| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/gnomon/ |
| H A D | gnomon_model.hpp | 541 …int FShiftedLen(TSignedSeqRange ab, bool withextras = true) const; // won't work if a/b is inse…
542 …int FShiftedLen(TSignedSeqPos a, TSignedSeqPos b, bool withextras = true) const { return FShifted… in FShiftedLen() function in CGeneModel
629 m_target_len = FShiftedLen(orig_a, orig_b); in CAlignMap()
644 m_target_len = FShiftedLen(orig_a, orig_b); in CAlignMap()
655 int FShiftedLen(TSignedSeqRange ab, ERangeEnd lend, ERangeEnd rend) const;
656 int FShiftedLen(TSignedSeqRange ab, bool withextras = true) const;
657 …int FShiftedLen(TSignedSeqPos a, TSignedSeqPos b, bool withextras = true) const { return FShiftedL… in FShiftedLen() function in CAlignMap
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/ |
| H A D | select_alignments_alt.cpp | 89 …if(a.FShiftedLen(acds.GetFrom(),common_point,false)%3 != b.FShiftedLen(bcds.GetFrom(),common_point… in AreSimilar()
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| H A D | parse.cpp | 614 if(localmap.FShiftedLen(local_reading_frame) <= del) { in GetGenes()
626 if(localmap.FShiftedLen(local_reading_frame) <= del) { in GetGenes()
641 …_ASSERT(gene.Limits().GetFrom() <= reading_frame.GetFrom() && gene.FShiftedLen(gene.Limits().GetFr… in GetGenes()
642 …_ASSERT(gene.Limits().GetTo() >= reading_frame.GetTo() && gene.FShiftedLen(reading_frame.GetTo(),g… in GetGenes()
651 …int utr_len = gene_map.FShiftedLen(TSignedSeqRange(gene.Limits().GetFrom(),reading_frame.GetFrom()… in GetGenes()
668 …int utr_len = gene_map.FShiftedLen(TSignedSeqRange(reading_frame.GetTo(),gene.Limits().GetTo()), C… in GetGenes()
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| H A D | aligncollapser.cpp | 385 if(seg.Empty() || amap.FShiftedLen(seg,false) < END_PART_LENGTH) { in ClipNotSupportedFlanks()
405 if(seg.Empty() || amap.FShiftedLen(seg,false) < END_PART_LENGTH) { in ClipNotSupportedFlanks()
435 if(segl.Empty() || amap.FShiftedLen(segl,false) < END_PART_LENGTH) { in ClipNotSupportedFlanks()
436 if(segr.Empty() || amap.FShiftedLen(segr,false) < END_PART_LENGTH) { in ClipNotSupportedFlanks()
444 } else if(segr.Empty() || amap.FShiftedLen(segr,false) < END_PART_LENGTH) { in ClipNotSupportedFlanks()
465 if(amap.FShiftedLen(a, b, false) < END_PART_LENGTH) { in ClipNotSupportedFlanks()
520 if(segl.Empty() || amap.FShiftedLen(segl,false) < END_PART_LENGTH) { in RemoveNotSupportedIntronsFromProt()
521 if(segr.Empty() || amap.FShiftedLen(segr,false) < END_PART_LENGTH) { in RemoveNotSupportedIntronsFromProt()
529 } else if(segr.Empty() || amap.FShiftedLen(segr,false) < END_PART_LENGTH) { in RemoveNotSupportedIntronsFromProt()
1712 … if(seg.Empty() || amap.FShiftedLen(seg,false) < END_PART_LENGTH) { // nothing left on right in FilterAlignments()
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| H A D | chainer.cpp | 533 TIVec acds_map(amap.FShiftedLen(a.GetCdsInfo().Cds()),0); in IsAlternative()
548 TIVec cds_map(gmap.FShiftedLen((*it)->GetCdsInfo().Cds()),0); in IsAlternative()
899 int algn_cds_len = algn.FShiftedLen(algn.GetCdsInfo().Cds(),false); in ReplacePseudoGeneSeeds()
2573 cds_overlap = mi.m_align_map->FShiftedLen(ai_rf&aj_rf,false); in LRCanChainItoJ()
2621 mi.m_cds = mi.m_align_map->FShiftedLen(ai_rf,false); in LRIinit()
3178 int cdslen = chain.FShiftedLen(chain.GetCdsInfo().Cds(),true); in MakeChains()
3204 if(chain.FShiftedLen(a,b,true)%3 != 0) in MakeChains()
4212 int mrna_len = amap.FShiftedLen(Limits()); in CChain()
5438 int mrna_len = amap.FShiftedLen(Limits()); in ClipLowCoverageUTR()
5638 int mrna_len = amap.FShiftedLen(Limits()); in CalculateDropLimits()
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| H A D | gnomon_model.cpp | 299 if(rf.NotEmpty() && amap.FShiftedLen(rf, true)%3 == 0) in MapFromEditedToOrig()
744 …_ASSERT( cds_info.ReadingFrame().Empty() || FShiftedLen(cds_info.Start()+cds_info.ReadingFrame()+c… in CombineCdsInfo()
926 int CGeneModel::FShiftedLen(TSignedSeqRange ab, bool withextras) const in FShiftedLen() function in CGeneModel
933 return GetAlignMap().FShiftedLen(ab, withextras); in FShiftedLen()
1321 return FShiftedLen(Limits(), false); in AlignLen()
1338 return FShiftedLen(RealCdsLimits(), false); in RealCdsLen()
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| H A D | gnomon_seq.cpp | 977 int CAlignMap::FShiftedLen(TSignedSeqRange ab, ERangeEnd lend, ERangeEnd rend) const { in FShiftedLen() function in CAlignMap
989 int CAlignMap::FShiftedLen(TSignedSeqRange ab, bool withextras) const { in FShiftedLen() function in CAlignMap
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| H A D | score.cpp | 471 _ASSERT(align.FShiftedLen(align.ReadingFrame(), false)%3==0); in Init()
1206 shift += mrnamap.FShiftedLen(exons[i-1].GetFrom(),exons[i-1].GetTo()); in SelectBestReadingFrame()
1241 shift -= mrnamap.FShiftedLen(exons[i-1].GetFrom(),exons[i-1].GetTo()); in SelectBestReadingFrame()
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