Merge branch 'master' into mmt-dev

Conflicts:
	Jamroot
	moses/TranslationModel/UG/mmsapt.h

42 files changed, 62 insertions, 491 deletions

diff --git a/moses/ChartManager.cpp b/moses/ChartManager.cpp
index d221bd0fc..4856b3656 100644
--- a/moses/ChartManager.cpp
+++ b/moses/ChartManager.cpp
@@ -19,7 +19,7 @@
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
  ***********************************************************************/
 
-#include <stdio.h>
+#include <cstdio>
 #include "ChartManager.h"
 #include "ChartCell.h"
 #include "ChartHypothesis.h"
diff --git a/moses/FF/ExternalFeature.cpp b/moses/FF/ExternalFeature.cpp
deleted file mode 100644
index 10800d24d..000000000
--- a/moses/FF/ExternalFeature.cpp
+++ /dev/null
@@ -1,72 +0,0 @@
-#include "ExternalFeature.h"
-#include <dlfcn.h>
-#include <stdlib.h>
-#include <iostream>
-#include "util/exception.hh"
-
-using namespace std;
-
-namespace Moses
-{
-ExternalFeatureState::ExternalFeatureState(int stateSize, void *data)
-{
-  m_stateSize = stateSize;
-  m_data = malloc(stateSize);
-  memcpy(m_data, data, stateSize);
-}
-
-void ExternalFeature::Load()
-{
-  string nparam = "testing";
-
-  if (m_path.size() < 1) {
-    UTIL_THROW2("External requires a path to a dynamic library");
-  }
-  lib_handle = dlopen(m_path.c_str(), RTLD_LAZY);
-  if (!lib_handle) {
-    UTIL_THROW2("dlopen reports: " << dlerror() << ". Did you provide a full path to the dynamic library?";);
-  }
-  CdecFF* (*fn)(const string&) =
-    (CdecFF* (*)(const string&))(dlsym(lib_handle, "create_ff"));
-  if (!fn) {
-    UTIL_THROW2("dlsym reports: " << dlerror());
-  }
-  ff_ext = (*fn)(nparam);
-  m_stateSize = ff_ext->StateSize();
-
-}
-
-ExternalFeature::~ExternalFeature()
-{
-  delete ff_ext;
-  dlclose(lib_handle);
-}
-
-void ExternalFeature::SetParameter(const std::string& key, const std::string& value)
-{
-  if (key == "path") {
-    m_path = value;
-  } else {
-    StatefulFeatureFunction::SetParameter(key, value);
-  }
-}
-
-FFState* ExternalFeature::EvaluateWhenApplied(
-  const Hypothesis& cur_hypo,
-  const FFState* prev_state,
-  ScoreComponentCollection* accumulator) const
-{
-  return new ExternalFeatureState(m_stateSize);
-}
-
-FFState* ExternalFeature::EvaluateWhenApplied(
-  const ChartHypothesis& /* cur_hypo */,
-  int /* featureID - used to index the state in the previous hypotheses */,
-  ScoreComponentCollection* accumulator) const
-{
-  return new ExternalFeatureState(m_stateSize);
-}
-
-
-}
-
diff --git a/moses/FF/ExternalFeature.h b/moses/FF/ExternalFeature.h
deleted file mode 100644
index 6c0fb829e..000000000
--- a/moses/FF/ExternalFeature.h
+++ /dev/null
@@ -1,100 +0,0 @@
-#pragma once
-
-#include <string>
-#include <cstring>
-#include <cstdlib>
-#include "StatefulFeatureFunction.h"
-#include "FFState.h"
-
-namespace Moses
-{
-class CdecFF;
-
-class ExternalFeatureState : public FFState
-{
-protected:
-  int m_stateSize;
-  void *m_data;
-public:
-  ExternalFeatureState(int stateSize)
-    :m_stateSize(stateSize)
-    ,m_data(NULL) {
-  }
-  ExternalFeatureState(int stateSize, void *data);
-
-  ~ExternalFeatureState() {
-    free(m_data);
-  }
-
-  int Compare(const FFState& other) const {
-    const ExternalFeatureState &otherFF = static_cast<const ExternalFeatureState&>(other);
-    int ret = memcmp(m_data, otherFF.m_data, m_stateSize);
-    return ret;
-  }
-};
-
-// copied from cdec
-class ExternalFeature : public StatefulFeatureFunction
-{
-public:
-  ExternalFeature(const std::string &line)
-    :StatefulFeatureFunction(line) {
-    ReadParameters();
-  }
-  ~ExternalFeature();
-
-  void Load();
-
-  bool IsUseable(const FactorMask &mask) const {
-    return true;
-  }
-
-  void SetParameter(const std::string& key, const std::string& value);
-
-  void EvaluateInIsolation(const Phrase &source
-                           , const TargetPhrase &targetPhrase
-                           , ScoreComponentCollection &scoreBreakdown
-                           , ScoreComponentCollection &estimatedFutureScore) const {
-  }
-  void EvaluateWithSourceContext(const InputType &input
-                                 , const InputPath &inputPath
-                                 , const TargetPhrase &targetPhrase
-                                 , const StackVec *stackVec
-                                 , ScoreComponentCollection &scoreBreakdown
-                                 , ScoreComponentCollection *estimatedFutureScore = NULL) const {
-  }
-
-  void EvaluateTranslationOptionListWithSourceContext(const InputType &input
-      , const TranslationOptionList &translationOptionList) const {
-  }
-
-  FFState* EvaluateWhenApplied(
-    const Hypothesis& cur_hypo,
-    const FFState* prev_state,
-    ScoreComponentCollection* accumulator) const;
-
-  FFState* EvaluateWhenApplied(
-    const ChartHypothesis& /* cur_hypo */,
-    int /* featureID - used to index the state in the previous hypotheses */,
-    ScoreComponentCollection* accumulator) const;
-
-  virtual const FFState* EmptyHypothesisState(const InputType &input) const {
-    return new ExternalFeatureState(m_stateSize);
-  }
-
-protected:
-  std::string m_path;
-  void* lib_handle;
-  CdecFF *ff_ext;
-  int m_stateSize;
-};
-
-class CdecFF
-{
-public:
-  virtual ~CdecFF() {}
-  virtual int StateSize() const = 0;
-};
-
-}
-
diff --git a/moses/FF/Factory.cpp b/moses/FF/Factory.cpp
index 218e458ff..80e4a4243 100644
--- a/moses/FF/Factory.cpp
+++ b/moses/FF/Factory.cpp
@@ -37,7 +37,6 @@
 #include "moses/FF/PhrasePenalty.h"
 #include "moses/FF/OSM-Feature/OpSequenceModel.h"
 #include "moses/FF/ControlRecombination.h"
-#include "moses/FF/ExternalFeature.h"
 #include "moses/FF/ConstrainedDecoding.h"
 #include "moses/FF/SoftSourceSyntacticConstraintsFeature.h"
 #include "moses/FF/CoveredReferenceFeature.h"
@@ -229,7 +228,6 @@ FeatureRegistry::FeatureRegistry()
   MOSES_FNAME(ControlRecombination);
   MOSES_FNAME(ConstrainedDecoding);
   MOSES_FNAME(CoveredReferenceFeature);
-  MOSES_FNAME(ExternalFeature);
   MOSES_FNAME(SourceGHKMTreeInputMatchFeature);
   MOSES_FNAME(SoftSourceSyntacticConstraintsFeature);
   MOSES_FNAME(TreeStructureFeature);
diff --git a/moses/FF/SoftSourceSyntacticConstraintsFeature.cpp b/moses/FF/SoftSourceSyntacticConstraintsFeature.cpp
index 05a3c92e0..d57c42d99 100644
--- a/moses/FF/SoftSourceSyntacticConstraintsFeature.cpp
+++ b/moses/FF/SoftSourceSyntacticConstraintsFeature.cpp
@@ -1,6 +1,6 @@
 #include <vector>
 #include <limits>
-#include <assert.h>
+#include <cassert>
 #include "SoftSourceSyntacticConstraintsFeature.h"
 #include "moses/StaticData.h"
 #include "moses/InputFileStream.h"
diff --git a/moses/FF/SourceGHKMTreeInputMatchFeature.cpp b/moses/FF/SourceGHKMTreeInputMatchFeature.cpp
index 15509f1e4..d33cbf94a 100644
--- a/moses/FF/SourceGHKMTreeInputMatchFeature.cpp
+++ b/moses/FF/SourceGHKMTreeInputMatchFeature.cpp
@@ -1,6 +1,6 @@
 #include <map>
 #include <vector>
-#include <assert.h>
+#include <cassert>
 #include "SourceGHKMTreeInputMatchFeature.h"
 #include "moses/StaticData.h"
 #include "moses/InputFileStream.h"
diff --git a/moses/FF/VW/VWFeatureBase.h b/moses/FF/VW/VWFeatureBase.h
index 04eb6974a..d0f5ebebe 100644
--- a/moses/FF/VW/VWFeatureBase.h
+++ b/moses/FF/VW/VWFeatureBase.h
@@ -3,7 +3,7 @@
 #include <string>
 #include <boost/thread/tss.hpp>
 
-#include "Classifier.h"
+#include "vw/Classifier.h"
 #include "moses/TypeDef.h"
 #include "moses/Util.h"
 #include "moses/FF/StatelessFeatureFunction.h"
diff --git a/moses/FF/WordTranslationFeature.cpp b/moses/FF/WordTranslationFeature.cpp
index 4c0233885..05883df12 100644
--- a/moses/FF/WordTranslationFeature.cpp
+++ b/moses/FF/WordTranslationFeature.cpp
@@ -22,8 +22,8 @@ WordTranslationFeature::WordTranslationFeature(const std::string &line)
   ,m_simple(true)
   ,m_sourceContext(false)
   ,m_targetContext(false)
-  ,m_ignorePunctuation(false)
   ,m_domainTrigger(false)
+  ,m_ignorePunctuation(false)
 {
   VERBOSE(1, "Initializing feature " << GetScoreProducerDescription() << " ...");
   ReadParameters();
diff --git a/moses/Hypothesis.cpp b/moses/Hypothesis.cpp
index 3707aed18..79a469523 100644
--- a/moses/Hypothesis.cpp
+++ b/moses/Hypothesis.cpp
@@ -484,9 +484,7 @@ namespace Moses
       
       targetOffset += tp.GetSize();
     }
-    // Removing std::endl here breaks -alignment-output-file, so stop doing that, please :)
-    // Or fix it somewhere else.
-    out << std::endl;
+    // Used by --print-alignment-info, so no endl
   }
 
   void 
diff --git a/moses/LM/Ken.cpp b/moses/LM/Ken.cpp
index 499886505..e86275050 100644
--- a/moses/LM/Ken.cpp
+++ b/moses/LM/Ken.cpp
@@ -22,7 +22,7 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 #include <cstring>
 #include <iostream>
 #include <memory>
-#include <stdlib.h>
+#include <cstdlib>
 #include <boost/shared_ptr.hpp>
 #include <boost/lexical_cast.hpp>
 
@@ -169,9 +169,9 @@ template <class Model> LanguageModelKen<Model>::LanguageModelKen(const LanguageM
   :LanguageModel(copy_from.GetArgLine()),
    m_ngram(copy_from.m_ngram),
 // TODO: don't copy this.
-   m_lmIdLookup(copy_from.m_lmIdLookup),
+   m_beginSentenceFactor(copy_from.m_beginSentenceFactor),
    m_factorType(copy_from.m_factorType),
-   m_beginSentenceFactor(copy_from.m_beginSentenceFactor)
+   m_lmIdLookup(copy_from.m_lmIdLookup)
 {
 }
 
diff --git a/moses/LM/Remote.cpp b/moses/LM/Remote.cpp
index 4527a52a7..af02a6617 100644
--- a/moses/LM/Remote.cpp
+++ b/moses/LM/Remote.cpp
@@ -1,5 +1,5 @@
-#include <stdio.h>
-#include <stdlib.h>
+#include <cstdio>
+#include <cstdlib>
 #include <unistd.h>
 #include <sys/types.h>
 #include <sys/socket.h>
diff --git a/moses/Manager.cpp b/moses/Manager.cpp
index e368c58f7..cb91a9d29 100644
--- a/moses/Manager.cpp
+++ b/moses/Manager.cpp
@@ -1876,8 +1876,7 @@ void Manager::OutputAlignment(ostream &out, const vector<const Hypothesis *> &ed
 
     targetOffset += tp.GetSize();
   }
-  // Removing std::endl here breaks -alignment-output-file, so stop doing that, please :)
-  // Or fix it somewhere else.
+  // Used by --alignment-output-file so requires endl
   out << std::endl;
 }
 
@@ -2032,6 +2031,8 @@ void Manager::OutputBestHypo(const Moses::TrellisPath &path, long /*translationI
 void Manager::OutputAlignment(std::ostringstream &out, const TrellisPath &path) const
 {
   Hypothesis::OutputAlignment(out, path.GetEdges());
+  // Used by --alignment-output-file so requires endl
+  out << std::endl;
 }
 
 } // namespace
diff --git a/moses/PDTAimp.cpp b/moses/PDTAimp.cpp
index 1b9e789ce..6770a5c17 100644
--- a/moses/PDTAimp.cpp
+++ b/moses/PDTAimp.cpp
@@ -222,7 +222,6 @@ void PDTAimp::CacheSource(ConfusionNet const& src)
     TRACE_ERR("\n");
   }
 
-  typedef StringTgtCand::Tokens sPhrase;
   typedef std::map<StringTgtCand::Tokens,TScores> E2Costs;
 
   std::map<Range,E2Costs> cov2cand;
diff --git a/moses/PP/CountsPhraseProperty.cpp b/moses/PP/CountsPhraseProperty.cpp
index 00bc08011..a8cefe37f 100644
--- a/moses/PP/CountsPhraseProperty.cpp
+++ b/moses/PP/CountsPhraseProperty.cpp
@@ -1,6 +1,6 @@
 #include "moses/PP/CountsPhraseProperty.h"
 #include <sstream>
-#include <assert.h>
+#include <cassert>
 
 namespace Moses
 {
diff --git a/moses/PP/NonTermContextProperty.cpp b/moses/PP/NonTermContextProperty.cpp
index d1ea6a554..3126e90d9 100644
--- a/moses/PP/NonTermContextProperty.cpp
+++ b/moses/PP/NonTermContextProperty.cpp
@@ -1,6 +1,6 @@
 #include "moses/PP/NonTermContextProperty.h"
 #include <string>
-#include <assert.h>
+#include <cassert>
 #include "moses/Util.h"
 #include "moses/FactorCollection.h"
 
diff --git a/moses/PP/SourceLabelsPhraseProperty.cpp b/moses/PP/SourceLabelsPhraseProperty.cpp
index efe5ae741..18229fd1a 100644
--- a/moses/PP/SourceLabelsPhraseProperty.cpp
+++ b/moses/PP/SourceLabelsPhraseProperty.cpp
@@ -5,7 +5,7 @@
 #include <sstream>
 #include <string>
 #include <queue>
-#include <assert.h>
+#include <cassert>
 #include <limits>
 
 namespace Moses
diff --git a/moses/SentenceStats.h b/moses/SentenceStats.h
index c1650eac1..998adc74f 100644
--- a/moses/SentenceStats.h
+++ b/moses/SentenceStats.h
@@ -25,7 +25,7 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 #include <iostream>
 #include <string>
 #include <vector>
-#include <time.h>
+#include <ctime>
 #include "Timer.h"
 #include "Phrase.h"
 #include "Hypothesis.h"
diff --git a/moses/Syntax/Cube.cpp b/moses/Syntax/Cube.cpp
index 0249291d3..6cbf72903 100644
--- a/moses/Syntax/Cube.cpp
+++ b/moses/Syntax/Cube.cpp
@@ -56,7 +56,7 @@ void Cube::CreateNeighbours(const std::vector<int> &coordinates)
 
   // Create each neighbour along the vertex stack dimensions.
   for (std::size_t i = 0; i < coordinates.size()-1; ++i) {
-    int x = coordinates[i];
+    const std::size_t x = coordinates[i];
     if (m_bundle.stacks[i]->size() > x+1) {
       ++tmpCoordinates[i];
       CreateNeighbour(tmpCoordinates);
@@ -64,7 +64,7 @@ void Cube::CreateNeighbours(const std::vector<int> &coordinates)
     }
   }
   // Create the neighbour along the translation dimension.
-  int x = coordinates.back();
+  const std::size_t x = coordinates.back();
   if (m_bundle.translations->GetSize() > x+1) {
     ++tmpCoordinates.back();
     CreateNeighbour(tmpCoordinates);
diff --git a/moses/Syntax/F2S/HyperTreeLoader.cpp b/moses/Syntax/F2S/HyperTreeLoader.cpp
index 0ffc3602f..f3caa2cec 100644
--- a/moses/Syntax/F2S/HyperTreeLoader.cpp
+++ b/moses/Syntax/F2S/HyperTreeLoader.cpp
@@ -3,7 +3,7 @@
 #include <sys/stat.h>
 
 #include <cmath>
-#include <stdlib.h>
+#include <cstdlib>
 #include <fstream>
 #include <string>
 #include <iterator>
diff --git a/moses/Syntax/F2S/RuleMatcherHyperTree-inl.h b/moses/Syntax/F2S/RuleMatcherHyperTree-inl.h
index d7ce2cf7c..74f2347a6 100644
--- a/moses/Syntax/F2S/RuleMatcherHyperTree-inl.h
+++ b/moses/Syntax/F2S/RuleMatcherHyperTree-inl.h
@@ -190,8 +190,9 @@ int RuleMatcherHyperTree<Callback>::SubSeqLength(const HyperPath::NodeSeq &seq,
     int pos)
 {
   int length = 0;
-  while (pos != seq.size() && seq[pos] != HyperPath::kComma) {
-    ++pos;
+  HyperPath::NodeSeq::size_type curpos = pos;
+  while (curpos != seq.size() && seq[curpos] != HyperPath::kComma) {
+    ++curpos;
     ++length;
   }
   return length;
diff --git a/moses/Syntax/S2T/Parsers/Scope3Parser/Parser-inl.h b/moses/Syntax/S2T/Parsers/Scope3Parser/Parser-inl.h
index f50cee3a0..24135c734 100644
--- a/moses/Syntax/S2T/Parsers/Scope3Parser/Parser-inl.h
+++ b/moses/Syntax/S2T/Parsers/Scope3Parser/Parser-inl.h
@@ -163,7 +163,7 @@ void Scope3Parser<Callback>::RecordPatternApplicationSpans(
       for (int j = std::max(e1, i+minSpan-1); j <= e2; ++j) {
         std::size_t span = j-i+1;
         assert(span >= 1);
-        if (span < minSpan) {
+        if (span < std::size_t(minSpan)) {
           continue;
         }
         if (m_maxChartSpan && span > m_maxChartSpan) {
diff --git a/moses/Syntax/S2T/Parsers/Scope3Parser/TailLatticeSearcher.h b/moses/Syntax/S2T/Parsers/Scope3Parser/TailLatticeSearcher.h
index 4e48429ab..4f815c78d 100644
--- a/moses/Syntax/S2T/Parsers/Scope3Parser/TailLatticeSearcher.h
+++ b/moses/Syntax/S2T/Parsers/Scope3Parser/TailLatticeSearcher.h
@@ -58,7 +58,7 @@ private:
 
     const int absStart = m_ranges[0].minStart + offset;
     const int minWidth = std::max(1, range.minEnd - absStart + 1);
-    const int maxWidth = range.maxEnd - absStart + 1;
+    const std::size_t maxWidth = range.maxEnd - absStart + 1;
 
     const std::vector<std::vector<const PVertex *> > &innerVec =
       m_lattice[offset][nonTermIndex+1];
diff --git a/moses/Syntax/S2T/RuleTrieLoader.cpp b/moses/Syntax/S2T/RuleTrieLoader.cpp
index b9f7484ad..a88c0f5fe 100644
--- a/moses/Syntax/S2T/RuleTrieLoader.cpp
+++ b/moses/Syntax/S2T/RuleTrieLoader.cpp
@@ -1,14 +1,14 @@
 #include "RuleTrieLoader.h"
 
 #include <sys/stat.h>
-#include <stdlib.h>
+#include <cstdlib>
 
 #include <fstream>
 #include <string>
 #include <iterator>
 #include <algorithm>
 #include <iostream>
-#include <math.h>
+#include <cmath>
 
 #include "moses/FactorCollection.h"
 #include "moses/Word.h"
diff --git a/moses/TargetPhrase.cpp b/moses/TargetPhrase.cpp
index 70568940d..d6abd16ff 100644
--- a/moses/TargetPhrase.cpp
+++ b/moses/TargetPhrase.cpp
@@ -20,7 +20,7 @@
  ***********************************************************************/
 
 #include <algorithm>
-#include <stdlib.h>
+#include <cstdlib>
 #include "util/exception.hh"
 #include "util/tokenize_piece.hh"
 
diff --git a/moses/ThreadPool.cpp b/moses/ThreadPool.cpp
index 1113cef9d..cba459697 100644
--- a/moses/ThreadPool.cpp
+++ b/moses/ThreadPool.cpp
@@ -57,9 +57,8 @@ void ThreadPool::Execute()
     if (task) {
       // must read from task before run. otherwise task may be deleted by main thread
       // race condition
-      bool del = task->DeleteAfterExecution();
+      task->DeleteAfterExecution();
       task->Run();
-      // if (del) delete task; // not needed any more, since we use shared ptrs.
     }
     m_threadAvailable.notify_all();
   } while (!m_stopped);
diff --git a/moses/TranslationModel/CompactPT/BlockHashIndex.h b/moses/TranslationModel/CompactPT/BlockHashIndex.h
index f8d526930..b3f5e6f4b 100644
--- a/moses/TranslationModel/CompactPT/BlockHashIndex.h
+++ b/moses/TranslationModel/CompactPT/BlockHashIndex.h
@@ -38,7 +38,7 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 #ifdef WITH_THREADS
 #include "moses/ThreadPool.h"
 #else
-#include <time.h>
+#include <ctime>
 #endif
 
 #include <boost/shared_ptr.hpp>
diff --git a/moses/TranslationModel/CompactPT/MurmurHash3.cpp b/moses/TranslationModel/CompactPT/MurmurHash3.cpp
index 4e4cd4258..fb6946bbc 100644
--- a/moses/TranslationModel/CompactPT/MurmurHash3.cpp
+++ b/moses/TranslationModel/CompactPT/MurmurHash3.cpp
@@ -18,7 +18,7 @@
 

 #define FORCE_INLINE	__forceinline

 

-#include <stdlib.h>

+#include <cstdlib>

 

 #define ROTL32(x,y)	_rotl(x,y)

 #define ROTL64(x,y)	_rotl64(x,y)

diff --git a/moses/TranslationModel/DynSAInclude/FileHandler.cpp b/moses/TranslationModel/DynSAInclude/FileHandler.cpp
index 8645833fe..9413ffd7c 100644
--- a/moses/TranslationModel/DynSAInclude/FileHandler.cpp
+++ b/moses/TranslationModel/DynSAInclude/FileHandler.cpp
@@ -1,5 +1,5 @@
 #include "FileHandler.h"
-#include <stdio.h>
+#include <cstdio>
 
 #ifdef WIN32
 #define popen(A, B) _popen(A, B)
diff --git a/moses/TranslationModel/PhraseDictionary.h b/moses/TranslationModel/PhraseDictionary.h
index f80c3febd..667b12bad 100644
--- a/moses/TranslationModel/PhraseDictionary.h
+++ b/moses/TranslationModel/PhraseDictionary.h
@@ -36,7 +36,7 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 #include <boost/thread/tss.hpp>
 #else
 #include <boost/scoped_ptr.hpp>
-#include <time.h>
+#include <ctime>
 #endif
 
 #include "moses/Phrase.h"
diff --git a/moses/TranslationModel/PhraseDictionaryTransliteration.cpp b/moses/TranslationModel/PhraseDictionaryTransliteration.cpp
index a336da759..69b7e9f5f 100644
--- a/moses/TranslationModel/PhraseDictionaryTransliteration.cpp
+++ b/moses/TranslationModel/PhraseDictionaryTransliteration.cpp
@@ -1,5 +1,7 @@
 // vim:tabstop=2
-#include <stdlib.h>
+#include <cstdlib>
+#include <boost/filesystem.hpp>
+
 #include "PhraseDictionaryTransliteration.h"
 #include "moses/TranslationModel/CYKPlusParser/ChartRuleLookupManagerSkeleton.h"
 #include "moses/DecodeGraph.h"
@@ -68,10 +70,9 @@ void PhraseDictionaryTransliteration::GetTargetPhraseCollection(InputPath &input
     inputPath.SetTargetPhrases(*this, tpColl, NULL);
   } else {
     // TRANSLITERATE
-    char *ptr = tmpnam(NULL);
-    string inFile(ptr);
-    ptr = tmpnam(NULL);
-    string outDir(ptr);
+    const boost::filesystem::path
+        inFile = boost::filesystem::unique_path(),
+        outDir = boost::filesystem::unique_path();
 
     ofstream inStream(inFile.c_str());
     inStream << sourcePhrase.ToString() << endl;
@@ -83,14 +84,14 @@ void PhraseDictionaryTransliteration::GetTargetPhraseCollection(InputPath &input
                  " --external-bin-dir " + m_externalDir +
                  " --input-extension " + m_inputLang +
                  " --output-extension " + m_outputLang +
-                 " --oov-file " + inFile +
-                 " --out-dir " + outDir;
+                 " --oov-file " + inFile.native() +
+                 " --out-dir " + outDir.native();
 
     int ret = system(cmd.c_str());
     UTIL_THROW_IF2(ret != 0, "Transliteration script error");
 
     TargetPhraseCollection *tpColl = new TargetPhraseCollection();
-    vector<TargetPhrase*> targetPhrases = CreateTargetPhrases(sourcePhrase, outDir);
+    vector<TargetPhrase*> targetPhrases = CreateTargetPhrases(sourcePhrase, outDir.native());
     vector<TargetPhrase*>::const_iterator iter;
     for (iter = targetPhrases.begin(); iter != targetPhrases.end(); ++iter) {
       TargetPhrase *tp = *iter;
@@ -104,9 +105,7 @@ void PhraseDictionaryTransliteration::GetTargetPhraseCollection(InputPath &input
 
     // clean up temporary files
     remove(inFile.c_str());
-
-    cmd = "rm -rf " + outDir;
-    system(cmd.c_str());
+    boost::filesystem::remove_all(outDir);
   }
 }
 
diff --git a/moses/TranslationModel/ProbingPT/huffmanish.hh b/moses/TranslationModel/ProbingPT/huffmanish.hh
index 46b7dbeea..14db53a69 100644
--- a/moses/TranslationModel/ProbingPT/huffmanish.hh
+++ b/moses/TranslationModel/ProbingPT/huffmanish.hh
@@ -3,7 +3,7 @@
 //Huffman encodes a line and also produces the vocabulary ids
 #include "hash.hh"
 #include "line_splitter.hh"
-#include <stdio.h>
+#include <cstdio>
 #include <fstream>
 #include <iostream>
 #include <sstream>
diff --git a/moses/TranslationModel/ProbingPT/line_splitter.hh b/moses/TranslationModel/ProbingPT/line_splitter.hh
index c699a28c0..36833616f 100644
--- a/moses/TranslationModel/ProbingPT/line_splitter.hh
+++ b/moses/TranslationModel/ProbingPT/line_splitter.hh
@@ -4,7 +4,7 @@
 #include "util/tokenize_piece.hh"
 #include "util/file_piece.hh"
 #include <vector>
-#include <stdlib.h> //atof
+#include <cstdlib> //atof
 #include "util/string_piece.hh"  //Tokenization and work with StringPiece
 #include "util/tokenize_piece.hh"
 #include <vector>
diff --git a/moses/TranslationModel/ProbingPT/storing.hh b/moses/TranslationModel/ProbingPT/storing.hh
index 821fd14ca..eb3b1ea53 100644
--- a/moses/TranslationModel/ProbingPT/storing.hh
+++ b/moses/TranslationModel/ProbingPT/storing.hh
@@ -1,6 +1,6 @@
 #pragma once
 
-#include <stdio.h>
+#include <cstdio>
 #include <fstream>
 #include <iostream>  
 
diff --git a/moses/TranslationModel/ProbingPT/tests/tokenization_tests.cpp b/moses/TranslationModel/ProbingPT/tests/tokenization_tests.cpp
deleted file mode 100644
index 528c9c37c..000000000
--- a/moses/TranslationModel/ProbingPT/tests/tokenization_tests.cpp
+++ /dev/null
@@ -1,206 +0,0 @@
-#include "line_splitter.hh"
-
-bool test_vectorinsert()
-{
-  StringPiece line1 = StringPiece("! ! ! ! ||| ! ! ! ! ||| 0.0804289 0.141656 0.0804289 0.443409 2.718 ||| 0-0 1-1 2-2 3-3 ||| 1 1 1");
-  StringPiece line2 = StringPiece("! ! ! ) , has ||| ! ! ! ) - , a ||| 0.0804289 0.0257627 0.0804289 0.00146736 2.718 ||| 0-0 1-1 2-2 3-3 4-4 4-5 5-6 ||| 1 1 1");
-  line_text output = splitLine(line1);
-  line_text output2 = splitLine(line2);
-
-  //Init container vector and iterator.
-  std::vector<char> container;
-  container.reserve(10000); //Reserve vector
-  std::vector<char>::iterator it = container.begin();
-  std::pair<std::vector<char>::iterator, int> binary_append_ret; //Return values from vector_append
-
-  //Put a value into the vector
-  binary_append_ret = vector_append(&output, &container, it, false);
-  it = binary_append_ret.first;
-  binary_append_ret = vector_append(&output2, &container, it, false);
-  it = binary_append_ret.first;
-
-  std::string test(container.begin(), container.end());
-  std::string should_be = "! ! ! ! 0.0804289 0.141656 0.0804289 0.443409 2.718 0-0 1-1 2-2 3-3 1 1 1! ! ! ) - , a 0.0804289 0.0257627 0.0804289 0.00146736 2.718 0-0 1-1 2-2 3-3 4-4 4-5 5-6 1 1 1";
-  if (test == should_be) {
-    return true;
-  } else {
-    return false;
-  }
-}
-
-bool probabilitiesTest()
-{
-  StringPiece line1 = StringPiece("0.536553 0.75961 0.634108 0.532927 2.718");
-  StringPiece line2 = StringPiece("1.42081e-05 3.91895e-09 0.0738539 0.749514 2.718");
-
-  std::vector<double> pesho;
-  bool peshobool = false;
-  bool kirobool = false;
-  std::vector<double> kiro;
-
-  pesho = splitProbabilities(line1);
-  kiro = splitProbabilities(line2);
-
-  if (pesho[0] == 0.536553 && pesho[1] == 0.75961 && pesho[2] == 0.634108 && pesho[3] == 0.532927 && pesho[4] == 2.718 && pesho.size() == 5) {
-    peshobool = true;
-  } else {
-    std::cout << "Processed: " << pesho[0] << " " << pesho[1] << " " << pesho[2] << " " << pesho[3] << " " << pesho[4] << std::endl;
-    std::cout << "Size is: " << pesho.size() << " Expected 5." << std::endl;
-    std::cout << "Expected: " << "0.536553 0.75961 0.634108 0.532927 2.718" << std::endl;
-  }
-
-  if (kiro[0] == 1.42081e-05 && kiro[1] == 3.91895e-09 && kiro[2] == 0.0738539 && kiro[3] == 0.749514 && kiro[4] == 2.718 && kiro.size() == 5) {
-    kirobool = true;
-  } else {
-    std::cout << "Processed: " << kiro[0] << " " << kiro[1] << " " << kiro[2] << " " << kiro[3] << " " << kiro[4] << std::endl;
-    std::cout << "Size is: " << kiro.size() << " Expected 5." << std::endl;
-    std::cout << "Expected: " << "1.42081e-05 3.91895e-09 0.0738539 0.749514 2.718" << std::endl;
-  }
-
-  return (peshobool && kirobool);
-}
-
-bool wordAll1test()
-{
-  StringPiece line1 = StringPiece("2-0 3-1 4-2 5-2");
-  StringPiece line2 = StringPiece("0-0 1-1 2-2 3-3 4-3 6-4 5-5");
-
-  std::vector<int> pesho;
-  bool peshobool = false;
-  bool kirobool = false;
-  std::vector<int> kiro;
-
-  pesho = splitWordAll1(line1);
-  kiro = splitWordAll1(line2);
-
-  if (pesho[0] == 2 && pesho[1] == 0 && pesho[2] == 3 && pesho[3] == 1 && pesho[4] == 4
-      && pesho[5] == 2 && pesho[6] == 5 && pesho[7] == 2 && pesho.size() == 8) {
-    peshobool = true;
-  } else {
-    std::cout << "Processed: " << pesho[0] << "-" << pesho[1] << " " << pesho[2] << "-" << pesho[3] << " "
-              << pesho[4] << "-" << pesho[5] << " " << pesho[6] << "-" << pesho[7] << std::endl;
-    std::cout << "Size is: " << pesho.size() << " Expected: 8." << std::endl;
-    std::cout << "Expected: " << "2-0 3-1 4-2 5-2" << std::endl;
-  }
-
-  if (kiro[0] == 0 && kiro[1] == 0 && kiro[2] == 1 && kiro[3] == 1 && kiro[4] == 2 && kiro[5] == 2
-      && kiro[6] == 3 && kiro[7] == 3 && kiro[8] == 4 && kiro[9] == 3 && kiro[10] == 6 && kiro[11] == 4
-      && kiro[12] == 5 && kiro[13] == 5 && kiro.size() == 14) {
-    kirobool = true;
-  } else {
-    std::cout << "Processed: " << kiro[0] << "-" << kiro[1] << " " << kiro[2] << "-" << kiro[3] << " "
-              << kiro[4] << "-" << kiro[5] << " " << kiro[6] << "-" << kiro[7] << " " << kiro[8] << "-" << kiro[9]
-              << " " << kiro[10] << "-" << kiro[11] << " " << kiro[12] << "-" << kiro[13] << std::endl;
-    std::cout << "Size is: " << kiro.size() << " Expected: 14" << std::endl;
-    std::cout << "Expected: " << "0-0 1-1 2-2 3-3 4-3 6-4 5-5" << std::endl;
-  }
-
-  return (peshobool && kirobool);
-}
-
-bool wordAll2test()
-{
-  StringPiece line1 = StringPiece("4 9 1");
-  StringPiece line2 = StringPiece("3255 9 1");
-
-  std::vector<int> pesho;
-  bool peshobool = false;
-  bool kirobool = false;
-  std::vector<int> kiro;
-
-  pesho = splitWordAll2(line1);
-  kiro = splitWordAll2(line2);
-
-  if (pesho[0] == 4 && pesho[1] == 9 && pesho[2] == 1 && pesho.size() == 3) {
-    peshobool = true;
-  } else {
-    std::cout << "Processed: " << pesho[0] << " " << pesho[1] << " " << pesho[2] << std::endl;
-    std::cout << "Size: " << pesho.size() << " Expected: 3" << std::endl;
-    std::cout << "Expected: " << "4 9 1" << std::endl;
-  }
-
-  if (kiro[0] == 3255 && kiro[1] == 9 && kiro[2] == 1 && kiro.size() == 3) {
-    kirobool = true;
-  } else {
-    std::cout << "Processed: " << kiro[0] << " " << kiro[1] << " " << kiro[2] << std::endl;
-    std::cout << "Size: " << kiro.size() << " Expected: 3" << std::endl;
-    std::cout << "Expected: " << "3255 9 1" << std::endl;
-  }
-
-  return (peshobool && kirobool);
-
-}
-
-bool test_tokenization()
-{
-  StringPiece line1 = StringPiece("! ! ! ! ||| ! ! ! ! ||| 0.0804289 0.141656 0.0804289 0.443409 2.718 ||| 0-0 1-1 2-2 3-3 ||| 1 1 1");
-  StringPiece line2 = StringPiece("! ! ! ) , has ||| ! ! ! ) - , a ||| 0.0804289 0.0257627 0.0804289 0.00146736 2.718 ||| 0-0 1-1 2-2 3-3 4-4 4-5 5-6 ||| 1 1 1");
-  StringPiece line3 = StringPiece("! ! ! ) , ||| ! ! ! ) - , ||| 0.0804289 0.075225 0.0804289 0.00310345 2.718 ||| 0-0 1-1 2-2 3-3 4-4 4-5 ||| 1 1 1");
-  StringPiece line4 = StringPiece("! ! ! ) ||| ! ! ! ) . ||| 0.0804289 0.177547 0.0268096 0.000872597 2.718 ||| 0-0 1-1 2-2 3-3 ||| 1 3 1");
-
-  line_text output1 = splitLine(line1);
-  line_text output2 = splitLine(line2);
-  line_text output3 = splitLine(line3);
-  line_text output4 = splitLine(line4);
-
-  bool test1 = output1.prob == StringPiece("0.0804289 0.141656 0.0804289 0.443409 2.718");
-  bool test2 = output2.word_all1 == StringPiece("0-0 1-1 2-2 3-3 4-4 4-5 5-6");
-  bool test3 = output2.target_phrase == StringPiece("! ! ! ) - , a");
-  bool test4 = output3.source_phrase == StringPiece("! ! ! ) ,");
-  bool test5 = output4.word_all2 == StringPiece("1 3 1");
-
-  //std::cout << test1 << " " << test2 << " " << test3 << " " << test4 << std::endl;
-
-  return (test1 && test2 && test3 && test4 && test5);
-
-}
-
-bool test_linesplitter()
-{
-  StringPiece line1 = StringPiece("! &#93;    0.0738539 0.901133 0.0738539 0.65207 2.718  0-0 1-1 1 1 1");
-  target_text ans1;
-  ans1 = splitSingleTargetLine(line1);
-
-  /* For testing purposes
-  std::cout << ans1.target_phrase[0] << " " <<ans1.target_phrase[1] << " Size: " << ans1.target_phrase.size() << std::endl;
-  std::cout << ans1.word_all1[3] << " " << ans1.word_all2[2] << " " << ans1.prob[3] << std::endl; */
-
-  return (ans1.target_phrase.size() == 2 && ans1.prob.size() == 5 && ans1.word_all1.size() == 4 && ans1.word_all2.size() == 3);
-}
-
-bool test_linessplitter()
-{
-  StringPiece line1 = StringPiece("! &#93;    0.0738539 0.901133 0.0738539 0.65207 2.718  0-0 1-1 1 1 1\n\n! ) . proto došlo 0.0738539 7.14446e-06");
-  StringPiece line2 = StringPiece("! &quot; ) 0.536553 0.75961 0.634108 0.532927 2.718    0-0 1-1 2-2 13 11 8\n! ) .  0.0369269 0.00049839 0.00671399 0.00372884 2.718    0-0 1-1 2-1 2-2 2 11 1\n&quot; ! )  0.0738539 0.75961 0.00671399 0.532927 2.718 1-0 0-1 2-2 1 11 1\nse ! &quot; )   0.0738539 0.75961 0.00671399 0.0225211 2.718    0-1 1-2 2-3 1 11 1\n\n! &quot; , a to   0.0738539 0.0894238 0.0738539 0.048");
-
-  std::vector<target_text> ans1;
-  std::vector<target_text> ans2;
-
-  ans1 = splitTargetLine(line1);
-  ans2 = splitTargetLine(line2);
-
-  bool sizes = ans1.size() == 1 && ans2.size() == 4;
-  bool prob = ans1[0].prob[3] == 0.65207 && ans2[1].prob[1] == 0.00049839;
-  bool word_alls = ans2[0].word_all2[1] == 11 && ans2[3].word_all1[5] == 3;
-
-  /* FOr testing
-  std::cout << ans1.size() << std::endl;
-  std::cout << ans2.size() << std::endl;
-  std::cout << ans1[0].prob[3] << std::endl;
-  std::cout << ans2[1].prob[1] << std::endl;
-  std::cout << ans2[0].word_all2[1] << std::endl;
-  std::cout << ans2[3].word_all1[5] << std::endl; */
-
-  return sizes && prob && word_alls;
-}
-
-int main()
-{
-  if (probabilitiesTest() && wordAll1test() && wordAll2test() && test_tokenization() && test_linesplitter() && test_linessplitter() && test_vectorinsert()) {
-    std::cout << "All tests pass!" << std::endl;
-  } else {
-    std::cout << "Failiure in some tests!" << std::endl;
-  }
-
-  return 1;
-}
\ No newline at end of file
diff --git a/moses/TranslationModel/ProbingPT/tests/vocabid_test.cpp b/moses/TranslationModel/ProbingPT/tests/vocabid_test.cpp
deleted file mode 100644
index fac439eeb..000000000
--- a/moses/TranslationModel/ProbingPT/tests/vocabid_test.cpp
+++ /dev/null
@@ -1,46 +0,0 @@
-#include <map> //Map for vocab ids
-
-#include "hash.hh"
-#include "vocabid.hh"
-
-int main(int argc, char* argv[])
-{
-
-  //Create a map and serialize it
-  std::map<uint64_t, std::string> vocabids;
-  StringPiece demotext = StringPiece("Demo text with 3 elements");
-  add_to_map(&vocabids, demotext);
-  //Serialize map
-  serialize_map(&vocabids, "/tmp/testmap.bin");
-
-  //Read the map and test if the values are the same
-  std::map<uint64_t, std::string> newmap;
-  read_map(&newmap, "/tmp/testmap.bin");
-
-  //Used hashes
-  uint64_t num1 = getHash(StringPiece("Demo"));
-  uint64_t num2 = getVocabID("text");
-  uint64_t num3 = getHash(StringPiece("with"));
-  uint64_t num4 = getVocabID("3");
-  uint64_t num5 = getHash(StringPiece("elements"));
-  uint64_t num6 = 0;
-
-  //Tests
-  bool test1 = getStringFromID(&newmap, num1) == getStringFromID(&vocabids, num1);
-  bool test2 = getStringFromID(&newmap, num2) == getStringFromID(&vocabids, num2);
-  bool test3 = getStringFromID(&newmap, num3) == getStringFromID(&vocabids, num3);
-  bool test4 = getStringFromID(&newmap, num4) == getStringFromID(&vocabids, num4);
-  bool test5 = getStringFromID(&newmap, num5) == getStringFromID(&vocabids, num5);
-  bool test6 = getStringFromID(&newmap, num6) == getStringFromID(&vocabids, num6);
-
-
-  if (test1 && test2 && test3 && test4 && test5 && test6) {
-    std::cout << "Map was successfully written and read!" << std::endl;
-  } else {
-    std::cout << "Error! " << test1 << " " << test2 << " " << test3 << " " << test4 << " " << test5 << " " << test6 << std::endl;
-  }
-
-
-  return 1;
-
-}
diff --git a/moses/TranslationModel/RuleTable/LoaderStandard.cpp b/moses/TranslationModel/RuleTable/LoaderStandard.cpp
index 95463feea..f9e6ac6fd 100644
--- a/moses/TranslationModel/RuleTable/LoaderStandard.cpp
+++ b/moses/TranslationModel/RuleTable/LoaderStandard.cpp
@@ -25,7 +25,7 @@
 #include <algorithm>
 #include <iostream>
 #include <sys/stat.h>
-#include <stdlib.h>
+#include <cstdlib>
 #include <boost/algorithm/string/predicate.hpp>
 #include "Trie.h"
 #include "moses/FactorCollection.h"
diff --git a/moses/TranslationModel/RuleTable/PhraseDictionaryFuzzyMatch.cpp b/moses/TranslationModel/RuleTable/PhraseDictionaryFuzzyMatch.cpp
index 0928cf1e4..1ca9dce67 100644
--- a/moses/TranslationModel/RuleTable/PhraseDictionaryFuzzyMatch.cpp
+++ b/moses/TranslationModel/RuleTable/PhraseDictionaryFuzzyMatch.cpp
@@ -19,10 +19,10 @@
  Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
  ***********************************************************************/
 
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <limits.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include <climits>
 #include <sys/types.h>
 #include <unistd.h>
 #include <dirent.h>
@@ -50,7 +50,7 @@ using namespace std;
 
 #if defined __MINGW32__ && !defined mkdtemp
 #include <windows.h>
-#include <errno.h>
+#include <cerrno>
 char *mkdtemp(char *tempbuf)
 {
   int rand_value = 0;
@@ -392,10 +392,10 @@ 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;
diff --git a/moses/TranslationModel/UG/mm/tpt_tightindex.cc b/moses/TranslationModel/UG/mm/tpt_tightindex.cc
index ff7153af7..da28c6d93 100644
--- a/moses/TranslationModel/UG/mm/tpt_tightindex.cc
+++ b/moses/TranslationModel/UG/mm/tpt_tightindex.cc
@@ -17,7 +17,7 @@
 //
 
 #include <iostream>
-#include <assert.h>
+#include <cassert>
 #include "tpt_tightindex.h"
 
 namespace ugdiss
diff --git a/moses/TranslationModel/UG/mm/tpt_tokenindex.cc b/moses/TranslationModel/UG/mm/tpt_tokenindex.cc
index 2273fefa7..c6704beac 100644
--- a/moses/TranslationModel/UG/mm/tpt_tokenindex.cc
+++ b/moses/TranslationModel/UG/mm/tpt_tokenindex.cc
@@ -1,7 +1,7 @@
 // -*- c++ -*-
 // (c) 2007-2013 Ulrich Germann
 #include <sstream>
-#include <string.h>
+#include <cstring>
 #include <algorithm>
 #include <iostream>
 #include <stdexcept>
diff --git a/moses/TranslationModel/fuzzy-match/Vocabulary.h b/moses/TranslationModel/fuzzy-match/Vocabulary.h
index 5a79e2f26..f5245ebe3 100644
--- a/moses/TranslationModel/fuzzy-match/Vocabulary.h
+++ b/moses/TranslationModel/fuzzy-match/Vocabulary.h
@@ -4,8 +4,8 @@
 
 #include <iostream>
 #include <fstream>
-#include <assert.h>
-#include <stdlib.h>
+#include <cassert>
+#include <cstdlib>
 #include <string>
 #include <queue>
 #include <map>
diff --git a/moses/Util.cpp b/moses/Util.cpp
index 1d1df7d58..a8175b58d 100644
--- a/moses/Util.cpp
+++ b/moses/Util.cpp
@@ -29,7 +29,7 @@
 #include <cstring>
 #include <cctype>
 #include <algorithm>
-#include <stdio.h>
+#include <cstdio>
 #include <iostream>
 #include <iomanip>
 #include <boost/algorithm/string/predicate.hpp>
diff --git a/moses/mbr.cpp b/moses/mbr.cpp
index 6a8dfa823..df2313b66 100644
--- a/moses/mbr.cpp
+++ b/moses/mbr.cpp
@@ -4,10 +4,10 @@
 #include <iomanip>
 #include <vector>
 #include <map>
-#include <stdlib.h>
-#include <math.h>
+#include <cstdlib>
+#include <cmath>
 #include <algorithm>
-#include <stdio.h>
+#include <cstdio>
 #include "moses/TrellisPathList.h"
 #include "moses/TrellisPath.h"
 #include "moses/StaticData.h"