Searched refs:GetAlignMap (Results 1 – 11 of 11) sorted by relevance
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/ |
H A D | gnomon_model.cpp | 96 CAlignMap amap = GetAlignMap(); in TranscriptExon() 117 CAlignMap amap = GetAlignMap(); in TranscriptLimits() 158 CAlignMap amap = GetAlignMap(); in isNMD() 227 m_alignmap = CGeneModel::GetAlignMap(); in ResetAlignMap() 933 return GetAlignMap().FShiftedLen(ab, withextras); in FShiftedLen() 938 return GetAlignMap().FShiftedMove(pos, len); in FShiftedMove() 1414 …TSignedSeqRange lim = GetAlignMap().MapRangeOrigToEdited(GetAlignMap().ShrinkToRealPoints(Limits()… in PolyALen() 1750 cds_info = cds_info.MapFromOrigToEdited(a.GetAlignMap()); in CollectAttributes() 1937 protcds = a.GetAlignMap().MapRangeOrigToEdited(protcds, false); in ParseAttributes() 2028 cds_info = cds_info.MapFromOrigToEdited(a.GetAlignMap()); in printGFF3() [all …]
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H A D | aligncollapser.cpp | 364 CAlignMap amap = align.GetAlignMap(); in ClipNotSupportedFlanks() 501 CAlignMap amap = align.GetAlignMap(); in RemoveNotSupportedIntronsFromProt() 546 CAlignMap amap = align.GetAlignMap(); in RemoveNotSupportedIntronsFromTranscript() 638 …transcript_exons, editedmodel.FrameShifts(), align.Orientation(), align.GetAlignMap().TargetLen()); in RemoveNotSupportedIntronsFromTranscript() 1490 l = a.GetAlignMap().ShrinkToRealPoints(l, false); in FilterAlignments() 1535 l = a.GetAlignMap().ShrinkToRealPoints(l, false); in FilterAlignments() 1565 l = a.GetAlignMap().ShrinkToRealPoints(l, false); in FilterAlignments() 1643 CAlignMap amap = align.GetAlignMap(); in FilterAlignments() 2186 …TSignedSeqRange texon = align.GetAlignMap().MapRangeOrigToEdited(TSignedSeqRange(e.GetTo(),align.E… in FillGapsInAlignmentAndAddToGenomicGaps() 2227 …ns(), transcript_exons, align.FrameShifts(), align.Orientation(), align.GetAlignMap().TargetLen()); in FillGapsInAlignmentAndAddToGenomicGaps() [all …]
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H A D | gnomon_objmgr.cpp | 479 CAlignMap amap = CGeneModel::GetAlignMap(); in GetCdsDnaSequence() 508 CAlignMap amap = GetAlignMap(); in GetProtein() 536 CAlignMap amap = GetAlignMap(); in GetProtein()
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H A D | asn1.cpp | 84 CAlignMap amap = model.GetAlignMap(); in SModelData() 359 CAlignMap amap = model.GetAlignMap(); in create_packed_int_seqloc() 678 …if (cds_info.ReadingFrame().NotEmpty() && model.GetAlignMap().MapRangeOrigToEdited(model.Limits(),… in create_internal_feature() 1072 CCDSInfo cds_info_g = cds_info_t.MapFromEditedToOrig(model.GetAlignMap()); in RestoreModelAttributes() 1084 rf = model.GetAlignMap().MapRangeOrigToEdited(rf, false); in RestoreModelReadingFrame()
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H A D | select_alignments_alt.cpp | 186 cds_info = cds_info.MapFromOrigToEdited(model.GetAlignMap()); in FilterGenes()
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H A D | parse.cpp | 649 CAlignMap gene_map = gene.GetAlignMap(); in GetGenes() 655 gene_map = gene.GetAlignMap(); in GetGenes() 672 gene_map = gene.GetAlignMap(); in GetGenes()
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H A D | chainer.cpp | 4211 CAlignMap amap = GetAlignMap(); in CChain() 4672 CAlignMap amap = GetAlignMap(); in RestoreReasonableConfirmedStart() 5257 CAlignMap amap = GetAlignMap(); in MainPeaks() 5436 CAlignMap amap = GetAlignMap(); in ClipLowCoverageUTR() 5636 CAlignMap amap = GetAlignMap(); in CalculateDropLimits() 5755 CAlignMap amap = GetAlignMap(); in SetConsistentCoverage() 5825 CAlignMap mrnamap = GetAlignMap(); in SetConfirmedStartStopForCompleteProteins() 6565 CAlignMap cdsmap(a.GetAlignMap()); in InframeFraction() 6669 CAlignMap cdsmap(a.GetAlignMap()); in transform_align() 7647 CAlignMap amap = align.GetAlignMap(); in MapOneModelToEditedContig() [all …]
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H A D | variations.cpp | 265 aligns.push_back(CAlignModel(a, a.GetAlignMap())); in GetVariationAlignList() 286 aligns.push_back(CAlignModel(a, a.GetAlignMap())); in GetVariationAlignList() 312 aligns.push_back(CAlignModel(a, a.GetAlignMap())); in GetVariationAlignList()
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H A D | annot.cpp | 732 CAlignMap mrnamap(m.GetAlignMap()); in transform_model()
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H A D | score.cpp | 442 CAlignMap mrnamap(al.GetAlignMap()); in Init()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/gnomon/ |
H A D | gnomon_model.hpp | 547 virtual CAlignMap GetAlignMap() const; 740 virtual CAlignMap GetAlignMap() const { return m_alignmap; } in GetAlignMap() function in CAlignModel
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