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Searched refs:CResidueVec (Results 1 – 16 of 16) sorted by relevance

/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/
H A Dgnomon_engine.hpp49 …SGnomonEngineImplData(CConstRef<CHMMParameters> hmm_params, CResidueVec&& sequence, TSignedSeqRang…
50 …SGnomonEngineImplData(CConstRef<CHMMParameters> hmm_params, const CResidueVec& sequence, TSignedSe…
53 CResidueVec m_seq;
H A Dgnomon_seq.hpp55 void Convert(const CResidueVec& src, CEResidueVec& dst);
56 void Convert(const CEResidueVec& src, CResidueVec& dst);
57 void Convert(const CResidueVec& src, CDoubleStrandSeq& dst);
H A Dgnomon_engine.cpp48 (CConstRef<CHMMParameters> hmm_params, CResidueVec&& sequence, TSignedSeqRange range) : m_seq(move(… in BEGIN_SCOPE()
51 (CConstRef<CHMMParameters> hmm_params, const CResidueVec& sequence, TSignedSeqRange range) : m_seq(… in SGnomonEngineImplData()
55 CGnomonEngine::CGnomonEngine(CConstRef<CHMMParameters> hmm_params, CResidueVec&& sequence, TSignedS… in CGnomonEngine()
64 CGnomonEngine::CGnomonEngine(CConstRef<CHMMParameters> hmm_params, const CResidueVec& sequence, TSi… in CGnomonEngine()
146 const CResidueVec& CGnomonEngine::GetSeq() const in GetSeq()
H A Dscore.hpp56 void Init(CResidueVec& original_sequence, bool leftwall,
118 …CResidueVec ConstructSequenceAndMaps(const TGeneModelList& aligns, const CResidueVec& original_seq…
H A Dgnomon_seq.cpp42 void Convert(const CResidueVec& src, CEResidueVec& dst) in Convert()
51 void Convert(const CResidueVec& src, CDoubleStrandSeq& dst) in Convert()
57 void Convert(const CEResidueVec& src, CResidueVec& dst) in Convert()
676 void CAlignMap::EditedSequence<CResidueVec>(const CResidueVec& original_sequence, CResidueVec& edit…
H A Dgnomon_objmgr.cpp474 string CGeneModel::GetCdsDnaSequence (const CResidueVec& contig_sequence) const in GetCdsDnaSequence()
486 CResidueVec mrna; in GetCdsDnaSequence()
498 string CGeneModel::GetProtein (const CResidueVec& contig_sequence) const in GetProtein()
520 string CGeneModel::GetProtein (const CResidueVec& contig_sequence, const CGenetic_code* gencode) co… in GetProtein()
H A Dscore.cpp162 CResidueVec CSeqScores::ConstructSequenceAndMaps(const TGeneModelList& aligns, const CResidueVec& o… in ConstructSequenceAndMaps()
172 CResidueVec sequence; in ConstructSequenceAndMaps()
272 void CSeqScores::Init( CResidueVec& original_sequence, bool leftwall, bool rightwall, double consen… in Init()
275 CResidueVec sequence = ConstructSequenceAndMaps(m_align_list,original_sequence); in Init()
H A Dchainer.cpp3296 const CResidueVec& contig = m_gnomon->GetSeq(); in MakeChains()
3425 const CResidueVec& contig = m_gnomon->GetSeq(); in MakeChains()
3984 const CResidueVec& contig = m_gnomon->GetSeq(); in SetFlagsForChains()
5042 CResidueVec mrna; in SetConfirmedEnds()
5118 CResidueVec block_of_As; in ValidPolyA()
6288 const CResidueVec& contig = m_gnomon->GetSeq(); in FindSelenoproteinsClipProteinsToStartStop()
6315 CResidueVec mrna; in FindSelenoproteinsClipProteinsToStartStop()
6600 const CResidueVec& seq;
6670 CResidueVec cds; in transform_align()
8015 CResidueVec seq; in SetGenomic()
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H A Dannot.cpp725 RemoveTrailingNs::RemoveTrailingNs(const CResidueVec& _seq) in RemoveTrailingNs()
733 CResidueVec vec; in transform_model()
H A Dasn1.cpp105 …CImplementationData(const string& contig_name, const CResidueVec& seq, IEvidence& evdnc, int genet…
177 …ementationData::CImplementationData(const string& a_contig_name, const CResidueVec& seq, IEvidence… in CImplementationData()
200 CAnnotationASN1::CAnnotationASN1(const string& contig_name, const CResidueVec& seq, IEvidence& evdn… in CAnnotationASN1()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/gnomon/
H A Dgnomon.hpp73 …CGnomonEngine(CConstRef<CHMMParameters> hmm_params, const CResidueVec& sequence, TSignedSeqRange r…
74 …CGnomonEngine(CConstRef<CHMMParameters> hmm_params, CResidueVec&& sequence, TSignedSeqRange range …
80 const CResidueVec& GetSeq() const;
H A Dannot.hpp130 RemoveTrailingNs(const CResidueVec& seq);
134 const CResidueVec& seq;
H A Dasn1.hpp62 CAnnotationASN1(const string& contig_name, const CResidueVec& seq, IEvidence& evidence,
H A Dgnomon_model.hpp70 typedef vector<TResidue> CResidueVec; typedef
549 string GetCdsDnaSequence (const CResidueVec& contig_sequence) const;
550 string GetProtein (const CResidueVec& contig_sequence) const;
551 string GetProtein (const CResidueVec& contig_sequence, const CGenetic_code* gencode) const;
H A Dchainer.hpp120 void SetGenomic(const CResidueVec& seq);
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/demo/
H A Dlocal_finder.cpp139 CResidueVec seq; in Run()