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Searched refs:CAlignMap (Results 1 – 15 of 15) sorted by relevance

/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/
H A Dgnomon_seq.cpp400 CAlignMap::SMapRangeEdge orig_from(orig_start, left_orige, left_type); in InsertOneToOneRange()
401 CAlignMap::SMapRangeEdge orig_to(orig_start+len-1, right_orige, right_type); in InsertOneToOneRange()
561 CAlignMap::CAlignMap(const CGeneModel::TExons& exons, const TInDels& indels, EStrand strand, TSigne… in CAlignMap() function in CAlignMap
670 int CAlignMap::FindLowerRange(const vector<CAlignMap::SMapRange>& a, TSignedSeqPos p) { in FindLowerRange()
813 TSignedSeqPos CAlignMap::FShiftedMove(TSignedSeqPos orig_pos, int len) const { in FShiftedMove()
826 TSignedSeqPos CAlignMap::MapAtoB(const vector<CAlignMap::SMapRange>& a, const vector<CAlignMap::SMa… in MapAtoB()
878 TSignedSeqPos CAlignMap::MapOrigToEdited(TSignedSeqPos orig_pos) const { in MapOrigToEdited()
887 TSignedSeqPos CAlignMap::MapEditedToOrig(TSignedSeqPos edited_pos) const { in MapEditedToOrig()
896 TSignedSeqRange CAlignMap::MapRangeAtoB(const vector<CAlignMap::SMapRange>& a, const vector<CAlignM… in MapRangeAtoB()
977 int CAlignMap::FShiftedLen(TSignedSeqRange ab, ERangeEnd lend, ERangeEnd rend) const { in FShiftedLen()
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H A Dgnomon_seq.hpp101 void FindAllStarts(TIVec codons[], const CEResidueVec& mrna, const CAlignMap& mrnamap, TSignedSeqRa…
102 void FindAllStops(TIVec codons[], const CEResidueVec& mrna, const CAlignMap& mrnamap, TSignedSeqRan…
103 …neModel& model, const CEResidueVec& contig_seq, const CEResidueVec& mrna, const CAlignMap& mrnamap,
H A Dgnomon_model.cpp96 CAlignMap amap = GetAlignMap(); in TranscriptExon()
117 CAlignMap amap = GetAlignMap(); in TranscriptLimits()
158 CAlignMap amap = GetAlignMap(); in isNMD()
194 CAlignMap CGeneModel::GetAlignMap() const { return CAlignMap(Exons(), FrameShifts(), Strand()); } in GetAlignMap()
232 m_alignmap = CAlignMap(); in RecalculateAlignMap()
242 … CAlignMap::ERangeEnd l = e.GetFrom() == left ? CAlignMap::eSinglePoint : CAlignMap::eLeftEnd; in RecalculateAlignMap()
243 … CAlignMap::ERangeEnd r = e.GetTo() == right ? CAlignMap::eSinglePoint : CAlignMap::eRightEnd; in RecalculateAlignMap()
699 CAlignMap mrnamap(Exons(),FrameShifts(),Strand()); in CdsInvariant()
996 auto_ptr<CAlignMap> pmapa(0), pmapb(0); in isCompatible()
2359 CAlignMap amap; in readGFF3()
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H A Dscore.hpp78 const CAlignMap& FrameShiftedSeqMap() const { return m_map; } in FrameShiftedSeqMap()
110 CAlignMap m_map;
H A Dparse.cpp550 const CAlignMap& seq_map = m_seqscr.FrameShiftedSeqMap(); in GetGenes()
600 CAlignMap localmap(local_gene.Exons(), local_gene.FrameShifts(), local_gene.Strand()); in GetGenes()
649 CAlignMap gene_map = gene.GetAlignMap(); in GetGenes()
651 …SeqRange(gene.Limits().GetFrom(),reading_frame.GetFrom()), CAlignMap::eSinglePoint, CAlignMap::eLe… in GetGenes()
668 …SignedSeqRange(reading_frame.GetTo(),gene.Limits().GetTo()), CAlignMap::eRightEnd, CAlignMap::eSin… in GetGenes()
711 const CAlignMap& seq_map = m_seqscr.FrameShiftedSeqMap(); in PrintInfo()
H A Dchainer.cpp136 const CAlignMap& m_edited_contig_map;
247 CAlignMap* m_align_map;
1875 list<CAlignMap> m_align_maps;
4211 CAlignMap amap = GetAlignMap(); in CChain()
4672 CAlignMap amap = GetAlignMap(); in RestoreReasonableConfirmedStart()
5436 CAlignMap amap = GetAlignMap(); in ClipLowCoverageUTR()
5636 CAlignMap amap = GetAlignMap(); in CalculateDropLimits()
5755 CAlignMap amap = GetAlignMap(); in SetConsistentCoverage()
5825 CAlignMap mrnamap = GetAlignMap(); in SetConfirmedStartStopForCompleteProteins()
7691 CAlignMap::ERangeEnd lend = CAlignMap::eLeftEnd; in MapOneModelToEditedContig()
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H A Dgnomon_objmgr.cpp358 m_alignmap = CAlignMap(Exons(), transcript_exons, indels, orientation, target_len ); in CAlignModel()
479 CAlignMap amap = CGeneModel::GetAlignMap(); in GetCdsDnaSequence()
508 CAlignMap amap = GetAlignMap(); in GetProtein()
536 CAlignMap amap = GetAlignMap(); in GetProtein()
H A Daligncollapser.cpp103 CAlignMap amap(a.Exons(), a.FrameShifts(), a.Strand()); in GetAlignment()
364 CAlignMap amap = align.GetAlignMap(); in ClipNotSupportedFlanks()
501 CAlignMap amap = align.GetAlignMap(); in RemoveNotSupportedIntronsFromProt()
546 CAlignMap amap = align.GetAlignMap(); in RemoveNotSupportedIntronsFromTranscript()
631 …d(e->Limits(),e->m_fsplice ? CAlignMap::eLeftEnd : CAlignMap::eSinglePoint, e->m_ssplice ? CAlignM… in RemoveNotSupportedIntronsFromTranscript()
638 …CAlignMap editedamap(editedmodel.Exons(), transcript_exons, editedmodel.FrameShifts(), align.Orien… in RemoveNotSupportedIntronsFromTranscript()
718 CAlignMap amap(exons,transcript_exons, align.FrameShifts(), ePlus, tlen); in CleanSelfTranscript()
943 …CAlignMap editedamap(editedmodel.Exons(),edited_transcript_exons, edited_indels, align.Orientation… in CleanSelfTranscript()
1643 CAlignMap amap = align.GetAlignMap(); in FilterAlignments()
2227 …CAlignMap editedamap(editedmodel.Exons(), transcript_exons, align.FrameShifts(), align.Orientation… in FillGapsInAlignmentAndAddToGenomicGaps()
H A Dgnomon_engine.cpp200 const CAlignMap& seq_map = m_data->m_ss->FrameShiftedSeqMap(); in PartialModelStepBack()
H A Dscore.cpp171 m_map = CAlignMap(m_chunk_start, m_chunk_stop, m_fshifts.begin(), m_fshifts.end()); in ConstructSequenceAndMaps()
197 CIndelMapper(const CAlignMap& seq_map): in CIndelMapper()
200 const CAlignMap& m_seq_map;
442 CAlignMap mrnamap(al.GetAlignMap()); in Init()
1187 …stReadingFrame(const CGeneModel& model, const CEResidueVec& mrna, const CAlignMap& mrnamap, TIVec … in SelectBestReadingFrame()
1393 CAlignMap mrnamap(model.Exons(),model.FrameShifts(),model.Strand()); in GetScore()
H A Dasn1.cpp84 CAlignMap amap = model.GetAlignMap(); in SModelData()
359 CAlignMap amap = model.GetAlignMap(); in create_packed_int_seqloc()
H A Dannot.cpp732 CAlignMap mrnamap(m.GetAlignMap()); in transform_model()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/gnomon/
H A Dgnomon_model.hpp221 class CAlignMap;
232 CCDSInfo MapFromOrigToEdited(const CAlignMap& amap) const;
547 virtual CAlignMap GetAlignMap() const;
620 class CAlignMap { class
625 CAlignMap() {}; in CAlignMap() function in CAlignMap
717 …static TSignedSeqPos MapAtoB(const vector<CAlignMap::SMapRange>& a, const vector<CAlignMap::SMapRa…
718 …static TSignedSeqRange MapRangeAtoB(const vector<CAlignMap::SMapRange>& a, const vector<CAlignMap:…
719 …static TSignedSeqRange MapRangeAtoB(const vector<CAlignMap::SMapRange>& a, const vector<CAlignMap:… in MapRangeAtoB()
739 CAlignModel(const CGeneModel& g, const CAlignMap& a);
740 virtual CAlignMap GetAlignMap() const { return m_alignmap; } in GetAlignMap()
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H A Dgnomon.hpp89 …SelectBestReadingFrame(const CGeneModel& model, const CEResidueVec& mrna, const CAlignMap& mrnamap,
H A Dchainer.hpp155 CAlignMap m_edited_contig_map;