Searched refs:m_ssplice (Results 1 – 10 of 10) sorted by relevance
673 new_exons.back().m_ssplice = Exons()[i].m_ssplice; in RemoveShortHolesAndRescore()770 MyExons()[i].m_ssplice = false; in CutExons()854 e->m_ssplice = false; in Clip()868 MyExons().back().m_ssplice = false; in Clip()1090 MyExons().back().m_ssplice = true; in AddExon()1097 e.m_ssplice = true; in AddExon()1119 MyExons().back().m_ssplice = true; in AddGgapExon()1126 e.m_ssplice = true; in AddGgapExon()1154 e.m_ssplice = true; in AddNormalExon()1173 m_ssplice =m_ssplice || e.m_ssplice; in Extend()[all …]
155 if(e[i-1].m_ssplice && e[i].m_fsplice) { in CAlignCommon()422 if(!(exonl.m_ssplice && exonr.m_fsplice)) { in ClipNotSupportedFlanks()701 if(!exons[ie].m_ssplice) { in CleanSelfTranscript()726 for( ; exons[piece_end].m_ssplice; ++piece_end); in CleanSelfTranscript()829 e.m_ssplice = false; in CleanSelfTranscript()851 for( ; edited_exons[piece_end].m_ssplice; ++piece_end); in CleanSelfTranscript()1482 if(a.Exons()[ie+1].m_ssplice) { in FilterAlignments()1526 if(a.Exons()[iie+1].m_ssplice) { in FilterAlignments()1866 } else if(a.m_ssplice != b.m_ssplice) { in OneExonCompare()1867 return a.m_ssplice < b.m_ssplice; in OneExonCompare()[all …]
243 if (!align.Exons()[i-1].m_ssplice || !align.Exons()[i].m_fsplice) { in CSeqScores()559 if (!e->m_ssplice && right < align.Limits().GetTo()) { in Init()638 if(algn.Exons()[k-1].m_ssplice) in Init()657 if(algn.Exons()[k-1].m_ssplice) in Init()673 if(algn.Exons()[k-1].m_ssplice && algn.Exons()[k].m_fsplice) in Init()980 if(algn.Exons()[k-1].m_ssplice && algn.Exons()[k].m_fsplice) continue; in Init()1165 …if(algn.Exons()[k].m_ssplice && algn.Exons()[k+1].m_fsplice && b >= cds_lim.GetFrom() && b <= cds_… in Init()1177 …if(a > 0 && algn.Exons()[k-1].m_ssplice && algn.Exons()[k].m_fsplice && a >= cds_lim.GetFrom() && … in Init()1208 if(exons[i-1].m_ssplice && exons[i-1].m_ssplice_sig != "XX") { in SelectBestReadingFrame()1243 if(exons[i-1].m_ssplice && exons[i-1].m_ssplice_sig != "XX") { in SelectBestReadingFrame()
481 if(b.Exons()[i-1].m_ssplice && b.Exons()[i].m_fsplice) { in IsAllowedAlternative()3802 if(!(exonl.m_ssplice && exonr.m_fsplice)) { in CreateChainsForPartialProteins()3828 if(!(exonl.m_ssplice && exonr.m_fsplice)) in CreateChainsForPartialProteins()3835 if(!(exonl.m_ssplice && exonr.m_fsplice)) { in CreateChainsForPartialProteins()4200 if(!e->m_ssplice) in CChain()4423 if(Exons()[i-1].m_ssplice && Exons()[i].m_fsplice) in CalculateSupportAndWeightFromMembers()4465 if(!m_gapped_helper_align.Exons()[i].m_ssplice) { in CalculateSupportAndWeightFromMembers()4478 if(!Exons()[i-1].m_ssplice || !Exons()[i].m_fsplice) { in CalculateSupportAndWeightFromMembers()5541 if(Exons()[i-1].m_ssplice && Exons()[i].m_fsplice) { in ClipLowCoverageUTR()6115 if(e->m_ssplice) in FilterOutChimeras()[all …]
143 if(check_in_holes || (algn.Exons()[i-1].m_ssplice && algn.Exons()[i].m_fsplice)) { in RangeNestedInIntron()
532 EEdgeType type_b = exons[i].m_ssplice ? eSplice : eBoundary; in CAlignMap()578 EEdgeType type_b = exons[i].m_ssplice ? eSplice : eBoundary; in CAlignMap()608 if(i != exons.size()-1 && (!exons[i+1].m_fsplice || !exons[i].m_ssplice)) in CAlignMap()
370 _ASSERT(piece_begin->m_ssplice); in CAlignModel()376 … for (piece_end = piece_begin; piece_end != Exons().end() && piece_end->m_ssplice; ++piece_end) ; in CAlignModel()
381 …if (i < model.Exons().size()-1 && (!e->m_ssplice || (model.Exons()[i+1].Limits().Empty() && extend… in create_packed_int_seqloc()733 if (e.m_ssplice) { in spliced_exon()
467 if(!ai.Exons()[i-1].m_ssplice || !ai.Exons()[i].m_fsplice) { in Predict()
186 …m_fsplice(fs), m_ssplice(ss), m_fsplice_sig(fsig), m_ssplice_sig(ssig), m_ident(ident), m_seq(seq)… in CModelExon()193 return (m_range==p.m_range && m_fsplice == p.m_fsplice && m_ssplice == p.m_ssplice); in operator ==()210 bool m_fsplice, m_ssplice; member in CModelExon497 if (!Exons()[i-1].m_ssplice || !Exons()[i].m_fsplice) in Continuous()898 if (!algn.Exons()[i-1].m_ssplice || !algn.Exons()[i].m_fsplice) { in GetAlignParts()