Searched refs:CAligner (Results 1 – 9 of 9) sorted by relevance
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/oligofar/ |
H A D | caligner.hpp | 17 class CAligner : public IAligner, public CTrBase class 20 CAligner( CScoringFactory * sf ) : in CAligner() function in CAligner 41 ~CAligner(); 223 static map<double,Uint8> CAligner::s_maxPenalty; 226 inline void CAligner::AppendTranscriptItem( const TTrItem& u ) in AppendTranscriptItem() 243 inline void CAligner::SetPenaltyLimit( double l ) { m_penaltyLimit = l; } in SetPenaltyLimit() 245 inline void CAligner::SetQueryStrand( CSeqCoding::EStrand s ) { m_qryStrand = s; } in SetQueryStrand() 253 inline void CAligner::SetSubjectGuideTranscript( const TTranscript& tr ) in SetSubjectGuideTranscript() 269 inline const CAligner::CCell& CAligner::GetMatrix( int q, int s ) const in GetMatrix() 274 inline const CAligner::CCell& CAligner::SetMatrix( int q, int s, double v, CCell::EEvent e, int cnt… in SetMatrix() [all …]
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H A D | caligner.cpp | 8 map<double,Uint8> CAligner::s_maxPenalty; 10 CAligner::~CAligner() in ~CAligner() 14 void CAligner::PrintStatistics( ostream& out ) in PrintStatistics()
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H A D | caligner-align.cpp | 12 inline void CAligner::AdjustMatrixSize() in AdjustMatrixSize() 26 bool CAligner::Align() in Align() 269 void CAligner::x_ColorspaceUpdatePenalty() in x_ColorspaceUpdatePenalty()
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H A D | caligner-alignwindow.cpp | 43 bool CAligner::AlignWindow( const char * & q, const char * & Q, const char * & s, const char * & S,… in AlignWindow() 165 void CAligner::AdjustWindowBoundary( const char * & q, const char * & Q, const char * & s, const ch… in AdjustWindowBoundary()
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H A D | caligner-aligntaildiag.cpp | 8 bool CAligner::AlignTailDiag( int size, int qdir, double pm, const char * qseq, const char * sseq, … in AlignTailDiag()
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H A D | caligner-aligntail.cpp | 9 void CAligner::MakeLocalSpliceSet( CIntron::TSet& iSet, int qdir, int qpos ) const in MakeLocalSpliceSet() 31 bool CAligner::AlignTail( int size, int qdir, const char * qseq, const char * sseq, int& qe, int& s… in AlignTail()
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H A D | caligner-aligndiag.cpp | 8 bool CAligner::AlignDiag( const char * q, const char * Q, const char * s, const char * S, bool reve… in AlignDiag()
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H A D | caligner-alignwintwodiag.cpp | 8 bool CAligner::AlignWinTwoDiag( in AlignWinTwoDiag()
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H A D | coligofarapp.cpp | 689 CAligner aligner( &scoringFactory ); in ProcessData()
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