| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/gnomon/ |
| H A D | aligncollapser.hpp | 84 CAlignModel GetAlignment(const SAlignIndividual& ali, const deque<char>& target_id_pool) const;
128 void AddAlignment(CAlignModel& align);
193 void CleanSelfTranscript(CAlignModel& align, const string& trans) const;
194 … void CleanExonEdge(int ie, CAlignModel& align, const string& transcript, bool right_edge) const;
195 CAlignModel FillGapsInAlignmentAndAddToGenomicGaps(const CAlignModel& align, int fill);
196 bool CheckAndInsert(const CAlignModel& align, TAlignModelClusterSet& clsset) const;
197 void ClipProteinToStartStop(CAlignModel& align);
198 bool RemoveNotSupportedIntronsFromProt(CAlignModel& align);
199 …bool RemoveNotSupportedIntronsFromTranscript(CAlignModel& align, bool check_introns_on_both_strand…
200 void ClipNotSupportedFlanks(CAlignModel& align, double clip_threshold);
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| H A D | chainer.hpp | 98 void operator()(CAlignModel& a) { transform_align(a); } in operator ()()
101 virtual void transform_align(CAlignModel& a) { transform_model(a); } in transform_align()
107 bool operator()(CAlignModel& a) { return align_predicate(a); } in operator ()()
110 virtual bool align_predicate(CAlignModel& a) { return model_predicate(a); } in align_predicate()
149 CAlignModel MapOneModelToEditedContig(const CGeneModel& align) const;
226 virtual void transform_align(CAlignModel& align);
233 virtual void transform_align(CAlignModel& align);
264 virtual void transform_align(CAlignModel& align);
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| H A D | asn1.hpp | 46 virtual const CAlignModel* GetModel(Int8 id) = 0;
53 virtual const CAlignModel* GetNext() =0;
67 void AddModel(const CAlignModel& model);
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| H A D | gnomon_model.hpp | 98 class CAlignModel;
735 class NCBI_XALGOGNOMON_EXPORT CAlignModel : public CGeneModel { class
737 CAlignModel() {} in CAlignModel() function in CAlignModel
738 CAlignModel(const objects::CSeq_align& seq_align);
739 CAlignModel(const CGeneModel& g, const CAlignMap& a);
779 NCBI_XALGOGNOMON_EXPORT CNcbiIstream& operator>>(CNcbiIstream& s, CAlignModel& a);
780 NCBI_XALGOGNOMON_EXPORT CNcbiOstream& operator<<(CNcbiOstream& s, const CAlignModel& a);
811 typedef CModelCluster<CAlignModel> TAlignModelCluster;
814 typedef list<CAlignModel> TAlignModelList;
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| H A D | variations.hpp | 107 …void AddAlignment(const CAlignModel& align); // adds each exon as a separate CLiteAlign; doesn't d…
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/ |
| H A D | asn1.cpp | 74 CAlignModel model;
108 void AddModel(const CAlignModel& model);
216 void CAnnotationASN1::AddModel(const CAlignModel& model) in AddModel()
398 if (m && (m->Type()&(CAlignModel::eChain|CAlignModel::eGnomon))!=0) { in ExpandSupport()
434 const CAlignModel* m = evidence.GetModel(id); in DumpEvidence()
521 const CAlignModel* m = evidence.GetModel(id); in create_ModelEvidence_user_object()
640 const CAlignModel& model = md.model; in create_internal_feature()
775 if (model.Status() & CAlignModel::ePolyA) { in AlignModelToSeqalign()
939 CAlignModel model = *this; in MakeSeqAlign()
987 const CAlignModel& model = md.model; in model2spliced_seq_align()
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| H A D | aligncollapser.cpp | 104 CAlignModel align(a, amap); in GetAlignment()
559 CAlignModel a = align; in RemoveNotSupportedIntronsFromTranscript()
992 CAlignModel& align = *i; in FilterAlignments()
1333 CAlignModel& align = *i; in FilterAlignments()
1336 CAlignModel a = align; in FilterAlignments()
1419 CAlignModel& align = *i; in FilterAlignments()
1448 CAlignModel& align = *i; in FilterAlignments()
1473 CAlignModel a = align; in FilterAlignments()
1638 CAlignModel& align = *i; in FilterAlignments()
2011 CAlignModel& align = *ia; in GetCollapsedAlgnments()
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| H A D | chainer.cpp | 79 typedef map<Int8,CAlignModel*> TOrigAligns;
268 CAlignModel* m_orig_align;
3947 const CAlignModel& align = *it->second; in SetFlagsForChains()
3962 const CAlignModel& align = *it->second; in SetFlagsForChains()
6035 bool operator()(const CAlignModel* a, const CAlignModel* b) in operator ()()
6162 vector<CAlignModel*> alignment_ptrs; in OverlapsSameAccessionAlignment()
6210 CAlignModel& algnj = *jtcl; in FindMultiplyIncluded()
6697 align = CAlignModel(b, b.GetAlignMap()); in transform_align()
6959 CAlignModel& algn = *i; in SetConfirmedStartStopForProteinAlignments()
7726 return CAlignModel(); in MapOneModelToEditedContig()
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| H A D | gnomon_model.cpp | 196 CAlignModel::CAlignModel(const CGeneModel& g, const CAlignMap& a) in CAlignModel() function in CAlignModel
224 void CAlignModel::ResetAlignMap() in ResetAlignMap()
230 void CAlignModel::RecalculateAlignMap(int left, int right) { in RecalculateAlignMap()
251 string CAlignModel::TargetAccession() const { in TargetAccession()
1410 int CAlignModel::PolyALen() const { in PolyALen()
2024 CNcbiOstream& printGFF3(CNcbiOstream& os, CAlignModel a) in printGFF3()
2220 CNcbiIstream& readGFF3(CNcbiIstream& is, CAlignModel& align) in readGFF3()
2366 align = CAlignModel(a, amap); in readGFF3()
2411 return operator<<(s, CAlignModel(a, a.GetAlignMap())); in operator <<()
2414 CNcbiOstream& operator<<(CNcbiOstream& os, const CAlignModel& a) in operator <<()
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| H A D | variations.cpp | 198 void CMultAlign::AddAlignment(const CAlignModel& align) { in AddAlignment()
265 aligns.push_back(CAlignModel(a, a.GetAlignMap())); in GetVariationAlignList()
286 aligns.push_back(CAlignModel(a, a.GetAlignMap())); in GetVariationAlignList()
312 aligns.push_back(CAlignModel(a, a.GetAlignMap())); in GetVariationAlignList()
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| H A D | annot.cpp | 757 m.Clip(new_lim,CAlignModel::eDontRemoveExons); in transform_model()
763 CAlignModel* a = dynamic_cast<CAlignModel*>(&m); in transform_model()
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| H A D | gnomon_objmgr.cpp | 75 CAlignModel::CAlignModel(const CSeq_align& seq_align) : in CAlignModel() function in CAlignModel
363 Clip(newlimits,CAlignModel::eRemoveExons); in CAlignModel()
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| /dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/demo/ |
| H A D | local_finder.cpp | 149 CAlignModel algn; in Run()
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