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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 Dcaligner.hpp17 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()
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H A Dcaligner.cpp8 map<double,Uint8> CAligner::s_maxPenalty;
10 CAligner::~CAligner() in ~CAligner()
14 void CAligner::PrintStatistics( ostream& out ) in PrintStatistics()
H A Dcaligner-align.cpp12 inline void CAligner::AdjustMatrixSize() in AdjustMatrixSize()
26 bool CAligner::Align() in Align()
269 void CAligner::x_ColorspaceUpdatePenalty() in x_ColorspaceUpdatePenalty()
H A Dcaligner-alignwindow.cpp43 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()
H A Dcaligner-aligntaildiag.cpp8 bool CAligner::AlignTailDiag( int size, int qdir, double pm, const char * qseq, const char * sseq, … in AlignTailDiag()
H A Dcaligner-aligntail.cpp9 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()
H A Dcaligner-aligndiag.cpp8 bool CAligner::AlignDiag( const char * q, const char * Q, const char * s, const char * S, bool reve… in AlignDiag()
H A Dcaligner-alignwintwodiag.cpp8 bool CAligner::AlignWinTwoDiag( in AlignWinTwoDiag()
H A Dcoligofarapp.cpp689 CAligner aligner( &scoringFactory ); in ProcessData()