Merge branch 'master' of https://github.com/moses-smt/mosesdecoder

Conflicts:
	moses-cmd/simulate-pe.cc

9 files changed, 172 insertions, 2180 deletions

diff --git a/moses-cmd/IOWrapper.cpp b/moses-cmd/IOWrapper.cpp
deleted file mode 100644
index 1483e0472..000000000
--- a/moses-cmd/IOWrapper.cpp
+++ /dev/null
@@ -1,661 +0,0 @@
-// $Id$
-
-/***********************************************************************
-Moses - factored phrase-based language decoder
-Copyright (c) 2006 University of Edinburgh
-All rights reserved.
-
-Redistribution and use in source and binary forms, with or without modification,
-are permitted provided that the following conditions are met:
-
- * Redistributions of source code must retain the above copyright notice,
-			this list of conditions and the following disclaimer.
- * Redistributions in binary form must reproduce the above copyright notice,
-			this list of conditions and the following disclaimer in the documentation
-			and/or other materials provided with the distribution.
- * Neither the name of the University of Edinburgh nor the names of its contributors
-			may be used to endorse or promote products derived from this software
-			without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
-THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
-PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS
-BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
-CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
-SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
-INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
-IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
-ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
-POSSIBILITY OF SUCH DAMAGE.
- ***********************************************************************/
-
-// example file on how to use moses library
-
-#include <iostream>
-#include <stack>
-#include <boost/algorithm/string.hpp>
-
-#include "moses/TypeDef.h"
-#include "moses/Util.h"
-#include "moses/Hypothesis.h"
-#include "moses/WordsRange.h"
-#include "moses/TrellisPathList.h"
-#include "moses/StaticData.h"
-#include "moses/FeatureVector.h"
-#include "moses/InputFileStream.h"
-#include "moses/FF/StatefulFeatureFunction.h"
-#include "moses/FF/StatelessFeatureFunction.h"
-#include "util/exception.hh"
-
-#include "IOWrapper.h"
-
-using namespace std;
-using namespace Moses;
-
-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)
-{
-  Initialization(inputFactorOrder, outputFactorOrder
-                 , 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)
-{
-  Initialization(inputFactorOrder, outputFactorOrder
-                 , inputFactorUsed
-                 , nBestSize, nBestFilePath);
-
-  m_inputStream = m_inputFile;
-}
-
-IOWrapper::~IOWrapper()
-{
-  if (m_inputFile != NULL)
-    delete m_inputFile;
-  if (m_nBestStream != NULL && !m_surpressSingleBestOutput) {
-    // outputting n-best to file, rather than stdout. need to close file and delete obj
-    delete m_nBestStream;
-  }
-  if (m_outputWordGraphStream != NULL) {
-    delete m_outputWordGraphStream;
-  }
-  if (m_outputSearchGraphStream != NULL) {
-    delete m_outputSearchGraphStream;
-  }
-  delete m_detailedTranslationReportingStream;
-  delete m_alignmentOutputStream;
-}
-
-void IOWrapper::Initialization(const std::vector<FactorType>	&/*inputFactorOrder*/
-                               , const std::vector<FactorType>			&/*outputFactorOrder*/
-                               , const FactorMask							&/*inputFactorUsed*/
-                               , size_t												nBestSize
-                               , const std::string							&nBestFilePath)
-{
-  const StaticData &staticData = StaticData::Instance();
-
-  // n-best
-  m_surpressSingleBestOutput = false;
-
-  if (nBestSize > 0) {
-    if (nBestFilePath == "-" || nBestFilePath == "/dev/stdout") {
-      m_nBestStream = &std::cout;
-      m_surpressSingleBestOutput = true;
-    } else {
-      std::ofstream *file = new std::ofstream;
-      m_nBestStream = file;
-      file->open(nBestFilePath.c_str());
-    }
-  }
-
-  // wordgraph output
-  if (staticData.GetOutputWordGraph()) {
-    string fileName = staticData.GetParam("output-word-graph")[0];
-    std::ofstream *file = new std::ofstream;
-    m_outputWordGraphStream  = file;
-    file->open(fileName.c_str());
-  }
-
-
-  // search graph output
-  if (staticData.GetOutputSearchGraph()) {
-    string fileName;
-    if (staticData.GetOutputSearchGraphExtended())
-      fileName = staticData.GetParam("output-search-graph-extended")[0];
-    else
-      fileName = staticData.GetParam("output-search-graph")[0];
-    std::ofstream *file = new std::ofstream;
-    m_outputSearchGraphStream = file;
-    file->open(fileName.c_str());
-  }
-
-  // detailed translation reporting
-  if (staticData.IsDetailedTranslationReportingEnabled()) {
-    const std::string &path = staticData.GetDetailedTranslationReportingFilePath();
-    m_detailedTranslationReportingStream = new std::ofstream(path.c_str());
-    UTIL_THROW_IF(!m_detailedTranslationReportingStream->good(),
-    		util::FileOpenException,
-    		"File for output of detailed translation report could not be open");
-  }
-
-  // sentence alignment output
-  if (! staticData.GetAlignmentOutputFile().empty()) {
-    m_alignmentOutputStream = new ofstream(staticData.GetAlignmentOutputFile().c_str());
-    UTIL_THROW_IF(!m_alignmentOutputStream->good(),
-    		util::FileOpenException,
-    		"File for output of word alignment could not be open");
-  }
-
-}
-
-InputType*
-IOWrapper::
-GetInput(InputType* inputType)
-{
-  if(inputType->Read(*m_inputStream, m_inputFactorOrder)) {
-    if (long x = inputType->GetTranslationId()) {
-      if (x>=m_translationId) m_translationId = x+1;
-    } else inputType->SetTranslationId(m_translationId++);
-
-    return inputType;
-  } else {
-    delete inputType;
-    return NULL;
-  }
-}
-
-std::map<size_t, const Factor*> GetPlaceholders(const Hypothesis &hypo, FactorType placeholderFactor)
-{
-  const InputPath &inputPath = hypo.GetTranslationOption().GetInputPath();
-  const Phrase &inputPhrase = inputPath.GetPhrase();
-
-  std::map<size_t, const Factor*> ret;
-
-  for (size_t sourcePos = 0; sourcePos < inputPhrase.GetSize(); ++sourcePos) {
-    const Factor *factor = inputPhrase.GetFactor(sourcePos, placeholderFactor);
-    if (factor) {
-      std::set<size_t> targetPos = hypo.GetTranslationOption().GetTargetPhrase().GetAlignTerm().GetAlignmentsForSource(sourcePos);
-      UTIL_THROW_IF2(targetPos.size() != 1,
-    		  "Placeholder should be aligned to 1, and only 1, word");
-      ret[*targetPos.begin()] = factor;
-    }
-  }
-
-  return ret;
-}
-
-/***
- * print surface factor only for the given phrase
- */
-void OutputSurface(std::ostream &out, const Hypothesis &edge, const std::vector<FactorType> &outputFactorOrder,
-                   char reportSegmentation, bool reportAllFactors)
-{
-  UTIL_THROW_IF2(outputFactorOrder.size() == 0,
-		  "Must specific at least 1 output factor");
-  const TargetPhrase& phrase = edge.GetCurrTargetPhrase();
-  bool markUnknown = StaticData::Instance().GetMarkUnknown();
-  if (reportAllFactors == true) {
-    out << phrase;
-  } else {
-    FactorType placeholderFactor = StaticData::Instance().GetPlaceholderFactor();
-
-    std::map<size_t, const Factor*> placeholders;
-    if (placeholderFactor != NOT_FOUND) {
-      // creates map of target position -> factor for placeholders
-      placeholders = GetPlaceholders(edge, placeholderFactor);
-    }
-
-    size_t size = phrase.GetSize();
-    for (size_t pos = 0 ; pos < size ; pos++) {
-      const Factor *factor = phrase.GetFactor(pos, outputFactorOrder[0]);
-
-      if (placeholders.size()) {
-        // do placeholders
-        std::map<size_t, const Factor*>::const_iterator iter = placeholders.find(pos);
-        if (iter != placeholders.end()) {
-          factor = iter->second;
-        }
-      }
-
-      UTIL_THROW_IF2(factor == NULL,
-    		  "No factor 0 at position " << pos);
-
-      //preface surface form with UNK if marking unknowns
-      const Word &word = phrase.GetWord(pos);
-      if(markUnknown && word.IsOOV()) {
-        out << "UNK" << *factor;
-      } else {
-        out << *factor;
-      }
-
-      for (size_t i = 1 ; i < outputFactorOrder.size() ; i++) {
-        const Factor *factor = phrase.GetFactor(pos, outputFactorOrder[i]);
-        UTIL_THROW_IF2(factor == NULL,
-      		  "No factor " << i << " at position " << pos);
-
-        out << "|" << *factor;
-      }
-      out << " ";
-    }
-  }
-
-  // trace ("report segmentation") option "-t" / "-tt"
-  if (reportSegmentation > 0 && phrase.GetSize() > 0) {
-    const WordsRange &sourceRange = edge.GetCurrSourceWordsRange();
-    const int sourceStart = sourceRange.GetStartPos();
-    const int sourceEnd = sourceRange.GetEndPos();
-    out << "|" << sourceStart << "-" << sourceEnd;    // enriched "-tt"
-    if (reportSegmentation == 2) {
-      out << ",wa=";
-      const AlignmentInfo &ai = edge.GetCurrTargetPhrase().GetAlignTerm();
-      OutputAlignment(out, ai, 0, 0);
-      out << ",total=";
-      out << edge.GetScore() - edge.GetPrevHypo()->GetScore();
-      out << ",";
-      ScoreComponentCollection scoreBreakdown(edge.GetScoreBreakdown());
-      scoreBreakdown.MinusEquals(edge.GetPrevHypo()->GetScoreBreakdown());
-      OutputAllFeatureScores(scoreBreakdown, out);
-    }
-    out << "| ";
-  }
-}
-
-void OutputBestSurface(std::ostream &out, const Hypothesis *hypo, const std::vector<FactorType> &outputFactorOrder,
-                       char reportSegmentation, bool reportAllFactors)
-{
-  if (hypo != NULL) {
-    // recursively retrace this best path through the lattice, starting from the end of the hypothesis sentence
-    OutputBestSurface(out, hypo->GetPrevHypo(), outputFactorOrder, reportSegmentation, reportAllFactors);
-    OutputSurface(out, *hypo, outputFactorOrder, reportSegmentation, reportAllFactors);
-  }
-}
-
-void OutputAlignment(ostream &out, const AlignmentInfo &ai, size_t sourceOffset, size_t targetOffset)
-{
-  typedef std::vector< const std::pair<size_t,size_t>* > AlignVec;
-  AlignVec alignments = ai.GetSortedAlignments();
-
-  AlignVec::const_iterator it;
-  for (it = alignments.begin(); it != alignments.end(); ++it) {
-    const std::pair<size_t,size_t> &alignment = **it;
-    out << alignment.first + sourceOffset << "-" << alignment.second + targetOffset << " ";
-  }
-
-}
-
-void OutputAlignment(ostream &out, const vector<const Hypothesis *> &edges)
-{
-  size_t targetOffset = 0;
-
-  for (int currEdge = (int)edges.size() - 1 ; currEdge >= 0 ; currEdge--) {
-    const Hypothesis &edge = *edges[currEdge];
-    const TargetPhrase &tp = edge.GetCurrTargetPhrase();
-    size_t sourceOffset = edge.GetCurrSourceWordsRange().GetStartPos();
-
-    OutputAlignment(out, tp.GetAlignTerm(), sourceOffset, targetOffset);
-
-    targetOffset += tp.GetSize();
-  }
-  out << std::endl;
-}
-
-void OutputAlignment(std::ostream &out, const Moses::Hypothesis *hypo)
-{
-  std::vector<const Hypothesis *> edges;
-  const Hypothesis *currentHypo = hypo;
-  while (currentHypo) {
-    edges.push_back(currentHypo);
-    currentHypo = currentHypo->GetPrevHypo();
-  }
-
-  OutputAlignment(out, edges);
-
-}
-
-void OutputAlignment(OutputCollector* collector, size_t lineNo , const vector<const Hypothesis *> &edges)
-{
-  ostringstream out;
-  OutputAlignment(out, edges);
-
-  collector->Write(lineNo,out.str());
-}
-
-void OutputAlignment(OutputCollector* collector, size_t lineNo , const Hypothesis *hypo)
-{
-  if (collector) {
-    std::vector<const Hypothesis *> edges;
-    const Hypothesis *currentHypo = hypo;
-    while (currentHypo) {
-      edges.push_back(currentHypo);
-      currentHypo = currentHypo->GetPrevHypo();
-    }
-
-    OutputAlignment(collector,lineNo, edges);
-  }
-}
-
-void OutputAlignment(OutputCollector* collector, size_t lineNo , const TrellisPath &path)
-{
-  if (collector) {
-    OutputAlignment(collector,lineNo, path.GetEdges());
-  }
-}
-
-void OutputBestHypo(const Moses::TrellisPath &path, long /*translationId*/, char reportSegmentation, bool reportAllFactors, std::ostream &out)
-{
-  const std::vector<const Hypothesis *> &edges = path.GetEdges();
-
-  for (int currEdge = (int)edges.size() - 1 ; currEdge >= 0 ; currEdge--) {
-    const Hypothesis &edge = *edges[currEdge];
-    OutputSurface(out, edge, StaticData::Instance().GetOutputFactorOrder(), reportSegmentation, reportAllFactors);
-  }
-  out << endl;
-}
-
-void IOWrapper::Backtrack(const Hypothesis *hypo)
-{
-
-  if (hypo->GetPrevHypo() != NULL) {
-    VERBOSE(3,hypo->GetId() << " <= ");
-    Backtrack(hypo->GetPrevHypo());
-  }
-}
-
-void OutputBestHypo(const std::vector<Word>&  mbrBestHypo, long /*translationId*/, char /*reportSegmentation*/, bool /*reportAllFactors*/, ostream& out)
-{
-
-  for (size_t i = 0 ; i < mbrBestHypo.size() ; i++) {
-    const Factor *factor = mbrBestHypo[i].GetFactor(StaticData::Instance().GetOutputFactorOrder()[0]);
-    UTIL_THROW_IF2(factor == NULL,
-  		  "No factor 0 at position " << i);
-    if (i>0) out << " " << *factor;
-    else     out << *factor;
-  }
-  out << endl;
-}
-
-
-void OutputInput(std::vector<const Phrase*>& map, const Hypothesis* hypo)
-{
-  if (hypo->GetPrevHypo()) {
-    OutputInput(map, hypo->GetPrevHypo());
-    map[hypo->GetCurrSourceWordsRange().GetStartPos()] = &hypo->GetTranslationOption().GetInputPath().GetPhrase();
-  }
-}
-
-void OutputInput(std::ostream& os, const Hypothesis* hypo)
-{
-  size_t len = hypo->GetInput().GetSize();
-  std::vector<const Phrase*> inp_phrases(len, 0);
-  OutputInput(inp_phrases, hypo);
-  for (size_t i=0; i<len; ++i)
-    if (inp_phrases[i]) os << *inp_phrases[i];
-}
-
-void IOWrapper::OutputBestHypo(const Hypothesis *hypo, long /*translationId*/, char reportSegmentation, bool reportAllFactors)
-{
-  if (hypo != NULL) {
-    VERBOSE(1,"BEST TRANSLATION: " << *hypo << endl);
-    VERBOSE(3,"Best path: ");
-    Backtrack(hypo);
-    VERBOSE(3,"0" << std::endl);
-    if (!m_surpressSingleBestOutput) {
-      if (StaticData::Instance().GetOutputHypoScore()) {
-        cout << hypo->GetTotalScore() << " ";
-      }
-
-      if (StaticData::Instance().IsPathRecoveryEnabled()) {
-        OutputInput(cout, hypo);
-        cout << "||| ";
-      }
-      OutputBestSurface(cout, hypo, m_outputFactorOrder, reportSegmentation, reportAllFactors);
-      cout << endl;
-    }
-  } else {
-    VERBOSE(1, "NO BEST TRANSLATION" << endl);
-    if (!m_surpressSingleBestOutput) {
-      cout << endl;
-    }
-  }
-}
-
-void OutputNBest(std::ostream& out
-                 , const Moses::TrellisPathList &nBestList
-                 , const std::vector<Moses::FactorType>& outputFactorOrder
-                 , long translationId
-                 , char reportSegmentation)
-{
-  const StaticData &staticData = StaticData::Instance();
-  bool reportAllFactors = staticData.GetReportAllFactorsNBest();
-  bool includeSegmentation = staticData.NBestIncludesSegmentation();
-  bool includeWordAlignment = staticData.PrintAlignmentInfoInNbest();
-
-  TrellisPathList::const_iterator iter;
-  for (iter = nBestList.begin() ; iter != nBestList.end() ; ++iter) {
-    const TrellisPath &path = **iter;
-    const std::vector<const Hypothesis *> &edges = path.GetEdges();
-
-    // print the surface factor of the translation
-    out << translationId << " ||| ";
-    for (int currEdge = (int)edges.size() - 1 ; currEdge >= 0 ; currEdge--) {
-      const Hypothesis &edge = *edges[currEdge];
-      OutputSurface(out, edge, outputFactorOrder, reportSegmentation, reportAllFactors);
-    }
-    out << " |||";
-
-    // print scores with feature names
-    OutputAllFeatureScores(path.GetScoreBreakdown(), out );
-
-    // total
-    out << " ||| " << path.GetTotalScore();
-
-    //phrase-to-phrase segmentation
-    if (includeSegmentation) {
-      out << " |||";
-      for (int currEdge = (int)edges.size() - 2 ; currEdge >= 0 ; currEdge--) {
-        const Hypothesis &edge = *edges[currEdge];
-        const WordsRange &sourceRange = edge.GetCurrSourceWordsRange();
-        WordsRange targetRange = path.GetTargetWordsRange(edge);
-        out << " " << sourceRange.GetStartPos();
-        if (sourceRange.GetStartPos() < sourceRange.GetEndPos()) {
-          out << "-" << sourceRange.GetEndPos();
-        }
-        out<< "=" << targetRange.GetStartPos();
-        if (targetRange.GetStartPos() < targetRange.GetEndPos()) {
-          out<< "-" << targetRange.GetEndPos();
-        }
-      }
-    }
-
-    if (includeWordAlignment) {
-      out << " ||| ";
-      for (int currEdge = (int)edges.size() - 2 ; currEdge >= 0 ; currEdge--) {
-        const Hypothesis &edge = *edges[currEdge];
-        const WordsRange &sourceRange = edge.GetCurrSourceWordsRange();
-        WordsRange targetRange = path.GetTargetWordsRange(edge);
-        const int sourceOffset = sourceRange.GetStartPos();
-        const int targetOffset = targetRange.GetStartPos();
-        const AlignmentInfo &ai = edge.GetCurrTargetPhrase().GetAlignTerm();
-
-        OutputAlignment(out, ai, sourceOffset, targetOffset);
-
-      }
-    }
-
-    if (StaticData::Instance().IsPathRecoveryEnabled()) {
-      out << " ||| ";
-      OutputInput(out, edges[0]);
-    }
-
-    out << endl;
-  }
-
-  out << std::flush;
-}
-
-void OutputAllFeatureScores(const Moses::ScoreComponentCollection &features
-                            , std::ostream &out)
-{
-  std::string lastName = "";
-  const vector<const StatefulFeatureFunction*>& sff = StatefulFeatureFunction::GetStatefulFeatureFunctions();
-  for( size_t i=0; i<sff.size(); i++ ) {
-    const StatefulFeatureFunction *ff = sff[i];
-    if (ff->GetScoreProducerDescription() != "BleuScoreFeature"
-        && ff->IsTuneable()) {
-      OutputFeatureScores( out, features, ff, lastName );
-    }
-  }
-  const vector<const StatelessFeatureFunction*>& slf = StatelessFeatureFunction::GetStatelessFeatureFunctions();
-  for( size_t i=0; i<slf.size(); i++ ) {
-    const StatelessFeatureFunction *ff = slf[i];
-    if (ff->IsTuneable()) {
-      OutputFeatureScores( out, features, ff, lastName );
-    }
-  }
-}
-
-void OutputFeatureScores( std::ostream& out
-                          , const ScoreComponentCollection &features
-                          , const FeatureFunction *ff
-                          , std::string &lastName )
-{
-  const StaticData &staticData = StaticData::Instance();
-  bool labeledOutput = staticData.IsLabeledNBestList();
-
-  // regular features (not sparse)
-  if (ff->GetNumScoreComponents() != 0) {
-    if( labeledOutput && lastName != ff->GetScoreProducerDescription() ) {
-      lastName = ff->GetScoreProducerDescription();
-      out << " " << lastName << "=";
-    }
-    vector<float> scores = features.GetScoresForProducer( ff );
-    for (size_t j = 0; j<scores.size(); ++j) {
-      out << " " << scores[j];
-    }
-  }
-
-  // sparse features
-  const FVector scores = features.GetVectorForProducer( ff );
-  for(FVector::FNVmap::const_iterator i = scores.cbegin(); i != scores.cend(); i++) {
-    out << " " << i->first << "= " << i->second;
-  }
-}
-
-void OutputLatticeMBRNBest(std::ostream& out, const vector<LatticeMBRSolution>& solutions,long translationId)
-{
-  for (vector<LatticeMBRSolution>::const_iterator si = solutions.begin(); si != solutions.end(); ++si) {
-    out << translationId;
-    out << " |||";
-    const vector<Word> mbrHypo = si->GetWords();
-    for (size_t i = 0 ; i < mbrHypo.size() ; i++) {
-      const Factor *factor = mbrHypo[i].GetFactor(StaticData::Instance().GetOutputFactorOrder()[0]);
-      if (i>0) out << " " << *factor;
-      else     out << *factor;
-    }
-    out << " |||";
-    out << " map: " << si->GetMapScore();
-    out << " w: " << mbrHypo.size();
-    const vector<float>& ngramScores = si->GetNgramScores();
-    for (size_t i = 0; i < ngramScores.size(); ++i) {
-      out << " " << ngramScores[i];
-    }
-    out << " ||| " << si->GetScore();
-
-    out << endl;
-  }
-}
-
-
-void IOWrapper::OutputLatticeMBRNBestList(const vector<LatticeMBRSolution>& solutions,long translationId)
-{
-  OutputLatticeMBRNBest(*m_nBestStream, solutions,translationId);
-}
-
-bool ReadInput(IOWrapper &ioWrapper, InputTypeEnum inputType, InputType*& source)
-{
-  if (source) delete source;
-  switch(inputType) {
-  case SentenceInput:
-    source = ioWrapper.GetInput(new Sentence);
-    break;
-  case ConfusionNetworkInput:
-    source = ioWrapper.GetInput(new ConfusionNet);
-    break;
-  case WordLatticeInput:
-    source = ioWrapper.GetInput(new WordLattice);
-    break;
-  default:
-    TRACE_ERR("Unknown input type: " << inputType << "\n");
-    source = NULL;
-  }
-  return (source ? true : false);
-}
-
-
-
-IOWrapper *GetIOWrapper(const StaticData &staticData)
-{
-  IOWrapper *ioWrapper;
-  const std::vector<FactorType> &inputFactorOrder = staticData.GetInputFactorOrder()
-      ,&outputFactorOrder = staticData.GetOutputFactorOrder();
-  FactorMask inputFactorUsed(inputFactorOrder);
-
-  // io
-  if (staticData.GetParam("input-file").size() == 1) {
-    VERBOSE(2,"IO from File" << endl);
-    string filePath = staticData.GetParam("input-file")[0];
-
-    ioWrapper = new IOWrapper(inputFactorOrder, outputFactorOrder, inputFactorUsed
-                              , staticData.GetNBestSize()
-                              , staticData.GetNBestFilePath()
-                              , filePath);
-  } else {
-    VERBOSE(1,"IO from STDOUT/STDIN" << endl);
-    ioWrapper = new IOWrapper(inputFactorOrder, outputFactorOrder, inputFactorUsed
-                              , staticData.GetNBestSize()
-                              , staticData.GetNBestFilePath());
-  }
-  ioWrapper->ResetTranslationId();
-
-  IFVERBOSE(1)
-  PrintUserTime("Created input-output object");
-
-  return ioWrapper;
-}
-
-}
-
diff --git a/moses-cmd/IOWrapper.h b/moses-cmd/IOWrapper.h
deleted file mode 100644
index ed2537986..000000000
--- a/moses-cmd/IOWrapper.h
+++ /dev/null
@@ -1,164 +0,0 @@
-// $Id$
-
-/***********************************************************************
-Moses - factored phrase-based language decoder
-Copyright (c) 2006 University of Edinburgh
-All rights reserved.
-
-Redistribution and use in source and binary forms, with or without modification,
-are permitted provided that the following conditions are met:
-
-    * Redistributions of source code must retain the above copyright notice,
-			this list of conditions and the following disclaimer.
-    * Redistributions in binary form must reproduce the above copyright notice,
-			this list of conditions and the following disclaimer in the documentation
-			and/or other materials provided with the distribution.
-    * Neither the name of the University of Edinburgh nor the names of its contributors
-			may be used to endorse or promote products derived from this software
-			without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
-THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
-PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS
-BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
-CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
-SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
-INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER
-IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
-ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
-POSSIBILITY OF SUCH DAMAGE.
-***********************************************************************/
-
-// example file on how to use moses library
-
-#ifndef moses_cmd_IOWrapper_h
-#define moses_cmd_IOWrapper_h
-
-#include <cassert>
-#include <fstream>
-#include <ostream>
-#include <vector>
-
-#include "moses/TypeDef.h"
-#include "moses/Sentence.h"
-#include "moses/FactorTypeSet.h"
-#include "moses/FactorCollection.h"
-#include "moses/Hypothesis.h"
-#include "moses/OutputCollector.h"
-#include "moses/TrellisPathList.h"
-#include "moses/InputFileStream.h"
-#include "moses/InputType.h"
-#include "moses/WordLattice.h"
-#include "moses/LatticeMBR.h"
-
-namespace Moses
-{
-class ScoreComponentCollection;
-class Hypothesis;
-class Factor;
-}
-
-namespace MosesCmd
-{
-
-/** Helper class that holds misc variables to write data out to command line.
- */
-class IOWrapper
-{
-protected:
-  long m_translationId;
-
-  const std::vector<Moses::FactorType>	&m_inputFactorOrder;
-  const std::vector<Moses::FactorType>	&m_outputFactorOrder;
-  const Moses::FactorMask							&m_inputFactorUsed;
-  std::string										m_inputFilePath;
-  Moses::InputFileStream				*m_inputFile;
-  std::istream									*m_inputStream;
-  std::ostream 									*m_nBestStream
-  ,*m_outputWordGraphStream,*m_outputSearchGraphStream;
-  std::ostream                  *m_detailedTranslationReportingStream;
-  std::ofstream *m_alignmentOutputStream;
-  bool													m_surpressSingleBestOutput;
-
-  void Initialization(const std::vector<Moses::FactorType>	&inputFactorOrder
-                      , const std::vector<Moses::FactorType>			&outputFactorOrder
-                      , const Moses::FactorMask							&inputFactorUsed
-                      , size_t												nBestSize
-                      , const std::string							&nBestFilePath);
-
-
-public:
-  IOWrapper(const std::vector<Moses::FactorType>	&inputFactorOrder
-            , const std::vector<Moses::FactorType>			&outputFactorOrder
-            , const Moses::FactorMask							&inputFactorUsed
-            , size_t												nBestSize
-            , const std::string							&nBestFilePath);
-
-  IOWrapper(const std::vector<Moses::FactorType>	&inputFactorOrder
-            , const std::vector<Moses::FactorType>	&outputFactorOrder
-            , const Moses::FactorMask							&inputFactorUsed
-            , size_t												nBestSize
-            , const std::string							&nBestFilePath
-            , const std::string                                                     &infilePath);
-  ~IOWrapper();
-
-  Moses::InputType* GetInput(Moses::InputType *inputType);
-
-  void OutputBestHypo(const Moses::Hypothesis *hypo, long translationId, char reportSegmentation, bool reportAllFactors);
-  void OutputLatticeMBRNBestList(const std::vector<LatticeMBRSolution>& solutions,long translationId);
-  void Backtrack(const Moses::Hypothesis *hypo);
-
-  void ResetTranslationId() {
-    m_translationId = 0;
-  }
-
-  std::ofstream *GetAlignmentOutputStream() {
-    return m_alignmentOutputStream;
-  }
-
-  std::ostream &GetOutputWordGraphStream() {
-    return *m_outputWordGraphStream;
-  }
-  std::ostream &GetOutputSearchGraphStream() {
-    return *m_outputSearchGraphStream;
-  }
-
-  std::ostream &GetDetailedTranslationReportingStream() {
-    assert (m_detailedTranslationReportingStream);
-    return *m_detailedTranslationReportingStream;
-  }
-};
-
-IOWrapper *GetIOWrapper(const Moses::StaticData &staticData);
-bool ReadInput(IOWrapper &ioWrapper, Moses::InputTypeEnum inputType, Moses::InputType*& source);
-void OutputLanguageModelOrder(std::ostream &out, const Moses::Hypothesis *hypo, Moses::Manager &manager);
-void OutputBestSurface(std::ostream &out, const Moses::Hypothesis *hypo, const std::vector<Moses::FactorType> &outputFactorOrder, char reportSegmentation, bool reportAllFactors);
-void OutputLatticeMBRNBest(std::ostream& out, const std::vector<LatticeMBRSolution>& solutions,long translationId);
-void OutputBestHypo(const std::vector<Moses::Word>&  mbrBestHypo, long /*translationId*/,
-                    char reportSegmentation, bool reportAllFactors, std::ostream& out);
-void OutputBestHypo(const Moses::TrellisPath &path, long /*translationId*/,char reportSegmentation, bool reportAllFactors, std::ostream &out);
-void OutputInput(std::ostream& os, const Moses::Hypothesis* hypo);
-void OutputAlignment(Moses::OutputCollector* collector, size_t lineNo, const Moses::Hypothesis *hypo);
-void OutputAlignment(Moses::OutputCollector* collector, size_t lineNo,  const Moses::TrellisPath &path);
-void OutputAlignment(std::ostream &out, const Moses::Hypothesis *hypo);
-void OutputAlignment(std::ostream &out, const Moses::AlignmentInfo &ai, size_t sourceOffset, size_t targetOffset);
-
-void OutputNBest(std::ostream& out
-                 , const Moses::TrellisPathList &nBestList
-                 , const std::vector<Moses::FactorType>& outputFactorOrder
-                 , long translationId
-                 , char reportSegmentation);
-void OutputAllFeatureScores(const Moses::ScoreComponentCollection &features
-                            , std::ostream &out);
-void OutputFeatureScores( std::ostream& out
-                          , const Moses::ScoreComponentCollection &features
-                          , const Moses::FeatureFunction *ff
-                          , std::string &lastName );
-
-// creates a map of TARGET positions which should be replaced by word using placeholder
-std::map<size_t, const Moses::Factor*> GetPlaceholders(const Moses::Hypothesis &hypo, Moses::FactorType placeholderFactor);
-
-}
-
-#endif
diff --git a/moses-cmd/Jamfile b/moses-cmd/Jamfile
index 8d54e0515..7ee90850c 100644
--- a/moses-cmd/Jamfile
+++ b/moses-cmd/Jamfile
@@ -1,4 +1,4 @@
-alias deps : IOWrapper.cpp mbr.cpp ..//z ..//boost_iostreams ..//boost_filesystem ../moses//moses ;
+alias deps :  ..//z ..//boost_iostreams ..//boost_filesystem ../moses//moses ;
 
 exe moses : Main.cpp deps ;
 exe lmbrgrid : LatticeMBRGrid.cpp deps ;
diff --git a/moses-cmd/LatticeMBRGrid.cpp b/moses-cmd/LatticeMBRGrid.cpp
index 904275339..f00f40fd0 100644
--- a/moses-cmd/LatticeMBRGrid.cpp
+++ b/moses-cmd/LatticeMBRGrid.cpp
@@ -46,7 +46,7 @@ POSSIBILITY OF SUCH DAMAGE.
 #include <stdexcept>
 #include <set>
 
-#include "IOWrapper.h"
+#include "moses/IOWrapper.h"
 #include "moses/LatticeMBR.h"
 #include "moses/Manager.h"
 #include "moses/StaticData.h"
@@ -55,12 +55,11 @@ POSSIBILITY OF SUCH DAMAGE.
 
 using namespace std;
 using namespace Moses;
-using namespace MosesCmd;
 
 //keys
 enum gridkey {lmbr_p,lmbr_r,lmbr_prune,lmbr_scale};
 
-namespace MosesCmd
+namespace Moses
 {
 
 class Grid
@@ -159,7 +158,7 @@ int main(int argc, char* argv[])
 
   StaticData& staticData = const_cast<StaticData&>(StaticData::Instance());
   staticData.SetUseLatticeMBR(true);
-  IOWrapper* ioWrapper = GetIOWrapper(staticData);
+  IOWrapper* ioWrapper = IOWrapper::GetIOWrapper(staticData);
 
   if (!ioWrapper) {
     throw runtime_error("Failed to initialise IOWrapper");
@@ -178,10 +177,11 @@ int main(int argc, char* argv[])
   const vector<float>& prune_grid = grid.getGrid(lmbr_prune);
   const vector<float>& scale_grid = grid.getGrid(lmbr_scale);
 
-  while(ReadInput(*ioWrapper,staticData.GetInputType(),source)) {
+  while(ioWrapper->ReadInput(staticData.GetInputType(),source)) {
     ++lineCount;
-    Sentence sentence;
-    Manager manager(lineCount, *source, staticData.GetSearchAlgorithm());
+    source->SetTranslationId(lineCount);
+
+    Manager manager(*source, staticData.GetSearchAlgorithm());
     manager.ProcessSentence();
     TrellisPathList nBestList;
     manager.CalcNBest(nBestSize, nBestList,true);
@@ -200,7 +200,7 @@ int main(int argc, char* argv[])
             staticData.SetMBRScale(scale);
             cout << lineCount << " ||| " << p << " " << r << " " << prune << " " << scale << " ||| ";
             vector<Word> mbrBestHypo = doLatticeMBR(manager,nBestList);
-            OutputBestHypo(mbrBestHypo, lineCount, staticData.GetReportSegmentation(),
+            ioWrapper->OutputBestHypo(mbrBestHypo, lineCount, staticData.GetReportSegmentation(),
                            staticData.GetReportAllFactors(),cout);
           }
         }
diff --git a/moses-cmd/Main.cpp b/moses-cmd/Main.cpp
index 713ded2e3..319aede20 100644
--- a/moses-cmd/Main.cpp
+++ b/moses-cmd/Main.cpp
@@ -34,389 +34,34 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 //#include <vld.h>
 #endif
 
-#include "moses/TranslationAnalysis.h"
-#include "IOWrapper.h"
-#include "mbr.h"
-
+#include "moses/IOWrapper.h"
 #include "moses/Hypothesis.h"
 #include "moses/HypergraphOutput.h"
 #include "moses/Manager.h"
 #include "moses/StaticData.h"
+#include "moses/TypeDef.h"
 #include "moses/Util.h"
 #include "moses/Timer.h"
-#include "moses/ThreadPool.h"
-#include "moses/OutputCollector.h"
 #include "moses/TranslationModel/PhraseDictionary.h"
 #include "moses/FF/StatefulFeatureFunction.h"
 #include "moses/FF/StatelessFeatureFunction.h"
+#include "moses/TranslationTask.h"
 
 #ifdef HAVE_PROTOBUF
 #include "hypergraph.pb.h"
 #endif
 
-using namespace std;
-using namespace Moses;
-using namespace MosesCmd;
-
-namespace MosesCmd
-{
-// output floats with five significant digits
-static const size_t PRECISION = 3;
-
-/** Enforce rounding */
-void fix(std::ostream& stream, size_t size)
-{
-  stream.setf(std::ios::fixed);
-  stream.precision(size);
-}
-
-/** Translates a sentence.
-  * - calls the search (Manager)
-  * - applies the decision rule
-  * - outputs best translation and additional reporting
-  **/
-class TranslationTask : public Task
-{
-
-public:
-
-  TranslationTask(size_t lineNumber,
-                  InputType* source, OutputCollector* outputCollector, OutputCollector* nbestCollector,
-                  OutputCollector* latticeSamplesCollector,
-                  OutputCollector* wordGraphCollector, OutputCollector* searchGraphCollector,
-                  OutputCollector* detailedTranslationCollector,
-                  OutputCollector* alignmentInfoCollector,
-                  OutputCollector* unknownsCollector,
-                  bool outputSearchGraphSLF,
-                  boost::shared_ptr<HypergraphOutput<Manager> > hypergraphOutput) :
-    m_source(source), m_lineNumber(lineNumber),
-    m_outputCollector(outputCollector), m_nbestCollector(nbestCollector),
-    m_latticeSamplesCollector(latticeSamplesCollector),
-    m_wordGraphCollector(wordGraphCollector), m_searchGraphCollector(searchGraphCollector),
-    m_detailedTranslationCollector(detailedTranslationCollector),
-    m_alignmentInfoCollector(alignmentInfoCollector),
-    m_unknownsCollector(unknownsCollector),
-    m_outputSearchGraphSLF(outputSearchGraphSLF),
-    m_hypergraphOutput(hypergraphOutput) {}
-
-  /** Translate one sentence
-   * gets called by main function implemented at end of this source file */
-  void Run() {
-    // shorthand for "global data"
-    const StaticData &staticData = StaticData::Instance();
-
-    // input sentence
-    Sentence sentence;
-
-    // report wall time spent on translation
-    Timer translationTime;
-    translationTime.start();
-
-    // report thread number
-#if defined(WITH_THREADS) && defined(BOOST_HAS_PTHREADS)
-    TRACE_ERR("Translating line " << m_lineNumber << "  in thread id " << pthread_self() << std::endl);
+#ifdef PT_UG
+#include <boost/foreach.hpp>
+#include "moses/TranslationModel/UG/mmsapt.h"
+#include "moses/TranslationModel/UG/generic/program_options/ug_splice_arglist.h"
 #endif
 
+using namespace std;
+using namespace Moses;
 
-    // execute the translation
-    // note: this executes the search, resulting in a search graph
-    //       we still need to apply the decision rule (MAP, MBR, ...)
-    Timer initTime;
-    initTime.start();
-    Manager manager(m_lineNumber, *m_source,staticData.GetSearchAlgorithm());
-    VERBOSE(1, "Line " << m_lineNumber << ": Initialize search took " << initTime << " seconds total" << endl);
-    manager.ProcessSentence();
-
-    // we are done with search, let's look what we got
-    Timer additionalReportingTime;
-    additionalReportingTime.start();
-
-    // output word graph
-    if (m_wordGraphCollector) {
-      ostringstream out;
-      fix(out,PRECISION);
-      manager.GetWordGraph(m_lineNumber, out);
-      m_wordGraphCollector->Write(m_lineNumber, out.str());
-    }
-
-    // output search graph
-    if (m_searchGraphCollector) {
-      ostringstream out;
-      fix(out,PRECISION);
-      manager.OutputSearchGraph(m_lineNumber, out);
-      m_searchGraphCollector->Write(m_lineNumber, out.str());
-
-#ifdef HAVE_PROTOBUF
-      if (staticData.GetOutputSearchGraphPB()) {
-        ostringstream sfn;
-        sfn << staticData.GetParam("output-search-graph-pb")[0] << '/' << m_lineNumber << ".pb" << ends;
-        string fn = sfn.str();
-        VERBOSE(2, "Writing search graph to " << fn << endl);
-        fstream output(fn.c_str(), ios::trunc | ios::binary | ios::out);
-        manager.SerializeSearchGraphPB(m_lineNumber, output);
-      }
-#endif
-    }
-
-    // Output search graph in HTK standard lattice format (SLF)
-    if (m_outputSearchGraphSLF) {
-      stringstream fileName;
-      fileName << staticData.GetParam("output-search-graph-slf")[0] << "/" << m_lineNumber << ".slf";
-      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();
-      } 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);
-      }
-      delete file;
-    }
-
-    // Output search graph in hypergraph format for Kenneth Heafield's lazy hypergraph decoder
-    if (m_hypergraphOutput.get()) {
-      m_hypergraphOutput->Write(manager);
-    }
-
-    additionalReportingTime.stop();
-
-    // apply decision rule and output best translation(s)
-    if (m_outputCollector) {
-      ostringstream out;
-      ostringstream debug;
-      fix(debug,PRECISION);
-
-      // all derivations - send them to debug stream
-      if (staticData.PrintAllDerivations()) {
-        additionalReportingTime.start();
-        manager.PrintAllDerivations(m_lineNumber, debug);
-        additionalReportingTime.stop();
-      }
-
-      Timer decisionRuleTime;
-      decisionRuleTime.start();
-
-      // MAP decoding: best hypothesis
-      const Hypothesis* bestHypo = NULL;
-      if (!staticData.UseMBR()) {
-        bestHypo = manager.GetBestHypothesis();
-        if (bestHypo) {
-          if (StaticData::Instance().GetOutputHypoScore()) {
-            out << bestHypo->GetTotalScore() << ' ';
-          }
-          if (staticData.IsPathRecoveryEnabled()) {
-            OutputInput(out, bestHypo);
-            out << "||| ";
-          }
-          if (staticData.GetParam("print-id").size() && Scan<bool>(staticData.GetParam("print-id")[0]) ) {
-            out << m_source->GetTranslationId() << " ";
-          }
-
-	  if (staticData.GetReportSegmentation() == 2) {
-	    manager.GetOutputLanguageModelOrder(out, bestHypo);
-	  }
-          OutputBestSurface(
-            out,
-            bestHypo,
-            staticData.GetOutputFactorOrder(),
-            staticData.GetReportSegmentation(),
-            staticData.GetReportAllFactors());
-          if (staticData.PrintAlignmentInfo()) {
-            out << "||| ";
-            OutputAlignment(out, bestHypo);
-          }
-
-          OutputAlignment(m_alignmentInfoCollector, m_lineNumber, bestHypo);
-          IFVERBOSE(1) {
-            debug << "BEST TRANSLATION: " << *bestHypo << endl;
-          }
-        } else {
-          VERBOSE(1, "NO BEST TRANSLATION" << endl);
-        }
-
-        out << endl;
-      }
-
-      // MBR decoding (n-best MBR, lattice MBR, consensus)
-      else {
-        // we first need the n-best translations
-        size_t nBestSize = staticData.GetMBRSize();
-        if (nBestSize <= 0) {
-          cerr << "ERROR: negative size for number of MBR candidate translations not allowed (option mbr-size)" << endl;
-          exit(1);
-        }
-        TrellisPathList nBestList;
-        manager.CalcNBest(nBestSize, nBestList,true);
-        VERBOSE(2,"size of n-best: " << nBestList.GetSize() << " (" << nBestSize << ")" << endl);
-        IFVERBOSE(2) {
-          PrintUserTime("calculated n-best list for (L)MBR decoding");
-        }
-
-        // lattice MBR
-        if (staticData.UseLatticeMBR()) {
-          if (m_nbestCollector) {
-            //lattice mbr nbest
-            vector<LatticeMBRSolution> solutions;
-            size_t n  = min(nBestSize, staticData.GetNBestSize());
-            getLatticeMBRNBest(manager,nBestList,solutions,n);
-            ostringstream out;
-            OutputLatticeMBRNBest(out, solutions,m_lineNumber);
-            m_nbestCollector->Write(m_lineNumber, out.str());
-          } else {
-            //Lattice MBR decoding
-            vector<Word> mbrBestHypo = doLatticeMBR(manager,nBestList);
-            OutputBestHypo(mbrBestHypo, m_lineNumber, staticData.GetReportSegmentation(),
-                           staticData.GetReportAllFactors(),out);
-            IFVERBOSE(2) {
-              PrintUserTime("finished Lattice MBR decoding");
-            }
-          }
-        }
-
-        // consensus decoding
-        else if (staticData.UseConsensusDecoding()) {
-          const TrellisPath &conBestHypo = doConsensusDecoding(manager,nBestList);
-          OutputBestHypo(conBestHypo, m_lineNumber,
-                         staticData.GetReportSegmentation(),
-                         staticData.GetReportAllFactors(),out);
-          OutputAlignment(m_alignmentInfoCollector, m_lineNumber, conBestHypo);
-          IFVERBOSE(2) {
-            PrintUserTime("finished Consensus decoding");
-          }
-        }
-
-        // n-best MBR decoding
-        else {
-          const Moses::TrellisPath &mbrBestHypo = doMBR(nBestList);
-          OutputBestHypo(mbrBestHypo, m_lineNumber,
-                         staticData.GetReportSegmentation(),
-                         staticData.GetReportAllFactors(),out);
-          OutputAlignment(m_alignmentInfoCollector, m_lineNumber, mbrBestHypo);
-          IFVERBOSE(2) {
-            PrintUserTime("finished MBR decoding");
-          }
-        }
-      }
-
-      // report best translation to output collector
-      m_outputCollector->Write(m_lineNumber,out.str(),debug.str());
-
-      decisionRuleTime.stop();
-      VERBOSE(1, "Line " << m_lineNumber << ": Decision rule took " << decisionRuleTime << " seconds total" << endl);
-    }
-
-    additionalReportingTime.start();
-
-    // output n-best list
-    if (m_nbestCollector && !staticData.UseLatticeMBR()) {
-      TrellisPathList nBestList;
-      ostringstream out;
-      manager.CalcNBest(staticData.GetNBestSize(), nBestList,staticData.GetDistinctNBest());
-      OutputNBest(out, nBestList, staticData.GetOutputFactorOrder(), m_lineNumber,
-                  staticData.GetReportSegmentation());
-      m_nbestCollector->Write(m_lineNumber, out.str());
-    }
-
-    //lattice samples
-    if (m_latticeSamplesCollector) {
-      TrellisPathList latticeSamples;
-      ostringstream out;
-      manager.CalcLatticeSamples(staticData.GetLatticeSamplesSize(), latticeSamples);
-      OutputNBest(out,latticeSamples, staticData.GetOutputFactorOrder(), m_lineNumber,
-                  staticData.GetReportSegmentation());
-      m_latticeSamplesCollector->Write(m_lineNumber, out.str());
-    }
-
-    // detailed translation reporting
-    if (m_detailedTranslationCollector) {
-      ostringstream out;
-      fix(out,PRECISION);
-      TranslationAnalysis::PrintTranslationAnalysis(out, manager.GetBestHypothesis());
-      m_detailedTranslationCollector->Write(m_lineNumber,out.str());
-    }
-
-    //list of unknown words
-    if (m_unknownsCollector) {
-      const vector<const Phrase*>& unknowns = manager.getSntTranslationOptions()->GetUnknownSources();
-      ostringstream out;
-      for (size_t i = 0; i < unknowns.size(); ++i) {
-        out << *(unknowns[i]);
-      }
-      out << endl;
-      m_unknownsCollector->Write(m_lineNumber, out.str());
-    }
-
-    // report additional statistics
-    manager.CalcDecoderStatistics();
-    VERBOSE(1, "Line " << m_lineNumber << ": Additional reporting took " << additionalReportingTime << " seconds total" << endl);
-    VERBOSE(1, "Line " << m_lineNumber << ": Translation took " << translationTime << " seconds total" << endl);
-    IFVERBOSE(2) {
-      PrintUserTime("Sentence Decoding Time:");
-    }
-  }
-
-  ~TranslationTask() {
-    delete m_source;
-  }
-
-private:
-  InputType* m_source;
-  size_t m_lineNumber;
-  OutputCollector* m_outputCollector;
-  OutputCollector* m_nbestCollector;
-  OutputCollector* m_latticeSamplesCollector;
-  OutputCollector* m_wordGraphCollector;
-  OutputCollector* m_searchGraphCollector;
-  OutputCollector* m_detailedTranslationCollector;
-  OutputCollector* m_alignmentInfoCollector;
-  OutputCollector* m_unknownsCollector;
-  bool m_outputSearchGraphSLF;
-  boost::shared_ptr<HypergraphOutput<Manager> > m_hypergraphOutput;
-  std::ofstream *m_alignmentStream;
-
-
-};
-
-static void PrintFeatureWeight(const FeatureFunction* ff)
+namespace Moses
 {
-  cout << ff->GetScoreProducerDescription() << "=";
-  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 << endl;
-}
-
-static void ShowWeights()
-{
-  //TODO: Find a way of ensuring this order is synced with the nbest
-  fix(cout,6);
-  const vector<const StatelessFeatureFunction*>& slf = StatelessFeatureFunction::GetStatelessFeatureFunctions();
-  const vector<const StatefulFeatureFunction*>& sff = StatefulFeatureFunction::GetStatefulFeatureFunctions();
-
-  for (size_t i = 0; i < sff.size(); ++i) {
-    const StatefulFeatureFunction *ff = sff[i];
-    if (ff->IsTuneable()) {
-      PrintFeatureWeight(ff);
-    }
-    else {
-      cout << ff->GetScoreProducerDescription() << " UNTUNEABLE" << endl;
-    }
-  }
-  for (size_t i = 0; i < slf.size(); ++i) {
-    const StatelessFeatureFunction *ff = slf[i];
-    if (ff->IsTuneable()) {
-      PrintFeatureWeight(ff);
-    }
-    else {
-      cout << ff->GetScoreProducerDescription() << " UNTUNEABLE" << endl;
-    }
-  }
-}
 
 void OutputFeatureWeightsForHypergraph(std::ostream &outputSearchGraphStream)
 {
@@ -445,8 +90,8 @@ int main(int argc, char** argv)
     }
 
     // set number of significant decimals in output
-    fix(cout,PRECISION);
-    fix(cerr,PRECISION);
+    IOWrapper::FixPrecision(cout);
+    IOWrapper::FixPrecision(cerr);
 
     // load all the settings into the Parameter class
     // (stores them as strings, or array of strings)
@@ -476,7 +121,7 @@ int main(int argc, char** argv)
     srand(time(NULL));
 
     // set up read/writing class
-    IOWrapper* ioWrapper = GetIOWrapper(staticData);
+    IOWrapper* ioWrapper = IOWrapper::GetIOWrapper(staticData);
     if (!ioWrapper) {
       cerr << "Error; Failed to create IO object" << endl;
       exit(1);
@@ -489,92 +134,17 @@ int main(int argc, char** argv)
       TRACE_ERR(weights);
       TRACE_ERR("\n");
     }
-    boost::shared_ptr<HypergraphOutput<Manager> > hypergraphOutput; 
-    if (staticData.GetOutputSearchGraphHypergraph()) {
-      hypergraphOutput.reset(new HypergraphOutput<Manager>(PRECISION));
-    }
-
 
-    // initialize output streams
-    // note: we can't just write to STDOUT or files
-    // because multithreading may return sentences in shuffled order
-    auto_ptr<OutputCollector> outputCollector; // for translations
-    auto_ptr<OutputCollector> nbestCollector;  // for n-best lists
-    auto_ptr<OutputCollector> latticeSamplesCollector; //for lattice samples
-    auto_ptr<ofstream> nbestOut;
-    auto_ptr<ofstream> latticeSamplesOut;
-    size_t nbestSize = staticData.GetNBestSize();
-    string nbestFile = staticData.GetNBestFilePath();
-    bool output1best = true;
-    if (nbestSize) {
-      if (nbestFile == "-" || nbestFile == "/dev/stdout") {
-        // nbest to stdout, no 1-best
-        nbestCollector.reset(new OutputCollector());
-        output1best = false;
-      } else {
-        // nbest to file, 1-best to stdout
-        nbestOut.reset(new ofstream(nbestFile.c_str()));
-        if (!nbestOut->good()) {
-          TRACE_ERR("ERROR: Failed to open " << nbestFile << " for nbest lists" << endl);
-          exit(1);
-        }
-        nbestCollector.reset(new OutputCollector(nbestOut.get()));
-      }
-    }
-    size_t latticeSamplesSize = staticData.GetLatticeSamplesSize();
-    string latticeSamplesFile = staticData.GetLatticeSamplesFilePath();
-    if (latticeSamplesSize) {
-      if (latticeSamplesFile == "-" || latticeSamplesFile == "/dev/stdout") {
-        latticeSamplesCollector.reset(new OutputCollector());
-        output1best = false;
-      } else {
-        latticeSamplesOut.reset(new ofstream(latticeSamplesFile.c_str()));
-        if (!latticeSamplesOut->good()) {
-          TRACE_ERR("ERROR: Failed to open " << latticeSamplesFile << " for lattice samples" << endl);
-          exit(1);
-        }
-        latticeSamplesCollector.reset(new OutputCollector(latticeSamplesOut.get()));
-      }
-    }
-    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()) {
-      alignmentInfoCollector.reset(new OutputCollector(ioWrapper->GetAlignmentOutputStream()));
-    }
+    boost::shared_ptr<HypergraphOutput<Manager> > hypergraphOutput; 
+    boost::shared_ptr<HypergraphOutput<ChartManager> > hypergraphOutputChart;
 
-    //initialise stream for unknown (oov) words
-    auto_ptr<OutputCollector> unknownsCollector;
-    auto_ptr<ofstream> unknownsStream;
-    if (!staticData.GetOutputUnknownsFile().empty()) {
-      unknownsStream.reset(new ofstream(staticData.GetOutputUnknownsFile().c_str()));
-      if (!unknownsStream->good()) {
-        TRACE_ERR("Unable to open " << staticData.GetOutputUnknownsFile() << " for unknowns");
-        exit(1);
-      }
-      unknownsCollector.reset(new OutputCollector(unknownsStream.get()));
+    if (staticData.GetOutputSearchGraphHypergraph()) {
+    	if (staticData.IsChart()) {
+    		hypergraphOutputChart.reset(new HypergraphOutput<ChartManager>(PRECISION));
+    	}
+    	else {
+    		hypergraphOutput.reset(new HypergraphOutput<Manager>(PRECISION));
+    	}
     }
 
 #ifdef WITH_THREADS
@@ -584,7 +154,8 @@ int main(int argc, char** argv)
     // main loop over set of input sentences
     InputType* source = NULL;
     size_t lineCount = staticData.GetStartTranslationId();
-    while(ReadInput(*ioWrapper,staticData.GetInputType(),source)) {
+    while(ioWrapper->ReadInput(staticData.GetInputType(),source)) {
+      source->SetTranslationId(lineCount);
       IFVERBOSE(1) {
         ResetUserTime();
       }
@@ -592,19 +163,44 @@ int main(int argc, char** argv)
       FeatureFunction::CallChangeSource(source);
 
       // set up task of translating one sentence
-      TranslationTask* task =
-        new TranslationTask(lineCount,source, outputCollector.get(),
-                            nbestCollector.get(),
-                            latticeSamplesCollector.get(),
-                            wordGraphCollector.get(),
-                            searchGraphCollector.get(),
-                            detailedTranslationCollector.get(),
-                            alignmentInfoCollector.get(),
-                            unknownsCollector.get(),
-                            staticData.GetOutputSearchGraphSLF(),
-                            hypergraphOutput);
+      TranslationTask* task;
+      if (staticData.IsChart()) {
+    	  // scfg
+          task = new TranslationTask(source, *ioWrapper, hypergraphOutputChart);
+      }
+      else {
+    	  // pb
+		  task = new TranslationTask(source, *ioWrapper,
+								staticData.GetOutputSearchGraphSLF(),
+								hypergraphOutput);
+      }
+
       // execute task
 #ifdef WITH_THREADS
+#ifdef PT_UG
+      bool spe = params.isParamSpecified("spe-src");
+      if (spe) {
+    	// simulated post-editing: always run single-threaded!
+        task->Run();
+        delete task;
+        string src,trg,aln;
+        UTIL_THROW_IF2(!getline(*ioWrapper->spe_src,src), "[" << HERE << "] "
+                       << "missing update data for simulated post-editing.");
+        UTIL_THROW_IF2(!getline(*ioWrapper->spe_trg,trg), "[" << HERE << "] "
+		       << "missing update data for simulated post-editing.");
+        UTIL_THROW_IF2(!getline(*ioWrapper->spe_aln,aln), "[" << HERE << "] "
+		       << "missing update data for simulated post-editing.");
+		BOOST_FOREACH (PhraseDictionary* pd, PhraseDictionary::GetColl())
+		  {
+			Mmsapt* sapt = dynamic_cast<Mmsapt*>(pd);
+			if (sapt) sapt->add(src,trg,aln);
+			VERBOSE(1,"[" << HERE << " added src] " << src << endl);
+			VERBOSE(1,"[" << HERE << " added trg] " << trg << endl);
+			VERBOSE(1,"[" << HERE << " added aln] " << aln << endl);
+		  }
+      }
+      else
+#endif
       pool.Submit(task);
 #else
       task->Run();
diff --git a/moses-cmd/Main.h b/moses-cmd/Main.h
index 362c1f245..49fee0219 100644
--- a/moses-cmd/Main.h
+++ b/moses-cmd/Main.h
@@ -1,3 +1,4 @@
+#pragma once
 // $Id$
 
 /***********************************************************************
@@ -32,12 +33,10 @@ POSSIBILITY OF SUCH DAMAGE.
 
 // example file on how to use moses library
 
-#ifndef moses_cmd_Main_h
-#define moses_cmd_Main_h
 
 #include "moses/StaticData.h"
 
 class IOWrapper;
 
 int main(int argc, char* argv[]);
-#endif
+
diff --git a/moses-cmd/mbr.cpp b/moses-cmd/mbr.cpp
deleted file mode 100644
index 6a8dfa823..000000000
--- a/moses-cmd/mbr.cpp
+++ /dev/null
@@ -1,178 +0,0 @@
-#include <iostream>
-#include <fstream>
-#include <sstream>
-#include <iomanip>
-#include <vector>
-#include <map>
-#include <stdlib.h>
-#include <math.h>
-#include <algorithm>
-#include <stdio.h>
-#include "moses/TrellisPathList.h"
-#include "moses/TrellisPath.h"
-#include "moses/StaticData.h"
-#include "moses/Util.h"
-#include "mbr.h"
-
-using namespace std ;
-using namespace Moses;
-
-
-/* Input :
-   1. a sorted  n-best list, with duplicates filtered out in the following  format
-   0 ||| amr moussa is currently on a visit to libya , tomorrow , sunday , to hold talks with regard to the in sudan . ||| 0 -4.94418 0 0 -2.16036 0 0 -81.4462 -106.593 -114.43 -105.55 -12.7873 -26.9057 -25.3715 -52.9336 7.99917 -24 ||| -4.58432
-
-   2. a weight vector
-   3. bleu order ( default = 4)
-   4. scaling factor to weigh the weight vector (default = 1.0)
-
-   Output :
-   translations that minimise the Bayes Risk of the n-best list
-
-
-*/
-
-int BLEU_ORDER = 4;
-int SMOOTH = 1;
-float min_interval = 1e-4;
-void extract_ngrams(const vector<const Factor* >& sentence, map < vector < const Factor* >, int >  & allngrams)
-{
-  vector< const Factor* > ngram;
-  for (int k = 0; k < BLEU_ORDER; k++) {
-    for(int i =0; i < max((int)sentence.size()-k,0); i++) {
-      for ( int j = i; j<= i+k; j++) {
-        ngram.push_back(sentence[j]);
-      }
-      ++allngrams[ngram];
-      ngram.clear();
-    }
-  }
-}
-
-float calculate_score(const vector< vector<const Factor*> > & sents, int ref, int hyp,  vector < map < vector < const Factor *>, int > > & ngram_stats )
-{
-  int comps_n = 2*BLEU_ORDER+1;
-  vector<int> comps(comps_n);
-  float logbleu = 0.0, brevity;
-
-  int hyp_length = sents[hyp].size();
-
-  for (int i =0; i<BLEU_ORDER; i++) {
-    comps[2*i] = 0;
-    comps[2*i+1] = max(hyp_length-i,0);
-  }
-
-  map< vector < const Factor * > ,int > & hyp_ngrams = ngram_stats[hyp] ;
-  map< vector < const Factor * >, int > & ref_ngrams = ngram_stats[ref] ;
-
-  for (map< vector< const Factor * >, int >::iterator it = hyp_ngrams.begin();
-       it != hyp_ngrams.end(); it++) {
-    map< vector< const Factor * >, int >::iterator ref_it = ref_ngrams.find(it->first);
-    if(ref_it != ref_ngrams.end()) {
-      comps[2* (it->first.size()-1)] += min(ref_it->second,it->second);
-    }
-  }
-  comps[comps_n-1] = sents[ref].size();
-
-  for (int i=0; i<BLEU_ORDER; i++) {
-    if (comps[0] == 0)
-      return 0.0;
-    if ( i > 0 )
-      logbleu += log((float)comps[2*i]+SMOOTH)-log((float)comps[2*i+1]+SMOOTH);
-    else
-      logbleu += log((float)comps[2*i])-log((float)comps[2*i+1]);
-  }
-  logbleu /= BLEU_ORDER;
-  brevity = 1.0-(float)comps[comps_n-1]/comps[1]; // comps[comps_n-1] is the ref length, comps[1] is the test length
-  if (brevity < 0.0)
-    logbleu += brevity;
-  return exp(logbleu);
-}
-
-const TrellisPath doMBR(const TrellisPathList& nBestList)
-{
-  float marginal = 0;
-
-  vector<float> joint_prob_vec;
-  vector< vector<const Factor*> > translations;
-  float joint_prob;
-  vector< map < vector <const Factor *>, int > > ngram_stats;
-
-  TrellisPathList::const_iterator iter;
-
-  // get max score to prevent underflow
-  float maxScore = -1e20;
-  for (iter = nBestList.begin() ; iter != nBestList.end() ; ++iter) {
-    const TrellisPath &path = **iter;
-    float score = StaticData::Instance().GetMBRScale()
-                  * path.GetScoreBreakdown().GetWeightedScore();
-    if (maxScore < score) maxScore = score;
-  }
-
-  for (iter = nBestList.begin() ; iter != nBestList.end() ; ++iter) {
-    const TrellisPath &path = **iter;
-    joint_prob = UntransformScore(StaticData::Instance().GetMBRScale() * path.GetScoreBreakdown().GetWeightedScore() - maxScore);
-    marginal += joint_prob;
-    joint_prob_vec.push_back(joint_prob);
-
-    // get words in translation
-    vector<const Factor*> translation;
-    GetOutputFactors(path, translation);
-
-    // collect n-gram counts
-    map < vector < const Factor *>, int > counts;
-    extract_ngrams(translation,counts);
-
-    ngram_stats.push_back(counts);
-    translations.push_back(translation);
-  }
-
-  vector<float> mbr_loss;
-  float bleu, weightedLoss;
-  float weightedLossCumul = 0;
-  float minMBRLoss = 1000000;
-  int minMBRLossIdx = -1;
-
-  /* Main MBR computation done here */
-  iter = nBestList.begin();
-  for (unsigned int i = 0; i < nBestList.GetSize(); i++) {
-    weightedLossCumul = 0;
-    for (unsigned int j = 0; j < nBestList.GetSize(); j++) {
-      if ( i != j) {
-        bleu = calculate_score(translations, j, i,ngram_stats );
-        weightedLoss = ( 1 - bleu) * ( joint_prob_vec[j]/marginal);
-        weightedLossCumul += weightedLoss;
-        if (weightedLossCumul > minMBRLoss)
-          break;
-      }
-    }
-    if (weightedLossCumul < minMBRLoss) {
-      minMBRLoss = weightedLossCumul;
-      minMBRLossIdx = i;
-    }
-    iter++;
-  }
-  /* Find sentence that minimises Bayes Risk under 1- BLEU loss */
-  return nBestList.at(minMBRLossIdx);
-  //return translations[minMBRLossIdx];
-}
-
-void GetOutputFactors(const TrellisPath &path, vector <const Factor*> &translation)
-{
-  const std::vector<const Hypothesis *> &edges = path.GetEdges();
-  const std::vector<FactorType>& outputFactorOrder = StaticData::Instance().GetOutputFactorOrder();
-  assert (outputFactorOrder.size() == 1);
-
-  // print the surface factor of the translation
-  for (int currEdge = (int)edges.size() - 1 ; currEdge >= 0 ; currEdge--) {
-    const Hypothesis &edge = *edges[currEdge];
-    const Phrase &phrase = edge.GetCurrTargetPhrase();
-    size_t size = phrase.GetSize();
-    for (size_t pos = 0 ; pos < size ; pos++) {
-
-      const Factor *factor = phrase.GetFactor(pos, outputFactorOrder[0]);
-      translation.push_back(factor);
-    }
-  }
-}
-
diff --git a/moses-cmd/mbr.h b/moses-cmd/mbr.h
deleted file mode 100644
index d08b11a98..000000000
--- a/moses-cmd/mbr.h
+++ /dev/null
@@ -1,28 +0,0 @@
-// $Id$
-
-/***********************************************************************
-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_cmd_mbr_h
-#define moses_cmd_mbr_h
-
-const Moses::TrellisPath doMBR(const Moses::TrellisPathList& nBestList);
-void GetOutputFactors(const Moses::TrellisPath &path, std::vector <const Moses::Factor*> &translation);
-float calculate_score(const std::vector< std::vector<const Moses::Factor*> > & sents, int ref, int hyp,  std::vector < std::map < std::vector < const Moses::Factor *>, int > > & ngram_stats );
-#endif
diff --git a/moses-cmd/simulate-pe.cc b/moses-cmd/simulate-pe.cc
index 9678e26c7..f05c0f510 100644
--- a/moses-cmd/simulate-pe.cc
+++ b/moses-cmd/simulate-pe.cc
@@ -20,44 +20,41 @@ 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 <boost/algorithm/string/predicate.hpp>
-#include <boost/filesystem.hpp>
-#include <boost/iostreams/device/file.hpp>
-#include <boost/iostreams/filter/bzip2.hpp>
-#include <boost/iostreams/filter/gzip.hpp>
-#include <boost/iostreams/filtering_stream.hpp>
-#include <boost/foreach.hpp>
-
+/**
+ * Moses main, for single-threaded and multi-threaded.
+ **/
 #include <exception>
 #include <fstream>
 #include <sstream>
 #include <vector>
 
+#include <boost/program_options.hpp>
 #include "util/usage.hh"
 #include "util/exception.hh"
 #include "moses/Util.h"
+
+#ifdef PT_UG
 #include "moses/TranslationModel/UG/mmsapt.h"
 #include "moses/TranslationModel/UG/generic/program_options/ug_splice_arglist.h"
+#endif
 
 #ifdef WIN32
 // Include Visual Leak Detector
 //#include <vld.h>
 #endif
 
-#include "moses/TranslationAnalysis.h"
-#include "IOWrapper.h"
-#include "mbr.h"
-
+#include "moses/IOWrapper.h"
 #include "moses/Hypothesis.h"
+#include "moses/HypergraphOutput.h"
 #include "moses/Manager.h"
 #include "moses/StaticData.h"
+#include "moses/TypeDef.h"
 #include "moses/Util.h"
 #include "moses/Timer.h"
-#include "moses/ThreadPool.h"
-#include "moses/OutputCollector.h"
 #include "moses/TranslationModel/PhraseDictionary.h"
 #include "moses/FF/StatefulFeatureFunction.h"
 #include "moses/FF/StatelessFeatureFunction.h"
+#include "moses/TranslationTask.h"
 
 #ifdef HAVE_PROTOBUF
 #include "hypergraph.pb.h"
@@ -65,522 +62,15 @@ Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
 
 using namespace std;
 using namespace Moses;
-using namespace MosesCmd;
-
-namespace MosesCmd
-{
-// output floats with five significant digits
-static const size_t PRECISION = 3;
-
-/** Enforce rounding */
-void fix(std::ostream& stream, size_t size)
-{
-  stream.setf(std::ios::fixed);
-  stream.precision(size);
-}
 
-/** Translates a sentence.
-  * - calls the search (Manager)
-  * - applies the decision rule
-  * - outputs best translation and additional reporting
-  **/
-class TranslationTask : public Task
+namespace Moses
 {
 
-public:
-
-  TranslationTask(size_t lineNumber,
-                  InputType* source, 
-		  OutputCollector* outputCollector, 
-		  OutputCollector* nbestCollector,
-                  OutputCollector* latticeSamplesCollector,
-                  OutputCollector* wordGraphCollector, 
-		  OutputCollector* searchGraphCollector,
-                  OutputCollector* detailedTranslationCollector,
-                  OutputCollector* alignmentInfoCollector,
-                  OutputCollector* unknownsCollector,
-                  bool outputSearchGraphSLF,
-                  bool outputSearchGraphHypergraph) 
-    : m_source(source)
-    , m_lineNumber(lineNumber)
-    , m_outputCollector(outputCollector)
-    , m_nbestCollector(nbestCollector)
-    , m_latticeSamplesCollector(latticeSamplesCollector)
-    , m_wordGraphCollector(wordGraphCollector)
-    , m_searchGraphCollector(searchGraphCollector)
-    , m_detailedTranslationCollector(detailedTranslationCollector)
-    , m_alignmentInfoCollector(alignmentInfoCollector)
-    , m_unknownsCollector(unknownsCollector)
-    , m_outputSearchGraphSLF(outputSearchGraphSLF)
-    , m_outputSearchGraphHypergraph(outputSearchGraphHypergraph) 
-  { }
-
-  /** Translate one sentence
-   * gets called by main function implemented at end of this source file */
-  void Run() {
-    // shorthand for "global data"
-    const StaticData &staticData = StaticData::Instance();
-
-    // input sentence
-    Sentence sentence;
-
-    // report wall time spent on translation
-    Timer translationTime;
-    translationTime.start();
-
-    // report thread number
-#if defined(WITH_THREADS) && defined(BOOST_HAS_PTHREADS)
-    TRACE_ERR("Translating line " << m_lineNumber << "  in thread id " << pthread_self() << std::endl);
-#endif
-
-
-    // execute the translation
-    // note: this executes the search, resulting in a search graph
-    //       we still need to apply the decision rule (MAP, MBR, ...)
-    Timer initTime;
-    initTime.start();
-    Manager manager(m_lineNumber, *m_source,staticData.GetSearchAlgorithm());
-    VERBOSE(1, "Line " << m_lineNumber << ": Initialize search took " << initTime << " seconds total" << endl);
-    manager.ProcessSentence();
-
-    // we are done with search, let's look what we got
-    Timer additionalReportingTime;
-    additionalReportingTime.start();
-
-    // output word graph
-    if (m_wordGraphCollector) {
-      ostringstream out;
-      fix(out,PRECISION);
-      manager.GetWordGraph(m_lineNumber, out);
-      m_wordGraphCollector->Write(m_lineNumber, out.str());
-    }
-
-    // output search graph
-    if (m_searchGraphCollector) {
-      ostringstream out;
-      fix(out,PRECISION);
-      manager.OutputSearchGraph(m_lineNumber, out);
-      m_searchGraphCollector->Write(m_lineNumber, out.str());
-
-#ifdef HAVE_PROTOBUF
-      if (staticData.GetOutputSearchGraphPB()) {
-        ostringstream sfn;
-        sfn << staticData.GetParam("output-search-graph-pb")[0] << '/' << m_lineNumber << ".pb" << ends;
-        string fn = sfn.str();
-        VERBOSE(2, "Writing search graph to " << fn << endl);
-        fstream output(fn.c_str(), ios::trunc | ios::binary | ios::out);
-        manager.SerializeSearchGraphPB(m_lineNumber, output);
-      }
-#endif
-    }
-
-    // Output search graph in HTK standard lattice format (SLF)
-    if (m_outputSearchGraphSLF) {
-      stringstream fileName;
-      fileName << staticData.GetParam("output-search-graph-slf")[0] << "/" << m_lineNumber << ".slf";
-      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();
-      } 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);
-      }
-      delete file;
-    }
-
-    // Output search graph in hypergraph format for Kenneth Heafield's lazy hypergraph decoder
-    if (m_outputSearchGraphHypergraph) {
-
-      vector<string> hypergraphParameters = staticData.GetParam("output-search-graph-hypergraph");
-
-      bool appendSuffix;
-      if (hypergraphParameters.size() > 0 && hypergraphParameters[0] == "true") {
-        appendSuffix = true;
-      } else {
-        appendSuffix = false;
-      }
-
-      string compression;
-      if (hypergraphParameters.size() > 1) {
-        compression = hypergraphParameters[1];
-      } else {
-        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().string() << "/hypergraph";
-          hypergraphDir = hypergraphDirName.str();
-        }
-      }
-
-      if ( ! boost::filesystem::exists(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);
-      } 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);
-      } 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(*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;
-      }
-    }
-    additionalReportingTime.stop();
-
-    // apply decision rule and output best translation(s)
-    if (m_outputCollector) {
-      ostringstream out;
-      ostringstream debug;
-      fix(debug,PRECISION);
-
-      // all derivations - send them to debug stream
-      if (staticData.PrintAllDerivations()) {
-        additionalReportingTime.start();
-        manager.PrintAllDerivations(m_lineNumber, debug);
-        additionalReportingTime.stop();
-      }
-
-      Timer decisionRuleTime;
-      decisionRuleTime.start();
-
-      // MAP decoding: best hypothesis
-      const Hypothesis* bestHypo = NULL;
-      if (!staticData.UseMBR()) {
-        bestHypo = manager.GetBestHypothesis();
-        if (bestHypo) {
-          if (StaticData::Instance().GetOutputHypoScore()) {
-            out << bestHypo->GetTotalScore() << ' ';
-          }
-          if (staticData.IsPathRecoveryEnabled()) {
-            OutputInput(out, bestHypo);
-            out << "||| ";
-          }
-          if (staticData.GetParam("print-id").size() && Scan<bool>(staticData.GetParam("print-id")[0]) ) {
-            out << m_source->GetTranslationId() << " ";
-          }
-
-	  if (staticData.GetReportSegmentation() == 2) {
-	    manager.GetOutputLanguageModelOrder(out, bestHypo);
-	  }
-          OutputBestSurface(
-            out,
-            bestHypo,
-            staticData.GetOutputFactorOrder(),
-            staticData.GetReportSegmentation(),
-            staticData.GetReportAllFactors());
-          if (staticData.PrintAlignmentInfo()) {
-            out << "||| ";
-            OutputAlignment(out, bestHypo);
-          }
-
-          OutputAlignment(m_alignmentInfoCollector, m_lineNumber, bestHypo);
-          IFVERBOSE(1) {
-            debug << "BEST TRANSLATION: " << *bestHypo << endl;
-          }
-        } else {
-          VERBOSE(1, "NO BEST TRANSLATION" << endl);
-        }
-
-        out << endl;
-      }
-
-      // MBR decoding (n-best MBR, lattice MBR, consensus)
-      else {
-        // we first need the n-best translations
-        size_t nBestSize = staticData.GetMBRSize();
-        if (nBestSize <= 0) {
-          cerr << "ERROR: negative size for number of MBR candidate translations not allowed (option mbr-size)" << endl;
-          exit(1);
-        }
-        TrellisPathList nBestList;
-        manager.CalcNBest(nBestSize, nBestList,true);
-        VERBOSE(2,"size of n-best: " << nBestList.GetSize() << " (" << nBestSize << ")" << endl);
-        IFVERBOSE(2) {
-          PrintUserTime("calculated n-best list for (L)MBR decoding");
-        }
-
-        // lattice MBR
-        if (staticData.UseLatticeMBR()) {
-          if (m_nbestCollector) {
-            //lattice mbr nbest
-            vector<LatticeMBRSolution> solutions;
-            size_t n  = min(nBestSize, staticData.GetNBestSize());
-            getLatticeMBRNBest(manager,nBestList,solutions,n);
-            ostringstream out;
-            OutputLatticeMBRNBest(out, solutions,m_lineNumber);
-            m_nbestCollector->Write(m_lineNumber, out.str());
-          } else {
-            //Lattice MBR decoding
-            vector<Word> mbrBestHypo = doLatticeMBR(manager,nBestList);
-            OutputBestHypo(mbrBestHypo, m_lineNumber, staticData.GetReportSegmentation(),
-                           staticData.GetReportAllFactors(),out);
-            IFVERBOSE(2) {
-              PrintUserTime("finished Lattice MBR decoding");
-            }
-          }
-        }
-
-        // consensus decoding
-        else if (staticData.UseConsensusDecoding()) {
-          const TrellisPath &conBestHypo = doConsensusDecoding(manager,nBestList);
-          OutputBestHypo(conBestHypo, m_lineNumber,
-                         staticData.GetReportSegmentation(),
-                         staticData.GetReportAllFactors(),out);
-          OutputAlignment(m_alignmentInfoCollector, m_lineNumber, conBestHypo);
-          IFVERBOSE(2) {
-            PrintUserTime("finished Consensus decoding");
-          }
-        }
-
-        // n-best MBR decoding
-        else {
-          const Moses::TrellisPath &mbrBestHypo = doMBR(nBestList);
-          OutputBestHypo(mbrBestHypo, m_lineNumber,
-                         staticData.GetReportSegmentation(),
-                         staticData.GetReportAllFactors(),out);
-          OutputAlignment(m_alignmentInfoCollector, m_lineNumber, mbrBestHypo);
-          IFVERBOSE(2) {
-            PrintUserTime("finished MBR decoding");
-          }
-        }
-      }
-
-      // report best translation to output collector
-      m_outputCollector->Write(m_lineNumber,out.str(),debug.str());
-
-      decisionRuleTime.stop();
-      VERBOSE(1, "Line " << m_lineNumber << ": Decision rule took " << decisionRuleTime << " seconds total" << endl);
-    }
-
-    additionalReportingTime.start();
-
-    // output n-best list
-    if (m_nbestCollector && !staticData.UseLatticeMBR()) {
-      TrellisPathList nBestList;
-      ostringstream out;
-      manager.CalcNBest(staticData.GetNBestSize(), nBestList,staticData.GetDistinctNBest());
-      OutputNBest(out, nBestList, staticData.GetOutputFactorOrder(), m_lineNumber,
-                  staticData.GetReportSegmentation());
-      m_nbestCollector->Write(m_lineNumber, out.str());
-    }
-
-    //lattice samples
-    if (m_latticeSamplesCollector) {
-      TrellisPathList latticeSamples;
-      ostringstream out;
-      manager.CalcLatticeSamples(staticData.GetLatticeSamplesSize(), latticeSamples);
-      OutputNBest(out,latticeSamples, staticData.GetOutputFactorOrder(), m_lineNumber,
-                  staticData.GetReportSegmentation());
-      m_latticeSamplesCollector->Write(m_lineNumber, out.str());
-    }
-
-    // detailed translation reporting
-    if (m_detailedTranslationCollector) {
-      ostringstream out;
-      fix(out,PRECISION);
-      TranslationAnalysis::PrintTranslationAnalysis(out, manager.GetBestHypothesis());
-      m_detailedTranslationCollector->Write(m_lineNumber,out.str());
-    }
-
-    //list of unknown words
-    if (m_unknownsCollector) {
-      const vector<const Phrase*>& unknowns = manager.getSntTranslationOptions()->GetUnknownSources();
-      ostringstream out;
-      for (size_t i = 0; i < unknowns.size(); ++i) {
-        out << *(unknowns[i]);
-      }
-      out << endl;
-      m_unknownsCollector->Write(m_lineNumber, out.str());
-    }
-
-    // report additional statistics
-    manager.CalcDecoderStatistics();
-    VERBOSE(1, "Line " << m_lineNumber << ": Additional reporting took " << additionalReportingTime << " seconds total" << endl);
-    VERBOSE(1, "Line " << m_lineNumber << ": Translation took " << translationTime << " seconds total" << endl);
-    IFVERBOSE(2) {
-      PrintUserTime("Sentence Decoding Time:");
-    }
-  }
-
-  ~TranslationTask() {
-    delete m_source;
-  }
-
-private:
-  InputType* m_source;
-  size_t m_lineNumber;
-  OutputCollector* m_outputCollector;
-  OutputCollector* m_nbestCollector;
-  OutputCollector* m_latticeSamplesCollector;
-  OutputCollector* m_wordGraphCollector;
-  OutputCollector* m_searchGraphCollector;
-  OutputCollector* m_detailedTranslationCollector;
-  OutputCollector* m_alignmentInfoCollector;
-  OutputCollector* m_unknownsCollector;
-  bool m_outputSearchGraphSLF;
-  bool m_outputSearchGraphHypergraph;
-  std::ofstream *m_alignmentStream;
-
-
-};
-
-static void PrintFeatureWeight(const FeatureFunction* ff)
-{
-  cout << ff->GetScoreProducerDescription() << "=";
-  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 << endl;
-}
-
-static void ShowWeights()
-{
-  //TODO: Find a way of ensuring this order is synced with the nbest
-  fix(cout,6);
-  const vector<const StatelessFeatureFunction*>& slf = StatelessFeatureFunction::GetStatelessFeatureFunctions();
-  const vector<const StatefulFeatureFunction*>& sff = StatefulFeatureFunction::GetStatefulFeatureFunctions();
-
-  for (size_t i = 0; i < sff.size(); ++i) {
-    const StatefulFeatureFunction *ff = sff[i];
-    if (ff->IsTuneable()) {
-      PrintFeatureWeight(ff);
-    }
-    else {
-      cout << ff->GetScoreProducerDescription() << " UNTUNEABLE" << endl;
-    }
-  }
-  for (size_t i = 0; i < slf.size(); ++i) {
-    const StatelessFeatureFunction *ff = slf[i];
-    if (ff->IsTuneable()) {
-      PrintFeatureWeight(ff);
-    }
-    else {
-      cout << ff->GetScoreProducerDescription() << " UNTUNEABLE" << endl;
-    }
-  }
-}
-
-size_t OutputFeatureWeightsForHypergraph(size_t index, const FeatureFunction* ff, std::ostream &outputSearchGraphStream)
-{
-  size_t numScoreComps = ff->GetNumScoreComponents();
-  if (numScoreComps != 0) {
-    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;
-      }
-    } else {
-      outputSearchGraphStream << ff->GetScoreProducerDescription()
-                              << "=" << values[0] << endl;
-    }
-    return index+numScoreComps;
-  } else {
-    UTIL_THROW2("Sparse features are not yet supported when outputting hypergraph format");
-  }
-}
-
 void OutputFeatureWeightsForHypergraph(std::ostream &outputSearchGraphStream)
 {
   outputSearchGraphStream.setf(std::ios::fixed);
   outputSearchGraphStream.precision(6);
-
-  const vector<const StatelessFeatureFunction*>& slf =StatelessFeatureFunction::GetStatelessFeatureFunctions();
-  const vector<const StatefulFeatureFunction*>& sff = StatefulFeatureFunction::GetStatefulFeatureFunctions();
-  size_t featureIndex = 1;
-  for (size_t i = 0; i < sff.size(); ++i) {
-    featureIndex = OutputFeatureWeightsForHypergraph(featureIndex, sff[i], outputSearchGraphStream);
-  }
-  for (size_t i = 0; i < slf.size(); ++i) {
-    /*
-    if (slf[i]->GetScoreProducerWeightShortName() != "u" &&
-          slf[i]->GetScoreProducerWeightShortName() != "tm" &&
-          slf[i]->GetScoreProducerWeightShortName() != "I" &&
-          slf[i]->GetScoreProducerWeightShortName() != "g")
-    */
-    {
-      featureIndex = OutputFeatureWeightsForHypergraph(featureIndex, slf[i], outputSearchGraphStream);
-    }
-  }
-  const vector<PhraseDictionary*>& pds = PhraseDictionary::GetColl();
-  for( size_t i=0; i<pds.size(); i++ ) {
-    featureIndex = OutputFeatureWeightsForHypergraph(featureIndex, pds[i], outputSearchGraphStream);
-  }
-  const vector<GenerationDictionary*>& gds = GenerationDictionary::GetColl();
-  for( size_t i=0; i<gds.size(); i++ ) {
-    featureIndex = OutputFeatureWeightsForHypergraph(featureIndex, gds[i], outputSearchGraphStream);
-  }
-
+  StaticData::Instance().GetAllWeights().Save(outputSearchGraphStream);
 }
 
 
@@ -603,9 +93,36 @@ int main(int argc, char** argv)
     }
 
     // set number of significant decimals in output
-    fix(cout,PRECISION);
-    fix(cerr,PRECISION);
-
+    // By the way, having a static member function in an Moses-specific class
+    // just to do 
+    // cout.setf(ios::fixed);cout.precision(3);
+    // doesn't make sense.
+    // 1. It makes the program harder to understand. If I see
+    //    cout.setf(ios::fixed);cout.precision(3);
+    //    I know immediately what's going on. If I see, 
+    //    IOWrapper::FixPrecision(cout); 
+    //    I assume that something much more elaborate is going on (side effects?)
+    //    and need to look it up. 
+    //    After all, one reads programs in order to understand them.
+    // 2. If you want to enforce a certain default behaviour on stdout,
+    //    that should happen only once. Other components should not do that. 
+    // 3. If you want to format locally, use
+    //    string IOWrapper::score_default_formatting = "%.3f";
+    //    cout << boost::format(IOWrapper::score_default_formatting) % my_variable;
+    //    This even allows you to do pretty printing by default if you wish. 
+    //    (Actually, the format variable should be constructed 
+    //    from an int IOWrapper::score_output_default_precision itself.)
+    // 4. If output speed is an issue and you are afraid of the overhead that 
+    //    boost::format may add, don't use streams to begin with.
+    // IOWrapper::FixPrecision(cout); 
+    // IOWrapper::FixPrecision(cerr);
+    cout.setf(ios::fixed); cout.precision(3);
+    cout.setf(ios::fixed); cout.precision(3);
+
+#ifdef PT_UG
+    // see my notes on the moses support mailing list, this is a hack around
+    // the misguided implementation of LoadParameter(), which should leave
+    // arguments it doesn't know alone.
     vector<pair<string,int> > argfilter(4);
     argfilter[0] = std::make_pair(string("--spe-src"),1);
     argfilter[1] = std::make_pair(string("--spe-trg"),1);
@@ -616,16 +133,16 @@ int main(int argc, char** argv)
     filter_arguments(argc, argv, mo_acnt, &mo_args, my_acnt, &my_args, argfilter);
 
     ifstream spe_src,spe_trg,spe_aln;
-    // instead of translating show coverage by phrase tables
     for (int i = 0; i < my_acnt; i += 2)
       {
-	if (!strcmp(my_args[i],"--spe-src"))
-	  spe_src.open(my_args[i+1]);
-	else if (!strcmp(my_args[i],"--spe-trg"))
-	  spe_trg.open(my_args[i+1]);
-	else if (!strcmp(my_args[i],"--spe-aln"))
-	  spe_aln.open(my_args[i+1]);
+        if (!strcmp(my_args[i],"--spe-src"))
+          spe_src.open(my_args[i+1]);
+        else if (!strcmp(my_args[i],"--spe-trg"))
+          spe_trg.open(my_args[i+1]);
+        else if (!strcmp(my_args[i],"--spe-aln"))
+          spe_aln.open(my_args[i+1]);
       }
+#endif
 
     // load all the settings into the Parameter class
     // (stores them as strings, or array of strings)
@@ -634,7 +151,6 @@ int main(int argc, char** argv)
       exit(1);
     }
 
-
     // initialize all "global" variables, which are stored in StaticData
     // note: this also loads models such as the language model, etc.
     if (!StaticData::LoadDataStatic(&params, argv[0])) {
@@ -650,12 +166,11 @@ int main(int argc, char** argv)
     // shorthand for accessing information in StaticData
     const StaticData& staticData = StaticData::Instance();
 
-
     //initialise random numbers
     srand(time(NULL));
 
     // set up read/writing class
-    IOWrapper* ioWrapper = GetIOWrapper(staticData);
+    IOWrapper* ioWrapper = IOWrapper::GetIOWrapper(staticData);
     if (!ioWrapper) {
       cerr << "Error; Failed to create IO object" << endl;
       exit(1);
@@ -668,113 +183,17 @@ int main(int argc, char** argv)
       TRACE_ERR(weights);
       TRACE_ERR("\n");
     }
-    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];
-      } 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().string() << "/hypergraph/weights";
-        }
-      }
-      boost::filesystem::path weightsFilePath(weightsFilename.str());
-      if ( ! boost::filesystem::exists(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());
-      OutputFeatureWeightsForHypergraph(*weightsOut);
-      weightsOut->flush();
-      weightsOut->close();
-      delete weightsOut;
-    }
-
-
-    // initialize output streams
-    // note: we can't just write to STDOUT or files
-    // because multithreading may return sentences in shuffled order
-    auto_ptr<OutputCollector> outputCollector; // for translations
-    auto_ptr<OutputCollector> nbestCollector;  // for n-best lists
-    auto_ptr<OutputCollector> latticeSamplesCollector; //for lattice samples
-    auto_ptr<ofstream> nbestOut;
-    auto_ptr<ofstream> latticeSamplesOut;
-    size_t nbestSize = staticData.GetNBestSize();
-    string nbestFile = staticData.GetNBestFilePath();
-    bool output1best = true;
-    if (nbestSize) {
-      if (nbestFile == "-" || nbestFile == "/dev/stdout") {
-        // nbest to stdout, no 1-best
-        nbestCollector.reset(new OutputCollector());
-        output1best = false;
-      } else {
-        // nbest to file, 1-best to stdout
-        nbestOut.reset(new ofstream(nbestFile.c_str()));
-        if (!nbestOut->good()) {
-          TRACE_ERR("ERROR: Failed to open " << nbestFile << " for nbest lists" << endl);
-          exit(1);
-        }
-        nbestCollector.reset(new OutputCollector(nbestOut.get()));
-      }
-    }
-    size_t latticeSamplesSize = staticData.GetLatticeSamplesSize();
-    string latticeSamplesFile = staticData.GetLatticeSamplesFilePath();
-    if (latticeSamplesSize) {
-      if (latticeSamplesFile == "-" || latticeSamplesFile == "/dev/stdout") {
-        latticeSamplesCollector.reset(new OutputCollector());
-        output1best = false;
-      } else {
-        latticeSamplesOut.reset(new ofstream(latticeSamplesFile.c_str()));
-        if (!latticeSamplesOut->good()) {
-          TRACE_ERR("ERROR: Failed to open " << latticeSamplesFile << " for lattice samples" << endl);
-          exit(1);
-        }
-        latticeSamplesCollector.reset(new OutputCollector(latticeSamplesOut.get()));
-      }
-    }
-    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()) {
-      alignmentInfoCollector.reset(new OutputCollector(ioWrapper->GetAlignmentOutputStream()));
-    }
+    boost::shared_ptr<HypergraphOutput<Manager> > hypergraphOutput; 
+    boost::shared_ptr<HypergraphOutput<ChartManager> > hypergraphOutputChart;
 
-    //initialise stream for unknown (oov) words
-    auto_ptr<OutputCollector> unknownsCollector;
-    auto_ptr<ofstream> unknownsStream;
-    if (!staticData.GetOutputUnknownsFile().empty()) {
-      unknownsStream.reset(new ofstream(staticData.GetOutputUnknownsFile().c_str()));
-      if (!unknownsStream->good()) {
-        TRACE_ERR("Unable to open " << staticData.GetOutputUnknownsFile() << " for unknowns");
-        exit(1);
-      }
-      unknownsCollector.reset(new OutputCollector(unknownsStream.get()));
+    if (staticData.GetOutputSearchGraphHypergraph()) {
+    	if (staticData.IsChart()) {
+    		hypergraphOutputChart.reset(new HypergraphOutput<ChartManager>(PRECISION));
+    	}
+    	else {
+    		hypergraphOutput.reset(new HypergraphOutput<Manager>(PRECISION));
+    	}
     }
 
 #ifdef WITH_THREADS
@@ -784,45 +203,54 @@ int main(int argc, char** argv)
     // main loop over set of input sentences
     InputType* source = NULL;
     size_t lineCount = staticData.GetStartTranslationId();
-    while(ReadInput(*ioWrapper,staticData.GetInputType(),source)) {
+    while(ioWrapper->ReadInput(staticData.GetInputType(),source)) {
+      source->SetTranslationId(lineCount);
       IFVERBOSE(1) {
         ResetUserTime();
       }
+
+      FeatureFunction::CallChangeSource(source);
+
       // set up task of translating one sentence
-      TranslationTask* task =
-        new TranslationTask(lineCount,source, outputCollector.get(),
-                            nbestCollector.get(),
-                            latticeSamplesCollector.get(),
-                            wordGraphCollector.get(),
-                            searchGraphCollector.get(),
-                            detailedTranslationCollector.get(),
-                            alignmentInfoCollector.get(),
-                            unknownsCollector.get(),
-                            staticData.GetOutputSearchGraphSLF(),
-                            staticData.GetOutputSearchGraphHypergraph());
+      TranslationTask* task;
+      if (staticData.IsChart()) {
+    	  // scfg
+          task = new TranslationTask(source, *ioWrapper, hypergraphOutputChart);
+      }
+      else {
+	// pb
+	task = new TranslationTask(source, *ioWrapper,
+				   staticData.GetOutputSearchGraphSLF(),
+				   hypergraphOutput);
+      }
+      
       // execute task
 #ifdef WITH_THREADS
+#ifdef PT_UG
       if (my_acnt)
-	{
-	  task->Run();
-	  delete task;
-	  string src,trg,aln;
-	  UTIL_THROW_IF2(!getline(spe_src,src), "[" << HERE << "] "
-			 << "missing update data for simulated post-editing.");
-	  UTIL_THROW_IF2(!getline(spe_trg,trg), "[" << HERE << "] "
-			 << "missing update data for simulated post-editing.");
-	  UTIL_THROW_IF2(!getline(spe_aln,aln), "[" << HERE << "] "
-			 << "missing update data for simulated post-editing.");
-	  BOOST_FOREACH (PhraseDictionary* pd, PhraseDictionary::GetColl())
-	    {
-	      Mmsapt* sapt = dynamic_cast<Mmsapt*>(pd);
-	      if (sapt) sapt->add(src,trg,aln);
-	      VERBOSE(1,"[" << HERE << " added src] " << src << endl);
-	      VERBOSE(1,"[" << HERE << " added trg] " << trg << endl);
-	      VERBOSE(1,"[" << HERE << " added aln] " << aln << endl);
-	    }
-	}
-      else pool.Submit(task);
+      {
+	// simulated post-editing: always run single-threaded!
+        task->Run();
+        delete task;
+        string src,trg,aln;
+        UTIL_THROW_IF2(!getline(spe_src,src), "[" << HERE << "] "
+                       << "missing update data for simulated post-editing.");
+	UTIL_THROW_IF2(!getline(spe_trg,trg), "[" << HERE << "] "
+		       << "missing update data for simulated post-editing.");
+	UTIL_THROW_IF2(!getline(spe_aln,aln), "[" << HERE << "] "
+		       << "missing update data for simulated post-editing.");
+	BOOST_FOREACH (PhraseDictionary* pd, PhraseDictionary::GetColl())
+	  {
+	    Mmsapt* sapt = dynamic_cast<Mmsapt*>(pd);
+	    if (sapt) sapt->add(src,trg,aln);
+	    VERBOSE(1,"[" << HERE << " added src] " << src << endl);
+	    VERBOSE(1,"[" << HERE << " added trg] " << trg << endl);
+	    VERBOSE(1,"[" << HERE << " added aln] " << aln << endl);
+	  }
+      }
+      else
+#endif
+	pool.Submit(task);
 #else
       task->Run();
       delete task;