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Searched refs:gapSeqSetV (Results 1 – 12 of 12) sorted by relevance

/dports/biology/seqan/seqan-library-2.4.0/include/seqan/align/
H A Dalign_interface_wrapper.h153 TSetV & gapSeqSetV, in _alignWrapperSequential() argument
166 auto zipCont = makeZipView(results, gapSeqSetH, gapSeqSetV); in _alignWrapperSequential()
H A Dglobal_alignment_unbanded.h752 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()
H A Ddp_align_simd_helper.h436 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()
H A Dlocal_alignment_unbanded.h329 StringSet<TGapSequenceV, TSetSpecV> & gapSeqSetV, in localAlignment() argument
336 return _alignWrapper(gapSeqSetH, gapSeqSetV, scoringScheme, TAlignConfig2(), TGapModel()); in localAlignment()
H A Dlocal_alignment_banded.h241 StringSet<TGapSequenceV, TSetSpecV> & gapSeqSetV, in localAlignment() argument
250 …return _alignWrapper(gapSeqSetH, gapSeqSetV, scoringScheme, TAlignConfig2(lowerDiag, upperDiag), T… in localAlignment()
H A Dglobal_alignment_banded.h664 StringSet<TGapSequenceV, TSetSpecV> & gapSeqSetV, in globalAlignment() argument
676 …return _alignWrapper(gapSeqSetH, gapSeqSetV, scoringScheme, TAlignConfig2(lowerDiag, upperDiag), T… in globalAlignment()
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align/
H A Dalign_interface_wrapper.h153 TSetV & gapSeqSetV, in _alignWrapperSequential() argument
166 auto zipCont = makeZipView(results, gapSeqSetH, gapSeqSetV); in _alignWrapperSequential()
H A Dglobal_alignment_unbanded.h752 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()
H A Ddp_align_simd_helper.h436 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()
H A Dlocal_alignment_unbanded.h329 StringSet<TGapSequenceV, TSetSpecV> & gapSeqSetV, in localAlignment() argument
336 return _alignWrapper(gapSeqSetH, gapSeqSetV, scoringScheme, TAlignConfig2(), TGapModel()); in localAlignment()
H A Dlocal_alignment_banded.h241 StringSet<TGapSequenceV, TSetSpecV> & gapSeqSetV, in localAlignment() argument
250 …return _alignWrapper(gapSeqSetH, gapSeqSetV, scoringScheme, TAlignConfig2(lowerDiag, upperDiag), T… in localAlignment()
H A Dglobal_alignment_banded.h664 StringSet<TGapSequenceV, TSetSpecV> & gapSeqSetV, in globalAlignment() argument
676 …return _alignWrapper(gapSeqSetH, gapSeqSetV, scoringScheme, TAlignConfig2(lowerDiag, upperDiag), T… in globalAlignment()