| /dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/seeds/ |
| H A D | banded_chain_alignment_impl.h | 766 TInfixH infixH; in _initializeBandedChain() local
777 infixH = infix(seqH, 0, upperDiagonal(band)); in _initializeBandedChain()
807 infixH = infix(seqH, gridBegin.i1, gridEnd.i1); in _initializeBandedChain()
830 1 - lowerDiagonal(band), length(infixH) - horizontalNextGridOrigin + 1, in _initializeBandedChain()
908 TInfixH infixH = infix(seqH, gridBegin.i1, gridEnd.i1); in _computeGapArea() local
965 TInfixH infixH = infix(seqH, gridBegin.i1, gridEnd.i1); in _computeAnchorArea() local
987 1 - lowerDiagonal(band), length(infixH) - horizontalNextGridOrigin + 1, in _computeAnchorArea()
1046 TInfixH infixH = infix(seqH, gridBegin.i1, gridEnd.i1); in _finishBandedChain() local
1057 length(infixV) + 1, length(infixH) - horizontalNextGridOrigin + 1, in _finishBandedChain()
1079 infixH = infix(seqH, gridBegin.i1, gridEnd.i1); in _finishBandedChain()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/seeds/ |
| H A D | banded_chain_alignment_impl.h | 854 TInfixH infixH; in _initializeBandedChain() local
864 infixH = infix(seqH, 0, upperDiagonal(band)); in _initializeBandedChain()
896 infixH = infix(seqH, gridBegin.i1, gridEnd.i1); in _initializeBandedChain()
919 1 - lowerDiagonal(band), length(infixH) - horizontalNextGridOrigin + 1, in _initializeBandedChain()
1000 TInfixH infixH = infix(seqH, gridBegin.i1, gridEnd.i1); in _computeGapArea() local
1058 TInfixH infixH = infix(seqH, gridBegin.i1, gridEnd.i1); in _computeAnchorArea() local
1080 1 - lowerDiagonal(band), length(infixH) - horizontalNextGridOrigin + 1, in _computeAnchorArea()
1140 TInfixH infixH = infix(seqH, gridBegin.i1, gridEnd.i1); in _finishBandedChain() local
1151 length(infixV) + 1, length(infixH) - horizontalNextGridOrigin + 1, in _finishBandedChain()
1173 infixH = infix(seqH, gridBegin.i1, gridEnd.i1); in _finishBandedChain()
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| /dports/biology/seqan/seqan-library-2.4.0/include/seqan/seeds/ |
| H A D | banded_chain_alignment_impl.h | 854 TInfixH infixH; in _initializeBandedChain() local
864 infixH = infix(seqH, 0, upperDiagonal(band)); in _initializeBandedChain()
896 infixH = infix(seqH, gridBegin.i1, gridEnd.i1); in _initializeBandedChain()
919 1 - lowerDiagonal(band), length(infixH) - horizontalNextGridOrigin + 1, in _initializeBandedChain()
1000 TInfixH infixH = infix(seqH, gridBegin.i1, gridEnd.i1); in _computeGapArea() local
1058 TInfixH infixH = infix(seqH, gridBegin.i1, gridEnd.i1); in _computeAnchorArea() local
1080 1 - lowerDiagonal(band), length(infixH) - horizontalNextGridOrigin + 1, in _computeAnchorArea()
1140 TInfixH infixH = infix(seqH, gridBegin.i1, gridEnd.i1); in _finishBandedChain() local
1151 length(infixV) + 1, length(infixH) - horizontalNextGridOrigin + 1, in _finishBandedChain()
1173 infixH = infix(seqH, gridBegin.i1, gridEnd.i1); in _finishBandedChain()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/stellar/ |
| H A D | stellar_extension.h | 367 …Segment<TSequenceA, InfixSegment> infixH(host(infH), beginPositionH(seed), beginPositionH(seedOld)… in _reverseLeftExtension()
369 reverse(infixH); in _reverseLeftExtension()
389 TInfix infixH(host(infH), beginPositionH(seed), beginPositionH(seedOld)); in _fillMatrixBestEndsLeft()
392 reverse(infixH); in _fillMatrixBestEndsLeft()
396 appendValue(str, infixH); in _fillMatrixBestEndsLeft()
437 TInfix infixH(host(infH), endPositionH(seedOld), endPositionH(seed)); in _fillMatrixBestEndsRight()
441 appendValue(str, infixH); in _fillMatrixBestEndsRight()
584 TInfix infixH(host(infH), beginPositionH(seed), beginPositionH(seedOld)); in _tracebackLeft()
586 appendValue(str, infixH); in _tracebackLeft()
635 TInfix infixH(host(infH), endPositionH(seedOld), endPositionH(seed)); in _tracebackRight()
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