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 D | gnomon_model.cpp | 99 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() [all …]
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H A D | gnomon_seq.cpp | 202 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()
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H A D | chainer.cpp | 5269 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() [all …]
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H A D | parse.cpp | 658 TSignedSeqRange rf = gene_map.MapRangeOrigToEdited(reading_frame, true); in GetGenes() 675 TSignedSeqRange rf = gene_map.MapRangeOrigToEdited(reading_frame, true); in GetGenes()
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H A D | asn1.cpp | 365 … 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()
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H A D | gnomon_objmgr.cpp | 417 TSignedSeqRange reading_frame = m_alignmap.MapRangeOrigToEdited(Limits(), true); in CAlignModel()
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H A D | aligncollapser.cpp | 631 …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()
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H A D | score.cpp | 206 return m_seq_map.MapRangeOrigToEdited(r, withextras); in operator ()()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/gnomon/ |
H A D | gnomon_model.hpp | 650 …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
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