NCBI C++ ToolKit
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Search Toolkit Book for CTwoStageNew
Private Member Functions | |
virtual int | stage1 () |
virtual void | stage2 (CAli &ali) |
Additional Inherited Members | |
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static CImplementation * | create (CProSplignScoring scoring, bool intronless, bool one_stage, bool just_second_stage, bool old) |
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bool | m_just_second_stage |
vector< pair< int, int > > | m_igi |
bool | m_lgap |
bool | m_rgap |
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CProSplignScaledScoring | m_scoring |
CSubstMatrix | m_matrix |
CScope * | m_scope |
const CSeq_id * | m_protein |
CRef< CSeq_loc > | m_genomic |
shared_ptr< CPSeq > | m_protseq |
shared_ptr< CNSeq > | m_cnseq |
CProSplignInterrupt | m_Interrupt |
Definition at line 904 of file prosplign.cpp.
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inline |
Definition at line 906 of file prosplign.cpp.
Referenced by clone().
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inlinevirtual |
Implements CProSplign::CImplementation.
Definition at line 907 of file prosplign.cpp.
References CTwoStageNew().
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privatevirtual |
Implements CProSplign::CImplementation.
Definition at line 944 of file prosplign.cpp.
References FindFGapIntronNog(), CProSplign::CImplementation::m_cnseq, CTwoStage::m_igi, CProSplign::CImplementation::m_Interrupt, CTwoStage::m_just_second_stage, CTwoStage::m_lgap, CProSplign::CImplementation::m_matrix, CProSplign::CImplementation::m_protseq, CTwoStage::m_rgap, and CProSplign::CImplementation::m_scoring.
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privatevirtual |
Implements CProSplign::CImplementation.
Definition at line 951 of file prosplign.cpp.
References FrAlignFNog1(), FrBackAlign(), CNSeq::Init(), CTBackAlignInfo< T >::Init(), CProSplign::CImplementation::m_cnseq, CTwoStage::m_igi, CProSplign::CImplementation::m_Interrupt, CTwoStage::m_lgap, CProSplign::CImplementation::m_matrix, CProSplign::CImplementation::m_protseq, CTwoStage::m_rgap, CProSplign::CImplementation::m_scoring, and CNSeq::size().