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Searched refs:m_ssplice_sig (Results 1 – 7 of 7) sorted by relevance

/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/
H A Dgnomon_model.cpp189 if(it->m_ssplice_sig != "XX") in ReverseComplementModel()
190 ReverseComplement(it->m_ssplice_sig.begin(),it->m_ssplice_sig.end()); in ReverseComplementModel()
771 MyExons()[i].m_ssplice_sig.clear(); in CutExons()
856 e->m_ssplice_sig.clear(); in Clip()
1127 e.m_ssplice_sig = "XX"; in AddGgapExon()
1145 MyExons().back().m_ssplice_sig = "XX"; in AddNormalExon()
1176 if(e.m_ssplice && !e.m_ssplice_sig.empty()) in Extend()
1177 m_ssplice_sig = e.m_ssplice_sig; in Extend()
2113 if(!e->m_fsplice_sig.empty() || !e->m_ssplice_sig.empty()) { in printGFF3()
2118 if(!e->m_ssplice_sig.empty()) in printGFF3()
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H A Daligncollapser.cpp158 sig = e[i-1].m_ssplice_sig+e[i].m_fsplice_sig; in CAlignCommon()
160 sig = e[i].m_fsplice_sig+e[i-1].m_ssplice_sig; in CAlignCommon()
712 exons[ie].m_ssplice_sig.clear(); in CleanSelfTranscript()
832 e.m_ssplice_sig.clear(); in CleanSelfTranscript()
898 edited_exons[piece_end].m_ssplice_sig = "NN"; in CleanSelfTranscript()
915 edited_exons[piece_end].m_ssplice_sig = splice; in CleanSelfTranscript()
926 editedmodel.AddExon(e.Limits(), e.m_fsplice_sig, e.m_ssplice_sig, e.m_ident); in CleanSelfTranscript()
2047 if(exons.front().m_ssplice_sig != "XX") in GetCollapsedAlgnments()
2182 editedmodel.AddExon(e.Limits(),e.m_fsplice_sig, e.m_ssplice_sig, e.m_ident); in FillGapsInAlignmentAndAddToGenomicGaps()
2350 sig = e[l-1].m_ssplice_sig+e[l].m_fsplice_sig; in AddAlignment()
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H A Dscore.cpp946 … if(algn.Exons().front().m_fsplice_sig == "XX" || algn.Exons().front().m_ssplice_sig == "XX") { in Init()
957 if(algn.Exons().back().m_fsplice_sig == "XX" || algn.Exons().back().m_ssplice_sig == "XX") { in Init()
1005 if(!algn.HasStart() && algn.Exons().front().m_ssplice_sig != "XX") in Init()
1085 if(!algn.HasStop() && algn.Exons().front().m_ssplice_sig != "XX") 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()
H A Dchainer.cpp465 if(e->m_fsplice_sig == "XX" || e->m_ssplice_sig == "XX") in IsAllowedAlternative()
470 if(e->m_fsplice_sig == "XX" || e->m_ssplice_sig == "XX") in IsAllowedAlternative()
744 if(b.Exons()[i-1].m_ssplice_sig == "XX" || b.Exons()[i].m_fsplice_sig == "XX") { in CheckCompatibility()
751 if(algn.Exons()[i-1].m_ssplice_sig == "XX" || algn.Exons()[i].m_fsplice_sig == "XX") { in CheckCompatibility()
2429 if(ai.Exons()[i-1].m_ssplice_sig == "XX" || ai.Exons()[i].m_fsplice_sig == "XX") in FindContainedAlignments()
4201 e->m_ssplice_sig.clear(); in CChain()
5799 if(Exons()[i].m_fsplice_sig == "XX" || Exons()[i].m_ssplice_sig == "XX") { in SetConsistentCoverage()
5953 if(ie->m_fsplice_sig == "XX" || ie->m_ssplice_sig == "XX") in CollectTrustedmRNAsProts()
6825 if(align.Exons().front().m_ssplice_sig == "XX") in TrimTranscript()
7561 model.AddNormalExon(exon, e.m_fsplice_sig, e.m_ssplice_sig, 0, false); in MapOneModelToOrigContig()
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H A Dasn1.cpp470 ggap = model.Exons()[i-1].m_ssplice_sig == "XX" || model.Exons()[i].m_fsplice_sig == "XX"; in ModelMethod()
736 se->SetDonor_after_exon().SetBases(e.m_ssplice_sig); in spliced_exon()
738 se->SetAcceptor_before_exon().SetBases(e.m_ssplice_sig); in spliced_exon()
H A Dannot.cpp620 if(ie->m_fsplice_sig == "XX" || ie->m_ssplice_sig == "XX") in Predict()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/gnomon/
H A Dgnomon_model.hpp186 …m_fsplice(fs), m_ssplice(ss), m_fsplice_sig(fsig), m_ssplice_sig(ssig), m_ident(ident), m_seq(seq)… in CModelExon()
211 string m_fsplice_sig, m_ssplice_sig; // obeys strand member in CModelExon
414 …f_sig, const string& s_sig) { m_exons[i].m_fsplice_sig = f_sig; m_exons[i].m_ssplice_sig = s_sig; } in SetSplices()