#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);
		// 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] = trg2SrcMLE; 
		scoreVector[1] = itrLexW->second.first;
		scoreVector[2] = 2.718; // exp(1); 
		phraseScores.insert(make_pair(scoreVector, &iterPhrases->first));
	}
	// return top scoring phrases
	std::multimap<Scores, const SAPhrase*, ScoresComp>::reverse_iterator ritr;
	for(ritr = phraseScores.rbegin(); ritr != phraseScores.rend(); ++ritr) {
		Scores scoreVector = ritr->first;
		TargetPhrase *targetPhrase = GetMosesFactorIDs(*ritr->second, src);
		target.push_back(make_pair( scoreVector, targetPhrase));
		if(target.size() == m_maxSampleSize) break;
	}
}

std::vector<int> BilingualDynSuffixArray::GetSntIndexes(std::vector<unsigned>& wrdIndices, 
	const int sourceSize, const std::vector<unsigned>& sntBreaks) const 
{
	std::vector<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);
  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);
  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