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Searched refs:EStrand (Results 1 – 25 of 41) sorted by relevance

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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/oligofar/
H A Dcseqcoding.hpp29 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()
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H A Dcsnpdb.hpp61 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…
H A Dcscoringfactory.hpp17 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()
H A Dialigner.hpp29 virtual void SetQueryStrand( CSeqCoding::EStrand ) = 0;
30 virtual void SetSubjectStrand( CSeqCoding::EStrand ) = 0;
H A Dcaligner.hpp46 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()
H A Dcquery.hpp89 …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()
H A Dtseqref.hpp39 …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()
H A Dcreadtagger.hpp90 ETagValue ProcessClippedRead( const char * iupac, int len, CSeqCoding::EStrand );
91 …essClippedRead( const vector<char>& ncbi8na, const CBitmaskAccess& bmaccess, CSeqCoding::EStrand );
H A Dcsnpdb.cpp52 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()
H A Dcsamalignments.hpp31 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…
H A Dtalignerbase.hpp46 CSeqCoding::EStrand GetReferenceStrandForQuery( int flags ) const;
47 CSeqCoding::EStrand GetReferenceStrandForSubject( int flags ) const;
H A Dcsamformatter.hpp24 …* seqdata, int seqlength, const TTrSequence& tr, const char * target, CSeqCoding::EStrand strand );
H A Dcscore-impl.hpp55 CSeqCoding::EStrand GetStrand() const { return CSeqCoding::eStrand_pos; } in GetStrand()
63 CSeqCoding::EStrand GetStrand() const { return CSeqCoding::eStrand_neg; } in GetStrand()
H A Dbmfilter-main.cpp94 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()
H A Dcoutputformatter.cpp274 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()
H A Dchit.hpp111 CSeqCoding::EStrand GetStrand( int pairmate ) const;
192 inline CSeqCoding::EStrand CHit::GetStrand( int pairmate ) const in GetStrand()
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/
H A Dhmm.hpp269 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…
H A Dgnomon_seq.hpp48 const CEResidueVec& operator[](EStrand s) const { return m_seq[s]; } in operator []()
49 CEResidueVec& operator[](EStrand s) { return m_seq[s]; } in operator []()
H A Dhmm.cpp57 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()
H A Dparse.cpp254 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()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objtools/eutils/api/
H A Defetch.hpp224 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;
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/eutils/api/
H A Defetch.hpp224 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;
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/algo/gnomon/
H A Dgnomon_model.hpp65 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()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objects/macro/
H A DMolinfo_field.cpp109 rval = CSeq_inst::ENUM_METHOD_NAME(EStrand)() in GetSequenceQualFromBioseq()
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objects/macro/
H A DMolinfo_field.cpp109 rval = CSeq_inst::ENUM_METHOD_NAME(EStrand)() in GetSequenceQualFromBioseq()

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