| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/gnomon/ |
| H A D | gnomon_model.hpp | 169 typedef vector<CInDelInfo> TInDels; typedef
535 TInDels& FrameShifts() { return m_fshifts; } in FrameShifts()
536 const TInDels& FrameShifts() const { return m_fshifts; } in FrameShifts()
537 TInDels FrameShifts(TSignedSeqPos a, TSignedSeqPos b) const;
538 TInDels GetInDels(bool fs_only) const;
539 TInDels GetInDels(TSignedSeqPos a, TSignedSeqPos b, bool fs_only) const;
600 TInDels m_fshifts;
631 …lignMap(TSignedSeqPos orig_a, TSignedSeqPos orig_b, TInDels::const_iterator fsi_begin, const TInDe… in CAlignMap()
639 TInDels::const_iterator fs = fsi_end-1; in CAlignMap()
725 …os orig_a, TSignedSeqPos orig_b, TSignedSeqPos edit_a, TInDels::const_iterator fsi_begin, TInDels:…
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| H A D | chainer.hpp | 145 typedef map<int,TInDels::const_iterator> TGgapInfo;
156 … TInDels m_editing_indels; // in original coordinates (include corrections, ggaps and Ns)
157 …TInDels m_reversed_corrections; // corrections from edited genome back to original (without gg…
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| H A D | aligncollapser.hpp | 120 TInDels m_correction_indels;
137 TInDels GetGenomicGaps() const { return m_correction_data.m_correction_indels; }; in GetGenomicGaps()
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| H A D | glb_align.hpp | 56 …TInDels GetInDels(int sstart, const char* const query, const char* subject) const; // sstart i…
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/ |
| H A D | score.hpp | 55 const TInDels& initial_fshifts, double mpp, const CGnomonEngine& gnomon);
77 const TInDels& SeqTInDels() const { return m_fshifts; } in SeqTInDels()
107 TInDels m_fshifts;
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| H A D | gnomon_model.cpp | 50 TInDels indels = GetInDels(fs_only); in GetInDels()
51 TInDels selected_indels; in GetInDels()
53 ITERATE(TInDels, i, indels) { in GetInDels()
63 TInDels selected_indels; in GetInDels()
65 ITERATE(TInDels, i, FrameShifts()) { in GetInDels()
210 ITERATE(TInDels, i, FrameShifts()) { in CAlignModel()
881 TInDels indels; in RemoveExtraFShifts()
915 TInDels fshifts; in FrameShifts()
917 ITERATE(TInDels, i, m_fshifts) { in FrameShifts()
1794 ITERATE(TInDels, indl, fs) { in CollectAttributes()
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| H A D | gnomon_seq.cpp | 315 void PushInDel(TInDels& indels, bool fs_only, TSignedSeqPos p, int len, CInDelInfo::EType type, con… in PushInDel()
411 …terval(TSignedSeqPos orig_a, TSignedSeqPos orig_b, TSignedSeqPos edit_a, TInDels::const_iterator f… in InsertIndelRangesForInterval()
412 …TInDels::const_iterator fsi_end, EEdgeType type_a, EEdgeType type_b, const string& gseq_a, const s… in InsertIndelRangesForInterval()
414 TInDels::const_iterator fsi = fsi_begin; in InsertIndelRangesForInterval()
504 …l::TExons& exons, const vector<TSignedSeqRange>& transcript_exons, const TInDels& indels, EStrand … in CAlignMap()
515 ITERATE(TInDels, f, indels) { in CAlignMap()
561 CAlignMap::CAlignMap(const CGeneModel::TExons& exons, const TInDels& indels, EStrand strand, TSigne… in CAlignMap()
563 TInDels::const_iterator fsi_begin = indels.begin(); in CAlignMap()
564 TInDels::const_iterator fsi_end = indels.end(); in CAlignMap()
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| H A D | chainer.cpp | 182 TInDels all_frameshifts;
2280 TInDels StrictlyContainedInDels(const TInDels& indels, const TSignedSeqRange& lim) { in StrictlyContainedInDels()
2281 TInDels fs; in StrictlyContainedInDels()
4846 TInDels fs; in RemoveFshiftsFromUTRs()
4973 TInDels fs; in SetConfirmedEnds()
5094 TInDels fs; in SetConfirmedEnds()
6488 TInDels m_fshifts;
7049 TInDels fshifts; in DropAlignmentInfo()
7348 TInDels combined_indels; in CombineCorrectionsAndIndels()
7534 TInDels erepl; in MapOneModelToOrigContig()
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| H A D | aligncollapser.cpp | 730 TInDels::const_iterator indl = indels.begin(); in CleanSelfTranscript()
846 TInDels edited_indels; in CleanSelfTranscript()
929 ITERATE(TInDels, indl, align.FrameShifts()) { in CleanSelfTranscript()
951 int TotalFrameShift(const TInDels& indels, int a, int b) { in TotalFrameShift()
953 ITERATE(TInDels, indl, indels) { in TotalFrameShift()
1403 ITERATE(TInDels, indl, m_correction_data.m_correction_indels) { in FilterAlignments()
1439 typedef pair<TSignedSeqRange,TInDels> TGapEnd; in FilterAlignments()
1684 TInDels pindels = align.GetInDels(true); in FilterAlignments()
1756 TInDels pindels = align.GetInDels(true); in FilterAlignments()
2253 TInDels corrections = a.FrameShifts(); in AddAlignment()
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| H A D | variations.cpp | 199 TInDels all_corrections = align.FrameShifts(); in AddAlignment()
202 TInDels corrections; in AddAlignment()
203 ITERATE(TInDels, i, all_corrections) { in AddAlignment()
221 ITERATE(TInDels, indl, corrections) { in AddAlignment()
234 ITERATE(TInDels, indl, corrections) { in AddAlignment()
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| H A D | gnomon_objmgr.cpp | 107 TInDels indels; in CAlignModel()
329 NON_CONST_ITERATE(TInDels, indl, indels) { in CAlignModel()
330 TInDels::iterator indl_next = indl; in CAlignModel()
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| H A D | gnomon_engine.cpp | 174 TInDels initial_fshifts; in Run()
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| H A D | glb_align.cpp | 87 TInDels CCigar::GetInDels(int sstart, const char* const query, const char* subject) const { in GetInDels()
88 TInDels indels; in GetInDels()
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| H A D | annot.cpp | 680 TInDels fs; in Predict()
682 ITERATE(TInDels, i, it->FrameShifts()) { in Predict()
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| H A D | asn1.cpp | 786 TInDels indels = (is_protalign ? model.GetInDels(false) : model.FrameShifts()); in AlignModelToSeqalign()
787 TInDels::const_iterator indel_i = indels.begin(); in AlignModelToSeqalign()
886 TInDels::const_iterator indl = model.FrameShifts().begin(); in AlignModelToSeqalign()
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| H A D | score.cpp | 233 …TSignedSeqPos from, TSignedSeqPos to, const TGeneModelList& cls, const TInDels& initial_fshifts, d… in CSeqScores()
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