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 D | gnomon_model.cpp | 187 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 D | aligncollapser.cpp | 158 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 D | score.cpp | 946 … 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 D | chainer.cpp | 465 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 D | asn1.cpp | 470 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 D | annot.cpp | 620 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 D | gnomon_model.hpp | 186 …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()
|