/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align/ |
H A D | align_interface_wrapper.h | 153 TSetV & gapSeqSetV, in _alignWrapperSequential() argument 166 auto zipCont = makeZipView(results, gapSeqSetH, gapSeqSetV); in _alignWrapperSequential()
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H A D | global_alignment_unbanded.h | 752 StringSet<Gaps<TSequenceV, TGapsSpecV>, TSetSpecV> & gapSeqSetV, in globalAlignment() argument 762 return _alignWrapper(gapSeqSetH, gapSeqSetV, scoringScheme, TAlignConfig2(), TGapModel()); in globalAlignment() 771 StringSet<Gaps<TSequenceV, TGapsSpecV>, TSetSpecV> & gapSeqSetV, in globalAlignment() argument 776 … return globalAlignment(gapSeqSetH, gapSeqSetV, scoringScheme, alignConfig, NeedlemanWunsch()); in globalAlignment() 778 return globalAlignment(gapSeqSetH, gapSeqSetV, scoringScheme, alignConfig, Gotoh()); in globalAlignment() 786 StringSet<Gaps<TSequenceV, TGapsSpecV>, TSetSpecV> & gapSeqSetV, in globalAlignment() argument 790 return globalAlignment(gapSeqSetH, gapSeqSetV, scoringScheme, alignConfig); in globalAlignment()
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H A D | dp_align_simd_helper.h | 436 TSetV & gapSeqSetV, in _alignWrapperSimd() argument 473 appendValue(depSetV, source(back(gapSeqSetV))); in _alignWrapperSimd() 478 appendValue(depSetV, source(gapSeqSetV[i])); in _alignWrapperSimd() 501 _adaptTraceSegmentsTo(gapSeqSetH[x], gapSeqSetV[x], trace[x - pos]); in _alignWrapperSimd()
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H A D | local_alignment_unbanded.h | 329 StringSet<TGapSequenceV, TSetSpecV> & gapSeqSetV, in localAlignment() argument 336 return _alignWrapper(gapSeqSetH, gapSeqSetV, scoringScheme, TAlignConfig2(), TGapModel()); in localAlignment()
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H A D | local_alignment_banded.h | 241 StringSet<TGapSequenceV, TSetSpecV> & gapSeqSetV, in localAlignment() argument 250 …return _alignWrapper(gapSeqSetH, gapSeqSetV, scoringScheme, TAlignConfig2(lowerDiag, upperDiag), T… in localAlignment()
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H A D | global_alignment_banded.h | 664 StringSet<TGapSequenceV, TSetSpecV> & gapSeqSetV, in globalAlignment() argument 676 …return _alignWrapper(gapSeqSetH, gapSeqSetV, scoringScheme, TAlignConfig2(lowerDiag, upperDiag), T… in globalAlignment()
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align/ |
H A D | align_interface_wrapper.h | 153 TSetV & gapSeqSetV, in _alignWrapperSequential() argument 166 auto zipCont = makeZipView(results, gapSeqSetH, gapSeqSetV); in _alignWrapperSequential()
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H A D | global_alignment_unbanded.h | 752 StringSet<Gaps<TSequenceV, TGapsSpecV>, TSetSpecV> & gapSeqSetV, in globalAlignment() argument 762 return _alignWrapper(gapSeqSetH, gapSeqSetV, scoringScheme, TAlignConfig2(), TGapModel()); in globalAlignment() 771 StringSet<Gaps<TSequenceV, TGapsSpecV>, TSetSpecV> & gapSeqSetV, in globalAlignment() argument 776 … return globalAlignment(gapSeqSetH, gapSeqSetV, scoringScheme, alignConfig, NeedlemanWunsch()); in globalAlignment() 778 return globalAlignment(gapSeqSetH, gapSeqSetV, scoringScheme, alignConfig, Gotoh()); in globalAlignment() 786 StringSet<Gaps<TSequenceV, TGapsSpecV>, TSetSpecV> & gapSeqSetV, in globalAlignment() argument 790 return globalAlignment(gapSeqSetH, gapSeqSetV, scoringScheme, alignConfig); in globalAlignment()
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H A D | dp_align_simd_helper.h | 436 TSetV & gapSeqSetV, in _alignWrapperSimd() argument 473 appendValue(depSetV, source(back(gapSeqSetV))); in _alignWrapperSimd() 478 appendValue(depSetV, source(gapSeqSetV[i])); in _alignWrapperSimd() 501 _adaptTraceSegmentsTo(gapSeqSetH[x], gapSeqSetV[x], trace[x - pos]); in _alignWrapperSimd()
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H A D | local_alignment_unbanded.h | 329 StringSet<TGapSequenceV, TSetSpecV> & gapSeqSetV, in localAlignment() argument 336 return _alignWrapper(gapSeqSetH, gapSeqSetV, scoringScheme, TAlignConfig2(), TGapModel()); in localAlignment()
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H A D | local_alignment_banded.h | 241 StringSet<TGapSequenceV, TSetSpecV> & gapSeqSetV, in localAlignment() argument 250 …return _alignWrapper(gapSeqSetH, gapSeqSetV, scoringScheme, TAlignConfig2(lowerDiag, upperDiag), T… in localAlignment()
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H A D | global_alignment_banded.h | 664 StringSet<TGapSequenceV, TSetSpecV> & gapSeqSetV, in globalAlignment() argument 676 …return _alignWrapper(gapSeqSetH, gapSeqSetV, scoringScheme, TAlignConfig2(lowerDiag, upperDiag), T… in globalAlignment()
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