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Searched refs:CModelExon (Results 1 – 6 of 6) sorted by relevance

/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/gnomon/
H A Dgnomon_model.hpp183 class NCBI_XALGOGNOMON_EXPORT CModelExon { class
185 …CModelExon(TSignedSeqPos f = 0, TSignedSeqPos s = 0, bool fs = false, bool ss = false, const strin… in CModelExon() function in CModelExon
191 bool operator==(const CModelExon& p) const in operator ==()
195 bool operator!=(const CModelExon& p) const in operator !=()
199 bool operator<(const CModelExon& p) const { return Precede(Limits(),p.Limits()); } in operator <()
206 void Extend(const CModelExon& e);
405 typedef vector<CModelExon> TExons;
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/
H A Daligncollapser.cpp420 CModelExon exonl = align.Exons()[k-1]; in ClipNotSupportedFlanks()
421 CModelExon exonr = align.Exons()[k]; in ClipNotSupportedFlanks()
507 CModelExon exonl = align.Exons()[k-1]; in RemoveNotSupportedIntronsFromProt()
508 CModelExon exonr = align.Exons()[k]; in RemoveNotSupportedIntronsFromProt()
565 CModelExon exonl = a.Exons()[k-1]; in RemoveNotSupportedIntronsFromTranscript()
566 CModelExon exonr = a.Exons()[k]; in RemoveNotSupportedIntronsFromTranscript()
575 CModelExon exonr = a.Exons()[k]; in RemoveNotSupportedIntronsFromTranscript()
819 CModelExon e = exons[ie]; in CleanSelfTranscript()
925 CModelExon& e = edited_exons[ie]; in CleanSelfTranscript()
1857 bool OneExonCompare(const CModelExon& a, const CModelExon& b) { in OneExonCompare()
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H A Dgnomon_model.cpp238 const CModelExon& e = Exons()[ie]; in RecalculateAlignMap()
1085 CModelExon e(exon_range.GetFrom(),exon_range.GetTo(),false,false,fs,ss,ident,seq,src); in AddExon()
1114 CModelExon e(exon_range.GetFrom(),exon_range.GetTo(),false,false,"","",ident,seq,src); in AddGgapExon()
1138 CModelExon e(exon_range.GetFrom(),exon_range.GetTo(),false,false,fs,ss,ident); in AddNormalExon()
1161 void CModelExon::Extend(const CModelExon& e) in Extend()
2079 const CModelExon *e = &a.Exons()[i]; in printGFF3()
2252 vector<CModelExon> exons; in readGFF3()
2299 exons.push_back(CModelExon(r->start,r->end,false,false,fs,ss,eident)); in readGFF3()
2314 exons.push_back(CModelExon(1,-1,false,false,fs,ss,eident,r->attributes["Seq"],src)); in readGFF3()
2346 const CModelExon& e = exons[i]; in readGFF3()
H A Dasn1.cpp362 const CModelExon* e = &model.Exons()[i]; in create_packed_int_seqloc()
701 CRef<CSpliced_exon> spliced_exon (const CModelExon& e, EStrand strand) in spliced_exon()
789 const CModelExon *e = &model.Exons()[i]; in AlignModelToSeqalign()
H A Dchainer.cpp3800 CModelExon exonl = chain.Exons()[k-1]; in CreateChainsForPartialProteins()
3801 CModelExon exonr = chain.Exons()[k]; in CreateChainsForPartialProteins()
3826 CModelExon exonl = unma.Exons()[k-1]; in CreateChainsForPartialProteins()
3827 CModelExon exonr = unma.Exons()[k]; in CreateChainsForPartialProteins()
3833 CModelExon exonl = palign.Exons()[k-1]; in CreateChainsForPartialProteins()
3834 CModelExon exonr = palign.Exons()[k]; in CreateChainsForPartialProteins()
6135 const CModelExon& e = align.Exons()[i]; in FilterOutChimeras()
7476 const CModelExon& e = srcmodel.Exons()[ie]; in MapOneModelToOrigContig()
7676 const CModelExon& e = aexons[i]; in MapOneModelToEditedContig()
7957 const CModelExon& e = i->Exons()[ie]; in SetGenomic()
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H A Dscore.cpp1197 const vector<CModelExon>& exons = model.Exons(); in SelectBestReadingFrame()