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Searched refs:TGeneModelList (Results 1 – 13 of 13) sorted by relevance

/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/gnomon/
H A Dannot.hpp70 void FilterGenes(TGeneModelList& chains, TGeneModelList& bad_aligns,
71 TGeneModelList& dest);
83 TGeneModelList FilterGenes(TGeneModelList& chains, TGeneModelList& bad_aligns);
95 void Predict(TGeneModelList& models, TGeneModelList& bad_aligns);
96 …void Predict(TGeneModelList& models, TGeneModelList& bad_aligns, TSignedSeqPos left, TSignedSeqPos…
104 …Predict(TSignedSeqPos llimit, TSignedSeqPos rlimit, TGeneModelList::const_iterator il, TGeneModelL…
105 TGeneModelList& models,
107 TGeneModelList& bad_aligns);
109 …double TryWithoutObviouslyBadAlignments(TGeneModelList& aligns, TGeneModelList& suspect_aligns, TG…
113 double TryToEliminateOneAlignment(TGeneModelList& suspect_aligns, TGeneModelList& bad_aligns,
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H A Dchainer.hpp121 …, objects::CScope& scope, const string& mask_annots = kEmptyStr, const TGeneModelList* models = 0);
142 void MapModelsToEditedContig(TGeneModelList& models) const;
143 void MapModelsToOrigContig(TGeneModelList& models) const;
194 void DropAlignmentInfo(TAlignModelList& alignments, TGeneModelList& models);
195 void FilterOutChimeras(TGeneModelList& clust);
196 void ScoreCDSes_FilterOutPoorAlignments(TGeneModelList& clust);
197 void FindSelenoproteinsClipProteinsToStartStop(TGeneModelList& clust);
198 void CutParts(TGeneModelList& models);
199 TGeneModelList MakeChains(TGeneModelList& models, bool coding_estimates_only = false);
H A Dgnomon.hpp95 …double Run(const TGeneModelList& chains, bool leftwall, bool rightwall, bool leftanchor, bool righ…
H A Dgnomon_model.hpp813 typedef list<CGeneModel> TGeneModelList; typedef
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/
H A Dannot.cpp82 TGeneModelList test_align; in ExtendJustThisChain()
92 …otator::TryWithoutObviouslyBadAlignments(TGeneModelList& aligns, TGeneModelList& suspect_aligns, T… in TryWithoutObviouslyBadAlignments()
137 double CGnomonAnnotator::TryToEliminateOneAlignment(TGeneModelList& suspect_aligns, TGeneModelList&… in TryToEliminateOneAlignment()
186 …Pos llimit, TSignedSeqPos rlimit, TGeneModelList::const_iterator il, TGeneModelList::const_iterato… in Predict()
189 TGeneModelList aligns(il, ir); in Predict()
206 TGeneModelList suspect_aligns; in Predict()
354 void FindPartials(TGeneModelList& models, TGeneModelList& aligns, EStrand strand) in FindPartials()
411 void CGnomonAnnotator::Predict(TGeneModelList& models, TGeneModelList& bad_aligns) in Predict()
563 TGeneModelList nested; in Predict()
661 TGeneModelList aligns; in Predict()
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H A Dselect_alignments_alt.cpp176 void CGeneSelector::FilterGenes(TGeneModelList& chains, TGeneModelList& bad_aligns, in FilterGenes()
177 TGeneModelList& dest) in FilterGenes()
179 NON_CONST_ITERATE(TGeneModelList, im, chains) { in FilterGenes()
204 ITERATE(TGeneModelList, it, chains) { in FilterGenes()
214 TGeneModelList CGeneSelector::FilterGenes(TGeneModelList& chains, TGeneModelList& bad_aligns) in FilterGenes()
216 TGeneModelList models; in FilterGenes()
H A Dscore.hpp54 TSignedSeqPos from, TSignedSeqPos to, const TGeneModelList& cls,
76 const TGeneModelList& Alignments() const { return m_align_list; } in Alignments()
106 TGeneModelList m_align_list;
118 …CResidueVec ConstructSequenceAndMaps(const TGeneModelList& aligns, const CResidueVec& original_seq…
H A Dgnomon_engine.cpp158 TGeneModelList cls; in Run()
167 double CGnomonEngine::Run(const TGeneModelList& cls, in Run()
H A Dchainer.cpp95 TGeneModelList MakeChains(TGeneModelList& models, bool coding_estimates_only);
101 void CutParts(TGeneModelList& clust);
120 …void SplitAlignmentsByStrand(const TGeneModelList& clust, TGeneModelList& clust_plus, TGeneModelLi…
213 TGeneModelList CChainer::MakeChains(TGeneModelList& models, bool coding_estimates_only) in MakeChains()
2944 TGeneModelList CChainer::CChainerImpl::MakeChains(TGeneModelList& clust, bool coding_estimates_only) in MakeChains()
3236 TGeneModelList chains; in MakeChains()
3324 TGeneModelList unma_aligns; in MakeChains()
3417 TGeneModelList chains; in MakeChains()
3864 TGeneModelList unmacl; in CreateChainsForPartialProteins()
6084 ITERATE(TGeneModelList, it, clust) { in FilterOutChimeras()
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H A Dparse.cpp486 void AddSupport(const TGeneModelList& align_list, TSignedSeqRange inside_range, CGeneModel& gene, T… in AddSupport()
492 ITERATE(TGeneModelList, it, align_list) { in AddSupport()
533 ITERATE(TGeneModelList, it, align_list) { in AddSupport()
546 TGeneModelList CParse::GetGenes() const in GetGenes()
548 TGeneModelList genes; in GetGenes()
H A Dscore.cpp162 CResidueVec CSeqScores::ConstructSequenceAndMaps(const TGeneModelList& aligns, const CResidueVec& o… in ConstructSequenceAndMaps()
165 ITERATE(TGeneModelList, it, aligns) { in ConstructSequenceAndMaps()
233 …TSignedSeqPos from, TSignedSeqPos to, const TGeneModelList& cls, const TInDels& initial_fshifts, d… in CSeqScores()
238 NON_CONST_ITERATE(TGeneModelList, it, m_align_list) { in CSeqScores()
395 ITERATE(TGeneModelList, it, m_align_list) { in Init()
406 ITERATE(TGeneModelList, jt, m_align_list) { in Init()
H A Dgnomon_objmgr.cpp582 TGeneModelList genes = GetGenes(); in GetAnnot()
592 ITERATE (TGeneModelList, it, genes) { in GetAnnot()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/demo/
H A Dlocal_finder.cpp144 TGeneModelList alignments; in Run()