#include "BilingualDynSuffixArray.h"
#include "moses/TranslationModel/DynSAInclude/utils.h"
#include "moses/FactorCollection.h"
#include "moses/StaticData.h"
#include "moses/TargetPhrase.h"
#include <iomanip>

using namespace std;

namespace Moses
{

BilingualDynSuffixArray::BilingualDynSuffixArray():
  m_maxPhraseLength(StaticData::Instance().GetMaxPhraseLength()),
  m_maxSampleSize(20)
{
  m_srcSA = 0;
  m_trgSA = 0;
  m_srcCorpus = new std::vector<wordID_t>();
  m_trgCorpus = new std::vector<wordID_t>();
  m_srcVocab = new Vocab(false);
  m_trgVocab = new Vocab(false);
  m_scoreCmp = 0;
}

BilingualDynSuffixArray::~BilingualDynSuffixArray()
{
  if(m_srcSA) delete m_srcSA;
  if(m_trgSA) delete m_trgSA;
  if(m_srcVocab) delete m_srcVocab;
  if(m_trgVocab) delete m_trgVocab;
  if(m_srcCorpus) delete m_srcCorpus;
  if(m_trgCorpus) delete m_trgCorpus;
  if(m_scoreCmp) delete m_scoreCmp;
}

bool BilingualDynSuffixArray::Load(
  const std::vector<FactorType>& inputFactors,
  const std::vector<FactorType>& outputFactors,
  std::string source, std::string target, std::string alignments,
  const std::vector<float> &weight)
{
  m_inputFactors = inputFactors;
  m_outputFactors = outputFactors;

  m_scoreCmp = new ScoresComp(weight);
  InputFileStream sourceStrme(source);
  InputFileStream targetStrme(target);
  cerr << "Loading source corpus...\n";
  LoadCorpus(Input, sourceStrme, m_inputFactors, *m_srcCorpus, m_srcSntBreaks, m_srcVocab);
  cerr << "Loading target corpus...\n";
  LoadCorpus(Output, targetStrme, m_outputFactors,*m_trgCorpus, m_trgSntBreaks, m_trgVocab);
  CHECK(m_srcSntBreaks.size() == m_trgSntBreaks.size());

  // build suffix arrays and auxilliary arrays
  cerr << "Building Source Suffix Array...\n";
  m_srcSA = new DynSuffixArray(m_srcCorpus);
  if(!m_srcSA) return false;
  cerr << "Building Target Suffix Array...\n";
  //m_trgSA = new DynSuffixArray(m_trgCorpus);
  //if(!m_trgSA) return false;
  cerr << "\t(Skipped. Not used)\n";

  InputFileStream alignStrme(alignments);
  cerr << "Loading Alignment File...\n";
  LoadRawAlignments(alignStrme);
  //LoadAlignments(alignStrme);
  cerr << "Building frequent word cache...\n";
  CacheFreqWords();
  return true;
}

bool BilingualDynSuffixArray::LoadTM(
  const std::vector<FactorType>& inputFactors,
  const std::vector<FactorType>& outputFactors,
  std::string source, std::string target, std::string alignments,
  const std::vector<float> &weight)
{
  m_inputFactors = inputFactors;
  m_outputFactors = outputFactors;

  m_scoreCmp = new ScoresComp(weight);
  InputFileStream sourceStrme(source);
  InputFileStream targetStrme(target);

  cerr << "Loading target corpus...\n";
  LoadCorpus(Output, targetStrme, m_outputFactors,*m_trgCorpus, m_trgSntBreaks, m_trgVocab);

  cerr << "Loading source corpus...\n";
  LoadCorpus(Input, sourceStrme, m_inputFactors, *m_srcCorpus, m_srcSntBreaks, m_srcVocab);

  CHECK(m_srcSntBreaks.size() == m_trgSntBreaks.size());

  // build suffix arrays and auxilliary arrays
  cerr << "Building Source Suffix Array...\n";
  m_srcSA = new DynSuffixArray(m_srcCorpus);
  if(!m_srcSA) return false;
  cerr << "Building Target Suffix Array...\n";
  //m_trgSA = new DynSuffixArray(m_trgCorpus);
  //if(!m_trgSA) return false;
  cerr << "\t(Skipped. Not used)\n";

  InputFileStream alignStrme(alignments);
  cerr << "Loading Alignment File...\n";
  LoadRawAlignments(alignStrme);
  //LoadAlignments(alignStrme);
  cerr << "Building frequent word cache...\n";
  CacheFreqWords();
  return true;

}

int BilingualDynSuffixArray::LoadRawAlignments(InputFileStream& align)
{
  // stores the alignments in the raw file format
  std::string line;
  std::vector<int> vtmp;
  int lineNum = 1;
  while(getline(align, line)) {
    if (lineNum % 10000 == 0)
      cerr << lineNum;
    Utils::splitToInt(line, vtmp, "- ");
    CHECK(vtmp.size() % 2 == 0);
    std::vector<short> vAlgn;	// store as short ints for memory
    for (std::vector<int>::const_iterator itr = vtmp.begin();
         itr != vtmp.end(); ++itr) {
      vAlgn.push_back(short(*itr));
    }
    m_rawAlignments.push_back(vAlgn);
    ++lineNum;
  }
  return m_rawAlignments.size();
}
int BilingualDynSuffixArray::LoadRawAlignments(string& align)
{
  // stores the alignments in the raw file format
  vector<int> vtmp;
  Utils::splitToInt(align, vtmp, "- ");
  CHECK(vtmp.size() % 2 == 0);
  vector<short> vAlgn;  // store as short ints for memory
  for (std::vector<int>::const_iterator itr = vtmp.begin();
       itr != vtmp.end(); ++itr) {
    vAlgn.push_back(short(*itr));
  }
  m_rawAlignments.push_back(vAlgn);
  return m_rawAlignments.size();
}

int BilingualDynSuffixArray::LoadAlignments(InputFileStream& align)
{
  std::string line;
  std::vector<int> vtmp;
  int sntIndex(0);

  while(getline(align, line)) {
    Utils::splitToInt(line, vtmp, "- ");
    CHECK(vtmp.size() % 2 == 0);

    int sourceSize = GetSourceSentenceSize(sntIndex);
    int targetSize = GetTargetSentenceSize(sntIndex);

    SentenceAlignment curSnt(sntIndex, sourceSize, targetSize); // initialize empty sentence
    for(int i=0; i < (int)vtmp.size(); i+=2) {
      int sourcePos = vtmp[i];
      int targetPos = vtmp[i+1];
      CHECK(sourcePos < sourceSize);
      CHECK(targetPos < targetSize);

      curSnt.alignedList[sourcePos].push_back(targetPos);	// list of target nodes for each source word
      curSnt.numberAligned[targetPos]++; // cnt of how many source words connect to this target word
    }
    curSnt.srcSnt = m_srcCorpus + sntIndex;	// point source and target sentence
    curSnt.trgSnt = m_trgCorpus + sntIndex;
    m_alignments.push_back(curSnt);

    sntIndex++;
  }
  return m_alignments.size();
}

SentenceAlignment BilingualDynSuffixArray::GetSentenceAlignment(const int sntIndex, bool trg2Src) const
{
  // retrieves the alignments in the format used by SentenceAlignment.Extract()
  int sntGiven = trg2Src ? GetTargetSentenceSize(sntIndex) : GetSourceSentenceSize(sntIndex);
  int sntExtract = trg2Src ? GetSourceSentenceSize(sntIndex) : GetTargetSentenceSize(sntIndex);
  std::vector<short> alignment = m_rawAlignments.at(sntIndex);
  SentenceAlignment curSnt(sntIndex, sntGiven, sntExtract); // initialize empty sentence
  for(size_t i=0; i < alignment.size(); i+=2) {
    int sourcePos = alignment[i];
    int targetPos = alignment[i+1];
    if(trg2Src) {
      curSnt.alignedList[targetPos].push_back(sourcePos);	// list of target nodes for each source word
      curSnt.numberAligned[sourcePos]++; // cnt of how many source words connect to this target word
    } else {
      curSnt.alignedList[sourcePos].push_back(targetPos);	// list of target nodes for each source word
      curSnt.numberAligned[targetPos]++; // cnt of how many source words connect to this target word
    }
  }
  curSnt.srcSnt = m_srcCorpus + sntIndex;	// point source and target sentence
  curSnt.trgSnt = m_trgCorpus + sntIndex;

  return curSnt;
}

bool BilingualDynSuffixArray::ExtractPhrases(const int& sntIndex, const int& wordIndex,
    const int& sourceSize, std::vector<PhrasePair*>& phrasePairs, bool trg2Src) const
{
  /* ExtractPhrases() can extract the matching phrases for both directions by using the trg2Src
   * parameter */
  SentenceAlignment curSnt = GetSentenceAlignment(sntIndex, trg2Src);
  // get span of phrase in source sentence
  int beginSentence = m_srcSntBreaks[sntIndex];
  int rightIdx = wordIndex - beginSentence
                 ,leftIdx = rightIdx - sourceSize + 1;
  return curSnt.Extract(m_maxPhraseLength, phrasePairs, leftIdx, rightIdx); // extract all phrase Alignments in sentence
}

int BilingualDynSuffixArray::LoadCorpus(FactorDirection direction, InputFileStream& corpus, const FactorList& factors,
                                        std::vector<wordID_t>& cArray, std::vector<wordID_t>& sntArray,
                                        Vocab* vocab)
{
  std::string line, word;
  int sntIdx(0);
//	corpus.seekg(0); Seems needless -> commented out to allow loading of gzipped corpora (gzfilebuf doesn't support seeking).
  const std::string& factorDelimiter = StaticData::Instance().GetFactorDelimiter();
  while(getline(corpus, line)) {
    sntArray.push_back(sntIdx);
    Phrase phrase(ARRAY_SIZE_INCR);
    // parse phrase
    phrase.CreateFromString(direction, factors, line, factorDelimiter, NULL);
    // store words in vocabulary and corpus
    for( size_t i = 0; i < phrase.GetSize(); ++i) {
      cArray.push_back( vocab->GetWordID(phrase.GetWord(i)) );
    }
    sntIdx += phrase.GetSize();
  }
  //cArray.push_back(vocab->GetkOOVWordID);	// signify end of corpus
  vocab->MakeClosed(); // avoid adding words
  return cArray.size();
}

bool BilingualDynSuffixArray::GetLocalVocabIDs(const Phrase& src, SAPhrase &output) const
{
  // looks up the SA vocab ids for the current src phrase
  size_t phraseSize = src.GetSize();
  for (size_t pos = 0; pos < phraseSize; ++pos) {
    const Word &word = src.GetWord(pos);
    wordID_t arrayId = m_srcVocab->GetWordID(word);
    if (arrayId == m_srcVocab->GetkOOVWordID()) {
      // oov
      return false;
    } else {
      output.SetId(pos, arrayId);
      //cerr << arrayId << " ";
    }
  }
  return true;
}

pair<float, float> BilingualDynSuffixArray::GetLexicalWeight(const PhrasePair& phrasepair) const
{
  //return pair<float, float>(1, 1);
  float srcLexWeight(1.0), trgLexWeight(1.0);
  std::map<pair<wordID_t, wordID_t>, float> targetProbs; // collect sum of target probs given source words
  //const SentenceAlignment& alignment = m_alignments[phrasepair.m_sntIndex];
  const SentenceAlignment& alignment = GetSentenceAlignment(phrasepair.m_sntIndex);
  std::map<pair<wordID_t, wordID_t>, pair<float, float> >::const_iterator itrCache;
  // for each source word
  for(int srcIdx = phrasepair.m_startSource; srcIdx <= phrasepair.m_endSource; ++srcIdx) {
    float srcSumPairProbs(0);
    wordID_t srcWord = m_srcCorpus->at(srcIdx + m_srcSntBreaks[phrasepair.m_sntIndex]);	// localIDs
    const std::vector<int>& srcWordAlignments = alignment.alignedList.at(srcIdx);
    // for each target word aligned to this source word in this alignment
    if(srcWordAlignments.size() == 0) { // get p(NULL|src)
      pair<wordID_t, wordID_t> wordpair = make_pair(srcWord, m_srcVocab->GetkOOVWordID());
      itrCache = m_wordPairCache.find(wordpair);
      if(itrCache == m_wordPairCache.end()) { // if not in cache
        CacheWordProbs(srcWord);
        itrCache = m_wordPairCache.find(wordpair); // search cache again
      }
      CHECK(itrCache != m_wordPairCache.end());
      srcSumPairProbs += itrCache->second.first;
      targetProbs[wordpair] = itrCache->second.second;
    } else { // extract p(trg|src)
      for(size_t i = 0; i < srcWordAlignments.size(); ++i) { // for each aligned word
        int trgIdx = srcWordAlignments[i];
        wordID_t trgWord = m_trgCorpus->at(trgIdx + m_trgSntBreaks[phrasepair.m_sntIndex]);
        // get probability of this source->target word pair
        pair<wordID_t, wordID_t> wordpair = make_pair(srcWord, trgWord);
        itrCache = m_wordPairCache.find(wordpair);
        if(itrCache == m_wordPairCache.end()) { // if not in cache
          CacheWordProbs(srcWord);
          itrCache = m_wordPairCache.find(wordpair); // search cache again
        }
        CHECK(itrCache != m_wordPairCache.end());
        srcSumPairProbs += itrCache->second.first;
        targetProbs[wordpair] = itrCache->second.second;
      }
    }
    float srcNormalizer = srcWordAlignments.size() < 2 ? 1.0 : 1.0 / float(srcWordAlignments.size());
    srcLexWeight *= (srcNormalizer * srcSumPairProbs);
  }	// end for each source word
  for(int trgIdx = phrasepair.m_startTarget; trgIdx <= phrasepair.m_endTarget; ++trgIdx) {
    float trgSumPairProbs(0);
    wordID_t trgWord = m_trgCorpus->at(trgIdx + m_trgSntBreaks[phrasepair.m_sntIndex]);
    for (std::map<pair<wordID_t, wordID_t>, float>::const_iterator trgItr
         = targetProbs.begin(); trgItr != targetProbs.end(); ++trgItr) {
      if(trgItr->first.second == trgWord)
        trgSumPairProbs += trgItr->second;
    }
    if(trgSumPairProbs == 0) continue;	// currently don't store target-side SA
    int noAligned = alignment.numberAligned.at(trgIdx);
    float trgNormalizer = noAligned < 2 ? 1.0 : 1.0 / float(noAligned);
    trgLexWeight *= (trgNormalizer * trgSumPairProbs);
  }
  // TODO::Need to get p(NULL|trg)
  return pair<float, float>(srcLexWeight, trgLexWeight);
}
void BilingualDynSuffixArray::CacheFreqWords() const
{
  std::multimap<int, wordID_t> wordCnts;
  // for each source word in vocab
  Vocab::Word2Id::const_iterator it;
  for(it = m_srcVocab->VocabStart(); it != m_srcVocab->VocabEnd(); ++it) {
    // get its frequency
    wordID_t srcWord = it->second;
    std::vector<wordID_t> sword(1, srcWord), wrdIndices;
    m_srcSA->GetCorpusIndex(&sword, &wrdIndices);
    if(wrdIndices.size() >= 1000) { // min count
      wordCnts.insert(make_pair(wrdIndices.size(), srcWord));
    }
  }
  int numSoFar(0);
  std::multimap<int, wordID_t>::reverse_iterator ritr;
  for(ritr = wordCnts.rbegin(); ritr != wordCnts.rend(); ++ritr) {
    m_freqWordsCached.insert(ritr->second);
    CacheWordProbs(ritr->second);
    if(++numSoFar == 50) break; // get top counts
  }
  cerr << "\tCached " << m_freqWordsCached.size() << " source words\n";
}
void BilingualDynSuffixArray::CacheWordProbs(wordID_t srcWord) const
{
  std::map<wordID_t, int> counts;
  std::vector<wordID_t> sword(1, srcWord), wrdIndices;
  bool ret = m_srcSA->GetCorpusIndex(&sword, &wrdIndices);
  CHECK(ret);
  std::vector<int> sntIndexes = GetSntIndexes(wrdIndices, 1, m_srcSntBreaks);
  float denom(0);
  // for each occurrence of this word
  for(size_t snt = 0; snt < sntIndexes.size(); ++snt) {
    int sntIdx = sntIndexes.at(snt); // get corpus index for sentence
    CHECK(sntIdx != -1);
    int srcWrdSntIdx = wrdIndices.at(snt) - m_srcSntBreaks.at(sntIdx); // get word index in sentence
    const std::vector<int> srcAlg = GetSentenceAlignment(sntIdx).alignedList.at(srcWrdSntIdx); // list of target words for this source word
    if(srcAlg.size() == 0) {
      ++counts[m_srcVocab->GetkOOVWordID()]; // if not alligned then align to NULL word
      ++denom;
    } else { //get target words aligned to srcword in this sentence
      for(size_t i=0; i < srcAlg.size(); ++i) {
        wordID_t trgWord = m_trgCorpus->at(srcAlg[i] + m_trgSntBreaks[sntIdx]);
        ++counts[trgWord];
        ++denom;
      }
    }
  }
  // now we've gotten counts of all target words aligned to this source word
  // get probs and cache all pairs
  for(std::map<wordID_t, int>::const_iterator itrCnt = counts.begin();
      itrCnt != counts.end(); ++itrCnt) {
    pair<wordID_t, wordID_t> wordPair = make_pair(srcWord, itrCnt->first);
    float srcTrgPrb = float(itrCnt->second) / float(denom);	// gives p(src->trg)
    float trgSrcPrb = float(itrCnt->second) / float(counts.size()); // gives p(trg->src)
    m_wordPairCache[wordPair] = pair<float, float>(srcTrgPrb, trgSrcPrb);
  }
}

SAPhrase BilingualDynSuffixArray::TrgPhraseFromSntIdx(const PhrasePair& phrasepair) const
{
  // takes sentence indexes and looks up vocab IDs
  SAPhrase phraseIds(phrasepair.GetTargetSize());
  int sntIndex = phrasepair.m_sntIndex;
  int id(-1), pos(0);
  for(int i=phrasepair.m_startTarget; i <= phrasepair.m_endTarget; ++i) { // look up trg words
    id = m_trgCorpus->at(m_trgSntBreaks[sntIndex] + i);
    phraseIds.SetId(pos++, id);
  }
  return phraseIds;
}

TargetPhrase* BilingualDynSuffixArray::GetMosesFactorIDs(const SAPhrase& phrase, const Phrase& sourcePhrase) const
{
  TargetPhrase* targetPhrase = new TargetPhrase();
  for(size_t i=0; i < phrase.words.size(); ++i) { // look up trg words
    Word& word = m_trgVocab->GetWord( phrase.words[i]);
    CHECK(word != m_trgVocab->GetkOOVWord());
    targetPhrase->AddWord(word);
  }
  targetPhrase->SetSourcePhrase(sourcePhrase);
  // scoring
  return targetPhrase;
}

void BilingualDynSuffixArray::GetTargetPhrasesByLexicalWeight(const Phrase& src, std::vector< std::pair<Scores, TargetPhrase*> > & target) const
{
  //cerr << "phrase is \"" << src << endl;
  size_t sourceSize = src.GetSize();
  SAPhrase localIDs(sourceSize);
  if(!GetLocalVocabIDs(src, localIDs)) return;
  float totalTrgPhrases(0);
  std::map<SAPhrase, int> phraseCounts;
  //std::map<SAPhrase, PhrasePair> phraseColl; // (one of) the word indexes this phrase was taken from
  std::map<SAPhrase, pair<float, float> > lexicalWeights;
  std::map<SAPhrase, pair<float, float> >::iterator itrLexW;
  std::vector<unsigned> wrdIndices;
  // extract sentence IDs from SA and return rightmost index of phrases
  if(!m_srcSA->GetCorpusIndex(&(localIDs.words), &wrdIndices)) return;
  SampleSelection(wrdIndices);
  std::vector<int> sntIndexes = GetSntIndexes(wrdIndices, sourceSize, m_srcSntBreaks);
  // for each sentence with this phrase
  for(size_t snt = 0; snt < sntIndexes.size(); ++snt) {
    std::vector<PhrasePair*> phrasePairs; // to store all phrases possible from current sentence
    int sntIndex = sntIndexes.at(snt); // get corpus index for sentence
    if(sntIndex == -1) continue;	// bad flag set by GetSntIndexes()
    ExtractPhrases(sntIndex, wrdIndices[snt], sourceSize, phrasePairs);
    //cerr << "extracted " << phrasePairs.size() << endl;
    totalTrgPhrases += phrasePairs.size(); // keep track of count of each extracted phrase pair
    std::vector<PhrasePair*>::iterator iterPhrasePair;
    for (iterPhrasePair = phrasePairs.begin(); iterPhrasePair != phrasePairs.end(); ++iterPhrasePair) {
      SAPhrase phrase = TrgPhraseFromSntIdx(**iterPhrasePair);
      phraseCounts[phrase]++;	// count each unique phrase
      // NOTE::Correct but slow to extract lexical weight here. could do
      // it later for only the top phrases chosen by phrase prob p(e|f)
      pair<float, float> lexWeight = GetLexicalWeight(**iterPhrasePair);	// get lexical weighting for this phrase pair
      itrLexW = lexicalWeights.find(phrase); // check if phrase already has lexical weight attached
      if((itrLexW != lexicalWeights.end()) && (itrLexW->second.first < lexWeight.first))
        itrLexW->second = lexWeight;	// if this lex weight is greater save it
      else lexicalWeights[phrase] = lexWeight; // else save
    }
    // done with sentence. delete SA phrase pairs
    RemoveAllInColl(phrasePairs);
  } // done with all sentences
  // convert to moses phrase pairs
  std::map<SAPhrase, int>::const_iterator iterPhrases;
  std::multimap<Scores, const SAPhrase*, ScoresComp> phraseScores (*m_scoreCmp);
  // get scores of all phrases
  for(iterPhrases = phraseCounts.begin(); iterPhrases != phraseCounts.end(); ++iterPhrases) {
    float trg2SrcMLE = float(iterPhrases->second) / totalTrgPhrases;
    itrLexW = lexicalWeights.find(iterPhrases->first);
    CHECK(itrLexW != lexicalWeights.end());
    Scores scoreVector(3);
    scoreVector[0] = std::log(trg2SrcMLE);
    scoreVector[1] = std::log(itrLexW->second.first);
    scoreVector[2] = 1; // exp(1);
    phraseScores.insert(make_pair(scoreVector, &iterPhrases->first));
  }
  // return top scoring phrases
  std::multimap<Scores, const SAPhrase*, ScoresComp>::reverse_iterator ritr;
  for(ritr = phraseScores.rbegin(); ritr != phraseScores.rend(); ++ritr) {
    Scores scoreVector = ritr->first;
    TargetPhrase *targetPhrase = GetMosesFactorIDs(*ritr->second, src);
    target.push_back(make_pair( scoreVector, targetPhrase));
    if(target.size() == m_maxSampleSize) break;
  }
}

std::vector<int> BilingualDynSuffixArray::GetSntIndexes(std::vector<unsigned>& wrdIndices,
    const int sourceSize, const std::vector<unsigned>& sntBreaks) const
{
  std::vector<unsigned>::const_iterator vit;
  std::vector<int> sntIndexes;
  for(size_t i=0; i < wrdIndices.size(); ++i) {
    vit = std::upper_bound(sntBreaks.begin(), sntBreaks.end(), wrdIndices[i]);
    int index = int(vit - sntBreaks.begin()) - 1;
    // check for phrases that cross sentence boundaries
    if(wrdIndices[i] - sourceSize + 1 < sntBreaks.at(index))
      sntIndexes.push_back(-1);	// set bad flag
    else
      sntIndexes.push_back(index);	// store the index of the sentence in the corpus
  }
  return sntIndexes;
}

int BilingualDynSuffixArray::SampleSelection(std::vector<unsigned>& sample,
    int sampleSize) const
{
  // only use top 'sampleSize' number of samples
  if(sample.size() > (size_t)sampleSize)
    sample.erase(sample.begin()+sampleSize, sample.end());
  return sample.size();
}

void BilingualDynSuffixArray::addSntPair(string& source, string& target, string& alignment)
{
  vuint_t srcFactor, trgFactor;
  cerr << "source, target, alignment = " << source << ", " << target << ", " << alignment << endl;
  const std::string& factorDelimiter = StaticData::Instance().GetFactorDelimiter();
  const unsigned oldSrcCrpSize = m_srcCorpus->size(), oldTrgCrpSize = m_trgCorpus->size();
  cerr << "old source corpus size = " << oldSrcCrpSize << "\told target size = " << oldTrgCrpSize << endl;
  Phrase sphrase(ARRAY_SIZE_INCR);
  sphrase.CreateFromString(Input, m_inputFactors, source, factorDelimiter, NULL);
  m_srcVocab->MakeOpen();
  std::vector<wordID_t> sIDs(sphrase.GetSize());
  // store words in vocabulary and corpus
  for(int i = sphrase.GetSize()-1; i >= 0; --i) {
    sIDs[i] = m_srcVocab->GetWordID(sphrase.GetWord(i));  // get vocab id backwards
  }
  for(size_t i = 0; i < sphrase.GetSize(); ++i) {
    srcFactor.push_back(sIDs[i]);
    cerr << "srcFactor[" << (srcFactor.size() - 1) << "] = " << srcFactor.back() << endl;
    m_srcCorpus->push_back(srcFactor.back()); // add word to corpus
  }
  m_srcSntBreaks.push_back(oldSrcCrpSize); // former end of corpus is index of new sentence
  m_srcVocab->MakeClosed();
  Phrase tphrase(ARRAY_SIZE_INCR);
  tphrase.CreateFromString(Output, m_outputFactors, target, factorDelimiter, NULL);
  m_trgVocab->MakeOpen();
  std::vector<wordID_t> tIDs(tphrase.GetSize());
  for(int i = tphrase.GetSize()-1; i >= 0; --i) {
    tIDs[i] = m_trgVocab->GetWordID(tphrase.GetWord(i));  // get vocab id
  }
  for(size_t i = 0; i < tphrase.GetSize(); ++i) {
    trgFactor.push_back(tIDs[i]);
    cerr << "trgFactor[" << (trgFactor.size() - 1) << "] = " << trgFactor.back() << endl;
    m_trgCorpus->push_back(trgFactor.back());
  }
  cerr << "gets to 1\n";
  m_trgSntBreaks.push_back(oldTrgCrpSize);
  cerr << "gets to 2\n";
  m_srcSA->Insert(&srcFactor, oldSrcCrpSize);
  cerr << "gets to 3\n";
  //m_trgSA->Insert(&trgFactor, oldTrgCrpSize);
  LoadRawAlignments(alignment);
  m_trgVocab->MakeClosed();
  //for(size_t i=0; i < sphrase.GetSize(); ++i)
  //ClearWordInCache(sIDs[i]);

}
void BilingualDynSuffixArray::ClearWordInCache(wordID_t srcWord)
{
  if(m_freqWordsCached.find(srcWord) != m_freqWordsCached.end())
    return;
  std::map<std::pair<wordID_t, wordID_t>, std::pair<float, float> >::iterator it,
      first, last;
  for(it = m_wordPairCache.begin(); it != m_wordPairCache.end(); ++it) {
    if(it->first.first == srcWord) {  // all source words grouped
      first = it; // copy first entry of srcWord
      last = it++;
      while(it != m_wordPairCache.end() && (it->first.first == srcWord)) {
        last = it++;
      }
    }
    m_wordPairCache.erase(first, last);
  }
}
SentenceAlignment::SentenceAlignment(int sntIndex, int sourceSize, int targetSize)
  :m_sntIndex(sntIndex)
  ,numberAligned(targetSize, 0)
  ,alignedList(sourceSize)
{
  for(int i=0; i < sourceSize; ++i) {
    std::vector<int> trgWrd;
    alignedList[i] = trgWrd;
  }
}

bool SentenceAlignment::Extract(int maxPhraseLength, std::vector<PhrasePair*> &ret, int startSource, int endSource) const
{
  // foreign = target, F=T
  // english = source, E=S
  int countTarget = numberAligned.size();

  int minTarget = 9999;
  int maxTarget = -1;
  std::vector< int > usedTarget = numberAligned;
  for(int sourcePos = startSource; sourcePos <= endSource; sourcePos++) {
    for(int ind=0; ind < (int)alignedList[sourcePos].size(); ind++) {
      int targetPos = alignedList[sourcePos][ind];
      // cout << "point (" << targetPos << ", " << sourcePos << ")\n";
      if (targetPos<minTarget) {
        minTarget = targetPos;
      }
      if (targetPos>maxTarget) {
        maxTarget = targetPos;
      }
      usedTarget[ targetPos ]--;
    } // for(int ind=0;ind<sentence
  } // for(int sourcePos=startSource

  // cout << "f projected ( " << minTarget << "-" << maxTarget << ", " << startSource << "," << endSource << ")\n";

  if (maxTarget >= 0 && // aligned to any foreign words at all
      maxTarget-minTarget < maxPhraseLength) {
    // foreign phrase within limits

    // check if foreign words are aligned to out of bound english words
    bool out_of_bounds = false;
    for(int targetPos=minTarget; targetPos <= maxTarget && !out_of_bounds; targetPos++) {
      if (usedTarget[targetPos]>0) {
        // cout << "ouf of bounds: " << targetPos << "\n";
        out_of_bounds = true;
      }
    }

    // cout << "doing if for ( " << minTarget << "-" << maxTarget << ", " << startSource << "," << endSource << ")\n";
    if (!out_of_bounds) {
      // start point of foreign phrase may retreat over unaligned
      for(int startTarget = minTarget;
          (startTarget >= 0 &&
           startTarget > maxTarget-maxPhraseLength && // within length limit
           (startTarget==minTarget || numberAligned[startTarget]==0)); // unaligned
          startTarget--) {
        // end point of foreign phrase may advance over unaligned
        for (int endTarget=maxTarget;
             (endTarget<countTarget &&
              endTarget<startTarget+maxPhraseLength && // within length limit
              (endTarget==maxTarget || numberAligned[endTarget]==0)); // unaligned
             endTarget++) {
          PhrasePair *phrasePair = new PhrasePair(startTarget,endTarget,startSource,endSource, m_sntIndex);
          ret.push_back(phrasePair);
        } // for (int endTarget=maxTarget;
      }	// for(int startTarget=minTarget;
    } // if (!out_of_bounds)
  } // if (maxTarget >= 0 &&
  return (ret.size() > 0);

}

}// end namepsace