Home
last modified time | relevance | path

Searched refs:m_fsplice_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.cpp187 if(it->m_fsplice_sig != "XX") in ReverseComplementModel()
188 ReverseComplement(it->m_fsplice_sig.begin(),it->m_fsplice_sig.end()); in ReverseComplementModel()
778 MyExons()[i].m_fsplice_sig.clear(); in CutExons()
852 e->m_fsplice_sig.clear(); in Clip()
1121 e.m_fsplice_sig = "XX"; in AddGgapExon()
1153 MyExons().front().m_fsplice_sig = "XX"; in AddNormalExon()
1174 if(e.m_fsplice && !e.m_fsplice_sig.empty()) in Extend()
1175 m_fsplice_sig = e.m_fsplice_sig; in Extend()
2113 if(!e->m_fsplice_sig.empty() || !e->m_ssplice_sig.empty()) { in printGFF3()
2115 if(!e->m_fsplice_sig.empty()) in printGFF3()
[all …]
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()
697 exons[ie].m_fsplice_sig.clear(); in CleanSelfTranscript()
825 e.m_fsplice_sig.clear(); in CleanSelfTranscript()
865 edited_exons[piece_begin].m_fsplice_sig = "NN"; in CleanSelfTranscript()
882 edited_exons[piece_begin].m_fsplice_sig = splice; in CleanSelfTranscript()
926 editedmodel.AddExon(e.Limits(), e.m_fsplice_sig, e.m_ssplice_sig, e.m_ident); in CleanSelfTranscript()
2049 if(exons.back().m_fsplice_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()
[all …]
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()
1031 if(!algn.HasStop() && algn.Exons().back().m_fsplice_sig != "XX") in Init()
1059 if(!algn.HasStart() && algn.Exons().back().m_fsplice_sig != "XX") in Init()
1223 if(exons[i].m_fsplice && exons[i].m_fsplice_sig != "XX") { in SelectBestReadingFrame()
1258 if(exons[i].m_fsplice && exons[i].m_fsplice_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()
4199 e->m_fsplice_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()
6827 if(align.Exons().back().m_fsplice_sig == "XX") in TrimTranscript()
7561 model.AddNormalExon(exon, e.m_fsplice_sig, e.m_ssplice_sig, 0, false); in MapOneModelToOrigContig()
[all …]
H A Dasn1.cpp470 ggap = model.Exons()[i-1].m_ssplice_sig == "XX" || model.Exons()[i].m_fsplice_sig == "XX"; in ModelMethod()
728 se->SetAcceptor_before_exon().SetBases(e.m_fsplice_sig); in spliced_exon()
730 se->SetDonor_after_exon().SetBases(e.m_fsplice_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 …void SetSplices(int i, const string& f_sig, const string& s_sig) { m_exons[i].m_fsplice_sig = f_si… in SetSplices()