Searched refs:ConfirmedStart (Results 1 – 5 of 5) sorted by relevance
244 …bool ConfirmedStart() const { return m_confirmed_start; } // start is confirmed by protein alignm… in ConfirmedStart() function in CCDSInfo294 _ASSERT( !ConfirmedStart() ); in Invariant()326 if (ConfirmedStart()) { in Invariant()506 bool CompleteCds() const { return FullCds() && (!Open5primeEnd() || ConfirmedStart()); } in CompleteCds()510 _ASSERT( !(OpenCds()&&ConfirmedStart()) ); in GoodEnoughToBeAnnotation()530 …bool ConfirmedStart() const { return m_cds_info.ConfirmedStart(); } // start is confirmed by prot… in ConfirmedStart() function in CGeneModel
569 if(align.ConfirmedStart()) { // enforcing confirmed start in Init()1384 …if(cds_info.ConfirmedStart() && cds_info.ConfirmedStop() && model.Continuous()) { // looks like a… in SelectBestReadingFrame()1513 is_open = !cds_info.ConfirmedStart(); in GetScore()1518 if(newlen >= max(6,oldlen/2) || cds_info.ConfirmedStart()) { in GetScore()1519 is_open = !cds_info.ConfirmedStart(); in GetScore()1524 …if (cds_info.ConfirmedStart() && best_start != starts[frame].back()) { // confirmed start was exp… in GetScore()1529 …bool confirmed_start = cds_info.ConfirmedStart(); //we wamnt to keep the status even if the actu… in GetScore()
307 new_cds.SetStart(start, ConfirmedStart()); in MapFromEditedToOrig()348 new_cds.SetStart(amap.MapRangeOrigToEdited(Start(), false), ConfirmedStart()); in MapFromOrigToEdited()704 _ASSERT( !(ConfirmedStart() && OpenCds()) ); in CdsInvariant()1776 _ASSERT( !(cds_info.ConfirmedStart() && cds_info.OpenCds()) ); in CollectAttributes()1778 if (cds_info.ConfirmedStart()) in CollectAttributes()
2191 if((algn.Type() & CGeneModel::eProt)!=0 || algn.ConfirmedStart()) in ScoreCdnas()4631 …if(ConfirmedStart() || !HasStart() || !HasStop() || OpenCds() || !Open5primeEnd() || (Type()&CGene… in SetOpenForPartialyAlignedProteins()4675 …if(align.Strand() != Strand() || !align.ConfirmedStart() || (align.TrustedProt().empty() && align.… in RestoreReasonableConfirmedStart()4764 …if(orig_align->ConfirmedStart() && Include((*it)->m_align->Limits(),orig_align->GetCdsInfo().Start… in RestoreReasonableConfirmedStart()5819 if(ConfirmedStart() && ConfirmedStop()) in SetConfirmedStartStopForCompleteProteins()5832 if(!ConfirmedStart() && HasStart()) in SetConfirmedStartStopForCompleteProteins()5852 … if(!ConfirmedStart() && HasStart() && fivep_exon.IntersectingWith((*i)->m_align->Limits()) && in SetConfirmedStartStopForCompleteProteins()5886 if((setconfstart || ConfirmedStart()) && (setconfstop || ConfirmedStop()) && Continuous()) { in SetConfirmedStartStopForCompleteProteins()5941 if(ConfirmedStart() && ConfirmedStop()) { in CollectTrustedmRNAsProts()6262 …if ((algn.Type() & CGeneModel::eProt)!=0 || algn.ConfirmedStart()) { // this includes protein al… in ScoreCDSes_FilterOutPoorAlignments()[all …]
692 cds_info.SetStart(start, gene.ConfirmedStart() && start == gene.GetCdsInfo().Start()); in GetGenes()