168 	typedef typename Size<TFragmentStore>::Type TSize;  in _loadContigReads()  typedef
183 	TSize numRead = 0;  in _loadContigReads()
186 	TSize lenRead = 0;  in _loadContigReads()
187 	TSize offset = 0;  in _loadContigReads()
208 template<typename TSpec, typename TConfig, typename TMatrix, typename TSize2, typename TSize, typen…
213 				 TSize& coverage,  in convertAlignment()
237 	typedef String<TSize> TFirstFreePos;  in convertAlignment()
240 	TSize pos = 0;  in convertAlignment()
241 	TSize maxTmp = 0;  in convertAlignment()
242 	TSize numCol = 0;  in convertAlignment()
263 	TSize readPos = 0;  in convertAlignment()
273 		TSize lenRead = length(myRead);  in convertAlignment()
274 		TSize offset = alignIt->beginPos;  in convertAlignment()
286 		TSize mySeqPos = 0;  in convertAlignment()
293 		TSize clr2 = lenRead;  in convertAlignment()
294 		TSize stop = 0;  in convertAlignment()
323 template<typename TSpec, typename TConfig, typename TMatrix, typename TSize2, typename TSize> 
328 				 TSize& coverage)  in convertAlignment()
331 	String<TSize> slot;  in convertAlignment()
343 	typedef typename Size<TFragmentStore>::Type TSize;  in convertAlignment()  typedef
344 	TSize coverage;  in convertAlignment()
350 template<typename TSpec, typename TConfig, typename TGappedConsensus, typename TSize> 
354 				   TSize contigId)  in getGappedConsensus()
384 template<typename TSpec, typename TConfig, typename TGappedConsensus, typename TSize> 
388 					  TSize contigId)  in assignGappedConsensus()
431 template<typename TStringSet, typename TCargo, typename TSpec, typename TSize, typename TConfigOpti…
434 				   String<Pair<TSize, TSize> >& begEndPos,  in consensusAlignment()  argument
467 	typedef Graph<Alignment<TStringSet, TSize> > TGraph;  in consensusAlignment()
490 template<typename TStringSet, typename TCargo, typename TSpec, typename TSize>
493 				   String<Pair<TSize, TSize> >& begEndPos)   in consensusAlignment()  argument
510 	typedef typename Size<TGraph>::Type TSize;  in updateContig()  typedef
513 	typedef std::map<TSize, TSize> TComponentLength;  in updateContig()
518 	TSize nseq = length(strSet);  in updateContig()
521 	TSize maxCoverage = 0;  in updateContig()
522 	TSize len = 0;  in updateContig()
526 	String<TSize> readBegEndRowPos;  in updateContig()
530 	String<TSize> component;  in updateContig()
531 	String<TSize> order;  in updateContig()
534 		TSize numOfComponents = length(order);  in updateContig()
537 		typedef String<std::pair<TSize, TSize> > TComponentToRank;  in updateContig()
539 		for(TSize compIndex = 0; compIndex < numOfComponents; ++compIndex)   in updateContig()
543 		typedef Pair<TSize, TSize> TRankPair;  in updateContig()
551 			TSize seq = idToPosition(strSet, sequenceId(g, vert));  in updateContig()
553 … Standard()), end(compToRank, Standard()), ::std::make_pair((TSize) component[vert], (TSize) 0))->…  in updateContig()
555 … Standard()), end(compToRank, Standard()), ::std::make_pair((TSize) component[vert], (TSize) 0))->…  in updateContig()
560 		String<TSize> seqToRow;  in updateContig()
567 		typedef String<std::pair<TSize, TSize> > TSeqToBegin;  in updateContig()
570 		TSize finishedSeq = 0;  in updateContig()
574 			for(TSize pos = 0; itL != itLEnd; ++itL, ++pos)   in updateContig()
578 			TSize endPos = 0;  in updateContig()
583 					TSize currentSeq = (*itSB).second;  in updateContig()
597 		String<TSize> compOffset;  in updateContig()
599 		for(TSize compIndex = 0; compIndex < numOfComponents; ++compIndex) {  in updateContig()
611 			TSize c = property(component, it->second);  in updateContig()
612 			TSize row = seqToRow[idToPosition(strSet, it->first.first)];  in updateContig()
620 			TSize i = compOffset[c];  in updateContig()
621 			for(TSize pCol = i;sIt!=sItEnd;++sIt, ++pCol, ++i)   in updateContig()
625 		for(TSize compIndex = 0; compIndex < numOfComponents; ++compIndex) {  in updateContig()
626 			TSize offset = compOffset[order[compIndex]];  in updateContig()
627 			TSize currentCompLength = compLength[order[compIndex]];  in updateContig()
633 			for(TSize i=0;i<nseq; ++i) {  in updateContig()
639 			for(TSize i = 0; i < maxCoverage; ++i) {  in updateContig()
641 					for(TSize pCol = offset;pCol < offset + currentCompLength;++pCol)   in updateContig()
648 		for(TSize i=0;i<nseq; ++i) {  in updateContig()
650 …TSize readBegin = compOffset[getProperty(component, findVertex(const_cast<TGraph&>(g), positionToI…  in updateContig()
651 …TSize readEnd = compOffset[getProperty(component, lastVertex)] + fragmentLength(const_cast<TGraph&…  in updateContig()
692 	for(TSize i = 0;alignIt != alignItEnd; ++alignIt, ++i) {  in updateContig()
693 		TSize lenRead = length(fragStore.readSeqStore[alignIt->readId]);  in updateContig()
703 …for(TSize column = readBegEndRowPos[3*i]; column<readBegEndRowPos[3*i + 1]; ++column, ++gappedPos)…  in updateContig()
736 template <typename TValue, typename TSpec, typename TCounters, typename TSize, typename TAlphabet>
740 			   TSize alignDepth,  in _countLetters()
748 	TSize len = length(mat) / alignDepth;  in _countLetters()
751 	TSize alphabetSize = ValueSize<TAlphabet>::VALUE;  in _countLetters()
757 	for(TSize i=0;i<len; ++i) {  in _countLetters()
767 	TSize pos = 0;  in _countLetters()
793 	typedef typename Size<String<TValue, TSpec> >::Type TSize;  in consensusCalling()  typedef
794 	TSize alphabetSize = ValueSize<TAlphabet>::VALUE;  in consensusCalling()
799 	typedef String<TSize> TCounter;  in consensusCalling()
806 	TSize len = length(mat) / maxCoverage;  in consensusCalling()
817 		TSize max = 0;  in consensusCalling()
821 		TSize pos = 0;  in consensusCalling()
835 	TSize run = 1;  in consensusCalling()
851 			for(TSize i = 0; i<(alphabetSize + 1); ++i)   in consensusCalling()
858 		for(TSize i = 0; i<length(pI); ++i)   in consensusCalling()
870 		TSize pos = 0;  in consensusCalling()
875 				TSize fragJ = (c != gapChar) ? ordValue(TAlphabet(c)) : alphabetSize;  in consensusCalling()
876 				for(TSize consI = 0; consI<(alphabetSize + 1); ++consI)   in consensusCalling()
885 …for(TSize diag = 0; diag<(alphabetSize + 1); ++diag) sumIJ += nIJ[diag * (alphabetSize + 1) + diag…  in consensusCalling()
886 		for(TSize consI = 0; consI<(alphabetSize + 1); ++consI)   in consensusCalling()
887 			for(TSize fragJ = 0; fragJ<(alphabetSize + 1); ++fragJ)  in consensusCalling()
892 		TSize col = 0;  in consensusCalling()
896 			for(TSize consI = 0; consI<(alphabetSize + 1); ++consI) {  in consensusCalling()
899 				for(TSize allI = 0; allI<(alphabetSize + 1); ++allI) {  in consensusCalling()
901 					for(TSize row = 0; row < maxCoverage; ++row) {  in consensusCalling()
904 							TSize fragJ = (c != gapChar) ? ordValue(TAlphabet(c)) : alphabetSize;  in consensusCalling()
923 		TSize runOld = run;  in consensusCalling()
968 		TSize ind = 0;  in consensusCalling()
969 		for(TSize consI = 0; consI<(alphabetSize + 1); ++consI) {  in consensusCalling()
993 	typedef typename Size<TFragmentStore>::Type TSize;  in consensusCalling()  typedef
1001 	TSize maxCoverage;  in consensusCalling()
1022 	typedef typename Size<String<TValue, TSpec> >::Type TSize;  in consensusCalling()  typedef
1023 	TSize alphabetSize = ValueSize<TAlphabet>::VALUE;  in consensusCalling()
1027 	typedef String<TSize> TCounter;  in consensusCalling()
1037 	TSize max = 0;  in consensusCalling()
1039 	TSize pos = 0;  in consensusCalling()
1067 	typedef typename Size<TFragmentStore>::Type TSize;  in consensusCalling()  typedef
1075 	TSize maxCoverage;  in consensusCalling()
1116 	typedef typename Size<TFragmentStore>::Type TSize;  in write()  typedef
1125 	for(TSize idCount = 0;contigIt != contigItEnd; ++contigIt, ++idCount) {  in write()
1129 		TSize maxCoverage;  in write()
1130 		String<TSize> readSlot;  in write()
1132 		TSize len = length(mat) / maxCoverage;  in write()
1140 		String<TSize> coverage;  in write()
1144 		TSize winSize = 60;  in write()
1146 		TSize column = 0;  in write()
1148 			TSize window_end = column + winSize;  in write()
1157 			for(TSize local_col = 1; local_col<window_end - column + 1; ++local_col) {  in write()
1164 			for(TSize row = 0; row<maxCoverage; ++row) {  in write()
1165 				TSize tmp = row;  in write()
1175 				for(TSize local_col = column; local_col<window_end; ++local_col) {  in write()
1216 		String<std::pair<TSize, TSize> > idToPos;  in write()
1218 		for(TSize iCount = 0; alignItTmp!=alignItTmpEnd; ++iCount, ++alignItTmp)   in write()
1228 		for(TSize iCount = 0;alignIt != alignItEnd; ++alignIt, ++iCount) {  in write()
1246 			TSize begClr = 0;  in write()
1247 			TSize endClr = 0;  in write()
1256 			TSize letterCount = 0;  in write()
1257 			TSize gapCount = 0;  in write()
1295 	typedef typename Size<TFragmentStore>::Type TSize;  in _convertSimpleReadFile()  typedef
1415 			TSize readLen = length(seq);  in _convertSimpleReadFile()
1671 	typedef typename Size<TFragmentStore>::Type TSize;  in _writeCeleraFrg()  typedef
1693 	for(TSize idCount = 0;readIt != readItEnd; goNext(readIt), ++idCount) {  in _writeCeleraFrg()
1717 		for(TSize k = 0;seqIt!=seqItEnd;goNext(seqIt), ++k) {  in _writeCeleraFrg()
1724 		for(TSize k = 0;seqIt!=seqItEnd;goNext(seqIt), ++k) {  in _writeCeleraFrg()
1752 	typedef typename Size<TFragmentStore>::Type TSize;  in _writeCeleraCgb()  typedef
1777 	TSize offsetLeft = _min(alignIt->beginPos, alignIt->endPos);  in _writeCeleraCgb()