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Searched refs:CGeneModel (Results 1 – 21 of 21) sorted by relevance

/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/gnomon/
H A Dannot.hpp117 double ExtendJustThisChain(CGeneModel& chain, TSignedSeqPos left, TSignedSeqPos right);
132 virtual void transform_model(CGeneModel& a);
139 static bool CanBeConnectedIntoOne(const CGeneModel& a, const CGeneModel& b);
140 static size_t CountCommonSplices(const CGeneModel& a, const CGeneModel& b);
141 static bool AreSimilar(const CGeneModel& a, const CGeneModel& b, int tolerance);
142 static bool BadOverlapTest(const CGeneModel& a, const CGeneModel& b);
143 …static bool RangeNestedInIntron(TSignedSeqRange r, const CGeneModel& algn, bool check_in_holes = t…
144 static bool HaveCommonExonOrIntron(const CGeneModel& a, const CGeneModel& b);
H A Dchainer.hpp75 (__first)->Status() |= CGeneModel::eSkipped; in remove_if()
100 virtual void transform_model(CGeneModel& /*a*/) {} in transform_model()
150 CGeneModel MapOneModelToOrigContig(const CGeneModel& srcmodel) const;
241 virtual bool model_predicate(CGeneModel& align);
245 virtual bool model_predicate(CGeneModel& align);
251 virtual bool model_predicate(CGeneModel& align);
257 virtual bool model_predicate(CGeneModel& align);
268 virtual bool model_predicate(CGeneModel& align);
272 virtual bool model_predicate(CGeneModel& align);
276 virtual bool model_predicate(CGeneModel& align);
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H A Dgnomon_model.hpp357 class NCBI_XALGOGNOMON_EXPORT CGeneModel class
398 virtual ~CGeneModel() {} in ~CGeneModel()
445 void SetCdsInfo(const CGeneModel& a);
562 bool operator==(const CGeneModel& a) const in operator ==()
748 CGeneModel::CutExons(hole); in CutExons()
813 typedef list<CGeneModel> TGeneModelList;
900 m.Status() &= ~CGeneModel::ePolyA; in GetAlignParts()
901 m.Status() &= ~CGeneModel::eCap; in GetAlignParts()
914 m.Status() &= ~CGeneModel::ePolyA; in GetAlignParts()
915 m.Status() &= ~CGeneModel::eCap; in GetAlignParts()
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H A Dgnomon.hpp88 void GetScore(CGeneModel& model, bool extend5p = false, bool obeystart = false) const;
89 …double SelectBestReadingFrame(const CGeneModel& model, const CEResidueVec& mrna, const CAlignMap& …
101 list<CGeneModel> GetGenes() const;
103 TSignedSeqPos PartialModelStepBack(list<CGeneModel>& genes) const;
H A Daligncollapser.hpp49 if(align.Status()&CGeneModel::eChangedByFilter) in SAlignIndividual()
82 CAlignCommon(const CGeneModel& align);
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/
H A Dannot.cpp67 bool s_AlignScoreOrder(const CGeneModel& ap, const CGeneModel& bp) in s_AlignScoreOrder()
114 if ((it->Type() & (CGeneModel::eWall | CGeneModel::eNested))==0 && in TryWithoutObviouslyBadAlignments()
142 if((it->Type() & (CGeneModel::eWall | CGeneModel::eNested))!=0) { in TryToEliminateOneAlignment()
146 CGeneModel algn = *it; in TryToEliminateOneAlignment()
330 bool s_AlignSeqOrder(const CGeneModel& ap, const CGeneModel& bp) in s_AlignSeqOrder()
345 if (wall_model.get() != 0 && wall_model->Type() == CGeneModel::eWall+CGeneModel::eGnomon) { in SaveWallModel()
357 auto_ptr<CGeneModel> wall_model; in FindPartials()
378 … CGeneModel new_nested_wall(ir->Strand(),ir->ID(),CGeneModel::eNested+CGeneModel::eGnomon); in FindPartials()
389 … wall_model.reset( new CGeneModel(ir->Strand(),ir->ID(),CGeneModel::eWall+CGeneModel::eGnomon)); in FindPartials()
612 CGeneModel& model = *im; in Predict()
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H A Daligncollapser.cpp57 CGeneModel a(isPlus() ? ePlus : eMinus, 0, isEST() ? CGeneModel::eEST : CGeneModel::eSR); in GetAlignment()
61 a.Status() |= CGeneModel::eCap; in GetAlignment()
135 if(align.Type()&CGeneModel::eSR) in CAlignCommon()
137 if(align.Type()&CGeneModel::eEST) in CAlignCommon()
548 CGeneModel editedmodel = align; in RemoveNotSupportedIntronsFromTranscript()
1355 if(align.Type()&(CGeneModel::emRNA|CGeneModel::eProt)) { in FilterAlignments()
1875 bool operator() (const CGeneModel::TExons& a, const CGeneModel::TExons& b) const { in operator ()()
2089 if((guest.Status()&CGeneModel::eCap) || (host.Status()&CGeneModel::eCap)) { in GetCollapsedAlgnments()
2307 CGeneModel galign(a.Strand(), a.ID(), CGeneModel::eSR); in AddAlignment()
2337 if((align.Type()&CGeneModel::eNotForChaining) && !(align.Status()&CGeneModel::eGapFiller)) in AddAlignment()
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H A Dgnomon_model.cpp729 void CGeneModel::SetCdsInfo(const CGeneModel& a) in SetCdsInfo()
735 void CGeneModel::CombineCdsInfo(const CGeneModel& a, bool ensure_cds_invariant) in CombineCdsInfo()
942 int CGeneModel::MutualExtension(const CGeneModel& a) const in MutualExtension()
949 …if((Status()&(CGeneModel::eLeftFlexible|CGeneModel::eRightFlexible)) == 0 && (a.Status()&(CGeneMod… in MutualExtension()
964 …} else if((Status()&(CGeneModel::eLeftFlexible|CGeneModel::eRightFlexible)) != (a.Status()&(CGeneM… in MutualExtension()
971 int CGeneModel::isCompatible(const CGeneModel& a) const in isCompatible()
1060 bool CGeneModel::IsSubAlignOf(const CGeneModel& a) const in IsSubAlignOf()
1104 void CGeneModel::AddHole() in AddHole()
1224 void CGeneModel::Extend(const CGeneModel& align, bool ensure_cds_invariant) in Extend()
1278 …SetType(Type() | ((CGeneModel::eProt|CGeneModel::eSR|CGeneModel::eEST|CGeneModel::emRNA|CGeneModel… in Extend()
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H A Dselect_alignments_alt.cpp45 bool CModelCompare::CanBeConnectedIntoOne(const CGeneModel& a, const CGeneModel& b) in BEGIN_SCOPE()
60 size_t CModelCompare::CountCommonSplices(const CGeneModel& a, const CGeneModel& b) { in CountCommonSplices()
76 bool CModelCompare::AreSimilar(const CGeneModel& a, const CGeneModel& b, int tolerance) in AreSimilar()
131 bool CModelCompare::BadOverlapTest(const CGeneModel& a, const CGeneModel& b) { // returns true … in BadOverlapTest()
141 bool CModelCompare::RangeNestedInIntron(TSignedSeqRange r, const CGeneModel& algn, bool check_in_ho… in RangeNestedInIntron()
153 bool CModelCompare::HaveCommonExonOrIntron(const CGeneModel& a, const CGeneModel& b) { in HaveCommonExonOrIntron()
180 CGeneModel& model = *im; in FilterGenes()
199 model.Status() |= CGeneModel::eSkipped; in FilterGenes()
205 if(it->Status()&CGeneModel::eSkipped) { in FilterGenes()
H A Dchainer.cpp245 CGeneModel* m_align;
2079 if(algn.Status()&(CGeneModel::eLeftFlexible|CGeneModel::eRightFlexible)) in CalculateSpliceWeights()
2293 if(ai.Status()&(CGeneModel::eLeftFlexible|CGeneModel::eRightFlexible)) in CanIncludeJinI()
2934 bool operator()(const CGeneModel& a, const CGeneModel& b) in operator ()()
2955 … int status = it->Status()&(CGeneModel::eLeftFlexible|CGeneModel::eCap|CGeneModel::ePolyA); in MakeChains()
2959 … int status = it->Status()&(CGeneModel::eRightFlexible|CGeneModel::eCap|CGeneModel::ePolyA); in MakeChains()
2972 CGeneModel galign(it->Strand(), it->ID(), CGeneModel::eSR); in MakeChains()
2999 CGeneModel galign(it->Strand(), it->ID(), CGeneModel::eSR); in MakeChains()
3469 bool operator()(const CGeneModel* ap, const CGeneModel* bp) in operator ()()
3746 CGeneModel palign(parts.front()->Strand(), id, CGeneModel::eProt); in CreateChainsForPartialProteins()
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H A Dscore.cpp166 const CGeneModel& align = *it; in ConstructSequenceAndMaps()
183 bool operator() (const CGeneModel& a, const CGeneModel& b) const in operator ()()
224 static bool s_AlignLeftLimitOrder(const CGeneModel& ap, const CGeneModel& bp) in s_AlignLeftLimitOrder()
239 CGeneModel& align = *it; in CSeqScores()
401 CGeneModel align = origalign; in Init()
405 if((align.Type() & CGeneModel::eNested)!=0 || (align.Type() & CGeneModel::eWall)!=0) { in Init()
409 if((aa.Type() & CGeneModel::eWall)==0 && (aa.Type() & CGeneModel::eNested)==0 && in Init()
422 if((align.Type()&CGeneModel::eWall)==0 && (align.Type()&CGeneModel::eNested)==0) { in Init()
423 CGeneModel al = align; in Init()
619 const CGeneModel& algn(*it); in Init()
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H A Dasn1.cpp281 const CGeneModel& model = md.model; in create_cdregion_feature()
407 const CGeneModel& model = md.model; in DumpEvidence()
466 string ModelMethod(const CGeneModel& model) { in ModelMethod()
472 if(model.Type()&CGeneModel::eChain) { in ModelMethod()
489 if(model.Type()&CGeneModel::eChain) { in create_ModelEvidence_user_object()
527 if (m->Type()&CGeneModel::eChain) { in create_ModelEvidence_user_object()
536 if (type&CGeneModel::eChain) { in create_ModelEvidence_user_object()
553 } else if (type&CGeneModel::eEST) { in create_ModelEvidence_user_object()
564 } else if (type&CGeneModel::eSR) { in create_ModelEvidence_user_object()
631 if(model.Status()&CGeneModel::eFullSupCDS) in create_ModelEvidence_user_object()
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H A Dparse.cpp488 CGeneModel support; in AddSupport()
490 const CGeneModel* supporting_align = NULL; in AddSupport()
493 const CGeneModel& algn(*it); in AddSupport()
495 if ((algn.Type() & (CGeneModel::eWall | CGeneModel::eNested))!=0) continue; in AddSupport()
504 gene.Status() |= CGeneModel::ePolyA; in AddSupport()
529 gene.Status() |= CGeneModel::eFullSupCDS; in AddSupport()
534 const CGeneModel& algn(*it); in AddSupport()
536 if ((algn.Type() & (CGeneModel::eWall | CGeneModel::eNested))!=0) continue; in AddSupport()
567 genes.push_front(CGeneModel(strand,0,CGeneModel::eGnomon)); in GetGenes()
568 CGeneModel& gene = genes.front(); in GetGenes()
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H A Dgnomon_objmgr.cpp92 Status() |= CGeneModel::eReversed; in CAlignModel()
375 CGeneModel::TExons::const_iterator piece_end; in CAlignModel()
379 CGeneModel::TExons::const_iterator piece_end_g = piece_end; in CAlignModel()
410 Clip(piece_range, CGeneModel::eDontRemoveExons); in CAlignModel()
447 Status() |= CGeneModel::ePolyA; in CAlignModel()
460 Status() |= CGeneModel::eBestPlacement; in CAlignModel()
462 Status() |= CGeneModel::eUnknownOrientation; in CAlignModel()
474 string CGeneModel::GetCdsDnaSequence (const CResidueVec& contig_sequence) const in GetCdsDnaSequence()
479 CAlignMap amap = CGeneModel::GetAlignMap(); in GetCdsDnaSequence()
498 string CGeneModel::GetProtein (const CResidueVec& contig_sequence) const in GetProtein()
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H A Dparse.hpp53 list<CGeneModel> GetGenes() const;
H A Dgnomon_engine.cpp191 list<CGeneModel> CGnomonEngine::GetGenes() const in GetGenes()
198 TSignedSeqPos CGnomonEngine::PartialModelStepBack(list<CGeneModel>& genes) const in PartialModelStepBack()
H A Dgnomon_seq.hpp103 void FindStartsStops(const CGeneModel& model, const CEResidueVec& contig_seq, const CEResidueVec& m…
H A Dvariations.cpp263 CGeneModel a(ePlus, 0, CGeneModel::eSR); in GetVariationAlignList()
282 CGeneModel a(ePlus, 0, CGeneModel::eSR); in GetVariationAlignList()
308 CGeneModel a(ePlus, 0, CGeneModel::eSR); in GetVariationAlignList()
H A Dgnomon_seq.cpp182 void FindStartsStops(const CGeneModel& model, const CEResidueVec& contig_seq, const CEResidueVec& m… in FindStartsStops()
504 CAlignMap::CAlignMap(const CGeneModel::TExons& exons, const vector<TSignedSeqRange>& transcript_exo… in CAlignMap()
561 CAlignMap::CAlignMap(const CGeneModel::TExons& exons, const TInDels& indels, EStrand strand, TSigne… in CAlignMap()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/sequence/
H A Dgene_model.hpp232 class NCBI_XALGOSEQ_EXPORT CGeneModel class
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/sequence/
H A Dgene_model.cpp85 void CGeneModel::CreateGeneModelFromAlign(const CSeq_align& align_in, in CreateGeneModelFromAlign()
100 void CGeneModel::CreateGeneModelsFromAligns(const list< CRef<objects::CSeq_align> > &aligns, in CreateGeneModelsFromAligns()
114 void CGeneModel::SetFeatureExceptions(CSeq_feat& feat, in SetFeatureExceptions()
131 void CGeneModel::SetPartialFlags(CScope& scope, in SetPartialFlags()
140 void CGeneModel::RecomputePartialFlags(CScope& scope, in RecomputePartialFlags()