Searched refs:ProtReadingFrame (Results 1 – 6 of 6) sorted by relevance
| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/gnomon/ |
| H A D | gnomon_model.hpp | 236 TSignedSeqRange ProtReadingFrame() const { return m_reading_frame_from_proteins; } in ProtReadingFrame() function in CCDSInfo
293 _ASSERT( ProtReadingFrame().Empty() && MaxCdsLimits().Empty() ); in Invariant()
304 _ASSERT( ProtReadingFrame().Empty() || Include(ReadingFrame(), ProtReadingFrame()) ); in Invariant()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/ |
| H A D | gnomon_seq.cpp | 229 if(model.GetCdsInfo().ProtReadingFrame().NotEmpty()) { in FindStartsStops()
230 … TSignedSeqRange protrf = mrnamap.MapRangeOrigToEdited(model.GetCdsInfo().ProtReadingFrame(),true); in FindStartsStops()
238 if(Include(model.GetCdsInfo().ProtReadingFrame(),model_start) && reading_frame_start < 3) { in FindStartsStops()
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| H A D | gnomon_model.cpp | 290 if(ProtReadingFrame().NotEmpty()) { in MapFromEditedToOrig()
291 TSignedSeqRange prot_rf = amap.MapRangeEditedToOrig(ProtReadingFrame(), true); in MapFromEditedToOrig()
339 if(ProtReadingFrame().NotEmpty()) { in MapFromOrigToEdited()
340 new_cds.SetReadingFrame(amap.MapRangeOrigToEdited(ProtReadingFrame(), true), true); in MapFromOrigToEdited()
341 _ASSERT(new_cds.ProtReadingFrame().NotEmpty()); in MapFromOrigToEdited()
1757 TSignedSeqRange protcds = cds_info.ProtReadingFrame(); in CollectAttributes()
1963 …eadingFrame(reading_frame, (a.Type()&CGeneModel::eProt)!=0 && cds_info.ProtReadingFrame().Empty()); in ParseAttributes()
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| H A D | parse.cpp | 688 if (gene.GetCdsInfo().ProtReadingFrame().NotEmpty()) in GetGenes()
689 cds_info.SetReadingFrame(gene.GetCdsInfo().ProtReadingFrame(), true); in GetGenes()
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| H A D | chainer.cpp | 2217 if(algn.GetCdsInfo().ProtReadingFrame().Empty() && algn.Score() < 5*minscor.m_min) { in Duplicate5pendsAndShortCDSes()
3179 if(chain.GetCdsInfo().ProtReadingFrame().Empty() && in MakeChains()
3963 if(align.GetCdsInfo().ProtReadingFrame().NotEmpty()) { in SetFlagsForChains()
4574 protreadingframe += align.GetCdsInfo().ProtReadingFrame(); in CalculateSupportAndWeightFromMembers()
4792 if(cds.ProtReadingFrame().NotEmpty()) { in RestoreReasonableConfirmedStart()
4793 if(Strand() == ePlus && cds.ProtReadingFrame().GetFrom() < conf_start.GetFrom()) in RestoreReasonableConfirmedStart()
4795 else if(Strand() == eMinus && cds.ProtReadingFrame().GetTo() > conf_start.GetTo()) in RestoreReasonableConfirmedStart()
4796 extra_cds = TSignedSeqRange(conf_start.GetTo(), cds.ProtReadingFrame().GetTo()); in RestoreReasonableConfirmedStart()
4804 TSignedSeqRange protreadingframe = cds.ProtReadingFrame(); in RestoreReasonableConfirmedStart()
5039 auto prot_rf = cds_info_t.ProtReadingFrame(); in SetConfirmedEnds()
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| H A D | score.cpp | 1541 …if (cds_info.ProtReadingFrame().NotEmpty() && !Include(best_reading_frame, cds_info.ProtReadingFra… in GetScore()
1543 cds_info.SetReadingFrame(best_reading_frame & cds_info.ProtReadingFrame(), true); in GetScore()
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