Searched refs:emRNA (Results 1 – 6 of 6) sorted by relevance
1349 if((align.Type()&CGeneModel::emRNA) && !m_filtermrna) in FilterAlignments()1355 if(align.Type()&(CGeneModel::emRNA|CGeneModel::eProt)) { in FilterAlignments()1647 if((align.Type()&CGeneModel::emRNA) && !m_filtermrna) in FilterAlignments()1897 if(i->Type() == CGeneModel::emRNA) { in GetOnlyOtherAlignments()2105 if(i->Type() == CGeneModel::emRNA) { in GetCollapsedAlgnments()2358 ((align.Type()&CGeneModel::emRNA) && !m_filtermrna) || in AddAlignment()2374 if(align.Type()&(CGeneModel::eEST|CGeneModel::emRNA)) in AddAlignment()
1278 …SetType(Type() | ((CGeneModel::eProt|CGeneModel::eSR|CGeneModel::eEST|CGeneModel::emRNA|CGeneModel… in Extend()1678 if ((type & (eSR|eEST|emRNA|eNotForChaining))!=0) return "Splign"; in TypeToString()1730 if ((a.Type() &CGeneModel::emRNA)!=0) attributes["flags"] += ",mRNA"; in CollectAttributes()1849 else if (*f == "mRNA") a.SetType(a.Type()| CGeneModel::emRNA); in ParseAttributes()
76 …gs().GetSpliced().GetGenomic_strand()==eNa_strand_minus?eMinus:ePlus, GetModelId(seq_align), emRNA) in CAlignModel()
3064 if(align.Type() == CGeneModel::emRNA) in MakeChains()4568 SetType(Type() & (~(eSR | eEST | emRNA | eProt | eNotForChaining))); in CalculateSupportAndWeightFromMembers()4573 SetType(Type() | (align.Type() & (eSR | eEST | emRNA | eProt | eNotForChaining))); in CalculateSupportAndWeightFromMembers()5515 …if(align.Type() == CGeneModel::emRNA || align.Type() == CGeneModel::eEST || align.Type() == CGeneM… in ClipLowCoverageUTR()5651 …if(align.Type() == CGeneModel::emRNA || align.Type() == CGeneModel::eEST) { //OK to clip protein… in CalculateDropLimits()5831 if((*i)->m_align->Type() & emRNA) { in SetConfirmedStartStopForCompleteProteins()6608 …if ((align.Type()&CAlignModel::emRNA)==0 || (align.Status()&CGeneModel::eTSA)!=0 || (align.Status(… in transform_align()8376 return m.Exons().size() <= 1 && (m.Type() & (CAlignModel::eProt|CAlignModel::emRNA))==0; in model_predicate()8389 …&& int(m.Support().size()) < minsupport && (m.Type() & (CAlignModel::eProt|CAlignModel::emRNA))==0; in model_predicate()
551 } else if (type&CGeneModel::emRNA) { in create_ModelEvidence_user_object()
365 emRNA = 16, enumerator