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Searched refs:GetCdsInfo (Results 1 – 10 of 10) sorted by relevance

/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/
H A Dselect_alignments_alt.cpp82 …!a.ReadingFrame().IntersectingWith(b.ReadingFrame()) || a.GetCdsInfo().PStops() != b.GetCdsInfo().… in AreSimilar()
86 TSignedSeqRange acds = a.GetCdsInfo().Cds(); in AreSimilar()
87 TSignedSeqRange bcds = b.GetCdsInfo().Cds(); in AreSimilar()
181 CCDSInfo cds_info = model.GetCdsInfo(); in FilterGenes()
H A Dchainer.cpp1916 mbr.m_cds_info = &algn.GetCdsInfo(); in InsertMember()
2134 CCDSInfo cds = algn.GetCdsInfo(); in ReplicatePStops()
3547 …mestop = (parts[p]->GetCdsInfo().HasStop() == mi.m_cds_info->HasStop() && (!parts[p]->GetCdsInfo(… in FindOptimalChainForProtein()
4065 if(!Include(jtt->GetCdsInfo().MaxCdsLimits(), itt->GetCdsInfo().MaxCdsLimits())) in CombineCompatibleChains()
4585 CCDSInfo cds = GetCdsInfo(); in CalculateSupportAndWeightFromMembers()
4654 CCDSInfo cds_info = GetCdsInfo(); in SetOpenForPartialyAlignedProteins()
4791 CCDSInfo cds = GetCdsInfo(); in RestoreReasonableConfirmedStart()
4894 CCDSInfo cds = GetCdsInfo(); in ClipChain()
4952 CCDSInfo cds_info = GetCdsInfo(); in SetConfirmedEnds()
5884 CCDSInfo cds_info = GetCdsInfo(); in SetConfirmedStartStopForCompleteProteins()
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H A Dasn1.cpp85 CCDSInfo cds = model.GetCdsInfo(); in SModelData()
282 const CCDSInfo& cds = model.GetCdsInfo(); in create_cdregion_feature()
670 const CCDSInfo& cds_info = model.GetCdsInfo(); in create_internal_feature()
941 _ASSERT(GetCdsInfo().IsMappedToGenome()); in MakeSeqAlign()
942 TSignedSeqRange lim = GetCdsInfo().Start()+GetCdsInfo().ReadingFrame(); in MakeSeqAlign()
1065 CCDSInfo cds_info = model.GetCdsInfo(); in RestoreModelAttributes()
1070 if(model.GetCdsInfo().ReadingFrame().NotEmpty()) { in RestoreModelAttributes()
1071 CCDSInfo cds_info_t = model.GetCdsInfo(); in RestoreModelAttributes()
H A Dannot.cpp574 CCDSInfo cds = nested.back().GetCdsInfo(); in Predict()
677 CCDSInfo cds_info = it->GetCdsInfo(); in Predict()
708 ITERATE(CCDSInfo::TPStops, stp, it->GetCdsInfo().PStops()) { in Predict()
718 CCDSInfo cds_info = it->GetCdsInfo(); in Predict()
758 CCDSInfo cds_info = m.GetCdsInfo(); in transform_model()
H A Dgnomon_model.cpp157 TSignedSeqRange cds = GetCdsInfo().Start()+GetCdsInfo().ReadingFrame()+GetCdsInfo().Stop(); in isNMD()
159 if(GetCdsInfo().IsMappedToGenome()) { in isNMD()
700 CCDSInfo cds_info = GetCdsInfo(); in CdsInvariant()
1329 cds.SetFrom(GetCdsInfo().Start().GetFrom()); in RealCdsLimits()
1331 cds.SetTo(GetCdsInfo().Start().GetTo()); in RealCdsLimits()
1346 return GetCdsInfo().MaxCdsLimits() & Limits(); in MaxCdsLimits()
1746 if (a.GetCdsInfo().ReadingFrame().NotEmpty()) { in CollectAttributes()
1748 CCDSInfo cds_info = a.GetCdsInfo(); in CollectAttributes()
1929 CCDSInfo cds_info = a.GetCdsInfo(); in ParseAttributes()
2026 CCDSInfo cds_info = a.GetCdsInfo(); in printGFF3()
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H A Dparse.cpp688 if (gene.GetCdsInfo().ProtReadingFrame().NotEmpty()) in GetGenes()
689 cds_info.SetReadingFrame(gene.GetCdsInfo().ProtReadingFrame(), true); in GetGenes()
692 cds_info.SetStart(start, gene.ConfirmedStart() && start == gene.GetCdsInfo().Start()); in GetGenes()
696 ITERATE(CCDSInfo::TPStops,s,gene.GetCdsInfo().PStops()) in GetGenes()
H A Dgnomon_seq.cpp229 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()
266 TSignedSeqRange start = mrnamap.MapRangeOrigToEdited(model.GetCdsInfo().Start(),false); in FindStartsStops()
H A Dgnomon_objmgr.cpp480 CCDSInfo cds_info = GetCdsInfo(); in GetCdsDnaSequence()
506 CCDSInfo cds_info = GetCdsInfo(); in GetProtein()
534 CCDSInfo cds_info = GetCdsInfo(); in GetProtein()
H A Dscore.cpp240 CCDSInfo cds_info = align.GetCdsInfo(); in CSeqScores()
588 if(align.GetCdsInfo().MaxCdsLimits().NotEmpty()) { in Init()
589 if(TSignedSeqRange::GetWholeFrom() < align.GetCdsInfo().MaxCdsLimits().GetFrom()) { in Init()
599 if(align.GetCdsInfo().MaxCdsLimits().GetTo() < TSignedSeqRange::GetWholeTo()) { in Init()
1303 CCDSInfo cds_info = model.GetCdsInfo(); in SelectBestReadingFrame()
1402 CCDSInfo cds_info = model.GetCdsInfo(); in GetScore()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/gnomon/
H A Dgnomon_model.hpp443 const CCDSInfo& GetCdsInfo() const { return m_cds_info; } in GetCdsInfo() function in CGeneModel
520 …return ReadingFrame().NotEmpty() && GetCdsInfo().MaxCdsLimits().GetFrom()==TSignedSeqRange::GetWho… in OpenLeftEnd()
524 …return ReadingFrame().NotEmpty() && GetCdsInfo().MaxCdsLimits().GetTo()==TSignedSeqRange::GetWhole… in OpenRightEnd()
561 …GetCdsInfo().PStops() == a.GetCdsInfo().PStops() && Type() == a.Type() && Status() == a.Status(); } in IdenticalAlign()