Home
last modified time | relevance | path

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 Dgnomon_model.cpp96 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 …]
H A Daligncollapser.cpp364 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 …]
H A Dgnomon_objmgr.cpp479 CAlignMap amap = CGeneModel::GetAlignMap(); in GetCdsDnaSequence()
508 CAlignMap amap = GetAlignMap(); in GetProtein()
536 CAlignMap amap = GetAlignMap(); in GetProtein()
H A Dasn1.cpp84 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()
H A Dselect_alignments_alt.cpp186 cds_info = cds_info.MapFromOrigToEdited(model.GetAlignMap()); in FilterGenes()
H A Dparse.cpp649 CAlignMap gene_map = gene.GetAlignMap(); in GetGenes()
655 gene_map = gene.GetAlignMap(); in GetGenes()
672 gene_map = gene.GetAlignMap(); in GetGenes()
H A Dchainer.cpp4211 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 …]
H A Dvariations.cpp265 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()
H A Dannot.cpp732 CAlignMap mrnamap(m.GetAlignMap()); in transform_model()
H A Dscore.cpp442 CAlignMap mrnamap(al.GetAlignMap()); in Init()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/gnomon/
H A Dgnomon_model.hpp547 virtual CAlignMap GetAlignMap() const;
740 virtual CAlignMap GetAlignMap() const { return m_alignmap; } in GetAlignMap() function in CAlignModel