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Searched refs:cds_info (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.cpp702 cds_info = cds_info.MapFromOrigToEdited(mrnamap); in CdsInvariant()
706 _ASSERT(Include(cds_info.MaxCdsLimits(), cds_info.Cds())); in CdsInvariant()
711 …_ASSERT(cds_info.ReadingFrame().GetFrom() < 3 || (cds_info.HasStart() && cds_info.Start().GetTo()+… in CdsInvariant()
712 …_ASSERT(cds_info.ReadingFrame().GetTo() >= mrnamap.TargetLen()-3 || (cds_info.HasStop() && cds_inf… in CdsInvariant()
715 _ASSERT(!cds_info.HasStart() || cds_info.Start().GetLength()==3); in CdsInvariant()
716 _ASSERT(!cds_info.HasStop() || cds_info.Stop().GetLength()==3); in CdsInvariant()
744 …_ASSERT( cds_info.ReadingFrame().Empty() || FShiftedLen(cds_info.Start()+cds_info.ReadingFrame()+c… in CombineCdsInfo()
1750 cds_info = cds_info.MapFromOrigToEdited(a.GetAlignMap()); in CollectAttributes()
1776 _ASSERT( !(cds_info.ConfirmedStart() && cds_info.OpenCds()) ); in CollectAttributes()
2019 cds_info.SetScore(cds_info.Score(), open_cds); in ParseAttributes()
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H A Dscore.cpp264 align.SetCdsInfo(cds_info); in CSeqScores()
1403 …if((cds_info.ReadingFrame().NotEmpty() || !cds_info.PStops().empty()) && cds_info.IsMappedToGenome… in GetScore()
1404 cds_info = cds_info.MapFromOrigToEdited(mrnamap); in GetScore()
1503 cds_info.Clear5PrimeCdsLimit(); in GetScore()
1506 cds_info.Clear(); in GetScore()
1507 model.SetCdsInfo( cds_info ); in GetScore()
1539 cds_info.ClearPStops(); in GetScore()
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()
1569 … cds_info = cds_info.MapFromEditedToOrig(mrnamap); // returns empty cds with badscore if con't map in GetScore()
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H A Dgnomon_objmgr.cpp480 CCDSInfo cds_info = GetCdsInfo(); in GetCdsDnaSequence() local
481 if(cds_info.IsMappedToGenome()) in GetCdsDnaSequence()
482 cds_info = cds_info.MapFromOrigToEdited(amap); in GetCdsDnaSequence()
483 int cds_len = cds_info.Cds().GetLength(); in GetCdsDnaSequence()
506 CCDSInfo cds_info = GetCdsInfo(); in GetProtein() local
507 if(cds_info.IsMappedToGenome()) { in GetProtein()
509 cds_info = cds_info.MapFromOrigToEdited(amap); in GetProtein()
511 ITERATE(CCDSInfo::TPStops, stp, cds_info.PStops()) { in GetProtein()
534 CCDSInfo cds_info = GetCdsInfo(); in GetProtein() local
535 if(cds_info.IsMappedToGenome()) { in GetProtein()
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H A Dselect_alignments_alt.cpp181 CCDSInfo cds_info = model.GetCdsInfo(); in FilterGenes() local
182 if(cds_info.ReadingFrame().Empty()) in FilterGenes()
185 if(cds_info.IsMappedToGenome()) in FilterGenes()
186 cds_info = cds_info.MapFromOrigToEdited(model.GetAlignMap()); in FilterGenes()
187 TSignedSeqRange cds = cds_info.Cds(); in FilterGenes()
H A Dannot.cpp677 CCDSInfo cds_info = it->GetCdsInfo(); in Predict() local
681 TSignedSeqRange fullcds = cds_info.Cds(); in Predict()
692 cds_info.ClearPStops(); in Predict()
695 cds_info.AddPStop(*ps); in Predict()
697 it->SetCdsInfo(cds_info); in Predict()
718 CCDSInfo cds_info = it->GetCdsInfo(); in Predict() local
719 cds_info.SetScore(cds_info.Score(),false); // kill the Open flag in Predict()
720 it->SetCdsInfo(cds_info); in Predict()
758 CCDSInfo cds_info = m.GetCdsInfo(); in transform_model() local
759 cds_info.SetScore(score, false); in transform_model()
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H A Dasn1.cpp670 const CCDSInfo& cds_info = model.GetCdsInfo(); in create_internal_feature() local
671 TSignedSeqRange rcds_on_mrna = cds_info.MaxCdsLimits() & model.TranscriptLimits(); in create_internal_feature()
673 if(cds_info.HasStart()) in create_internal_feature()
674 rcds_on_mrna.SetFrom(cds_info.Start().GetFrom()); in create_internal_feature()
676 frame = (cds_info.Cds().GetFrom()-rcds_on_mrna.GetFrom())%3; in create_internal_feature()
1065 CCDSInfo cds_info = model.GetCdsInfo(); in RestoreModelAttributes() local
1066 cds_info.SetScore(score, cds_info.OpenCds()); in RestoreModelAttributes()
1067 model.SetCdsInfo(cds_info); in RestoreModelAttributes()
1116 … CCDSInfo cds_info(false); // mrna coordinates; will be projected to genome at the end if possible in RestoreModelReadingFrame() local
1117 cds_info.SetReadingFrame(rf, false); in RestoreModelReadingFrame()
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H A Dparse.cpp687 CCDSInfo cds_info; in GetGenes() local
689 cds_info.SetReadingFrame(gene.GetCdsInfo().ProtReadingFrame(), true); in GetGenes()
690 cds_info.SetReadingFrame(reading_frame); in GetGenes()
692 cds_info.SetStart(start, gene.ConfirmedStart() && start == gene.GetCdsInfo().Start()); in GetGenes()
694 cds_info.SetStop(stop, gene.ConfirmedStop()); in GetGenes()
697 cds_info.AddPStop(*s); in GetGenes()
699 cds_info.SetScore(score); in GetGenes()
700 gene.SetCdsInfo(cds_info); in GetGenes()
H A Dchainer.cpp4593 CCDSInfo cds_info = cds; in CalculateSupportAndWeightFromMembers() local
4595 cds_info = cds_info.MapFromOrigToEdited(mrnamap); in CalculateSupportAndWeightFromMembers()
4656 SetCdsInfo(cds_info); in SetOpenForPartialyAlignedProteins()
4952 CCDSInfo cds_info = GetCdsInfo(); in SetConfirmedEnds() local
5093 auto cds = cds_info.Cds(); in SetConfirmedEnds()
5107 SetCdsInfo(cds_info); in SetConfirmedEnds()
5884 CCDSInfo cds_info = GetCdsInfo(); in SetConfirmedStartStopForCompleteProteins() local
5885 double score = cds_info.Score(); in SetConfirmedStartStopForCompleteProteins()
5893 cds_info.SetStart(cds_info.Start(), true); // confirmed start in SetConfirmedStartStopForCompleteProteins()
5897 cds_info.SetStop(cds_info.Stop(), true); // confirmed stop in SetConfirmedStartStopForCompleteProteins()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/gnomon/
H A Dgnomon_model.hpp444 void SetCdsInfo(const CCDSInfo& cds_info);
447 void CombineCdsInfo(const CCDSInfo& cds_info, bool ensure_cds_invariant = true);