NCBI C++ ToolKit
Public Member Functions | Static Public Member Functions | Protected Attributes | Private Member Functions | List of all members
CProSplign::CImplementation Class Referenceabstract

Search Toolkit Book for CProSplign::CImplementation

+ Inheritance diagram for CProSplign::CImplementation:
+ Collaboration diagram for CProSplign::CImplementation:

Public Member Functions

 CImplementation (CProSplignScoring scoring)
 
virtual ~CImplementation ()
 
virtual CImplementation * clone ()=0
 
int FindGlobalAlignment_stage1 (CScope &scope, const CSeq_id &protein, const CSeq_loc &genomic)
 
CRef< CSeq_align > FindGlobalAlignment_stage2 ()
 
CRef< CSeq_align > FindGlobalAlignment (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 CProSplignScaledScoring & GetScaleScoring () const
 
const CSubstMatrix & GetSubstMatrix () const
 
virtual const vector< pair< int, int > > & GetExons () const
 
virtual vector< pair< int, int > > & SetExons ()
 
virtual void GetFlanks (bool &, bool &) const
 
virtual void SetFlanks (bool, bool)
 
void Interrupt (void)
 
void SetInterruptCallback (CProSplign::TInterruptFnPtr prg_callback, void *data)
 
void SetScope (CScope &scope)
 
void SetTranslationTable (int gcode)
 

Static Public Member Functions

static CImplementation * create (CProSplignScoring scoring, bool intronless, bool one_stage, bool just_second_stage, bool old)
 

Protected Attributes

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
 

Private Member Functions

virtual int stage1 ()=0
 
virtual void stage2 (CAli &ali)=0
 

Detailed Description

Definition at line 756 of file prosplign.cpp.

Constructor & Destructor Documentation

◆ CImplementation()

CProSplign::CImplementation::CImplementation ( CProSplignScoring  scoring)
inline

Definition at line 759 of file prosplign.cpp.

◆ ~CImplementation()

virtual CProSplign::CImplementation::~CImplementation ( )
inlinevirtual

Definition at line 761 of file prosplign.cpp.

Member Function Documentation

◆ clone()

virtual CImplementation* CProSplign::CImplementation::clone ( )
pure virtual

Implemented in CIntronlessNew, CIntronlessOld, CTwoStageNew, CTwoStageOld, and COneStage.

◆ create()

CProSplign::CImplementation * CProSplign::CImplementation::create ( CProSplignScoring  scoring,
bool  intronless,
bool  one_stage,
bool  just_second_stage,
bool  old 
)
static

Definition at line 1011 of file prosplign.cpp.

◆ FindGlobalAlignment()

CRef<CSeq_align> CProSplign::CImplementation::FindGlobalAlignment ( CScope &  scope,
const CSeq_id &  protein,
const CSeq_loc &  genomic_orig 
)
inline

Definition at line 768 of file prosplign.cpp.

References FindGlobalAlignment_stage1(), and FindGlobalAlignment_stage2().

◆ FindGlobalAlignment_stage1()

int CProSplign::CImplementation::FindGlobalAlignment_stage1 ( CScope &  scope,
const CSeq_id &  protein,
const CSeq_loc &  genomic 
)

Definition at line 1190 of file prosplign.cpp.

References CSeq_loc::Assign(), CProSplignOptions_Base::GetAltStarts(), CScope::GetBioseqHandle(), COrg_ref::GetGcode(), GetOrg_ref(), m_cnseq, m_genomic, m_matrix, m_protein, m_protseq, m_scope, m_scoring, CRef< C, Locker >::Reset(), CSubstMatrix::SetTranslationTable(), and stage1().

Referenced by FindGlobalAlignment().

◆ FindGlobalAlignment_stage2()

CRef< CSeq_align > CProSplign::CImplementation::FindGlobalAlignment_stage2 ( )

Definition at line 1210 of file prosplign.cpp.

References CSeq_align_Base::eType_disc, CSeq_align_Base::GetSegs(), CSeq_align_Base::C_Segs::GetSpliced(), CAliToSeq_align::MakeSeq_align(), and CSeq_align_Base::SetType().

Referenced by FindGlobalAlignment().

◆ GetExons()

virtual const vector<pair<int, int> >& CProSplign::CImplementation::GetExons ( void  ) const
inlinevirtual

Reimplemented in CTwoStage.

Definition at line 790 of file prosplign.cpp.

References NCBI_THROW.

◆ GetFlanks()

virtual void CProSplign::CImplementation::GetFlanks ( bool &  ,
bool &   
) const
inlinevirtual

Reimplemented in CTwoStage.

Definition at line 798 of file prosplign.cpp.

References NCBI_THROW.

◆ GetScaleScoring()

const CProSplignScaledScoring& CProSplign::CImplementation::GetScaleScoring ( ) const
inline

Definition at line 780 of file prosplign.cpp.

References m_scoring.

◆ GetSubstMatrix()

const CSubstMatrix& CProSplign::CImplementation::GetSubstMatrix ( ) const
inline

Definition at line 785 of file prosplign.cpp.

References m_matrix.

◆ HasStartOnNuc()

bool CProSplign::CImplementation::HasStartOnNuc ( const CSpliced_seg &  sps)

Definition at line 1265 of file prosplign.cpp.

References CSeq_id::Assign(), buf, CBioseq_Handle::eCoding_Iupac, CSpliced_exon_chunk_Base::GetDiag(), CSpliced_seg_Base::GetExons(), CProt_pos::GetFrame(), CSpliced_exon_Base::GetGenomic_end(), CSpliced_seg_Base::GetGenomic_id(), CSpliced_exon_Base::GetGenomic_start(), CSpliced_seg_Base::GetGenomic_strand(), CSpliced_exon_chunk_Base::GetMatch(), CSpliced_exon_chunk_Base::GetMismatch(), CSpliced_exon_Base::GetParts(), CSpliced_exon_Base::GetProduct_start(), CProduct_pos_Base::GetProtpos(), CSeqVector_CI::GetSeqData(), CSpliced_exon_chunk_Base::IsDiag(), CSpliced_exon_chunk_Base::IsGenomic_ins(), CSpliced_exon_chunk_Base::IsMatch(), CSpliced_exon_chunk_Base::IsMismatch(), CSpliced_exon_chunk_Base::IsProduct_ins(), and len.

◆ HasStopOnNuc()

bool CProSplign::CImplementation::HasStopOnNuc ( const CSpliced_seg &  sps)

Definition at line 1306 of file prosplign.cpp.

References CSeq_id::Assign(), buf, CBioseq_Handle::eCoding_Iupac, eNa_strand_minus, eNa_strand_plus, CSpliced_seg_Base::GetExons(), CProt_pos::GetFrame(), CSpliced_exon_Base::GetGenomic_end(), CSpliced_seg_Base::GetGenomic_id(), CSpliced_exon_Base::GetGenomic_start(), CSpliced_seg_Base::GetGenomic_strand(), GetLength(), CSpliced_exon_Base::GetProduct_end(), CProduct_pos_Base::GetProtpos(), and CSeqVector_CI::GetSeqData().

◆ Interrupt()

void CProSplign::CImplementation::Interrupt ( void  )
inline

Definition at line 807 of file prosplign.cpp.

References CProSplignInterrupt::Interrupt(), and m_Interrupt.

◆ SeekStartStop()

void CProSplign::CImplementation::SeekStartStop ( CSeq_align &  seq_align)

Definition at line 1344 of file prosplign.cpp.

References _ASSERT, CSeq_id::Assign(), CProt_pos_Base::GetAmin(), CSpliced_seg_Base::GetModifiers(), CSpliced_seg_Base::GetProduct_id(), CSpliced_exon_Base::GetProduct_start(), CProduct_pos_Base::GetProtpos(), CPSeq::HasStart(), CSpliced_seg_Base::IsSetModifiers(), len, CRef< C, Locker >::Reset(), CSpliced_seg_Base::ResetModifiers(), CSpliced_seg_Base::SetExons(), CSpliced_seg_Base::SetModifiers(), CSpliced_exon_Base::SetParts(), and CSeq_align_Base::SetSegs().

◆ SetExons()

virtual vector<pair<int, int> >& CProSplign::CImplementation::SetExons ( void  )
inlinevirtual

Reimplemented in CTwoStage.

Definition at line 794 of file prosplign.cpp.

References NCBI_THROW.

◆ SetFlanks()

virtual void CProSplign::CImplementation::SetFlanks ( bool  ,
bool   
)
inlinevirtual

Reimplemented in CTwoStage.

Definition at line 802 of file prosplign.cpp.

References NCBI_THROW.

◆ SetInterruptCallback()

void CProSplign::CImplementation::SetInterruptCallback ( CProSplign::TInterruptFnPtr  prg_callback,
void *  data 
)
inline

Definition at line 812 of file prosplign.cpp.

References data, m_Interrupt, and CProSplignInterrupt::SetInterruptCallback().

◆ SetScope()

void CProSplign::CImplementation::SetScope ( CScope &  scope)
inline

Definition at line 817 of file prosplign.cpp.

References m_scope.

◆ SetTranslationTable()

void CProSplign::CImplementation::SetTranslationTable ( int  gcode)
inline

Definition at line 820 of file prosplign.cpp.

References CProSplignOptions_Base::GetAltStarts(), m_matrix, m_scoring, and CSubstMatrix::SetTranslationTable().

◆ stage1()

virtual int CProSplign::CImplementation::stage1 ( )
privatepure virtual

Implemented in CIntronlessNew, CIntronlessOld, CTwoStageNew, CTwoStageOld, and COneStage.

Referenced by FindGlobalAlignment_stage1().

◆ stage2()

virtual void CProSplign::CImplementation::stage2 ( CAli &  ali)
privatepure virtual

Implemented in CIntronless, CTwoStageNew, CTwoStageOld, and COneStage.

Member Data Documentation

◆ m_cnseq

shared_ptr<CNSeq> CProSplign::CImplementation::m_cnseq
protected

Definition at line 835 of file prosplign.cpp.

Referenced by FindGlobalAlignment_stage1(), COneStage::stage1(), CTwoStageOld::stage1(), CTwoStageNew::stage1(), CIntronlessOld::stage1(), CIntronlessNew::stage1(), CTwoStageOld::stage2(), and CTwoStageNew::stage2().

◆ m_genomic

CRef<CSeq_loc> CProSplign::CImplementation::m_genomic
protected

Definition at line 833 of file prosplign.cpp.

Referenced by FindGlobalAlignment_stage1().

◆ m_Interrupt

CProSplignInterrupt CProSplign::CImplementation::m_Interrupt
protected

Definition at line 837 of file prosplign.cpp.

Referenced by Interrupt(), SetInterruptCallback(), COneStage::stage1(), CTwoStageOld::stage1(), CTwoStageNew::stage1(), CIntronlessOld::stage1(), CIntronlessNew::stage1(), CTwoStageOld::stage2(), and CTwoStageNew::stage2().

◆ m_matrix

CSubstMatrix CProSplign::CImplementation::m_matrix
protected

Definition at line 829 of file prosplign.cpp.

Referenced by FindGlobalAlignment_stage1(), GetSubstMatrix(), SetTranslationTable(), COneStage::stage1(), CTwoStageOld::stage1(), CTwoStageNew::stage1(), CIntronlessOld::stage1(), CIntronlessNew::stage1(), CTwoStageOld::stage2(), and CTwoStageNew::stage2().

◆ m_protein

const CSeq_id* CProSplign::CImplementation::m_protein
protected

Definition at line 832 of file prosplign.cpp.

Referenced by FindGlobalAlignment_stage1().

◆ m_protseq

shared_ptr<CPSeq> CProSplign::CImplementation::m_protseq
protected

Definition at line 834 of file prosplign.cpp.

Referenced by FindGlobalAlignment_stage1(), COneStage::stage1(), CTwoStageOld::stage1(), CTwoStageNew::stage1(), CIntronlessOld::stage1(), CIntronlessNew::stage1(), CTwoStageOld::stage2(), and CTwoStageNew::stage2().

◆ m_scope

CScope* CProSplign::CImplementation::m_scope
protected

Definition at line 831 of file prosplign.cpp.

Referenced by FindGlobalAlignment_stage1(), and SetScope().

◆ m_scoring

CProSplignScaledScoring CProSplign::CImplementation::m_scoring
protected

Definition at line 828 of file prosplign.cpp.

Referenced by FindGlobalAlignment_stage1(), GetScaleScoring(), SetTranslationTable(), COneStage::stage1(), CTwoStageOld::stage1(), CTwoStageNew::stage1(), CIntronlessOld::stage1(), CIntronlessNew::stage1(), CTwoStageOld::stage2(), and CTwoStageNew::stage2().

The documentation for this class was generated from the following file:
Generated by doxygen 1.9.0
Modified on Fri Sep 20 14:57:23 2024 by modify_doxy.py rev. 669887