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Searched refs:GetInDels (Results 1 – 9 of 9) sorted by relevance

/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/gnomon/
H A Dglb_align.hpp56 …TInDels GetInDels(int sstart, const char* const query, const char* subject) const; // sstart i…
H A Dvariations.hpp58 TLiteInDelsP GetInDels() const { in GetInDels() function in CLiteAlign
H A Dgnomon_model.hpp538 TInDels GetInDels(bool fs_only) const;
539 TInDels GetInDels(TSignedSeqPos a, TSignedSeqPos b, bool fs_only) const;
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/
H A Dvariations.cpp284 …a.FrameShifts() = cigar.GetInDels(range.GetFrom()+m_word, seq.c_str()+m_word, m_contigt.c_str()+ra… in GetVariationAlignList()
310 …a.FrameShifts() = selected_cigar.GetInDels(range.GetFrom()+m_word, selected_seq.c_str()+m_word, m_… in GetVariationAlignList()
356 TLiteInDelsP indels = m_alignsp[ir]->GetInDels(); in InsertDashesInBase()
421 TLiteInDelsP indels = m_alignsp[ir]->GetInDels(); in InsertDashesInReads()
H A Dgnomon_model.cpp48 TInDels CGeneModel::GetInDels(TSignedSeqPos a, TSignedSeqPos b, bool fs_only) const { in GetInDels() function in CGeneModel
50 TInDels indels = GetInDels(fs_only); in GetInDels()
61 TInDels CGeneModel::GetInDels(bool fs_only) const { in GetInDels() function in CGeneModel
1793 TInDels fs = a.GetInDels(true); in CollectAttributes()
H A Dglb_align.cpp87 TInDels CCigar::GetInDels(int sstart, const char* const query, const char* subject) const { in GetInDels() function in CCigar
H A Daligncollapser.cpp729 … TInDels indels = align.GetInDels(exons[piece_begin].GetFrom(), exons[piece_end].GetTo(), false); in CleanSelfTranscript()
1458 TInDels fs = align.GetInDels(ie->GetFrom(), ie->GetTo(), true); in FilterAlignments()
1684 TInDels pindels = align.GetInDels(true); in FilterAlignments()
1756 TInDels pindels = align.GetInDels(true); in FilterAlignments()
H A Dasn1.cpp786 TInDels indels = (is_protalign ? model.GetInDels(false) : model.FrameShifts()); in AlignModelToSeqalign()
H A Dchainer.cpp5050 …return (a < 0 || b < 0 || map.MapEditedToOrig(i+1) < 0 || !GetInDels(a, b, false).empty()); // gen… in SetConfirmedEnds()
6570 TInDels indels = a.GetInDels(left, right, true); in InframeFraction()
7048 TInDels alignfshifts = i->GetInDels(true); in DropAlignmentInfo()
7654 TInDels aindels = align.GetInDels(false); in MapOneModelToEditedContig()