/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/oligofar/ |
H A D | cseqcoding.hpp | 29 enum EStrand { enum in CSeqCoding 34 friend EStrand operator ^ ( EStrand a, EStrand b ) { return EStrand( int(a) ^ int(b) ); } in operator ^() 51 CIupacnaBase Get( EStrand strand ) const { return strand == eStrand_neg ? Complement() : *this; } in Get() 113 CNcbi8naBase( char c, EStrand strand = eStrand_pos ); 114 CNcbi8naBase( int c, EStrand strand = eStrand_pos ); 115 CNcbi8naBase( unsigned int c, EStrand strand = eStrand_pos ); 174 CColorTwoBase( char c, EStrand ) : m_base( c ) {} in CColorTwoBase() argument 176 CColorTwoBase( const char * c, EStrand ) : m_base( *c ) {} in CColorTwoBase() argument 340 inline CNcbi8naBase::CNcbi8naBase( char c, EStrand strand ) : m_base( c ) in CNcbi8naBase() 345 inline CNcbi8naBase::CNcbi8naBase( int c, EStrand strand ) : m_base( c ) in CNcbi8naBase() [all …]
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H A D | csnpdb.hpp | 61 enum EStrand { enum in CSnpDbCreator 69 …bool Insert( const string& fullId, int pos, double a, double c, double g, double t, EStrand strand… 70 …bool Insert( const string& fullId, int pos, unsigned base = 0x0f, EStrand strand = eStrand_forward…
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H A D | cscoringfactory.hpp | 17 static unsigned Sel( CSeqCoding::ECoding c, CSeqCoding::EStrand s, EConvertionTable t ) in Sel() 20 void SetSubjectStrand( CSeqCoding::EStrand s ) { m_sel = ( m_sel & ~1 ) | s; } in SetSubjectStrand() 25 CSeqCoding::EStrand GetSubjectStrand() const { return CSeqCoding::EStrand( m_sel & 1 ); } in GetSubjectStrand()
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H A D | ialigner.hpp | 29 virtual void SetQueryStrand( CSeqCoding::EStrand ) = 0; 30 virtual void SetSubjectStrand( CSeqCoding::EStrand ) = 0;
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H A D | caligner.hpp | 46 virtual void SetQueryStrand( CSeqCoding::EStrand ); 47 virtual void SetSubjectStrand( CSeqCoding::EStrand ); 183 CSeqCoding::EStrand m_qryStrand; 184 CSeqCoding::EStrand m_sbjStrand; 245 inline void CAligner::SetQueryStrand( CSeqCoding::EStrand s ) { m_qryStrand = s; } in SetQueryStrand() 247 inline void CAligner::SetSubjectStrand( CSeqCoding::EStrand s ) { m_sbjStrand = s; } in SetSubjectStrand()
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H A D | cquery.hpp | 89 …ostream& PrintIupac( ostream& dest, int component, CSeqCoding::EStrand = CSeqCoding::eStrand_pos )… 91 …ostream& PrintSeq( ostream& out, int component, CSeqCoding::EStrand = CSeqCoding::eStrand_pos ) co… 93 Iter Export( Iter dest, int component, CSeqCoding::EStrand = CSeqCoding::eStrand_pos ) const; 95 ostream& PrintDibaseAsIupac( ostream& dest, int component, CSeqCoding::EStrand ) const; 345 inline ostream& CQuery::PrintIupac( ostream& dest, int component, CSeqCoding::EStrand strand ) cons… in PrintIupac() 357 inline ostream& CQuery::PrintSeq( ostream& out, int component, CSeqCoding::EStrand strand ) const in PrintSeq() 364 inline Iter CQuery::Export( Iter dest, int component, CSeqCoding::EStrand strand ) const in Export() 374 inline ostream& CQuery::PrintDibaseAsIupac( ostream& dest, int component, CSeqCoding::EStrand stran… in PrintDibaseAsIupac()
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H A D | tseqref.hpp | 39 …static CSeqCoding::EStrand GetStrand() { return incr < 0 ? CSeqCoding::eStrand_neg : CSeqCoding::e… in GetStrand() 44 Base GetBase( CSeqCoding::EStrand strand ) const { return Base( m_ptr, strand ); } in GetBase()
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H A D | creadtagger.hpp | 90 ETagValue ProcessClippedRead( const char * iupac, int len, CSeqCoding::EStrand ); 91 …essClippedRead( const vector<char>& ncbi8na, const CBitmaskAccess& bmaccess, CSeqCoding::EStrand );
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H A D | csnpdb.cpp | 52 bool CSnpDbCreator::Insert( const string& fullId, int pos, unsigned base, EStrand strand ) in Insert() 63 …reator::Insert( const string& id, int pos, double a, double c, double g, double t, EStrand strand ) in Insert()
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H A D | csamalignments.hpp | 31 string GetIupacna( CSeqCoding::EStrand = CSeqCoding::eStrand_pos ) const; 110 …CSeqCoding::EStrand GetStrand() const { return IsReverseComplement() ? CSeqCoding::eStrand_neg : C… in GetStrand() 135 … query, CContig * subject, int from, const TTrVector& cigar, CSeqCoding::EStrand strand, int flags…
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H A D | talignerbase.hpp | 46 CSeqCoding::EStrand GetReferenceStrandForQuery( int flags ) const; 47 CSeqCoding::EStrand GetReferenceStrandForSubject( int flags ) const;
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H A D | csamformatter.hpp | 24 …* seqdata, int seqlength, const TTrSequence& tr, const char * target, CSeqCoding::EStrand strand );
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H A D | cscore-impl.hpp | 55 CSeqCoding::EStrand GetStrand() const { return CSeqCoding::eStrand_pos; } in GetStrand() 63 CSeqCoding::EStrand GetStrand() const { return CSeqCoding::eStrand_neg; } in GetStrand()
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H A D | bmfilter-main.cpp | 94 ETagValue ProcessClippedRead( const char * iupac, int len, CSeqCoding::EStrand ); 95 …essClippedRead( const vector<char>& ncbi8na, const CBitmaskAccess& bmaccess, CSeqCoding::EStrand ); 321 …TagValue CReadTagger::ProcessClippedRead( const char * iupac, int len, CSeqCoding::EStrand strand ) in ProcessClippedRead() 346 …ClippedRead( const vector<char>& read, const CBitmaskAccess& bmaccess, CSeqCoding::EStrand strand ) in ProcessClippedRead()
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H A D | coutputformatter.cpp | 274 CSeqCoding::EStrand strand = hit->GetStrand( matepair ); in CoTranslate() 346 inline char * Reverse( char * c, int cnt, CSeqCoding::EStrand s ) { in Reverse() 350 inline char * ReverseComplement( char * c, int cnt, CSeqCoding::EStrand s ) { in ReverseComplement() 367 CSeqCoding::EStrand strand = hit->GetStrand( matepair ); in CoTranslate()
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H A D | chit.hpp | 111 CSeqCoding::EStrand GetStrand( int pairmate ) const; 192 inline CSeqCoding::EStrand CHit::GetStrand( int pairmate ) const in GetStrand()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/ |
H A D | hmm.hpp | 269 CHMM_State(EStrand strn, int point, const CSeqScores& seqscr); 279 EStrand Strand() const { return m_strand; } in Strand() 300 EStrand m_strand; 324 CExon(EStrand strn, int point, int ph, const CSeqScores& seqscr, const CExonParameters& params); 353 CSingleExon(EStrand strn, int point, const CSeqScores& seqscr, const CExonParameters& params); 373 …CFirstExon(EStrand strn, int ph, int point, const CSeqScores& seqscr, const CExonParameters& param… 393 …CInternalExon(EStrand strn, int ph, int point, const CSeqScores& seqscr, const CExonParameters& pa… 410 …CLastExon(EStrand strn, int ph, int point, const CSeqScores& seqscr, const CExonParameters& params… 449 …CIntron(EStrand strn, int ph, int point, const CSeqScores& seqscr,const CIntronParameters& params); 540 …CIntergenic(EStrand strn, int point, const CSeqScores& seqscr, const CIntergenicParameters& params…
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H A D | gnomon_seq.hpp | 48 const CEResidueVec& operator[](EStrand s) const { return m_seq[s]; } in operator []() 49 CEResidueVec& operator[](EStrand s) { return m_seq[s]; } in operator []()
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H A D | hmm.cpp | 57 CHMM_State::CHMM_State(EStrand strn, int point, const CSeqScores& seqscr) in CHMM_State() 109 CExon::CExon(EStrand strn, int point, int ph, const CSeqScores& seqscr, const CExonParameters& exon… in CExon() 175 CSingleExon::CSingleExon(EStrand strn, int point, const CSeqScores& seqscr, const CExonParameters& … in CSingleExon() 201 CFirstExon::CFirstExon(EStrand strn, int ph, int point, const CSeqScores& seqscr, const CExonParame… in CFirstExon() 239 CInternalExon::CInternalExon(EStrand strn, int ph, int point, const CSeqScores& seqscr, const CExon… in CInternalExon() 272 CLastExon::CLastExon(EStrand strn, int ph, int point, const CSeqScores& seqscr, const CExonParamete… in CLastExon() 306 CIntron::CIntron(EStrand strn, int ph, int point, const CSeqScores& seqscr, const CIntronParameters… in CIntron() 340 CIntergenic::CIntergenic(EStrand strn, int point, const CSeqScores& seqscr, const CIntergenicParame… in CIntergenic()
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H A D | parse.cpp | 254 inline void s_MakeStep(const CSeqScores& seqscr, const CExonParameters& exon_params, EStrand strand… in s_MakeStep() 262 inline void s_MakeStep(const CSeqScores& seqscr, const CExonParameters& exon_params, EStrand strand… in s_MakeStep() 276 inline void s_MakeStep(const CSeqScores& seqscr, const CExonParameters& exon_params, EStrand strand… in s_MakeStep() 289 inline void s_MakeStep(const CSeqScores& seqscr, const CExonParameters& exon_params, EStrand strand… in s_MakeStep() 309 inline void s_MakeStep(const CSeqScores& seqscr, const CIntronParameters& intron_params, EStrand st… in s_MakeStep() 566 EStrand strand = g_it->back()->Strand(); in GetGenes()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objtools/eutils/api/ |
H A D | efetch.hpp | 224 enum EStrand { enum in CEFetch_Sequence_Request 231 EStrand GetStrand(void) const { return m_Strand; } in GetStrand() 232 void SetStrand(EStrand strand) { Disconnect(); m_Strand = strand; } in SetStrand() 266 EStrand m_Strand;
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/eutils/api/ |
H A D | efetch.hpp | 224 enum EStrand { enum in CEFetch_Sequence_Request 231 EStrand GetStrand(void) const { return m_Strand; } in GetStrand() 232 void SetStrand(EStrand strand) { Disconnect(); m_Strand = strand; } in SetStrand() 266 EStrand m_Strand;
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/gnomon/ |
H A D | gnomon_model.hpp | 65 enum EStrand { ePlus, eMinus}; enum 66 inline EStrand OtherStrand(EStrand s) { return (s == ePlus ? eMinus : ePlus); } in OtherStrand() 107 EStrand m_strand; 396 CGeneModel(EStrand s = ePlus, Int8 id = 0, int type = 0) : in CGeneModel() 460 void SetStrand(EStrand s) { m_strand = s; } in SetStrand() 461 EStrand Strand() const { return m_strand; } in Strand() 462 EStrand Orientation() const { in Orientation() 599 EStrand m_strand; 647 …CAlignMap(const CGeneModel::TExons& exons, const TInDels& frameshifts, EStrand strand, TSignedSeqR… 665 EStrand Orientation() const { return m_orientation; } in Orientation() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objects/macro/ |
H A D | Molinfo_field.cpp | 109 rval = CSeq_inst::ENUM_METHOD_NAME(EStrand)() in GetSequenceQualFromBioseq()
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objects/macro/ |
H A D | Molinfo_field.cpp | 109 rval = CSeq_inst::ENUM_METHOD_NAME(EStrand)() in GetSequenceQualFromBioseq()
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