NCBI C++ ToolKit
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CTwoStageNew Class Reference

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+ Inheritance diagram for CTwoStageNew:
+ Collaboration diagram for CTwoStageNew:

Public Member Functions

 CTwoStageNew (CProSplignScoring scoring, bool just_second_stage)
 
virtual CTwoStageNewclone ()
 
- Public Member Functions inherited from CTwoStage
 CTwoStage (CProSplignScoring scoring, bool just_second_stage)
 
virtual const vector< pair< int, int > > & GetExons () const
 
virtual vector< pair< int, int > > & SetExons ()
 
virtual void GetFlanks (bool &lgap, bool &rgap) const
 
virtual void SetFlanks (bool lgap, bool rgap)
 
- Public Member Functions inherited from CProSplign::CImplementation
 CImplementation (CProSplignScoring scoring)
 
virtual ~CImplementation ()
 
int FindGlobalAlignment_stage1 (CScope &scope, const CSeq_id &protein, const CSeq_loc &genomic)
 
CRef< CSeq_alignFindGlobalAlignment_stage2 ()
 
CRef< CSeq_alignFindGlobalAlignment (CScope &scope, const CSeq_id &protein, const CSeq_loc &genomic_orig)
 
bool HasStartOnNuc (const CSpliced_seg &sps)
 
bool HasStopOnNuc (const CSpliced_seg &sps)
 
void SeekStartStop (CSeq_align &seq_align)
 
const CProSplignScaledScoringGetScaleScoring () const
 
const CSubstMatrixGetSubstMatrix () const
 
void Interrupt (void)
 
void SetInterruptCallback (CProSplign::TInterruptFnPtr prg_callback, void *data)
 
void SetScope (CScope &scope)
 
void SetTranslationTable (int gcode)
 

Private Member Functions

virtual int stage1 ()
 
virtual void stage2 (CAli &ali)
 

Additional Inherited Members

- Static Public Member Functions inherited from CProSplign::CImplementation
static CImplementationcreate (CProSplignScoring scoring, bool intronless, bool one_stage, bool just_second_stage, bool old)
 
- Protected Attributes inherited from CTwoStage
bool m_just_second_stage
 
vector< pair< int, int > > m_igi
 
bool m_lgap
 
bool m_rgap
 
- Protected Attributes inherited from CProSplign::CImplementation
CProSplignScaledScoring m_scoring
 
CSubstMatrix m_matrix
 
CScopem_scope
 
const CSeq_idm_protein
 
CRef< CSeq_locm_genomic
 
shared_ptr< CPSeqm_protseq
 
shared_ptr< CNSeqm_cnseq
 
CProSplignInterrupt m_Interrupt
 

Detailed Description

Definition at line 904 of file prosplign.cpp.

Constructor & Destructor Documentation

◆ CTwoStageNew()

CTwoStageNew::CTwoStageNew ( CProSplignScoring  scoring,
bool  just_second_stage 
)
inline

Definition at line 906 of file prosplign.cpp.

Referenced by clone().

Member Function Documentation

◆ clone()

virtual CTwoStageNew* CTwoStageNew::clone ( )
inlinevirtual

Implements CProSplign::CImplementation.

Definition at line 907 of file prosplign.cpp.

References CTwoStageNew().

◆ stage1()

int CTwoStageNew::stage1 ( )
privatevirtual

◆ stage2()

void CTwoStageNew::stage2 ( CAli ali)
privatevirtual

The documentation for this class was generated from the following file:
Modified on Fri Sep 20 14:57:58 2024 by modify_doxy.py rev. 669887