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

/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/
H A Dgnomon_model.cpp99 return amap.MapRangeOrigToEdited(Exons()[i].Limits(), true); in TranscriptExon()
123 l = amap.MapRangeOrigToEdited(Exons().front().Limits(),true).GetFrom(); in TranscriptLimits()
129 r = amap.MapRangeOrigToEdited(Exons().back().Limits(),true).GetTo(); in TranscriptLimits()
136 r = amap.MapRangeOrigToEdited(Exons().front().Limits(),true).GetTo(); in TranscriptLimits()
142 l = amap.MapRangeOrigToEdited(Exons().back().Limits(),true).GetFrom(); in TranscriptLimits()
160 cds = amap.MapRangeOrigToEdited(cds); in isNMD()
167 l = amap.MapRangeOrigToEdited(Exons()[i],true).GetFrom(); in isNMD()
174 l = amap.MapRangeOrigToEdited(Exons()[i],true).GetFrom(); in isNMD()
356 TSignedSeqRange p = amap.MapRangeOrigToEdited(*i, false); in MapFromOrigToEdited()
1937 protcds = a.GetAlignMap().MapRangeOrigToEdited(protcds, false); in ParseAttributes()
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H A Dgnomon_seq.cpp202 TSignedSeqRange rf = mrnamap.MapRangeOrigToEdited(model.ReadingFrame(),true); in FindStartsStops()
230 … TSignedSeqRange protrf = mrnamap.MapRangeOrigToEdited(model.GetCdsInfo().ProtReadingFrame(),true); in FindStartsStops()
266 TSignedSeqRange start = mrnamap.MapRangeOrigToEdited(model.GetCdsInfo().Start(),false); in FindStartsStops()
922 TSignedSeqRange CAlignMap::MapRangeOrigToEdited(TSignedSeqRange orig_range, ERangeEnd lend, ERangeE… in MapRangeOrigToEdited() function in CAlignMap
979 int len = MapRangeOrigToEdited(ab, lend, rend).GetLength(); in FShiftedLen()
991 int len = MapRangeOrigToEdited(ab, withextras).GetLength(); in FShiftedLen()
H A Dchainer.cpp5269 TSignedSeqRange core_lim = amap.MapRangeOrigToEdited(genome_core_lim); in MainPeaks()
5462 TSignedSeqRange core_lim = amap.MapRangeOrigToEdited(genome_core_lim); in ClipLowCoverageUTR()
5513 TSignedSeqRange overlap_on_mrna = amap.MapRangeOrigToEdited(overlap); in ClipLowCoverageUTR()
5613 int new_5p = amap.MapRangeOrigToEdited(Limits()).GetFrom(); in ClipLowCoverageUTR()
5649 TSignedSeqRange overlap_on_mrna = amap.MapRangeOrigToEdited(overlap); in CalculateDropLimits()
5676 soft_limit = amap.MapRangeOrigToEdited(soft_limit); in CalculateDropLimits()
5768 TSignedSeqRange overlap_on_mrna = amap.MapRangeOrigToEdited(overlap); in SetConsistentCoverage()
6314 TSignedSeqRange tstop = amap.MapRangeOrigToEdited(*stp,false); in FindSelenoproteinsClipProteinsToStartStop()
6318 TSignedSeqRange ostop = origmap.MapRangeOrigToEdited(*stp,false); in FindSelenoproteinsClipProteinsToStartStop()
7797 TSignedSeqRange texon = amap.MapRangeOrigToEdited(orig_exon, lend, rend); in MapOneModelToEditedContig()
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H A Dparse.cpp658 TSignedSeqRange rf = gene_map.MapRangeOrigToEdited(reading_frame, true); in GetGenes()
675 TSignedSeqRange rf = gene_map.MapRangeOrigToEdited(reading_frame, true); in GetGenes()
H A Dasn1.cpp365 … TSignedSeqRange interval_range_on_mrna = amap.MapRangeOrigToEdited(e->Limits()) & limits_on_mrna; in create_packed_int_seqloc()
678 …if (cds_info.ReadingFrame().NotEmpty() && model.GetAlignMap().MapRangeOrigToEdited(model.Limits(),… in create_internal_feature()
1084 rf = model.GetAlignMap().MapRangeOrigToEdited(rf, false); in RestoreModelReadingFrame()
H A Dgnomon_objmgr.cpp417 TSignedSeqRange reading_frame = m_alignmap.MapRangeOrigToEdited(Limits(), true); in CAlignModel()
H A Daligncollapser.cpp631 …TSignedSeqRange te = amap.MapRangeOrigToEdited(e->Limits(),e->m_fsplice ? CAlignMap::eLeftEnd : CA… in RemoveNotSupportedIntronsFromTranscript()
2186 …TSignedSeqRange texon = align.GetAlignMap().MapRangeOrigToEdited(TSignedSeqRange(e.GetTo(),align.E… in FillGapsInAlignmentAndAddToGenomicGaps()
H A Dscore.cpp206 return m_seq_map.MapRangeOrigToEdited(r, withextras); in operator ()()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/gnomon/
H A Dgnomon_model.hpp650 …TSignedSeqRange MapRangeOrigToEdited(TSignedSeqRange orig_range, ERangeEnd lend, ERangeEnd rend) c…
651 …TSignedSeqRange MapRangeOrigToEdited(TSignedSeqRange orig_range, bool withextras = true) const { r… in MapRangeOrigToEdited() function in CAlignMap