++) {
 
-        CrossEntropyCounts * ObjectiveFunction = new CrossEntropyCounts(optimizerStats, this, iFeature);
+    CrossEntropyCounts * ObjectiveFunction = new CrossEntropyCounts(optimizerStats, this, iFeature);
 
-        vector<float> weight_vector = Optimize(ObjectiveFunction, m_numModels);
+    vector<float> weight_vector = Optimize(ObjectiveFunction, m_numModels);
 
-        if (m_mode == "interpolate") {
-            weight_vector = normalizeWeights(weight_vector);
-        }
-        else if (m_mode == "instance_weighting") {
-            float first_value = weight_vector[0];
-            for (size_t i=0; i < m_numModels; i++) {
-                weight_vector[i] = weight_vector[i]/first_value;
-            }
-        }
-        cerr << "Weight vector for feature " << iFeature << ": ";
-        for (size_t i=0; i < m_numModels; i++) {
-            ret[(iFeature*m_numModels)+i] = weight_vector[i];
-            cerr << weight_vector[i] << " ";
-        }
-        cerr << endl;
-        delete ObjectiveFunction;
+    if (m_mode == "interpolate") {
+      weight_vector = normalizeWeights(weight_vector);
+    } else if (m_mode == "instance_weighting") {
+      float first_value = weight_vector[0];
+      for (size_t i=0; i < m_numModels; i++) {
+        weight_vector[i] = weight_vector[i]/first_value;
+      }
+    }
+    cerr << "Weight vector for feature " << iFeature << ": ";
+    for (size_t i=0; i < m_numModels; i++) {
+      ret[(iFeature*m_numModels)+i] = weight_vector[i];
+      cerr << weight_vector[i] << " ";
     }
+    cerr << endl;
+    delete ObjectiveFunction;
+  }
 
-    RemoveAllInColl(optimizerStats);
-    return ret;
+  RemoveAllInColl(optimizerStats);
+  return ret;
 
 }
 
 double CrossEntropyCounts::operator() ( const dlib::matrix<double,0,1>& arg) const
 {
-    double total = 0.0;
-    double n = 0.0;
-    std::vector<float> weight_vector (m_model->m_numModels);
+  double total = 0.0;
+  double n = 0.0;
+  std::vector<float> weight_vector (m_model->m_numModels);
 
-    for (int i=0; i < arg.nr(); i++) {
-        weight_vector[i] = arg(i);
-    }
-    if (m_model->m_mode == "interpolate") {
-        weight_vector = m_model->normalizeWeights(weight_vector);
-    }
-
-    for ( std::vector<multiModelCountsStatisticsOptimization*>::const_iterator iter = m_optimizerStats.begin(); iter != m_optimizerStats.end(); ++iter ) {
-        multiModelCountsStatisticsOptimization* statistics = *iter;
-        size_t f = statistics->f;
+  for (int i=0; i < arg.nr(); i++) {
+    weight_vector[i] = arg(i);
+  }
+  if (m_model->m_mode == "interpolate") {
+    weight_vector = m_model->normalizeWeights(weight_vector);
+  }
 
-        double score;
-        if (m_iFeature == 0) {
-            score = m_model->m_combineFunction(statistics->fst, statistics->ft, weight_vector);
-        }
-        else if (m_iFeature == 1) {
-            score = m_model->ComputeWeightedLexicalTranslationFromCache(statistics->lexCachee2f, weight_vector);
-        }
-        else if (m_iFeature == 2) {
-            score = m_model->m_combineFunction(statistics->fst, statistics->fs, weight_vector);
-        }
-        else if (m_iFeature == 3) {
-            score = m_model->ComputeWeightedLexicalTranslationFromCache(statistics->lexCachef2e, weight_vector);
-        }
-        else {
-            score = 0;
-            UTIL_THROW(util::Exception, "Trying to optimize feature that I don't know. Aborting");
-        }
-        total -= (FloorScore(TransformScore(score))/TransformScore(2))*f;
-        n += f;
+  for ( std::vector<multiModelCountsStatisticsOptimization*>::const_iterator iter = m_optimizerStats.begin(); iter != m_optimizerStats.end(); ++iter ) {
+    multiModelCountsStatisticsOptimization* statistics = *iter;
+    size_t f = statistics->f;
+
+    double score;
+    if (m_iFeature == 0) {
+      score = m_model->m_combineFunction(statistics->fst, statistics->ft, weight_vector);
+    } else if (m_iFeature == 1) {
+      score = m_model->ComputeWeightedLexicalTranslationFromCache(statistics->lexCachee2f, weight_vector);
+    } else if (m_iFeature == 2) {
+      score = m_model->m_combineFunction(statistics->fst, statistics->fs, weight_vector);
+    } else if (m_iFeature == 3) {
+      score = m_model->ComputeWeightedLexicalTranslationFromCache(statistics->lexCachef2e, weight_vector);
+    } else {
+      score = 0;
+      UTIL_THROW(util::Exception, "Trying to optimize feature that I don't know. Aborting");
     }
-    return total/n;
+    total -= (FloorScore(TransformScore(score))/TransformScore(2))*f;
+    n += f;
+  }
+  return total/n;
 }
 
 #endif
 
 // calculate weighted probability based on instance weighting of joint counts and marginal counts
-double InstanceWeighting(vector<float> &joint_counts, vector<float> &marginals, vector<float> &multimodelweights) {
+double InstanceWeighting(vector<float> &joint_counts, vector<float> &marginals, vector<float> &multimodelweights)
+{
 
-    double joint_counts_weighted =  inner_product(joint_counts.begin(), joint_counts.end(), multimodelweights.begin(), 0.0);
-    double marginals_weighted = inner_product(marginals.begin(), marginals.end(), multimodelweights.begin(), 0.0);
+  double joint_counts_weighted =  inner_product(joint_counts.begin(), joint_counts.end(), multimodelweights.begin(), 0.0);
+  double marginals_weighted = inner_product(marginals.begin(), marginals.end(), multimodelweights.begin(), 0.0);
 
-    if (marginals_weighted == 0) {
-        return 0;
-    }
-    else {
-        return joint_counts_weighted/marginals_weighted;
-    }
+  if (marginals_weighted == 0) {
+    return 0;
+  } else {
+    return joint_counts_weighted/marginals_weighted;
+  }
 }
 
 
 // calculate linear interpolation of relative frequency estimates based on joint count and marginal counts
 //unused for now; enable in config?
-double LinearInterpolationFromCounts(vector<float> &joint_counts, vector<float> &marginals, vector<float> &multimodelweights) {
+double LinearInterpolationFromCounts(vector<float> &joint_counts, vector<float> &marginals, vector<float> &multimodelweights)
+{
 
-    vector<float> p(marginals.size());
+  vector<float> p(marginals.size());
 
-    for (size_t i=0;i < marginals.size();i++) {
-        if (marginals[i] != 0) {
-            p[i] = joint_counts[i]/marginals[i];
-        }
+  for (size_t i=0; i < marginals.size(); i++) {
+    if (marginals[i] != 0) {
+      p[i] = joint_counts[i]/marginals[i];
     }
+  }
 
-    double p_weighted = inner_product(p.begin(), p.end(), multimodelweights.begin(), 0.0);
+  double p_weighted = inner_product(p.begin(), p.end(), multimodelweights.begin(), 0.0);
 
-    return p_weighted;
+  return p_weighted;
 }
 
 
diff --git a/moses/TranslationModel/PhraseDictionaryMultiModelCounts.h b/moses/TranslationModel/PhraseDictionaryMultiModelCounts.h
index ef89272c3..04be77dd6 100644
--- a/moses/TranslationModel/PhraseDictionaryMultiModelCounts.h
+++ b/moses/TranslationModel/PhraseDictionaryMultiModelCounts.h
@@ -35,32 +35,33 @@ extern std::vector<std::string> tokenize( const char*);
 namespace Moses
 {
 
-  typedef boost::unordered_map<std::string, double > lexicalMap;
-  typedef boost::unordered_map<std::string, lexicalMap > lexicalMapJoint;
-  typedef std::pair<std::vector<float>, std::vector<float> > lexicalPair;
-  typedef std::vector<std::vector<lexicalPair> > lexicalCache;
+typedef boost::unordered_map<std::string, double > lexicalMap;
+typedef boost::unordered_map<std::string, lexicalMap > lexicalMapJoint;
+typedef std::pair<std::vector<float>, std::vector<float> > lexicalPair;
+typedef std::vector<std::vector<lexicalPair> > lexicalCache;
 
-  struct multiModelCountsStatistics : multiModelStatistics {
-    std::vector<float> fst, ft;
-  };
+struct multiModelCountsStatistics : multiModelStatistics {
+  std::vector<float> fst, ft;
+};
 
-  struct multiModelCountsStatisticsOptimization: multiModelCountsStatistics {
-    std::vector<float> fs;
-    lexicalCache lexCachee2f, lexCachef2e;
-    size_t f;
-  };
+struct multiModelCountsStatisticsOptimization: multiModelCountsStatistics {
+  std::vector<float> fs;
+  lexicalCache lexCachee2f, lexCachef2e;
+  size_t f;
+};
 
-  struct lexicalTable {
-    lexicalMapJoint joint;
-    lexicalMap marginal;
-  };
+struct lexicalTable {
+  lexicalMapJoint joint;
+  lexicalMap marginal;
+};
 
-  double InstanceWeighting(std::vector<float> &joint_counts, std::vector<float> &marginals, std::vector<float> &multimodelweights);
-  double LinearInterpolationFromCounts(std::vector<float> &joint_counts, std::vector<float> &marginals, std::vector<float> &multimodelweights);
+double InstanceWeighting(std::vector<float> &joint_counts, std::vector<float> &marginals, std::vector<float> &multimodelweights);
+double LinearInterpolationFromCounts(std::vector<float> &joint_counts, std::vector<float> &marginals, std::vector<float> &multimodelweights);
 
 
 //thrown if alignment information does not match phrase pair (out-of-bound alignment points)
-class AlignmentException : public std::runtime_error {
+class AlignmentException : public std::runtime_error
+{
 public:
   AlignmentException() : std::runtime_error("AlignmentException") { }
 };
@@ -72,10 +73,10 @@ class PhraseDictionaryMultiModelCounts: public PhraseDictionaryMultiModel
 {
 
 #ifdef WITH_DLIB
-friend class CrossEntropyCounts;
+  friend class CrossEntropyCounts;
 #endif
 
-typedef std::vector< std::set<size_t> > AlignVector;
+  typedef std::vector< std::set<size_t> > AlignVector;
 
 
 public:
@@ -116,23 +117,22 @@ class CrossEntropyCounts: public OptimizationObjective
 {
 public:
 
-    CrossEntropyCounts (
-        std::vector<multiModelCountsStatisticsOptimization*> &optimizerStats,
-        PhraseDictionaryMultiModelCounts * model,
-        size_t iFeature
-    )
-    {
-        m_optimizerStats = optimizerStats;
-        m_model = model;
-        m_iFeature = iFeature;
-    }
+  CrossEntropyCounts (
+    std::vector<multiModelCountsStatisticsOptimization*> &optimizerStats,
+    PhraseDictionaryMultiModelCounts * model,
+    size_t iFeature
+  ) {
+    m_optimizerStats = optimizerStats;
+    m_model = model;
+    m_iFeature = iFeature;
+  }
 
-    double operator() ( const dlib::matrix<double,0,1>& arg) const;
+  double operator() ( const dlib::matrix<double,0,1>& arg) const;
 
 private:
-    std::vector<multiModelCountsStatisticsOptimization*> m_optimizerStats;
-    PhraseDictionaryMultiModelCounts * m_model;
-    size_t m_iFeature;
+  std::vector<multiModelCountsStatisticsOptimization*> m_optimizerStats;
+  PhraseDictionaryMultiModelCounts * m_model;
+  size_t m_iFeature;
 };
 #endif
 
diff --git a/moses/TranslationModel/PhraseDictionaryNodeMemory.cpp b/moses/TranslationModel/PhraseDictionaryNodeMemory.cpp
index 465c076d5..389c74394 100644
--- a/moses/TranslationModel/PhraseDictionaryNodeMemory.cpp
+++ b/moses/TranslationModel/PhraseDictionaryNodeMemory.cpp
@@ -31,8 +31,8 @@ namespace Moses
 PhraseDictionaryNodeMemory::~PhraseDictionaryNodeMemory()
 {
   for (TerminalMap::iterator iter = m_sourceTermMap.begin(); iter != m_sourceTermMap.end(); ++iter) {
-	const PhraseDictionaryNodeMemory *node = iter->second;
-	delete node;
+    const PhraseDictionaryNodeMemory *node = iter->second;
+    delete node;
   }
   for (NonTerminalMap::iterator iter = m_nonTermMap.begin(); iter != m_nonTermMap.end(); ++iter) {
     const PhraseDictionaryNodeMemory *node = iter->second;
@@ -41,7 +41,8 @@ PhraseDictionaryNodeMemory::~PhraseDictionaryNodeMemory()
   delete m_targetPhraseCollection;
 }
 
-TargetPhraseCollection &PhraseDictionaryNodeMemory::GetOrCreateTargetPhraseCollection() {
+TargetPhraseCollection &PhraseDictionaryNodeMemory::GetOrCreateTargetPhraseCollection()
+{
   if (m_targetPhraseCollection == NULL)
     m_targetPhraseCollection = new TargetPhraseCollection();
   return *m_targetPhraseCollection;
@@ -138,9 +139,9 @@ void PhraseDictionaryNodeMemory::Clear()
   m_sourceTermMap.clear();
   m_nonTermMap.clear();
   delete m_targetPhraseCollection;
-  
+
 }
-  
+
 std::ostream& operator<<(std::ostream &out, const PhraseDictionaryNodeMemory &node)
 {
   out << node.GetTargetPhraseCollection();
diff --git a/moses/TranslationModel/PhraseDictionaryNodeMemory.h b/moses/TranslationModel/PhraseDictionaryNodeMemory.h
index 672196ba2..136e10c0a 100644
--- a/moses/TranslationModel/PhraseDictionaryNodeMemory.h
+++ b/moses/TranslationModel/PhraseDictionaryNodeMemory.h
@@ -39,8 +39,8 @@ namespace Moses
 
 class PhraseDictionaryMemory;
 class PhraseDictionaryFuzzyMatch;
-  
-  //! @todo why?
+
+//! @todo why?
 class NonTerminalMapKeyHasher
 {
 public:
@@ -152,7 +152,7 @@ public:
   }
 
   void Clear();
-  
+
   TO_STRING();
 };
 
diff --git a/moses/TranslationModel/PhraseDictionaryTree.cpp b/moses/TranslationModel/PhraseDictionaryTree.cpp
index 321924dfe..c5eefc290 100644
--- a/moses/TranslationModel/PhraseDictionaryTree.cpp
+++ b/moses/TranslationModel/PhraseDictionaryTree.cpp
@@ -157,7 +157,8 @@ PhraseDictionaryTree::PrefixPtr::operator bool() const
 typedef LVoc<std::string> WordVoc;
 
 
-class PDTimp {
+class PDTimp
+{
 public:
   typedef PrefixTreeF<LabelId,OFF_T> PTF;
   typedef FilePtr<PTF> CPT;
@@ -481,7 +482,7 @@ int PhraseDictionaryTree::Create(std::istream& inFile,const std::string& out)
   std::vector<OFF_T> vo;
   size_t lnc=0;
   size_t numElement = NOT_FOUND; // 3=old format, 5=async format which include word alignment info
-  size_t missingAlignmentCount = 0; 
+  size_t missingAlignmentCount = 0;
 
   while(getline(inFile, line)) {
     ++lnc;
@@ -553,9 +554,9 @@ int PhraseDictionaryTree::Create(std::istream& inFile,const std::string& out)
     if (!sparseFeatureString.empty()) {
       std::vector<std::string> sparseTokens = Tokenize(sparseFeatureString);
       if (sparseTokens.size() % 2 != 0) {
-        TRACE_ERR("ERROR: incorrectly formatted sparse feature string: " << 
-          sparseFeatureString << std::endl);
-        abort();  
+        TRACE_ERR("ERROR: incorrectly formatted sparse feature string: " <<
+                  sparseFeatureString << std::endl);
+        abort();
       }
       for (size_t i = 0; i < sparseTokens.size(); i+=2) {
         fnames.push_back(imp->tv.add(sparseTokens[i]));
@@ -624,7 +625,7 @@ int PhraseDictionaryTree::Create(std::istream& inFile,const std::string& out)
 
   if ( PrintWordAlignment()) {
     TRACE_ERR("Count of lines with missing alignments: " <<
-      missingAlignmentCount << "/" << lnc << "\n");
+              missingAlignmentCount << "/" << lnc << "\n");
   }
 
   fClose(os);
diff --git a/moses/TranslationModel/PhraseDictionaryTree.h b/moses/TranslationModel/PhraseDictionaryTree.h
index 1b88637c3..6214c8194 100644
--- a/moses/TranslationModel/PhraseDictionaryTree.h
+++ b/moses/TranslationModel/PhraseDictionaryTree.h
@@ -31,8 +31,7 @@ class PDTimp;
 typedef PrefixTreeF<LabelId,OFF_T> PTF;
 
 //typedef std::pair<std::vector<std::string const*>,Scores > StringTgtCand;
-struct StringTgtCand
-{
+struct StringTgtCand {
   typedef std::vector<std::string const*> Tokens;
   Tokens tokens;
   Scores scores;
@@ -86,7 +85,7 @@ public:
   // get the target candidates for a given phrase
   void GetTargetCandidates(const std::vector<std::string>& src,
                            std::vector<StringTgtCand>& rv) const;
-                           
+
 
   // get the target candidates for a given phrase
   void GetTargetCandidates(const std::vector<std::string>& src,
diff --git a/moses/TranslationModel/RuleTable/Loader.h b/moses/TranslationModel/RuleTable/Loader.h
index 4d3e03351..48390e37e 100644
--- a/moses/TranslationModel/RuleTable/Loader.h
+++ b/moses/TranslationModel/RuleTable/Loader.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -32,7 +32,7 @@ namespace Moses
  */
 class RuleTableLoader
 {
- public:
+public:
   virtual ~RuleTableLoader() {}
 
   virtual bool Load(const std::vector<FactorType> &input,
@@ -41,7 +41,7 @@ class RuleTableLoader
                     size_t tableLimit,
                     RuleTableTrie &) = 0;
 
- protected:
+protected:
   // Provide access to RuleTableTrie's private SortAndPrune function.
   void SortAndPrune(RuleTableTrie &ruleTable) {
     ruleTable.SortAndPrune();
@@ -50,10 +50,10 @@ class RuleTableLoader
   // Provide access to RuleTableTrie's private
   // GetOrCreateTargetPhraseCollection function.
   TargetPhraseCollection &GetOrCreateTargetPhraseCollection(
-      RuleTableTrie &ruleTable
-      , const Phrase &source
-      , const TargetPhrase &target
-      , const Word *sourceLHS) {
+    RuleTableTrie &ruleTable
+    , const Phrase &source
+    , const TargetPhrase &target
+    , const Word *sourceLHS) {
     return ruleTable.GetOrCreateTargetPhraseCollection(source, target, sourceLHS);
   }
 };
diff --git a/moses/TranslationModel/RuleTable/LoaderCompact.cpp b/moses/TranslationModel/RuleTable/LoaderCompact.cpp
index f235b3e79..2b4a6003a 100644
--- a/moses/TranslationModel/RuleTable/LoaderCompact.cpp
+++ b/moses/TranslationModel/RuleTable/LoaderCompact.cpp
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -84,9 +84,9 @@ bool RuleTableLoaderCompact::Load(const std::vector<FactorType> &input,
 }
 
 void RuleTableLoaderCompact::LoadVocabularySection(
-    LineReader &reader,
-    const std::vector<FactorType> &factorTypes,
-    std::vector<Word> &vocabulary)
+  LineReader &reader,
+  const std::vector<FactorType> &factorTypes,
+  std::vector<Word> &vocabulary)
 {
   // Read symbol count.
   reader.ReadLine();
@@ -106,10 +106,10 @@ void RuleTableLoaderCompact::LoadVocabularySection(
 }
 
 void RuleTableLoaderCompact::LoadPhraseSection(
-    LineReader &reader,
-    const std::vector<Word> &vocab,
-    std::vector<Phrase> &rhsPhrases,
-    std::vector<size_t> &lhsIds)
+  LineReader &reader,
+  const std::vector<Word> &vocab,
+  std::vector<Phrase> &rhsPhrases,
+  std::vector<size_t> &lhsIds)
 {
   // Read phrase count.
   reader.ReadLine();
@@ -132,7 +132,7 @@ void RuleTableLoaderCompact::LoadPhraseSection(
 }
 
 void RuleTableLoaderCompact::LoadAlignmentSection(
-    LineReader &reader, std::vector<const AlignmentInfo *> &alignmentSets, std::vector<Phrase> &sourcePhrases)
+  LineReader &reader, std::vector<const AlignmentInfo *> &alignmentSets, std::vector<Phrase> &sourcePhrases)
 {
   // Read alignment set count.
   reader.ReadLine();
@@ -144,8 +144,8 @@ void RuleTableLoaderCompact::LoadAlignmentSection(
   std::vector<size_t> points;
   for (size_t i = 0; i < alignmentSetCount; ++i) {
     // Read alignment set, lookup in collection, and store pointer.
-  	alignTerm.clear();
-  	alignNonTerm.clear();
+    alignTerm.clear();
+    alignNonTerm.clear();
     tokens.clear();
 
     reader.ReadLine();
@@ -157,11 +157,10 @@ void RuleTableLoaderCompact::LoadAlignmentSection(
       std::pair<size_t, size_t> alignmentPair(points[0], points[1]);
 
       if (sourcePhrases[i].GetWord(alignmentPair.first).IsNonTerminal()) {
-      	alignNonTerm.insert(alignmentPair);
+        alignNonTerm.insert(alignmentPair);
+      } else {
+        alignTerm.insert(alignmentPair);
       }
-    	else {
-    		alignTerm.insert(alignmentPair);
-    	}
 
     }
     alignmentSets[i*2] = AlignmentInfoCollection::Instance().Add(alignNonTerm);
@@ -170,13 +169,13 @@ void RuleTableLoaderCompact::LoadAlignmentSection(
 }
 
 bool RuleTableLoaderCompact::LoadRuleSection(
-    LineReader &reader,
-    const std::vector<Word> &vocab,
-    const std::vector<Phrase> &sourcePhrases,
-    const std::vector<Phrase> &targetPhrases,
-    const std::vector<size_t> &targetLhsIds,
-    const std::vector<const AlignmentInfo *> &alignmentSets,
-    RuleTableTrie &ruleTable)
+  LineReader &reader,
+  const std::vector<Word> &vocab,
+  const std::vector<Phrase> &sourcePhrases,
+  const std::vector<Phrase> &targetPhrases,
+  const std::vector<size_t> &targetLhsIds,
+  const std::vector<const AlignmentInfo *> &alignmentSets,
+  RuleTableTrie &ruleTable)
 {
   // Read rule count.
   reader.ReadLine();
@@ -232,7 +231,7 @@ bool RuleTableLoaderCompact::LoadRuleSection(
 
     // Insert rule into table.
     TargetPhraseCollection &coll = GetOrCreateTargetPhraseCollection(
-        ruleTable, sourcePhrase, *targetPhrase, &sourceLHS);
+                                     ruleTable, sourcePhrase, *targetPhrase, &sourceLHS);
     coll.Add(targetPhrase);
   }
 
diff --git a/moses/TranslationModel/RuleTable/LoaderCompact.h b/moses/TranslationModel/RuleTable/LoaderCompact.h
index 314cfca57..26e19fce6 100644
--- a/moses/TranslationModel/RuleTable/LoaderCompact.h
+++ b/moses/TranslationModel/RuleTable/LoaderCompact.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -35,14 +35,14 @@ class RuleTableTrie;
 //! @todo ask phil williams
 class RuleTableLoaderCompact : public RuleTableLoader
 {
- public:
+public:
   bool Load(const std::vector<FactorType> &input,
             const std::vector<FactorType> &output,
             const std::string &inFile,
             size_t tableLimit,
             RuleTableTrie &);
 
- private:
+private:
   struct LineReader {
     LineReader(std::istream &input) : m_input(input), m_lineNum(0) {}
     void ReadLine() {
@@ -78,8 +78,7 @@ class RuleTableLoaderCompact : public RuleTableLoader
 
   // Like Tokenize() but records starting positions of tokens (instead of
   // copying substrings) and assumes delimiter is ASCII space character.
-  void FindTokens(std::vector<size_t> &output, const std::string &str) const
-  {
+  void FindTokens(std::vector<size_t> &output, const std::string &str) const {
     // Skip delimiters at beginning.
     size_t lastPos = str.find_first_not_of(' ', 0);
     // Find first "non-delimiter".
diff --git a/moses/TranslationModel/RuleTable/LoaderFactory.cpp b/moses/TranslationModel/RuleTable/LoaderFactory.cpp
index b3bd00555..cdbfc965a 100644
--- a/moses/TranslationModel/RuleTable/LoaderFactory.cpp
+++ b/moses/TranslationModel/RuleTable/LoaderFactory.cpp
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -37,7 +37,7 @@ namespace Moses
 // Determines the rule table type by peeking inside the file then creates
 // a suitable RuleTableLoader object.
 std::auto_ptr<RuleTableLoader> RuleTableLoaderFactory::Create(
-    const std::string &path)
+  const std::string &path)
 {
   InputFileStream input(path);
   std::string line;
@@ -54,17 +54,15 @@ std::auto_ptr<RuleTableLoader> RuleTableLoaderFactory::Create(
       msg << "Unsupported compact rule table format: " << tokens[0];
       UserMessage::Add(msg.str());
       return std::auto_ptr<RuleTableLoader>();
+    } else if (tokens[0] == "[X]" && tokens[1] == "|||") {
+      return std::auto_ptr<RuleTableLoader>(new
+                                            RuleTableLoaderHiero());
+
     }
-    else if (tokens[0] == "[X]" && tokens[1] == "|||") {
-      return std::auto_ptr<RuleTableLoader>(new 
-          RuleTableLoaderHiero());
-      
-    }
-    
+
     return std::auto_ptr<RuleTableLoader>(new RuleTableLoaderStandard());
-  }
-  else
-  { // empty phrase table
+  } else {
+    // empty phrase table
     return std::auto_ptr<RuleTableLoader>(new RuleTableLoaderStandard());
   }
 }
diff --git a/moses/TranslationModel/RuleTable/LoaderFactory.h b/moses/TranslationModel/RuleTable/LoaderFactory.h
index 01c168680..c695738e4 100644
--- a/moses/TranslationModel/RuleTable/LoaderFactory.h
+++ b/moses/TranslationModel/RuleTable/LoaderFactory.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -30,7 +30,7 @@ class RuleTableLoader;
 //! Creates a RuleTableLoader object suitable for loading the specified file.
 class RuleTableLoaderFactory
 {
- public:
+public:
   static std::auto_ptr<RuleTableLoader> Create(const std::string &);
 };
 
diff --git a/moses/TranslationModel/RuleTable/LoaderHiero.cpp b/moses/TranslationModel/RuleTable/LoaderHiero.cpp
index c0526be02..81289d9b2 100644
--- a/moses/TranslationModel/RuleTable/LoaderHiero.cpp
+++ b/moses/TranslationModel/RuleTable/LoaderHiero.cpp
@@ -11,19 +11,20 @@
 
 using namespace std;
 
-namespace Moses {
-  
+namespace Moses
+{
+
 bool RuleTableLoaderHiero::Load(const std::vector<FactorType> &input,
-          const std::vector<FactorType> &output,
-          const std::string &inFile,
-          size_t tableLimit,
-          RuleTableTrie &ruleTable)
+                                const std::vector<FactorType> &output,
+                                const std::string &inFile,
+                                size_t tableLimit,
+                                RuleTableTrie &ruleTable)
 {
   bool ret = RuleTableLoaderStandard::Load(HieroFormat
-              ,input, output
-              ,inFile
-              ,tableLimit
-              ,ruleTable);
+             ,input, output
+             ,inFile
+             ,tableLimit
+             ,ruleTable);
   return ret;
 }
 
diff --git a/moses/TranslationModel/RuleTable/LoaderHiero.h b/moses/TranslationModel/RuleTable/LoaderHiero.h
index 1f6b66725..099787281 100644
--- a/moses/TranslationModel/RuleTable/LoaderHiero.h
+++ b/moses/TranslationModel/RuleTable/LoaderHiero.h
@@ -11,7 +11,8 @@
 
 #include "LoaderStandard.h"
 
-namespace Moses {
+namespace Moses
+{
 
 //! specific implementation of SCFG loader to load rule tables formatted in Hiero-style format
 class RuleTableLoaderHiero : public RuleTableLoaderStandard
diff --git a/moses/TranslationModel/RuleTable/LoaderStandard.cpp b/moses/TranslationModel/RuleTable/LoaderStandard.cpp
index 566684775..fb5052c40 100644
--- a/moses/TranslationModel/RuleTable/LoaderStandard.cpp
+++ b/moses/TranslationModel/RuleTable/LoaderStandard.cpp
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -59,38 +59,34 @@ bool RuleTableLoaderStandard::Load(const std::vector<FactorType> &input
   return ret;
 
 }
-  
+
 void ReformatHieroRule(int sourceTarget, string &phrase, map<size_t, pair<size_t, size_t> > &ntAlign)
 {
   vector<string> toks;
   Tokenize(toks, phrase, " ");
 
-  for (size_t i = 0; i < toks.size(); ++i)
-  {
+  for (size_t i = 0; i < toks.size(); ++i) {
     string &tok = toks[i];
     size_t tokLen = tok.size();
-    if (tok.substr(0, 1) == "[" && tok.substr(tokLen - 1, 1) == "]")
-    { // no-term
+    if (tok.substr(0, 1) == "[" && tok.substr(tokLen - 1, 1) == "]") {
+      // no-term
       vector<string> split = Tokenize(tok, ",");
       CHECK(split.size() == 2);
-      
+
       tok = "[X]" + split[0] + "]";
       size_t coIndex = Scan<size_t>(split[1]);
-      
+
       pair<size_t, size_t> &alignPoint = ntAlign[coIndex];
-      if (sourceTarget == 0)
-      {
+      if (sourceTarget == 0) {
         alignPoint.first = i;
-      }
-      else
-      {
+      } else {
         alignPoint.second = i;
       }
     }
   }
-  
+
   phrase = Join(" ", toks) + " [X]";
-  
+
 }
 
 void ReformateHieroScore(string &scoreString)
@@ -98,8 +94,7 @@ void ReformateHieroScore(string &scoreString)
   vector<string> toks;
   Tokenize(toks, scoreString, " ");
 
-  for (size_t i = 0; i < toks.size(); ++i)
-  {
+  for (size_t i = 0; i < toks.size(); ++i) {
     string &tok = toks[i];
     vector<string> nameValue = Tokenize(tok, "=");
     CHECK(nameValue.size() == 2);
@@ -108,49 +103,48 @@ void ReformateHieroScore(string &scoreString)
     score = exp(-score);
     tok = SPrint(score);
   }
-  
+
   scoreString = Join(" ", toks);
 }
-  
+
 void ReformatHieroRule(const string &lineOrig, string &out)
-{  
+{
   vector<string> tokens;
   vector<float> scoreVector;
-  
+
   TokenizeMultiCharSeparator(tokens, lineOrig, "|||" );
 
   string &sourcePhraseString = tokens[1]
-              , &targetPhraseString = tokens[2]
-              , &scoreString        = tokens[3];
+                               , &targetPhraseString = tokens[2]
+                                   , &scoreString        = tokens[3];
 
   map<size_t, pair<size_t, size_t> > ntAlign;
   ReformatHieroRule(0, sourcePhraseString, ntAlign);
   ReformatHieroRule(1, targetPhraseString, ntAlign);
   ReformateHieroScore(scoreString);
-  
+
   stringstream align;
   map<size_t, pair<size_t, size_t> >::const_iterator iterAlign;
-  for (iterAlign = ntAlign.begin(); iterAlign != ntAlign.end(); ++iterAlign)
-  {
+  for (iterAlign = ntAlign.begin(); iterAlign != ntAlign.end(); ++iterAlign) {
     const pair<size_t, size_t> &alignPoint = iterAlign->second;
     align << alignPoint.first << "-" << alignPoint.second << " ";
   }
-  
+
   stringstream ret;
   ret << sourcePhraseString << " ||| "
-      << targetPhraseString << " ||| " 
+      << targetPhraseString << " ||| "
       << scoreString << " ||| "
       << align.str();
-  
+
   out = ret.str();
 }
-  
+
 bool RuleTableLoaderStandard::Load(FormatType format
-                                , const std::vector<FactorType> &input
-                                , const std::vector<FactorType> &output
-                                , const std::string &inFile
-                                , size_t /* tableLimit */
-                                , RuleTableTrie &ruleTable)
+                                   , const std::vector<FactorType> &input
+                                   , const std::vector<FactorType> &output
+                                   , const std::string &inFile
+                                   , size_t /* tableLimit */
+                                   , RuleTableTrie &ruleTable)
 {
   PrintUserTime(string("Start loading text SCFG phrase table. ") + (format==MosesFormat?"Moses ":"Hiero ") + " format");
 
@@ -174,7 +168,9 @@ bool RuleTableLoaderStandard::Load(FormatType format
   while(true) {
     try {
       line = in.ReadLine();
-    } catch (const util::EndOfFileException &e) { break; }
+    } catch (const util::EndOfFileException &e) {
+      break;
+    }
 
     if (format == HieroFormat) { // inefficiently reformat line
       hiero_before.assign(line.data(), line.size());
@@ -186,7 +182,7 @@ bool RuleTableLoaderStandard::Load(FormatType format
     StringPiece sourcePhraseString(*pipes);
     StringPiece targetPhraseString(*++pipes);
     StringPiece scoreString(*++pipes);
-    
+
     StringPiece alignString;
     if (++pipes) {
       StringPiece temp(*pipes);
@@ -237,9 +233,9 @@ bool RuleTableLoaderStandard::Load(FormatType format
     // rest of target phrase
     targetPhrase->SetAlignmentInfo(alignString);
     targetPhrase->SetTargetLHS(targetLHS);
-    
+
     //targetPhrase->SetDebugOutput(string("New Format pt ") + line);
-    
+
     if (++pipes) {
       StringPiece sparseString(*pipes);
       targetPhrase->SetSparseScore(&ruleTable, sparseString);
diff --git a/moses/TranslationModel/RuleTable/LoaderStandard.h b/moses/TranslationModel/RuleTable/LoaderStandard.h
index 4beefea39..b47f7c00b 100644
--- a/moses/TranslationModel/RuleTable/LoaderStandard.h
+++ b/moses/TranslationModel/RuleTable/LoaderStandard.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -35,7 +35,7 @@ protected:
             const std::string &inFile,
             size_t tableLimit,
             RuleTableTrie &);
- public:
+public:
   bool Load(const std::vector<FactorType> &input,
             const std::vector<FactorType> &output,
             const std::string &inFile,
diff --git a/moses/TranslationModel/RuleTable/PhraseDictionaryALSuffixArray.cpp b/moses/TranslationModel/RuleTable/PhraseDictionaryALSuffixArray.cpp
index 8f736af60..1f8ebab15 100644
--- a/moses/TranslationModel/RuleTable/PhraseDictionaryALSuffixArray.cpp
+++ b/moses/TranslationModel/RuleTable/PhraseDictionaryALSuffixArray.cpp
@@ -18,14 +18,14 @@
 
 using namespace std;
 
-namespace Moses 
+namespace Moses
 {
 PhraseDictionaryALSuffixArray::PhraseDictionaryALSuffixArray(const std::string &line)
-: PhraseDictionaryMemory("PhraseDictionaryALSuffixArray", line)
+  : PhraseDictionaryMemory("PhraseDictionaryALSuffixArray", line)
 {
   const StaticData &staticData = StaticData::Instance();
   if (staticData.ThreadCount() > 1) {
-	throw runtime_error("Suffix array implementation is not threadsafe");
+    throw runtime_error("Suffix array implementation is not threadsafe");
   }
 }
 
@@ -33,14 +33,14 @@ void PhraseDictionaryALSuffixArray::InitializeForInput(InputType const& source)
 {
   // populate with rules for this sentence
   long translationId = source.GetTranslationId();
-  
+
   string grammarFile = GetFilePath() + "/grammar." + SPrint(translationId) + ".gz";
-  
+
   std::auto_ptr<RuleTableLoader> loader =
-  RuleTableLoaderFactory::Create(grammarFile);
+    RuleTableLoaderFactory::Create(grammarFile);
   bool ret = loader->Load(m_input, m_output, grammarFile, m_tableLimit,
                           *this);
-  
+
   CHECK(ret);
 }
 
diff --git a/moses/TranslationModel/RuleTable/PhraseDictionaryALSuffixArray.h b/moses/TranslationModel/RuleTable/PhraseDictionaryALSuffixArray.h
index 81e1e02cf..aa4c15258 100644
--- a/moses/TranslationModel/RuleTable/PhraseDictionaryALSuffixArray.h
+++ b/moses/TranslationModel/RuleTable/PhraseDictionaryALSuffixArray.h
@@ -11,26 +11,28 @@
 
 #include "moses/TranslationModel/PhraseDictionaryMemory.h"
 
-namespace Moses {
-  
+namespace Moses
+{
+
 /** Implementation of in-memory phrase table for use with Adam Lopez's suffix array.
  * Does 2 things that the normal in-memory pt doesn't do:
  *  1. Loads grammar for a sentence to be decoded only when the sentence is being decoded. Unload afterwards
     2. Format of the pt file follows Hiero, rather than Moses
- */   
+ */
 class PhraseDictionaryALSuffixArray : public PhraseDictionaryMemory
 {
 public:
   PhraseDictionaryALSuffixArray(const std::string &line);
-  bool InitDictionary()
-  { return true; }
+  bool InitDictionary() {
+    return true;
+  }
   void InitializeForInput(InputType const& source);
   void CleanUpAfterSentenceProcessing(const InputType& source);
 
 protected:
-  
+
 };
-  
+
 
 }
 
diff --git a/moses/TranslationModel/RuleTable/PhraseDictionaryFuzzyMatch.cpp b/moses/TranslationModel/RuleTable/PhraseDictionaryFuzzyMatch.cpp
index be6996399..669e7306b 100644
--- a/moses/TranslationModel/RuleTable/PhraseDictionaryFuzzyMatch.cpp
+++ b/moses/TranslationModel/RuleTable/PhraseDictionaryFuzzyMatch.cpp
@@ -3,17 +3,17 @@
 /***********************************************************************
  Moses - factored phrase-based language decoder
  Copyright (C) 2006 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -49,316 +49,312 @@ using namespace std;
 namespace Moses
 {
 
-  PhraseDictionaryFuzzyMatch::PhraseDictionaryFuzzyMatch(const std::string &line)
+PhraseDictionaryFuzzyMatch::PhraseDictionaryFuzzyMatch(const std::string &line)
   : PhraseDictionary("PhraseDictionaryFuzzyMatch", line)
-  {}
-
-  bool PhraseDictionaryFuzzyMatch::Load(const std::vector<FactorType> &input
-            , const std::vector<FactorType> &output
-            , const std::string &initStr
-            , size_t tableLimit)
-  {
-    m_tableLimit = tableLimit;
-    m_input		= &input;
-    m_output	= &output;
-    
-   
-    cerr << "initStr=" << initStr << endl;
-    m_config = Tokenize(initStr, ";");
-    assert(m_config.size() == 3);
-
-    m_FuzzyMatchWrapper = new tmmt::FuzzyMatchWrapper(m_config[0], m_config[1], m_config[2]);
-    
-    return true;
+{}
+
+bool PhraseDictionaryFuzzyMatch::Load(const std::vector<FactorType> &input
+                                      , const std::vector<FactorType> &output
+                                      , const std::string &initStr
+                                      , size_t tableLimit)
+{
+  m_tableLimit = tableLimit;
+  m_input		= &input;
+  m_output	= &output;
+
+
+  cerr << "initStr=" << initStr << endl;
+  m_config = Tokenize(initStr, ";");
+  assert(m_config.size() == 3);
+
+  m_FuzzyMatchWrapper = new tmmt::FuzzyMatchWrapper(m_config[0], m_config[1], m_config[2]);
+
+  return true;
+}
+
+ChartRuleLookupManager *PhraseDictionaryFuzzyMatch::CreateRuleLookupManager(
+  const InputType &sentence,
+  const ChartCellCollectionBase &cellCollection)
+{
+  return new ChartRuleLookupManagerMemoryPerSentence(sentence, cellCollection, *this);
+}
+
+
+int removedirectoryrecursively(const char *dirname)
+{
+  DIR *dir;
+  struct dirent *entry;
+  char path[PATH_MAX];
+
+  if (path == NULL) {
+    fprintf(stderr, "Out of memory error\n");
+    return 0;
   }
-    
-  ChartRuleLookupManager *PhraseDictionaryFuzzyMatch::CreateRuleLookupManager(
-                                                                        const InputType &sentence,
-                                                                        const ChartCellCollectionBase &cellCollection)
-  {
-    return new ChartRuleLookupManagerMemoryPerSentence(sentence, cellCollection, *this);
+  dir = opendir(dirname);
+  if (dir == NULL) {
+    perror("Error opendir()");
+    return 0;
   }
-    
-  
-  int removedirectoryrecursively(const char *dirname)
-  {
-    DIR *dir;
-    struct dirent *entry;
-    char path[PATH_MAX];
-    
-    if (path == NULL) {
-      fprintf(stderr, "Out of memory error\n");
-      return 0;
-    }
-    dir = opendir(dirname);
-    if (dir == NULL) {
-      perror("Error opendir()");
-      return 0;
-    }
-    
-    while ((entry = readdir(dir)) != NULL) {
-      if (strcmp(entry->d_name, ".") && strcmp(entry->d_name, "..")) {
-        snprintf(path, (size_t) PATH_MAX, "%s/%s", dirname, entry->d_name);
-        if (entry->d_type == DT_DIR) {
-          removedirectoryrecursively(path);
-        }
-        
-        remove(path);
-        /*
-         * Here, the actual deletion must be done.  Beacuse this is
-         * quite a dangerous thing to do, and this program is not very
-         * well tested, we are just printing as if we are deleting.
-         */
-        //printf("(not really) Deleting: %s\n", path);
-        /*
-         * When you are finished testing this and feel you are ready to do the real
-         * deleting, use this: remove*STUB*(path);
-         * (see "man 3 remove")
-         * Please note that I DONT TAKE RESPONSIBILITY for data you delete with this!
-         */
+
+  while ((entry = readdir(dir)) != NULL) {
+    if (strcmp(entry->d_name, ".") && strcmp(entry->d_name, "..")) {
+      snprintf(path, (size_t) PATH_MAX, "%s/%s", dirname, entry->d_name);
+      if (entry->d_type == DT_DIR) {
+        removedirectoryrecursively(path);
       }
-      
+
+      remove(path);
+      /*
+       * Here, the actual deletion must be done.  Beacuse this is
+       * quite a dangerous thing to do, and this program is not very
+       * well tested, we are just printing as if we are deleting.
+       */
+      //printf("(not really) Deleting: %s\n", path);
+      /*
+       * When you are finished testing this and feel you are ready to do the real
+       * deleting, use this: remove*STUB*(path);
+       * (see "man 3 remove")
+       * Please note that I DONT TAKE RESPONSIBILITY for data you delete with this!
+       */
     }
-    closedir(dir);
-    
-    rmdir(dirname);
-    /*
-     * Now the directory is emtpy, finally delete the directory itself. (Just
-     * printing here, see above) 
-     */
-    //printf("(not really) Deleting: %s\n", dirname);
-    
-    return 1;
+
+  }
+  closedir(dir);
+
+  rmdir(dirname);
+  /*
+   * Now the directory is emtpy, finally delete the directory itself. (Just
+   * printing here, see above)
+   */
+  //printf("(not really) Deleting: %s\n", dirname);
+
+  return 1;
+}
+
+void PhraseDictionaryFuzzyMatch::InitializeForInput(InputType const& inputSentence)
+{
+  char dirName[] = "/tmp/moses.XXXXXX";
+  char *temp = mkdtemp(dirName);
+  CHECK(temp);
+  string dirNameStr(dirName);
+
+  string inFileName(dirNameStr + "/in");
+
+  ofstream inFile(inFileName.c_str());
+
+  for (size_t i = 1; i < inputSentence.GetSize() - 1; ++i) {
+    inFile << inputSentence.GetWord(i);
   }
+  inFile << endl;
+  inFile.close();
+
+  long translationId = inputSentence.GetTranslationId();
+  string ptFileName = m_FuzzyMatchWrapper->Extract(translationId, dirNameStr);
+
+  // populate with rules for this sentence
+  PhraseDictionaryNodeMemory &rootNode = m_collection[translationId];
+  FormatType format = MosesFormat;
 
-  void PhraseDictionaryFuzzyMatch::InitializeForInput(InputType const& inputSentence)
-  {
-    char dirName[] = "/tmp/moses.XXXXXX";
-    char *temp = mkdtemp(dirName);
-    CHECK(temp);
-    string dirNameStr(dirName);
-    
-    string inFileName(dirNameStr + "/in");
-    
-    ofstream inFile(inFileName.c_str());
-    
-    for (size_t i = 1; i < inputSentence.GetSize() - 1; ++i)
-    {
-      inFile << inputSentence.GetWord(i);
+  // data from file
+  InputFileStream inStream(ptFileName);
+
+  // copied from class LoaderStandard
+  PrintUserTime("Start loading fuzzy-match phrase model");
+
+  const StaticData &staticData = StaticData::Instance();
+  const std::string& factorDelimiter = staticData.GetFactorDelimiter();
+
+
+  string lineOrig;
+  size_t count = 0;
+
+  while(getline(inStream, lineOrig)) {
+    const string *line;
+    if (format == HieroFormat) { // reformat line
+      assert(false);
+      //line = ReformatHieroRule(lineOrig);
+    } else {
+      // do nothing to format of line
+      line = &lineOrig;
     }
-    inFile << endl;
-    inFile.close();
-        
-    long translationId = inputSentence.GetTranslationId();
-    string ptFileName = m_FuzzyMatchWrapper->Extract(translationId, dirNameStr);
-
-    // populate with rules for this sentence
-    PhraseDictionaryNodeMemory &rootNode = m_collection[translationId];
-    FormatType format = MosesFormat;
-        
-    // data from file
-    InputFileStream inStream(ptFileName);
-    
-    // copied from class LoaderStandard
-    PrintUserTime("Start loading fuzzy-match phrase model");
-    
-    const StaticData &staticData = StaticData::Instance();
-    const std::string& factorDelimiter = staticData.GetFactorDelimiter();
-    
-    
-    string lineOrig;
-    size_t count = 0;
-    
-    while(getline(inStream, lineOrig)) {
-      const string *line;
-      if (format == HieroFormat) { // reformat line
-        assert(false);
-        //line = ReformatHieroRule(lineOrig);
-      }
-      else
-      { // do nothing to format of line
-        line = &lineOrig;
-      }
-      
-      vector<string> tokens;
-      vector<float> scoreVector;
-      
-      TokenizeMultiCharSeparator(tokens, *line , "|||" );
-      
-      if (tokens.size() != 4 && tokens.size() != 5) {
-        stringstream strme;
-        strme << "Syntax error at " << ptFileName << ":" << count;
-        UserMessage::Add(strme.str());
-        abort();
-      }
-      
-      const string &sourcePhraseString = tokens[0]
-      , &targetPhraseString = tokens[1]
-      , &scoreString        = tokens[2]
-      , &alignString        = tokens[3];
-      
-      bool isLHSEmpty = (sourcePhraseString.find_first_not_of(" \t", 0) == string::npos);
-      if (isLHSEmpty && !staticData.IsWordDeletionEnabled()) {
-        TRACE_ERR( ptFileName << ":" << count << ": pt entry contains empty target, skipping\n");
-        continue;
-      }
-      
-      Tokenize<float>(scoreVector, scoreString);
-      const size_t numScoreComponents = GetNumScoreComponents();
-      if (scoreVector.size() != numScoreComponents) {
-        stringstream strme;
-        strme << "Size of scoreVector != number (" << scoreVector.size() << "!="
-        << numScoreComponents << ") of score components on line " << count;
-        UserMessage::Add(strme.str());
-        abort();
-      }
-      CHECK(scoreVector.size() == numScoreComponents);
-      
-      // parse source & find pt node
-      
-      // constituent labels
-      Word *sourceLHS;
-      Word *targetLHS;
-      
-      // source
-      Phrase sourcePhrase( 0);
-      sourcePhrase.CreateFromString(Input, *m_input, sourcePhraseString, factorDelimiter, &sourceLHS);
-      
-      // create target phrase obj
-      TargetPhrase *targetPhrase = new TargetPhrase();
-      targetPhrase->CreateFromString(Output, *m_output, targetPhraseString, factorDelimiter, &targetLHS);
-      
-      // rest of target phrase
-      targetPhrase->SetAlignmentInfo(alignString);
-      targetPhrase->SetTargetLHS(targetLHS);
-      //targetPhrase->SetDebugOutput(string("New Format pt ") + line);
-      
-      // component score, for n-best output
-      std::transform(scoreVector.begin(),scoreVector.end(),scoreVector.begin(),TransformScore);
-      std::transform(scoreVector.begin(),scoreVector.end(),scoreVector.begin(),FloorScore);
-      
-      targetPhrase->GetScoreBreakdown().Assign(this, scoreVector);
-      targetPhrase->Evaluate(sourcePhrase);
-      
-      TargetPhraseCollection &phraseColl = GetOrCreateTargetPhraseCollection(rootNode, sourcePhrase, *targetPhrase, sourceLHS);
-      phraseColl.Add(targetPhrase);
-      
-      count++;
-      
-      if (format == HieroFormat) { // reformat line
-        delete line;
-      }
-      else
-      { // do nothing
-      }
-      
+
+    vector<string> tokens;
+    vector<float> scoreVector;
+
+    TokenizeMultiCharSeparator(tokens, *line , "|||" );
+
+    if (tokens.size() != 4 && tokens.size() != 5) {
+      stringstream strme;
+      strme << "Syntax error at " << ptFileName << ":" << count;
+      UserMessage::Add(strme.str());
+      abort();
     }
-    
-    // sort and prune each target phrase collection
-    SortAndPrune(rootNode);
-   
-    //removedirectoryrecursively(dirName);
-  }
-  
-  TargetPhraseCollection &PhraseDictionaryFuzzyMatch::GetOrCreateTargetPhraseCollection(PhraseDictionaryNodeMemory &rootNode
-                                                                                  , const Phrase &source
-                                                                                  , const TargetPhrase &target
-                                                                                  , const Word *sourceLHS)
-  {
-    PhraseDictionaryNodeMemory &currNode = GetOrCreateNode(rootNode, source, target, sourceLHS);
-    return currNode.GetOrCreateTargetPhraseCollection();
-  }
 
-  PhraseDictionaryNodeMemory &PhraseDictionaryFuzzyMatch::GetOrCreateNode(PhraseDictionaryNodeMemory &rootNode
-                                                                  , const Phrase &source
-                                                                  , const TargetPhrase &target
-                                                                  , const Word *sourceLHS)
-  {
-    cerr << source << endl << target << endl;
-    const size_t size = source.GetSize();
-    
-    const AlignmentInfo &alignmentInfo = target.GetAlignNonTerm();
-    AlignmentInfo::const_iterator iterAlign = alignmentInfo.begin();
-    
-    PhraseDictionaryNodeMemory *currNode = &rootNode;
-    for (size_t pos = 0 ; pos < size ; ++pos) {
-      const Word& word = source.GetWord(pos);
-      
-      if (word.IsNonTerminal()) {
-        // indexed by source label 1st
-        const Word &sourceNonTerm = word;
-        
-        CHECK(iterAlign != alignmentInfo.end());
-        CHECK(iterAlign->first == pos);
-        size_t targetNonTermInd = iterAlign->second;
-        ++iterAlign;
-        const Word &targetNonTerm = target.GetWord(targetNonTermInd);
-        
-        currNode = currNode->GetOrCreateChild(sourceNonTerm, targetNonTerm);
-      } else {
-        currNode = currNode->GetOrCreateChild(word);
-      }
-      
-      CHECK(currNode != NULL);
+    const string &sourcePhraseString = tokens[0]
+                                       , &targetPhraseString = tokens[1]
+                                           , &scoreString        = tokens[2]
+                                               , &alignString        = tokens[3];
+
+    bool isLHSEmpty = (sourcePhraseString.find_first_not_of(" \t", 0) == string::npos);
+    if (isLHSEmpty && !staticData.IsWordDeletionEnabled()) {
+      TRACE_ERR( ptFileName << ":" << count << ": pt entry contains empty target, skipping\n");
+      continue;
     }
-    
-    // finally, the source LHS
-    //currNode = currNode->GetOrCreateChild(sourceLHS);
-    //CHECK(currNode != NULL);
-    
-    
-    return *currNode;
-  }
 
-  void PhraseDictionaryFuzzyMatch::SortAndPrune(PhraseDictionaryNodeMemory &rootNode)
-  {
-    if (GetTableLimit())
-    {
-      rootNode.Sort(GetTableLimit());
+    Tokenize<float>(scoreVector, scoreString);
+    const size_t numScoreComponents = GetNumScoreComponents();
+    if (scoreVector.size() != numScoreComponents) {
+      stringstream strme;
+      strme << "Size of scoreVector != number (" << scoreVector.size() << "!="
+            << numScoreComponents << ") of score components on line " << count;
+      UserMessage::Add(strme.str());
+      abort();
     }
+    CHECK(scoreVector.size() == numScoreComponents);
+
+    // parse source & find pt node
+
+    // constituent labels
+    Word *sourceLHS;
+    Word *targetLHS;
+
+    // source
+    Phrase sourcePhrase( 0);
+    sourcePhrase.CreateFromString(Input, *m_input, sourcePhraseString, factorDelimiter, &sourceLHS);
+
+    // create target phrase obj
+    TargetPhrase *targetPhrase = new TargetPhrase();
+    targetPhrase->CreateFromString(Output, *m_output, targetPhraseString, factorDelimiter, &targetLHS);
+
+    // rest of target phrase
+    targetPhrase->SetAlignmentInfo(alignString);
+    targetPhrase->SetTargetLHS(targetLHS);
+    //targetPhrase->SetDebugOutput(string("New Format pt ") + line);
+
+    // component score, for n-best output
+    std::transform(scoreVector.begin(),scoreVector.end(),scoreVector.begin(),TransformScore);
+    std::transform(scoreVector.begin(),scoreVector.end(),scoreVector.begin(),FloorScore);
+
+    targetPhrase->GetScoreBreakdown().Assign(this, scoreVector);
+    targetPhrase->Evaluate(sourcePhrase);
+
+    TargetPhraseCollection &phraseColl = GetOrCreateTargetPhraseCollection(rootNode, sourcePhrase, *targetPhrase, sourceLHS);
+    phraseColl.Add(targetPhrase);
+
+    count++;
+
+    if (format == HieroFormat) { // reformat line
+      delete line;
+    } else {
+      // do nothing
+    }
+
   }
-  
-  void PhraseDictionaryFuzzyMatch::CleanUpAfterSentenceProcessing(const InputType &source)
-  {
-    m_collection.erase(source.GetTranslationId());
+
+  // sort and prune each target phrase collection
+  SortAndPrune(rootNode);
+
+  //removedirectoryrecursively(dirName);
+}
+
+TargetPhraseCollection &PhraseDictionaryFuzzyMatch::GetOrCreateTargetPhraseCollection(PhraseDictionaryNodeMemory &rootNode
+    , const Phrase &source
+    , const TargetPhrase &target
+    , const Word *sourceLHS)
+{
+  PhraseDictionaryNodeMemory &currNode = GetOrCreateNode(rootNode, source, target, sourceLHS);
+  return currNode.GetOrCreateTargetPhraseCollection();
+}
+
+PhraseDictionaryNodeMemory &PhraseDictionaryFuzzyMatch::GetOrCreateNode(PhraseDictionaryNodeMemory &rootNode
+    , const Phrase &source
+    , const TargetPhrase &target
+    , const Word *sourceLHS)
+{
+  cerr << source << endl << target << endl;
+  const size_t size = source.GetSize();
+
+  const AlignmentInfo &alignmentInfo = target.GetAlignNonTerm();
+  AlignmentInfo::const_iterator iterAlign = alignmentInfo.begin();
+
+  PhraseDictionaryNodeMemory *currNode = &rootNode;
+  for (size_t pos = 0 ; pos < size ; ++pos) {
+    const Word& word = source.GetWord(pos);
+
+    if (word.IsNonTerminal()) {
+      // indexed by source label 1st
+      const Word &sourceNonTerm = word;
+
+      CHECK(iterAlign != alignmentInfo.end());
+      CHECK(iterAlign->first == pos);
+      size_t targetNonTermInd = iterAlign->second;
+      ++iterAlign;
+      const Word &targetNonTerm = target.GetWord(targetNonTermInd);
+
+      currNode = currNode->GetOrCreateChild(sourceNonTerm, targetNonTerm);
+    } else {
+      currNode = currNode->GetOrCreateChild(word);
+    }
+
+    CHECK(currNode != NULL);
   }
 
-  const PhraseDictionaryNodeMemory &PhraseDictionaryFuzzyMatch::GetRootNode(const InputType &source) const 
-  {
-    long transId = source.GetTranslationId();
-    std::map<long, PhraseDictionaryNodeMemory>::const_iterator iter = m_collection.find(transId);
-    CHECK(iter != m_collection.end());
-    return iter->second; 
+  // finally, the source LHS
+  //currNode = currNode->GetOrCreateChild(sourceLHS);
+  //CHECK(currNode != NULL);
+
+
+  return *currNode;
+}
+
+void PhraseDictionaryFuzzyMatch::SortAndPrune(PhraseDictionaryNodeMemory &rootNode)
+{
+  if (GetTableLimit()) {
+    rootNode.Sort(GetTableLimit());
   }
-  PhraseDictionaryNodeMemory &PhraseDictionaryFuzzyMatch::GetRootNode(const InputType &source) 
-  {
-    long transId = source.GetTranslationId();
-    std::map<long, PhraseDictionaryNodeMemory>::iterator iter = m_collection.find(transId);
-    CHECK(iter != m_collection.end());
-    return iter->second; 
+}
+
+void PhraseDictionaryFuzzyMatch::CleanUpAfterSentenceProcessing(const InputType &source)
+{
+  m_collection.erase(source.GetTranslationId());
+}
+
+const PhraseDictionaryNodeMemory &PhraseDictionaryFuzzyMatch::GetRootNode(const InputType &source) const
+{
+  long transId = source.GetTranslationId();
+  std::map<long, PhraseDictionaryNodeMemory>::const_iterator iter = m_collection.find(transId);
+  CHECK(iter != m_collection.end());
+  return iter->second;
+}
+PhraseDictionaryNodeMemory &PhraseDictionaryFuzzyMatch::GetRootNode(const InputType &source)
+{
+  long transId = source.GetTranslationId();
+  std::map<long, PhraseDictionaryNodeMemory>::iterator iter = m_collection.find(transId);
+  CHECK(iter != m_collection.end());
+  return iter->second;
+}
+
+TO_STRING_BODY(PhraseDictionaryFuzzyMatch);
+
+// friend
+ostream& operator<<(ostream& out, const PhraseDictionaryFuzzyMatch& phraseDict)
+{
+  typedef PhraseDictionaryNodeMemory::TerminalMap TermMap;
+  typedef PhraseDictionaryNodeMemory::NonTerminalMap NonTermMap;
+
+  /*
+  const PhraseDictionaryNodeMemory &coll = phraseDict.m_collection;
+  for (NonTermMap::const_iterator p = coll.m_nonTermMap.begin(); p != coll.m_nonTermMap.end(); ++p) {
+    const Word &sourceNonTerm = p->first.first;
+    out << sourceNonTerm;
   }
-  
-  TO_STRING_BODY(PhraseDictionaryFuzzyMatch);
-  
-  // friend
-  ostream& operator<<(ostream& out, const PhraseDictionaryFuzzyMatch& phraseDict)
-  {
-    typedef PhraseDictionaryNodeMemory::TerminalMap TermMap;
-    typedef PhraseDictionaryNodeMemory::NonTerminalMap NonTermMap;
-    
-    /*
-    const PhraseDictionaryNodeMemory &coll = phraseDict.m_collection;
-    for (NonTermMap::const_iterator p = coll.m_nonTermMap.begin(); p != coll.m_nonTermMap.end(); ++p) {
-      const Word &sourceNonTerm = p->first.first;
-      out << sourceNonTerm;
-    }
-    for (TermMap::const_iterator p = coll.m_sourceTermMap.begin(); p != coll.m_sourceTermMap.end(); ++p) {
-      const Word &sourceTerm = p->first;
-      out << sourceTerm;
-    }
-     */
-    
-    return out;
+  for (TermMap::const_iterator p = coll.m_sourceTermMap.begin(); p != coll.m_sourceTermMap.end(); ++p) {
+    const Word &sourceTerm = p->first;
+    out << sourceTerm;
   }
-  
+   */
+
+  return out;
+}
+
 }
diff --git a/moses/TranslationModel/RuleTable/PhraseDictionaryFuzzyMatch.h b/moses/TranslationModel/RuleTable/PhraseDictionaryFuzzyMatch.h
index 8e4d20423..94966b175 100644
--- a/moses/TranslationModel/RuleTable/PhraseDictionaryFuzzyMatch.h
+++ b/moses/TranslationModel/RuleTable/PhraseDictionaryFuzzyMatch.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -29,61 +29,60 @@
 
 namespace Moses
 {
-  class PhraseDictionaryNodeMemory;
-  
-  /** Implementation of a SCFG rule table in a trie.  Looking up a rule of
-   * length n symbols requires n look-ups to find the TargetPhraseCollection.
-   */
-  class PhraseDictionaryFuzzyMatch : public PhraseDictionary
-  {
-    friend std::ostream& operator<<(std::ostream&, const PhraseDictionaryFuzzyMatch&);
-    friend class RuleTableLoader;
-    
-  public:
-    PhraseDictionaryFuzzyMatch(const std::string &line);
-    bool Load(const std::vector<FactorType> &input
-              , const std::vector<FactorType> &output
-              , const std::string &initStr
-              , size_t tableLimit);
-    
-    const PhraseDictionaryNodeMemory &GetRootNode(const InputType &source) const;
-    
-    ChartRuleLookupManager *CreateRuleLookupManager(
-                                                    const InputType &,
-                                                    const ChartCellCollectionBase &);
-    void InitializeForInput(InputType const& inputSentence);
-    void CleanUpAfterSentenceProcessing(const InputType& source);
-    
-    virtual const TargetPhraseCollection *GetTargetPhraseCollection(const Phrase& src) const
-    {
-      assert(false);
-      return NULL;
-    }
-    
-    TO_STRING();
-    
-  protected:
-    TargetPhraseCollection &GetOrCreateTargetPhraseCollection(PhraseDictionaryNodeMemory &rootNode
-                                                              , const Phrase &source
-                                                              , const TargetPhrase &target
-                                                              , const Word *sourceLHS);
-    
-    PhraseDictionaryNodeMemory &GetOrCreateNode(PhraseDictionaryNodeMemory &rootNode
-                                              , const Phrase &source
-                                              , const TargetPhrase &target
-                                              , const Word *sourceLHS);
-    
-    void SortAndPrune(PhraseDictionaryNodeMemory &rootNode);
-    PhraseDictionaryNodeMemory &GetRootNode(const InputType &source);
-
-    std::map<long, PhraseDictionaryNodeMemory> m_collection;
-    std::vector<std::string> m_config;
-    
-    const std::vector<FactorType> *m_input, *m_output;
-    const std::vector<float> *m_weight;
-    
-    tmmt::FuzzyMatchWrapper *m_FuzzyMatchWrapper;
-
-  };
-  
+class PhraseDictionaryNodeMemory;
+
+/** Implementation of a SCFG rule table in a trie.  Looking up a rule of
+ * length n symbols requires n look-ups to find the TargetPhraseCollection.
+ */
+class PhraseDictionaryFuzzyMatch : public PhraseDictionary
+{
+  friend std::ostream& operator<<(std::ostream&, const PhraseDictionaryFuzzyMatch&);
+  friend class RuleTableLoader;
+
+public:
+  PhraseDictionaryFuzzyMatch(const std::string &line);
+  bool Load(const std::vector<FactorType> &input
+            , const std::vector<FactorType> &output
+            , const std::string &initStr
+            , size_t tableLimit);
+
+  const PhraseDictionaryNodeMemory &GetRootNode(const InputType &source) const;
+
+  ChartRuleLookupManager *CreateRuleLookupManager(
+    const InputType &,
+    const ChartCellCollectionBase &);
+  void InitializeForInput(InputType const& inputSentence);
+  void CleanUpAfterSentenceProcessing(const InputType& source);
+
+  virtual const TargetPhraseCollection *GetTargetPhraseCollection(const Phrase& src) const {
+    assert(false);
+    return NULL;
+  }
+
+  TO_STRING();
+
+protected:
+  TargetPhraseCollection &GetOrCreateTargetPhraseCollection(PhraseDictionaryNodeMemory &rootNode
+      , const Phrase &source
+      , const TargetPhrase &target
+      , const Word *sourceLHS);
+
+  PhraseDictionaryNodeMemory &GetOrCreateNode(PhraseDictionaryNodeMemory &rootNode
+      , const Phrase &source
+      , const TargetPhrase &target
+      , const Word *sourceLHS);
+
+  void SortAndPrune(PhraseDictionaryNodeMemory &rootNode);
+  PhraseDictionaryNodeMemory &GetRootNode(const InputType &source);
+
+  std::map<long, PhraseDictionaryNodeMemory> m_collection;
+  std::vector<std::string> m_config;
+
+  const std::vector<FactorType> *m_input, *m_output;
+  const std::vector<float> *m_weight;
+
+  tmmt::FuzzyMatchWrapper *m_FuzzyMatchWrapper;
+
+};
+
 }  // namespace Moses
diff --git a/moses/TranslationModel/RuleTable/PhraseDictionaryOnDisk.cpp b/moses/TranslationModel/RuleTable/PhraseDictionaryOnDisk.cpp
index cd509f544..38cf247af 100644
--- a/moses/TranslationModel/RuleTable/PhraseDictionaryOnDisk.cpp
+++ b/moses/TranslationModel/RuleTable/PhraseDictionaryOnDisk.cpp
@@ -1,4 +1,4 @@
-  // vim:tabstop=2
+// vim:tabstop=2
 /***********************************************************************
  Moses - factored phrase-based language decoder
  Copyright (C) 2010 Hieu Hoang
diff --git a/moses/TranslationModel/RuleTable/PhraseDictionaryOnDisk.h b/moses/TranslationModel/RuleTable/PhraseDictionaryOnDisk.h
index 9b186def9..874478cdc 100644
--- a/moses/TranslationModel/RuleTable/PhraseDictionaryOnDisk.h
+++ b/moses/TranslationModel/RuleTable/PhraseDictionaryOnDisk.h
@@ -35,7 +35,7 @@ class TargetPhraseCollection;
 class DottedRuleStackOnDisk;
 
 /** Implementation of on-disk phrase table for hierarchical/syntax model.
- */   
+ */
 class PhraseDictionaryOnDisk : public PhraseDictionary
 {
   typedef PhraseDictionary MyBase;
diff --git a/moses/TranslationModel/RuleTable/Trie.cpp b/moses/TranslationModel/RuleTable/Trie.cpp
index c3590074d..950271d29 100644
--- a/moses/TranslationModel/RuleTable/Trie.cpp
+++ b/moses/TranslationModel/RuleTable/Trie.cpp
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2012 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -38,7 +38,7 @@ bool RuleTableTrie::InitDictionary()
 {
 
   std::auto_ptr<Moses::RuleTableLoader> loader =
-      Moses::RuleTableLoaderFactory::Create(m_filePath);
+    Moses::RuleTableLoaderFactory::Create(m_filePath);
   if (!loader.get()) {
     return false;
   }
diff --git a/moses/TranslationModel/RuleTable/Trie.h b/moses/TranslationModel/RuleTable/Trie.h
index 822ef8b92..c2f757ab8 100644
--- a/moses/TranslationModel/RuleTable/Trie.h
+++ b/moses/TranslationModel/RuleTable/Trie.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2012 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -39,28 +39,27 @@ class Word;
  */
 class RuleTableTrie : public PhraseDictionary
 {
- public:
+public:
   RuleTableTrie(const std::string &description, const std::string &line)
-      : PhraseDictionary(description, line)
- {}
+    : PhraseDictionary(description, line)
+  {}
 
   virtual ~RuleTableTrie();
 
   bool InitDictionary();
 
   // Required by PhraseDictionary.
-  virtual const TargetPhraseCollection *GetTargetPhraseCollection(const Phrase &) const
-  {
+  virtual const TargetPhraseCollection *GetTargetPhraseCollection(const Phrase &) const {
     CHECK(false);
     return NULL;
   }
 
- private:
+private:
   friend class RuleTableLoader;
 
   virtual TargetPhraseCollection &GetOrCreateTargetPhraseCollection(
-      const Phrase &source, const TargetPhrase &target,
-      const Word *sourceLHS) = 0;
+    const Phrase &source, const TargetPhrase &target,
+    const Word *sourceLHS) = 0;
 
   virtual void SortAndPrune() = 0;
 
diff --git a/moses/TranslationModel/RuleTable/UTrie.cpp b/moses/TranslationModel/RuleTable/UTrie.cpp
index bcfc0d538..17f457f22 100644
--- a/moses/TranslationModel/RuleTable/UTrie.cpp
+++ b/moses/TranslationModel/RuleTable/UTrie.cpp
@@ -39,15 +39,15 @@ namespace Moses
 {
 
 TargetPhraseCollection &RuleTableUTrie::GetOrCreateTargetPhraseCollection(
-    const Phrase &source, const TargetPhrase &target, const Word *sourceLHS)
+  const Phrase &source, const TargetPhrase &target, const Word *sourceLHS)
 {
   UTrieNode &currNode = GetOrCreateNode(source, target, sourceLHS);
   return currNode.GetOrCreateTargetPhraseCollection(target);
 }
 
 UTrieNode &RuleTableUTrie::GetOrCreateNode(const Phrase &source,
-                                           const TargetPhrase &target,
-                                           const Word */*sourceLHS*/)
+    const TargetPhrase &target,
+    const Word */*sourceLHS*/)
 {
   const size_t size = source.GetSize();
 
diff --git a/moses/TranslationModel/RuleTable/UTrie.h b/moses/TranslationModel/RuleTable/UTrie.h
index d31e22cc7..a8f218158 100644
--- a/moses/TranslationModel/RuleTable/UTrie.h
+++ b/moses/TranslationModel/RuleTable/UTrie.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2012 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -43,21 +43,23 @@ class Word;
  */
 class RuleTableUTrie : public RuleTableTrie
 {
- public:
+public:
   RuleTableUTrie(const std::string &line)
-      : RuleTableTrie("RuleTableUTrie", line)
+    : RuleTableTrie("RuleTableUTrie", line)
   {}
 
-  const UTrieNode &GetRootNode() const { return m_root; }
+  const UTrieNode &GetRootNode() const {
+    return m_root;
+  }
 
   ChartRuleLookupManager *CreateRuleLookupManager(const InputType &,
-                                                  const ChartCellCollectionBase &);
+      const ChartCellCollectionBase &);
 
- private:
+private:
   const TargetPhraseCollection *GetTargetPhraseCollection(const Phrase &) const;
 
   TargetPhraseCollection &GetOrCreateTargetPhraseCollection(
-      const Phrase &source, const TargetPhrase &target, const Word *sourceLHS);
+    const Phrase &source, const TargetPhrase &target, const Word *sourceLHS);
 
   UTrieNode &GetOrCreateNode(const Phrase &source, const TargetPhrase &target,
                              const Word *sourceLHS);
diff --git a/moses/TranslationModel/RuleTable/UTrieNode.cpp b/moses/TranslationModel/RuleTable/UTrieNode.cpp
index d2275422e..725f02c97 100644
--- a/moses/TranslationModel/RuleTable/UTrieNode.cpp
+++ b/moses/TranslationModel/RuleTable/UTrieNode.cpp
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2012 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -90,7 +90,7 @@ UTrieNode *UTrieNode::GetOrCreateNonTerminalChild(const Word &targetNonTerm)
 }
 
 TargetPhraseCollection &UTrieNode::GetOrCreateTargetPhraseCollection(
-    const TargetPhrase &target)
+  const TargetPhrase &target)
 {
   const AlignmentInfo &alignmentInfo = target.GetAlignNonTerm();
   const size_t rank = alignmentInfo.GetSize();
diff --git a/moses/TranslationModel/RuleTable/UTrieNode.h b/moses/TranslationModel/RuleTable/UTrieNode.h
index b3d82cddc..436bcbea1 100644
--- a/moses/TranslationModel/RuleTable/UTrieNode.h
+++ b/moses/TranslationModel/RuleTable/UTrieNode.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2012 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -42,49 +42,62 @@ class RuleTableUTrie;
 //! @todo ask phil williams - whats the diff between this and phrasedictionaryNode
 class UTrieNode
 {
- public:
+public:
   typedef std::vector<std::vector<Word> > LabelTable;
 #if defined(BOOST_VERSION) && (BOOST_VERSION >= 104200)
   typedef boost::unordered_map<Word,
-                               UTrieNode,
-                               TerminalHasher,
-                               TerminalEqualityPred> TerminalMap;
+          UTrieNode,
+          TerminalHasher,
+          TerminalEqualityPred> TerminalMap;
 
   typedef boost::unordered_map<std::vector<int>,
-                               TargetPhraseCollection> LabelMap;
+          TargetPhraseCollection> LabelMap;
 #else
   typedef std::map<Word, UTrieNode> TerminalMap;
   typedef std::map<std::vector<int>, TargetPhraseCollection> LabelMap;
 #endif
 
-  ~UTrieNode() { delete m_gapNode; }
+  ~UTrieNode() {
+    delete m_gapNode;
+  }
 
-  const LabelTable &GetLabelTable() const { return m_labelTable; }
-  const LabelMap &GetLabelMap() const { return m_labelMap; }
-  const TerminalMap &GetTerminalMap() const { return m_terminalMap; }
+  const LabelTable &GetLabelTable() const {
+    return m_labelTable;
+  }
+  const LabelMap &GetLabelMap() const {
+    return m_labelMap;
+  }
+  const TerminalMap &GetTerminalMap() const {
+    return m_terminalMap;
+  }
 
-  const UTrieNode *GetNonTerminalChild() const { return m_gapNode; }
+  const UTrieNode *GetNonTerminalChild() const {
+    return m_gapNode;
+  }
 
   UTrieNode *GetOrCreateTerminalChild(const Word &sourceTerm);
   UTrieNode *GetOrCreateNonTerminalChild(const Word &targetNonTerm);
 
   TargetPhraseCollection &GetOrCreateTargetPhraseCollection(
-      const TargetPhrase &);
+    const TargetPhrase &);
 
-  bool IsLeaf() const { return m_terminalMap.empty() && m_gapNode == NULL; }
+  bool IsLeaf() const {
+    return m_terminalMap.empty() && m_gapNode == NULL;
+  }
 
-  bool HasRules() const { return !m_labelMap.empty(); }
+  bool HasRules() const {
+    return !m_labelMap.empty();
+  }
 
   void Prune(size_t tableLimit);
   void Sort(size_t tableLimit);
 
- private:
+private:
   friend class RuleTableUTrie;
 
   UTrieNode() : m_gapNode(NULL) {}
 
-  int InsertLabel(int i, const Word &w)
-  {
+  int InsertLabel(int i, const Word &w) {
     std::vector<Word> &inner = m_labelTable[i];
     for (size_t j = 0; j < inner.size(); ++j) {
       if (inner[j] == w) {
diff --git a/moses/TranslationModel/Scope3Parser/ApplicableRuleTrie.cpp b/moses/TranslationModel/Scope3Parser/ApplicableRuleTrie.cpp
index ec5c1d8f1..b635dc050 100644
--- a/moses/TranslationModel/Scope3Parser/ApplicableRuleTrie.cpp
+++ b/moses/TranslationModel/Scope3Parser/ApplicableRuleTrie.cpp
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2012 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -39,7 +39,7 @@ void ApplicableRuleTrie::Extend(const UTrieNode &root, int minPos,
       size_t index = *r;
       if (index == (size_t)minPos || (followsGap && index > (size_t)minPos) || minPos == -1) {
         ApplicableRuleTrie *subTrie = new ApplicableRuleTrie(index, index,
-                                                             child);
+            child);
         subTrie->Extend(child, index+1, sentMap, false);
         m_children.push_back(subTrie);
       }
diff --git a/moses/TranslationModel/Scope3Parser/ApplicableRuleTrie.h b/moses/TranslationModel/Scope3Parser/ApplicableRuleTrie.h
index 35243adde..9d2f2cda9 100644
--- a/moses/TranslationModel/Scope3Parser/ApplicableRuleTrie.h
+++ b/moses/TranslationModel/Scope3Parser/ApplicableRuleTrie.h
@@ -33,14 +33,13 @@ struct VarSpanNode;
 
 /** @todo what is this?
  */
-struct ApplicableRuleTrie
-{
- public:
+struct ApplicableRuleTrie {
+public:
   ApplicableRuleTrie(int start, int end, const UTrieNode &node)
-      : m_start(start)
-      , m_end(end)
-      , m_node(&node)
-      , m_vstNode(NULL) {}
+    : m_start(start)
+    , m_end(end)
+    , m_node(&node)
+    , m_vstNode(NULL) {}
 
   ~ApplicableRuleTrie() {
     RemoveAllInColl(m_children);
diff --git a/moses/TranslationModel/Scope3Parser/IntermediateVarSpanNode.h b/moses/TranslationModel/Scope3Parser/IntermediateVarSpanNode.h
index 353fabf22..499085127 100644
--- a/moses/TranslationModel/Scope3Parser/IntermediateVarSpanNode.h
+++ b/moses/TranslationModel/Scope3Parser/IntermediateVarSpanNode.h
@@ -26,9 +26,8 @@ namespace Moses
 
 /** @todo what is this?
  */
-struct IntermediateVarSpanNode
-{
- public:
+struct IntermediateVarSpanNode {
+public:
   typedef std::pair<int, int> Range;
 
   IntermediateVarSpanNode()
@@ -41,8 +40,12 @@ struct IntermediateVarSpanNode
     , m_end(end)
     , m_numSplitPoints(0) {}
 
-  bool isOpen() { return m_end.second == -1; }
-  bool isClosed() { return !isOpen(); }
+  bool isOpen() {
+    return m_end.second == -1;
+  }
+  bool isClosed() {
+    return !isOpen();
+  }
 
   Range m_start;
   Range m_end;
diff --git a/moses/TranslationModel/Scope3Parser/Parser.cpp b/moses/TranslationModel/Scope3Parser/Parser.cpp
index bfcacb1ed..81e156b3d 100644
--- a/moses/TranslationModel/Scope3Parser/Parser.cpp
+++ b/moses/TranslationModel/Scope3Parser/Parser.cpp
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2012 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -38,8 +38,8 @@ namespace Moses
 {
 
 void Scope3Parser::GetChartRuleCollection(
-    const WordsRange &range,
-    ChartParserCallback &outColl)
+  const WordsRange &range,
+  ChartParserCallback &outColl)
 {
   const size_t start = range.GetStartPos();
   const size_t end = range.GetEndPos();
@@ -122,7 +122,7 @@ void Scope3Parser::InitRuleApplicationVector()
 }
 
 void Scope3Parser::FillSentenceMap(
-    const Sentence &sent, SentenceMap &sentMap)
+  const Sentence &sent, SentenceMap &sentMap)
 {
   for (size_t i = 0; i < sent.GetSize(); ++i) {
     sentMap[sent.GetWord(i)].push_back(i);
@@ -130,10 +130,10 @@ void Scope3Parser::FillSentenceMap(
 }
 
 void Scope3Parser::AddRulesToCells(
-    const ApplicableRuleTrie &node,
-    std::pair<int, int> start,
-    int maxPos,
-    int depth)
+  const ApplicableRuleTrie &node,
+  std::pair<int, int> start,
+  int maxPos,
+  int depth)
 {
   if (depth > 0) {
     // Determine the start range for this path if not already known.
@@ -183,7 +183,7 @@ void Scope3Parser::AddRulesToCells(
           break;
         }
         m_ruleApplications[i][span].push_back(std::make_pair(node.m_node,
-                                                             node.m_vstNode));
+                                              node.m_vstNode));
       }
     }
   }
diff --git a/moses/TranslationModel/Scope3Parser/Parser.h b/moses/TranslationModel/Scope3Parser/Parser.h
index 0b5e63d95..2a46de9a8 100644
--- a/moses/TranslationModel/Scope3Parser/Parser.h
+++ b/moses/TranslationModel/Scope3Parser/Parser.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2012 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -46,15 +46,14 @@ class WordsRange;
  */
 class Scope3Parser : public ChartRuleLookupManager
 {
- public:
+public:
   Scope3Parser(const InputType &sentence,
                const ChartCellCollectionBase &cellColl,
                const RuleTableUTrie &ruleTable,
                size_t maxChartSpan)
-      : ChartRuleLookupManager(sentence, cellColl)
-      , m_ruleTable(ruleTable)
-      , m_maxChartSpan(maxChartSpan)
-  {
+    : ChartRuleLookupManager(sentence, cellColl)
+    , m_ruleTable(ruleTable)
+    , m_maxChartSpan(maxChartSpan) {
     Init();
   }
 
@@ -62,23 +61,21 @@ class Scope3Parser : public ChartRuleLookupManager
     const WordsRange &range,
     ChartParserCallback &outColl);
 
- private:
+private:
   // Define a callback type for use by StackLatticeSearcher.
-  struct MatchCallback
-  {
-    public:
-      MatchCallback(const WordsRange &range,
-                    ChartParserCallback &out)
-          : m_range(range)
-          , m_out(out)
-          , m_tpc(NULL) {}
-      void operator()(const StackVec &stackVec)
-      {
-        m_out.Add(*m_tpc, stackVec, m_range);
-      }
-      const WordsRange &m_range;
-      ChartParserCallback &m_out;
-      const TargetPhraseCollection *m_tpc;
+  struct MatchCallback {
+  public:
+    MatchCallback(const WordsRange &range,
+                  ChartParserCallback &out)
+      : m_range(range)
+      , m_out(out)
+      , m_tpc(NULL) {}
+    void operator()(const StackVec &stackVec) {
+      m_out.Add(*m_tpc, stackVec, m_range);
+    }
+    const WordsRange &m_range;
+    ChartParserCallback &m_out;
+    const TargetPhraseCollection *m_tpc;
   };
 
   void Init();
@@ -89,7 +86,7 @@ class Scope3Parser : public ChartRuleLookupManager
 
   const RuleTableUTrie &m_ruleTable;
   std::vector<std::vector<std::vector<
-    std::pair<const UTrieNode *, const VarSpanNode *> > > > m_ruleApplications;
+  std::pair<const UTrieNode *, const VarSpanNode *> > > > m_ruleApplications;
   std::auto_ptr<VarSpanNode> m_varSpanTrie;
   StackVec m_emptyStackVec;
   const size_t m_maxChartSpan;
diff --git a/moses/TranslationModel/Scope3Parser/SentenceMap.h b/moses/TranslationModel/Scope3Parser/SentenceMap.h
index 9bc46db93..a7a1fdad9 100644
--- a/moses/TranslationModel/Scope3Parser/SentenceMap.h
+++ b/moses/TranslationModel/Scope3Parser/SentenceMap.h
@@ -29,7 +29,7 @@
 namespace Moses
 {
 typedef boost::unordered_map<Word,
-                             std::vector<size_t>,
-                             TerminalHasher,
-                             TerminalEqualityPred> SentenceMap;
+        std::vector<size_t>,
+        TerminalHasher,
+        TerminalEqualityPred> SentenceMap;
 }
diff --git a/moses/TranslationModel/Scope3Parser/StackLatticeBuilder.cpp b/moses/TranslationModel/Scope3Parser/StackLatticeBuilder.cpp
index bb553a116..26e4e6aca 100644
--- a/moses/TranslationModel/Scope3Parser/StackLatticeBuilder.cpp
+++ b/moses/TranslationModel/Scope3Parser/StackLatticeBuilder.cpp
@@ -28,14 +28,14 @@ namespace Moses
 {
 
 void StackLatticeBuilder::Build(
-    int start,
-    int end,
-    const UTrieNode &ruleNode,
-    const VarSpanNode &varSpanNode,
-    const std::vector<VarSpanNode::NonTermRange> &ranges,
-    const ChartRuleLookupManager &manager,
-    StackLattice &lattice,
-    std::vector<std::vector<bool> > &checkTable)
+  int start,
+  int end,
+  const UTrieNode &ruleNode,
+  const VarSpanNode &varSpanNode,
+  const std::vector<VarSpanNode::NonTermRange> &ranges,
+  const ChartRuleLookupManager &manager,
+  StackLattice &lattice,
+  std::vector<std::vector<bool> > &checkTable)
 {
   // Extend the lattice if necessary.  Do not shrink it.
   const size_t span = end - start + 1;
diff --git a/moses/TranslationModel/Scope3Parser/StackLatticeBuilder.h b/moses/TranslationModel/Scope3Parser/StackLatticeBuilder.h
index 7091e8f18..551655e30 100644
--- a/moses/TranslationModel/Scope3Parser/StackLatticeBuilder.h
+++ b/moses/TranslationModel/Scope3Parser/StackLatticeBuilder.h
@@ -32,7 +32,7 @@ class ChartCellCollection;
  */
 class StackLatticeBuilder
 {
- public:
+public:
   StackLatticeBuilder() {}
 
   void Build(int, int, const UTrieNode &, const VarSpanNode &,
diff --git a/moses/TranslationModel/Scope3Parser/StackLatticeSearcher.h b/moses/TranslationModel/Scope3Parser/StackLatticeSearcher.h
index 749a3a2c1..4deac31f8 100644
--- a/moses/TranslationModel/Scope3Parser/StackLatticeSearcher.h
+++ b/moses/TranslationModel/Scope3Parser/StackLatticeSearcher.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2012 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -33,22 +33,20 @@ class ChartHypothesisCollection;
 template<typename MatchCallBackType>
 class StackLatticeSearcher
 {
- public:
+public:
   StackLatticeSearcher(const StackLattice &lattice,
                        const std::vector<VarSpanNode::NonTermRange> &ranges)
-      : m_lattice(lattice)
-      , m_ranges(ranges) {}
+    : m_lattice(lattice)
+    , m_ranges(ranges) {}
 
-  void Search(const std::vector<int> &labels, MatchCallBackType &callback)
-  {
+  void Search(const std::vector<int> &labels, MatchCallBackType &callback) {
     m_labels = &labels;
     m_matchCB = &callback;
     SearchInner(0, 0);
   }
 
- private:
-  void SearchInner(int start, size_t index)
-  {
+private:
+  void SearchInner(int start, size_t index) {
     assert(m_stackVec.size() == index);
 
     const VarSpanNode::NonTermRange &range = m_ranges[index];
diff --git a/moses/TranslationModel/Scope3Parser/VarSpanNode.h b/moses/TranslationModel/Scope3Parser/VarSpanNode.h
index 52dc32382..0dda6a787 100644
--- a/moses/TranslationModel/Scope3Parser/VarSpanNode.h
+++ b/moses/TranslationModel/Scope3Parser/VarSpanNode.h
@@ -33,9 +33,8 @@ namespace Moses
 
 /** @todo what is this?
  */
-struct VarSpanNode
-{
- public:
+struct VarSpanNode {
+public:
   struct NonTermRange {
     size_t s1;
     size_t s2;
@@ -48,8 +47,7 @@ struct VarSpanNode
 
   VarSpanNode() : m_parent(0), m_label(0), m_rank(0) {}
 
-  VarSpanNode &Insert(const NodeVec &vec)
-  {
+  VarSpanNode &Insert(const NodeVec &vec) {
     if (vec.empty()) {
       return *this;
     }
@@ -59,8 +57,7 @@ struct VarSpanNode
   // Given a span, determine the ranges of possible start and end offsets
   // for each non-terminal.
   void CalculateRanges(int start, int end,
-                       std::vector<NonTermRange> &ranges) const
-  {
+                       std::vector<NonTermRange> &ranges) const {
     ranges.resize(m_rank);
     const VarSpanNode *n = this;
     size_t firstIndex = m_rank;
@@ -103,10 +100,9 @@ struct VarSpanNode
   size_t m_rank;
   MapType m_children;
 
- private:
+private:
   VarSpanNode &Insert(NodeVec::const_iterator first,
-                      NodeVec::const_iterator last)
-  {
+                      NodeVec::const_iterator last) {
     assert(first != last);
 
     KeyType key;
@@ -117,7 +113,7 @@ struct VarSpanNode
     key[4] = first->m_numSplitPoints;
 
     std::pair<MapType::iterator, bool> result = m_children.insert(
-        std::make_pair(key, VarSpanNode()));
+          std::make_pair(key, VarSpanNode()));
     VarSpanNode &child = result.first->second;
     if (result.second) {
       child.m_parent = this;
diff --git a/moses/TranslationModel/Scope3Parser/VarSpanTrieBuilder.cpp b/moses/TranslationModel/Scope3Parser/VarSpanTrieBuilder.cpp
index 16b180ea5..35e66978b 100644
--- a/moses/TranslationModel/Scope3Parser/VarSpanTrieBuilder.cpp
+++ b/moses/TranslationModel/Scope3Parser/VarSpanTrieBuilder.cpp
@@ -30,7 +30,7 @@ namespace Moses
 {
 
 std::auto_ptr<VarSpanNode> VarSpanTrieBuilder::Build(
-    ApplicableRuleTrie &root)
+  ApplicableRuleTrie &root)
 {
   std::auto_ptr<VarSpanNode> vstRoot(new VarSpanNode());
   NodeVec vec;
diff --git a/moses/TranslationModel/Scope3Parser/VarSpanTrieBuilder.h b/moses/TranslationModel/Scope3Parser/VarSpanTrieBuilder.h
index 13c701b4f..2513a2878 100644
--- a/moses/TranslationModel/Scope3Parser/VarSpanTrieBuilder.h
+++ b/moses/TranslationModel/Scope3Parser/VarSpanTrieBuilder.h
@@ -34,13 +34,12 @@ struct VarSpanNode;
  */
 class VarSpanTrieBuilder
 {
- public:
+public:
   std::auto_ptr<VarSpanNode> Build(ApplicableRuleTrie &);
 
- private:
+private:
   typedef std::vector<IntermediateVarSpanNode> NodeVec;
-  struct NodeVecState
-  {
+  struct NodeVecState {
     std::size_t m_size;
     IntermediateVarSpanNode m_lastNode;
   };
diff --git a/moses/TranslationModel/fuzzy-match/Alignments.cpp b/moses/TranslationModel/fuzzy-match/Alignments.cpp
index f15d82a5e..142aff251 100644
--- a/moses/TranslationModel/fuzzy-match/Alignments.cpp
+++ b/moses/TranslationModel/fuzzy-match/Alignments.cpp
@@ -8,12 +8,11 @@ using namespace std;
 using namespace Moses;
 
 Alignments::Alignments(const std::string &str, size_t sourceSize, size_t targetSize)
-:m_alignS2T(sourceSize)
-,m_alignT2S(targetSize)
+  :m_alignS2T(sourceSize)
+  ,m_alignT2S(targetSize)
 {
   vector<string> toks   = Tokenize(str, " ");
-  for (size_t i = 0; i < toks.size(); ++i)
-  {
+  for (size_t i = 0; i < toks.size(); ++i) {
     string &tok = toks[i];
 
     vector<int> point = Tokenize<int>(tok, "-");
@@ -25,20 +24,18 @@ Alignments::Alignments(const std::string &str, size_t sourceSize, size_t targetS
     std::map<int, int> &targets = m_alignS2T[ point[0] ];
     iter = targets.find(point[1]);
     if (iter == targets .end()) {
-    	targets[ point[1] ] = 0;
-    }
-    else {
-    	++(iter->second);
+      targets[ point[1] ] = 0;
+    } else {
+      ++(iter->second);
     }
 
     // m_alignedToS
     std::map<int, int> &sources = m_alignT2S[ point[1] ];
     iter = sources.find(point[0]);
     if (iter == targets .end()) {
-    	sources[ point[0] ] = 0;
-    }
-    else {
-    	++(iter->second);
+      sources[ point[0] ] = 0;
+    } else {
+      ++(iter->second);
     }
   }
 
diff --git a/moses/TranslationModel/fuzzy-match/FuzzyMatchWrapper.cpp b/moses/TranslationModel/fuzzy-match/FuzzyMatchWrapper.cpp
index 065368ca7..a4264f6a4 100644
--- a/moses/TranslationModel/fuzzy-match/FuzzyMatchWrapper.cpp
+++ b/moses/TranslationModel/fuzzy-match/FuzzyMatchWrapper.cpp
@@ -17,10 +17,10 @@
 
 using namespace std;
 
-namespace tmmt 
+namespace tmmt
 {
 
-  FuzzyMatchWrapper::FuzzyMatchWrapper(const std::string &sourcePath, const std::string &targetPath, const std::string &alignmentPath)
+FuzzyMatchWrapper::FuzzyMatchWrapper(const std::string &sourcePath, const std::string &targetPath, const std::string &alignmentPath)
   :basic_flag(false)
   ,lsed_flag(true)
   ,refined_flag(true)
@@ -30,790 +30,735 @@ namespace tmmt
   ,multiple_flag(true)
   ,multiple_slack(0)
   ,multiple_max(100)
-  {
-    cerr << "creating suffix array" << endl;
-    suffixArray = new tmmt::SuffixArray( sourcePath );
+{
+  cerr << "creating suffix array" << endl;
+  suffixArray = new tmmt::SuffixArray( sourcePath );
 
-    //cerr << "loading source data" << endl;
-    //load_corpus(sourcePath, source);
+  //cerr << "loading source data" << endl;
+  //load_corpus(sourcePath, source);
 
-    cerr << "loading target data" << endl;
-    load_target(targetPath, targetAndAlignment);
+  cerr << "loading target data" << endl;
+  load_target(targetPath, targetAndAlignment);
 
-    cerr << "loading alignment" << endl;
-    load_alignment(alignmentPath, targetAndAlignment);
+  cerr << "loading alignment" << endl;
+  load_alignment(alignmentPath, targetAndAlignment);
 
-    // create suffix array
-    //load_corpus(m_config[0], input);
-    
-    cerr << "loading completed" << endl;
-  }
+  // create suffix array
+  //load_corpus(m_config[0], input);
+
+  cerr << "loading completed" << endl;
+}
 
-  string FuzzyMatchWrapper::Extract(long translationId, const string &dirNameStr)
-  {
-    const Moses::StaticData &staticData = Moses::StaticData::Instance();
+string FuzzyMatchWrapper::Extract(long translationId, const string &dirNameStr)
+{
+  const Moses::StaticData &staticData = Moses::StaticData::Instance();
+
+  WordIndex wordIndex;
 
-    WordIndex wordIndex;
+  string fuzzyMatchFile = ExtractTM(wordIndex, translationId, dirNameStr);
 
-    string fuzzyMatchFile = ExtractTM(wordIndex, translationId, dirNameStr);
-    
-    // create extrac files
-    create_xml(fuzzyMatchFile);
+  // create extrac files
+  create_xml(fuzzyMatchFile);
 
-    // create phrase table with usual Moses scoring and consolidate programs
-    string cmd;
-    cmd = "LC_ALL=C sort " + fuzzyMatchFile + ".extract | gzip -c > "
-    	+ fuzzyMatchFile + ".extract.sorted.gz";
-    system(cmd.c_str());
-    cmd = "LC_ALL=C sort " + fuzzyMatchFile + ".extract.inv | gzip -c > "
-    	+ fuzzyMatchFile + ".extract.inv.sorted.gz";
-    system(cmd.c_str());
+  // create phrase table with usual Moses scoring and consolidate programs
+  string cmd;
+  cmd = "LC_ALL=C sort " + fuzzyMatchFile + ".extract | gzip -c > "
+        + fuzzyMatchFile + ".extract.sorted.gz";
+  system(cmd.c_str());
+  cmd = "LC_ALL=C sort " + fuzzyMatchFile + ".extract.inv | gzip -c > "
+        + fuzzyMatchFile + ".extract.inv.sorted.gz";
+  system(cmd.c_str());
 
 #ifdef IS_XCODE
-    cmd = "/Users/hieuhoang/unison/workspace/github/moses-smt/bin";
+  cmd = "/Users/hieuhoang/unison/workspace/github/moses-smt/bin";
 #elif IS_ECLIPSE
-    cmd = "/home/hieu/workspace/github/moses-smt/bin";
+  cmd = "/home/hieu/workspace/github/moses-smt/bin";
 #else
-    cmd = staticData.GetBinDirectory();
+  cmd = staticData.GetBinDirectory();
 #endif
 
-    cmd += string("/../scripts/training/train-model.perl -dont-zip -first-step 6 -last-step 6 -f en -e fr -hierarchical ")
-		    	+ " -extract-file " + fuzzyMatchFile + ".extract -lexical-file - -score-options \"--NoLex\" "
-		    	+ " -phrase-translation-table " + fuzzyMatchFile + ".pt";
-    system(cmd.c_str());
+  cmd += string("/../scripts/training/train-model.perl -dont-zip -first-step 6 -last-step 6 -f en -e fr -hierarchical ")
+         + " -extract-file " + fuzzyMatchFile + ".extract -lexical-file - -score-options \"--NoLex\" "
+         + " -phrase-translation-table " + fuzzyMatchFile + ".pt";
+  system(cmd.c_str());
+
+
+  return fuzzyMatchFile + ".pt.gz";
+}
+
+string FuzzyMatchWrapper::ExtractTM(WordIndex &wordIndex, long translationId, const string &dirNameStr)
+{
+  const std::vector< std::vector< WORD_ID > > &source = suffixArray->GetCorpus();
+
+  string inputPath = dirNameStr + "/in";
+  string fuzzyMatchFile = dirNameStr + "/fuzzyMatchFile";
+  ofstream fuzzyMatchStream(fuzzyMatchFile.c_str());
+
+  vector< vector< WORD_ID > > input;
+  load_corpus(inputPath, input);
+
+  assert(input.size() == 1);
+  size_t sentenceInd = 0;
+
+  clock_t start_clock = clock();
+  // if (i % 10 == 0) cerr << ".";
+
+  // establish some basic statistics
 
+  // int input_length = compute_length( input[i] );
+  int input_length = input[sentenceInd].size();
+  int best_cost = input_length * (100-min_match) / 100 + 1;
 
-    return fuzzyMatchFile + ".pt.gz";
+  int match_count = 0; // how many substring matches to be considered
+  //cerr << endl << "sentence " << i << ", length " << input_length << ", best_cost " << best_cost << endl;
+
+  // find match ranges in suffix array
+  vector< vector< pair< SuffixArray::INDEX, SuffixArray::INDEX > > > match_range;
+  for(size_t start=0; start<input[sentenceInd].size(); start++) {
+    SuffixArray::INDEX prior_first_match = 0;
+    SuffixArray::INDEX prior_last_match = suffixArray->GetSize()-1;
+    vector< string > substring;
+    bool stillMatched = true;
+    vector< pair< SuffixArray::INDEX, SuffixArray::INDEX > > matchedAtThisStart;
+    //cerr << "start: " << start;
+    for(int word=start; stillMatched && word<input[sentenceInd].size(); word++) {
+      substring.push_back( GetVocabulary().GetWord( input[sentenceInd][word] ) );
+
+      // only look up, if needed (i.e. no unnecessary short gram lookups)
+      //				if (! word-start+1 <= short_match_max_length( input_length ) )
+      //			{
+      SuffixArray::INDEX first_match, last_match;
+      stillMatched = false;
+      if (suffixArray->FindMatches( substring, first_match, last_match, prior_first_match, prior_last_match ) ) {
+        stillMatched = true;
+        matchedAtThisStart.push_back( make_pair( first_match, last_match ) );
+        //cerr << " (" << first_match << "," << last_match << ")";
+        //cerr << " " << ( last_match - first_match + 1 );
+        prior_first_match = first_match;
+        prior_last_match = last_match;
+      }
+      //}
+    }
+    //cerr << endl;
+    match_range.push_back( matchedAtThisStart );
   }
-  
-  string FuzzyMatchWrapper::ExtractTM(WordIndex &wordIndex, long translationId, const string &dirNameStr)
-  {
-    const std::vector< std::vector< WORD_ID > > &source = suffixArray->GetCorpus();
-
-    string inputPath = dirNameStr + "/in";    
-    string fuzzyMatchFile = dirNameStr + "/fuzzyMatchFile";
-    ofstream fuzzyMatchStream(fuzzyMatchFile.c_str());
- 
-    vector< vector< WORD_ID > > input;
-    load_corpus(inputPath, input);
-    
-    assert(input.size() == 1);
-    size_t sentenceInd = 0;
-    
-		clock_t start_clock = clock();
-		// if (i % 10 == 0) cerr << ".";
-    
-		// establish some basic statistics
-    
-		// int input_length = compute_length( input[i] );
-		int input_length = input[sentenceInd].size();
-		int best_cost = input_length * (100-min_match) / 100 + 1;
-    
-		int match_count = 0; // how many substring matches to be considered
-		//cerr << endl << "sentence " << i << ", length " << input_length << ", best_cost " << best_cost << endl;
-    
-		// find match ranges in suffix array
-		vector< vector< pair< SuffixArray::INDEX, SuffixArray::INDEX > > > match_range;
-		for(size_t start=0;start<input[sentenceInd].size();start++) 
-		{
-			SuffixArray::INDEX prior_first_match = 0;
-			SuffixArray::INDEX prior_last_match = suffixArray->GetSize()-1;
-			vector< string > substring;
-			bool stillMatched = true;
-			vector< pair< SuffixArray::INDEX, SuffixArray::INDEX > > matchedAtThisStart;
-			//cerr << "start: " << start;
-			for(int word=start; stillMatched && word<input[sentenceInd].size(); word++)
-			{
-				substring.push_back( GetVocabulary().GetWord( input[sentenceInd][word] ) );
-        
-				// only look up, if needed (i.e. no unnecessary short gram lookups)
-        //				if (! word-start+1 <= short_match_max_length( input_length ) )
-				//			{
-				SuffixArray::INDEX first_match, last_match;
-				stillMatched = false;
-				if (suffixArray->FindMatches( substring, first_match, last_match, prior_first_match, prior_last_match ) )
-				{
-					stillMatched = true;
-					matchedAtThisStart.push_back( make_pair( first_match, last_match ) );
-					//cerr << " (" << first_match << "," << last_match << ")";
-					//cerr << " " << ( last_match - first_match + 1 );
-					prior_first_match = first_match;
-					prior_last_match = last_match;
-				}
-        //}
-			}
-			//cerr << endl;
-			match_range.push_back( matchedAtThisStart );
-		}
-    
-		clock_t clock_range = clock();
-    
-		map< int, vector< Match > > sentence_match;
-		map< int, int > sentence_match_word_count;
-    
-		// go through all matches, longest first
-		for(int length = input[sentenceInd].size(); length >= 1; length--)
-		{
-			// do not create matches, if these are handled by the short match function
-			if (length <= short_match_max_length( input_length ) )
-			{
-				continue;
-			}
-      
-			unsigned int count = 0;
-			for(int start = 0; start <= input[sentenceInd].size() - length; start++)
-			{
-				if (match_range[start].size() >= length)
-				{
-					pair< SuffixArray::INDEX, SuffixArray::INDEX > &range = match_range[start][length-1];
-					// cerr << " (" << range.first << "," << range.second << ")";
-					count += range.second - range.first + 1;
-          
-					for(SuffixArray::INDEX i=range.first; i<=range.second; i++)
-					{
-						int position = suffixArray->GetPosition( i );
-            
-						// sentence length mismatch
-						size_t sentence_id = suffixArray->GetSentence( position );
-						int sentence_length = suffixArray->GetSentenceLength( sentence_id );
-						int diff = abs( (int)sentence_length - (int)input_length );
-						// cerr << endl << i << "\tsentence " << sentence_id << ", length " << sentence_length;
-						//if (length <= 2 && input_length>=5 &&
-						//		sentence_match.find( sentence_id ) == sentence_match.end())
-						//	continue;
-            
-						if (diff > best_cost)
-							continue;
-            
-						// compute minimal cost
-						int start_pos = suffixArray->GetWordInSentence( position );
-						int end_pos = start_pos + length-1;
-						// cerr << endl << "\t" << start_pos << "-" << end_pos << " (" << sentence_length << ") vs. " 
-						// << start << "-" << (start+length-1) << " (" << input_length << ")"; 
-						// different number of prior words -> cost is at least diff
-						int min_cost = abs( start - start_pos );
-						
-						// same number of words, but not sent. start -> cost is at least 1 
-						if (start == start_pos && start>0)
-							min_cost++;
-            
-						// different number of remaining words -> cost is at least diff
-						min_cost += abs( ( sentence_length-1 - end_pos ) -
-                            ( input_length-1 - (start+length-1) ) );
-            
-						// same number of words, but not sent. end -> cost is at least 1
-						if ( sentence_length-1 - end_pos ==
-                input_length-1 - (start+length-1)
-                && end_pos != sentence_length-1 )
-							min_cost++;
-            
-						// cerr << " -> min_cost " << min_cost;
-						if (min_cost > best_cost)
-							continue;
-            
-						// valid match
-						match_count++;
-            
-						// compute maximal cost
-						int max_cost = max( start, start_pos )
-            + max( sentence_length-1 - end_pos,
-                  input_length-1 - (start+length-1) );
-						// cerr << ", max_cost " << max_cost;
-						
-						Match m = Match( start, start+length-1, 
-                            start_pos, start_pos+length-1, 
-                            min_cost, max_cost, 0);
-						sentence_match[ sentence_id ].push_back( m );
-						sentence_match_word_count[ sentence_id ] += length;
-            
-						if (max_cost < best_cost)
-						{
-							best_cost = max_cost;
-							if (best_cost == 0) break;
-						}
-						//if (match_count >= MAX_MATCH_COUNT) break;
-					}
-				}
-				// cerr << endl;
-				if (best_cost == 0) break;
-				//if (match_count >= MAX_MATCH_COUNT) break;
-			}
-			// cerr << count << " matches at length " << length << " in " << sentence_match.size() << " tm." << endl;
-      
-			if (best_cost == 0) break;
-			//if (match_count >= MAX_MATCH_COUNT) break;
-		}
-		cerr << match_count << " matches in " << sentence_match.size() << " sentences." << endl;
-    
-		clock_t clock_matches = clock();
-    
-		// consider each sentence for which we have matches
-		int old_best_cost = best_cost;
-		int tm_count_word_match = 0;
-		int tm_count_word_match2 = 0;
-		int pruned_match_count = 0;
-		if (short_match_max_length( input_length ))
-		{
-			init_short_matches(wordIndex, translationId, input[sentenceInd] );
-		}
-		vector< int > best_tm;
-		typedef map< int, vector< Match > >::iterator I;
-    
-		clock_t clock_validation_sum = 0;
-    
-		for(I tm=sentence_match.begin(); tm!=sentence_match.end(); tm++)
-		{
-			int tmID = tm->first;
-			int tm_length = suffixArray->GetSentenceLength(tmID);
-			vector< Match > &match = tm->second;
-			add_short_matches(wordIndex, translationId, match, source[tmID], input_length, best_cost );
-      
-			//cerr << "match in sentence " << tmID << ": " << match.size() << " [" << tm_length << "]" << endl;
-      
-			// quick look: how many words are matched
-			int words_matched = 0;
-			for(int m=0;m<match.size();m++) {
-        
-				if (match[m].min_cost <= best_cost) // makes no difference
-					words_matched += match[m].input_end - match[m].input_start + 1;
-			}
-			if (max(input_length,tm_length) - words_matched > best_cost)
-			{
-				if (length_filter_flag) continue;
-			}
-			tm_count_word_match++;
-      
-			// prune, check again how many words are matched
-			vector< Match > pruned = prune_matches( match, best_cost );
-			words_matched = 0;
-			for(int p=0;p<pruned.size();p++) {
-				words_matched += pruned[p].input_end - pruned[p].input_start + 1;
-			}
-			if (max(input_length,tm_length) - words_matched > best_cost)
-			{
-				if (length_filter_flag) continue;
-			}
-			tm_count_word_match2++;
-      
-			pruned_match_count += pruned.size();
-			int prior_best_cost = best_cost;
-			int cost;
-      
-			clock_t clock_validation_start = clock();
-			if (! parse_flag ||
-			    pruned.size()>=10) // to prevent worst cases
-			{
-				string path;
-				cost = sed( input[sentenceInd], source[tmID], path, false );
-				if (cost <  best_cost) 
-				{
-					best_cost = cost;
-				}
-			}
-      
-			else
-			{
-				cost = parse_matches( pruned, input_length, tm_length, best_cost );
-				if (prior_best_cost != best_cost)
-				{
-					best_tm.clear();
-				}
-			}
-			clock_validation_sum += clock() - clock_validation_start;
-			if (cost == best_cost)
-			{
-				best_tm.push_back( tmID );
-			}
-		}
-		cerr << "reduced best cost from " << old_best_cost << " to " << best_cost << endl;
-		cerr << "tm considered: " << sentence_match.size()
-    << " word-matched: " << tm_count_word_match 
-    << " word-matched2: " << tm_count_word_match2 
-    << " best: " << best_tm.size() << endl;
-    
-		cerr << "pruned matches: " << ((float)pruned_match_count/(float)tm_count_word_match2) << endl;
-    
-    // create xml and extract files
-    string inputStr, sourceStr;
-    for (size_t pos = 0; pos < input_length; ++pos) {
-      inputStr += GetVocabulary().GetWord(input[sentenceInd][pos]) + " ";
+
+  clock_t clock_range = clock();
+
+  map< int, vector< Match > > sentence_match;
+  map< int, int > sentence_match_word_count;
+
+  // go through all matches, longest first
+  for(int length = input[sentenceInd].size(); length >= 1; length--) {
+    // do not create matches, if these are handled by the short match function
+    if (length <= short_match_max_length( input_length ) ) {
+      continue;
     }
-    
-		// do not try to find the best ... report multiple matches
-		if (multiple_flag) {
-			int input_letter_length = compute_length( input[sentenceInd] );
-			for(int si=0; si<best_tm.size(); si++) {
-				int s = best_tm[si];
-				string path;
-				unsigned int letter_cost = sed( input[sentenceInd], source[s], path, true );
-				// do not report multiple identical sentences, but just their count
-				//cout << sentenceInd << " "; // sentence number
-				//cout << letter_cost << "/" << input_letter_length << " ";
-				//cout << "(" << best_cost <<"/" << input_length <<") ";
-				//cout << "||| " << s << " ||| " << path << endl;
-        
-        const vector<WORD_ID> &sourceSentence = source[s];
-        vector<SentenceAlignment> &targets = targetAndAlignment[s];
-        create_extract(sentenceInd, best_cost, sourceSentence, targets, inputStr, path, fuzzyMatchStream);
-        
-			}
-		} // if (multiple_flag)
-    else {
-      
-      // find the best matches according to letter sed
-      string best_path = "";
-      int best_match = -1;
-      int best_letter_cost;
-      if (lsed_flag) {
-        best_letter_cost = compute_length( input[sentenceInd] ) * min_match / 100 + 1;
-        for(int si=0; si<best_tm.size(); si++)
-        {
-          int s = best_tm[si];
-          string path;
-          unsigned int letter_cost = sed( input[sentenceInd], source[s], path, true );
-          if (letter_cost < best_letter_cost)
-          {
-            best_letter_cost = letter_cost;
-            best_path = path;
-            best_match = s;
+
+    unsigned int count = 0;
+    for(int start = 0; start <= input[sentenceInd].size() - length; start++) {
+      if (match_range[start].size() >= length) {
+        pair< SuffixArray::INDEX, SuffixArray::INDEX > &range = match_range[start][length-1];
+        // cerr << " (" << range.first << "," << range.second << ")";
+        count += range.second - range.first + 1;
+
+        for(SuffixArray::INDEX i=range.first; i<=range.second; i++) {
+          int position = suffixArray->GetPosition( i );
+
+          // sentence length mismatch
+          size_t sentence_id = suffixArray->GetSentence( position );
+          int sentence_length = suffixArray->GetSentenceLength( sentence_id );
+          int diff = abs( (int)sentence_length - (int)input_length );
+          // cerr << endl << i << "\tsentence " << sentence_id << ", length " << sentence_length;
+          //if (length <= 2 && input_length>=5 &&
+          //		sentence_match.find( sentence_id ) == sentence_match.end())
+          //	continue;
+
+          if (diff > best_cost)
+            continue;
+
+          // compute minimal cost
+          int start_pos = suffixArray->GetWordInSentence( position );
+          int end_pos = start_pos + length-1;
+          // cerr << endl << "\t" << start_pos << "-" << end_pos << " (" << sentence_length << ") vs. "
+          // << start << "-" << (start+length-1) << " (" << input_length << ")";
+          // different number of prior words -> cost is at least diff
+          int min_cost = abs( start - start_pos );
+
+          // same number of words, but not sent. start -> cost is at least 1
+          if (start == start_pos && start>0)
+            min_cost++;
+
+          // different number of remaining words -> cost is at least diff
+          min_cost += abs( ( sentence_length-1 - end_pos ) -
+                           ( input_length-1 - (start+length-1) ) );
+
+          // same number of words, but not sent. end -> cost is at least 1
+          if ( sentence_length-1 - end_pos ==
+               input_length-1 - (start+length-1)
+               && end_pos != sentence_length-1 )
+            min_cost++;
+
+          // cerr << " -> min_cost " << min_cost;
+          if (min_cost > best_cost)
+            continue;
+
+          // valid match
+          match_count++;
+
+          // compute maximal cost
+          int max_cost = max( start, start_pos )
+                         + max( sentence_length-1 - end_pos,
+                                input_length-1 - (start+length-1) );
+          // cerr << ", max_cost " << max_cost;
+
+          Match m = Match( start, start+length-1,
+                           start_pos, start_pos+length-1,
+                           min_cost, max_cost, 0);
+          sentence_match[ sentence_id ].push_back( m );
+          sentence_match_word_count[ sentence_id ] += length;
+
+          if (max_cost < best_cost) {
+            best_cost = max_cost;
+            if (best_cost == 0) break;
           }
+          //if (match_count >= MAX_MATCH_COUNT) break;
         }
       }
-      // if letter sed turned off, just compute path for first match
-      else {
-        if (best_tm.size() > 0) {
-          string path;
-          sed( input[sentenceInd], source[best_tm[0]], path, false );
-          best_path = path;
-          best_match = best_tm[0];
-        }
-      }
-      cerr << "elapsed: " << (1000 * (clock()-start_clock) / CLOCKS_PER_SEC)
-      << " ( range: " << (1000 * (clock_range-start_clock) / CLOCKS_PER_SEC)
-      << " match: " << (1000 * (clock_matches-clock_range) / CLOCKS_PER_SEC)
-      << " tm: " << (1000 * (clock()-clock_matches) / CLOCKS_PER_SEC)
-      << " (validation: " << (1000 * (clock_validation_sum) / CLOCKS_PER_SEC) << ")"
-      << " )" << endl;
-      if (lsed_flag) {
-        //cout << best_letter_cost << "/" << compute_length( input[sentenceInd] ) << " (";
-      }
-      //cout << best_cost <<"/" << input_length;
-      if (lsed_flag) {
-        //cout << ")";
-      }
-      //cout << " ||| " << best_match << " ||| " << best_path << endl;
-      
-      if (best_match == -1) {
-        CHECK(source.size());
-        best_match = 0;
-      }
-      
-      // creat xml & extracts
-      const vector<WORD_ID> &sourceSentence = source[best_match];
-      vector<SentenceAlignment> &targets = targetAndAlignment[best_match];
-      create_extract(sentenceInd, best_cost, sourceSentence, targets, inputStr, best_path, fuzzyMatchStream);
-      
-    } // else if (multiple_flag)
-    
-    fuzzyMatchStream.close();
-    
-    return fuzzyMatchFile;
+      // cerr << endl;
+      if (best_cost == 0) break;
+      //if (match_count >= MAX_MATCH_COUNT) break;
+    }
+    // cerr << count << " matches at length " << length << " in " << sentence_match.size() << " tm." << endl;
+
+    if (best_cost == 0) break;
+    //if (match_count >= MAX_MATCH_COUNT) break;
   }
+  cerr << match_count << " matches in " << sentence_match.size() << " sentences." << endl;
 
-  void FuzzyMatchWrapper::load_corpus( const std::string &fileName, vector< vector< WORD_ID > > &corpus )
-  { // source 
-    ifstream fileStream;
-    fileStream.open(fileName.c_str());
-    if (!fileStream) {
-      cerr << "file not found: " << fileName << endl;
-      exit(1);
+  clock_t clock_matches = clock();
+
+  // consider each sentence for which we have matches
+  int old_best_cost = best_cost;
+  int tm_count_word_match = 0;
+  int tm_count_word_match2 = 0;
+  int pruned_match_count = 0;
+  if (short_match_max_length( input_length )) {
+    init_short_matches(wordIndex, translationId, input[sentenceInd] );
+  }
+  vector< int > best_tm;
+  typedef map< int, vector< Match > >::iterator I;
+
+  clock_t clock_validation_sum = 0;
+
+  for(I tm=sentence_match.begin(); tm!=sentence_match.end(); tm++) {
+    int tmID = tm->first;
+    int tm_length = suffixArray->GetSentenceLength(tmID);
+    vector< Match > &match = tm->second;
+    add_short_matches(wordIndex, translationId, match, source[tmID], input_length, best_cost );
+
+    //cerr << "match in sentence " << tmID << ": " << match.size() << " [" << tm_length << "]" << endl;
+
+    // quick look: how many words are matched
+    int words_matched = 0;
+    for(int m=0; m<match.size(); m++) {
+
+      if (match[m].min_cost <= best_cost) // makes no difference
+        words_matched += match[m].input_end - match[m].input_start + 1;
     }
-    cerr << "loading " << fileName << endl;
-    
-    istream *fileStreamP = &fileStream;
-    
-    char line[LINE_MAX_LENGTH];
-    while(true)
-    {
-      SAFE_GETLINE((*fileStreamP), line, LINE_MAX_LENGTH, '\n');
-      if (fileStreamP->eof()) break;
-      corpus.push_back( GetVocabulary().Tokenize( line ) );
+    if (max(input_length,tm_length) - words_matched > best_cost) {
+      if (length_filter_flag) continue;
     }
-  }
-  
-  void FuzzyMatchWrapper::load_target(const std::string &fileName, vector< vector< SentenceAlignment > > &corpus)
-  { 
-    ifstream fileStream;
-    fileStream.open(fileName.c_str());
-    if (!fileStream) {
-      cerr << "file not found: " << fileName << endl;
-      exit(1);
+    tm_count_word_match++;
+
+    // prune, check again how many words are matched
+    vector< Match > pruned = prune_matches( match, best_cost );
+    words_matched = 0;
+    for(int p=0; p<pruned.size(); p++) {
+      words_matched += pruned[p].input_end - pruned[p].input_start + 1;
     }
-    cerr << "loading " << fileName << endl;
-    
-    istream *fileStreamP = &fileStream;
-    
-    WORD_ID delimiter = GetVocabulary().StoreIfNew("|||");
-    
-    int lineNum = 0;
-    char line[LINE_MAX_LENGTH];
-    while(true)
-    {
-      SAFE_GETLINE((*fileStreamP), line, LINE_MAX_LENGTH, '\n');
-      if (fileStreamP->eof()) break;
-      
-      vector<WORD_ID> toks = GetVocabulary().Tokenize( line );
-      
-      corpus.push_back(vector< SentenceAlignment >());
-      vector< SentenceAlignment > &vec = corpus.back();
-      
-      vec.push_back(SentenceAlignment());
-      SentenceAlignment *sentence = &vec.back();
-      
-      const WORD &countStr = GetVocabulary().GetWord(toks[0]);
-      sentence->count = atoi(countStr.c_str());
-      
-      for (size_t i = 1; i < toks.size(); ++i) {
-        WORD_ID wordId = toks[i];
-        
-        if (wordId == delimiter) {
-          // target and alignments can have multiple sentences.
-          vec.push_back(SentenceAlignment());
-          sentence = &vec.back();
-          
-          // count
-          ++i;
-          
-          const WORD &countStr = GetVocabulary().GetWord(toks[i]);
-          sentence->count = atoi(countStr.c_str());
-        }
-        else {
-          // just a normal word, add
-          sentence->target.push_back(wordId);
-        }
+    if (max(input_length,tm_length) - words_matched > best_cost) {
+      if (length_filter_flag) continue;
+    }
+    tm_count_word_match2++;
+
+    pruned_match_count += pruned.size();
+    int prior_best_cost = best_cost;
+    int cost;
+
+    clock_t clock_validation_start = clock();
+    if (! parse_flag ||
+        pruned.size()>=10) { // to prevent worst cases
+      string path;
+      cost = sed( input[sentenceInd], source[tmID], path, false );
+      if (cost <  best_cost) {
+        best_cost = cost;
+      }
+    }
+
+    else {
+      cost = parse_matches( pruned, input_length, tm_length, best_cost );
+      if (prior_best_cost != best_cost) {
+        best_tm.clear();
       }
-      
-      ++lineNum;
-      
     }
-    
+    clock_validation_sum += clock() - clock_validation_start;
+    if (cost == best_cost) {
+      best_tm.push_back( tmID );
+    }
+  }
+  cerr << "reduced best cost from " << old_best_cost << " to " << best_cost << endl;
+  cerr << "tm considered: " << sentence_match.size()
+       << " word-matched: " << tm_count_word_match
+       << " word-matched2: " << tm_count_word_match2
+       << " best: " << best_tm.size() << endl;
+
+  cerr << "pruned matches: " << ((float)pruned_match_count/(float)tm_count_word_match2) << endl;
+
+  // create xml and extract files
+  string inputStr, sourceStr;
+  for (size_t pos = 0; pos < input_length; ++pos) {
+    inputStr += GetVocabulary().GetWord(input[sentenceInd][pos]) + " ";
   }
-  
-  
-  void FuzzyMatchWrapper::load_alignment(const std::string &fileName, vector< vector< SentenceAlignment > > &corpus )
-  { 
-    ifstream fileStream;
-    fileStream.open(fileName.c_str());
-    if (!fileStream) {
-      cerr << "file not found: " << fileName << endl;
-      exit(1);
+
+  // do not try to find the best ... report multiple matches
+  if (multiple_flag) {
+    int input_letter_length = compute_length( input[sentenceInd] );
+    for(int si=0; si<best_tm.size(); si++) {
+      int s = best_tm[si];
+      string path;
+      unsigned int letter_cost = sed( input[sentenceInd], source[s], path, true );
+      // do not report multiple identical sentences, but just their count
+      //cout << sentenceInd << " "; // sentence number
+      //cout << letter_cost << "/" << input_letter_length << " ";
+      //cout << "(" << best_cost <<"/" << input_length <<") ";
+      //cout << "||| " << s << " ||| " << path << endl;
+
+      const vector<WORD_ID> &sourceSentence = source[s];
+      vector<SentenceAlignment> &targets = targetAndAlignment[s];
+      create_extract(sentenceInd, best_cost, sourceSentence, targets, inputStr, path, fuzzyMatchStream);
+
     }
-    cerr << "loading " << fileName << endl;
-    
-    istream *fileStreamP = &fileStream;
-    
-    string delimiter = "|||";
-    
-    int lineNum = 0;
-    char line[LINE_MAX_LENGTH];
-    while(true)
-    {
-      SAFE_GETLINE((*fileStreamP), line, LINE_MAX_LENGTH, '\n');
-      if (fileStreamP->eof()) break;
-      
-      vector< SentenceAlignment > &vec = corpus[lineNum];
-      size_t targetInd = 0;
-      SentenceAlignment *sentence = &vec[targetInd];
-      
-      vector<string> toks = Moses::Tokenize(line);
-      
-      for (size_t i = 0; i < toks.size(); ++i) {
-        string &tok = toks[i];
-        
-        if (tok == delimiter) {
-          // target and alignments can have multiple sentences.
-          ++targetInd;
-          sentence = &vec[targetInd];
-          
-          ++i;
-        }
-        else {
-          // just a normal alignment, add
-          vector<int> alignPoint = Moses::Tokenize<int>(tok, "-");
-          assert(alignPoint.size() == 2);
-          sentence->alignment.push_back(pair<int,int>(alignPoint[0], alignPoint[1]));
+  } // if (multiple_flag)
+  else {
+
+    // find the best matches according to letter sed
+    string best_path = "";
+    int best_match = -1;
+    int best_letter_cost;
+    if (lsed_flag) {
+      best_letter_cost = compute_length( input[sentenceInd] ) * min_match / 100 + 1;
+      for(int si=0; si<best_tm.size(); si++) {
+        int s = best_tm[si];
+        string path;
+        unsigned int letter_cost = sed( input[sentenceInd], source[s], path, true );
+        if (letter_cost < best_letter_cost) {
+          best_letter_cost = letter_cost;
+          best_path = path;
+          best_match = s;
         }
       }
-      
-      ++lineNum;
-      
     }
+    // if letter sed turned off, just compute path for first match
+    else {
+      if (best_tm.size() > 0) {
+        string path;
+        sed( input[sentenceInd], source[best_tm[0]], path, false );
+        best_path = path;
+        best_match = best_tm[0];
+      }
+    }
+    cerr << "elapsed: " << (1000 * (clock()-start_clock) / CLOCKS_PER_SEC)
+         << " ( range: " << (1000 * (clock_range-start_clock) / CLOCKS_PER_SEC)
+         << " match: " << (1000 * (clock_matches-clock_range) / CLOCKS_PER_SEC)
+         << " tm: " << (1000 * (clock()-clock_matches) / CLOCKS_PER_SEC)
+         << " (validation: " << (1000 * (clock_validation_sum) / CLOCKS_PER_SEC) << ")"
+         << " )" << endl;
+    if (lsed_flag) {
+      //cout << best_letter_cost << "/" << compute_length( input[sentenceInd] ) << " (";
+    }
+    //cout << best_cost <<"/" << input_length;
+    if (lsed_flag) {
+      //cout << ")";
+    }
+    //cout << " ||| " << best_match << " ||| " << best_path << endl;
+
+    if (best_match == -1) {
+      CHECK(source.size());
+      best_match = 0;
+    }
+
+    // creat xml & extracts
+    const vector<WORD_ID> &sourceSentence = source[best_match];
+    vector<SentenceAlignment> &targets = targetAndAlignment[best_match];
+    create_extract(sentenceInd, best_cost, sourceSentence, targets, inputStr, best_path, fuzzyMatchStream);
+
+  } // else if (multiple_flag)
+
+  fuzzyMatchStream.close();
+
+  return fuzzyMatchFile;
+}
+
+void FuzzyMatchWrapper::load_corpus( const std::string &fileName, vector< vector< WORD_ID > > &corpus )
+{
+  // source
+  ifstream fileStream;
+  fileStream.open(fileName.c_str());
+  if (!fileStream) {
+    cerr << "file not found: " << fileName << endl;
+    exit(1);
   }
-  
-  bool FuzzyMatchWrapper::GetLSEDCache(const std::pair< WORD_ID, WORD_ID > &key, unsigned int &value) const
-  {
-#ifdef WITH_THREADS
-    boost::shared_lock<boost::shared_mutex> read_lock(m_accessLock);
-#endif
-    map< pair< WORD_ID, WORD_ID >, unsigned int >::const_iterator lookup = m_lsed.find( key );
-    if (lookup != m_lsed.end()) {
-      value = lookup->second;
-      return true;
+  cerr << "loading " << fileName << endl;
+
+  istream *fileStreamP = &fileStream;
+
+  char line[LINE_MAX_LENGTH];
+  while(true) {
+    SAFE_GETLINE((*fileStreamP), line, LINE_MAX_LENGTH, '\n');
+    if (fileStreamP->eof()) break;
+    corpus.push_back( GetVocabulary().Tokenize( line ) );
+  }
+}
+
+void FuzzyMatchWrapper::load_target(const std::string &fileName, vector< vector< SentenceAlignment > > &corpus)
+{
+  ifstream fileStream;
+  fileStream.open(fileName.c_str());
+  if (!fileStream) {
+    cerr << "file not found: " << fileName << endl;
+    exit(1);
+  }
+  cerr << "loading " << fileName << endl;
+
+  istream *fileStreamP = &fileStream;
+
+  WORD_ID delimiter = GetVocabulary().StoreIfNew("|||");
+
+  int lineNum = 0;
+  char line[LINE_MAX_LENGTH];
+  while(true) {
+    SAFE_GETLINE((*fileStreamP), line, LINE_MAX_LENGTH, '\n');
+    if (fileStreamP->eof()) break;
+
+    vector<WORD_ID> toks = GetVocabulary().Tokenize( line );
+
+    corpus.push_back(vector< SentenceAlignment >());
+    vector< SentenceAlignment > &vec = corpus.back();
+
+    vec.push_back(SentenceAlignment());
+    SentenceAlignment *sentence = &vec.back();
+
+    const WORD &countStr = GetVocabulary().GetWord(toks[0]);
+    sentence->count = atoi(countStr.c_str());
+
+    for (size_t i = 1; i < toks.size(); ++i) {
+      WORD_ID wordId = toks[i];
+
+      if (wordId == delimiter) {
+        // target and alignments can have multiple sentences.
+        vec.push_back(SentenceAlignment());
+        sentence = &vec.back();
+
+        // count
+        ++i;
+
+        const WORD &countStr = GetVocabulary().GetWord(toks[i]);
+        sentence->count = atoi(countStr.c_str());
+      } else {
+        // just a normal word, add
+        sentence->target.push_back(wordId);
+      }
+    }
+
+    ++lineNum;
+
+  }
+
+}
+
+
+void FuzzyMatchWrapper::load_alignment(const std::string &fileName, vector< vector< SentenceAlignment > > &corpus )
+{
+  ifstream fileStream;
+  fileStream.open(fileName.c_str());
+  if (!fileStream) {
+    cerr << "file not found: " << fileName << endl;
+    exit(1);
+  }
+  cerr << "loading " << fileName << endl;
+
+  istream *fileStreamP = &fileStream;
+
+  string delimiter = "|||";
+
+  int lineNum = 0;
+  char line[LINE_MAX_LENGTH];
+  while(true) {
+    SAFE_GETLINE((*fileStreamP), line, LINE_MAX_LENGTH, '\n');
+    if (fileStreamP->eof()) break;
+
+    vector< SentenceAlignment > &vec = corpus[lineNum];
+    size_t targetInd = 0;
+    SentenceAlignment *sentence = &vec[targetInd];
+
+    vector<string> toks = Moses::Tokenize(line);
+
+    for (size_t i = 0; i < toks.size(); ++i) {
+      string &tok = toks[i];
+
+      if (tok == delimiter) {
+        // target and alignments can have multiple sentences.
+        ++targetInd;
+        sentence = &vec[targetInd];
+
+        ++i;
+      } else {
+        // just a normal alignment, add
+        vector<int> alignPoint = Moses::Tokenize<int>(tok, "-");
+        assert(alignPoint.size() == 2);
+        sentence->alignment.push_back(pair<int,int>(alignPoint[0], alignPoint[1]));
+      }
     }
 
-    return false;
+    ++lineNum;
+
   }
+}
 
-  void FuzzyMatchWrapper::SetLSEDCache(const std::pair< WORD_ID, WORD_ID > &key, const unsigned int &value)
-  {
+bool FuzzyMatchWrapper::GetLSEDCache(const std::pair< WORD_ID, WORD_ID > &key, unsigned int &value) const
+{
 #ifdef WITH_THREADS
-    boost::unique_lock<boost::shared_mutex> lock(m_accessLock);
+  boost::shared_lock<boost::shared_mutex> read_lock(m_accessLock);
 #endif
-    m_lsed[ key ] = value;
+  map< pair< WORD_ID, WORD_ID >, unsigned int >::const_iterator lookup = m_lsed.find( key );
+  if (lookup != m_lsed.end()) {
+    value = lookup->second;
+    return true;
   }
 
+  return false;
+}
+
+void FuzzyMatchWrapper::SetLSEDCache(const std::pair< WORD_ID, WORD_ID > &key, const unsigned int &value)
+{
+#ifdef WITH_THREADS
+  boost::unique_lock<boost::shared_mutex> lock(m_accessLock);
+#endif
+  m_lsed[ key ] = value;
+}
+
 /* Letter string edit distance, e.g. sub 'their' to 'there' costs 2 */
 
 unsigned int FuzzyMatchWrapper::letter_sed( WORD_ID aIdx, WORD_ID bIdx )
 {
-	// check if already computed -> lookup in cache
-	pair< WORD_ID, WORD_ID > pIdx = make_pair( aIdx, bIdx );
-	unsigned int value;
-	bool ret = GetLSEDCache(pIdx, value);
-	if (ret) {
-		return value;
-	}
-  
-	// get surface strings for word indices
-	const string &a = GetVocabulary().GetWord( aIdx );
-	const string &b = GetVocabulary().GetWord( bIdx );
-  
-	// initialize cost matrix
-	unsigned int **cost  = (unsigned int**) calloc( sizeof( unsigned int*  ), a.size()+1 );
-	for( unsigned int i=0; i<=a.size(); i++ ) {
-		cost[i] = (unsigned int*) calloc( sizeof(unsigned int), b.size()+1 );
-		cost[i][0] = i;
-	}
-	for( unsigned int j=0; j<=b.size(); j++ ) {
-		cost[0][j] = j;
-	}
-  
-	// core string edit distance loop
-	for( unsigned int i=1; i<=a.size(); i++ ) {
-		for( unsigned int j=1; j<=b.size(); j++ ) {
-      
-			unsigned int ins = cost[i-1][j] + 1;
-			unsigned int del = cost[i][j-1] + 1;
-			bool match = (a.substr(i-1,1).compare( b.substr(j-1,1) ) == 0);
-			unsigned int diag = cost[i-1][j-1] + (match ? 0 : 1);
-      
-			unsigned int min = (ins < del) ? ins : del;
-			min = (diag < min) ? diag : min;
-      
-			cost[i][j] = min;
-		}
-	}
-  
-	// clear out memory
-	unsigned int final = cost[a.size()][b.size()];
-	for( unsigned int i=0; i<=a.size(); i++ ) {
-		free( cost[i] );
-	}
-	free( cost );
-  
-	// cache and return result
-	SetLSEDCache(pIdx, final);
-	return final;
-}
-  
-  /* string edit distance implementation */
-  
-  unsigned int FuzzyMatchWrapper::sed( const vector< WORD_ID > &a, const vector< WORD_ID > &b, string &best_path, bool use_letter_sed ) {
-
-    // initialize cost and path matrices
-    unsigned int **cost  = (unsigned int**) calloc( sizeof( unsigned int* ), a.size()+1 );
-    char **path = (char**) calloc( sizeof( char* ), a.size()+1 );
-
-    for( unsigned int i=0; i<=a.size(); i++ ) {
-      cost[i] = (unsigned int*) calloc( sizeof(unsigned int), b.size()+1 );
-      path[i] = (char*) calloc( sizeof(char), b.size()+1 );
-      if (i>0)
-      {
-        cost[i][0] = cost[i-1][0];
-        if (use_letter_sed)
-        {
-          cost[i][0] += GetVocabulary().GetWord( a[i-1] ).size();
-        }
-        else
-        {
-          cost[i][0]++;
-        }
-      }
-      else
-      {
-        cost[i][0] = 0;
-      }
-      path[i][0] = 'I';
-    }
+  // check if already computed -> lookup in cache
+  pair< WORD_ID, WORD_ID > pIdx = make_pair( aIdx, bIdx );
+  unsigned int value;
+  bool ret = GetLSEDCache(pIdx, value);
+  if (ret) {
+    return value;
+  }
 
-    for( unsigned int j=0; j<=b.size(); j++ ) {
-      if (j>0)
-      {
-        cost[0][j] = cost[0][j-1];
-        if (use_letter_sed)
-        {
-          cost[0][j] +=	GetVocabulary().GetWord( b[j-1] ).size();
-        }
-        else
-        {
-          cost[0][j]++;
-        }
-      }
-      else
-      {
-        cost[0][j] = 0;
-      }
-      path[0][j] = 'D';
+  // get surface strings for word indices
+  const string &a = GetVocabulary().GetWord( aIdx );
+  const string &b = GetVocabulary().GetWord( bIdx );
+
+  // initialize cost matrix
+  unsigned int **cost  = (unsigned int**) calloc( sizeof( unsigned int*  ), a.size()+1 );
+  for( unsigned int i=0; i<=a.size(); i++ ) {
+    cost[i] = (unsigned int*) calloc( sizeof(unsigned int), b.size()+1 );
+    cost[i][0] = i;
+  }
+  for( unsigned int j=0; j<=b.size(); j++ ) {
+    cost[0][j] = j;
+  }
+
+  // core string edit distance loop
+  for( unsigned int i=1; i<=a.size(); i++ ) {
+    for( unsigned int j=1; j<=b.size(); j++ ) {
+
+      unsigned int ins = cost[i-1][j] + 1;
+      unsigned int del = cost[i][j-1] + 1;
+      bool match = (a.substr(i-1,1).compare( b.substr(j-1,1) ) == 0);
+      unsigned int diag = cost[i-1][j-1] + (match ? 0 : 1);
+
+      unsigned int min = (ins < del) ? ins : del;
+      min = (diag < min) ? diag : min;
+
+      cost[i][j] = min;
     }
+  }
 
-    // core string edit distance algorithm
-    for( unsigned int i=1; i<=a.size(); i++ ) {
-      for( unsigned int j=1; j<=b.size(); j++ ) {
-        unsigned int ins = cost[i-1][j];
-        unsigned int del = cost[i][j-1];
-        unsigned int match;
-        if (use_letter_sed)
-        {
-          ins += GetVocabulary().GetWord( a[i-1] ).size();
-          del += GetVocabulary().GetWord( b[j-1] ).size();
-          match = letter_sed( a[i-1], b[j-1] );
-        }
-        else
-        {
-          ins++;
-          del++;
-          match = ( a[i-1] == b[j-1] ) ? 0 : 1;
-        }
-        unsigned int diag = cost[i-1][j-1] + match;
-
-        char action = (ins < del) ? 'I' : 'D';
-        unsigned int min = (ins < del) ? ins : del;
-        if (diag < min)
-        {
-          action = (match>0) ? 'S' : 'M';
-          min = diag;
-        }
+  // clear out memory
+  unsigned int final = cost[a.size()][b.size()];
+  for( unsigned int i=0; i<=a.size(); i++ ) {
+    free( cost[i] );
+  }
+  free( cost );
+
+  // cache and return result
+  SetLSEDCache(pIdx, final);
+  return final;
+}
+
+/* string edit distance implementation */
 
-        cost[i][j] = min;
-        path[i][j] = action;
+unsigned int FuzzyMatchWrapper::sed( const vector< WORD_ID > &a, const vector< WORD_ID > &b, string &best_path, bool use_letter_sed )
+{
+
+  // initialize cost and path matrices
+  unsigned int **cost  = (unsigned int**) calloc( sizeof( unsigned int* ), a.size()+1 );
+  char **path = (char**) calloc( sizeof( char* ), a.size()+1 );
+
+  for( unsigned int i=0; i<=a.size(); i++ ) {
+    cost[i] = (unsigned int*) calloc( sizeof(unsigned int), b.size()+1 );
+    path[i] = (char*) calloc( sizeof(char), b.size()+1 );
+    if (i>0) {
+      cost[i][0] = cost[i-1][0];
+      if (use_letter_sed) {
+        cost[i][0] += GetVocabulary().GetWord( a[i-1] ).size();
+      } else {
+        cost[i][0]++;
       }
+    } else {
+      cost[i][0] = 0;
     }
+    path[i][0] = 'I';
+  }
 
-    // construct string for best path
-    unsigned int i = a.size();
-    unsigned int j = b.size();
-    best_path = "";
-    while( i>0 || j>0 )
-    {
-      best_path = path[i][j] + best_path;
-      if (path[i][j] == 'I')
-      {
-        i--;
+  for( unsigned int j=0; j<=b.size(); j++ ) {
+    if (j>0) {
+      cost[0][j] = cost[0][j-1];
+      if (use_letter_sed) {
+        cost[0][j] +=	GetVocabulary().GetWord( b[j-1] ).size();
+      } else {
+        cost[0][j]++;
       }
-      else if (path[i][j] == 'D')
-      {
-        j--;
+    } else {
+      cost[0][j] = 0;
+    }
+    path[0][j] = 'D';
+  }
+
+  // core string edit distance algorithm
+  for( unsigned int i=1; i<=a.size(); i++ ) {
+    for( unsigned int j=1; j<=b.size(); j++ ) {
+      unsigned int ins = cost[i-1][j];
+      unsigned int del = cost[i][j-1];
+      unsigned int match;
+      if (use_letter_sed) {
+        ins += GetVocabulary().GetWord( a[i-1] ).size();
+        del += GetVocabulary().GetWord( b[j-1] ).size();
+        match = letter_sed( a[i-1], b[j-1] );
+      } else {
+        ins++;
+        del++;
+        match = ( a[i-1] == b[j-1] ) ? 0 : 1;
       }
-      else
-      {
-        i--;
-        j--;
+      unsigned int diag = cost[i-1][j-1] + match;
+
+      char action = (ins < del) ? 'I' : 'D';
+      unsigned int min = (ins < del) ? ins : del;
+      if (diag < min) {
+        action = (match>0) ? 'S' : 'M';
+        min = diag;
       }
+
+      cost[i][j] = min;
+      path[i][j] = action;
     }
+  }
 
+  // construct string for best path
+  unsigned int i = a.size();
+  unsigned int j = b.size();
+  best_path = "";
+  while( i>0 || j>0 ) {
+    best_path = path[i][j] + best_path;
+    if (path[i][j] == 'I') {
+      i--;
+    } else if (path[i][j] == 'D') {
+      j--;
+    } else {
+      i--;
+      j--;
+    }
+  }
 
-    // clear out memory
-    unsigned int final = cost[a.size()][b.size()];
 
-    for( unsigned int i=0; i<=a.size(); i++ ) {
-      free( cost[i] );
-      free( path[i] );
-    }
-    free( cost );
-    free( path );
+  // clear out memory
+  unsigned int final = cost[a.size()][b.size()];
 
-    // return result
-    return final;
+  for( unsigned int i=0; i<=a.size(); i++ ) {
+    free( cost[i] );
+    free( path[i] );
   }
+  free( cost );
+  free( path );
+
+  // return result
+  return final;
+}
 
-/* utlility function: compute length of sentence in characters 
+/* utlility function: compute length of sentence in characters
  (spaces do not count) */
 
 unsigned int FuzzyMatchWrapper::compute_length( const vector< WORD_ID > &sentence )
 {
-	unsigned int length = 0; for( unsigned int i=0; i<sentence.size(); i++ )
-	{
-		length += GetVocabulary().GetWord( sentence[i] ).size();
-	}
-	return length;
+  unsigned int length = 0;
+  for( unsigned int i=0; i<sentence.size(); i++ ) {
+    length += GetVocabulary().GetWord( sentence[i] ).size();
+  }
+  return length;
 }
 
 /* brute force method: compare input to all corpus sentences */
 
-  int FuzzyMatchWrapper::basic_fuzzy_match( vector< vector< WORD_ID > > source, 
-                      vector< vector< WORD_ID > > input ) 
+int FuzzyMatchWrapper::basic_fuzzy_match( vector< vector< WORD_ID > > source,
+    vector< vector< WORD_ID > > input )
 {
-	// go through input set...
-	for(unsigned int i=0;i<input.size();i++)
-	{
-		bool use_letter_sed = false;
-    
-		// compute sentence length and worst allowed cost
-		unsigned int input_length;
-		if (use_letter_sed)
-		{
-			input_length = compute_length( input[i] );
-		}
-		else
-		{
-			input_length = input[i].size();
-		}
-		unsigned int best_cost = input_length * (100-min_match) / 100 + 2;
-		string best_path = "";
-		int best_match = -1;
-    
-		// go through all corpus sentences
-		for(unsigned int s=0;s<source.size();s++)
-		{
-			int source_length;
-			if (use_letter_sed)
-			{
-				source_length = compute_length( source[s] );
-			}
-			else
-			{
-				source_length = source[s].size();
-			}
-			int diff = abs((int)source_length - (int)input_length);
-			if (length_filter_flag && (diff >= best_cost))
-			{
-				continue;
-			}
-      
-			// compute string edit distance
-			string path;
-			unsigned int cost = sed( input[i], source[s], path, use_letter_sed );
-      
-			// update if new best
-			if (cost < best_cost) 
-			{
-				best_cost = cost;
-				best_path = path;
-				best_match = s;
-			}
-		}
-		//cout << best_cost << " ||| " << best_match << " ||| " << best_path << endl;
-	}
+  // go through input set...
+  for(unsigned int i=0; i<input.size(); i++) {
+    bool use_letter_sed = false;
+
+    // compute sentence length and worst allowed cost
+    unsigned int input_length;
+    if (use_letter_sed) {
+      input_length = compute_length( input[i] );
+    } else {
+      input_length = input[i].size();
+    }
+    unsigned int best_cost = input_length * (100-min_match) / 100 + 2;
+    string best_path = "";
+    int best_match = -1;
+
+    // go through all corpus sentences
+    for(unsigned int s=0; s<source.size(); s++) {
+      int source_length;
+      if (use_letter_sed) {
+        source_length = compute_length( source[s] );
+      } else {
+        source_length = source[s].size();
+      }
+      int diff = abs((int)source_length - (int)input_length);
+      if (length_filter_flag && (diff >= best_cost)) {
+        continue;
+      }
+
+      // compute string edit distance
+      string path;
+      unsigned int cost = sed( input[i], source[s], path, use_letter_sed );
+
+      // update if new best
+      if (cost < best_cost) {
+        best_cost = cost;
+        best_path = path;
+        best_match = s;
+      }
+    }
+    //cout << best_cost << " ||| " << best_match << " ||| " << best_path << endl;
+  }
 }
 
 /* definition of short matches
@@ -823,274 +768,250 @@ unsigned int FuzzyMatchWrapper::compute_length( const vector< WORD_ID > &sentenc
 
 int FuzzyMatchWrapper::short_match_max_length( int input_length )
 {
-  if ( ! refined_flag ) 
+  if ( ! refined_flag )
     return 0;
   if ( input_length >= 5 )
     return 1;
-  return 0;	
+  return 0;
 }
 
 
 /* if we have non-short matches in a sentence, we need to
- take a closer look at it. 
+ take a closer look at it.
  this function creates a hash map for all input words and their positions
- (to be used by the next function) 
+ (to be used by the next function)
  (done here, because this has be done only once for an input sentence) */
 
 void FuzzyMatchWrapper::init_short_matches(WordIndex &wordIndex, long translationId, const vector< WORD_ID > &input )
 {
-	int max_length = short_match_max_length( input.size() );
-	if (max_length == 0)
-		return;
-  
-	wordIndex.clear();
-	
-	// store input words and their positions in hash map
-	for(int i=0; i<input.size(); i++)
-	{
-		if (wordIndex.find( input[i] ) == wordIndex.end())
-		{
-			vector< int > position_vector;
-			wordIndex[ input[i] ] = position_vector;
-		}
-		wordIndex[ input[i] ].push_back( i );
-	}	
+  int max_length = short_match_max_length( input.size() );
+  if (max_length == 0)
+    return;
+
+  wordIndex.clear();
+
+  // store input words and their positions in hash map
+  for(int i=0; i<input.size(); i++) {
+    if (wordIndex.find( input[i] ) == wordIndex.end()) {
+      vector< int > position_vector;
+      wordIndex[ input[i] ] = position_vector;
+    }
+    wordIndex[ input[i] ].push_back( i );
+  }
 }
 
 /* add all short matches to list of matches for a sentence */
 
 void FuzzyMatchWrapper::add_short_matches(WordIndex &wordIndex, long translationId, vector< Match > &match, const vector< WORD_ID > &tm, int input_length, int best_cost )
-{	
-	int max_length = short_match_max_length( input_length );
-	if (max_length == 0)
-		return;
-  
-	int tm_length = tm.size();
-	map< WORD_ID,vector< int > >::iterator input_word_hit;
-	for(int t_pos=0; t_pos<tm.size(); t_pos++)
-	{
-		input_word_hit = wordIndex.find( tm[t_pos] );
-		if (input_word_hit != wordIndex.end())
-		{
-			vector< int > &position_vector = input_word_hit->second;
-			for(int j=0; j<position_vector.size(); j++)
-			{
-				int &i_pos = position_vector[j];
-        
-				// before match
-				int max_cost = max( i_pos , t_pos );
-				int min_cost = abs( i_pos - t_pos );
-				if ( i_pos>0 && i_pos == t_pos ) 
-					min_cost++;
-				
-				// after match
-				max_cost += max( (input_length-i_pos) , (tm_length-t_pos));
-				min_cost += abs( (input_length-i_pos) - (tm_length-t_pos));
-				if ( i_pos != input_length-1 && (input_length-i_pos) == (tm_length-t_pos))
-					min_cost++;
-				
-				if (min_cost <= best_cost)
-				{
-					Match new_match( i_pos,i_pos, t_pos,t_pos, min_cost,max_cost,0 );
-					match.push_back( new_match );
-				}
-			}
-		} 
-	}
+{
+  int max_length = short_match_max_length( input_length );
+  if (max_length == 0)
+    return;
+
+  int tm_length = tm.size();
+  map< WORD_ID,vector< int > >::iterator input_word_hit;
+  for(int t_pos=0; t_pos<tm.size(); t_pos++) {
+    input_word_hit = wordIndex.find( tm[t_pos] );
+    if (input_word_hit != wordIndex.end()) {
+      vector< int > &position_vector = input_word_hit->second;
+      for(int j=0; j<position_vector.size(); j++) {
+        int &i_pos = position_vector[j];
+
+        // before match
+        int max_cost = max( i_pos , t_pos );
+        int min_cost = abs( i_pos - t_pos );
+        if ( i_pos>0 && i_pos == t_pos )
+          min_cost++;
+
+        // after match
+        max_cost += max( (input_length-i_pos) , (tm_length-t_pos));
+        min_cost += abs( (input_length-i_pos) - (tm_length-t_pos));
+        if ( i_pos != input_length-1 && (input_length-i_pos) == (tm_length-t_pos))
+          min_cost++;
+
+        if (min_cost <= best_cost) {
+          Match new_match( i_pos,i_pos, t_pos,t_pos, min_cost,max_cost,0 );
+          match.push_back( new_match );
+        }
+      }
+    }
+  }
 }
 
 /* remove matches that are subsumed by a larger match */
 
 vector< Match > FuzzyMatchWrapper::prune_matches( const vector< Match > &match, int best_cost )
 {
-	//cerr << "\tpruning";
-	vector< Match > pruned;
-	for(int i=match.size()-1; i>=0; i--)
-	{
-		//cerr << " (" << match[i].input_start << "," << match[i].input_end 
-		//		 << " ; " << match[i].tm_start << "," << match[i].tm_end 
-		//		 << " * " << match[i].min_cost << ")";
-    
-		//if (match[i].min_cost > best_cost)
-		//	continue;
-    
-		bool subsumed = false;
-		for(int j=match.size()-1; j>=0; j--)
-		{
-			if (i!=j // do not compare match with itself
-					&& ( match[i].input_end - match[i].input_start <= 
-              match[j].input_end - match[j].input_start ) // i shorter than j
-					&& ((match[i].input_start == match[j].input_start &&
-							 match[i].tm_start    == match[j].tm_start	) ||
-							(match[i].input_end   == match[j].input_end &&
-							 match[i].tm_end      == match[j].tm_end) ) )
-			{
-				subsumed = true;
-			}
-		}
-		if (! subsumed && match[i].min_cost <= best_cost)
-		{
-			//cerr << "*";
-			pruned.push_back( match[i] );
-		}
-	}
-	//cerr << endl;
-	return pruned;
+  //cerr << "\tpruning";
+  vector< Match > pruned;
+  for(int i=match.size()-1; i>=0; i--) {
+    //cerr << " (" << match[i].input_start << "," << match[i].input_end
+    //		 << " ; " << match[i].tm_start << "," << match[i].tm_end
+    //		 << " * " << match[i].min_cost << ")";
+
+    //if (match[i].min_cost > best_cost)
+    //	continue;
+
+    bool subsumed = false;
+    for(int j=match.size()-1; j>=0; j--) {
+      if (i!=j // do not compare match with itself
+          && ( match[i].input_end - match[i].input_start <=
+               match[j].input_end - match[j].input_start ) // i shorter than j
+          && ((match[i].input_start == match[j].input_start &&
+               match[i].tm_start    == match[j].tm_start	) ||
+              (match[i].input_end   == match[j].input_end &&
+               match[i].tm_end      == match[j].tm_end) ) ) {
+        subsumed = true;
+      }
+    }
+    if (! subsumed && match[i].min_cost <= best_cost) {
+      //cerr << "*";
+      pruned.push_back( match[i] );
+    }
+  }
+  //cerr << endl;
+  return pruned;
 }
 
 /* A* parsing method to compute string edit distance */
 
 int FuzzyMatchWrapper::parse_matches( vector< Match > &match, int input_length, int tm_length, int &best_cost )
-{	
-	// cerr << "sentence has " << match.size() << " matches, best cost: " << best_cost << ", lengths input: " << input_length << " tm: " << tm_length << endl;
-  
-	if (match.size() == 1)
-		return match[0].max_cost;
-	if (match.size() == 0)
-		return input_length+tm_length;
-	
-	int this_best_cost = input_length + tm_length;
-	for(int i=0;i<match.size();i++)
-	{
-		this_best_cost = min( this_best_cost, match[i].max_cost );
-	}
-	// cerr << "\tthis best cost: " << this_best_cost << endl;
-	
-	// bottom up combination of spans
-	vector< vector< Match > > multi_match;
-	multi_match.push_back( match );
-	
-	int match_level = 1;
-	while(multi_match[ match_level-1 ].size()>0)
-	{
-		// init vector
-		vector< Match > empty;
-		multi_match.push_back( empty );
-    
-		for(int first_level = 0; first_level <= (match_level-1)/2; first_level++)
-		{
-			int second_level = match_level - first_level -1;
-			//cerr << "\tcombining level " << first_level << " and " << second_level << endl;
-			
-			vector< Match > &first_match  = multi_match[ first_level ];
-			vector< Match > &second_match = multi_match[ second_level ];
-      
-			for(int i1 = 0; i1 < first_match.size(); i1++) {
-				for(int i2 = 0; i2 < second_match.size(); i2++) {
-          
-					// do not combine the same pair twice
-					if (first_level == second_level && i2 <= i1) 
-					{
-						continue;
-					}
-          
-					// get sorted matches (first is before second)
-					Match *first, *second;
-					if (first_match[i1].input_start < second_match[i2].input_start )
-					{
-						first = &first_match[i1];
-						second = &second_match[i2];
-					}
-					else
-					{
-						second = &first_match[i1];
-						first = &second_match[i2];
-					}
-          
-					//cerr << "\tcombining " 
-					//		 << "(" << first->input_start << "," << first->input_end << "), "
-					//		 << first->tm_start << " [" << first->internal_cost << "]"
-					//		 << " with "
-					//		 << "(" << second->input_start << "," << second->input_end << "), "
-					//		 << second->tm_start<< " [" << second->internal_cost << "]"
-					//		 << endl;
-          
-					// do not process overlapping matches
-					if (first->input_end >= second->input_start) 
-					{
-						continue;
-					}
-          
-					// no overlap / mismatch in tm
-					if (first->tm_end >= second->tm_start)
-					{
-						continue;
-					}
-          
-					// compute cost
-					int min_cost = 0;
-					int max_cost = 0;
-          
-					// initial
-					min_cost += abs( first->input_start - first->tm_start );
-					max_cost += max( first->input_start, first->tm_start );				 
-          
-					// same number of words, but not sent. start -> cost is at least 1 
-					if (first->input_start == first->tm_start && first->input_start > 0)
-					{
-						min_cost++;
-					}
-          
-					// in-between
-					int skipped_words = second->input_start - first->input_end -1;
-					int skipped_words_tm = second->tm_start - first->tm_end -1;
-					int internal_cost = max( skipped_words, skipped_words_tm );
-					internal_cost += first->internal_cost + second->internal_cost;
-					min_cost += internal_cost;
-					max_cost += internal_cost;
-					
-					// final
-					min_cost += abs( (tm_length-1 - second->tm_end) -
-                          (input_length-1 - second->input_end) );
-					max_cost += max( (tm_length-1 - second->tm_end),
-                          (input_length-1 - second->input_end) );
-          
-					// same number of words, but not sent. end -> cost is at least 1
-					if ( ( input_length-1 - second->input_end 
-                == tm_length-1 - second->tm_end )
-              && input_length-1 != second->input_end )
-					{
-						min_cost++;
-					}
-          
-					// cerr << "\tcost: " << min_cost << "-" << max_cost << endl;
-          
-					// if worst than best cost, forget it
-					if (min_cost > best_cost)					
-					{
-						continue;
-					}
-					
-					// add match
-					Match new_match( first->input_start,
-                          second->input_end,
-                          first->tm_start,
-                          second->tm_end,
-                          min_cost,
-                          max_cost,
-                          internal_cost);
-					multi_match[ match_level ].push_back( new_match );
-					// cerr << "\tstored\n";
-					
-					// possibly updating this_best_cost
-					if (max_cost < this_best_cost)
-					{
-						// cerr << "\tupdating this best cost to " << max_cost << "\n";
-						this_best_cost = max_cost;
-            
-						// possibly updating best_cost
-						if (max_cost < best_cost)
-						{
-							// cerr << "\tupdating best cost to " << max_cost << "\n";
-							best_cost = max_cost;
-						}					
-					}
-				}
-			}
-		}
-		match_level++;
-	}
-	return this_best_cost;
+{
+  // cerr << "sentence has " << match.size() << " matches, best cost: " << best_cost << ", lengths input: " << input_length << " tm: " << tm_length << endl;
+
+  if (match.size() == 1)
+    return match[0].max_cost;
+  if (match.size() == 0)
+    return input_length+tm_length;
+
+  int this_best_cost = input_length + tm_length;
+  for(int i=0; i<match.size(); i++) {
+    this_best_cost = min( this_best_cost, match[i].max_cost );
+  }
+  // cerr << "\tthis best cost: " << this_best_cost << endl;
+
+  // bottom up combination of spans
+  vector< vector< Match > > multi_match;
+  multi_match.push_back( match );
+
+  int match_level = 1;
+  while(multi_match[ match_level-1 ].size()>0) {
+    // init vector
+    vector< Match > empty;
+    multi_match.push_back( empty );
+
+    for(int first_level = 0; first_level <= (match_level-1)/2; first_level++) {
+      int second_level = match_level - first_level -1;
+      //cerr << "\tcombining level " << first_level << " and " << second_level << endl;
+
+      vector< Match > &first_match  = multi_match[ first_level ];
+      vector< Match > &second_match = multi_match[ second_level ];
+
+      for(int i1 = 0; i1 < first_match.size(); i1++) {
+        for(int i2 = 0; i2 < second_match.size(); i2++) {
+
+          // do not combine the same pair twice
+          if (first_level == second_level && i2 <= i1) {
+            continue;
+          }
+
+          // get sorted matches (first is before second)
+          Match *first, *second;
+          if (first_match[i1].input_start < second_match[i2].input_start ) {
+            first = &first_match[i1];
+            second = &second_match[i2];
+          } else {
+            second = &first_match[i1];
+            first = &second_match[i2];
+          }
+
+          //cerr << "\tcombining "
+          //		 << "(" << first->input_start << "," << first->input_end << "), "
+          //		 << first->tm_start << " [" << first->internal_cost << "]"
+          //		 << " with "
+          //		 << "(" << second->input_start << "," << second->input_end << "), "
+          //		 << second->tm_start<< " [" << second->internal_cost << "]"
+          //		 << endl;
+
+          // do not process overlapping matches
+          if (first->input_end >= second->input_start) {
+            continue;
+          }
+
+          // no overlap / mismatch in tm
+          if (first->tm_end >= second->tm_start) {
+            continue;
+          }
+
+          // compute cost
+          int min_cost = 0;
+          int max_cost = 0;
+
+          // initial
+          min_cost += abs( first->input_start - first->tm_start );
+          max_cost += max( first->input_start, first->tm_start );
+
+          // same number of words, but not sent. start -> cost is at least 1
+          if (first->input_start == first->tm_start && first->input_start > 0) {
+            min_cost++;
+          }
+
+          // in-between
+          int skipped_words = second->input_start - first->input_end -1;
+          int skipped_words_tm = second->tm_start - first->tm_end -1;
+          int internal_cost = max( skipped_words, skipped_words_tm );
+          internal_cost += first->internal_cost + second->internal_cost;
+          min_cost += internal_cost;
+          max_cost += internal_cost;
+
+          // final
+          min_cost += abs( (tm_length-1 - second->tm_end) -
+                           (input_length-1 - second->input_end) );
+          max_cost += max( (tm_length-1 - second->tm_end),
+                           (input_length-1 - second->input_end) );
+
+          // same number of words, but not sent. end -> cost is at least 1
+          if ( ( input_length-1 - second->input_end
+                 == tm_length-1 - second->tm_end )
+               && input_length-1 != second->input_end ) {
+            min_cost++;
+          }
+
+          // cerr << "\tcost: " << min_cost << "-" << max_cost << endl;
+
+          // if worst than best cost, forget it
+          if (min_cost > best_cost) {
+            continue;
+          }
+
+          // add match
+          Match new_match( first->input_start,
+                           second->input_end,
+                           first->tm_start,
+                           second->tm_end,
+                           min_cost,
+                           max_cost,
+                           internal_cost);
+          multi_match[ match_level ].push_back( new_match );
+          // cerr << "\tstored\n";
+
+          // possibly updating this_best_cost
+          if (max_cost < this_best_cost) {
+            // cerr << "\tupdating this best cost to " << max_cost << "\n";
+            this_best_cost = max_cost;
+
+            // possibly updating best_cost
+            if (max_cost < best_cost) {
+              // cerr << "\tupdating best cost to " << max_cost << "\n";
+              best_cost = max_cost;
+            }
+          }
+        }
+      }
+    }
+    match_level++;
+  }
+  return this_best_cost;
 }
 
 
@@ -1101,22 +1022,22 @@ void FuzzyMatchWrapper::create_extract(int sentenceInd, int cost, const vector<
     WORD_ID wordId = sourceSentence[pos];
     sourceStr += GetVocabulary().GetWord(wordId) + " ";
   }
-    
+
   for (size_t targetInd = 0; targetInd < targets.size(); ++targetInd) {
-    const SentenceAlignment &sentenceAlignment = targets[targetInd]; 
+    const SentenceAlignment &sentenceAlignment = targets[targetInd];
     string targetStr = sentenceAlignment.getTargetString(GetVocabulary());
     string alignStr = sentenceAlignment.getAlignmentString();
-    
+
     outputFile
-    << sentenceInd << endl
-    << cost << endl
-    << sourceStr << endl 
-    << inputStr << endl
-    << targetStr << endl
-    << alignStr << endl
-    << path << endl
-    << sentenceAlignment.count << endl;
-    
+        << sentenceInd << endl
+        << cost << endl
+        << sourceStr << endl
+        << inputStr << endl
+        << targetStr << endl
+        << alignStr << endl
+        << path << endl
+        << sentenceAlignment.count << endl;
+
   }
 }
 
diff --git a/moses/TranslationModel/fuzzy-match/FuzzyMatchWrapper.h b/moses/TranslationModel/fuzzy-match/FuzzyMatchWrapper.h
index a6f772fb9..d8813a65c 100644
--- a/moses/TranslationModel/fuzzy-match/FuzzyMatchWrapper.h
+++ b/moses/TranslationModel/fuzzy-match/FuzzyMatchWrapper.h
@@ -20,18 +20,18 @@
 #include "Match.h"
 #include "moses/InputType.h"
 
-namespace tmmt 
+namespace tmmt
 {
 class Match;
 class SentenceAlignment;
-  
+
 class FuzzyMatchWrapper
 {
 public:
   FuzzyMatchWrapper(const std::string &source, const std::string &target, const std::string &alignment);
 
   std::string Extract(long translationId, const std::string &dirNameStr);
-  
+
 protected:
   // tm-mt
   std::vector< std::vector< tmmt::SentenceAlignment > > targetAndAlignment;
@@ -58,13 +58,13 @@ protected:
   void load_corpus( const std::string &fileName, std::vector< std::vector< tmmt::WORD_ID > > &corpus );
   void load_target( const std::string &fileName, std::vector< std::vector< tmmt::SentenceAlignment > > &corpus);
   void load_alignment( const std::string &fileName, std::vector< std::vector< tmmt::SentenceAlignment > > &corpus );
-  
+
   /** brute force method: compare input to all corpus sentences */
-  int basic_fuzzy_match( std::vector< std::vector< tmmt::WORD_ID > > source, 
-                        std::vector< std::vector< tmmt::WORD_ID > > input ) ;
-  
-  /** utlility function: compute length of sentence in characters 
-   (spaces do not count) */    
+  int basic_fuzzy_match( std::vector< std::vector< tmmt::WORD_ID > > source,
+                         std::vector< std::vector< tmmt::WORD_ID > > input ) ;
+
+  /** utlility function: compute length of sentence in characters
+   (spaces do not count) */
   unsigned int compute_length( const std::vector< tmmt::WORD_ID > &sentence );
   unsigned int letter_sed( WORD_ID aIdx, WORD_ID bIdx );
   unsigned int sed( const std::vector< WORD_ID > &a, const std::vector< WORD_ID > &b, std::string &best_path, bool use_letter_sed );
@@ -77,8 +77,9 @@ protected:
   void create_extract(int sentenceInd, int cost, const std::vector< WORD_ID > &sourceSentence, const std::vector<SentenceAlignment> &targets, const std::string &inputStr, const std::string  &path, std::ofstream &outputFile);
 
   std::string ExtractTM(WordIndex &wordIndex, long translationId, const std::string &inputPath);
-  Vocabulary &GetVocabulary()
-  { return suffixArray->GetVocabulary(); }
+  Vocabulary &GetVocabulary() {
+    return suffixArray->GetVocabulary();
+  }
 
   bool GetLSEDCache(const std::pair< WORD_ID, WORD_ID > &key, unsigned int &value) const;
   void SetLSEDCache(const std::pair< WORD_ID, WORD_ID > &key, const unsigned int &value);
diff --git a/moses/TranslationModel/fuzzy-match/Match.h b/moses/TranslationModel/fuzzy-match/Match.h
index 7feb25769..f2ba2c150 100644
--- a/moses/TranslationModel/fuzzy-match/Match.h
+++ b/moses/TranslationModel/fuzzy-match/Match.h
@@ -14,17 +14,18 @@ namespace tmmt
 
 /* data structure for n-gram match between input and corpus */
 
-class Match {
+class Match
+{
 public:
-	int input_start;
-	int input_end;
-	int tm_start;
-	int tm_end;
-	int min_cost;
-	int max_cost;
-	int internal_cost;
-	Match( int is, int ie, int ts, int te, int min, int max, int i )
-  :input_start(is), input_end(ie), tm_start(ts), tm_end(te), min_cost(min), max_cost(max), internal_cost(i)
+  int input_start;
+  int input_end;
+  int tm_start;
+  int tm_end;
+  int min_cost;
+  int max_cost;
+  int internal_cost;
+  Match( int is, int ie, int ts, int te, int min, int max, int i )
+    :input_start(is), input_end(ie), tm_start(ts), tm_end(te), min_cost(min), max_cost(max), internal_cost(i)
   {}
 };
 
diff --git a/moses/TranslationModel/fuzzy-match/SentenceAlignment.h b/moses/TranslationModel/fuzzy-match/SentenceAlignment.h
index 30c887fc1..466baa149 100644
--- a/moses/TranslationModel/fuzzy-match/SentenceAlignment.h
+++ b/moses/TranslationModel/fuzzy-match/SentenceAlignment.h
@@ -15,20 +15,18 @@
 
 namespace tmmt
 {
-  
-struct SentenceAlignment
-{
+
+struct SentenceAlignment {
   int count;
   std::vector< WORD_ID > target;
   std::vector< std::pair<int,int> > alignment;
-  
+
   SentenceAlignment()
   {}
-  
+
   std::string getTargetString(const Vocabulary &vocab) const;
-  
-  std::string getAlignmentString() const
-  {
+
+  std::string getAlignmentString() const {
     std::stringstream strme;
     for (size_t i = 0; i < alignment.size(); ++i) {
       const std::pair<int,int> &alignPair = alignment[i];
@@ -36,7 +34,7 @@ struct SentenceAlignment
     }
     return strme.str();
   }
-  
+
 };
 
 }
diff --git a/moses/TranslationModel/fuzzy-match/SuffixArray.cpp b/moses/TranslationModel/fuzzy-match/SuffixArray.cpp
index 8a67fd954..5f49952ce 100644
--- a/moses/TranslationModel/fuzzy-match/SuffixArray.cpp
+++ b/moses/TranslationModel/fuzzy-match/SuffixArray.cpp
@@ -8,247 +8,235 @@ using namespace std;
 namespace tmmt
 {
 
-SuffixArray::SuffixArray( string fileName ) 
+SuffixArray::SuffixArray( string fileName )
 {
-	m_vcb.StoreIfNew( "<uNk>" );
-	m_endOfSentence = m_vcb.StoreIfNew( "<s>" );
-
-	ifstream extractFile;
-	char line[LINE_MAX_LENGTH];
-
-	// count the number of words first;
-	extractFile.open(fileName.c_str());
-	istream *fileP = &extractFile;
-	m_size = 0;
-	size_t sentenceCount = 0;
-	while(!fileP->eof()) {
-		SAFE_GETLINE((*fileP), line, LINE_MAX_LENGTH, '\n');
-		if (fileP->eof()) break;
-		vector< WORD_ID > words = m_vcb.Tokenize( line );
-		m_size += words.size() + 1;
-		sentenceCount++;
-	}
-	extractFile.close();
-	cerr << m_size << " words (incl. sentence boundaries)" << endl;
-
-	// allocate memory
-	m_array = (WORD_ID*) calloc( sizeof( WORD_ID ), m_size );
-	m_index = (INDEX*) calloc( sizeof( INDEX ), m_size );
-	m_wordInSentence = (char*) calloc( sizeof( char ), m_size );
-	m_sentence = (size_t*) calloc( sizeof( size_t ), m_size );
-	m_sentenceLength = (char*) calloc( sizeof( char ), sentenceCount );
-
-	// fill the array
-	int wordIndex = 0;
-	int sentenceId = 0;
-	extractFile.open(fileName.c_str());
-	fileP = &extractFile;
-	while(!fileP->eof()) {
-		SAFE_GETLINE((*fileP), line, LINE_MAX_LENGTH, '\n');
-		if (fileP->eof()) break;
-		vector< WORD_ID > words = m_vcb.Tokenize( line );
-
-		// add to corpus vector
-		corpus.push_back(words);
-
-		// create SA
-		
-		vector< WORD_ID >::const_iterator i;
-		for( i=words.begin(); i!=words.end(); i++)
-		{
-			m_index[ wordIndex ] = wordIndex;
-			m_sentence[ wordIndex ] = sentenceId;
-			m_wordInSentence[ wordIndex ] = i-words.begin();
-			m_array[ wordIndex++ ] = *i;
-		}
-		m_index[ wordIndex ] = wordIndex;
-		m_array[ wordIndex++ ] = m_endOfSentence;
-		m_sentenceLength[ sentenceId++ ] = words.size();
-	}
-	extractFile.close();
-	cerr << "done reading " << wordIndex << " words, " << sentenceId << " sentences." << endl;
-	// List(0,9);
-
-	// sort
-	m_buffer = (INDEX*) calloc( sizeof( INDEX ), m_size );
-	Sort( 0, m_size-1 );
-	free( m_buffer );
-	cerr << "done sorting" << endl;
+  m_vcb.StoreIfNew( "<uNk>" );
+  m_endOfSentence = m_vcb.StoreIfNew( "<s>" );
+
+  ifstream extractFile;
+  char line[LINE_MAX_LENGTH];
+
+  // count the number of words first;
+  extractFile.open(fileName.c_str());
+  istream *fileP = &extractFile;
+  m_size = 0;
+  size_t sentenceCount = 0;
+  while(!fileP->eof()) {
+    SAFE_GETLINE((*fileP), line, LINE_MAX_LENGTH, '\n');
+    if (fileP->eof()) break;
+    vector< WORD_ID > words = m_vcb.Tokenize( line );
+    m_size += words.size() + 1;
+    sentenceCount++;
+  }
+  extractFile.close();
+  cerr << m_size << " words (incl. sentence boundaries)" << endl;
+
+  // allocate memory
+  m_array = (WORD_ID*) calloc( sizeof( WORD_ID ), m_size );
+  m_index = (INDEX*) calloc( sizeof( INDEX ), m_size );
+  m_wordInSentence = (char*) calloc( sizeof( char ), m_size );
+  m_sentence = (size_t*) calloc( sizeof( size_t ), m_size );
+  m_sentenceLength = (char*) calloc( sizeof( char ), sentenceCount );
+
+  // fill the array
+  int wordIndex = 0;
+  int sentenceId = 0;
+  extractFile.open(fileName.c_str());
+  fileP = &extractFile;
+  while(!fileP->eof()) {
+    SAFE_GETLINE((*fileP), line, LINE_MAX_LENGTH, '\n');
+    if (fileP->eof()) break;
+    vector< WORD_ID > words = m_vcb.Tokenize( line );
+
+    // add to corpus vector
+    corpus.push_back(words);
+
+    // create SA
+
+    vector< WORD_ID >::const_iterator i;
+    for( i=words.begin(); i!=words.end(); i++) {
+      m_index[ wordIndex ] = wordIndex;
+      m_sentence[ wordIndex ] = sentenceId;
+      m_wordInSentence[ wordIndex ] = i-words.begin();
+      m_array[ wordIndex++ ] = *i;
+    }
+    m_index[ wordIndex ] = wordIndex;
+    m_array[ wordIndex++ ] = m_endOfSentence;
+    m_sentenceLength[ sentenceId++ ] = words.size();
+  }
+  extractFile.close();
+  cerr << "done reading " << wordIndex << " words, " << sentenceId << " sentences." << endl;
+  // List(0,9);
+
+  // sort
+  m_buffer = (INDEX*) calloc( sizeof( INDEX ), m_size );
+  Sort( 0, m_size-1 );
+  free( m_buffer );
+  cerr << "done sorting" << endl;
 }
 
 // good ol' quick sort
-void SuffixArray::Sort(INDEX start, INDEX end) {
-	if (start == end) return;
-	INDEX mid = (start+end+1)/2;
-	Sort( start, mid-1 );
-	Sort( mid, end );
-
-	// merge
-	int i = start;
-	int j = mid;
-	int k = 0;
-	int length = end-start+1;
-	while( k<length )
-	{
-		if (i == mid ) 
-		{
-			m_buffer[ k++ ] = m_index[ j++ ];
-		}
-		else if (j > end ) 
-		{
-			m_buffer[ k++ ] = m_index[ i++ ];
-		}
-		else {
-			if (CompareIndex( m_index[i], m_index[j] ) < 0) 
-			{
-				m_buffer[ k++ ] = m_index[ i++ ];
-			}	
-			else 
-			{
-				m_buffer[ k++ ] = m_index[ j++ ];
-			}
-		}
-	}
-	
-	memcpy( ((char*)m_index) + sizeof( INDEX ) * start,
-					((char*)m_buffer), sizeof( INDEX ) * (end-start+1) );
+void SuffixArray::Sort(INDEX start, INDEX end)
+{
+  if (start == end) return;
+  INDEX mid = (start+end+1)/2;
+  Sort( start, mid-1 );
+  Sort( mid, end );
+
+  // merge
+  int i = start;
+  int j = mid;
+  int k = 0;
+  int length = end-start+1;
+  while( k<length ) {
+    if (i == mid ) {
+      m_buffer[ k++ ] = m_index[ j++ ];
+    } else if (j > end ) {
+      m_buffer[ k++ ] = m_index[ i++ ];
+    } else {
+      if (CompareIndex( m_index[i], m_index[j] ) < 0) {
+        m_buffer[ k++ ] = m_index[ i++ ];
+      } else {
+        m_buffer[ k++ ] = m_index[ j++ ];
+      }
+    }
+  }
+
+  memcpy( ((char*)m_index) + sizeof( INDEX ) * start,
+          ((char*)m_buffer), sizeof( INDEX ) * (end-start+1) );
 }
 
 SuffixArray::~SuffixArray()
-{ 
-	free(m_index); 
-	free(m_array);
+{
+  free(m_index);
+  free(m_array);
 }
 
 int SuffixArray::CompareIndex( INDEX a, INDEX b ) const
 {
-	// skip over identical words
-	INDEX offset = 0;
-	while( a+offset < m_size &&
-				 b+offset < m_size &&
-				 m_array[ a+offset ] == m_array[ b+offset ] )
-	{ offset++; }
-	
-	if( a+offset == m_size ) return -1;
-	if( b+offset == m_size ) return 1;
-	return CompareWord( m_array[ a+offset ], m_array[ b+offset ] );
+  // skip over identical words
+  INDEX offset = 0;
+  while( a+offset < m_size &&
+         b+offset < m_size &&
+         m_array[ a+offset ] == m_array[ b+offset ] ) {
+    offset++;
+  }
+
+  if( a+offset == m_size ) return -1;
+  if( b+offset == m_size ) return 1;
+  return CompareWord( m_array[ a+offset ], m_array[ b+offset ] );
 }
 
 inline int SuffixArray::CompareWord( WORD_ID a, WORD_ID b ) const
 {
-	// cerr << "c(" << m_vcb.GetWord(a) << ":" << m_vcb.GetWord(b) << ")=" << m_vcb.GetWord(a).compare( m_vcb.GetWord(b) ) << endl;
-	return m_vcb.GetWord(a).compare( m_vcb.GetWord(b) );
+  // cerr << "c(" << m_vcb.GetWord(a) << ":" << m_vcb.GetWord(b) << ")=" << m_vcb.GetWord(a).compare( m_vcb.GetWord(b) ) << endl;
+  return m_vcb.GetWord(a).compare( m_vcb.GetWord(b) );
 }
 
 int SuffixArray::Count( const vector< WORD > &phrase )
 {
-	INDEX dummy;
-	return LimitedCount( phrase, m_size, dummy, dummy, 0, m_size-1 );
+  INDEX dummy;
+  return LimitedCount( phrase, m_size, dummy, dummy, 0, m_size-1 );
 }
 
 bool SuffixArray::MinCount( const vector< WORD > &phrase, INDEX min )
 {
-	INDEX dummy;
-	return LimitedCount( phrase, min, dummy, dummy, 0, m_size-1 ) >= min;
+  INDEX dummy;
+  return LimitedCount( phrase, min, dummy, dummy, 0, m_size-1 ) >= min;
 }
 
 bool SuffixArray::Exists( const vector< WORD > &phrase )
 {
-	INDEX dummy;
-	return LimitedCount( phrase, 1, dummy, dummy, 0, m_size-1 ) == 1;
+  INDEX dummy;
+  return LimitedCount( phrase, 1, dummy, dummy, 0, m_size-1 ) == 1;
 }
 
 int SuffixArray::FindMatches( const vector< WORD > &phrase, INDEX &firstMatch, INDEX &lastMatch, INDEX search_start, INDEX search_end )
 {
-	return LimitedCount( phrase, m_size, firstMatch, lastMatch, search_start, search_end );
+  return LimitedCount( phrase, m_size, firstMatch, lastMatch, search_start, search_end );
 }
 
 int SuffixArray::LimitedCount( const vector< WORD > &phrase, INDEX min, INDEX &firstMatch, INDEX &lastMatch, INDEX search_start, INDEX search_end )
 {
-	// cerr << "FindFirst\n";
-	INDEX start = search_start;
-	INDEX end = (search_end == -1) ? (m_size-1) : search_end;
-	INDEX mid = FindFirst( phrase, start, end );
-	// cerr << "done\n";
-	if (mid == m_size) return 0; // no matches
-	if (min == 1) return 1;      // only existance check
+  // cerr << "FindFirst\n";
+  INDEX start = search_start;
+  INDEX end = (search_end == -1) ? (m_size-1) : search_end;
+  INDEX mid = FindFirst( phrase, start, end );
+  // cerr << "done\n";
+  if (mid == m_size) return 0; // no matches
+  if (min == 1) return 1;      // only existance check
 
-	int matchCount = 1;
+  int matchCount = 1;
 
-	//cerr << "before...\n";
-	firstMatch = FindLast( phrase, mid, start, -1 );
-	matchCount += mid - firstMatch;
+  //cerr << "before...\n";
+  firstMatch = FindLast( phrase, mid, start, -1 );
+  matchCount += mid - firstMatch;
 
-	//cerr << "after...\n";
-	lastMatch = FindLast( phrase, mid, end, 1 );
-	matchCount += lastMatch - mid;
+  //cerr << "after...\n";
+  lastMatch = FindLast( phrase, mid, end, 1 );
+  matchCount += lastMatch - mid;
 
-	return matchCount;
+  return matchCount;
 }
 
 SuffixArray::INDEX SuffixArray::FindLast( const vector< WORD > &phrase, INDEX start, INDEX end, int direction )
 {
-	end += direction;
-	while(true)
-	{
-		INDEX mid = ( start + end + (direction>0 ? 0 : 1) )/2;
-		
-		int match = Match( phrase, mid );
-		int matchNext = Match( phrase, mid+direction );
-		//cerr << "\t" << start << ";" << mid << ";" << end << " -> " << match << "," << matchNext << endl;
-		
-		if (match == 0 && matchNext != 0) return mid;
-
-		if (match == 0) // mid point is a match
-			start = mid;
-		else
-			end = mid;
-	}
+  end += direction;
+  while(true) {
+    INDEX mid = ( start + end + (direction>0 ? 0 : 1) )/2;
+
+    int match = Match( phrase, mid );
+    int matchNext = Match( phrase, mid+direction );
+    //cerr << "\t" << start << ";" << mid << ";" << end << " -> " << match << "," << matchNext << endl;
+
+    if (match == 0 && matchNext != 0) return mid;
+
+    if (match == 0) // mid point is a match
+      start = mid;
+    else
+      end = mid;
+  }
 }
 
 SuffixArray::INDEX SuffixArray::FindFirst( const vector< WORD > &phrase, INDEX &start, INDEX &end )
 {
-	while(true)
-	{
-		INDEX mid = ( start + end + 1 )/2;
-		//cerr << "FindFirst(" << start << ";" << mid << ";" << end << ")\n";
-		int match = Match( phrase, mid );
-		
-		if (match == 0) return mid;
-		if (start >= end && match != 0 ) return m_size;
-		
-		if (match > 0)
-			start = mid+1;
-		else
-			end = mid-1;	
-	}
+  while(true) {
+    INDEX mid = ( start + end + 1 )/2;
+    //cerr << "FindFirst(" << start << ";" << mid << ";" << end << ")\n";
+    int match = Match( phrase, mid );
+
+    if (match == 0) return mid;
+    if (start >= end && match != 0 ) return m_size;
+
+    if (match > 0)
+      start = mid+1;
+    else
+      end = mid-1;
+  }
 }
 
 int SuffixArray::Match( const vector< WORD > &phrase, INDEX index )
 {
-	INDEX pos = m_index[ index ];
-	for(INDEX i=0; i<phrase.size() && i+pos<m_size; i++)
-	{
-		int match = CompareWord( m_vcb.GetWordID( phrase[i] ), m_array[ pos+i ] );
-		// cerr << "{" << index << "+" << i << "," << pos+i << ":" << match << "}" << endl;
-		if (match != 0) 
-			return match;
-	}
-	return 0;
+  INDEX pos = m_index[ index ];
+  for(INDEX i=0; i<phrase.size() && i+pos<m_size; i++) {
+    int match = CompareWord( m_vcb.GetWordID( phrase[i] ), m_array[ pos+i ] );
+    // cerr << "{" << index << "+" << i << "," << pos+i << ":" << match << "}" << endl;
+    if (match != 0)
+      return match;
+  }
+  return 0;
 }
 
 void SuffixArray::List(INDEX start, INDEX end)
 {
-	for(INDEX i=start; i<=end; i++)
-	{
-		INDEX pos = m_index[ i ];
-		// cerr << i << ":" << pos << "\t";
-		for(int j=0; j<5 && j+pos<m_size; j++)
-		{
-			//cout << " " << m_vcb.GetWord( m_array[ pos+j ] );
-		}
-		// cerr << "\n";
-	}
+  for(INDEX i=start; i<=end; i++) {
+    INDEX pos = m_index[ i ];
+    // cerr << i << ":" << pos << "\t";
+    for(int j=0; j<5 && j+pos<m_size; j++) {
+      //cout << " " << m_vcb.GetWord( m_array[ pos+j ] );
+    }
+    // cerr << "\n";
+  }
 }
 
 }
diff --git a/moses/TranslationModel/fuzzy-match/SuffixArray.h b/moses/TranslationModel/fuzzy-match/SuffixArray.h
index 5cfb120d6..a2dbf892c 100644
--- a/moses/TranslationModel/fuzzy-match/SuffixArray.h
+++ b/moses/TranslationModel/fuzzy-match/SuffixArray.h
@@ -6,51 +6,63 @@
 
 namespace tmmt
 {
-  
-class SuffixArray 
+
+class SuffixArray
 {
 public:
-	typedef unsigned int INDEX;
+  typedef unsigned int INDEX;
 
 private:
   std::vector< std::vector< WORD_ID > > corpus;
 
   WORD_ID *m_array;
-	INDEX *m_index;
-	INDEX *m_buffer;
-	char *m_wordInSentence;
-	size_t *m_sentence;
-	char *m_sentenceLength;
-	WORD_ID m_endOfSentence;
-	Vocabulary m_vcb;
-	INDEX m_size;
+  INDEX *m_index;
+  INDEX *m_buffer;
+  char *m_wordInSentence;
+  size_t *m_sentence;
+  char *m_sentenceLength;
+  WORD_ID m_endOfSentence;
+  Vocabulary m_vcb;
+  INDEX m_size;
 
 public:
-	SuffixArray( std::string fileName );
-	~SuffixArray();
-
-	void Sort(INDEX start, INDEX end);
-	int CompareIndex( INDEX a, INDEX b ) const;
-	inline int CompareWord( WORD_ID a, WORD_ID b ) const;
-	int Count( const std::vector< WORD > &phrase );
-	bool MinCount( const std::vector< WORD > &phrase, INDEX min );
-	bool Exists( const std::vector< WORD > &phrase );
-	int FindMatches( const std::vector< WORD > &phrase, INDEX &firstMatch, INDEX &lastMatch, INDEX search_start = 0, INDEX search_end = -1 );
-	int LimitedCount( const std::vector< WORD > &phrase, INDEX min, INDEX &firstMatch, INDEX &lastMatch, INDEX search_start = -1, INDEX search_end = 0 );
-	INDEX FindFirst( const std::vector< WORD > &phrase, INDEX &start, INDEX &end );
-	INDEX FindLast( const std::vector< WORD > &phrase, INDEX start, INDEX end, int direction );
-	int Match( const std::vector< WORD > &phrase, INDEX index );
-	void List( INDEX start, INDEX end );
-	inline INDEX GetPosition( INDEX index ) { return m_index[ index ]; }
-	inline size_t GetSentence( INDEX position ) { return m_sentence[position]; }
-	inline char GetWordInSentence( INDEX position ) { return m_wordInSentence[position]; }
-	inline char GetSentenceLength( size_t sentenceId ) { return m_sentenceLength[sentenceId]; }
-	inline INDEX GetSize() { return m_size; }
-
-	Vocabulary &GetVocabulary()
-	{ return m_vcb; }
-	const std::vector< std::vector< WORD_ID > > &GetCorpus() const
-  { return corpus; }
+  SuffixArray( std::string fileName );
+  ~SuffixArray();
+
+  void Sort(INDEX start, INDEX end);
+  int CompareIndex( INDEX a, INDEX b ) const;
+  inline int CompareWord( WORD_ID a, WORD_ID b ) const;
+  int Count( const std::vector< WORD > &phrase );
+  bool MinCount( const std::vector< WORD > &phrase, INDEX min );
+  bool Exists( const std::vector< WORD > &phrase );
+  int FindMatches( const std::vector< WORD > &phrase, INDEX &firstMatch, INDEX &lastMatch, INDEX search_start = 0, INDEX search_end = -1 );
+  int LimitedCount( const std::vector< WORD > &phrase, INDEX min, INDEX &firstMatch, INDEX &lastMatch, INDEX search_start = -1, INDEX search_end = 0 );
+  INDEX FindFirst( const std::vector< WORD > &phrase, INDEX &start, INDEX &end );
+  INDEX FindLast( const std::vector< WORD > &phrase, INDEX start, INDEX end, int direction );
+  int Match( const std::vector< WORD > &phrase, INDEX index );
+  void List( INDEX start, INDEX end );
+  inline INDEX GetPosition( INDEX index ) {
+    return m_index[ index ];
+  }
+  inline size_t GetSentence( INDEX position ) {
+    return m_sentence[position];
+  }
+  inline char GetWordInSentence( INDEX position ) {
+    return m_wordInSentence[position];
+  }
+  inline char GetSentenceLength( size_t sentenceId ) {
+    return m_sentenceLength[sentenceId];
+  }
+  inline INDEX GetSize() {
+    return m_size;
+  }
+
+  Vocabulary &GetVocabulary() {
+    return m_vcb;
+  }
+  const std::vector< std::vector< WORD_ID > > &GetCorpus() const {
+    return corpus;
+  }
 };
 
 }
diff --git a/moses/TranslationModel/fuzzy-match/Vocabulary.cpp b/moses/TranslationModel/fuzzy-match/Vocabulary.cpp
index 0c833ff78..ab1439a29 100644
--- a/moses/TranslationModel/fuzzy-match/Vocabulary.cpp
+++ b/moses/TranslationModel/fuzzy-match/Vocabulary.cpp
@@ -10,7 +10,8 @@ namespace tmmt
 {

 

 // as in beamdecoder/tables.cpp

-vector<WORD_ID> Vocabulary::Tokenize( const char input[] ) {

+vector<WORD_ID> Vocabulary::Tokenize( const char input[] )

+{

   vector< WORD_ID > token;

   bool betweenWords = true;

   int start=0;

@@ -21,8 +22,7 @@ vector<WORD_ID> Vocabulary::Tokenize( const char input[] ) {
     if (!isSpace && betweenWords) {

       start = i;

       betweenWords = false;

-    }

-    else if (isSpace && !betweenWords) {

+    } else if (isSpace && !betweenWords) {

       token.push_back( StoreIfNew ( string( input+start, i-start ) ) );

       betweenWords = true;

     }

@@ -32,9 +32,11 @@ vector<WORD_ID> Vocabulary::Tokenize( const char input[] ) {
   return token;

 }

 

-WORD_ID Vocabulary::StoreIfNew( const WORD& word ) {

+WORD_ID Vocabulary::StoreIfNew( const WORD& word )

+{

 

-  { // read=lock scope

+  {

+    // read=lock scope

 #ifdef WITH_THREADS

     boost::shared_lock<boost::shared_mutex> read_lock(m_accessLock);

 #endif

@@ -43,17 +45,18 @@ WORD_ID Vocabulary::StoreIfNew( const WORD& word ) {
     if( i != lookup.end() )

       return i->second;

   }

-  

+

 #ifdef WITH_THREADS

   boost::unique_lock<boost::shared_mutex> lock(m_accessLock);

 #endif

   WORD_ID id = vocab.size();

   vocab.push_back( word );

   lookup[ word ] = id;

-  return id;  

+  return id;

 }

 

-WORD_ID Vocabulary::GetWordID( const WORD &word ) {

+WORD_ID Vocabulary::GetWordID( const WORD &word )

+{

 #ifdef WITH_THREADS

   boost::shared_lock<boost::shared_mutex> read_lock(m_accessLock);

 #endif

diff --git a/moses/TranslationModel/fuzzy-match/Vocabulary.h b/moses/TranslationModel/fuzzy-match/Vocabulary.h
index 7be82bcbe..dfa11c1db 100644
--- a/moses/TranslationModel/fuzzy-match/Vocabulary.h
+++ b/moses/TranslationModel/fuzzy-match/Vocabulary.h
@@ -34,16 +34,20 @@ namespace tmmt
 typedef std::string WORD;
 typedef unsigned int WORD_ID;
 
-class Vocabulary {
- public:
+class Vocabulary
+{
+public:
   std::map<WORD, WORD_ID> lookup;
   std::vector< WORD > vocab;
   WORD_ID StoreIfNew( const WORD& );
   WORD_ID GetWordID( const WORD& );
   std::vector<WORD_ID> Tokenize( const char[] );
-  inline WORD &GetWord( WORD_ID id ) const { WORD &i = (WORD&) vocab[ id ]; return i; }
+  inline WORD &GetWord( WORD_ID id ) const {
+    WORD &i = (WORD&) vocab[ id ];
+    return i;
+  }
 
- protected:
+protected:
 #ifdef WITH_THREADS
   //reader-writer lock
   mutable boost::shared_mutex m_accessLock;
diff --git a/moses/TranslationModel/fuzzy-match/create_xml.cpp b/moses/TranslationModel/fuzzy-match/create_xml.cpp
index 783fb93eb..44c1efc9f 100644
--- a/moses/TranslationModel/fuzzy-match/create_xml.cpp
+++ b/moses/TranslationModel/fuzzy-match/create_xml.cpp
@@ -42,12 +42,10 @@ void create_xml(const string &inPath)
   string inLine;
 
   int step = 0;
-  while (!inStrme.eof())
-  {
+  while (!inStrme.eof()) {
     getline(inStrme, inLine);
     //cout << inLine << endl;
-    switch (step)
-    {
+    switch (step) {
     case 0:
       setenceId = Scan<int>(inLine);
       ++step;
@@ -63,8 +61,7 @@ void create_xml(const string &inPath)
     case 3:
       if (input == NULL) {
         input = new string(inLine);
-      }
-      else {
+      } else {
         assert(inLine == *input);
       }
       ++step;
@@ -87,9 +84,9 @@ void create_xml(const string &inPath)
 
       //print STDOUT $frame."\n";
       rule << ret.ruleS << " [X] ||| " << ret.ruleT << " [X] ||| " << ret.ruleAlignment
-          << " ||| " << count << endl;
+           << " ||| " << count << endl;
       ruleInv << ret.ruleT << " [X] ||| " << ret.ruleS << " [X] ||| " << ret.ruleAlignmentInv
-          << " ||| " << count << endl;
+              << " ||| " << count << endl;
 
       //print STDOUT "$sentenceInd ||| $score ||| $count\n";
       ++ruleCount;
@@ -112,8 +109,8 @@ CreateXMLRetValues createXML(int ruleCount, const string &source, const string &
 {
   CreateXMLRetValues ret;
   vector<string> sourceToks   = Tokenize(source, " ")
-                		    ,inputToks    = Tokenize(input, " ")
-                		    ,targetsToks  = Tokenize(target, " ");
+                                ,inputToks    = Tokenize(input, " ")
+                                    ,targetsToks  = Tokenize(target, " ");
   Alignments alignments(align, sourceToks.size(), targetsToks.size());
   map<int, string> frameInput;
   map<int, int> alignI2S;
@@ -241,8 +238,7 @@ CreateXMLRetValues createXML(int ruleCount, const string &source, const string &
 
     if (action == "M") {
       inputBitmap.push_back(1);
-    }
-    else if (action == "I" || action == "S") {
+    } else if (action == "I" || action == "S") {
       inputBitmap.push_back(0);
     }
 
@@ -358,9 +354,8 @@ CreateXMLRetValues createXML(int ruleCount, const string &source, const string &
     }
     // end of tm target inclusion (not included word or inserted input)
     else if (currently_included
-        && ( targetBitmap[t] || frameInput.find(t) != frameInput.end() )
-    )
-    {
+             && ( targetBitmap[t] || frameInput.find(t) != frameInput.end() )
+            ) {
       // add xml (unless change is at the beginning of the sentence
       if ( start_t >= 0 ) {
         string target = "";
diff --git a/moses/TranslationOption.cpp b/moses/TranslationOption.cpp
index 87721bc52..dfe3312fc 100644
--- a/moses/TranslationOption.cpp
+++ b/moses/TranslationOption.cpp
@@ -42,11 +42,11 @@ TranslationOption::TranslationOption(const WordsRange &wordsRange
 }
 
 TranslationOption::TranslationOption(const TranslationOption &copy, const WordsRange &sourceWordsRange)
-: m_targetPhrase(copy.m_targetPhrase)
+  : m_targetPhrase(copy.m_targetPhrase)
 //, m_sourcePhrase(new Phrase(*copy.m_sourcePhrase)) // TODO use when confusion network trans opt for confusion net properly implemented
-, m_sourceWordsRange(sourceWordsRange)
-, m_futureScore(copy.m_futureScore)
-, m_lexReorderingScores(copy.m_lexReorderingScores)
+  , m_sourceWordsRange(sourceWordsRange)
+  , m_futureScore(copy.m_futureScore)
+  , m_lexReorderingScores(copy.m_lexReorderingScores)
 {}
 
 bool TranslationOption::IsCompatible(const Phrase& phrase, const std::vector<FactorType>& featuresToCheck) const
diff --git a/moses/TranslationOption.h b/moses/TranslationOption.h
index 8e2064f83..b1de31eb1 100644
--- a/moses/TranslationOption.h
+++ b/moses/TranslationOption.h
@@ -146,18 +146,18 @@ public:
   void CacheLexReorderingScores(const LexicalReordering &scoreProducer, const Scores &score);
 
   TO_STRING();
-	
-	bool operator== (const TranslationOption &rhs) const
-	{
+
+  bool operator== (const TranslationOption &rhs) const {
     return m_sourceWordsRange == rhs.m_sourceWordsRange &&
-      m_targetPhrase == rhs.m_targetPhrase;
-	}
+           m_targetPhrase == rhs.m_targetPhrase;
+  }
 
 };
 
 
 //XXX: This doesn't look at the alignment. Is this correct?
-inline size_t hash_value(const TranslationOption& translationOption) {
+inline size_t hash_value(const TranslationOption& translationOption)
+{
   size_t  seed = 0;
   boost::hash_combine(seed, translationOption.GetTargetPhrase());
   boost::hash_combine(seed, translationOption.GetStartPos());
diff --git a/moses/TranslationOptionCollection.cpp b/moses/TranslationOptionCollection.cpp
index 16bcce791..2d7024c7a 100644
--- a/moses/TranslationOptionCollection.cpp
+++ b/moses/TranslationOptionCollection.cpp
@@ -48,11 +48,11 @@ bool CompareTranslationOption(const TranslationOption *a, const TranslationOptio
 	* This fn should be called by inherited classes
 */
 TranslationOptionCollection::TranslationOptionCollection(
-    InputType const& src, size_t maxNoTransOptPerCoverage, float translationOptionThreshold)
+  InputType const& src, size_t maxNoTransOptPerCoverage, float translationOptionThreshold)
   : m_source(src)
-    ,m_futureScore(src.GetSize())
-    ,m_maxNoTransOptPerCoverage(maxNoTransOptPerCoverage)
-    ,m_translationOptionThreshold(translationOptionThreshold)
+  ,m_futureScore(src.GetSize())
+  ,m_maxNoTransOptPerCoverage(maxNoTransOptPerCoverage)
+  ,m_translationOptionThreshold(translationOptionThreshold)
 {
   // create 2-d vector
   size_t size = src.GetSize();
@@ -202,73 +202,68 @@ void TranslationOptionCollection::ProcessOneUnknownWord(const Word &sourceWord,s
   const UnknownWordPenaltyProducer *unknownWordPenaltyProducer = staticData.GetUnknownWordPenaltyProducer();
   float unknownScore = FloorScore(TransformScore(0));
 
-	// unknown word, add as trans opt
-	FactorCollection &factorCollection = FactorCollection::Instance();
-
-	size_t isDigit = 0;
-	
-	const Factor *f = sourceWord[0]; // TODO hack. shouldn't know which factor is surface
-	const StringPiece s = f->GetString();
-	bool isEpsilon = (s=="" || s==EPSILON);
-	if (StaticData::Instance().GetDropUnknown())
-	{
-
-
-		isDigit = s.find_first_of("0123456789");
-		if (isDigit == 1) 
-			isDigit = 1;
-		else 
-			isDigit = 0;
-		// modify the starting bitmap
-	}
-	
-	Phrase* m_unksrc = new Phrase(1);
+  // unknown word, add as trans opt
+  FactorCollection &factorCollection = FactorCollection::Instance();
+
+  size_t isDigit = 0;
+
+  const Factor *f = sourceWord[0]; // TODO hack. shouldn't know which factor is surface
+  const StringPiece s = f->GetString();
+  bool isEpsilon = (s=="" || s==EPSILON);
+  if (StaticData::Instance().GetDropUnknown()) {
+
+
+    isDigit = s.find_first_of("0123456789");
+    if (isDigit == 1)
+      isDigit = 1;
+    else
+      isDigit = 0;
+    // modify the starting bitmap
+  }
+
+  Phrase* m_unksrc = new Phrase(1);
   m_unksrc->AddWord() = sourceWord;
-	m_unksrcs.push_back(m_unksrc);
-
-	TranslationOption *transOpt;
-	TargetPhrase targetPhrase;
-	targetPhrase.SetSourcePhrase(*m_unksrc);
-	
-	if (!(staticData.GetDropUnknown() || isEpsilon) || isDigit)
-	{
-		// add to dictionary
-
-		Word &targetWord = targetPhrase.AddWord();
-					
-		for (unsigned int currFactor = 0 ; currFactor < MAX_NUM_FACTORS ; currFactor++)
-		{
-			FactorType factorType = static_cast<FactorType>(currFactor);
-			
-			const Factor *sourceFactor = sourceWord[currFactor];
-			if (sourceFactor == NULL)
-				targetWord[factorType] = factorCollection.AddFactor(UNKNOWN_FACTOR);
-			else
-				targetWord[factorType] = factorCollection.AddFactor(sourceFactor->GetString());
-		}
-		//create a one-to-one alignment between UNKNOWN_FACTOR and its verbatim translation	
-        
-		targetPhrase.SetAlignmentInfo("0-0");
-		
-	}
-	else 
-	{ 
-		// drop source word. create blank trans opt
-
-		//targetPhrase.SetAlignment();
-
-	}
+  m_unksrcs.push_back(m_unksrc);
+
+  TranslationOption *transOpt;
+  TargetPhrase targetPhrase;
+  targetPhrase.SetSourcePhrase(*m_unksrc);
+
+  if (!(staticData.GetDropUnknown() || isEpsilon) || isDigit) {
+    // add to dictionary
+
+    Word &targetWord = targetPhrase.AddWord();
+
+    for (unsigned int currFactor = 0 ; currFactor < MAX_NUM_FACTORS ; currFactor++) {
+      FactorType factorType = static_cast<FactorType>(currFactor);
+
+      const Factor *sourceFactor = sourceWord[currFactor];
+      if (sourceFactor == NULL)
+        targetWord[factorType] = factorCollection.AddFactor(UNKNOWN_FACTOR);
+      else
+        targetWord[factorType] = factorCollection.AddFactor(sourceFactor->GetString());
+    }
+    //create a one-to-one alignment between UNKNOWN_FACTOR and its verbatim translation
+
+    targetPhrase.SetAlignmentInfo("0-0");
+
+  } else {
+    // drop source word. create blank trans opt
+
+    //targetPhrase.SetAlignment();
+
+  }
 
   targetPhrase.GetScoreBreakdown().Assign(unknownWordPenaltyProducer, unknownScore);
 
-	if (inputScores != NULL) {
-		targetPhrase.SetInputScore(*inputScores);
-	}
+  if (inputScores != NULL) {
+    targetPhrase.SetInputScore(*inputScores);
+  }
 
-	targetPhrase.Evaluate(*m_unksrc);
+  targetPhrase.Evaluate(*m_unksrc);
 
-	transOpt = new TranslationOption(WordsRange(sourcePos, sourcePos + length - 1), targetPhrase);
-	Add(transOpt);
+  transOpt = new TranslationOption(WordsRange(sourcePos, sourcePos + length - 1), targetPhrase);
+  Add(transOpt);
 
 
 }
@@ -426,19 +421,19 @@ void TranslationOptionCollection::EvaluateWithSource()
 {
   const size_t size = m_source.GetSize();
   for (size_t startPos = 0 ; startPos < size ; ++startPos) {
-	size_t maxSize = m_source.GetSize() - startPos;
-	size_t maxSizePhrase = StaticData::Instance().GetMaxPhraseLength();
-	maxSize = std::min(maxSize, maxSizePhrase);
-
-	for (size_t endPos = startPos ; endPos < startPos + maxSize ; ++endPos) {
-	  TranslationOptionList &transOptList = GetTranslationOptionList(startPos, endPos);
-
-	  TranslationOptionList::const_iterator iterTransOpt;
-	  for(iterTransOpt = transOptList.begin() ; iterTransOpt != transOptList.end() ; ++iterTransOpt) {
-		TranslationOption &transOpt = **iterTransOpt;
-		transOpt.Evaluate(m_source);
-	  }
-	}
+    size_t maxSize = m_source.GetSize() - startPos;
+    size_t maxSizePhrase = StaticData::Instance().GetMaxPhraseLength();
+    maxSize = std::min(maxSize, maxSizePhrase);
+
+    for (size_t endPos = startPos ; endPos < startPos + maxSize ; ++endPos) {
+      TranslationOptionList &transOptList = GetTranslationOptionList(startPos, endPos);
+
+      TranslationOptionList::const_iterator iterTransOpt;
+      for(iterTransOpt = transOptList.begin() ; iterTransOpt != transOptList.end() ; ++iterTransOpt) {
+        TranslationOption &transOpt = **iterTransOpt;
+        transOpt.Evaluate(m_source);
+      }
+    }
   }
 
 }
@@ -514,7 +509,7 @@ void TranslationOptionCollection::CreateTranslationOptionsForRange(
 
       for (++iterStep ; iterStep != decodeGraph.end() ; ++iterStep) {
 
-    	const DecodeStep &decodeStep = **iterStep;
+        const DecodeStep &decodeStep = **iterStep;
         PartialTranslOptColl* newPtoc = new PartialTranslOptColl;
 
         // go thru each intermediate trans opt just created
@@ -634,7 +629,7 @@ std::ostream& operator<<(std::ostream& out, const TranslationOptionCollection& c
   return out;
 }
 
-const std::vector<Phrase*>& TranslationOptionCollection::GetUnknownSources() const 
+const std::vector<Phrase*>& TranslationOptionCollection::GetUnknownSources() const
 {
   return m_unksrcs;
 }
diff --git a/moses/TranslationOptionCollection.h b/moses/TranslationOptionCollection.h
index 36164f135..171a082e2 100644
--- a/moses/TranslationOptionCollection.h
+++ b/moses/TranslationOptionCollection.h
@@ -42,7 +42,7 @@ class InputType;
 class FactorMask;
 class Word;
 class DecodeGraph;
-  
+
 /** Contains all phrase translations applicable to current input type (a sentence or confusion network).
  * A key insight into efficient decoding is that various input
  * conditions (trelliss, factored input, normal text, xml markup)
diff --git a/moses/TranslationOptionCollectionConfusionNet.cpp b/moses/TranslationOptionCollectionConfusionNet.cpp
index a25e8cffb..93953ba8a 100644
--- a/moses/TranslationOptionCollectionConfusionNet.cpp
+++ b/moses/TranslationOptionCollectionConfusionNet.cpp
@@ -10,8 +10,8 @@ namespace Moses
 
 /** constructor; just initialize the base class */
 TranslationOptionCollectionConfusionNet::TranslationOptionCollectionConfusionNet(
-    const ConfusionNet &input
-    , size_t maxNoTransOptPerCoverage, float translationOptionThreshold)
+  const ConfusionNet &input
+  , size_t maxNoTransOptPerCoverage, float translationOptionThreshold)
   : TranslationOptionCollection(input, maxNoTransOptPerCoverage, translationOptionThreshold) {}
 
 /* forcibly create translation option for a particular source word.
diff --git a/moses/TreeInput.cpp b/moses/TreeInput.cpp
index acae0bdb1..166445602 100644
--- a/moses/TreeInput.cpp
+++ b/moses/TreeInput.cpp
@@ -149,7 +149,7 @@ bool TreeInput::ProcessAndStripXMLTags(string &line, std::vector<XMLParseOutput>
           return false;
         }
 
-	// may be either a input span label ("label"), or a specified output translation "translation"
+        // may be either a input span label ("label"), or a specified output translation "translation"
         string label = ParseXmlTagAttribute(tagContent,"label");
         string translation = ParseXmlTagAttribute(tagContent,"translation");
 
@@ -165,18 +165,17 @@ bool TreeInput::ProcessAndStripXMLTags(string &line, std::vector<XMLParseOutput>
           vector<string> altTexts = TokenizeMultiCharSeparator(translation, "||");
           vector<string> altLabel = TokenizeMultiCharSeparator(label, "||");
           vector<string> altProbs = TokenizeMultiCharSeparator(ParseXmlTagAttribute(tagContent,"prob"), "||");
-	  //TRACE_ERR("number of translations: " << altTexts.size() << endl);
+          //TRACE_ERR("number of translations: " << altTexts.size() << endl);
           for (size_t i=0; i<altTexts.size(); ++i) {
             // set target phrase
             TargetPhrase targetPhrase;
             targetPhrase.CreateFromString(Output, outputFactorOrder,altTexts[i],factorDelimiter, NULL);
 
             // set constituent label
-	    string targetLHSstr;
+            string targetLHSstr;
             if (altLabel.size() > i && altLabel[i].size() > 0) {
               targetLHSstr = altLabel[i];
-            }
-            else {
+            } else {
               const UnknownLHSList &lhsList = StaticData::Instance().GetUnknownLHS();
               UnknownLHSList::const_iterator iterLHS = lhsList.begin();
               targetLHSstr = iterLHS->first;
diff --git a/moses/TrellisPath.cpp b/moses/TrellisPath.cpp
index c73575b2c..fed8f9658 100644
--- a/moses/TrellisPath.cpp
+++ b/moses/TrellisPath.cpp
@@ -41,7 +41,8 @@ TrellisPath::TrellisPath(const Hypothesis *hypo)
   }
 }
 
-void TrellisPath::InitScore() {
+void TrellisPath::InitScore()
+{
   m_totalScore		= m_path[0]->GetWinningHypo()->GetTotalScore();
   m_scoreBreakdown= m_path[0]->GetWinningHypo()->GetScoreBreakdown();
 
@@ -82,8 +83,8 @@ TrellisPath::TrellisPath(const TrellisPath &copy, size_t edgeIndex, const Hypoth
   InitScore();
 }
 
-TrellisPath::TrellisPath(const vector<const Hypothesis*> edges) 
-:m_prevEdgeChanged(NOT_FOUND)
+TrellisPath::TrellisPath(const vector<const Hypothesis*> edges)
+  :m_prevEdgeChanged(NOT_FOUND)
 {
   m_path.resize(edges.size());
   copy(edges.rbegin(),edges.rend(),m_path.begin());
diff --git a/moses/TrellisPath.h b/moses/TrellisPath.h
index d8005435c..26e722696 100644
--- a/moses/TrellisPath.h
+++ b/moses/TrellisPath.h
@@ -59,36 +59,36 @@ protected:
   void InitScore();
 
 public:
-	TrellisPath(); // not implemented
-	
-	//! create path OF pure hypo
-	TrellisPath(const Hypothesis *hypo);
-		
-	/** create path from another path, deviate at edgeIndex by using arc instead, 
-		* which may change other hypo back from there
-		*/
-	TrellisPath(const TrellisPath &copy, size_t edgeIndex, const Hypothesis *arc);
-
-	//! get score for this path throught trellis
-	inline float GetTotalScore() const { return m_totalScore; }
-
-	/** list of each hypo/arcs in path. For anything other than the best hypo, it is not possible just to follow the
-		* m_prevHypo variable in the hypothesis object
-		*/
-	inline const std::vector<const Hypothesis *> &GetEdges() const
-	{
-		return m_path;
-	}
-
-	inline size_t GetSize() const
-	{
-		return m_path.size();
-	}
-	
-	//! create a set of next best paths by wiggling 1 of the node at a time. 
-	void CreateDeviantPaths(TrellisPathCollection &pathColl) const;
-  
-  //! create a list of next best paths by wiggling 1 of the node at a time. 
+  TrellisPath(); // not implemented
+
+  //! create path OF pure hypo
+  TrellisPath(const Hypothesis *hypo);
+
+  /** create path from another path, deviate at edgeIndex by using arc instead,
+  	* which may change other hypo back from there
+  	*/
+  TrellisPath(const TrellisPath &copy, size_t edgeIndex, const Hypothesis *arc);
+
+  //! get score for this path throught trellis
+  inline float GetTotalScore() const {
+    return m_totalScore;
+  }
+
+  /** list of each hypo/arcs in path. For anything other than the best hypo, it is not possible just to follow the
+  	* m_prevHypo variable in the hypothesis object
+  	*/
+  inline const std::vector<const Hypothesis *> &GetEdges() const {
+    return m_path;
+  }
+
+  inline size_t GetSize() const {
+    return m_path.size();
+  }
+
+  //! create a set of next best paths by wiggling 1 of the node at a time.
+  void CreateDeviantPaths(TrellisPathCollection &pathColl) const;
+
+  //! create a list of next best paths by wiggling 1 of the node at a time.
   void CreateDeviantPaths(TrellisPathList &pathColl) const;
 
   inline const ScoreComponentCollection &GetScoreBreakdown() const {
diff --git a/moses/TypeDef.h b/moses/TypeDef.h
index e44946a2f..2b98b5bc3 100644
--- a/moses/TypeDef.h
+++ b/moses/TypeDef.h
@@ -129,7 +129,7 @@ enum InputTypeEnum {
   ,WordLatticeInput				= 2
   ,TreeInputType					= 3
   ,WordLatticeInput2			= 4
-  
+
 };
 
 enum XmlInputType {
@@ -169,8 +169,7 @@ enum WordAlignmentSort {
   ,TargetOrder = 1
 };
 
-enum FormatType
-{
+enum FormatType {
   MosesFormat
   ,HieroFormat
 };
diff --git a/moses/Util.cpp b/moses/Util.cpp
index 13cee27f9..f92c32dbb 100644
--- a/moses/Util.cpp
+++ b/moses/Util.cpp
@@ -182,8 +182,7 @@ std::string PassthroughSGML(std::string &line, const std::string tagName, const
 
   size_t close = lline.find(rbrack, open);
   //check whether the tag is closed with '/>'; if not return the empty string
-  if (close == std::string::npos)
-  {
+  if (close == std::string::npos) {
     TRACE_ERR("PassthroughSGML error: the <passthrough info/> tag does not end properly\n");
     return meta;
   }
@@ -198,8 +197,7 @@ std::string PassthroughSGML(std::string &line, const std::string tagName, const
 
   lline = ToLower(line);
   open = lline.find(lbrack+tagName);
-  if (open != std::string::npos)
-  {
+  if (open != std::string::npos) {
     TRACE_ERR("PassthroughSGML error: there are two <passthrough> tags\n");
   }
   return meta;
diff --git a/moses/Util.h b/moses/Util.h
index 9f43d9dc3..e5bdc820a 100644
--- a/moses/Util.h
+++ b/moses/Util.h
@@ -363,27 +363,27 @@ std::string PassthroughSGML(std::string &line, const std::string tagName,const s
  */
 inline std::string GetFirstString(const std::string& str, int& first_pos,  const std::string& delimiters = " \t")
 {
-	
-	std::string first_str;
-	// Skip delimiters at beginning.
-	std::string::size_type lastPos = str.find_first_not_of(delimiters, first_pos);
-	
-	// Find first "non-delimiter".
-	std::string::size_type pos     = str.find_first_of(delimiters, lastPos);
-	
-	if (std::string::npos != pos || std::string::npos != lastPos){
-		
-		first_str = str.substr(lastPos, pos - lastPos);
-		
-		// Skip delimiters.  Note the "not_of"
-		lastPos = str.find_first_not_of(delimiters, pos);
-		
-	}
-	
-	first_pos = lastPos;
-	return first_str;
+
+  std::string first_str;
+  // Skip delimiters at beginning.
+  std::string::size_type lastPos = str.find_first_not_of(delimiters, first_pos);
+
+  // Find first "non-delimiter".
+  std::string::size_type pos     = str.find_first_of(delimiters, lastPos);
+
+  if (std::string::npos != pos || std::string::npos != lastPos) {
+
+    first_str = str.substr(lastPos, pos - lastPos);
+
+    // Skip delimiters.  Note the "not_of"
+    lastPos = str.find_first_not_of(delimiters, pos);
+
+  }
+
+  first_pos = lastPos;
+  return first_str;
 }
-	
+
 template<class T>
 T log_sum (T log_a, T log_b)
 {
diff --git a/moses/Word.cpp b/moses/Word.cpp
index 69d382c8a..41e5fae03 100644
--- a/moses/Word.cpp
+++ b/moses/Word.cpp
@@ -87,7 +87,8 @@ std::string Word::GetString(const vector<FactorType> factorType,bool endWithBlan
   return strme.str();
 }
 
-StringPiece Word::GetString(FactorType factorType) const {
+StringPiece Word::GetString(FactorType factorType) const
+{
   return m_factorArray[factorType]->GetString();
 }
 
diff --git a/moses/Word.h b/moses/Word.h
index d650fb67e..e88b0441b 100644
--- a/moses/Word.h
+++ b/moses/Word.h
@@ -152,8 +152,9 @@ struct WordComparer {
 };
 
 
-inline size_t hash_value(const Word& word) {
-  return word.hash();    
+inline size_t hash_value(const Word& word)
+{
+  return word.hash();
 }
 
 }
diff --git a/moses/XmlOption.cpp b/moses/XmlOption.cpp
index c8d639e0a..4b703b247 100644
--- a/moses/XmlOption.cpp
+++ b/moses/XmlOption.cpp
@@ -83,8 +83,8 @@ string TrimXml(const string& str, const std::string& lbrackStr, const std::strin
  */
 bool isXmlTag(const string& tag, const std::string& lbrackStr, const std::string& rbrackStr)
 {
-   return (tag.substr(0,lbrackStr.length()) == lbrackStr &&
-	   (tag[lbrackStr.length()] == '/' ||
+  return (tag.substr(0,lbrackStr.length()) == lbrackStr &&
+          (tag[lbrackStr.length()] == '/' ||
            (tag[lbrackStr.length()] >= 'a' && tag[lbrackStr.length()] <= 'z') ||
            (tag[lbrackStr.length()] >= 'A' && tag[lbrackStr.length()] <= 'Z')));
 }
@@ -111,7 +111,7 @@ vector<string> TokenizeXml(const string& str, const std::string& lbrackStr, cons
   // walk thorugh the string (loop vver cpos)
   while (cpos != str.size()) {
     // find the next opening "<" of an xml tag
-       lpos = str.find(lbrack, cpos);			// lpos = str.find_first_of(lbrack, cpos);
+    lpos = str.find(lbrack, cpos);			// lpos = str.find_first_of(lbrack, cpos);
     if (lpos != string::npos) {
       // find the end of the xml tag
       rpos = str.find(rbrack, lpos+lbrackStr.length()-1);			// rpos = str.find_first_of(rbrack, lpos);
@@ -149,8 +149,8 @@ vector<string> TokenizeXml(const string& str, const std::string& lbrackStr, cons
  * \param lbrackStr xml tag's left bracket string, typically "<"
  * \param rbrackStr xml tag's right bracket string, typically ">"
  */
-bool ProcessAndStripXMLTags(string &line, vector<XmlOption*> &res, ReorderingConstraint &reorderingConstraint, vector< size_t > &walls, 
-	const std::string& lbrackStr, const std::string& rbrackStr)
+bool ProcessAndStripXMLTags(string &line, vector<XmlOption*> &res, ReorderingConstraint &reorderingConstraint, vector< size_t > &walls,
+                            const std::string& lbrackStr, const std::string& rbrackStr)
 {
   //parse XML markup in translation line
 
diff --git a/moses/XmlOption.h b/moses/XmlOption.h
index 45989c841..942446b26 100644
--- a/moses/XmlOption.h
+++ b/moses/XmlOption.h
@@ -30,8 +30,8 @@ std::string TrimXml(const std::string& str, const std::string& lbrackStr="<", co
 bool isXmlTag(const std::string& tag, const std::string& lbrackStr="<", const std::string& rbrackStr=">");
 std::vector<std::string> TokenizeXml(const std::string& str, const std::string& lbrackStr="<", const std::string& rbrackStr=">");
 
-bool ProcessAndStripXMLTags(std::string &line, std::vector<XmlOption*> &res, ReorderingConstraint &reorderingConstraint, std::vector< size_t > &walls, 
-	const std::string& lbrackStr="<", const std::string& rbrackStr=">");
+bool ProcessAndStripXMLTags(std::string &line, std::vector<XmlOption*> &res, ReorderingConstraint &reorderingConstraint, std::vector< size_t > &walls,
+                            const std::string& lbrackStr="<", const std::string& rbrackStr=">");
 
 }
 
diff --git a/phrase-extract/AlignmentPhrase.h b/phrase-extract/AlignmentPhrase.h
index ec6431f18..52d9c85ea 100644
--- a/phrase-extract/AlignmentPhrase.h
+++ b/phrase-extract/AlignmentPhrase.h
@@ -25,7 +25,7 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 
 namespace MosesTraining
 {
-  
+
 class WordsRange;
 
 class AlignmentElement
diff --git a/phrase-extract/ExtractedRule.cpp b/phrase-extract/ExtractedRule.cpp
index 985f2f093..50d9085e6 100644
--- a/phrase-extract/ExtractedRule.cpp
+++ b/phrase-extract/ExtractedRule.cpp
@@ -23,20 +23,19 @@ void ExtractedRule::OutputNTLengths(std::ostream &out) const
 void ExtractedRule::OutputNTLengths(std::ostringstream &outString) const
 {
   std::map<size_t, std::pair<size_t, size_t> >::const_iterator iter;
-  for (iter = m_ntLengths.begin(); iter != m_ntLengths.end(); ++iter)
-  {
+  for (iter = m_ntLengths.begin(); iter != m_ntLengths.end(); ++iter) {
     size_t sourcePos = iter->first;
     const std::pair<size_t, size_t> &spanLengths = iter->second;
-    outString << sourcePos << "=" << spanLengths.first << "," <<spanLengths.second << " "; 
+    outString << sourcePos << "=" << spanLengths.first << "," <<spanLengths.second << " ";
   }
 }
 
 std::ostream& operator<<(std::ostream &out, const ExtractedRule &obj)
 {
-  out << obj.source << " ||| " << obj.target << " ||| " 
+  out << obj.source << " ||| " << obj.target << " ||| "
       << obj.alignment << " ||| "
       << obj.alignmentInv << " ||| ";
-  
+
   obj.OutputNTLengths(out);
 
   return out;
diff --git a/phrase-extract/ExtractedRule.h b/phrase-extract/ExtractedRule.h
index 992a807b3..c26de37ca 100644
--- a/phrase-extract/ExtractedRule.h
+++ b/phrase-extract/ExtractedRule.h
@@ -49,7 +49,7 @@ public:
   double pcfgScore;
 
   std::map<size_t, std::pair<size_t, size_t> > m_ntLengths;
-  
+
   ExtractedRule(int sT, int eT, int sS, int eS)
     : source()
     , target()
@@ -64,12 +64,11 @@ public:
     , count(0)
     , pcfgScore(0.0)
   {}
-  
-  void SetSpanLength(size_t sourcePos, size_t sourceLength, size_t targetLength)
-  {
+
+  void SetSpanLength(size_t sourcePos, size_t sourceLength, size_t targetLength) {
     m_ntLengths[sourcePos] = std::pair<size_t, size_t>(sourceLength, targetLength);
   }
-  
+
   void OutputNTLengths(std::ostream &out) const;
   void OutputNTLengths(std::ostringstream &out) const;
 };
diff --git a/phrase-extract/Hole.h b/phrase-extract/Hole.h
index c570ec7a1..efedf2f53 100644
--- a/phrase-extract/Hole.h
+++ b/phrase-extract/Hole.h
@@ -72,7 +72,7 @@ public:
   int GetSize(size_t direction) const {
     return m_end[direction] - m_start[direction] + 1;
   }
-  
+
   void SetPos(int pos, size_t direction) {
     m_pos[direction] = pos;
   }
diff --git a/phrase-extract/HoleCollection.cpp b/phrase-extract/HoleCollection.cpp
index fba295993..e63e2eacc 100644
--- a/phrase-extract/HoleCollection.cpp
+++ b/phrase-extract/HoleCollection.cpp
@@ -64,7 +64,7 @@ int HoleCollection::Scope(const Hole &proposedHole) const
   const int holeEnd = proposedHole.GetEnd(0);
   int scope = m_scope.back();
   if (holeStart == m_sourcePhraseStart.back() ||
-     find(m_sourceHoleEndPoints.begin(), m_sourceHoleEndPoints.end(), holeStart-1) != m_sourceHoleEndPoints.end()) {
+      find(m_sourceHoleEndPoints.begin(), m_sourceHoleEndPoints.end(), holeStart-1) != m_sourceHoleEndPoints.end()) {
     ++scope; // Adding hole would introduce choice point at start of hole.
   }
   if (holeEnd == m_sourcePhraseEnd.back() ||
diff --git a/phrase-extract/OutputFileStream.cpp b/phrase-extract/OutputFileStream.cpp
index 2cad33bb9..a61ce1ab1 100644
--- a/phrase-extract/OutputFileStream.cpp
+++ b/phrase-extract/OutputFileStream.cpp
@@ -46,11 +46,11 @@ OutputFileStream::~OutputFileStream()
 
 bool OutputFileStream::Open(const std::string &filePath)
 {
-  m_outFile = new ofstream(filePath.c_str(), ios_base::out | ios_base::binary);    
+  m_outFile = new ofstream(filePath.c_str(), ios_base::out | ios_base::binary);
   if (m_outFile->fail()) {
     return false;
   }
-  
+
   if (filePath.size() > 3 && filePath.substr(filePath.size() - 3, 3) == ".gz") {
     this->push(boost::iostreams::gzip_compressor());
   }
@@ -64,10 +64,10 @@ void OutputFileStream::Close()
   if (m_outFile == NULL) {
     return;
   }
-  
+
   this->flush();
   this->pop(); // file
-  
+
   m_outFile->close();
   delete m_outFile;
   m_outFile = NULL;
diff --git a/phrase-extract/PhraseAlignment.cpp b/phrase-extract/PhraseAlignment.cpp
index bdfead082..f830e411f 100644
--- a/phrase-extract/PhraseAlignment.cpp
+++ b/phrase-extract/PhraseAlignment.cpp
@@ -29,10 +29,10 @@ extern bool hierarchicalFlag;
 template<typename T>
 inline T Scan(const std::string &input)
 {
-	std::stringstream stream(input);
-	T ret;
-	stream >> ret;
-	return ret;
+  std::stringstream stream(input);
+  T ret;
+  stream >> ret;
+  return ret;
 }
 
 
@@ -40,11 +40,10 @@ inline T Scan(const std::string &input)
 template<typename T>
 inline void Scan(std::vector<T> &output, const std::vector< std::string > &input)
 {
-	output.resize(input.size());
-	for (size_t i = 0 ; i < input.size() ; i++)
-	{
-		output[i] = Scan<T>( input[i] );
-	}
+  output.resize(input.size());
+  for (size_t i = 0 ; i < input.size() ; i++) {
+    output[i] = Scan<T>( input[i] );
+  }
 }
 
 
@@ -56,7 +55,7 @@ inline void Tokenize(std::vector<std::string> &output
   std::string::size_type lastPos = str.find_first_not_of(delimiters, 0);
   // Find first "non-delimiter".
   std::string::size_type pos     = str.find_first_of(delimiters, lastPos);
-  
+
   while (std::string::npos != pos || std::string::npos != lastPos) {
     // Found a token, add it to the vector.
     output.push_back(str.substr(lastPos, pos - lastPos));
@@ -70,12 +69,12 @@ inline void Tokenize(std::vector<std::string> &output
 // speeded up version of above
 template<typename T>
 inline void Tokenize( std::vector<T> &output
-										 , const std::string &input
-										 , const std::string& delimiters = " \t")
+                      , const std::string &input
+                      , const std::string& delimiters = " \t")
 {
-	std::vector<std::string> stringVector;
-	Tokenize(stringVector, input, delimiters);
-	return Scan<T>(output, stringVector );
+  std::vector<std::string> stringVector;
+  Tokenize(stringVector, input, delimiters);
+  return Scan<T>(output, stringVector );
 }
 
 // read in a phrase pair and store it
@@ -94,8 +93,7 @@ void PhraseAlignment::create( char line[], int lineID, bool includeSentenceIdFla
 
     else if (item == 2) { // target phrase
       phraseT.push_back( vcbT.storeIfNew( token[j] ) );
-    }
-    else if (item == 3) { // alignment
+    } else if (item == 3) { // alignment
       int s,t;
       sscanf(token[j].c_str(), "%d-%d", &s, &t);
       if ((size_t)t >= phraseT.size() || (size_t)s >= phraseS.size()) {
@@ -135,17 +133,17 @@ void PhraseAlignment::create( char line[], int lineID, bool includeSentenceIdFla
 void PhraseAlignment::addNTLength(const std::string &tok)
 {
   vector< string > tokens;
-  
+
   Tokenize(tokens, tok, "=");
   assert(tokens.size() == 2);
-  
+
   size_t sourcePos = Scan<size_t>(tokens[0]);
   assert(sourcePos < phraseS.size());
-  
+
   vector< size_t > ntLengths;
   Tokenize<size_t>(ntLengths, tokens[1], ",");
   assert(ntLengths.size() == 2);
-  
+
   m_ntLengths[sourcePos] = std::pair<size_t, size_t>(ntLengths[0], ntLengths[1]);
 }
 
@@ -211,13 +209,13 @@ int PhraseAlignment::Compare(const PhraseAlignment &other) const
   if (this == &other) // comparing with itself
     return 0;
 
-  if (GetTarget() != other.GetTarget()) 
+  if (GetTarget() != other.GetTarget())
     return ( GetTarget() < other.GetTarget() ) ? -1 : +1;
 
   if (GetSource() != other.GetSource())
-   return ( GetSource() < other.GetSource() ) ? -1 : +1;
+    return ( GetSource() < other.GetSource() ) ? -1 : +1;
 
-  if (!hierarchicalFlag) 
+  if (!hierarchicalFlag)
     return 0;
 
   // loop over all words (note: 0 = left hand side of rule)
@@ -228,15 +226,14 @@ int PhraseAlignment::Compare(const PhraseAlignment &other) const
 
       if (alignedToT[i].size() != 1 ||
           other.alignedToT[i].size() != 1 ||
-          thisAlign != otherAlign)
-      {
+          thisAlign != otherAlign) {
         int ret = (thisAlign < otherAlign) ? -1 : +1;
         return ret;
       }
     }
   }
   return 0;
-  
+
 }
 
 }
diff --git a/phrase-extract/PhraseAlignment.h b/phrase-extract/PhraseAlignment.h
index c0df2aa37..06d9cfad0 100644
--- a/phrase-extract/PhraseAlignment.h
+++ b/phrase-extract/PhraseAlignment.h
@@ -24,7 +24,7 @@ protected:
   PHRASE phraseT;
 
   std::map<size_t, std::pair<size_t, size_t> > m_ntLengths;
-  
+
   void createAlignVec(size_t sourceSize, size_t targetSize);
   void addNTLength(const std::string &tok);
 public:
@@ -41,11 +41,10 @@ public:
   bool equals( const PhraseAlignment& );
   bool match( const PhraseAlignment& );
 
-	int Compare(const PhraseAlignment &compare) const;
-	inline bool operator<(const PhraseAlignment &compare) const
-	{ 
-		return Compare(compare) < 0;
-	}
+  int Compare(const PhraseAlignment &compare) const;
+  inline bool operator<(const PhraseAlignment &compare) const {
+    return Compare(compare) < 0;
+  }
 
   const PHRASE &GetSource() const {
     return phraseS;
@@ -53,9 +52,10 @@ public:
   const PHRASE &GetTarget() const {
     return phraseT;
   }
-  
-  const std::map<size_t, std::pair<size_t, size_t> > &GetNTLengths() const
-  { return m_ntLengths; }
+
+  const std::map<size_t, std::pair<size_t, size_t> > &GetNTLengths() const {
+    return m_ntLengths;
+  }
 
 };
 
@@ -67,8 +67,7 @@ typedef std::vector<PhraseAlignment*>          PhraseAlignmentCollection;
 class PhraseAlignmentCollectionOrderer
 {
 public:
-	bool operator()(const PhraseAlignmentCollection &collA, const PhraseAlignmentCollection &collB) const
-	{
+  bool operator()(const PhraseAlignmentCollection &collA, const PhraseAlignmentCollection &collB) const {
     assert(collA.size() > 0);
     assert(collB.size() > 0);
 
@@ -77,7 +76,7 @@ public:
     bool ret = objA < objB;
 
     return ret;
-	}
+  }
 };
 
 
@@ -97,10 +96,12 @@ public:
 
   std::pair<Coll::iterator,bool> insert ( const PhraseAlignmentCollection& obj );
 
-  const SortedColl &GetSortedColl() const
-  { return m_sortedColl; }
-  size_t GetSize() const
-  { return m_coll.size(); }
+  const SortedColl &GetSortedColl() const {
+    return m_sortedColl;
+  }
+  size_t GetSize() const {
+    return m_coll.size();
+  }
 
 private:
   SortedColl m_sortedColl;
diff --git a/phrase-extract/PhraseExtractionOptions.h b/phrase-extract/PhraseExtractionOptions.h
index 2daeaf0ca..60e56b08c 100644
--- a/phrase-extract/PhraseExtractionOptions.h
+++ b/phrase-extract/PhraseExtractionOptions.h
@@ -29,11 +29,12 @@ enum REO_MODEL_TYPE {REO_MSD, REO_MSLR, REO_MONO};
 enum REO_POS {LEFT, RIGHT, DLEFT, DRIGHT, UNKNOWN};
 
 
-class PhraseExtractionOptions {
-  
- public: 
-     const int maxPhraseLength;
- private:
+class PhraseExtractionOptions
+{
+
+public:
+  const int maxPhraseLength;
+private:
   bool allModelsOutputFlag;
   bool wordModel;
   REO_MODEL_TYPE wordType;
@@ -48,103 +49,103 @@ class PhraseExtractionOptions {
   bool gzOutput;
   std::string instanceWeightsFile; //weights for each sentence
 
-public:  
+public:
   PhraseExtractionOptions(const int initmaxPhraseLength):
-            maxPhraseLength(initmaxPhraseLength),
-            allModelsOutputFlag(false),
-            wordModel(false),
-            wordType(REO_MSD),
-            phraseModel(false),
-            phraseType(REO_MSD),
-            hierModel(false),
-            hierType(REO_MSD),
-            orientationFlag(false),
-            translationFlag(true),
-            includeSentenceIdFlag(false),
-            onlyOutputSpanInfo(false),
-            gzOutput(false){}
- 
-    //functions for initialization of options
-    void initAllModelsOutputFlag(const bool initallModelsOutputFlag){
-        allModelsOutputFlag=initallModelsOutputFlag;
-    }
-    void initWordModel(const bool initwordModel){
-        wordModel=initwordModel;
-    }
-    void initWordType(REO_MODEL_TYPE initwordType ){
-        wordType=initwordType; 
-    } 
-    void initPhraseModel(const bool initphraseModel ){
-        phraseModel=initphraseModel;  
-    } 
-    void initPhraseType(REO_MODEL_TYPE initphraseType){
-        phraseType=initphraseType;
-    }  
-    void initHierModel(const bool inithierModel){
-        hierModel=inithierModel;
-    }
-    void initHierType(REO_MODEL_TYPE inithierType){
-        hierType=inithierType;
-    }
-    void initOrientationFlag(const bool initorientationFlag){
-        orientationFlag=initorientationFlag;
-    }
-    void initTranslationFlag(const bool inittranslationFlag){
-        translationFlag=inittranslationFlag;
-    }
-    void initIncludeSentenceIdFlag(const bool initincludeSentenceIdFlag){
-        includeSentenceIdFlag=initincludeSentenceIdFlag;
-    }
-    void initOnlyOutputSpanInfo(const bool initonlyOutputSpanInfo){
-        onlyOutputSpanInfo= initonlyOutputSpanInfo;
-    } 
-    void initGzOutput (const bool initgzOutput){
-        gzOutput= initgzOutput;
-    }
-    void initInstanceWeightsFile(const char* initInstanceWeightsFile) {
-      instanceWeightsFile = std::string(initInstanceWeightsFile);
-    }
-     
-    // functions for getting values
-    bool isAllModelsOutputFlag() const {
-        return allModelsOutputFlag;
-    }
-    bool isWordModel() const {
-        return wordModel;
-    }
-    REO_MODEL_TYPE isWordType() const {
-        return wordType; 
-    } 
-    bool isPhraseModel() const {
-        return phraseModel;  
-    } 
-    REO_MODEL_TYPE isPhraseType() const {
-        return phraseType;
-    }  
-    bool isHierModel() const {
-        return hierModel; 
-    }
-    REO_MODEL_TYPE isHierType() const {
-        return hierType;
-    }
-    bool isOrientationFlag() const {
-        return orientationFlag;
-    }
-    bool isTranslationFlag() const {
-        return translationFlag;
-    }
-    bool isIncludeSentenceIdFlag() const {
-        return includeSentenceIdFlag;
-    }
-    bool isOnlyOutputSpanInfo() const {
-        return onlyOutputSpanInfo;
-    } 
-    bool isGzOutput () const {
-        return gzOutput;
-    }
-    std::string getInstanceWeightsFile() const {
-      return instanceWeightsFile;
-    }
+    maxPhraseLength(initmaxPhraseLength),
+    allModelsOutputFlag(false),
+    wordModel(false),
+    wordType(REO_MSD),
+    phraseModel(false),
+    phraseType(REO_MSD),
+    hierModel(false),
+    hierType(REO_MSD),
+    orientationFlag(false),
+    translationFlag(true),
+    includeSentenceIdFlag(false),
+    onlyOutputSpanInfo(false),
+    gzOutput(false) {}
+
+  //functions for initialization of options
+  void initAllModelsOutputFlag(const bool initallModelsOutputFlag) {
+    allModelsOutputFlag=initallModelsOutputFlag;
+  }
+  void initWordModel(const bool initwordModel) {
+    wordModel=initwordModel;
+  }
+  void initWordType(REO_MODEL_TYPE initwordType ) {
+    wordType=initwordType;
+  }
+  void initPhraseModel(const bool initphraseModel ) {
+    phraseModel=initphraseModel;
+  }
+  void initPhraseType(REO_MODEL_TYPE initphraseType) {
+    phraseType=initphraseType;
+  }
+  void initHierModel(const bool inithierModel) {
+    hierModel=inithierModel;
+  }
+  void initHierType(REO_MODEL_TYPE inithierType) {
+    hierType=inithierType;
+  }
+  void initOrientationFlag(const bool initorientationFlag) {
+    orientationFlag=initorientationFlag;
+  }
+  void initTranslationFlag(const bool inittranslationFlag) {
+    translationFlag=inittranslationFlag;
+  }
+  void initIncludeSentenceIdFlag(const bool initincludeSentenceIdFlag) {
+    includeSentenceIdFlag=initincludeSentenceIdFlag;
+  }
+  void initOnlyOutputSpanInfo(const bool initonlyOutputSpanInfo) {
+    onlyOutputSpanInfo= initonlyOutputSpanInfo;
+  }
+  void initGzOutput (const bool initgzOutput) {
+    gzOutput= initgzOutput;
+  }
+  void initInstanceWeightsFile(const char* initInstanceWeightsFile) {
+    instanceWeightsFile = std::string(initInstanceWeightsFile);
+  }
+
+  // functions for getting values
+  bool isAllModelsOutputFlag() const {
+    return allModelsOutputFlag;
+  }
+  bool isWordModel() const {
+    return wordModel;
+  }
+  REO_MODEL_TYPE isWordType() const {
+    return wordType;
+  }
+  bool isPhraseModel() const {
+    return phraseModel;
+  }
+  REO_MODEL_TYPE isPhraseType() const {
+    return phraseType;
+  }
+  bool isHierModel() const {
+    return hierModel;
+  }
+  REO_MODEL_TYPE isHierType() const {
+    return hierType;
+  }
+  bool isOrientationFlag() const {
+    return orientationFlag;
+  }
+  bool isTranslationFlag() const {
+    return translationFlag;
+  }
+  bool isIncludeSentenceIdFlag() const {
+    return includeSentenceIdFlag;
+  }
+  bool isOnlyOutputSpanInfo() const {
+    return onlyOutputSpanInfo;
+  }
+  bool isGzOutput () const {
+    return gzOutput;
+  }
+  std::string getInstanceWeightsFile() const {
+    return instanceWeightsFile;
+  }
 };
 
 }
diff --git a/phrase-extract/RuleExtractionOptions.h b/phrase-extract/RuleExtractionOptions.h
index 431be58b0..772d803a4 100644
--- a/phrase-extract/RuleExtractionOptions.h
+++ b/phrase-extract/RuleExtractionOptions.h
@@ -54,7 +54,7 @@ public:
   bool unpairedExtractFormat;
   bool conditionOnTargetLhs;
   bool boundaryRules;
-  
+
   RuleExtractionOptions()
     : maxSpan(10)
     , minHoleSource(2)
diff --git a/phrase-extract/ScoreFeature.cpp b/phrase-extract/ScoreFeature.cpp
index 5998c528c..25e497df2 100644
--- a/phrase-extract/ScoreFeature.cpp
+++ b/phrase-extract/ScoreFeature.cpp
@@ -22,82 +22,81 @@
 
 using namespace std;
 
-namespace MosesTraining 
+namespace MosesTraining
 {
 
 
-  const string& ScoreFeatureManager::usage() const
-  {
-    const static string& usage = "[--[Sparse]Domain[Indicator|Ratio|Subset|Bin] domain-file [bins]]"  ;
-    return usage;
-  }
+const string& ScoreFeatureManager::usage() const
+{
+  const static string& usage = "[--[Sparse]Domain[Indicator|Ratio|Subset|Bin] domain-file [bins]]"  ;
+  return usage;
+}
 
-  void ScoreFeatureManager::configure(const std::vector<std::string> args)
-  {
-    bool domainAdded = false;
-    bool sparseDomainAdded = false;
-    for (size_t i = 0; i < args.size(); ++i) {
-      if (args[i] == "--IgnoreSentenceId") {
-        m_includeSentenceId = true;
+void ScoreFeatureManager::configure(const std::vector<std::string> args)
+{
+  bool domainAdded = false;
+  bool sparseDomainAdded = false;
+  for (size_t i = 0; i < args.size(); ++i) {
+    if (args[i] == "--IgnoreSentenceId") {
+      m_includeSentenceId = true;
+    } else if (args[i].substr(0,8) == "--Domain") {
+      string type = args[i].substr(8);
+      ++i;
+      UTIL_THROW_IF(i == args.size(), ScoreFeatureArgumentException, "Missing domain file");
+      string domainFile = args[i];
+      UTIL_THROW_IF(domainAdded, ScoreFeatureArgumentException,
+                    "Only allowed one domain feature");
+      if (type == "Subset") {
+        m_features.push_back(ScoreFeaturePtr(new SubsetDomainFeature(domainFile)));
+      } else if (type == "Ratio") {
+        m_features.push_back(ScoreFeaturePtr(new RatioDomainFeature(domainFile)));
+      } else if (type == "Indicator") {
+        m_features.push_back(ScoreFeaturePtr(new IndicatorDomainFeature(domainFile)));
+      } else {
+        UTIL_THROW(ScoreFeatureArgumentException, "Unknown domain feature type " << type);
       }
-      else if (args[i].substr(0,8) == "--Domain") {
-        string type = args[i].substr(8);
-        ++i;
-        UTIL_THROW_IF(i == args.size(), ScoreFeatureArgumentException, "Missing domain file");
-        string domainFile = args[i];
-        UTIL_THROW_IF(domainAdded, ScoreFeatureArgumentException,
-             "Only allowed one domain feature");
-        if (type == "Subset") {
-          m_features.push_back(ScoreFeaturePtr(new SubsetDomainFeature(domainFile)));
-        } else if (type == "Ratio") {
-          m_features.push_back(ScoreFeaturePtr(new RatioDomainFeature(domainFile)));
-        } else if (type == "Indicator") {
-          m_features.push_back(ScoreFeaturePtr(new IndicatorDomainFeature(domainFile)));
-        } else {
-          UTIL_THROW(ScoreFeatureArgumentException, "Unknown domain feature type " << type);
-        }
-        domainAdded = true;
-        m_includeSentenceId = true;
-      } else if (args[i].substr(0,14) == "--SparseDomain") {
-        string type = args[i].substr(14);
-        ++i;
-        UTIL_THROW_IF(i == args.size(), ScoreFeatureArgumentException, "Missing domain file");
-        string domainFile = args[i];
-        UTIL_THROW_IF(sparseDomainAdded, ScoreFeatureArgumentException,
-             "Only allowed one sparse domain feature");
-        if (type == "Subset") {
-          m_features.push_back(ScoreFeaturePtr(new SparseSubsetDomainFeature(domainFile)));
-        } else if (type == "Ratio") {
-          m_features.push_back(ScoreFeaturePtr(new SparseRatioDomainFeature(domainFile)));
-        } else if (type == "Indicator") {
-          m_features.push_back(ScoreFeaturePtr(new SparseIndicatorDomainFeature(domainFile)));
-        } else {
-          UTIL_THROW(ScoreFeatureArgumentException, "Unknown domain feature type " << type);
-        }
-        sparseDomainAdded = true;
-        m_includeSentenceId = true;
+      domainAdded = true;
+      m_includeSentenceId = true;
+    } else if (args[i].substr(0,14) == "--SparseDomain") {
+      string type = args[i].substr(14);
+      ++i;
+      UTIL_THROW_IF(i == args.size(), ScoreFeatureArgumentException, "Missing domain file");
+      string domainFile = args[i];
+      UTIL_THROW_IF(sparseDomainAdded, ScoreFeatureArgumentException,
+                    "Only allowed one sparse domain feature");
+      if (type == "Subset") {
+        m_features.push_back(ScoreFeaturePtr(new SparseSubsetDomainFeature(domainFile)));
+      } else if (type == "Ratio") {
+        m_features.push_back(ScoreFeaturePtr(new SparseRatioDomainFeature(domainFile)));
+      } else if (type == "Indicator") {
+        m_features.push_back(ScoreFeaturePtr(new SparseIndicatorDomainFeature(domainFile)));
       } else {
-        UTIL_THROW(ScoreFeatureArgumentException,"Unknown score argument " << args[i]);
+        UTIL_THROW(ScoreFeatureArgumentException, "Unknown domain feature type " << type);
       }
+      sparseDomainAdded = true;
+      m_includeSentenceId = true;
+    } else {
+      UTIL_THROW(ScoreFeatureArgumentException,"Unknown score argument " << args[i]);
     }
-
   }
 
-  bool ScoreFeatureManager::equals(const PhraseAlignment& lhs, const PhraseAlignment& rhs) const
-  {
-    for (size_t i = 0; i < m_features.size(); ++i) {
-      if (!m_features[i]->equals(lhs,rhs)) return false;
-    }
-    return true;
+}
+
+bool ScoreFeatureManager::equals(const PhraseAlignment& lhs, const PhraseAlignment& rhs) const
+{
+  for (size_t i = 0; i < m_features.size(); ++i) {
+    if (!m_features[i]->equals(lhs,rhs)) return false;
   }
+  return true;
+}
 
- void ScoreFeatureManager::addFeatures(const ScoreFeatureContext& context,
-           std::vector<float>& denseValues,
-           std::map<std::string,float>& sparseValues) const
- {
-    for (size_t i = 0; i < m_features.size(); ++i) {
-      m_features[i]->add(context, denseValues, sparseValues);
-    }
- }
+void ScoreFeatureManager::addFeatures(const ScoreFeatureContext& context,
+                                      std::vector<float>& denseValues,
+                                      std::map<std::string,float>& sparseValues) const
+{
+  for (size_t i = 0; i < m_features.size(); ++i) {
+    m_features[i]->add(context, denseValues, sparseValues);
+  }
+}
 }
 
diff --git a/phrase-extract/ScoreFeature.h b/phrase-extract/ScoreFeature.h
index c7d856bcf..76939436f 100644
--- a/phrase-extract/ScoreFeature.h
+++ b/phrase-extract/ScoreFeature.h
@@ -20,7 +20,7 @@
 /**
  * This contains extra features that can be added to the scorer. To add a new feature:
  * 1. Implement a subclass of ScoreFeature
- * 2. Updated ScoreFeatureManager.configure() to configure your feature, and usage() to 
+ * 2. Updated ScoreFeatureManager.configure() to configure your feature, and usage() to
  *    display usage info.
  * 3. Write unit tests (see ScoreFeatureTest.cpp) and regression tests
 **/
@@ -37,35 +37,37 @@
 
 #include "PhraseAlignment.h"
 
-namespace MosesTraining 
+namespace MosesTraining
 {
 
-struct MaybeLog{
+struct MaybeLog {
   MaybeLog(bool useLog, float negativeLog):
     m_useLog(useLog), m_negativeLog(negativeLog) {}
-    
-  inline float operator() (float a) const    
-   { return m_useLog ? m_negativeLog*log(a) : a; }
+
+  inline float operator() (float a) const {
+    return m_useLog ? m_negativeLog*log(a) : a;
+  }
 
   float m_useLog;
   float m_negativeLog;
 };
 
-class ScoreFeatureArgumentException : public util::Exception 
+class ScoreFeatureArgumentException : public util::Exception
 {
-  public:
-    ScoreFeatureArgumentException() throw() {*this << "Unable to configure features: ";}
-    ~ScoreFeatureArgumentException() throw() {}
+public:
+  ScoreFeatureArgumentException() throw() {
+    *this << "Unable to configure features: ";
+  }
+  ~ScoreFeatureArgumentException() throw() {}
 };
 
 /** Passed to each feature to be used to calculate its values */
-struct ScoreFeatureContext
-{
+struct ScoreFeatureContext {
   ScoreFeatureContext(
     const PhraseAlignmentCollection &thePhrasePair,
     float theCount, /* Total counts of all phrase pairs*/
     const MaybeLog& theMaybeLog
-    ) :
+  ) :
     phrasePair(thePhrasePair),
     count(theCount),
     maybeLog(theMaybeLog)
@@ -82,53 +84,57 @@ struct ScoreFeatureContext
   **/
 class ScoreFeature
 {
-  public:
-    /** Add the values for this feature function. */
-    virtual void add(const ScoreFeatureContext& context, 
-             std::vector<float>& denseValues,
-             std::map<std::string,float>& sparseValues) const = 0;
+public:
+  /** Add the values for this feature function. */
+  virtual void add(const ScoreFeatureContext& context,
+                   std::vector<float>& denseValues,
+                   std::map<std::string,float>& sparseValues) const = 0;
 
-    /** Return true if the two phrase pairs are equal from the point of this feature. Assume
-        that they already compare true according to PhraseAlignment.equals()
-     **/
-    virtual bool equals(const PhraseAlignment& lhs, const PhraseAlignment& rhs) const = 0;
+  /** Return true if the two phrase pairs are equal from the point of this feature. Assume
+      that they already compare true according to PhraseAlignment.equals()
+   **/
+  virtual bool equals(const PhraseAlignment& lhs, const PhraseAlignment& rhs) const = 0;
 
-    virtual ~ScoreFeature() {}
+  virtual ~ScoreFeature() {}
 
 };
 
 typedef boost::shared_ptr<ScoreFeature> ScoreFeaturePtr;
 class ScoreFeatureManager
 {
-  public:
-    ScoreFeatureManager():
-      m_includeSentenceId(false) {}
-
-   /** To be appended to the score usage message */
-   const std::string& usage() const;
-   
-   /** Pass the unused command-line arguments to configure the extra features */
-   void configure(const std::vector<std::string> args);
-
-   /** Add all the features */
-   void addFeatures(const ScoreFeatureContext& context,
-             std::vector<float>& denseValues,
-             std::map<std::string,float>& sparseValues) const;
-
-    /** 
-      * Used to tell if the PhraseAlignment should be considered the same by all
-      * extended features. 
-     **/
-    bool equals(const PhraseAlignment& lhs, const PhraseAlignment& rhs) const;
-
-   const std::vector<ScoreFeaturePtr>& getFeatures() const {return m_features;}
-
-   /** Do we need to include sentence ids in phrase pairs? */
-   bool includeSentenceId() const {return m_includeSentenceId;}
-
-  private:
-    std::vector<ScoreFeaturePtr> m_features;
-    bool m_includeSentenceId;
+public:
+  ScoreFeatureManager():
+    m_includeSentenceId(false) {}
+
+  /** To be appended to the score usage message */
+  const std::string& usage() const;
+
+  /** Pass the unused command-line arguments to configure the extra features */
+  void configure(const std::vector<std::string> args);
+
+  /** Add all the features */
+  void addFeatures(const ScoreFeatureContext& context,
+                   std::vector<float>& denseValues,
+                   std::map<std::string,float>& sparseValues) const;
+
+  /**
+    * Used to tell if the PhraseAlignment should be considered the same by all
+    * extended features.
+   **/
+  bool equals(const PhraseAlignment& lhs, const PhraseAlignment& rhs) const;
+
+  const std::vector<ScoreFeaturePtr>& getFeatures() const {
+    return m_features;
+  }
+
+  /** Do we need to include sentence ids in phrase pairs? */
+  bool includeSentenceId() const {
+    return m_includeSentenceId;
+  }
+
+private:
+  std::vector<ScoreFeaturePtr> m_features;
+  bool m_includeSentenceId;
 };
 
 }
diff --git a/phrase-extract/ScoreFeatureTest.cpp b/phrase-extract/ScoreFeatureTest.cpp
index fecde015a..f4570fe30 100644
--- a/phrase-extract/ScoreFeatureTest.cpp
+++ b/phrase-extract/ScoreFeatureTest.cpp
@@ -31,14 +31,16 @@ using namespace MosesTraining;
 using namespace std;
 
 //pesky global variables
-namespace MosesTraining {
-  bool hierarchicalFlag = false;
-  Vocabulary vcbT;
-  Vocabulary vcbS;
+namespace MosesTraining
+{
+bool hierarchicalFlag = false;
+Vocabulary vcbT;
+Vocabulary vcbS;
 }
 
 
-const char *DomainFileLocation() {
+const char *DomainFileLocation()
+{
   if (boost::unit_test::framework::master_test_suite().argc < 2) {
     return "test.domain";
   }
@@ -62,7 +64,7 @@ BOOST_AUTO_TEST_CASE(manager_configure_domain_except)
 
 template <class Expected>
 static void checkDomainConfigured(
-      const vector<string>& args) 
+  const vector<string>& args)
 {
   ScoreFeatureManager manager;
   manager.configure(args);
@@ -76,17 +78,17 @@ static void checkDomainConfigured(
 BOOST_AUTO_TEST_CASE(manager_config_domain)
 {
   checkDomainConfigured<RatioDomainFeature>
-    (boost::assign::list_of ("--DomainRatio")("/dev/null"));
+  (boost::assign::list_of ("--DomainRatio")("/dev/null"));
   checkDomainConfigured<IndicatorDomainFeature>
-    (boost::assign::list_of("--DomainIndicator")("/dev/null"));
+  (boost::assign::list_of("--DomainIndicator")("/dev/null"));
   checkDomainConfigured<SubsetDomainFeature>
-    (boost::assign::list_of("--DomainSubset")("/dev/null"));
+  (boost::assign::list_of("--DomainSubset")("/dev/null"));
   checkDomainConfigured<SparseRatioDomainFeature>
-    (boost::assign::list_of("--SparseDomainRatio")("/dev/null"));
+  (boost::assign::list_of("--SparseDomainRatio")("/dev/null"));
   checkDomainConfigured<SparseIndicatorDomainFeature>
-    (boost::assign::list_of("--SparseDomainIndicator")("/dev/null"));
+  (boost::assign::list_of("--SparseDomainIndicator")("/dev/null"));
   checkDomainConfigured<SparseSubsetDomainFeature>
-    (boost::assign::list_of("--SparseDomainSubset")("/dev/null"));
+  (boost::assign::list_of("--SparseDomainSubset")("/dev/null"));
 }
 
 
@@ -98,8 +100,8 @@ BOOST_AUTO_TEST_CASE(domain_equals)
   char buf2[] = "a ||| b ||| 0-0 ||| 2";
   char buf3[] = "a ||| b ||| 0-0 ||| 3";
   a1.create(buf1, 0, true); //domain a
-  a2.create(buf2, 1, true); //domain c  
-  a3.create(buf3, 2, true); //domain c 
+  a2.create(buf2, 1, true); //domain c
+  a3.create(buf3, 2, true); //domain c
   BOOST_CHECK(feature.equals(a2,a3));
   BOOST_CHECK(!feature.equals(a1,a3));
   BOOST_CHECK(!feature.equals(a1,a3));
diff --git a/phrase-extract/SentenceAlignment.cpp b/phrase-extract/SentenceAlignment.cpp
index 96ef02865..b2d5520aa 100644
--- a/phrase-extract/SentenceAlignment.cpp
+++ b/phrase-extract/SentenceAlignment.cpp
@@ -94,12 +94,12 @@ bool SentenceAlignment::create( char targetString[], char sourceString[], char a
       cerr << "T: " << targetString << endl << "S: " << sourceString << endl;
       return false;
     }
-    
+
     if (boundaryRules) {
       ++s;
       ++t;
     }
-    
+
     // cout << "alignmentSequence[i] " << alignmentSequence[i] << " is " << s << ", " << t << endl;
     if ((size_t)t >= target.size() || (size_t)s >= source.size()) {
       cerr << "WARNING: sentence " << sentenceID << " has alignment point (" << s << ", " << t << ") out of bounds (" << source.size() << ", " << target.size() << ")\n";
@@ -109,16 +109,16 @@ bool SentenceAlignment::create( char targetString[], char sourceString[], char a
     alignedToT[t].push_back( s );
     alignedCountS[s]++;
   }
-  
+
   if (boundaryRules) {
     alignedToT[0].push_back(0);
     alignedCountS[0]++;
-    
+
     alignedToT.back().push_back(alignedCountS.size() - 1);
     alignedCountS.back()++;
-    
+
   }
-  
+
   return true;
 }
 
diff --git a/phrase-extract/SentenceAlignment.h b/phrase-extract/SentenceAlignment.h
index 76cf950d4..e215f5fef 100644
--- a/phrase-extract/SentenceAlignment.h
+++ b/phrase-extract/SentenceAlignment.h
@@ -45,7 +45,7 @@ public:
 
   bool create(char targetString[], char sourceString[],
               char alignmentString[], char weightString[], int sentenceID, bool boundaryRules);
-  
+
 };
 
 }
diff --git a/phrase-extract/XmlTree.cpp b/phrase-extract/XmlTree.cpp
index 05bcefe20..eedb3b260 100644
--- a/phrase-extract/XmlTree.cpp
+++ b/phrase-extract/XmlTree.cpp
@@ -364,7 +364,7 @@ bool ProcessAndStripXMLTags(string &line, SyntaxTree &tree, set< string > &label
 
         string pcfgString = ParseXmlTagAttribute(tagContent,"pcfg");
         float pcfgScore = pcfgString == "" ? 0.0f
-                                           : std::atof(pcfgString.c_str());
+                          : std::atof(pcfgString.c_str());
 
         // report what we have processed so far
         if (0) {
diff --git a/phrase-extract/consolidate-direct-main.cpp b/phrase-extract/consolidate-direct-main.cpp
index e7e68e977..3b38f741c 100644
--- a/phrase-extract/consolidate-direct-main.cpp
+++ b/phrase-extract/consolidate-direct-main.cpp
@@ -89,21 +89,20 @@ int main(int argc, char* argv[])
 
   char* &fileNameConsolidated = argv[2];
   ostream *fileConsolidated;
-	
-	if (strcmp(fileNameConsolidated, "-") == 0) {
-		fileConsolidated = &cout;
-	}
-	else {
+
+  if (strcmp(fileNameConsolidated, "-") == 0) {
+    fileConsolidated = &cout;
+  } else {
     Moses::OutputFileStream *outputFile = new Moses::OutputFileStream();
-		bool success = outputFile->Open(fileNameConsolidated);
-		if (!success) {
-			cerr << "ERROR: could not open file phrase table file "
-			<< fileNameConsolidated << endl;
-			exit(1);
-		}
-		fileConsolidated = outputFile;
-	}
-	
+    bool success = outputFile->Open(fileNameConsolidated);
+    if (!success) {
+      cerr << "ERROR: could not open file phrase table file "
+           << fileNameConsolidated << endl;
+      exit(1);
+    }
+    fileConsolidated = outputFile;
+  }
+
   int i=0;
   while(true) {
     i++;
@@ -119,8 +118,8 @@ int main(int argc, char* argv[])
 
     // output alignment and probabilities
     (*fileConsolidated)	<< itemDirect[2]						// prob direct
-                      << " 2.718" // phrase count feature
-                      << " ||| " << itemDirect[3];	// alignment
+                        << " 2.718" // phrase count feature
+                        << " ||| " << itemDirect[3];	// alignment
 
     // counts
     (*fileConsolidated) << "||| 0 " << itemDirect[4]; // indirect
@@ -128,11 +127,11 @@ int main(int argc, char* argv[])
 
   }
 
-	fileConsolidated->flush();
-	if (fileConsolidated != &cout) {
-		delete fileConsolidated;
-	}
-	
+  fileConsolidated->flush();
+  if (fileConsolidated != &cout) {
+    delete fileConsolidated;
+  }
+
   cerr << "Finished" << endl;
 }
 
diff --git a/phrase-extract/consolidate-main.cpp b/phrase-extract/consolidate-main.cpp
index fd33907de..67a097910 100644
--- a/phrase-extract/consolidate-main.cpp
+++ b/phrase-extract/consolidate-main.cpp
@@ -42,7 +42,10 @@ bool goodTuringFlag = false;
 bool kneserNeyFlag = false;
 bool logProbFlag = false;
 bool outputNTLengths = false;
-inline float maybeLogProb( float a ) { return logProbFlag ? log(a) : a; }
+inline float maybeLogProb( float a )
+{
+  return logProbFlag ? log(a) : a;
+}
 
 char line[LINE_MAX_LENGTH];
 void processFiles( char*, char*, char*, char* );
@@ -79,7 +82,7 @@ int main(int argc, char* argv[])
       cerr << "not including the phrase count feature\n";
     } else if (strcmp(argv[i],"--GoodTuring") == 0) {
       goodTuringFlag = true;
-      if (i+1==argc) { 
+      if (i+1==argc) {
         cerr << "ERROR: specify count of count files for Good Turing discounting!\n";
         exit(1);
       }
@@ -87,7 +90,7 @@ int main(int argc, char* argv[])
       cerr << "adjusting phrase translation probabilities with Good Turing discounting\n";
     } else if (strcmp(argv[i],"--KneserNey") == 0) {
       kneserNeyFlag = true;
-      if (i+1==argc) { 
+      if (i+1==argc) {
         cerr << "ERROR: specify count of count files for Kneser Ney discounting!\n";
         exit(1);
       }
@@ -105,8 +108,11 @@ int main(int argc, char* argv[])
       while(i+1<argc && argv[i+1][0]>='0' && argv[i+1][0]<='9') {
         int binCount = atoi(argv[++i]);
         countBin.push_back( binCount );
-        if (prev+1 == binCount) { cerr << " " << binCount; }
-        else { cerr << " " << (prev+1) << "-" << binCount; }
+        if (prev+1 == binCount) {
+          cerr << " " << binCount;
+        } else {
+          cerr << " " << (prev+1) << "-" << binCount;
+        }
         prev = binCount;
       }
       cerr << " " << (prev+1) << "+\n";
@@ -152,7 +158,7 @@ void loadCountOfCounts( char* fileNameCountOfCounts )
   if (goodTuringFlag) {
     goodTuringDiscount.push_back(0.01); // floor value
     for( size_t i=1; i<countOfCounts.size()-1; i++ ) {
-      goodTuringDiscount.push_back(((float)i+1)/(float)i*((countOfCounts[i+1]+0.1) / ((float)countOfCounts[i]+0.1))); 
+      goodTuringDiscount.push_back(((float)i+1)/(float)i*((countOfCounts[i+1]+0.1) / ((float)countOfCounts[i]+0.1)));
       if (goodTuringDiscount[i]>1)
         goodTuringDiscount[i] = 1;
       if (goodTuringDiscount[i]<goodTuringDiscount[i-1])
@@ -253,21 +259,21 @@ void processFiles( char* fileNameDirect, char* fileNameIndirect, char* fileNameC
     float adjustedCountEF_indirect = adjustedCountEF;
 
     // Kneser Ney discounting [Foster et al, 2006]
-   if (kneserNeyFlag) {
-     float D = kneserNey_D3;
-     if (countEF < 2) D = kneserNey_D1;
-     else if (countEF < 3) D = kneserNey_D2;
-     if (D > countEF) D = countEF - 0.01; // sanity constraint
-
-     float p_b_E = n1_E / totalCount; // target phrase prob based on distinct
-     float alpha_F = D * n1_F / countF; // available mass
-     adjustedCountEF = countEF - D + countF * alpha_F * p_b_E;
-
-     // for indirect
-     float p_b_F = n1_F / totalCount; // target phrase prob based on distinct
-     float alpha_E = D * n1_E / countE; // available mass
-     adjustedCountEF_indirect = countEF - D + countE * alpha_E * p_b_F;
-   }
+    if (kneserNeyFlag) {
+      float D = kneserNey_D3;
+      if (countEF < 2) D = kneserNey_D1;
+      else if (countEF < 3) D = kneserNey_D2;
+      if (D > countEF) D = countEF - 0.01; // sanity constraint
+
+      float p_b_E = n1_E / totalCount; // target phrase prob based on distinct
+      float alpha_F = D * n1_F / countF; // available mass
+      adjustedCountEF = countEF - D + countF * alpha_F * p_b_E;
+
+      // for indirect
+      float p_b_F = n1_F / totalCount; // target phrase prob based on distinct
+      float alpha_E = D * n1_E / countE; // available mass
+      adjustedCountEF_indirect = countEF - D + countE * alpha_E * p_b_F;
+    }
 
     // prob indirect
     if (!onlyDirectFlag) {
@@ -296,30 +302,27 @@ void processFiles( char* fileNameDirect, char* fileNameIndirect, char* fileNameC
         if (!foundBin && countEF <= countBin[i]) {
           fileConsolidated << " " << maybeLogProb(2.718);
           foundBin = true;
-        }
-        else {
+        } else {
           fileConsolidated << " " << maybeLogProb(1);
         }
       }
-      fileConsolidated << " " << maybeLogProb( foundBin ? 1 : 2.718 );   
+      fileConsolidated << " " << maybeLogProb( foundBin ? 1 : 2.718 );
     }
 
     // alignment
     fileConsolidated << " ||| " << itemDirect[3];
 
     // counts, for debugging
-    fileConsolidated << "||| " << countE << " " << countF << " " << countEF; 
+    fileConsolidated << "||| " << countE << " " << countF << " " << countEF;
 
-    if (outputNTLengths)
-    {
+    if (outputNTLengths) {
       fileConsolidated << " ||| " << itemDirect[5];
     }
-    
+
     // count bin feature (as a sparse feature)
-    if (sparseCountBinFeatureFlag || 
-        directSparseScores.compare("") != 0 || 
-        indirectSparseScores.compare("") != 0)
-    {
+    if (sparseCountBinFeatureFlag ||
+        directSparseScores.compare("") != 0 ||
+        indirectSparseScores.compare("") != 0) {
       fileConsolidated << " |||";
       if (directSparseScores.compare("") != 0)
         fileConsolidated << " " << directSparseScores;
@@ -351,13 +354,13 @@ void processFiles( char* fileNameDirect, char* fileNameIndirect, char* fileNameC
   fileConsolidated.Close();
 }
 
-void breakdownCoreAndSparse( string combined, string &core, string &sparse ) 
+void breakdownCoreAndSparse( string combined, string &core, string &sparse )
 {
   core = "";
   sparse = "";
   vector<string> score = tokenize( combined.c_str() );
   for(size_t i=0; i<score.size(); i++) {
-    if ((score[i][0] >= '0' && score[i][0] <= '9') || i+1 == score.size()) 
+    if ((score[i][0] >= '0' && score[i][0] <= '9') || i+1 == score.size())
       core += " " + score[i];
     else {
       sparse += " " + score[i];
diff --git a/phrase-extract/consolidate-reverse-main.cpp b/phrase-extract/consolidate-reverse-main.cpp
index c86d870c8..6843bf3aa 100644
--- a/phrase-extract/consolidate-reverse-main.cpp
+++ b/phrase-extract/consolidate-reverse-main.cpp
@@ -229,13 +229,12 @@ string reverseAlignment(const string &alignments)
 
   vector<string> alignToks = tokenize(alignments.c_str());
 
-  for (size_t i = 0; i < alignToks.size(); ++i)
-  {
+  for (size_t i = 0; i < alignToks.size(); ++i) {
     string &alignPair = alignToks[i];
     vector<string> alignPoints;
     Tokenize(alignPoints, alignPair, "-");
     assert(alignPoints.size() == 2);
-    
+
     ret << alignPoints[1] << "-" << alignPoints[0] << " ";
   }
 
diff --git a/phrase-extract/domain.cpp b/phrase-extract/domain.cpp
index 29ba8ee64..67b4a13c3 100644
--- a/phrase-extract/domain.cpp
+++ b/phrase-extract/domain.cpp
@@ -13,7 +13,8 @@ namespace MosesTraining
 {
 
 // handling of domain names: load database with sentence-id / domain name info
-void Domain::load( const std::string &domainFileName ) {
+void Domain::load( const std::string &domainFileName )
+{
   Moses::InputFileStream fileS( domainFileName );
   istream *fileP = &fileS;
   while(true) {
@@ -39,7 +40,8 @@ void Domain::load( const std::string &domainFileName ) {
 }
 
 // get domain name based on sentence number
-string Domain::getDomainOfSentence( int sentenceId ) const {
+string Domain::getDomainOfSentence( int sentenceId ) const
+{
   for(size_t i=0; i<spec.size(); i++) {
     if (sentenceId <= spec[i].first) {
       return spec[i].second;
@@ -54,9 +56,9 @@ DomainFeature::DomainFeature(const string& domainFile)
   m_domain.load(domainFile);
 }
 
-void DomainFeature::add(const ScoreFeatureContext& context, 
-         std::vector<float>& denseValues,
-         std::map<std::string,float>& sparseValues)  const
+void DomainFeature::add(const ScoreFeatureContext& context,
+                        std::vector<float>& denseValues,
+                        std::map<std::string,float>& sparseValues)  const
 {
   map< string, float > domainCount;
   for(size_t i=0; i<context.phrasePair.size(); i++) {
@@ -71,13 +73,13 @@ void DomainFeature::add(const ScoreFeatureContext& context,
 }
 
 void SubsetDomainFeature::add(const map<string,float>& domainCount,float count,
-         const MaybeLog& maybeLog,
-         std::vector<float>& denseValues,
-         std::map<std::string,float>& sparseValues)  const
+                              const MaybeLog& maybeLog,
+                              std::vector<float>& denseValues,
+                              std::map<std::string,float>& sparseValues)  const
 {
- if (m_domain.list.size() > 6) {
+  if (m_domain.list.size() > 6) {
     UTIL_THROW_IF(m_domain.list.size() > 6, ScoreFeatureArgumentException,
-      "too many domains for core domain subset features");
+                  "too many domains for core domain subset features");
   }
   size_t bitmap = 0;
   for(size_t bit = 0; bit < m_domain.list.size(); bit++) {
@@ -87,13 +89,13 @@ void SubsetDomainFeature::add(const map<string,float>& domainCount,float count,
   }
   for(size_t i = 1; i < (1 << m_domain.list.size()); i++) {
     denseValues.push_back(maybeLog( (bitmap == i) ? 2.718 : 1 ));
-  } 
+  }
 }
 
 void SparseSubsetDomainFeature::add(const map<string,float>& domainCount,float count,
-         const MaybeLog& maybeLog,
-         std::vector<float>& denseValues,
-         std::map<std::string,float>& sparseValues)  const
+                                    const MaybeLog& maybeLog,
+                                    std::vector<float>& denseValues,
+                                    std::map<std::string,float>& sparseValues)  const
 {
   typedef vector<string>::const_iterator I;
   ostringstream key;
@@ -108,9 +110,9 @@ void SparseSubsetDomainFeature::add(const map<string,float>& domainCount,float c
 
 
 void RatioDomainFeature::add(const map<string,float>& domainCount,float count,
-         const MaybeLog& maybeLog,
-         std::vector<float>& denseValues,
-         std::map<std::string,float>& sparseValues)  const
+                             const MaybeLog& maybeLog,
+                             std::vector<float>& denseValues,
+                             std::map<std::string,float>& sparseValues)  const
 {
   typedef vector< string >::const_iterator I;
   for (I i = m_domain.list.begin(); i != m_domain.list.end(); i++ ) {
@@ -125,9 +127,9 @@ void RatioDomainFeature::add(const map<string,float>& domainCount,float count,
 
 
 void SparseRatioDomainFeature::add(const map<string,float>& domainCount,float count,
-         const MaybeLog& maybeLog,
-         std::vector<float>& denseValues,
-         std::map<std::string,float>& sparseValues)  const
+                                   const MaybeLog& maybeLog,
+                                   std::vector<float>& denseValues,
+                                   std::map<std::string,float>& sparseValues)  const
 {
   typedef map< string, float >::const_iterator I;
   for (I i=domainCount.begin(); i != domainCount.end(); i++) {
@@ -137,9 +139,9 @@ void SparseRatioDomainFeature::add(const map<string,float>& domainCount,float co
 
 
 void IndicatorDomainFeature::add(const map<string,float>& domainCount,float count,
-         const MaybeLog& maybeLog,
-         std::vector<float>& denseValues,
-         std::map<std::string,float>& sparseValues)  const
+                                 const MaybeLog& maybeLog,
+                                 std::vector<float>& denseValues,
+                                 std::map<std::string,float>& sparseValues)  const
 {
   typedef vector< string >::const_iterator I;
   for (I i = m_domain.list.begin(); i != m_domain.list.end(); i++ ) {
@@ -154,20 +156,20 @@ void IndicatorDomainFeature::add(const map<string,float>& domainCount,float coun
 }
 
 void SparseIndicatorDomainFeature::add(const map<string,float>& domainCount,float count,
-         const MaybeLog& maybeLog,
-         std::vector<float>& denseValues,
-         std::map<std::string,float>& sparseValues)  const
+                                       const MaybeLog& maybeLog,
+                                       std::vector<float>& denseValues,
+                                       std::map<std::string,float>& sparseValues)  const
 {
   typedef map< string, float >::const_iterator I;
   for (I i=domainCount.begin(); i != domainCount.end(); i++) {
-      sparseValues["dom_" + i->first] = 1;
+    sparseValues["dom_" + i->first] = 1;
   }
 }
 
-bool DomainFeature::equals(const PhraseAlignment& lhs, const PhraseAlignment& rhs) const 
+bool DomainFeature::equals(const PhraseAlignment& lhs, const PhraseAlignment& rhs) const
 {
   return m_domain.getDomainOfSentence(lhs.sentenceId) ==
-    m_domain.getDomainOfSentence( rhs.sentenceId);
+         m_domain.getDomainOfSentence( rhs.sentenceId);
 }
 
 
diff --git a/phrase-extract/domain.h b/phrase-extract/domain.h
index f3e1e92a3..279496e01 100644
--- a/phrase-extract/domain.h
+++ b/phrase-extract/domain.h
@@ -31,106 +31,106 @@ public:
 
 class DomainFeature : public ScoreFeature
 {
-  public:
+public:
+
+  DomainFeature(const std::string& domainFile);
+  bool equals(const PhraseAlignment& lhs, const PhraseAlignment& rhs) const;
+  void add(const ScoreFeatureContext& context,
+           std::vector<float>& denseValues,
+           std::map<std::string,float>& sparseValues) const;
 
-    DomainFeature(const std::string& domainFile);
-    bool equals(const PhraseAlignment& lhs, const PhraseAlignment& rhs) const;
-    void add(const ScoreFeatureContext& context, 
-             std::vector<float>& denseValues,
-             std::map<std::string,float>& sparseValues) const;
+protected:
+  /** Overriden in subclass */
+  virtual void add(const std::map<std::string,float>& domainCounts, float count,
+                   const MaybeLog& maybeLog,
+                   std::vector<float>& denseValues,
+                   std::map<std::string,float>& sparseValues) const = 0;
 
-  protected:
-    /** Overriden in subclass */
-    virtual void add(const std::map<std::string,float>& domainCounts, float count,
-             const MaybeLog& maybeLog,
-             std::vector<float>& denseValues,
-             std::map<std::string,float>& sparseValues) const = 0;
-      
 
-    Domain m_domain;
+  Domain m_domain;
 
 };
 
 class SubsetDomainFeature : public DomainFeature
 {
-  public:
-    SubsetDomainFeature(const std::string& domainFile) :
-      DomainFeature(domainFile) {}
-
-  protected:
-    virtual void add(const std::map<std::string,float>& domainCounts, float count,
-             const MaybeLog& maybeLog,
-             std::vector<float>& denseValues,
-             std::map<std::string,float>& sparseValues) const;
+public:
+  SubsetDomainFeature(const std::string& domainFile) :
+    DomainFeature(domainFile) {}
+
+protected:
+  virtual void add(const std::map<std::string,float>& domainCounts, float count,
+                   const MaybeLog& maybeLog,
+                   std::vector<float>& denseValues,
+                   std::map<std::string,float>& sparseValues) const;
 };
 
 class SparseSubsetDomainFeature : public DomainFeature
 {
- public:
-    SparseSubsetDomainFeature(const std::string& domainFile) :
-      DomainFeature(domainFile) {}
+public:
+  SparseSubsetDomainFeature(const std::string& domainFile) :
+    DomainFeature(domainFile) {}
 
-  protected:
-    virtual void add(const std::map<std::string,float>& domainCounts, float count,
-             const MaybeLog& maybeLog,
-             std::vector<float>& denseValues,
-             std::map<std::string,float>& sparseValues) const;
+protected:
+  virtual void add(const std::map<std::string,float>& domainCounts, float count,
+                   const MaybeLog& maybeLog,
+                   std::vector<float>& denseValues,
+                   std::map<std::string,float>& sparseValues) const;
 
 };
 
 class IndicatorDomainFeature : public DomainFeature
 {
-  public:
-    IndicatorDomainFeature(const std::string& domainFile) :
-      DomainFeature(domainFile) {}
-
-  protected:
-    virtual void add(const std::map<std::string,float>& domainCounts, float count,
-             const MaybeLog& maybeLog,
-             std::vector<float>& denseValues,
-             std::map<std::string,float>& sparseValues) const;
+public:
+  IndicatorDomainFeature(const std::string& domainFile) :
+    DomainFeature(domainFile) {}
+
+protected:
+  virtual void add(const std::map<std::string,float>& domainCounts, float count,
+                   const MaybeLog& maybeLog,
+                   std::vector<float>& denseValues,
+                   std::map<std::string,float>& sparseValues) const;
 };
 
 
 class SparseIndicatorDomainFeature : public DomainFeature
 {
-  public:
-    SparseIndicatorDomainFeature(const std::string& domainFile) :
-      DomainFeature(domainFile) {}
-
-  protected:
-    virtual void add(const std::map<std::string,float>& domainCounts, float count,
-             const MaybeLog& maybeLog,
-             std::vector<float>& denseValues,
-             std::map<std::string,float>& sparseValues) const;
+public:
+  SparseIndicatorDomainFeature(const std::string& domainFile) :
+    DomainFeature(domainFile) {}
+
+protected:
+  virtual void add(const std::map<std::string,float>& domainCounts, float count,
+                   const MaybeLog& maybeLog,
+                   std::vector<float>& denseValues,
+                   std::map<std::string,float>& sparseValues) const;
 };
 
 
 class RatioDomainFeature : public DomainFeature
 {
-  public:
-    RatioDomainFeature(const std::string& domainFile) :
-      DomainFeature(domainFile) {}
-
-  protected:
-    virtual void add(const std::map<std::string,float>& domainCounts, float count,
-             const MaybeLog& maybeLog,
-             std::vector<float>& denseValues,
-             std::map<std::string,float>& sparseValues) const;
+public:
+  RatioDomainFeature(const std::string& domainFile) :
+    DomainFeature(domainFile) {}
+
+protected:
+  virtual void add(const std::map<std::string,float>& domainCounts, float count,
+                   const MaybeLog& maybeLog,
+                   std::vector<float>& denseValues,
+                   std::map<std::string,float>& sparseValues) const;
 };
 
 
 class SparseRatioDomainFeature : public DomainFeature
 {
-  public:
-    SparseRatioDomainFeature(const std::string& domainFile) :
-      DomainFeature(domainFile) {}
-
-  protected:
-    virtual void add(const std::map<std::string,float>& domainCounts, float count,
-             const MaybeLog& maybeLog,
-             std::vector<float>& denseValues,
-             std::map<std::string,float>& sparseValues) const;
+public:
+  SparseRatioDomainFeature(const std::string& domainFile) :
+    DomainFeature(domainFile) {}
+
+protected:
+  virtual void add(const std::map<std::string,float>& domainCounts, float count,
+                   const MaybeLog& maybeLog,
+                   std::vector<float>& denseValues,
+                   std::map<std::string,float>& sparseValues) const;
 };
 
 
diff --git a/phrase-extract/extract-ghkm/Alignment.cpp b/phrase-extract/extract-ghkm/Alignment.cpp
index fcd5e14e1..744b4b1a2 100644
--- a/phrase-extract/extract-ghkm/Alignment.cpp
+++ b/phrase-extract/extract-ghkm/Alignment.cpp
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -24,8 +24,10 @@
 #include <cassert>
 #include <cstdlib>
 
-namespace Moses {
-namespace GHKM {
+namespace Moses
+{
+namespace GHKM
+{
 
 Alignment ReadAlignment(const std::string &s)
 {
diff --git a/phrase-extract/extract-ghkm/Alignment.h b/phrase-extract/extract-ghkm/Alignment.h
index bc42191e1..051d5ca92 100644
--- a/phrase-extract/extract-ghkm/Alignment.h
+++ b/phrase-extract/extract-ghkm/Alignment.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -25,8 +25,10 @@
 #include <utility>
 #include <vector>
 
-namespace Moses {
-namespace GHKM {
+namespace Moses
+{
+namespace GHKM
+{
 
 typedef std::vector<std::pair<int, int> > Alignment;
 
diff --git a/phrase-extract/extract-ghkm/AlignmentGraph.cpp b/phrase-extract/extract-ghkm/AlignmentGraph.cpp
index 6bd32a13b..974188dbd 100644
--- a/phrase-extract/extract-ghkm/AlignmentGraph.cpp
+++ b/phrase-extract/extract-ghkm/AlignmentGraph.cpp
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -30,8 +30,10 @@
 #include <memory>
 #include <stack>
 
-namespace Moses {
-namespace GHKM {
+namespace Moses
+{
+namespace GHKM
+{
 
 AlignmentGraph::AlignmentGraph(const ParseTree *t,
                                const std::vector<std::string> &s,
@@ -84,8 +86,8 @@ AlignmentGraph::~AlignmentGraph()
 }
 
 Subgraph AlignmentGraph::ComputeMinimalFrontierGraphFragment(
-    Node *root,
-    const std::set<Node *> &frontierSet)
+  Node *root,
+  const std::set<Node *> &frontierSet)
 {
   std::stack<Node *> expandableNodes;
   std::set<const Node *> expandedNodes;
@@ -302,7 +304,7 @@ void AlignmentGraph::CalcComplementSpans(Node *root)
 }
 
 void AlignmentGraph::GetTargetTreeLeaves(Node *root,
-                                         std::vector<Node *> &leaves)
+    std::vector<Node *> &leaves)
 {
   if (root->IsSink()) {
     leaves.push_back(root);
diff --git a/phrase-extract/extract-ghkm/AlignmentGraph.h b/phrase-extract/extract-ghkm/AlignmentGraph.h
index 94948758a..cf26b8c27 100644
--- a/phrase-extract/extract-ghkm/AlignmentGraph.h
+++ b/phrase-extract/extract-ghkm/AlignmentGraph.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -28,8 +28,10 @@
 #include <string>
 #include <vector>
 
-namespace Moses {
-namespace GHKM {
+namespace Moses
+{
+namespace GHKM
+{
 
 class Node;
 class ParseTree;
@@ -37,20 +39,24 @@ class Subgraph;
 
 class AlignmentGraph
 {
- public:
+public:
   AlignmentGraph(const ParseTree *,
                  const std::vector<std::string> &,
                  const Alignment &);
 
   ~AlignmentGraph();
 
-  Node *GetRoot() { return m_root; }
-  const std::vector<Node *> &GetTargetNodes() { return m_targetNodes; }
+  Node *GetRoot() {
+    return m_root;
+  }
+  const std::vector<Node *> &GetTargetNodes() {
+    return m_targetNodes;
+  }
 
   void ExtractMinimalRules(const Options &);
   void ExtractComposedRules(const Options &);
 
- private:
+private:
   // Disallow copying
   AlignmentGraph(const AlignmentGraph &);
   AlignmentGraph &operator=(const AlignmentGraph &);
@@ -58,11 +64,11 @@ class AlignmentGraph
   Node *CopyParseTree(const ParseTree *);
   void ComputeFrontierSet(Node *, const Options &, std::set<Node *> &) const;
   void CalcComplementSpans(Node *);
-  void GetTargetTreeLeaves(Node *, std::vector<Node *> &); 
+  void GetTargetTreeLeaves(Node *, std::vector<Node *> &);
   void AttachUnalignedSourceWords();
   Node *DetermineAttachmentPoint(int);
   Subgraph ComputeMinimalFrontierGraphFragment(Node *,
-                                               const std::set<Node *> &);
+      const std::set<Node *> &);
   void ExtractComposedRules(Node *, const Options &);
 
   Node *m_root;
diff --git a/phrase-extract/extract-ghkm/ComposedRule.cpp b/phrase-extract/extract-ghkm/ComposedRule.cpp
index 8bf3cfc72..e9fc826b7 100644
--- a/phrase-extract/extract-ghkm/ComposedRule.cpp
+++ b/phrase-extract/extract-ghkm/ComposedRule.cpp
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -27,14 +27,16 @@
 #include <vector>
 #include <queue>
 
-namespace Moses {
-namespace GHKM {
+namespace Moses
+{
+namespace GHKM
+{
 
 ComposedRule::ComposedRule(const Subgraph &baseRule)
-    : m_baseRule(baseRule)
-    , m_depth(baseRule.GetDepth())
-    , m_size(baseRule.GetSize())
-    , m_nodeCount(baseRule.GetNodeCount())
+  : m_baseRule(baseRule)
+  , m_depth(baseRule.GetDepth())
+  , m_size(baseRule.GetSize())
+  , m_nodeCount(baseRule.GetNodeCount())
 {
   const std::set<const Node *> &leaves = baseRule.GetLeaves();
   for (std::set<const Node *>::const_iterator p = leaves.begin();
@@ -47,12 +49,12 @@ ComposedRule::ComposedRule(const Subgraph &baseRule)
 
 ComposedRule::ComposedRule(const ComposedRule &other, const Subgraph &rule,
                            int depth)
-    : m_baseRule(other.m_baseRule)
-    , m_attachedRules(other.m_attachedRules)
-    , m_openAttachmentPoints(other.m_openAttachmentPoints)
-    , m_depth(depth)
-    , m_size(other.m_size+rule.GetSize())
-    , m_nodeCount(other.m_nodeCount+rule.GetNodeCount()-1)
+  : m_baseRule(other.m_baseRule)
+  , m_attachedRules(other.m_attachedRules)
+  , m_openAttachmentPoints(other.m_openAttachmentPoints)
+  , m_depth(depth)
+  , m_size(other.m_size+rule.GetSize())
+  , m_nodeCount(other.m_nodeCount+rule.GetNodeCount()-1)
 {
   m_attachedRules.push_back(&rule);
   m_openAttachmentPoints.pop();
@@ -71,7 +73,7 @@ void ComposedRule::CloseAttachmentPoint()
 }
 
 ComposedRule *ComposedRule::AttemptComposition(const Subgraph &rule,
-                                               const Options &options) const
+    const Options &options) const
 {
   // The smallest possible rule fragment should be rooted at a tree node.
   // Note that this differs from the original GHKM definition.
diff --git a/phrase-extract/extract-ghkm/ComposedRule.h b/phrase-extract/extract-ghkm/ComposedRule.h
index 65ce9ac70..b5f72a492 100644
--- a/phrase-extract/extract-ghkm/ComposedRule.h
+++ b/phrase-extract/extract-ghkm/ComposedRule.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -26,15 +26,17 @@
 #include <vector>
 #include <queue>
 
-namespace Moses {
-namespace GHKM {
+namespace Moses
+{
+namespace GHKM
+{
 
 class Node;
 struct Options;
 
 class ComposedRule
 {
- public:
+public:
   // Form a 'trivial' ComposedRule from a single existing rule.
   ComposedRule(const Subgraph &baseRule);
 
@@ -53,7 +55,7 @@ class ComposedRule
   // Constructs a Subgraph object corresponding to the composed rule.
   Subgraph CreateSubgraph();
 
- private:
+private:
   ComposedRule(const ComposedRule &, const Subgraph &, int);
 
   const Subgraph &m_baseRule;
diff --git a/phrase-extract/extract-ghkm/Exception.h b/phrase-extract/extract-ghkm/Exception.h
index 9928785f0..a1e623cd1 100644
--- a/phrase-extract/extract-ghkm/Exception.h
+++ b/phrase-extract/extract-ghkm/Exception.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -23,16 +23,20 @@
 
 #include <string>
 
-namespace Moses {
-namespace GHKM {
+namespace Moses
+{
+namespace GHKM
+{
 
 class Exception
 {
- public:
+public:
   Exception(const char *msg) : m_msg(msg) {}
   Exception(const std::string &msg) : m_msg(msg) {}
-  const std::string &GetMsg() const { return m_msg; }
- private:
+  const std::string &GetMsg() const {
+    return m_msg;
+  }
+private:
   std::string m_msg;
 };
 
diff --git a/phrase-extract/extract-ghkm/ExtractGHKM.cpp b/phrase-extract/extract-ghkm/ExtractGHKM.cpp
index e3b52943c..80568ccd5 100644
--- a/phrase-extract/extract-ghkm/ExtractGHKM.cpp
+++ b/phrase-extract/extract-ghkm/ExtractGHKM.cpp
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -43,8 +43,10 @@
 #include <sstream>
 #include <vector>
 
-namespace Moses {
-namespace GHKM {
+namespace Moses
+{
+namespace GHKM
+{
 
 int ExtractGHKM::Main(int argc, char *argv[])
 {
@@ -107,7 +109,7 @@ int ExtractGHKM::Main(int argc, char *argv[])
     ++lineNum;
 
     // Parse target tree.
-    if (targetLine.size() == 0) { 
+    if (targetLine.size() == 0) {
       std::cerr << "skipping line " << lineNum << " with empty target tree\n";
       continue;
     }
@@ -263,64 +265,64 @@ void ExtractGHKM::ProcessOptions(int argc, char *argv[],
   // Declare the command line options that are visible to the user.
   po::options_description visible(usageTop.str());
   visible.add_options()
-    //("help", "print this help message and exit")
-    ("AllowUnary",
-        "allow fully non-lexical unary rules")
-    ("ConditionOnTargetLHS",
-        "write target LHS instead of \"X\" as source LHS")
-    ("GlueGrammar",
-        po::value(&options.glueGrammarFile),
-        "write glue grammar to named file")
-    ("GZOutput",
-        "write gzipped extract files")
-    ("MaxNodes",
-        po::value(&options.maxNodes)->default_value(options.maxNodes),
-        "set maximum number of tree nodes for composed rules")
-    ("MaxRuleDepth",
-        po::value(&options.maxRuleDepth)->default_value(options.maxRuleDepth),
-        "set maximum depth for composed rules")
-    ("MaxRuleSize",
-        po::value(&options.maxRuleSize)->default_value(options.maxRuleSize),
-        "set maximum size for composed rules")
-    ("MaxScope",
-        po::value(&options.maxScope)->default_value(options.maxScope),
-        "set maximum allowed scope")
-    ("Minimal",
-        "extract minimal rules only")
-    ("PCFG",
-        "include score based on PCFG scores in target corpus")
-    ("SentenceOffset",
-        po::value(&options.sentenceOffset)->default_value(options.sentenceOffset),
-        "set sentence number offset if processing split corpus")
-    ("UnknownWordLabel",
-        po::value(&options.unknownWordFile),
-        "write unknown word labels to named file")
-    ("UnknownWordMinRelFreq",
-        po::value(&options.unknownWordMinRelFreq)->default_value(
-          options.unknownWordMinRelFreq),
-        "set minimum relative frequency for unknown word labels")
-    ("UnknownWordUniform",
-        "write uniform weights to unknown word label file")
-    ("UnpairedExtractFormat",
-        "do not pair non-terminals in extract files")
+  //("help", "print this help message and exit")
+  ("AllowUnary",
+   "allow fully non-lexical unary rules")
+  ("ConditionOnTargetLHS",
+   "write target LHS instead of \"X\" as source LHS")
+  ("GlueGrammar",
+   po::value(&options.glueGrammarFile),
+   "write glue grammar to named file")
+  ("GZOutput",
+   "write gzipped extract files")
+  ("MaxNodes",
+   po::value(&options.maxNodes)->default_value(options.maxNodes),
+   "set maximum number of tree nodes for composed rules")
+  ("MaxRuleDepth",
+   po::value(&options.maxRuleDepth)->default_value(options.maxRuleDepth),
+   "set maximum depth for composed rules")
+  ("MaxRuleSize",
+   po::value(&options.maxRuleSize)->default_value(options.maxRuleSize),
+   "set maximum size for composed rules")
+  ("MaxScope",
+   po::value(&options.maxScope)->default_value(options.maxScope),
+   "set maximum allowed scope")
+  ("Minimal",
+   "extract minimal rules only")
+  ("PCFG",
+   "include score based on PCFG scores in target corpus")
+  ("SentenceOffset",
+   po::value(&options.sentenceOffset)->default_value(options.sentenceOffset),
+   "set sentence number offset if processing split corpus")
+  ("UnknownWordLabel",
+   po::value(&options.unknownWordFile),
+   "write unknown word labels to named file")
+  ("UnknownWordMinRelFreq",
+   po::value(&options.unknownWordMinRelFreq)->default_value(
+     options.unknownWordMinRelFreq),
+   "set minimum relative frequency for unknown word labels")
+  ("UnknownWordUniform",
+   "write uniform weights to unknown word label file")
+  ("UnpairedExtractFormat",
+   "do not pair non-terminals in extract files")
   ;
 
   // Declare the command line options that are hidden from the user
   // (these are used as positional options).
   po::options_description hidden("Hidden options");
   hidden.add_options()
-    ("TargetFile",
-        po::value(&options.targetFile),
-        "target file")
-    ("SourceFile",
-        po::value(&options.sourceFile),
-        "source file")
-    ("AlignmentFile",
-        po::value(&options.alignmentFile),
-        "alignment file")
-    ("ExtractFile",
-        po::value(&options.extractFile),
-        "extract file")
+  ("TargetFile",
+   po::value(&options.targetFile),
+   "target file")
+  ("SourceFile",
+   po::value(&options.sourceFile),
+   "source file")
+  ("AlignmentFile",
+   po::value(&options.alignmentFile),
+   "alignment file")
+  ("ExtractFile",
+   po::value(&options.extractFile),
+   "extract file")
   ;
 
   // Compose the full set of command-line options.
@@ -337,8 +339,8 @@ void ExtractGHKM::ProcessOptions(int argc, char *argv[],
   // Process the command-line.
   po::variables_map vm;
   const int optionStyle = cls::allow_long
-                        | cls::long_allow_adjacent
-                        | cls::long_allow_next;
+                          | cls::long_allow_adjacent
+                          | cls::long_allow_next;
   try {
     po::store(po::command_line_parser(argc, argv).style(optionStyle).
               options(cmdLineOptions).positional(p).run(), vm);
@@ -424,9 +426,9 @@ std::vector<std::string> ExtractGHKM::ReadTokens(const std::string &s)
 }
 
 void ExtractGHKM::WriteGlueGrammar(
-    const std::set<std::string> &labelSet,
-    const std::map<std::string, int> &topLabelSet,
-    std::ostream &out)
+  const std::set<std::string> &labelSet,
+  const std::map<std::string, int> &topLabelSet,
+  std::ostream &out)
 {
   // chose a top label that is not already a label
   std::string topLabel = "QQQQQQ";
@@ -457,10 +459,10 @@ void ExtractGHKM::WriteGlueGrammar(
 }
 
 void ExtractGHKM::CollectWordLabelCounts(
-    ParseTree &root,
-    const Options &options,
-    std::map<std::string, int> &wordCount,
-    std::map<std::string, std::string> &wordLabel)
+  ParseTree &root,
+  const Options &options,
+  std::map<std::string, int> &wordCount,
+  std::map<std::string, std::string> &wordLabel)
 {
   std::vector<const ParseTree*> leaves;
   root.GetLeaves(std::back_inserter(leaves));
@@ -486,10 +488,10 @@ void ExtractGHKM::CollectWordLabelCounts(
 }
 
 void ExtractGHKM::WriteUnknownWordLabel(
-    const std::map<std::string, int> &wordCount,
-    const std::map<std::string, std::string> &wordLabel,
-    const Options &options,
-    std::ostream &out)
+  const std::map<std::string, int> &wordCount,
+  const std::map<std::string, std::string> &wordLabel,
+  const Options &options,
+  std::ostream &out)
 {
   std::map<std::string, int> labelCount;
   int total = 0;
diff --git a/phrase-extract/extract-ghkm/ExtractGHKM.h b/phrase-extract/extract-ghkm/ExtractGHKM.h
index 6519bf675..c78aea109 100644
--- a/phrase-extract/extract-ghkm/ExtractGHKM.h
+++ b/phrase-extract/extract-ghkm/ExtractGHKM.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -27,22 +27,26 @@
 #include <string>
 #include <vector>
 
-namespace Moses {
+namespace Moses
+{
 
 class OutputFileStream;
 
-namespace GHKM {
+namespace GHKM
+{
 
 struct Options;
 class ParseTree;
 
 class ExtractGHKM
 {
- public:
+public:
   ExtractGHKM() : m_name("extract-ghkm") {}
-  const std::string &GetName() const { return m_name; }
+  const std::string &GetName() const {
+    return m_name;
+  }
   int Main(int argc, char *argv[]);
- private:
+private:
   void Error(const std::string &) const;
   void OpenInputFileOrDie(const std::string &, std::ifstream &);
   void OpenOutputFileOrDie(const std::string &, std::ofstream &);
@@ -60,7 +64,7 @@ class ExtractGHKM
                         const std::map<std::string, int> &,
                         std::ostream &);
   std::vector<std::string> ReadTokens(const std::string &);
-  
+
   void ProcessOptions(int, char *[], Options &) const;
 
   std::string m_name;
diff --git a/phrase-extract/extract-ghkm/Main.cpp b/phrase-extract/extract-ghkm/Main.cpp
index faf3230a6..14064406b 100644
--- a/phrase-extract/extract-ghkm/Main.cpp
+++ b/phrase-extract/extract-ghkm/Main.cpp
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
diff --git a/phrase-extract/extract-ghkm/Node.cpp b/phrase-extract/extract-ghkm/Node.cpp
index beb7470b8..e14d8c050 100644
--- a/phrase-extract/extract-ghkm/Node.cpp
+++ b/phrase-extract/extract-ghkm/Node.cpp
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -21,8 +21,10 @@
 
 #include "Subgraph.h"
 
-namespace Moses {
-namespace GHKM {
+namespace Moses
+{
+namespace GHKM
+{
 
 Node::~Node()
 {
diff --git a/phrase-extract/extract-ghkm/Node.h b/phrase-extract/extract-ghkm/Node.h
index 775473362..2eed01311 100644
--- a/phrase-extract/extract-ghkm/Node.h
+++ b/phrase-extract/extract-ghkm/Node.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -28,8 +28,10 @@
 #include <string>
 #include <vector>
 
-namespace Moses {
-namespace GHKM {
+namespace Moses
+{
+namespace GHKM
+{
 
 class Subgraph;
 
@@ -37,34 +39,68 @@ enum NodeType { SOURCE, TARGET, TREE };
 
 class Node
 {
- public:
+public:
   Node(const std::string &label, NodeType type)
-      : m_label(label)
-      , m_type(type)
-      , m_pcfgScore(0.0f) {}
+    : m_label(label)
+    , m_type(type)
+    , m_pcfgScore(0.0f) {}
 
   ~Node();
 
-  const std::string &GetLabel() const { return m_label; }
-  NodeType GetType() const { return m_type; }
-  const std::vector<Node*> &GetChildren() const { return m_children; }
-  const std::vector<Node*> &GetParents() const { return m_parents; }
-  float GetPcfgScore() const { return m_pcfgScore; }
-  const Span &GetSpan() const { return m_span; }
-  const Span &GetComplementSpan() const { return m_complementSpan; }
-  const std::vector<const Subgraph*> &GetRules() const { return m_rules; }
-
-  void SetChildren(const std::vector<Node*> &c) { m_children = c; }
-  void SetParents(const std::vector<Node*> &p) { m_parents = p; }
-  void SetPcfgScore(float s) { m_pcfgScore = s; }
-  void SetSpan(const Span &s) { m_span = s; }
-  void SetComplementSpan(const Span &cs) { m_complementSpan = cs; }
-
-  void AddChild(Node *c) { m_children.push_back(c); }
-  void AddParent(Node *p) { m_parents.push_back(p); }
-  void AddRule(const Subgraph *s) { m_rules.push_back(s); }
-
-  bool IsSink() const { return m_children.empty(); }
+  const std::string &GetLabel() const {
+    return m_label;
+  }
+  NodeType GetType() const {
+    return m_type;
+  }
+  const std::vector<Node*> &GetChildren() const {
+    return m_children;
+  }
+  const std::vector<Node*> &GetParents() const {
+    return m_parents;
+  }
+  float GetPcfgScore() const {
+    return m_pcfgScore;
+  }
+  const Span &GetSpan() const {
+    return m_span;
+  }
+  const Span &GetComplementSpan() const {
+    return m_complementSpan;
+  }
+  const std::vector<const Subgraph*> &GetRules() const {
+    return m_rules;
+  }
+
+  void SetChildren(const std::vector<Node*> &c) {
+    m_children = c;
+  }
+  void SetParents(const std::vector<Node*> &p) {
+    m_parents = p;
+  }
+  void SetPcfgScore(float s) {
+    m_pcfgScore = s;
+  }
+  void SetSpan(const Span &s) {
+    m_span = s;
+  }
+  void SetComplementSpan(const Span &cs) {
+    m_complementSpan = cs;
+  }
+
+  void AddChild(Node *c) {
+    m_children.push_back(c);
+  }
+  void AddParent(Node *p) {
+    m_parents.push_back(p);
+  }
+  void AddRule(const Subgraph *s) {
+    m_rules.push_back(s);
+  }
+
+  bool IsSink() const {
+    return m_children.empty();
+  }
   bool IsPreterminal() const;
 
   void PropagateIndex(int);
@@ -82,7 +118,7 @@ class Node
   template<typename InputIterator>
   static Node *LowestCommonAncestor(InputIterator first, InputIterator last);
 
- private:
+private:
   // Disallow copying
   Node(const Node &);
   Node &operator=(const Node &);
diff --git a/phrase-extract/extract-ghkm/Options.h b/phrase-extract/extract-ghkm/Options.h
index d348a57d8..e54a9ddae 100644
--- a/phrase-extract/extract-ghkm/Options.h
+++ b/phrase-extract/extract-ghkm/Options.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -23,25 +23,27 @@
 
 #include <string>
 
-namespace Moses {
-namespace GHKM {
+namespace Moses
+{
+namespace GHKM
+{
 
 struct Options {
- public:
+public:
   Options()
-      : allowUnary(false)
-      , conditionOnTargetLhs(false)
-      , gzOutput(false)
-      , maxNodes(15)
-      , maxRuleDepth(3)
-      , maxRuleSize(3)
-      , maxScope(3)
-      , minimal(false)
-      , pcfg(false)
-      , sentenceOffset(0)
-      , unpairedExtractFormat(false)
-      , unknownWordMinRelFreq(0.03f)
-      , unknownWordUniform(false) {}
+    : allowUnary(false)
+    , conditionOnTargetLhs(false)
+    , gzOutput(false)
+    , maxNodes(15)
+    , maxRuleDepth(3)
+    , maxRuleSize(3)
+    , maxScope(3)
+    , minimal(false)
+    , pcfg(false)
+    , sentenceOffset(0)
+    , unpairedExtractFormat(false)
+    , unknownWordMinRelFreq(0.03f)
+    , unknownWordUniform(false) {}
 
   // Positional options
   std::string targetFile;
diff --git a/phrase-extract/extract-ghkm/ParseTree.cpp b/phrase-extract/extract-ghkm/ParseTree.cpp
index 052b8dee1..f86486487 100644
--- a/phrase-extract/extract-ghkm/ParseTree.cpp
+++ b/phrase-extract/extract-ghkm/ParseTree.cpp
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -19,8 +19,10 @@
 
 #include "ParseTree.h"
 
-namespace Moses {
-namespace GHKM {
+namespace Moses
+{
+namespace GHKM
+{
 
 ParseTree::~ParseTree()
 {
diff --git a/phrase-extract/extract-ghkm/ParseTree.h b/phrase-extract/extract-ghkm/ParseTree.h
index 273e2e04e..03da17735 100644
--- a/phrase-extract/extract-ghkm/ParseTree.h
+++ b/phrase-extract/extract-ghkm/ParseTree.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -24,27 +24,39 @@
 #include <string>
 #include <vector>
 
-namespace Moses {
-namespace GHKM {
+namespace Moses
+{
+namespace GHKM
+{
 
 class ParseTree
 {
- public:
+public:
   ParseTree(const std::string &label)
-      : m_label(label)
-      , m_parent(0)
-      , m_pcfgScore(0.0) {}
+    : m_label(label)
+    , m_parent(0)
+    , m_pcfgScore(0.0) {}
 
   ~ParseTree();
 
-  const std::string &GetLabel() const { return m_label; }
-  const std::vector<ParseTree*> &GetChildren() const { return m_children; }
-  const ParseTree *GetParent() const { return m_parent; }
-  float GetPcfgScore() const { return m_pcfgScore; }
+  const std::string &GetLabel() const {
+    return m_label;
+  }
+  const std::vector<ParseTree*> &GetChildren() const {
+    return m_children;
+  }
+  const ParseTree *GetParent() const {
+    return m_parent;
+  }
+  float GetPcfgScore() const {
+    return m_pcfgScore;
+  }
 
   void SetParent(ParseTree *);
   void SetChildren(const std::vector<ParseTree*> &);
-  void SetPcfgScore(float score) { m_pcfgScore = score; }
+  void SetPcfgScore(float score) {
+    m_pcfgScore = score;
+  }
 
   void AddChild(ParseTree *);
 
@@ -53,7 +65,7 @@ class ParseTree
   template<typename OutputIterator>
   void GetLeaves(OutputIterator);
 
- private:
+private:
   // Disallow copying
   ParseTree(const ParseTree &);
   ParseTree &operator=(const ParseTree &);
diff --git a/phrase-extract/extract-ghkm/ScfgRule.cpp b/phrase-extract/extract-ghkm/ScfgRule.cpp
index 5dc70052c..2c901413d 100644
--- a/phrase-extract/extract-ghkm/ScfgRule.cpp
+++ b/phrase-extract/extract-ghkm/ScfgRule.cpp
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -24,13 +24,15 @@
 
 #include <algorithm>
 
-namespace Moses {
-namespace GHKM {
+namespace Moses
+{
+namespace GHKM
+{
 
 ScfgRule::ScfgRule(const Subgraph &fragment)
-    : m_sourceLHS("X", NonTerminal)
-    , m_targetLHS(fragment.GetRoot()->GetLabel(), NonTerminal)
-    , m_pcfgScore(fragment.GetPcfgScore())
+  : m_sourceLHS("X", NonTerminal)
+  , m_targetLHS(fragment.GetRoot()->GetLabel(), NonTerminal)
+  , m_pcfgScore(fragment.GetPcfgScore())
 {
   // Source RHS
 
diff --git a/phrase-extract/extract-ghkm/ScfgRule.h b/phrase-extract/extract-ghkm/ScfgRule.h
index 2405d8fa3..21a9e9900 100644
--- a/phrase-extract/extract-ghkm/ScfgRule.h
+++ b/phrase-extract/extract-ghkm/ScfgRule.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -26,42 +26,59 @@
 #include <string>
 #include <vector>
 
-namespace Moses {
-namespace GHKM {
+namespace Moses
+{
+namespace GHKM
+{
 
 class Node;
 class Subgraph;
 
 enum SymbolType { Terminal, NonTerminal };
 
-struct Symbol
-{
- public:
+struct Symbol {
+public:
   Symbol(const std::string &v, SymbolType t) : m_value(v) , m_type(t) {}
 
-  const std::string &GetValue() const { return m_value; }
-  SymbolType GetType() const { return m_type; }
+  const std::string &GetValue() const {
+    return m_value;
+  }
+  SymbolType GetType() const {
+    return m_type;
+  }
 
- private:
+private:
   std::string m_value;
   SymbolType m_type;
 };
 
 class ScfgRule
 {
- public:
+public:
   ScfgRule(const Subgraph &fragment);
 
-  const Symbol &GetSourceLHS() const { return m_sourceLHS; }
-  const Symbol &GetTargetLHS() const { return m_targetLHS; }
-  const std::vector<Symbol> &GetSourceRHS() const { return m_sourceRHS; }
-  const std::vector<Symbol> &GetTargetRHS() const { return m_targetRHS; }
-  const Alignment &GetAlignment() const { return m_alignment; }
-  float GetPcfgScore() const { return m_pcfgScore; }
+  const Symbol &GetSourceLHS() const {
+    return m_sourceLHS;
+  }
+  const Symbol &GetTargetLHS() const {
+    return m_targetLHS;
+  }
+  const std::vector<Symbol> &GetSourceRHS() const {
+    return m_sourceRHS;
+  }
+  const std::vector<Symbol> &GetTargetRHS() const {
+    return m_targetRHS;
+  }
+  const Alignment &GetAlignment() const {
+    return m_alignment;
+  }
+  float GetPcfgScore() const {
+    return m_pcfgScore;
+  }
 
   int Scope() const;
 
- private:
+private:
   static bool PartitionOrderComp(const Node *, const Node *);
 
   Symbol m_sourceLHS;
diff --git a/phrase-extract/extract-ghkm/ScfgRuleWriter.cpp b/phrase-extract/extract-ghkm/ScfgRuleWriter.cpp
index cd993d6e8..54b3978d1 100644
--- a/phrase-extract/extract-ghkm/ScfgRuleWriter.cpp
+++ b/phrase-extract/extract-ghkm/ScfgRuleWriter.cpp
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -30,8 +30,10 @@
 #include <sstream>
 #include <vector>
 
-namespace Moses {
-namespace GHKM {
+namespace Moses
+{
+namespace GHKM
+{
 
 void ScfgRuleWriter::Write(const ScfgRule &rule)
 {
@@ -70,8 +72,8 @@ void ScfgRuleWriter::Write(const ScfgRule &rule)
 }
 
 void ScfgRuleWriter::WriteStandardFormat(const ScfgRule &rule,
-                                         std::ostream &sourceSS,
-                                         std::ostream &targetSS)
+    std::ostream &sourceSS,
+    std::ostream &targetSS)
 {
   const std::vector<Symbol> &sourceRHS = rule.GetSourceRHS();
   const std::vector<Symbol> &targetRHS = rule.GetTargetRHS();
@@ -122,8 +124,8 @@ void ScfgRuleWriter::WriteStandardFormat(const ScfgRule &rule,
 }
 
 void ScfgRuleWriter::WriteUnpairedFormat(const ScfgRule &rule,
-                                         std::ostream &sourceSS,
-                                         std::ostream &targetSS)
+    std::ostream &sourceSS,
+    std::ostream &targetSS)
 {
   const std::vector<Symbol> &sourceRHS = rule.GetSourceRHS();
   const std::vector<Symbol> &targetRHS = rule.GetTargetRHS();
diff --git a/phrase-extract/extract-ghkm/ScfgRuleWriter.h b/phrase-extract/extract-ghkm/ScfgRuleWriter.h
index b92a432a1..ee29e49e5 100644
--- a/phrase-extract/extract-ghkm/ScfgRuleWriter.h
+++ b/phrase-extract/extract-ghkm/ScfgRuleWriter.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -23,8 +23,10 @@
 
 #include <ostream>
 
-namespace Moses {
-namespace GHKM {
+namespace Moses
+{
+namespace GHKM
+{
 
 struct Options;
 class ScfgRule;
@@ -32,15 +34,15 @@ struct Symbol;
 
 class ScfgRuleWriter
 {
- public:
+public:
   ScfgRuleWriter(std::ostream &fwd, std::ostream &inv, const Options &options)
-      : m_fwd(fwd)
-      , m_inv(inv)
-      , m_options(options) {}
+    : m_fwd(fwd)
+    , m_inv(inv)
+    , m_options(options) {}
 
   void Write(const ScfgRule &);
 
- private:
+private:
   // Disallow copying
   ScfgRuleWriter(const ScfgRuleWriter &);
   ScfgRuleWriter &operator=(const ScfgRuleWriter &);
diff --git a/phrase-extract/extract-ghkm/Span.cpp b/phrase-extract/extract-ghkm/Span.cpp
index f0eccbdf2..d637ec3d2 100644
--- a/phrase-extract/extract-ghkm/Span.cpp
+++ b/phrase-extract/extract-ghkm/Span.cpp
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -19,8 +19,10 @@
 
 #include "Span.h"
 
-namespace Moses {
-namespace GHKM {
+namespace Moses
+{
+namespace GHKM
+{
 
 bool SpansIntersect(const Span &a, const ContiguousSpan &b)
 {
diff --git a/phrase-extract/extract-ghkm/Span.h b/phrase-extract/extract-ghkm/Span.h
index 003d1ef84..c4d146c4e 100644
--- a/phrase-extract/extract-ghkm/Span.h
+++ b/phrase-extract/extract-ghkm/Span.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -24,8 +24,10 @@
 #include <map>
 #include <set>
 
-namespace Moses {
-namespace GHKM {
+namespace Moses
+{
+namespace GHKM
+{
 
 typedef std::set<int> Span;
 typedef std::pair<int, int> ContiguousSpan;
diff --git a/phrase-extract/extract-ghkm/Subgraph.cpp b/phrase-extract/extract-ghkm/Subgraph.cpp
index e048f2c55..3c0503010 100644
--- a/phrase-extract/extract-ghkm/Subgraph.cpp
+++ b/phrase-extract/extract-ghkm/Subgraph.cpp
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -21,8 +21,10 @@
 
 #include "Node.h"
 
-namespace Moses {
-namespace GHKM {
+namespace Moses
+{
+namespace GHKM
+{
 
 void Subgraph::GetTargetLeaves(std::vector<const Node *> &result) const
 {
diff --git a/phrase-extract/extract-ghkm/Subgraph.h b/phrase-extract/extract-ghkm/Subgraph.h
index ede1233e9..f4d1e0c8d 100644
--- a/phrase-extract/extract-ghkm/Subgraph.h
+++ b/phrase-extract/extract-ghkm/Subgraph.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -26,47 +26,62 @@
 #include <set>
 #include <vector>
 
-namespace Moses {
-namespace GHKM {
+namespace Moses
+{
+namespace GHKM
+{
 
 class Node;
 
 class Subgraph
 {
- public:
+public:
   Subgraph(const Node *root)
-      : m_root(root)
-      , m_depth(0)
-      , m_size(root->GetType() == TREE ? 1 : 0)
-      , m_nodeCount(1)
-      , m_pcfgScore(0.0f) {}
+    : m_root(root)
+    , m_depth(0)
+    , m_size(root->GetType() == TREE ? 1 : 0)
+    , m_nodeCount(1)
+    , m_pcfgScore(0.0f) {}
 
   Subgraph(const Node *root, const std::set<const Node *> &leaves)
-      : m_root(root)
-      , m_leaves(leaves)
-      , m_depth(-1)
-      , m_size(-1)
-      , m_nodeCount(-1)
-      , m_pcfgScore(0.0f)
-  {
+    : m_root(root)
+    , m_leaves(leaves)
+    , m_depth(-1)
+    , m_size(-1)
+    , m_nodeCount(-1)
+    , m_pcfgScore(0.0f) {
     m_depth = CalcDepth(m_root);
     m_size = CalcSize(m_root);
     m_nodeCount = CountNodes(m_root);
     m_pcfgScore = CalcPcfgScore();
   }
 
-  const Node *GetRoot() const { return m_root; }
-  const std::set<const Node *> &GetLeaves() const { return m_leaves; }
-  int GetDepth() const { return m_depth; }
-  int GetSize() const { return m_size; }
-  int GetNodeCount() const { return m_nodeCount; }
-  float GetPcfgScore() const { return m_pcfgScore; }
+  const Node *GetRoot() const {
+    return m_root;
+  }
+  const std::set<const Node *> &GetLeaves() const {
+    return m_leaves;
+  }
+  int GetDepth() const {
+    return m_depth;
+  }
+  int GetSize() const {
+    return m_size;
+  }
+  int GetNodeCount() const {
+    return m_nodeCount;
+  }
+  float GetPcfgScore() const {
+    return m_pcfgScore;
+  }
 
-  bool IsTrivial() const { return m_leaves.empty(); }
+  bool IsTrivial() const {
+    return m_leaves.empty();
+  }
 
   void GetTargetLeaves(std::vector<const Node *> &) const;
 
- private:
+private:
   void GetTargetLeaves(const Node *, std::vector<const Node *> &) const;
   int CalcDepth(const Node *) const;
   int CalcSize(const Node *) const;
diff --git a/phrase-extract/extract-ghkm/XmlTreeParser.cpp b/phrase-extract/extract-ghkm/XmlTreeParser.cpp
index 66024ff01..2f28c3244 100644
--- a/phrase-extract/extract-ghkm/XmlTreeParser.cpp
+++ b/phrase-extract/extract-ghkm/XmlTreeParser.cpp
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -29,13 +29,15 @@
 
 using namespace MosesTraining;
 
-namespace Moses {
-namespace GHKM {
+namespace Moses
+{
+namespace GHKM
+{
 
 XmlTreeParser::XmlTreeParser(std::set<std::string> &labelSet,
                              std::map<std::string, int> &topLabelSet)
-    : m_labelSet(labelSet)
-    , m_topLabelSet(topLabelSet)
+  : m_labelSet(labelSet)
+  , m_topLabelSet(topLabelSet)
 {
 }
 
@@ -60,8 +62,8 @@ std::auto_ptr<ParseTree> XmlTreeParser::Parse(const std::string &line)
 
 // Converts a SyntaxNode tree to a Moses::GHKM::ParseTree.
 std::auto_ptr<ParseTree> XmlTreeParser::ConvertTree(
-    const SyntaxNode &tree,
-    const std::vector<std::string> &words)
+  const SyntaxNode &tree,
+  const std::vector<std::string> &words)
 {
   std::auto_ptr<ParseTree> root(new ParseTree(tree.GetLabel()));
   root->SetPcfgScore(tree.GetPcfgScore());
diff --git a/phrase-extract/extract-ghkm/XmlTreeParser.h b/phrase-extract/extract-ghkm/XmlTreeParser.h
index 7b63ae1e4..d00fd7d9f 100644
--- a/phrase-extract/extract-ghkm/XmlTreeParser.h
+++ b/phrase-extract/extract-ghkm/XmlTreeParser.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2011 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -31,18 +31,21 @@
 #include <string>
 #include <vector>
 
-namespace Moses {
-namespace GHKM {
+namespace Moses
+{
+namespace GHKM
+{
 
 class ParseTree;
 
 // Parses a string in Moses' XML parse tree format and returns a ParseTree
 // object.
-class XmlTreeParser {
- public:
+class XmlTreeParser
+{
+public:
   XmlTreeParser(std::set<std::string> &, std::map<std::string, int> &);
   std::auto_ptr<ParseTree> Parse(const std::string &);
- private:
+private:
   std::auto_ptr<ParseTree> ConvertTree(const MosesTraining::SyntaxNode &,
                                        const std::vector<std::string> &);
 
diff --git a/phrase-extract/extract-lex-main.cpp b/phrase-extract/extract-lex-main.cpp
index a59450da8..f63015a6a 100644
--- a/phrase-extract/extract-lex-main.cpp
+++ b/phrase-extract/extract-lex-main.cpp
@@ -10,16 +10,16 @@ using namespace MosesTraining;
 
 float COUNT_INCR = 1;
 
-void fix(std::ostream& stream) 
+void fix(std::ostream& stream)
 {
-    stream.setf(std::ios::fixed);
-    stream.precision(7);
+  stream.setf(std::ios::fixed);
+  stream.precision(7);
 }
 
 int main(int argc, char* argv[])
 {
   cerr << "Starting...\n";
-  
+
   assert(argc == 6);
   char* &filePathTarget = argv[1];
   char* &filePathSource = argv[2];
@@ -43,8 +43,7 @@ int main(int argc, char* argv[])
 
   size_t lineCount = 0;
   string lineTarget, lineSource, lineAlign;
-  while (getline(streamTarget, lineTarget))
-  {
+  while (getline(streamTarget, lineTarget)) {
     if (lineCount % 10000 == 0)
       cerr << lineCount << " ";
 
@@ -52,7 +51,7 @@ int main(int argc, char* argv[])
     assert(isSource);
     istream &isAlign = getline(streamAlign, lineAlign);
     assert(isAlign);
-    
+
     vector<string> toksTarget, toksSource, toksAlign;
     Tokenize(toksTarget, lineTarget);
     Tokenize(toksSource, lineSource);
@@ -61,13 +60,13 @@ int main(int argc, char* argv[])
     /*
     cerr  << endl
           << toksTarget.size() << " " << lineTarget << endl
-          << toksSource.size() << " " << lineSource << endl 
+          << toksSource.size() << " " << lineSource << endl
           << toksAlign.size() << " " << lineAlign << endl;
     */
 
     extractSingleton.Process(toksTarget, toksSource, toksAlign, lineCount);
-   
-    ++lineCount; 
+
+    ++lineCount;
   }
 
   extractSingleton.Output(streamLexS2T, streamLexT2S);
@@ -86,35 +85,32 @@ namespace MosesTraining
 
 const std::string *Vocab::GetOrAdd(const std::string &word)
 {
- 	const string *ret = &(*m_coll.insert(word).first);
+  const string *ret = &(*m_coll.insert(word).first);
   return ret;
 }
 
 void ExtractLex::Process(vector<string> &toksTarget, vector<string> &toksSource, vector<string> &toksAlign, size_t lineCount)
 {
   std::vector<bool> m_sourceAligned(toksSource.size(), false)
-                    , m_targetAligned(toksTarget.size(), false);
+  , m_targetAligned(toksTarget.size(), false);
 
   vector<string>::const_iterator iterAlign;
-  for (iterAlign = toksAlign.begin(); iterAlign != toksAlign.end(); ++iterAlign)
-  {
+  for (iterAlign = toksAlign.begin(); iterAlign != toksAlign.end(); ++iterAlign) {
     const string &alignTok = *iterAlign;
-    
+
     vector<size_t> alignPos;
     Tokenize(alignPos, alignTok, "-");
     assert(alignPos.size() == 2);
 
-	if (alignPos[0] >= toksSource.size())
-	{
-		cerr << "ERROR: alignment over source length. Alignment " << alignPos[0] << " at line " << lineCount << endl;
-		continue;
-	}
-	if (alignPos[1] >= toksTarget.size())
-	{
-		cerr << "ERROR: alignment over target length. Alignment " << alignPos[1] << " at line " << lineCount << endl;
-		continue;
-	}
-	
+    if (alignPos[0] >= toksSource.size()) {
+      cerr << "ERROR: alignment over source length. Alignment " << alignPos[0] << " at line " << lineCount << endl;
+      continue;
+    }
+    if (alignPos[1] >= toksTarget.size()) {
+      cerr << "ERROR: alignment over target length. Alignment " << alignPos[1] << " at line " << lineCount << endl;
+      continue;
+    }
+
     assert(alignPos[0] < toksSource.size());
     assert(alignPos[1] < toksTarget.size());
 
@@ -123,12 +119,12 @@ void ExtractLex::Process(vector<string> &toksTarget, vector<string> &toksSource,
 
     const string &tmpSource = toksSource[ alignPos[0] ];
     const string &tmpTarget = toksTarget[ alignPos[1] ];
- 
+
     const string *source = m_vocab.GetOrAdd(tmpSource);
     const string *target = m_vocab.GetOrAdd(tmpTarget);
 
     Process(target, source);
-    
+
   }
 
   ProcessUnaligned(toksTarget, toksSource, m_sourceAligned, m_targetAligned);
@@ -154,15 +150,13 @@ void ExtractLex::Process(WordCount &wcIn, const std::string *out)
 }
 
 void ExtractLex::ProcessUnaligned(vector<string> &toksTarget, vector<string> &toksSource
-                                , const std::vector<bool> &m_sourceAligned, const std::vector<bool> &m_targetAligned)
+                                  , const std::vector<bool> &m_sourceAligned, const std::vector<bool> &m_targetAligned)
 {
-  const string *nullWord = m_vocab.GetOrAdd("NULL"); 
+  const string *nullWord = m_vocab.GetOrAdd("NULL");
 
-  for (size_t pos = 0; pos < m_sourceAligned.size(); ++pos)
-  {
+  for (size_t pos = 0; pos < m_sourceAligned.size(); ++pos) {
     bool isAlignedCurr = m_sourceAligned[pos];
-    if (!isAlignedCurr)
-    {
+    if (!isAlignedCurr) {
       const string &tmpWord = toksSource[pos];
       const string *sourceWord = m_vocab.GetOrAdd(tmpWord);
 
@@ -170,11 +164,9 @@ void ExtractLex::ProcessUnaligned(vector<string> &toksTarget, vector<string> &to
     }
   }
 
-  for (size_t pos = 0; pos < m_targetAligned.size(); ++pos)
-  {
+  for (size_t pos = 0; pos < m_targetAligned.size(); ++pos) {
     bool isAlignedCurr = m_targetAligned[pos];
-    if (!isAlignedCurr)
-    {
+    if (!isAlignedCurr) {
       const string &tmpWord = toksTarget[pos];
       const string *targetWord = m_vocab.GetOrAdd(tmpWord);
 
@@ -193,16 +185,14 @@ void ExtractLex::Output(std::ofstream &streamLexS2T, std::ofstream &streamLexT2S
 void ExtractLex::Output(const std::map<const std::string*, WordCount> &coll, std::ofstream &outStream)
 {
   std::map<const std::string*, WordCount>::const_iterator iterOuter;
-  for (iterOuter = coll.begin(); iterOuter != coll.end(); ++iterOuter)
-  {
+  for (iterOuter = coll.begin(); iterOuter != coll.end(); ++iterOuter) {
     const string &inStr = *iterOuter->first;
     const WordCount &inWC = iterOuter->second;
 
     const std::map<const std::string*, WordCount> &outColl = inWC.GetColl();
 
     std::map<const std::string*, WordCount>::const_iterator iterInner;
-    for (iterInner = outColl.begin(); iterInner != outColl.end(); ++iterInner)
-    {
+    for (iterInner = outColl.begin(); iterInner != outColl.end(); ++iterInner) {
       const string &outStr = *iterInner->first;
       const WordCount &outWC = iterInner->second;
 
diff --git a/phrase-extract/extract-lex.h b/phrase-extract/extract-lex.h
index d272cf6ff..d79038fc6 100644
--- a/phrase-extract/extract-lex.h
+++ b/phrase-extract/extract-lex.h
@@ -14,10 +14,10 @@ namespace MosesTraining
 template<typename T>
 inline T Scan(const std::string &input)
 {
-	std::stringstream stream(input);
-	T ret;
-	stream >> ret;
-	return ret;
+  std::stringstream stream(input);
+  T ret;
+  stream >> ret;
+  return ret;
 }
 
 
@@ -25,13 +25,12 @@ inline T Scan(const std::string &input)
 template<typename T>
 inline void Scan(std::vector<T> &output, const std::vector< std::string > &input)
 {
-	output.resize(input.size());
-	for (size_t i = 0 ; i < input.size() ; i++)
-	{
-		output[i] = Scan<T>( input[i] );
-	}
+  output.resize(input.size());
+  for (size_t i = 0 ; i < input.size() ; i++) {
+    output[i] = Scan<T>( input[i] );
+  }
 }
-	
+
 
 inline void Tokenize(std::vector<std::string> &output
                      , const std::string& str
@@ -55,17 +54,17 @@ inline void Tokenize(std::vector<std::string> &output
 // speeded up version of above
 template<typename T>
 inline void Tokenize( std::vector<T> &output
-										 , const std::string &input
-										 , const std::string& delimiters = " \t")
+                      , const std::string &input
+                      , const std::string& delimiters = " \t")
 {
-	std::vector<std::string> stringVector;
-	Tokenize(stringVector, input, delimiters);
-	return Scan<T>(output, stringVector );
+  std::vector<std::string> stringVector;
+  Tokenize(stringVector, input, delimiters);
+  return Scan<T>(output, stringVector );
 }
 
 class WordCount
 {
-	friend std::ostream& operator<<(std::ostream&, const WordCount&);
+  friend std::ostream& operator<<(std::ostream&, const WordCount&);
 public:
   float m_count;
 
@@ -83,13 +82,16 @@ public:
 
   void AddCount(float incr);
 
-  std::map<const std::string*, WordCount> &GetColl()
-  { return m_coll; }
-  const std::map<const std::string*, WordCount> &GetColl() const
-  { return m_coll; }
+  std::map<const std::string*, WordCount> &GetColl() {
+    return m_coll;
+  }
+  const std::map<const std::string*, WordCount> &GetColl() const {
+    return m_coll;
+  }
 
-  const float GetCount() const
-  { return m_count; }
+  const float GetCount() const {
+    return m_count;
+  }
 
 };
 
diff --git a/phrase-extract/extract-main.cpp b/phrase-extract/extract-main.cpp
index cab91e92d..a8edb298a 100644
--- a/phrase-extract/extract-main.cpp
+++ b/phrase-extract/extract-main.cpp
@@ -29,7 +29,8 @@
 using namespace std;
 using namespace MosesTraining;
 
-namespace MosesTraining {
+namespace MosesTraining
+{
 
 
 const long int LINE_MAX_LENGTH = 500000 ;
@@ -49,37 +50,38 @@ typedef vector < HPhrase > HPhraseVector;
 // The key of the map is the English index and the value is a set of the source ones
 typedef map <int, set<int> > HSentenceVertices;
 
-  REO_POS getOrientWordModel(SentenceAlignment &, REO_MODEL_TYPE, bool, bool,
+REO_POS getOrientWordModel(SentenceAlignment &, REO_MODEL_TYPE, bool, bool,
                            int, int, int, int, int, int, int,
                            bool (*)(int, int), bool (*)(int, int));
-  REO_POS getOrientPhraseModel(SentenceAlignment &, REO_MODEL_TYPE, bool, bool,
+REO_POS getOrientPhraseModel(SentenceAlignment &, REO_MODEL_TYPE, bool, bool,
                              int, int, int, int, int, int, int,
                              bool (*)(int, int), bool (*)(int, int),
                              const HSentenceVertices &, const HSentenceVertices &);
-  REO_POS getOrientHierModel(SentenceAlignment &, REO_MODEL_TYPE, bool, bool,
+REO_POS getOrientHierModel(SentenceAlignment &, REO_MODEL_TYPE, bool, bool,
                            int, int, int, int, int, int, int,
                            bool (*)(int, int), bool (*)(int, int),
                            const HSentenceVertices &, const HSentenceVertices &,
                            const HSentenceVertices &, const HSentenceVertices &,
                            REO_POS);
 
-  void insertVertex(HSentenceVertices &, int, int);
-  void insertPhraseVertices(HSentenceVertices &, HSentenceVertices &, HSentenceVertices &, HSentenceVertices &,
+void insertVertex(HSentenceVertices &, int, int);
+void insertPhraseVertices(HSentenceVertices &, HSentenceVertices &, HSentenceVertices &, HSentenceVertices &,
                           int, int, int, int);
-  string getOrientString(REO_POS, REO_MODEL_TYPE);
+string getOrientString(REO_POS, REO_MODEL_TYPE);
 
-  bool ge(int, int);
-  bool le(int, int);
-  bool lt(int, int);
+bool ge(int, int);
+bool le(int, int);
+bool lt(int, int);
 
-  bool isAligned (SentenceAlignment &, int, int);
-  int sentenceOffset = 0;
+bool isAligned (SentenceAlignment &, int, int);
+int sentenceOffset = 0;
 
 }
 
-namespace MosesTraining{
+namespace MosesTraining
+{
 
-class ExtractTask 
+class ExtractTask
 {
 public:
   ExtractTask(size_t id, SentenceAlignment &sentence,PhraseExtractionOptions &initoptions, Moses::OutputFileStream &extractFile, Moses::OutputFileStream &extractFileInv,Moses::OutputFileStream &extractFileOrientation):
@@ -87,8 +89,8 @@ public:
     m_options(initoptions),
     m_extractFile(extractFile),
     m_extractFileInv(extractFileInv),
-    m_extractFileOrientation(extractFileOrientation){}
-void Run();
+    m_extractFileOrientation(extractFileOrientation) {}
+  void Run();
 private:
   vector< string > m_extractedPhrases;
   vector< string > m_extractedPhrasesInv;
@@ -98,7 +100,7 @@ private:
   void extract(SentenceAlignment &);
   void addPhrase(SentenceAlignment &, int, int, int, int, string &);
   void writePhrasesToFile();
-  
+
   SentenceAlignment &m_sentence;
   const PhraseExtractionOptions &m_options;
   Moses::OutputFileStream &m_extractFile;
@@ -112,7 +114,7 @@ int main(int argc, char* argv[])
   cerr	<< "PhraseExtract v1.4, written by Philipp Koehn\n"
         << "phrase extraction from an aligned parallel corpus\n";
 
- if (argc < 6) {
+  if (argc < 6) {
     cerr << "syntax: extract en de align extract max-length [orientation [ --model [wbe|phrase|hier]-[msd|mslr|mono] ] ";
     cerr<<"| --OnlyOutputSpanInfo | --NoTTable | --GZOutput | --IncludeSentenceId | --SentenceOffset n | --InstanceWeights filename ]\n";
     exit(1);
@@ -135,7 +137,7 @@ int main(int argc, char* argv[])
     } else if (strcmp(argv[i],"--NoTTable") == 0) {
       options.initTranslationFlag(false);
     } else if (strcmp(argv[i], "--IncludeSentenceId") == 0) {
-      options.initIncludeSentenceIdFlag(true);  
+      options.initIncludeSentenceIdFlag(true);
     } else if (strcmp(argv[i], "--SentenceOffset") == 0) {
       if (i+1 >= argc || argv[i+1][0] < '0' || argv[i+1][0] > '9') {
         cerr << "extract: syntax error, used switch --SentenceOffset without a number" << endl;
@@ -143,7 +145,7 @@ int main(int argc, char* argv[])
       }
       sentenceOffset = atoi(argv[++i]);
     } else if (strcmp(argv[i], "--GZOutput") == 0) {
-      options.initGzOutput(true);  
+      options.initGzOutput(true);
     } else if (strcmp(argv[i], "--InstanceWeights") == 0) {
       if (i+1 >= argc) {
         cerr << "extract: syntax error, used switch --InstanceWeights without file name" << endl;
@@ -260,7 +262,7 @@ int main(int argc, char* argv[])
       SAFE_GETLINE((*iwFileP), weightString, LINE_MAX_LENGTH, '\n', __FILE__);
     }
     SentenceAlignment sentence;
-	// cout << "read in: " << englishString << " & " << foreignString << " & " << alignmentString << endl;
+    // cout << "read in: " << englishString << " & " << foreignString << " & " << alignmentString << endl;
     //az: output src, tgt, and alingment line
     if (options.isOnlyOutputSpanInfo()) {
       cout << "LOG: SRC: " << foreignString << endl;
@@ -268,8 +270,8 @@ int main(int argc, char* argv[])
       cout << "LOG: ALT: " << alignmentString << endl;
       cout << "LOG: PHRASES_BEGIN:" << endl;
     }
-	if (sentence.create( englishString, foreignString, alignmentString, weightString, i, false)) {
-   	ExtractTask *task = new ExtractTask(i-1, sentence, options, extractFile , extractFileInv, extractFileOrientation);
+    if (sentence.create( englishString, foreignString, alignmentString, weightString, i, false)) {
+      ExtractTask *task = new ExtractTask(i-1, sentence, options, extractFile , extractFileInv, extractFileOrientation);
       task->Run();
       delete task;
 
@@ -286,17 +288,18 @@ int main(int argc, char* argv[])
     if (options.isTranslationFlag()) {
       extractFile.Close();
       extractFileInv.Close();
-      
+
+    }
+    if (options.isOrientationFlag()) {
+      extractFileOrientation.Close();
     }
-    if (options.isOrientationFlag()){ 
-	extractFileOrientation.Close();
-	}
   }
 }
 
 namespace MosesTraining
 {
-void ExtractTask::Run() {
+void ExtractTask::Run()
+{
   extract(m_sentence);
   writePhrasesToFile();
   m_extractedPhrases.clear();
@@ -665,16 +668,16 @@ void ExtractTask::addPhrase( SentenceAlignment &sentence, int startE, int endE,
 {
   // source
   //   // cout << "adding ( " << startF << "-" << endF << ", " << startE << "-" << endE << ")\n";
-  	ostringstream outextractstr;
-  	ostringstream outextractstrInv;
-  	ostringstream outextractstrOrientation;
+  ostringstream outextractstr;
+  ostringstream outextractstrInv;
+  ostringstream outextractstrOrientation;
 
   if (m_options.isOnlyOutputSpanInfo()) {
     cout << startF << " " << endF << " " << startE << " " << endE << endl;
     return;
   }
 
-for(int fi=startF; fi<=endF; fi++) {
+  for(int fi=startF; fi<=endF; fi++) {
     if (m_options.isTranslationFlag()) outextractstr << sentence.source[fi] << " ";
     if (m_options.isOrientationFlag()) outextractstrOrientation << sentence.source[fi] << " ";
   }
@@ -693,13 +696,13 @@ for(int fi=startF; fi<=endF; fi++) {
 
   // source (for inverse)
 
- if (m_options.isTranslationFlag()) {
+  if (m_options.isTranslationFlag()) {
     for(int fi=startF; fi<=endF; fi++)
       outextractstrInv << sentence.source[fi] << " ";
     outextractstrInv << "|||";
   }
   // alignment
- if (m_options.isTranslationFlag()) {
+  if (m_options.isTranslationFlag()) {
     for(int ei=startE; ei<=endE; ei++) {
       for(unsigned int i=0; i<sentence.alignedToT[ei].size(); i++) {
         int fi = sentence.alignedToT[ei][i];
@@ -732,39 +735,40 @@ for(int fi=startF; fi<=endF; fi++) {
   if (m_options.isOrientationFlag()) outextractstrOrientation << "\n";
 
 
-    m_extractedPhrases.push_back(outextractstr.str());
-    m_extractedPhrasesInv.push_back(outextractstrInv.str());
-    m_extractedPhrasesOri.push_back(outextractstrOrientation.str());
+  m_extractedPhrases.push_back(outextractstr.str());
+  m_extractedPhrasesInv.push_back(outextractstrInv.str());
+  m_extractedPhrasesOri.push_back(outextractstrOrientation.str());
 }
 
 
-void ExtractTask::writePhrasesToFile(){
+void ExtractTask::writePhrasesToFile()
+{
 
-    ostringstream outextractFile;
-    ostringstream outextractFileInv;
-    ostringstream outextractFileOrientation;
+  ostringstream outextractFile;
+  ostringstream outextractFileInv;
+  ostringstream outextractFileOrientation;
 
-    for(vector<string>::const_iterator phrase=m_extractedPhrases.begin();phrase!=m_extractedPhrases.end();phrase++){
-        outextractFile<<phrase->data();
-    }
-    for(vector<string>::const_iterator phrase=m_extractedPhrasesInv.begin();phrase!=m_extractedPhrasesInv.end();phrase++){
-        outextractFileInv<<phrase->data();
-    }
-    for(vector<string>::const_iterator phrase=m_extractedPhrasesOri.begin();phrase!=m_extractedPhrasesOri.end();phrase++){
-        outextractFileOrientation<<phrase->data();
-    }
+  for(vector<string>::const_iterator phrase=m_extractedPhrases.begin(); phrase!=m_extractedPhrases.end(); phrase++) {
+    outextractFile<<phrase->data();
+  }
+  for(vector<string>::const_iterator phrase=m_extractedPhrasesInv.begin(); phrase!=m_extractedPhrasesInv.end(); phrase++) {
+    outextractFileInv<<phrase->data();
+  }
+  for(vector<string>::const_iterator phrase=m_extractedPhrasesOri.begin(); phrase!=m_extractedPhrasesOri.end(); phrase++) {
+    outextractFileOrientation<<phrase->data();
+  }
 
-      m_extractFile << outextractFile.str();
-      m_extractFileInv  << outextractFileInv.str();
-      m_extractFileOrientation << outextractFileOrientation.str();
+  m_extractFile << outextractFile.str();
+  m_extractFileInv  << outextractFileInv.str();
+  m_extractFileOrientation << outextractFileOrientation.str();
 }
 
 // if proper conditioning, we need the number of times a source phrase occured
 
 void ExtractTask::extractBase( SentenceAlignment &sentence )
 {
-    ostringstream outextractFile;
-    ostringstream outextractFileInv;
+  ostringstream outextractFile;
+  ostringstream outextractFileInv;
 
   int countF = sentence.source.size();
   for(int startF=0; startF<countF; startF++) {
@@ -772,8 +776,8 @@ void ExtractTask::extractBase( SentenceAlignment &sentence )
         (endF<countF && endF<startF+m_options.maxPhraseLength);
         endF++) {
       for(int fi=startF; fi<=endF; fi++) {
-         outextractFile << sentence.source[fi] << " ";
-	}
+        outextractFile << sentence.source[fi] << " ";
+      }
       outextractFile << "|||" << endl;
     }
   }
@@ -789,8 +793,8 @@ void ExtractTask::extractBase( SentenceAlignment &sentence )
       outextractFileInv << "|||" << endl;
     }
   }
-    m_extractFile << outextractFile.str();
-    m_extractFileInv << outextractFileInv.str();
+  m_extractFile << outextractFile.str();
+  m_extractFileInv << outextractFileInv.str();
 
 }
 
diff --git a/phrase-extract/extract-rules-main.cpp b/phrase-extract/extract-rules-main.cpp
index 368aae1f5..f8e315e2c 100644
--- a/phrase-extract/extract-rules-main.cpp
+++ b/phrase-extract/extract-rules-main.cpp
@@ -55,7 +55,7 @@ using namespace MosesTraining;
 typedef vector< int > LabelIndex;
 typedef map< int, int > WordIndex;
 
-class ExtractTask 
+class ExtractTask
 {
 private:
   SentenceAlignmentWithSyntax &m_sentence;
@@ -64,31 +64,30 @@ private:
   Moses::OutputFileStream& m_extractFileInv;
 
   vector< ExtractedRule > m_extractedRules;
-  
+
   // main functions
   void extractRules();
   void addRuleToCollection(ExtractedRule &rule);
   void consolidateRules();
   void writeRulesToFile();
-  
+
   // subs
   void addRule( int, int, int, int, int, RuleExist &ruleExist);
   void addHieroRule( int startT, int endT, int startS, int endS
-                    , RuleExist &ruleExist, HoleCollection &holeColl, int numHoles, int initStartF, int wordCountT, int wordCountS);
+                     , RuleExist &ruleExist, HoleCollection &holeColl, int numHoles, int initStartF, int wordCountT, int wordCountS);
   void saveHieroPhrase( int startT, int endT, int startS, int endS
                         , HoleCollection &holeColl, LabelIndex &labelIndex, int countS);
   string saveTargetHieroPhrase(  int startT, int endT, int startS, int endS
-                                , WordIndex &indexT, HoleCollection &holeColl, const LabelIndex &labelIndex, double &logPCFGScore, int countS);
+                                 , WordIndex &indexT, HoleCollection &holeColl, const LabelIndex &labelIndex, double &logPCFGScore, int countS);
   string saveSourceHieroPhrase( int startT, int endT, int startS, int endS
                                 , HoleCollection &holeColl, const LabelIndex &labelIndex);
   void preprocessSourceHieroPhrase( int startT, int endT, int startS, int endS
-                                   , WordIndex &indexS, HoleCollection &holeColl, const LabelIndex &labelIndex);
+                                    , WordIndex &indexS, HoleCollection &holeColl, const LabelIndex &labelIndex);
   void saveHieroAlignment(  int startT, int endT, int startS, int endS
-                           , const WordIndex &indexS, const WordIndex &indexT, HoleCollection &holeColl, ExtractedRule &rule);
+                            , const WordIndex &indexS, const WordIndex &indexT, HoleCollection &holeColl, ExtractedRule &rule);
   void saveAllHieroPhrases( int startT, int endT, int startS, int endS, HoleCollection &holeColl, int countS);
-  
-  inline string IntToString( int i )
-  {
+
+  inline string IntToString( int i ) {
     stringstream out;
     out << i;
     return out.str();
@@ -123,7 +122,7 @@ int main(int argc, char* argv[])
   if (argc < 5) {
     cerr << "syntax: extract-rules corpus.target corpus.source corpus.align extract ["
 
-    << " --GlueGrammar FILE"
+         << " --GlueGrammar FILE"
          << " | --UnknownWordLabel FILE"
          << " | --OnlyDirect"
          << " | --OutputNTLengths"
@@ -139,8 +138,8 @@ int main(int argc, char* argv[])
          << " | --AllowOnlyUnalignedWords | --DisallowNonTermConsecTarget |--NonTermConsecSource |  --NoNonTermFirstWord | --NoFractionalCounting"
          << " | --UnpairedExtractFormat"
          << " | --ConditionOnTargetLHS ]"
-        << " | --BoundaryRules[" << options.boundaryRules << "]";
-    
+         << " | --BoundaryRules[" << options.boundaryRules << "]";
+
     exit(1);
   }
   char* &fileNameT = argv[1];
@@ -212,10 +211,9 @@ int main(int argc, char* argv[])
         cerr << "extract error: --MaxScope should be at least 0" << endl;
         exit(1);
       }
+    } else if (strcmp(argv[i], "--GZOutput") == 0) {
+      options.gzOutput = true;
     }
-    else if (strcmp(argv[i], "--GZOutput") == 0) {
-      options.gzOutput = true;  
-    } 
     // allow consecutive non-terminals (X Y | X Y)
     else if (strcmp(argv[i],"--TargetSyntax") == 0) {
       options.targetSyntax = true;
@@ -265,7 +263,7 @@ int main(int argc, char* argv[])
       options.unpairedExtractFormat = true;
     } else if (strcmp(argv[i],"--ConditionOnTargetLHS") == 0) {
       options.conditionOnTargetLhs = true;
-    } else if (strcmp(argv[i],"-threads") == 0 || 
+    } else if (strcmp(argv[i],"-threads") == 0 ||
                strcmp(argv[i],"--threads") == 0 ||
                strcmp(argv[i],"--Threads") == 0) {
 #ifdef WITH_THREADS
@@ -327,8 +325,8 @@ int main(int argc, char* argv[])
     SAFE_GETLINE((*aFileP), alignmentString, LINE_MAX_LENGTH, '\n', __FILE__);
 
     SentenceAlignmentWithSyntax sentence
-      (targetLabelCollection, sourceLabelCollection, 
-       targetTopLabelCollection, sourceTopLabelCollection, options);
+    (targetLabelCollection, sourceLabelCollection,
+     targetTopLabelCollection, sourceTopLabelCollection, options);
     //az: output src, tgt, and alingment line
     if (options.onlyOutputSpanInfo) {
       cout << "LOG: SRC: " << sourceString << endl;
@@ -364,7 +362,8 @@ int main(int argc, char* argv[])
     writeUnknownWordLabel(fileNameUnknownWordLabel);
 }
 
-void ExtractTask::Run() {
+void ExtractTask::Run()
+{
   extractRules();
   consolidateRules();
   writeRulesToFile();
@@ -471,7 +470,7 @@ void ExtractTask::extractRules()
 }
 
 void ExtractTask::preprocessSourceHieroPhrase( int startT, int endT, int startS, int endS
-                                  , WordIndex &indexS, HoleCollection &holeColl, const LabelIndex &labelIndex)
+    , WordIndex &indexS, HoleCollection &holeColl, const LabelIndex &labelIndex)
 {
   vector<Hole*>::iterator iterHoleList = holeColl.GetSortedSourceHoles().begin();
   assert(iterHoleList != holeColl.GetSortedSourceHoles().end());
@@ -509,8 +508,8 @@ void ExtractTask::preprocessSourceHieroPhrase( int startT, int endT, int startS,
 }
 
 string ExtractTask::saveTargetHieroPhrase( int startT, int endT, int startS, int endS
-                              , WordIndex &indexT, HoleCollection &holeColl, const LabelIndex &labelIndex, double &logPCFGScore
-                              , int countS)
+    , WordIndex &indexT, HoleCollection &holeColl, const LabelIndex &labelIndex, double &logPCFGScore
+    , int countS)
 {
   HoleList::iterator iterHoleList = holeColl.GetHoles().begin();
   assert(iterHoleList != holeColl.GetHoles().end());
@@ -536,11 +535,11 @@ string ExtractTask::saveTargetHieroPhrase( int startT, int endT, int startS, int
       if (m_options.targetSyntax) {
         targetLabel = m_sentence.targetTree.GetNodes(currPos,hole.GetEnd(1))[labelI]->GetLabel();
       } else if (m_options.boundaryRules && (startS == 0 || endS == countS - 1)) {
-         targetLabel = "S"; 
+        targetLabel = "S";
       } else {
         targetLabel = "X";
       }
-      
+
       hole.SetLabel(targetLabel, 1);
 
       if (m_options.unpairedExtractFormat) {
@@ -571,7 +570,7 @@ string ExtractTask::saveTargetHieroPhrase( int startT, int endT, int startS, int
 }
 
 string ExtractTask::saveSourceHieroPhrase( int startT, int endT, int startS, int endS
-                               , HoleCollection &holeColl, const LabelIndex &labelIndex)
+    , HoleCollection &holeColl, const LabelIndex &labelIndex)
 {
   vector<Hole*>::iterator iterHoleList = holeColl.GetSortedSourceHoles().begin();
   assert(iterHoleList != holeColl.GetSortedSourceHoles().end());
@@ -615,7 +614,7 @@ string ExtractTask::saveSourceHieroPhrase( int startT, int endT, int startS, int
 }
 
 void ExtractTask::saveHieroAlignment( int startT, int endT, int startS, int endS
-                         , const WordIndex &indexS, const WordIndex &indexT, HoleCollection &holeColl, ExtractedRule &rule)
+                                      , const WordIndex &indexS, const WordIndex &indexT, HoleCollection &holeColl, ExtractedRule &rule)
 {
   // print alignment of words
   for(int ti=startT; ti<=endT; ti++) {
@@ -636,13 +635,13 @@ void ExtractTask::saveHieroAlignment( int startT, int endT, int startS, int endS
   HoleList::const_iterator iterHole;
   for (iterHole = holeColl.GetHoles().begin(); iterHole != holeColl.GetHoles().end(); ++iterHole) {
     const Hole &hole = *iterHole;
-        
+
     std::string sourceSymbolIndex = IntToString(hole.GetPos(0));
     std::string targetSymbolIndex = IntToString(hole.GetPos(1));
     rule.alignment      += sourceSymbolIndex + "-" + targetSymbolIndex + " ";
     if (!m_options.onlyDirectFlag)
       rule.alignmentInv += targetSymbolIndex + "-" + sourceSymbolIndex + " ";
-  
+
     rule.SetSpanLength(hole.GetPos(0), hole.GetSize(0), hole.GetSize(1) ) ;
 
   }
@@ -654,7 +653,7 @@ void ExtractTask::saveHieroAlignment( int startT, int endT, int startS, int endS
 }
 
 void ExtractTask::saveHieroPhrase( int startT, int endT, int startS, int endS
-                       , HoleCollection &holeColl, LabelIndex &labelIndex, int countS)
+                                   , HoleCollection &holeColl, LabelIndex &labelIndex, int countS)
 {
   WordIndex indexS, indexT; // to keep track of word positions in rule
 
@@ -680,12 +679,12 @@ void ExtractTask::saveHieroPhrase( int startT, int endT, int startS, int endS
   if (m_options.pcfgScore) {
     double logPCFGScore = m_sentence.targetTree.GetNodes(startT,endT)[labelIndex[0]]->GetPcfgScore();
     rule.target = saveTargetHieroPhrase(startT, endT, startS, endS, indexT, holeColl, labelIndex, logPCFGScore, countS)
-                + " [" + targetLabel + "]";
+                  + " [" + targetLabel + "]";
     rule.pcfgScore = std::exp(logPCFGScore);
   } else {
     double logPCFGScore = 0.0f;
     rule.target = saveTargetHieroPhrase(startT, endT, startS, endS, indexT, holeColl, labelIndex, logPCFGScore, countS)
-                + " [" + targetLabel + "]";
+                  + " [" + targetLabel + "]";
   }
 
   // source
@@ -754,8 +753,8 @@ void ExtractTask::saveAllHieroPhrases( int startT, int endT, int startS, int end
 // this function is called recursively
 // it pokes a new hole into the phrase pair, and then calls itself for more holes
 void ExtractTask::addHieroRule( int startT, int endT, int startS, int endS
-                   , RuleExist &ruleExist, HoleCollection &holeColl
-                   , int numHoles, int initStartT, int wordCountT, int wordCountS)
+                                , RuleExist &ruleExist, HoleCollection &holeColl
+                                , int numHoles, int initStartT, int wordCountT, int wordCountS)
 {
   // done, if already the maximum number of non-terminals in phrase pair
   if (numHoles >= m_options.maxNonTerm)
@@ -862,7 +861,7 @@ void ExtractTask::addHieroRule( int startT, int endT, int startS, int endS
           allowablePhrase = false;
 
         // passed all checks...
-        if (allowablePhrase) 
+        if (allowablePhrase)
           saveAllHieroPhrases(startT, endT, startS, endS, holeColl, wordCountS);
 
         // recursively search for next hole
@@ -880,12 +879,12 @@ void ExtractTask::addHieroRule( int startT, int endT, int startS, int endS
 void ExtractTask::addRule( int startT, int endT, int startS, int endS, int countS, RuleExist &ruleExist)
 {
   // contains only <s> or </s>. Don't output
-  if (m_options.boundaryRules 
-      && (   (startS == 0         && endS == 0) 
-          || (startS == countS-1  && endS == countS-1))) {
+  if (m_options.boundaryRules
+      && (   (startS == 0         && endS == 0)
+             || (startS == countS-1  && endS == countS-1))) {
     return;
   }
-  
+
   if (m_options.onlyOutputSpanInfo) {
     cout << startS << " " << endS << " " << startT << " " << endT << endl;
     return;
@@ -897,11 +896,10 @@ void ExtractTask::addRule( int startT, int endT, int startS, int endS, int count
   string targetLabel,sourceLabel;
   if (m_options.targetSyntax && m_options.conditionOnTargetLhs) {
     sourceLabel = targetLabel = m_sentence.targetTree.GetNodes(startT,endT)[0]->GetLabel();
-  }
-  else {
+  } else {
     sourceLabel = m_options.sourceSyntax ?
                   m_sentence.sourceTree.GetNodes(startS,endS)[0]->GetLabel() : "X";
-    
+
     if (m_options.targetSyntax) {
       targetLabel = m_sentence.targetTree.GetNodes(startT,endT)[0]->GetLabel();
     } else if (m_options.boundaryRules && (startS == 0 || endS == countS - 1)) {
@@ -1008,7 +1006,7 @@ void ExtractTask::writeRulesToFile()
         << rule->alignment << " ||| "
         << rule->count << " ||| ";
     if (m_options.outputNTLengths) {
-      rule->OutputNTLengths(out); 
+      rule->OutputNTLengths(out);
     }
     if (m_options.pcfgScore) {
       out << " ||| " << rule->pcfgScore;
diff --git a/phrase-extract/lexical-reordering/reordering_classes.cpp b/phrase-extract/lexical-reordering/reordering_classes.cpp
index e5b3fe7cd..8c5163f9b 100644
--- a/phrase-extract/lexical-reordering/reordering_classes.cpp
+++ b/phrase-extract/lexical-reordering/reordering_classes.cpp
@@ -57,7 +57,7 @@ void ModelScore::reset_f()
 }
 
 void ModelScore::add_example
-  (const StringPiece& previous, const StringPiece& next, float weight)
+(const StringPiece& previous, const StringPiece& next, float weight)
 {
   count_fe_prev[getType(previous)]+=weight;
   count_f_prev[getType(previous)]+=weight;
diff --git a/phrase-extract/lexical-reordering/score.cpp b/phrase-extract/lexical-reordering/score.cpp
index 545abf303..d404822b8 100644
--- a/phrase-extract/lexical-reordering/score.cpp
+++ b/phrase-extract/lexical-reordering/score.cpp
@@ -29,11 +29,11 @@ void get_orientations(const StringPiece& pair, StringPiece& previous, StringPiec
 
 class FileFormatException : public util::Exception
 {
-  public:
-    FileFormatException() throw() {
-     *this << "Invalid extract file format: ";
-    }
-    ~FileFormatException() throw() {}
+public:
+  FileFormatException() throw() {
+    *this << "Invalid extract file format: ";
+  }
+  ~FileFormatException() throw() {}
 };
 
 int main(int argc, char* argv[])
@@ -214,9 +214,10 @@ int main(int argc, char* argv[])
 }
 
 template <class It> StringPiece
-GrabOrDie(It &it, const StringPiece& line) {
-    UTIL_THROW_IF(!it, FileFormatException, line.as_string());
-    return *it++;
+GrabOrDie(It &it, const StringPiece& line)
+{
+  UTIL_THROW_IF(!it, FileFormatException, line.as_string());
+  return *it++;
 }
 
 
@@ -236,12 +237,12 @@ void split_line(
        | phrase | hier
        | phrase | hier ||| weight
   */
-  
+
   util::TokenIter<util::MultiCharacter> pipes(line, util::MultiCharacter(" ||| "));
   foreign = GrabOrDie(pipes,line);
   english = GrabOrDie(pipes,line);
   StringPiece next = GrabOrDie(pipes,line);
-  
+
   util::TokenIter<util::MultiCharacter> singlePipe(next, util::MultiCharacter(" | "));
   wbe = GrabOrDie(singlePipe,line);
   if (singlePipe) {
diff --git a/phrase-extract/pcfg-common/exception.h b/phrase-extract/pcfg-common/exception.h
index 3dbd59d0e..d9266ca36 100644
--- a/phrase-extract/pcfg-common/exception.h
+++ b/phrase-extract/pcfg-common/exception.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2012 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -23,15 +23,20 @@
 
 #include <string>
 
-namespace Moses {
-namespace PCFG {
+namespace Moses
+{
+namespace PCFG
+{
 
-class Exception {
- public:
+class Exception
+{
+public:
   Exception(const char *msg) : msg_(msg) {}
   Exception(const std::string &msg) : msg_(msg) {}
-  const std::string &msg() const { return msg_; }
- private:
+  const std::string &msg() const {
+    return msg_;
+  }
+private:
   std::string msg_;
 };
 
diff --git a/phrase-extract/pcfg-common/numbered_set.h b/phrase-extract/pcfg-common/numbered_set.h
index 15e768b4c..66e960404 100644
--- a/phrase-extract/pcfg-common/numbered_set.h
+++ b/phrase-extract/pcfg-common/numbered_set.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2012 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -29,32 +29,45 @@
 #include <sstream>
 #include <vector>
 
-namespace Moses {
-namespace PCFG {
+namespace Moses
+{
+namespace PCFG
+{
 
 // Stores a set of elements of type T, each of which is allocated an integral
 // ID of type I.  IDs are contiguous starting at 0.  Individual elements cannot
 // be removed once inserted (but the whole set can be cleared).
 template<typename T, typename I=std::size_t>
-class NumberedSet {
- private:
+class NumberedSet
+{
+private:
   typedef boost::unordered_map<T, I> ElementToIdMap;
   typedef std::vector<const T *> IdToElementMap;
 
- public:
+public:
   typedef I IdType;
   typedef typename IdToElementMap::const_iterator const_iterator;
 
   NumberedSet() {}
 
-  const_iterator begin() const { return id_to_element_.begin(); }
-  const_iterator end() const { return id_to_element_.end(); }
+  const_iterator begin() const {
+    return id_to_element_.begin();
+  }
+  const_iterator end() const {
+    return id_to_element_.end();
+  }
 
   // Static value
-  static I NullId() { return std::numeric_limits<I>::max(); }
+  static I NullId() {
+    return std::numeric_limits<I>::max();
+  }
 
-  bool Empty() const { return id_to_element_.empty(); }
-  std::size_t Size() const { return id_to_element_.size(); }
+  bool Empty() const {
+    return id_to_element_.empty();
+  }
+  std::size_t Size() const {
+    return id_to_element_.size();
+  }
 
   // Insert the given object and return its ID.
   I Insert(const T &);
@@ -64,19 +77,21 @@ class NumberedSet {
 
   void Clear();
 
- private:
+private:
   ElementToIdMap element_to_id_;
   IdToElementMap id_to_element_;
 };
 
 template<typename T, typename I>
-I NumberedSet<T, I>::Lookup(const T &s) const {
+I NumberedSet<T, I>::Lookup(const T &s) const
+{
   typename ElementToIdMap::const_iterator p = element_to_id_.find(s);
   return (p == element_to_id_.end()) ? NullId() : p->second;
 }
 
 template<typename T, typename I>
-const T &NumberedSet<T, I>::Lookup(I id) const {
+const T &NumberedSet<T, I>::Lookup(I id) const
+{
   if (id < 0 || id >= id_to_element_.size()) {
     std::ostringstream msg;
     msg << "Value not found: " << id;
@@ -86,10 +101,11 @@ const T &NumberedSet<T, I>::Lookup(I id) const {
 }
 
 template<typename T, typename I>
-I NumberedSet<T, I>::Insert(const T &x) {
+I NumberedSet<T, I>::Insert(const T &x)
+{
   std::pair<T, I> value(x, id_to_element_.size());
   std::pair<typename ElementToIdMap::iterator, bool> result =
-      element_to_id_.insert(value);
+    element_to_id_.insert(value);
   if (result.second) {
     // x is a new element.
     id_to_element_.push_back(&result.first->first);
@@ -98,7 +114,8 @@ I NumberedSet<T, I>::Insert(const T &x) {
 }
 
 template<typename T, typename I>
-void NumberedSet<T, I>::Clear() {
+void NumberedSet<T, I>::Clear()
+{
   element_to_id_.clear();
   id_to_element_.clear();
 }
diff --git a/phrase-extract/pcfg-common/pcfg.h b/phrase-extract/pcfg-common/pcfg.h
index b87336584..5398cd97e 100644
--- a/phrase-extract/pcfg-common/pcfg.h
+++ b/phrase-extract/pcfg-common/pcfg.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2012 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -28,11 +28,14 @@
 #include <ostream>
 #include <vector>
 
-namespace Moses {
-namespace PCFG {
+namespace Moses
+{
+namespace PCFG
+{
 
-class Pcfg {
- public:
+class Pcfg
+{
+public:
   typedef std::vector<std::size_t> Key;
   typedef std::map<Key, double> Map;
   typedef Map::iterator iterator;
@@ -40,18 +43,26 @@ class Pcfg {
 
   Pcfg() {}
 
-  iterator begin() { return rules_.begin(); }
-  const_iterator begin() const { return rules_.begin(); }
+  iterator begin() {
+    return rules_.begin();
+  }
+  const_iterator begin() const {
+    return rules_.begin();
+  }
 
-  iterator end() { return rules_.end(); }
-  const_iterator end() const { return rules_.end(); }
+  iterator end() {
+    return rules_.end();
+  }
+  const_iterator end() const {
+    return rules_.end();
+  }
 
   void Add(const Key &, double);
   bool Lookup(const Key &, double &) const;
   void Read(std::istream &, Vocabulary &);
   void Write(const Vocabulary &, std::ostream &) const;
 
- private:
+private:
   Map rules_;
 };
 
diff --git a/phrase-extract/pcfg-common/pcfg_tree.h b/phrase-extract/pcfg-common/pcfg_tree.h
index bdac64dfc..d125cad16 100644
--- a/phrase-extract/pcfg-common/pcfg_tree.h
+++ b/phrase-extract/pcfg-common/pcfg_tree.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2012 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -26,34 +26,43 @@
 
 #include <string>
 
-namespace Moses {
-namespace PCFG {
+namespace Moses
+{
+namespace PCFG
+{
 
 template<typename DerivedType>
-class PcfgTreeBase : public SyntaxTreeBase<std::string, DerivedType> {
- public:
+class PcfgTreeBase : public SyntaxTreeBase<std::string, DerivedType>
+{
+public:
   typedef std::string LabelType;
   typedef SyntaxTreeBase<LabelType, DerivedType> BaseType;
 
   PcfgTreeBase(const LabelType &label) : BaseType(label), score_(0.0) {}
 
-  double score() const { return score_; }
-  void set_score(double s) { score_ = s; }
+  double score() const {
+    return score_;
+  }
+  void set_score(double s) {
+    score_ = s;
+  }
 
- private:
+private:
   double score_;
 };
 
-class PcfgTree : public PcfgTreeBase<PcfgTree> {
- public:
+class PcfgTree : public PcfgTreeBase<PcfgTree>
+{
+public:
   typedef PcfgTreeBase<PcfgTree> BaseType;
   PcfgTree(const BaseType::LabelType &label) : BaseType(label) {}
 };
 
 // Specialise XmlOutputHandler for PcfgTree.
 template<>
-class XmlOutputHandler<PcfgTree> {
- public:
+class XmlOutputHandler<PcfgTree>
+{
+public:
   typedef std::map<std::string, std::string> AttributeMap;
 
   void GetLabel(const PcfgTree &tree, std::string &label) const {
diff --git a/phrase-extract/pcfg-common/syntax_tree.h b/phrase-extract/pcfg-common/syntax_tree.h
index 89c6ec0c3..93d9dbec9 100644
--- a/phrase-extract/pcfg-common/syntax_tree.h
+++ b/phrase-extract/pcfg-common/syntax_tree.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2012 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -24,62 +24,87 @@
 #include <cassert>
 #include <vector>
 
-namespace Moses {
-namespace PCFG {
+namespace Moses
+{
+namespace PCFG
+{
 
 // Base class for SyntaxTree, AgreementTree, and friends.
 template<typename T, typename DerivedType>
-class SyntaxTreeBase {
- public:
+class SyntaxTreeBase
+{
+public:
   // Constructors
   SyntaxTreeBase(const T &label)
-      : label_(label)
-      , children_()
-      , parent_(0) {}
+    : label_(label)
+    , children_()
+    , parent_(0) {}
 
   SyntaxTreeBase(const T &label, const std::vector<DerivedType *> &children)
-      : label_(label)
-      , children_(children)
-      , parent_(0) {}
+    : label_(label)
+    , children_(children)
+    , parent_(0) {}
 
   // Destructor
   virtual ~SyntaxTreeBase();
 
-  const T &label() const { return label_; }
-  const DerivedType *parent() const { return parent_; }
-  DerivedType *parent() { return parent_; }
-  const std::vector<DerivedType *> &children() const { return children_; }
-  std::vector<DerivedType *> &children() { return children_; }
+  const T &label() const {
+    return label_;
+  }
+  const DerivedType *parent() const {
+    return parent_;
+  }
+  DerivedType *parent() {
+    return parent_;
+  }
+  const std::vector<DerivedType *> &children() const {
+    return children_;
+  }
+  std::vector<DerivedType *> &children() {
+    return children_;
+  }
 
-  void set_label(const T &label) { label_ = label; }
-  void set_parent(DerivedType *parent) { parent_ = parent; }
-  void set_children(const std::vector<DerivedType *> &c) { children_ = c; }
+  void set_label(const T &label) {
+    label_ = label;
+  }
+  void set_parent(DerivedType *parent) {
+    parent_ = parent;
+  }
+  void set_children(const std::vector<DerivedType *> &c) {
+    children_ = c;
+  }
 
-  bool IsLeaf() const { return children_.empty(); }
+  bool IsLeaf() const {
+    return children_.empty();
+  }
 
   bool IsPreterminal() const {
     return children_.size() == 1 && children_[0]->IsLeaf();
   }
 
-  void AddChild(DerivedType *child) { children_.push_back(child); }
+  void AddChild(DerivedType *child) {
+    children_.push_back(child);
+  }
 
- private:
+private:
   T label_;
   std::vector<DerivedType *> children_;
   DerivedType *parent_;
 };
 
 template<typename T>
-class SyntaxTree : public SyntaxTreeBase<T, SyntaxTree<T> > {
- public:
+class SyntaxTree : public SyntaxTreeBase<T, SyntaxTree<T> >
+{
+public:
   typedef SyntaxTreeBase<T, SyntaxTree<T> > BaseType;
   SyntaxTree(const T &label) : BaseType(label) {}
   SyntaxTree(const T &label, const std::vector<SyntaxTree *> &children)
-      : BaseType(label, children) {}
+    : BaseType(label, children) {}
 };
 
 template<typename T, typename DerivedType>
-SyntaxTreeBase<T, DerivedType>::~SyntaxTreeBase() {
+SyntaxTreeBase<T, DerivedType>::~SyntaxTreeBase()
+{
   for (std::size_t i = 0; i < children_.size(); ++i) {
     delete children_[i];
   }
diff --git a/phrase-extract/pcfg-common/tool.h b/phrase-extract/pcfg-common/tool.h
index 0af342569..aada036e3 100644
--- a/phrase-extract/pcfg-common/tool.h
+++ b/phrase-extract/pcfg-common/tool.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2012 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -28,18 +28,23 @@
 #include <iostream>
 #include <string>
 
-namespace Moses {
-namespace PCFG {
+namespace Moses
+{
+namespace PCFG
+{
 
-class Tool {
- public:
+class Tool
+{
+public:
   virtual ~Tool() {}
 
-  const std::string &name() const { return name_; }
+  const std::string &name() const {
+    return name_;
+  }
 
   virtual int Main(int argc, char *argv[]) = 0;
 
- protected:
+protected:
   Tool(const std::string &name) : name_(name) {}
 
   // Returns the boost::program_options style that should be used by all tools.
@@ -77,7 +82,7 @@ class Tool {
   // the file cannot be opened for writing.
   void OpenNamedOutputOrDie(const std::string &, std::ofstream &);
 
- private:
+private:
   std::string name_;
   std::istream *input_ptr_;
   std::ifstream input_file_stream_;
diff --git a/phrase-extract/pcfg-common/typedef.h b/phrase-extract/pcfg-common/typedef.h
index 49a12d681..ce3e0423b 100644
--- a/phrase-extract/pcfg-common/typedef.h
+++ b/phrase-extract/pcfg-common/typedef.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2012 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -26,8 +26,10 @@
 
 #include <string>
 
-namespace Moses {
-namespace PCFG {
+namespace Moses
+{
+namespace PCFG
+{
 
 typedef NumberedSet<std::string> Vocabulary;
 
diff --git a/phrase-extract/pcfg-common/xml_tree_parser.h b/phrase-extract/pcfg-common/xml_tree_parser.h
index 7d01b0684..7eec14033 100644
--- a/phrase-extract/pcfg-common/xml_tree_parser.h
+++ b/phrase-extract/pcfg-common/xml_tree_parser.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2012 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -30,16 +30,19 @@
 #include <string>
 #include <vector>
 
-namespace Moses {
-namespace PCFG {
+namespace Moses
+{
+namespace PCFG
+{
 
 // Parses a string in Moses' XML parse tree format and returns a PcfgTree
 // object.
-class XmlTreeParser {
- public:
+class XmlTreeParser
+{
+public:
   XmlTreeParser();
   std::auto_ptr<PcfgTree> Parse(const std::string &);
- private:
+private:
   std::auto_ptr<PcfgTree> ConvertTree(const MosesTraining::SyntaxNode &,
                                       const std::vector<std::string> &);
 
diff --git a/phrase-extract/pcfg-common/xml_tree_writer.h b/phrase-extract/pcfg-common/xml_tree_writer.h
index 6a9a3de05..426efec17 100644
--- a/phrase-extract/pcfg-common/xml_tree_writer.h
+++ b/phrase-extract/pcfg-common/xml_tree_writer.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2012 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -32,12 +32,15 @@
 #include <vector>
 #include <string>
 
-namespace Moses {
-namespace PCFG {
+namespace Moses
+{
+namespace PCFG
+{
 
 template<typename InputTree>
-class XmlOutputHandler {
- public:
+class XmlOutputHandler
+{
+public:
   typedef std::map<std::string, std::string> AttributeMap;
 
   void GetLabel(const InputTree &, std::string &) const;
@@ -45,17 +48,19 @@ class XmlOutputHandler {
 };
 
 template<typename InputTree>
-class XmlTreeWriter : public XmlOutputHandler<InputTree> {
- public:
+class XmlTreeWriter : public XmlOutputHandler<InputTree>
+{
+public:
   typedef XmlOutputHandler<InputTree> Base;
   void Write(const InputTree &, std::ostream &) const;
- private:
+private:
   std::string Escape(const std::string &) const;
 };
 
 template<typename InputTree>
 void XmlTreeWriter<InputTree>::Write(const InputTree &tree,
-                                     std::ostream &out) const {
+                                     std::ostream &out) const
+{
   assert(!tree.IsLeaf());
 
   // Opening tag
@@ -99,7 +104,8 @@ void XmlTreeWriter<InputTree>::Write(const InputTree &tree,
 
 // Escapes XML special characters.
 template<typename InputTree>
-std::string XmlTreeWriter<InputTree>::Escape(const std::string &s) const {
+std::string XmlTreeWriter<InputTree>::Escape(const std::string &s) const
+{
   std::string t;
   std::size_t len = s.size();
   t.reserve(len);
diff --git a/phrase-extract/pcfg-extract/options.h b/phrase-extract/pcfg-extract/options.h
index 3acb31b58..2633f025a 100644
--- a/phrase-extract/pcfg-extract/options.h
+++ b/phrase-extract/pcfg-extract/options.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2012 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -23,8 +23,10 @@
 
 #include <string>
 
-namespace Moses {
-namespace PCFG {
+namespace Moses
+{
+namespace PCFG
+{
 
 struct Options {
   std::string corpus_file;
diff --git a/phrase-extract/pcfg-extract/pcfg_extract.h b/phrase-extract/pcfg-extract/pcfg_extract.h
index 1af6cb4fe..e8c306876 100644
--- a/phrase-extract/pcfg-extract/pcfg_extract.h
+++ b/phrase-extract/pcfg-extract/pcfg_extract.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2012 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -23,16 +23,19 @@
 
 #include "pcfg-common/tool.h"
 
-namespace Moses {
-namespace PCFG {
+namespace Moses
+{
+namespace PCFG
+{
 
 class Options;
 
-class PcfgExtract : public Tool {
- public:
+class PcfgExtract : public Tool
+{
+public:
   PcfgExtract() : Tool("pcfg-extract") {}
   virtual int Main(int, char *[]);
- private:
+private:
   void ProcessOptions(int, char *[], Options &) const;
 };
 
diff --git a/phrase-extract/pcfg-extract/rule_collection.h b/phrase-extract/pcfg-extract/rule_collection.h
index 452fa0e97..32cb2dc05 100644
--- a/phrase-extract/pcfg-extract/rule_collection.h
+++ b/phrase-extract/pcfg-extract/rule_collection.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2012 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -27,12 +27,15 @@
 
 #include <vector>
 
-namespace Moses {
-namespace PCFG {
+namespace Moses
+{
+namespace PCFG
+{
 
 // Contains PCFG rules and their counts.
-class RuleCollection {
- public:
+class RuleCollection
+{
+public:
   typedef boost::unordered_map<std::vector<std::size_t>, std::size_t> RhsCountMap;
   typedef boost::unordered_map<std::size_t, RhsCountMap> Map;
   typedef Map::iterator iterator;
@@ -40,16 +43,24 @@ class RuleCollection {
 
   RuleCollection() {}
 
-  iterator begin() { return collection_.begin(); }
-  const_iterator begin() const { return collection_.begin(); }
+  iterator begin() {
+    return collection_.begin();
+  }
+  const_iterator begin() const {
+    return collection_.begin();
+  }
 
-  iterator end() { return collection_.end(); }
-  const_iterator end() const { return collection_.end(); }
+  iterator end() {
+    return collection_.end();
+  }
+  const_iterator end() const {
+    return collection_.end();
+  }
 
   void Add(std::size_t, const std::vector<std::size_t> &);
   void CreatePcfg(Pcfg &);
 
- private:
+private:
   Map collection_;
 };
 
diff --git a/phrase-extract/pcfg-extract/rule_extractor.h b/phrase-extract/pcfg-extract/rule_extractor.h
index 6bcffbc61..e4b411c01 100644
--- a/phrase-extract/pcfg-extract/rule_extractor.h
+++ b/phrase-extract/pcfg-extract/rule_extractor.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2012 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -25,17 +25,20 @@
 
 #include "pcfg-common/typedef.h"
 
-namespace Moses {
-namespace PCFG {
+namespace Moses
+{
+namespace PCFG
+{
 
 class PcfgTree;
 
 // Extracts PCFG rules from syntax trees and adds them to a RuleCollection.
-class RuleExtractor {
- public:
+class RuleExtractor
+{
+public:
   RuleExtractor(Vocabulary &);
   void Extract(const PcfgTree &, RuleCollection &) const;
- private:
+private:
   Vocabulary &non_term_vocab_;
 };
 
diff --git a/phrase-extract/pcfg-score/options.h b/phrase-extract/pcfg-score/options.h
index e54b2a0b9..fd54b4b6b 100644
--- a/phrase-extract/pcfg-score/options.h
+++ b/phrase-extract/pcfg-score/options.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2012 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -23,8 +23,10 @@
 
 #include <string>
 
-namespace Moses {
-namespace PCFG {
+namespace Moses
+{
+namespace PCFG
+{
 
 struct Options {
   std::string pcfg_file;
diff --git a/phrase-extract/pcfg-score/pcfg_score.h b/phrase-extract/pcfg-score/pcfg_score.h
index 5e506c39d..f49c9a0be 100644
--- a/phrase-extract/pcfg-score/pcfg_score.h
+++ b/phrase-extract/pcfg-score/pcfg_score.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2012 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -23,16 +23,19 @@
 
 #include "pcfg-common/tool.h"
 
-namespace Moses {
-namespace PCFG {
+namespace Moses
+{
+namespace PCFG
+{
 
 class Options;
 
-class PcfgScore : public Tool {
- public:
+class PcfgScore : public Tool
+{
+public:
   PcfgScore() : Tool("pcfg-score") {}
   virtual int Main(int, char *[]);
- private:
+private:
   void ProcessOptions(int, char *[], Options &) const;
 };
 
diff --git a/phrase-extract/pcfg-score/tree_scorer.h b/phrase-extract/pcfg-score/tree_scorer.h
index 36f4e1e99..8cb59c0c2 100644
--- a/phrase-extract/pcfg-score/tree_scorer.h
+++ b/phrase-extract/pcfg-score/tree_scorer.h
@@ -1,17 +1,17 @@
 /***********************************************************************
  Moses - statistical machine translation system
  Copyright (C) 2006-2012 University of Edinburgh
- 
+
  This library is free software; you can redistribute it and/or
  modify it under the terms of the GNU Lesser General Public
  License as published by the Free Software Foundation; either
  version 2.1 of the License, or (at your option) any later version.
- 
+
  This library is distributed in the hope that it will be useful,
  but WITHOUT ANY WARRANTY; without even the implied warranty of
  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  Lesser General Public License for more details.
- 
+
  You should have received a copy of the GNU Lesser General Public
  License along with this library; if not, write to the Free Software
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
@@ -25,18 +25,21 @@
 #include "pcfg-common/pcfg_tree.h"
 #include "pcfg-common/typedef.h"
 
-namespace Moses {
-namespace PCFG {
+namespace Moses
+{
+namespace PCFG
+{
 
-class TreeScorer {
- public:
+class TreeScorer
+{
+public:
   TreeScorer(const Pcfg &, const Vocabulary &);
 
   // Score tree according to PCFG.  Returns false if unsuccessful (due to
   // missing rule).
   bool Score(PcfgTree &) const;
 
- private:
+private:
   const Pcfg &pcfg_;
   const Vocabulary &non_term_vocab_;
 };
diff --git a/phrase-extract/score-main.cpp b/phrase-extract/score-main.cpp
index 0e4ad57f4..3042cbe3e 100644
--- a/phrase-extract/score-main.cpp
+++ b/phrase-extract/score-main.cpp
@@ -68,7 +68,7 @@ float minCountHierarchical = 0;
 
 Vocabulary vcbT;
 Vocabulary vcbS;
-  
+
 } // namespace
 
 vector<string> tokenize( const char [] );
@@ -130,18 +130,18 @@ int main(int argc, char* argv[])
       cerr << "not computing lexical translation score\n";
     } else if (strcmp(argv[i],"--GoodTuring") == 0) {
       goodTuringFlag = true;
-			fileNameCountOfCounts = string(fileNamePhraseTable) + ".coc";
+      fileNameCountOfCounts = string(fileNamePhraseTable) + ".coc";
       cerr << "adjusting phrase translation probabilities with Good Turing discounting\n";
     } else if (strcmp(argv[i],"--KneserNey") == 0) {
       kneserNeyFlag = true;
-			fileNameCountOfCounts = string(fileNamePhraseTable) + ".coc";
+      fileNameCountOfCounts = string(fileNamePhraseTable) + ".coc";
       cerr << "adjusting phrase translation probabilities with Kneser Ney discounting\n";
     } else if (strcmp(argv[i],"--UnalignedPenalty") == 0) {
       unalignedFlag = true;
       cerr << "using unaligned word penalty\n";
     } else if (strcmp(argv[i],"--UnalignedFunctionWordPenalty") == 0) {
       unalignedFWFlag = true;
-      if (i+1==argc) { 
+      if (i+1==argc) {
         cerr << "ERROR: specify count of count files for Kneser Ney discounting!\n";
         exit(1);
       }
@@ -204,22 +204,21 @@ int main(int argc, char* argv[])
   istream &extractFileP = extractFile;
 
   // output file: phrase translation table
-	ostream *phraseTableFile;
-
-	if (fileNamePhraseTable == "-") {
-		phraseTableFile = &cout;
-	}
-	else {
-		Moses::OutputFileStream *outputFile = new Moses::OutputFileStream();
-		bool success = outputFile->Open(fileNamePhraseTable);
-		if (!success) {
-			cerr << "ERROR: could not open file phrase table file "
-					 << fileNamePhraseTable << endl;
-			exit(1);
-		}
-		phraseTableFile = outputFile;
-	}
-	
+  ostream *phraseTableFile;
+
+  if (fileNamePhraseTable == "-") {
+    phraseTableFile = &cout;
+  } else {
+    Moses::OutputFileStream *outputFile = new Moses::OutputFileStream();
+    bool success = outputFile->Open(fileNamePhraseTable);
+    if (!success) {
+      cerr << "ERROR: could not open file phrase table file "
+           << fileNamePhraseTable << endl;
+      exit(1);
+    }
+    phraseTableFile = outputFile;
+  }
+
   // loop through all extracted phrase translations
   float lastCount = 0.0f;
   float lastPcfgSum = 0.0f;
@@ -250,25 +249,23 @@ int main(int argc, char* argv[])
     lastPcfgSum = phrasePair.pcfgSum;
 
     // only differs in count? just add count
-    if (lastPhrasePair != NULL 
-	    && lastPhrasePair->equals( phrasePair )
-	    && featureManager.equals(*lastPhrasePair, phrasePair)) {
+    if (lastPhrasePair != NULL
+        && lastPhrasePair->equals( phrasePair )
+        && featureManager.equals(*lastPhrasePair, phrasePair)) {
       lastPhrasePair->count += phrasePair.count;
       lastPhrasePair->pcfgSum += phrasePair.pcfgSum;
       continue;
     }
-    
+
     // if new source phrase, process last batch
     if (lastPhrasePair != NULL &&
         lastPhrasePair->GetSource() != phrasePair.GetSource()) {
       processPhrasePairs( phrasePairsWithSameF, *phraseTableFile, isSingleton, featureManager, maybeLogProb );
-      
+
       phrasePairsWithSameF.clear();
       isSingleton = false;
       lastPhrasePair = NULL;
-    }
-    else
-    {
+    } else {
       isSingleton = true;
     }
 
@@ -277,11 +274,11 @@ int main(int argc, char* argv[])
     lastPhrasePair = &phrasePairsWithSameF.back();
   }
   processPhrasePairs( phrasePairsWithSameF, *phraseTableFile, isSingleton, featureManager, maybeLogProb );
-	
-	phraseTableFile->flush();
-	if (phraseTableFile != &cout) {
-		delete phraseTableFile;
-	}
+
+  phraseTableFile->flush();
+  if (phraseTableFile != &cout) {
+    delete phraseTableFile;
+  }
 
   // output count of count statistics
   if (goodTuringFlag || kneserNeyFlag) {
@@ -292,13 +289,13 @@ int main(int argc, char* argv[])
 void writeCountOfCounts( const string &fileNameCountOfCounts )
 {
   // open file
-	Moses::OutputFileStream countOfCountsFile;
-	bool success = countOfCountsFile.Open(fileNameCountOfCounts.c_str());
-	if (!success) {
-		cerr << "ERROR: could not open count-of-counts file "
-				 << fileNameCountOfCounts << endl;
+  Moses::OutputFileStream countOfCountsFile;
+  bool success = countOfCountsFile.Open(fileNameCountOfCounts.c_str());
+  if (!success) {
+    cerr << "ERROR: could not open count-of-counts file "
+         << fileNameCountOfCounts << endl;
     return;
-	}
+  }
 
   // Kneser-Ney needs the total number of phrase pairs
   countOfCountsFile << totalDistinct << endl;
@@ -307,7 +304,7 @@ void writeCountOfCounts( const string &fileNameCountOfCounts )
   for(int i=1; i<=COC_MAX; i++) {
     countOfCountsFile << countOfCounts[ i ] << endl;
   }
-	countOfCountsFile.Close();
+  countOfCountsFile.Close();
 }
 
 void processPhrasePairs( vector< PhraseAlignment > &phrasePair, ostream &phraseTableFile, bool isSingleton, const ScoreFeatureManager& featureManager, const MaybeLog& maybeLogProb )
@@ -317,65 +314,63 @@ void processPhrasePairs( vector< PhraseAlignment > &phrasePair, ostream &phraseT
   // group phrase pairs based on alignments that matter
   // (i.e. that re-arrange non-terminals)
   PhrasePairGroup phrasePairGroup;
-  
+
   float totalSource = 0;
 
   //cerr << "phrasePair.size() = " << phrasePair.size() << endl;
-  
+
   // loop through phrase pairs
   for(size_t i=0; i<phrasePair.size(); i++) {
     // add to total count
     PhraseAlignment &currPhrasePair = phrasePair[i];
-    
+
     totalSource += phrasePair[i].count;
-    
+
     // check for matches
     //cerr << "phrasePairGroup.size() = " << phrasePairGroup.size() << endl;
-    
+
     PhraseAlignmentCollection phraseAlignColl;
     phraseAlignColl.push_back(&currPhrasePair);
     pair<PhrasePairGroup::iterator, bool> retInsert;
     retInsert = phrasePairGroup.insert(phraseAlignColl);
-    if (!retInsert.second)
-    { // already exist. Add to that collection instead
+    if (!retInsert.second) {
+      // already exist. Add to that collection instead
       PhraseAlignmentCollection &existingColl = const_cast<PhraseAlignmentCollection&>(*retInsert.first);
       existingColl.push_back(&currPhrasePair);
     }
-    
+
   }
 
   // output the distinct phrase pairs, one at a time
   const PhrasePairGroup::SortedColl &sortedColl = phrasePairGroup.GetSortedColl();
   PhrasePairGroup::SortedColl::const_iterator iter;
 
-  for(iter = sortedColl.begin(); iter != sortedColl.end(); ++iter) 
-  {
+  for(iter = sortedColl.begin(); iter != sortedColl.end(); ++iter) {
     const PhraseAlignmentCollection &group = **iter;
     outputPhrasePair( group, totalSource, phrasePairGroup.GetSize(), phraseTableFile, isSingleton, featureManager, maybeLogProb );
   }
-  
+
 }
 
 const PhraseAlignment &findBestAlignment(const PhraseAlignmentCollection &phrasePair )
 {
   float bestAlignmentCount = -1;
   PhraseAlignment* bestAlignment = NULL;
-  
+
   for(size_t i=0; i<phrasePair.size(); i++) {
     size_t alignInd;
-    if (inverseFlag) 
-    { // count backwards, so that alignments for ties will be the same for both normal & inverse scores
+    if (inverseFlag) {
+      // count backwards, so that alignments for ties will be the same for both normal & inverse scores
       alignInd = phrasePair.size() - i - 1;
-    }
-    else {
+    } else {
       alignInd = i;
     }
-    
+
     if (phrasePair[alignInd]->count > bestAlignmentCount) {
       bestAlignmentCount = phrasePair[alignInd]->count;
       bestAlignment = phrasePair[alignInd];
     }
-  }    
+  }
 
   return *bestAlignment;
 }
@@ -386,14 +381,12 @@ void calcNTLengthProb(const map<size_t, map<size_t, size_t> > &lengths
                       , map<size_t, map<size_t, float> > &probs)
 {
   map<size_t, map<size_t, size_t> >::const_iterator iterOuter;
-  for (iterOuter = lengths.begin(); iterOuter != lengths.end(); ++iterOuter)
-  {
+  for (iterOuter = lengths.begin(); iterOuter != lengths.end(); ++iterOuter) {
     size_t sourcePos = iterOuter->first;
     const map<size_t, size_t> &inner = iterOuter->second;
-    
+
     map<size_t, size_t>::const_iterator iterInner;
-    for (iterInner = inner.begin(); iterInner != inner.end(); ++iterInner)
-    {
+    for (iterInner = inner.begin(); iterInner != inner.end(); ++iterInner) {
       size_t length = iterInner->first;
       size_t count = iterInner->second;
       float prob = (float) count / (float) total;
@@ -411,54 +404,49 @@ void calcNTLengthProb(const vector< PhraseAlignment* > &phrasePairs
   map<size_t, size_t> totals;
   // 1st = position in source phrase, 2nd = total counts
   // each source pos should have same count?
-  
+
   vector< PhraseAlignment* >::const_iterator iterOuter;
-  for (iterOuter = phrasePairs.begin(); iterOuter != phrasePairs.end(); ++iterOuter)
-  {
+  for (iterOuter = phrasePairs.begin(); iterOuter != phrasePairs.end(); ++iterOuter) {
     const PhraseAlignment &phrasePair = **iterOuter;
     const std::map<size_t, std::pair<size_t, size_t> > &ntLengths = phrasePair.GetNTLengths();
-    
+
     std::map<size_t, std::pair<size_t, size_t> >::const_iterator iterInner;
-    for (iterInner = ntLengths.begin(); iterInner != ntLengths.end(); ++iterInner)
-    {
+    for (iterInner = ntLengths.begin(); iterInner != ntLengths.end(); ++iterInner) {
       size_t sourcePos = iterInner->first;
       size_t sourceLength = iterInner->second.first;
       size_t targetLength = iterInner->second.second;
-      
+
       sourceLengths[sourcePos][sourceLength]++;
       targetLengths[sourcePos][targetLength]++;
 
       totals[sourcePos]++;
     }
   }
-    
-  if (totals.size() == 0)
-  { // no non-term. Don't bother
+
+  if (totals.size() == 0) {
+    // no non-term. Don't bother
     return;
   }
 
   size_t total = totals.begin()->second;
-  if (totals.size() > 1)
-  {
+  if (totals.size() > 1) {
     assert(total == (++totals.begin())->second );
   }
-  
+
   calcNTLengthProb(sourceLengths, total, sourceProb);
   calcNTLengthProb(targetLengths, total, targetProb);
-  
+
 }
 
 void outputNTLengthProbs(ostream &phraseTableFile, const map<size_t, map<size_t, float> > &probs, const string &prefix)
 {
   map<size_t, map<size_t, float> >::const_iterator iterOuter;
-  for (iterOuter = probs.begin(); iterOuter != probs.end(); ++iterOuter)
-  {
+  for (iterOuter = probs.begin(); iterOuter != probs.end(); ++iterOuter) {
     size_t sourcePos = iterOuter->first;
     const map<size_t, float> &inner = iterOuter->second;
-    
+
     map<size_t, float>::const_iterator iterInner;
-    for (iterInner = inner.begin(); iterInner != inner.end(); ++iterInner)
-    {
+    for (iterInner = inner.begin(); iterInner != inner.end(); ++iterInner) {
       size_t length = iterInner->first;
       float prob = iterInner->second;
 
@@ -470,47 +458,40 @@ void outputNTLengthProbs(ostream &phraseTableFile, const map<size_t, map<size_t,
 
 bool calcCrossedNonTerm(size_t sourcePos, size_t targetPos, const std::vector< std::set<size_t> > &alignedToS)
 {
-  for (size_t currSource = 0; currSource < alignedToS.size(); ++currSource)
-  {
-    if (currSource == sourcePos)
-    { // skip
-    }
-    else 
-    {
+  for (size_t currSource = 0; currSource < alignedToS.size(); ++currSource) {
+    if (currSource == sourcePos) {
+      // skip
+    } else {
       const std::set<size_t> &targetSet = alignedToS[currSource];
       std::set<size_t>::const_iterator iter;
-      for (iter = targetSet.begin(); iter != targetSet.end(); ++iter)
-      {
+      for (iter = targetSet.begin(); iter != targetSet.end(); ++iter) {
         size_t currTarget = *iter;
-        
+
         if ((currSource < sourcePos && currTarget > targetPos)
             || (currSource > sourcePos && currTarget < targetPos)
-          )
-        {
+           ) {
           return true;
         }
       }
-      
+
     }
   }
-  
+
   return false;
 }
 
 int calcCrossedNonTerm(const PHRASE &phraseS, const PhraseAlignment &bestAlignment)
 {
   const std::vector< std::set<size_t> > &alignedToS = bestAlignment.alignedToS;
-  
-  for (size_t sourcePos = 0; sourcePos < alignedToS.size(); ++sourcePos)
-  {
+
+  for (size_t sourcePos = 0; sourcePos < alignedToS.size(); ++sourcePos) {
     const std::set<size_t> &targetSet = alignedToS[sourcePos];
-    
+
     WORD_ID wordId = phraseS[sourcePos];
     const WORD &word = vcbS.getWord(wordId);
     bool isNonTerm = isNonTerminal(word);
-    
-    if (isNonTerm)
-    {
+
+    if (isNonTerm) {
       assert(targetSet.size() == 1);
       size_t targetPos = *targetSet.begin();
       bool ret = calcCrossedNonTerm(sourcePos, targetPos, alignedToS);
@@ -518,17 +499,17 @@ int calcCrossedNonTerm(const PHRASE &phraseS, const PhraseAlignment &bestAlignme
         return 1;
     }
   }
-  
+
   return 0;
 }
 
 void outputPhrasePair(const PhraseAlignmentCollection &phrasePair, float totalCount, int distinctCount, ostream &phraseTableFile, bool isSingleton, const ScoreFeatureManager& featureManager,
-  const MaybeLog& maybeLogProb )
+                      const MaybeLog& maybeLogProb )
 {
   if (phrasePair.size() == 0) return;
 
   const PhraseAlignment &bestAlignment = findBestAlignment( phrasePair );
-    
+
   // compute count
   float count = 0;
   for(size_t i=0; i<phrasePair.size(); i++) {
@@ -550,7 +531,7 @@ void outputPhrasePair(const PhraseAlignmentCollection &phrasePair, float totalCo
   if (pcfgFlag && !inverseFlag) {
     float pcfgSum = 0;
     for(size_t i=0; i<phrasePair.size(); ++i) {
-        pcfgSum += phrasePair[i]->pcfgSum;
+      pcfgSum += phrasePair[i]->pcfgSum;
     }
     pcfgScore = pcfgSum / count;
   }
@@ -604,11 +585,11 @@ void outputPhrasePair(const PhraseAlignmentCollection &phrasePair, float totalCo
   if (singletonFeature) {
     phraseTableFile << " " << (isSingleton ? 1 : 0);
   }
-  
+
   if (crossedNonTerm && !inverseFlag) {
     phraseTableFile << " " << calcCrossedNonTerm(phraseS, bestAlignment);
   }
-  
+
   // target-side PCFG score
   if (pcfgFlag && !inverseFlag) {
     phraseTableFile << " " << maybeLogProb(pcfgScore );
@@ -624,7 +605,7 @@ void outputPhrasePair(const PhraseAlignmentCollection &phrasePair, float totalCo
   }
 
   for (map<string,float>::const_iterator i = extraSparse.begin();
-        i != extraSparse.end(); ++i) {
+       i != extraSparse.end(); ++i) {
     phraseTableFile << " " << i->first << " " << i->second;
   }
 
@@ -633,8 +614,8 @@ void outputPhrasePair(const PhraseAlignmentCollection &phrasePair, float totalCo
   // alignment info for non-terminals
   if (! inverseFlag) {
     if (hierarchicalFlag) {
-      // always output alignment if hiero style, but only for non-terms 
-      // (eh: output all alignments, needed for some feature functions) 
+      // always output alignment if hiero style, but only for non-terms
+      // (eh: output all alignments, needed for some feature functions)
       assert(phraseT.size() == bestAlignment.alignedToT.size() + 1);
       std::vector<std::string> alignment;
       for(size_t j = 0; j < phraseT.size() - 1; j++) {
@@ -657,15 +638,15 @@ void outputPhrasePair(const PhraseAlignmentCollection &phrasePair, float totalCo
             std::stringstream point;
             point << sourcePos << "-" << j;
             alignment.push_back(point.str());
-           }
-         }
-       }
-       // now print all alignments, sorted by source index
-       sort(alignment.begin(), alignment.end());
-       for (size_t i = 0; i < alignment.size(); ++i) {
-          phraseTableFile << alignment[i] << " ";
-       }
-     } else if (wordAlignmentFlag) {
+          }
+        }
+      }
+      // now print all alignments, sorted by source index
+      sort(alignment.begin(), alignment.end());
+      for (size_t i = 0; i < alignment.size(); ++i) {
+        phraseTableFile << alignment[i] << " ";
+      }
+    } else if (wordAlignmentFlag) {
       // alignment info in pb model
       for(size_t j=0; j<bestAlignment.alignedToT.size(); j++) {
         const set< size_t > &aligned = bestAlignment.alignedToT[j];
@@ -678,28 +659,26 @@ void outputPhrasePair(const PhraseAlignmentCollection &phrasePair, float totalCo
 
 
   // counts
-  
+
   phraseTableFile << " ||| " << totalCount << " " << count;
-  if (kneserNeyFlag) 
+  if (kneserNeyFlag)
     phraseTableFile << " " << distinctCount;
-  
-  // nt lengths  
-  if (outputNTLengths)
-  {
+
+  // nt lengths
+  if (outputNTLengths) {
     phraseTableFile << " ||| ";
 
-    if (!inverseFlag)
-    {
+    if (!inverseFlag) {
       map<size_t, map<size_t, float> > sourceProb, targetProb;
       // 1st sourcePos, 2nd = length, 3rd = prob
 
       calcNTLengthProb(phrasePair, sourceProb, targetProb);
-      
+
       outputNTLengthProbs(phraseTableFile, sourceProb, "S");
       outputNTLengthProbs(phraseTableFile, targetProb, "T");
-    }    
+    }
   }
-  
+
   phraseTableFile << endl;
 }
 
@@ -878,13 +857,13 @@ void printTargetPhrase(const PHRASE &phraseS, const PHRASE &phraseT,
 std::pair<PhrasePairGroup::Coll::iterator,bool> PhrasePairGroup::insert ( const PhraseAlignmentCollection& obj )
 {
   std::pair<iterator,bool> ret = m_coll.insert(obj);
-  
-  if (ret.second)
-  { // obj inserted. Also add to sorted vector
+
+  if (ret.second) {
+    // obj inserted. Also add to sorted vector
     const PhraseAlignmentCollection &insertedObj = *ret.first;
     m_sortedColl.push_back(&insertedObj);
   }
-  
+
   return ret;
 }
 
diff --git a/phrase-extract/score.h b/phrase-extract/score.h
index 59d2cf58f..6a10536c1 100644
--- a/phrase-extract/score.h
+++ b/phrase-extract/score.h
@@ -32,6 +32,6 @@ inline bool isNonTerminal( const std::string &word )
   return (word.length()>=3 && word[0] == '[' && word[word.length()-1] == ']');
 }
 
-  
+
 }
 
diff --git a/phrase-extract/tables-core.cpp b/phrase-extract/tables-core.cpp
index 6b35f371b..30c1544e9 100644
--- a/phrase-extract/tables-core.cpp
+++ b/phrase-extract/tables-core.cpp
@@ -33,8 +33,9 @@ vector<string> tokenize( const char* input )
 namespace MosesTraining
 {
 
-bool isNonTerminal( const WORD &symbol ) {
-   return symbol.substr(0, 1) == "[" && symbol.substr(symbol.size()-1, 1) == "]";
+bool isNonTerminal( const WORD &symbol )
+{
+  return symbol.substr(0, 1) == "[" && symbol.substr(symbol.size()-1, 1) == "]";
 }
 
 WORD_ID Vocabulary::storeIfNew( const WORD& word )
@@ -105,7 +106,7 @@ void DTable::load( const string& fileName )
       std::cerr << "Error reading from " << fileName << std::endl;
       abort();
     }
-    
+
     vector<string> token = tokenize(line.c_str());
     if (token.size() < 2) {
       cerr << "line " << i << " in " << fileName << " too short, skipping\n";
diff --git a/scripts/other/beautify.perl b/scripts/other/beautify.perl
index 110539893..01afb1af2 100755
--- a/scripts/other/beautify.perl
+++ b/scripts/other/beautify.perl
@@ -1,31 +1,46 @@
-#!/usr/bin/perl
+#!/usr/bin/perl 
 
 use strict;
+use File::Basename;
 
-#my $cmd = "astyle --style='k&r' -s2 -v --recursive *.h *.cpp";
-#print STDERR "Executing: $cmd \n";
-#system($cmd);
+sub Beautify($);
 
-opendir(DIR,".") or die "Can't open the current directory: $!\n";
+Beautify("/home/hieu/workspace/github/mosesdecoder");
+
+sub Beautify($)
+{
+my $path = shift;
+opendir(DIR, $path) or die "Can't open the current directory: $!\n";
 
 # read file/directory names in that directory into @names 
 my @names = readdir(DIR) or die "Unable to read current dir:$!\n";
 
 foreach my $name (@names) {
-   next if ($name eq ".");   # skip the current directory entry
-   next if ($name eq "..");  # skip the parent  directory entry
-   next if ($name eq "boost");  # skip the parent  directory entry
-   next if ($name eq "contrib");  # skip the parent  directory entry
-   next if ($name eq "jam-files");  # skip the parent  directory entry
-   next if ($name eq ".git");  # skip the parent  directory entry
-
-   if (-d $name){            # is this a directory?
-      my $cmd = "astyle --style='k&r' -s2 -v --recursive $name/*.h $name/*.cpp";
-      print STDERR "Executing: $cmd \n";
-      system($cmd);
-
-      next;                  # can skip to the next name in the for loop 
+   next if ($name eq ".");
+   next if ($name eq "..");
+   next if ($name eq "boost");
+   next if ($name eq "contrib");
+   next if ($name eq "jam-files");
+   next if ($name eq ".git");
+   next if ($name eq "util");
+   next if ($name eq "lm");
+   next if ($name eq "search");
+
+   $name = $path ."/" .$name;
+   if (-d $name) {
+      print STDERR "Into: $name \n";
+      Beautify($name);
+   }
+   else {            # is this a directory?
+      (my $nameOnly, my $pathOnly,my $suffix) = fileparse($name,qr"\..[^.]*$");
+      if ($suffix eq ".cpp" || $suffix eq ".h") {
+        my $cmd = "astyle --style='k&r' -s2 -v $name";
+        print STDERR "Executing: $cmd \n";
+        system($cmd);
+      }
    }
 }
 
 closedir(DIR);
+}
+
diff --git a/symal/symal.cpp b/symal/symal.cpp
index da386d973..dbe68f1b9 100644
--- a/symal/symal.cpp
+++ b/symal/symal.cpp
@@ -411,7 +411,7 @@ int main(int argc, char** argv)
                 "o", CMDSTRINGTYPE, &output,
                 "v", CMDENUMTYPE,  &verbose, BoolEnum,
                 "verbose", CMDENUMTYPE,  &verbose, BoolEnum,
-                
+
                 (char*)NULL);
 
   GetParams(&argc, &argv, (char*)NULL);
diff --git a/util/double-conversion/bignum-dtoa.h b/util/double-conversion/bignum-dtoa.h
index 34b961992..652a4db9a 100644
--- a/util/double-conversion/bignum-dtoa.h
+++ b/util/double-conversion/bignum-dtoa.h
@@ -30,7 +30,8 @@
 
 #include "utils.h"
 
-namespace double_conversion {
+namespace double_conversion
+{
 
 enum BignumDtoaMode {
   // Return the shortest correct representation.
diff --git a/util/double-conversion/bignum.h b/util/double-conversion/bignum.h
index 5ec3544f5..5deadbfbe 100644
--- a/util/double-conversion/bignum.h
+++ b/util/double-conversion/bignum.h
@@ -30,10 +30,12 @@
 
 #include "utils.h"
 
-namespace double_conversion {
+namespace double_conversion
+{
 
-class Bignum {
- public:
+class Bignum
+{
+public:
   // 3584 = 128 * 28. We can represent 2^3584 > 10^1000 accurately.
   // This bignum can encode much bigger numbers, since it contains an
   // exponent.
@@ -60,7 +62,9 @@ class Bignum {
   void MultiplyByUInt32(uint32_t factor);
   void MultiplyByUInt64(uint64_t factor);
   void MultiplyByPowerOfTen(int exponent);
-  void Times10() { return MultiplyByUInt32(10); }
+  void Times10() {
+    return MultiplyByUInt32(10);
+  }
   // Pseudocode:
   //  int result = this / other;
   //  this = this % other;
@@ -97,7 +101,7 @@ class Bignum {
   static bool PlusLess(const Bignum& a, const Bignum& b, const Bignum& c) {
     return PlusCompare(a, b, c) < 0;
   }
- private:
+private:
   typedef uint32_t Chunk;
   typedef uint64_t DoubleChunk;
 
@@ -125,7 +129,9 @@ class Bignum {
   // shift_amount must be < kBigitSize.
   void BigitsShiftLeft(int shift_amount);
   // BigitLength includes the "hidden" digits encoded in the exponent.
-  int BigitLength() const { return used_digits_ + exponent_; }
+  int BigitLength() const {
+    return used_digits_ + exponent_;
+  }
   Chunk BigitAt(int index) const;
   void SubtractTimes(const Bignum& other, int factor);
 
diff --git a/util/double-conversion/cached-powers.h b/util/double-conversion/cached-powers.h
index 61a50614c..3daf52d51 100644
--- a/util/double-conversion/cached-powers.h
+++ b/util/double-conversion/cached-powers.h
@@ -30,10 +30,12 @@
 
 #include "diy-fp.h"
 
-namespace double_conversion {
+namespace double_conversion
+{
 
-class PowersOfTenCache {
- public:
+class PowersOfTenCache
+{
+public:
 
   // Not all powers of ten are cached. The decimal exponent of two neighboring
   // cached numbers will differ by kDecimalExponentDistance.
@@ -45,9 +47,9 @@ class PowersOfTenCache {
   // Returns a cached power-of-ten with a binary exponent in the range
   // [min_exponent; max_exponent] (boundaries included).
   static void GetCachedPowerForBinaryExponentRange(int min_exponent,
-                                                   int max_exponent,
-                                                   DiyFp* power,
-                                                   int* decimal_exponent);
+      int max_exponent,
+      DiyFp* power,
+      int* decimal_exponent);
 
   // Returns a cached power of ten x ~= 10^k such that
   //   k <= decimal_exponent < k + kCachedPowersDecimalDistance.
@@ -55,8 +57,8 @@ class PowersOfTenCache {
   //   kMinDecimalExponent <= requested_exponent, and
   //   requested_exponent < kMaxDecimalExponent + kDecimalExponentDistance.
   static void GetCachedPowerForDecimalExponent(int requested_exponent,
-                                               DiyFp* power,
-                                               int* found_exponent);
+      DiyFp* power,
+      int* found_exponent);
 };
 
 }  // namespace double_conversion
diff --git a/util/double-conversion/diy-fp.h b/util/double-conversion/diy-fp.h
index 9dcf8fbdb..39a6bd7dd 100644
--- a/util/double-conversion/diy-fp.h
+++ b/util/double-conversion/diy-fp.h
@@ -30,15 +30,17 @@
 
 #include "utils.h"
 
-namespace double_conversion {
+namespace double_conversion
+{
 
 // This "Do It Yourself Floating Point" class implements a floating-point number
 // with a uint64 significand and an int exponent. Normalized DiyFp numbers will
 // have the most significant bit of the significand set.
 // Multiplication and Subtraction do not normalize their results.
 // DiyFp are not designed to contain special doubles (NaN and Infinity).
-class DiyFp {
- public:
+class DiyFp
+{
+public:
   static const int kSignificandSize = 64;
 
   DiyFp() : f_(0), e_(0) {}
@@ -100,13 +102,21 @@ class DiyFp {
     return result;
   }
 
-  uint64_t f() const { return f_; }
-  int e() const { return e_; }
+  uint64_t f() const {
+    return f_;
+  }
+  int e() const {
+    return e_;
+  }
 
-  void set_f(uint64_t new_value) { f_ = new_value; }
-  void set_e(int new_value) { e_ = new_value; }
+  void set_f(uint64_t new_value) {
+    f_ = new_value;
+  }
+  void set_e(int new_value) {
+    e_ = new_value;
+  }
 
- private:
+private:
   static const uint64_t kUint64MSB = UINT64_2PART_C(0x80000000, 00000000);
 
   uint64_t f_;
diff --git a/util/double-conversion/double-conversion.h b/util/double-conversion/double-conversion.h
index 1c3387d4f..b3e51bae8 100644
--- a/util/double-conversion/double-conversion.h
+++ b/util/double-conversion/double-conversion.h
@@ -30,10 +30,12 @@
 
 #include "utils.h"
 
-namespace double_conversion {
+namespace double_conversion
+{
 
-class DoubleToStringConverter {
- public:
+class DoubleToStringConverter
+{
+public:
   // When calling ToFixed with a double > 10^kMaxFixedDigitsBeforePoint
   // or a requested_digits parameter > kMaxFixedDigitsAfterPoint then the
   // function returns false.
@@ -112,20 +114,20 @@ class DoubleToStringConverter {
                           int decimal_in_shortest_high,
                           int max_leading_padding_zeroes_in_precision_mode,
                           int max_trailing_padding_zeroes_in_precision_mode)
-      : flags_(flags),
-        infinity_symbol_(infinity_symbol),
-        nan_symbol_(nan_symbol),
-        exponent_character_(exponent_character),
-        decimal_in_shortest_low_(decimal_in_shortest_low),
-        decimal_in_shortest_high_(decimal_in_shortest_high),
-        max_leading_padding_zeroes_in_precision_mode_(
-            max_leading_padding_zeroes_in_precision_mode),
-        max_trailing_padding_zeroes_in_precision_mode_(
-            max_trailing_padding_zeroes_in_precision_mode) {
+    : flags_(flags),
+      infinity_symbol_(infinity_symbol),
+      nan_symbol_(nan_symbol),
+      exponent_character_(exponent_character),
+      decimal_in_shortest_low_(decimal_in_shortest_low),
+      decimal_in_shortest_high_(decimal_in_shortest_high),
+      max_leading_padding_zeroes_in_precision_mode_(
+        max_leading_padding_zeroes_in_precision_mode),
+      max_trailing_padding_zeroes_in_precision_mode_(
+        max_trailing_padding_zeroes_in_precision_mode) {
     // When 'trailing zero after the point' is set, then 'trailing point'
     // must be set too.
     ASSERT(((flags & EMIT_TRAILING_DECIMAL_POINT) != 0) ||
-        !((flags & EMIT_TRAILING_ZERO_AFTER_POINT) != 0));
+           !((flags & EMIT_TRAILING_ZERO_AFTER_POINT) != 0));
   }
 
   // Returns a converter following the EcmaScript specification.
@@ -341,7 +343,7 @@ class DoubleToStringConverter {
                             int* length,
                             int* point);
 
- private:
+private:
   // Implementation for ToShortest and ToShortestSingle.
   bool ToShortestIeeeNumber(double value,
                             StringBuilder* result_builder,
@@ -378,8 +380,9 @@ class DoubleToStringConverter {
 };
 
 
-class StringToDoubleConverter {
- public:
+class StringToDoubleConverter
+{
+public:
   // Enumeration for allowing octals and ignoring junk when converting
   // strings to numbers.
   enum Flags {
@@ -488,11 +491,11 @@ class StringToDoubleConverter {
                           double junk_string_value,
                           const char* infinity_symbol,
                           const char* nan_symbol)
-      : flags_(flags),
-        empty_string_value_(empty_string_value),
-        junk_string_value_(junk_string_value),
-        infinity_symbol_(infinity_symbol),
-        nan_symbol_(nan_symbol) {
+    : flags_(flags),
+      empty_string_value_(empty_string_value),
+      junk_string_value_(junk_string_value),
+      infinity_symbol_(infinity_symbol),
+      nan_symbol_(nan_symbol) {
   }
 
   // Performs the conversion.
@@ -516,7 +519,7 @@ class StringToDoubleConverter {
                                            processed_characters_count, false));
   }
 
- private:
+private:
   const int flags_;
   const double empty_string_value_;
   const double junk_string_value_;
diff --git a/util/double-conversion/fast-dtoa.h b/util/double-conversion/fast-dtoa.h
index 5f1e8eee5..184f9cade 100644
--- a/util/double-conversion/fast-dtoa.h
+++ b/util/double-conversion/fast-dtoa.h
@@ -30,7 +30,8 @@
 
 #include "utils.h"
 
-namespace double_conversion {
+namespace double_conversion
+{
 
 enum FastDtoaMode {
   // Computes the shortest representation of the given input. The returned
diff --git a/util/double-conversion/fixed-dtoa.h b/util/double-conversion/fixed-dtoa.h
index 3bdd08e21..9383cb936 100644
--- a/util/double-conversion/fixed-dtoa.h
+++ b/util/double-conversion/fixed-dtoa.h
@@ -30,7 +30,8 @@
 
 #include "utils.h"
 
-namespace double_conversion {
+namespace double_conversion
+{
 
 // Produces digits necessary to print a given number with
 // 'fractional_count' digits after the decimal point.
diff --git a/util/double-conversion/ieee.h b/util/double-conversion/ieee.h
index 839dc47d4..0922129d5 100644
--- a/util/double-conversion/ieee.h
+++ b/util/double-conversion/ieee.h
@@ -30,17 +30,31 @@
 
 #include "diy-fp.h"
 
-namespace double_conversion {
+namespace double_conversion
+{
 
 // We assume that doubles and uint64_t have the same endianness.
-static uint64_t double_to_uint64(double d) { return BitCast<uint64_t>(d); }
-static double uint64_to_double(uint64_t d64) { return BitCast<double>(d64); }
-static uint32_t float_to_uint32(float f) { return BitCast<uint32_t>(f); }
-static float uint32_to_float(uint32_t d32) { return BitCast<float>(d32); }
+static uint64_t double_to_uint64(double d)
+{
+  return BitCast<uint64_t>(d);
+}
+static double uint64_to_double(uint64_t d64)
+{
+  return BitCast<double>(d64);
+}
+static uint32_t float_to_uint32(float f)
+{
+  return BitCast<uint32_t>(f);
+}
+static float uint32_to_float(uint32_t d32)
+{
+  return BitCast<float>(d32);
+}
 
 // Helper functions for doubles.
-class Double {
- public:
+class Double
+{
+public:
   static const uint64_t kSignMask = UINT64_2PART_C(0x80000000, 00000000);
   static const uint64_t kExponentMask = UINT64_2PART_C(0x7FF00000, 00000000);
   static const uint64_t kSignificandMask = UINT64_2PART_C(0x000FFFFF, FFFFFFFF);
@@ -113,7 +127,7 @@ class Double {
 
     uint64_t d64 = AsUint64();
     int biased_e =
-        static_cast<int>((d64 & kExponentMask) >> kPhysicalSignificandSize);
+      static_cast<int>((d64 & kExponentMask) >> kPhysicalSignificandSize);
     return biased_e - kExponentBias;
   }
 
@@ -143,13 +157,13 @@ class Double {
   bool IsNan() const {
     uint64_t d64 = AsUint64();
     return ((d64 & kExponentMask) == kExponentMask) &&
-        ((d64 & kSignificandMask) != 0);
+           ((d64 & kSignificandMask) != 0);
   }
 
   bool IsInfinite() const {
     uint64_t d64 = AsUint64();
     return ((d64 & kExponentMask) == kExponentMask) &&
-        ((d64 & kSignificandMask) == 0);
+           ((d64 & kSignificandMask) == 0);
   }
 
   int Sign() const {
@@ -197,7 +211,9 @@ class Double {
     return physical_significand_is_zero && (Exponent() != kDenormalExponent);
   }
 
-  double value() const { return uint64_to_double(d64_); }
+  double value() const {
+    return uint64_to_double(d64_);
+  }
 
   // Returns the significand size for a given order of magnitude.
   // If v = f*2^e with 2^p-1 <= f <= 2^p then p+e is v's order of magnitude.
@@ -221,7 +237,7 @@ class Double {
     return Double(kNaN).value();
   }
 
- private:
+private:
   static const int kExponentBias = 0x3FF + kPhysicalSignificandSize;
   static const int kDenormalExponent = -kExponentBias + 1;
   static const int kMaxExponent = 0x7FF - kExponentBias;
@@ -254,12 +270,13 @@ class Double {
       biased_exponent = static_cast<uint64_t>(exponent + kExponentBias);
     }
     return (significand & kSignificandMask) |
-        (biased_exponent << kPhysicalSignificandSize);
+           (biased_exponent << kPhysicalSignificandSize);
   }
 };
 
-class Single {
- public:
+class Single
+{
+public:
   static const uint32_t kSignMask = 0x80000000;
   static const uint32_t kExponentMask = 0x7F800000;
   static const uint32_t kSignificandMask = 0x007FFFFF;
@@ -289,7 +306,7 @@ class Single {
 
     uint32_t d32 = AsUint32();
     int biased_e =
-        static_cast<int>((d32 & kExponentMask) >> kPhysicalSignificandSize);
+      static_cast<int>((d32 & kExponentMask) >> kPhysicalSignificandSize);
     return biased_e - kExponentBias;
   }
 
@@ -319,13 +336,13 @@ class Single {
   bool IsNan() const {
     uint32_t d32 = AsUint32();
     return ((d32 & kExponentMask) == kExponentMask) &&
-        ((d32 & kSignificandMask) != 0);
+           ((d32 & kSignificandMask) != 0);
   }
 
   bool IsInfinite() const {
     uint32_t d32 = AsUint32();
     return ((d32 & kExponentMask) == kExponentMask) &&
-        ((d32 & kSignificandMask) == 0);
+           ((d32 & kSignificandMask) == 0);
   }
 
   int Sign() const {
@@ -373,7 +390,9 @@ class Single {
     return physical_significand_is_zero && (Exponent() != kDenormalExponent);
   }
 
-  float value() const { return uint32_to_float(d32_); }
+  float value() const {
+    return uint32_to_float(d32_);
+  }
 
   static float Infinity() {
     return Single(kInfinity).value();
@@ -383,7 +402,7 @@ class Single {
     return Single(kNaN).value();
   }
 
- private:
+private:
   static const int kExponentBias = 0x7F + kPhysicalSignificandSize;
   static const int kDenormalExponent = -kExponentBias + 1;
   static const int kMaxExponent = 0xFF - kExponentBias;
diff --git a/util/double-conversion/strtod.h b/util/double-conversion/strtod.h
index ed0293b8f..1d81078d2 100644
--- a/util/double-conversion/strtod.h
+++ b/util/double-conversion/strtod.h
@@ -30,7 +30,8 @@
 
 #include "utils.h"
 
-namespace double_conversion {
+namespace double_conversion
+{
 
 // The buffer must only contain digits in the range [0-9]. It must not
 // contain a dot or a sign. It must not start with '0', and must not be empty.
diff --git a/util/double-conversion/utils.h b/util/double-conversion/utils.h
index 2bd716050..91f1e6c48 100644
--- a/util/double-conversion/utils.h
+++ b/util/double-conversion/utils.h
@@ -126,25 +126,29 @@ typedef unsigned __int64 uint64_t;
   DISALLOW_COPY_AND_ASSIGN(TypeName)
 #endif
 
-namespace double_conversion {
+namespace double_conversion
+{
 
 static const int kCharSize = sizeof(char);
 
 // Returns the maximum of the two parameters.
 template <typename T>
-static T Max(T a, T b) {
+static T Max(T a, T b)
+{
   return a < b ? b : a;
 }
 
 
 // Returns the minimum of the two parameters.
 template <typename T>
-static T Min(T a, T b) {
+static T Min(T a, T b)
+{
   return a < b ? a : b;
 }
 
 
-inline int StrLength(const char* string) {
+inline int StrLength(const char* string)
+{
   size_t length = strlen(string);
   ASSERT(length == static_cast<size_t>(static_cast<int>(length)));
   return static_cast<int>(length);
@@ -152,8 +156,9 @@ inline int StrLength(const char* string) {
 
 // This is a simplified version of V8's Vector class.
 template <typename T>
-class Vector {
- public:
+class Vector
+{
+public:
   Vector() : start_(NULL), length_(0) {}
   Vector(T* data, int length) : start_(data), length_(length) {
     ASSERT(length == 0 || (length > 0 && data != NULL));
@@ -169,13 +174,19 @@ class Vector {
   }
 
   // Returns the length of the vector.
-  int length() const { return length_; }
+  int length() const {
+    return length_;
+  }
 
   // Returns whether or not the vector is empty.
-  bool is_empty() const { return length_ == 0; }
+  bool is_empty() const {
+    return length_ == 0;
+  }
 
   // Returns the pointer to the start of the data in the vector.
-  T* start() const { return start_; }
+  T* start() const {
+    return start_;
+  }
 
   // Access individual vector elements - checks bounds in debug mode.
   T& operator[](int index) const {
@@ -183,11 +194,15 @@ class Vector {
     return start_[index];
   }
 
-  T& first() { return start_[0]; }
+  T& first() {
+    return start_[0];
+  }
 
-  T& last() { return start_[length_ - 1]; }
+  T& last() {
+    return start_[length_ - 1];
+  }
 
- private:
+private:
   T* start_;
   int length_;
 };
@@ -196,14 +211,19 @@ class Vector {
 // Helper class for building result strings in a character buffer. The
 // purpose of the class is to use safe operations that checks the
 // buffer bounds on all operations in debug mode.
-class StringBuilder {
- public:
+class StringBuilder
+{
+public:
   StringBuilder(char* buffer, int size)
-      : buffer_(buffer, size), position_(0) { }
+    : buffer_(buffer, size), position_(0) { }
 
-  ~StringBuilder() { if (!is_finalized()) Finalize(); }
+  ~StringBuilder() {
+    if (!is_finalized()) Finalize();
+  }
 
-  int size() const { return buffer_.length(); }
+  int size() const {
+    return buffer_.length();
+  }
 
   // Get the current position in the builder.
   int position() const {
@@ -212,7 +232,9 @@ class StringBuilder {
   }
 
   // Reset the position.
-  void Reset() { position_ = 0; }
+  void Reset() {
+    position_ = 0;
+  }
 
   // Add a single character to the builder. It is not allowed to add
   // 0-characters; use the Finalize() method to terminate the string
@@ -262,11 +284,13 @@ class StringBuilder {
     return buffer_.start();
   }
 
- private:
+private:
   Vector<char> buffer_;
   int position_;
 
-  bool is_finalized() const { return position_ < 0; }
+  bool is_finalized() const {
+    return position_ < 0;
+  }
 
   DISALLOW_IMPLICIT_CONSTRUCTORS(StringBuilder);
 };
@@ -296,7 +320,8 @@ class StringBuilder {
 // enough that it can no longer see that you have cast one pointer type to
 // another thus avoiding the warning.
 template <class Dest, class Source>
-inline Dest BitCast(const Source& source) {
+inline Dest BitCast(const Source& source)
+{
   // Compile time assertion: sizeof(Dest) == sizeof(Source)
   // A compile error here means your Dest and Source have different sizes.
   typedef char VerifySizesAreEqual[sizeof(Dest) == sizeof(Source) ? 1 : -1];
@@ -307,7 +332,8 @@ inline Dest BitCast(const Source& source) {
 }
 
 template <class Dest, class Source>
-inline Dest BitCast(Source* source) {
+inline Dest BitCast(Source* source)
+{
   return BitCast<Dest>(reinterpret_cast<uintptr_t>(source));
 }