/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/gnomon/ |
H A D | annot.hpp | 70 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, [all …]
|
H A D | chainer.hpp | 121 …, 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 D | gnomon.hpp | 95 …double Run(const TGeneModelList& chains, bool leftwall, bool rightwall, bool leftanchor, bool righ…
|
H A D | gnomon_model.hpp | 813 typedef list<CGeneModel> TGeneModelList; typedef
|
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/ |
H A D | annot.cpp | 82 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() [all …]
|
H A D | select_alignments_alt.cpp | 176 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 D | score.hpp | 54 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 D | gnomon_engine.cpp | 158 TGeneModelList cls; in Run() 167 double CGnomonEngine::Run(const TGeneModelList& cls, in Run()
|
H A D | chainer.cpp | 95 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() [all …]
|
H A D | parse.cpp | 486 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 D | score.cpp | 162 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 D | gnomon_objmgr.cpp | 582 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 D | local_finder.cpp | 144 TGeneModelList alignments; in Run()
|