126     typedef typename Size<TFragmentString>::Type TSize;  in buildAlignmentGraph()  typedef
154         TSize pos1 = fragmentBegin(*it, id1);  in buildAlignmentGraph()
155         TSize pos2 = fragmentBegin(*it, id2);  in buildAlignmentGraph()
156         TSize fragLen = fragmentLength(*it, id1);  in buildAlignmentGraph()
157         TSize end1 = pos1 + fragLen;  in buildAlignmentGraph()
161             TSize vertexLen = fragmentLength(outGraph, p1);  in buildAlignmentGraph()
208 template<typename TString, typename TSpec, typename TScoreType, typename TSize, typename TSpec2, ty…
212               String<Fragment<TSize, ExactFragment<> >, TSpec2> const & matches,  in _scoreMatches()  argument
216     typedef String<Fragment<TSize, ExactFragment<> >, TSpec2> const TFragmentString;  in _scoreMatches()
228     TSize pos1 = 0; TSize pos2 = 0;    TSize fragLen = 0;  in _scoreMatches()
240         for(TSize i = 0; i<fragLen; ++i, ++itS1, ++itS2)  in _scoreMatches()
390 template<typename TGuideTree, typename TSeqGroups, typename TGroupRoot, typename TSize>
395                TSize minMembers)  in _subTreeSearch()
402     TSize nVertices = numVertices(guideTree);  in _subTreeSearch()
403     TSize nSeq = (nVertices / 2) + 1;  in _subTreeSearch()
407     String<TSize> numLeaves;  in _subTreeSearch()
417     TSize pos = length(vertices) - 1;  in _subTreeSearch()
442             TSize elem = length(seqGroups) - 1;  in _subTreeSearch()
463     typedef Pair<TSize, TSize> TDistGroup; // Distance, group index  in _subTreeSearch()
466     for(TSize i=0; i< (TSize) length(groupRoot); ++i) {  in _subTreeSearch()
468         TSize dist = 0;  in _subTreeSearch()
482     for(TSize i=0; i< (TSize) length(seqGroups); ++i) {  in _subTreeSearch()
492     TSize leftover = 0;  in _subTreeSearch()
526 template<typename TStringSet, typename TCargo, typename TSpec, typename TGuideTree, typename TSize>
530                         TSize minMembers)  in tripletLibraryExtension()
537     TSize nSeq = length(strSet);  in tripletLibraryExtension()
540     typedef String<TSize> TSequenceGroups;  in tripletLibraryExtension()
547     String<TSize> seqLabels;  in tripletLibraryExtension()
550     for(TSize i=0; i< (TSize) length(seqGroup); ++i) {  in tripletLibraryExtension()
579     for(TSize i=0; i< (TSize) length(seqGroup); ++i) {  in tripletLibraryExtension()
583             TSize seq1 = idToPosition(strSet, sequenceId(g, (*itInitial).v1));  in tripletLibraryExtension()
584             TSize seq2 = idToPosition(strSet, sequenceId(g, (*itInitial).v2));  in tripletLibraryExtension()
788     typedef typename Size<TGraph>::Type TSize;  in sumOfPairsScore()  typedef
799     TSize nseq = length(stringSet(g));  in sumOfPairsScore()
800     TSize len = length(mat) / nseq;  in sumOfPairsScore()
805     for(TSize i = 0; i<nseq-1; ++i) {  in sumOfPairsScore()
806         for(TSize j=i+1; j<nseq; ++j) {  in sumOfPairsScore()
807             for(TSize k=0;k<len; ++k) {  in sumOfPairsScore()
845     typedef typename Size<TGraph>::Type TSize;  in sumOfPairsScoreInd()  typedef
855     TSize nseq = length(stringSet(g));  in sumOfPairsScoreInd()
856     TSize len = length(mat) / nseq;  in sumOfPairsScoreInd()
859     for(TSize k=0;k<len; ++k) {  in sumOfPairsScoreInd()
860         for(TSize i = 0; i<nseq-1; ++i) {  in sumOfPairsScoreInd()
861             for(TSize j=i+1; j<nseq; ++j) {  in sumOfPairsScoreInd()
898 template<typename TStringSet, typename TCargo, typename TSpec, typename TScore, typename TSize>
902                     TSize& gapExCount,  in alignmentEvaluation()
903                     TSize& gapCount,  in alignmentEvaluation()
904                     TSize& pairCount,  in alignmentEvaluation()
905                     String<TSize> & numPairs,  in alignmentEvaluation()
906                     TSize& len)  in alignmentEvaluation()
911     TSize alphSize = ValueSize<TAlphabet>::VALUE;  in alignmentEvaluation()
926     TSize nseq = length(stringSet(g));  in alignmentEvaluation()
933     for(TSize i = 0; i<nseq-1; ++i) {  in alignmentEvaluation()
934         for(TSize j=i+1; j<nseq; ++j) {  in alignmentEvaluation()
935             for(TSize k=0;k<len; ++k) {  in alignmentEvaluation()
941                         TSize index1 = ordValue(TAlphabet(value(mat, i*len+k)));  in alignmentEvaluation()
942                         TSize index2 = ordValue(TAlphabet(value(mat, j*len + k)));  in alignmentEvaluation()
982         typedef typename Size<TAlign>::Type TSize;  in convertAlignment()  typedef
986         TSize nseq = length(sourceSet);  in convertAlignment()
990             for(TSize i = 0; i<nseq; ++i) assignSource(row(align, i), sourceSet[i]);  in convertAlignment()
994         for(TSize i = 0; i<nseq; ++i) value(rowIter, i) = begin(row(align, i));  in convertAlignment()
995         TSize lenMat = length(mat);  in convertAlignment()
996         TSize colLen = lenMat / nseq;  in convertAlignment()
997         TSize gapCount = 0;  in convertAlignment()
999         for(TSize alignRow = 0; alignRow < nseq; ++alignRow) {  in convertAlignment()
1000             for(TSize pos = alignRow * colLen; pos < (alignRow + 1) * colLen; ++pos) {  in convertAlignment()
1030     typedef typename Size<TAlign>::Type TSize;  in convertAlignment()  typedef
1038     TSize nseq = length(rows(align));  in convertAlignment()
1043     for(TSize i = 0; i<nseq; ++i) {  in convertAlignment()
1048     for(TSize alignRow1 = 0; alignRow1 < nseq; ++alignRow1) {  in convertAlignment()
1049         for(TSize alignRow2 = alignRow1 + 1; alignRow2 < nseq; ++alignRow2) {  in convertAlignment()
1052             TSize alignPos = 0;  in convertAlignment()
1053             TSize length = 0;  in convertAlignment()
1054             TSize offset1 = 0;  in convertAlignment()
1055             TSize offset2 = 0;  in convertAlignment()