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Searched refs:TAlignModelList (Results 1 – 9 of 9) sorted by relevance

/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/gnomon/
H A Dchainer.hpp141 void MapAlignmentsToEditedContig(TAlignModelList& alignments) const;
183 void SetGenomicRange(const TAlignModelList& alignments);
189 Predicate* OverlapsSameAccessionAlignment(TAlignModelList& alignments);
190 Predicate* ConnectsParalogs(TAlignModelList& alignments);
193 void SetConfirmedStartStopForProteinAlignments(TAlignModelList& alignments);
194 void DropAlignmentInfo(TAlignModelList& alignments, TGeneModelList& models);
H A Dasn1.hpp70 TAlignModelList& model_list,
71 TAlignModelList& evidence_models,
H A Dvariations.hpp108 TAlignModelList GetVariationAlignList(bool correctionsonly);
H A Daligncollapser.hpp207 TAlignModelList m_aligns_for_filtering_only;
H A Dgnomon_model.hpp814 typedef list<CAlignModel> TAlignModelList; typedef
939 void MapAlignsToOrigContig(TAlignModelList& aligns, const TInDels& corrections, int contig_size);
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/
H A Daligncollapser.cpp991 TAlignModelList::iterator i = it++; in FilterAlignments()
1332 TAlignModelList::iterator i = it++; in FilterAlignments()
1418 TAlignModelList::iterator i = it++; in FilterAlignments()
1447 TAlignModelList::iterator i = it++; in FilterAlignments()
1637 TAlignModelList::iterator i = it++; in FilterAlignments()
1840 …bool operator() (TAlignModelList::const_iterator a, TAlignModelList::const_iterator b) { // left … in operator ()()
1929 TAlignModelList rnaseq_or_est; in GetCollapsedAlgnments()
1996 ITERATE(TAlignModelList, ia, rnaseq_or_est) { in GetCollapsedAlgnments()
2010 NON_CONST_ITERATE(TAlignModelList, ia, rnaseq_or_est) { in GetCollapsedAlgnments()
2032 ITERATE(TAlignModelList, ia, rnaseq_or_est) { in GetCollapsedAlgnments()
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H A Dchainer.cpp90 void SetGenomicRange(const TAlignModelList& alignments);
6152 OverlapsSameAccessionAlignment(TAlignModelList& alignments);
6163 NON_CONST_ITERATE(TAlignModelList, a, alignments) { in OverlapsSameAccessionAlignment()
6199 string FindMultiplyIncluded(CAlignModel& algn, TAlignModelList& clust) in FindMultiplyIncluded()
6209 NON_CONST_ITERATE(TAlignModelList, jtcl, clust) { in FindMultiplyIncluded()
6234 ConnectsParalogs(TAlignModelList& _alignments) in ConnectsParalogs()
6237 TAlignModelList& alignments;
6248 Predicate* CChainer::ConnectsParalogs(TAlignModelList& alignments) in ConnectsParalogs()
6880 void CChainer::SetGenomicRange(const TAlignModelList& alignments) in SetGenomicRange()
6892 ITERATE(TAlignModelList, i, alignments) { in SetGenomicRange()
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H A Dvariations.cpp249 TAlignModelList CMultAlign::GetVariationAlignList(bool correctionsonly) { in GetVariationAlignList()
252 TAlignModelList aligns; in GetVariationAlignList()
H A Dasn1.cpp1188 … TAlignModelList& evidence_models, list<CRef<CSeq_align> >& evidence_alignments, in ExtractSupportModels()
1228 TAlignModelList& model_list, in ExtractModels()
1229 TAlignModelList& evidence_models, in ExtractModels()