NCBI C++ ToolKit
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CNgAligner Class Reference

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#include <algo/align/ngalign/ngalign.hpp>

+ Collaboration diagram for CNgAligner:

Public Member Functions

 CNgAligner (objects::CScope &Scope, objects::CGC_Assembly *GenColl=NULL, bool AllowDupes=false)
 
virtual ~CNgAligner ()
 
void SetQuery (ISequenceSet *Set)
 
void SetSubject (ISequenceSet *Set)
 
void AddFilter (IAlignmentFilter *Filter)
 
void AddAligner (IAlignmentFactory *Aligner)
 
void AddScorer (IAlignmentScorer *Scorer)
 
TAlignSetRef Align ()
 

Protected Member Functions

virtual TAlignSetRef x_Align_Impl ()
 

Private Types

typedef list< CIRef< IAlignmentFilter > > TFilters
 
typedef list< CIRef< IAlignmentFactory > > TFactories
 
typedef list< CIRef< IAlignmentScorer > > TScorers
 

Private Member Functions

 CNgAligner (const CNgAligner &)
 
CNgAligneroperator= (const CNgAligner &)
 

Private Attributes

CRef< objects::CScope > m_Scope
 
bool m_AllowDupes
 
CRef< objects::CGC_Assembly > m_GenColl
 
CIRef< ISequenceSetm_Query
 
CIRef< ISequenceSetm_Subject
 
TFilters m_Filters
 
TFactories m_Aligners
 
TScorers m_Scorers
 

Detailed Description

Definition at line 61 of file ngalign.hpp.

Member Typedef Documentation

◆ TFactories

Definition at line 94 of file ngalign.hpp.

◆ TFilters

typedef list<CIRef<IAlignmentFilter> > CNgAligner::TFilters
private

Definition at line 93 of file ngalign.hpp.

◆ TScorers

typedef list<CIRef<IAlignmentScorer> > CNgAligner::TScorers
private

Definition at line 95 of file ngalign.hpp.

Constructor & Destructor Documentation

◆ CNgAligner() [1/2]

CNgAligner::CNgAligner ( objects::CScope &  Scope,
objects::CGC_Assembly *  GenColl = NULL,
bool  AllowDupes = false 
)

◆ ~CNgAligner()

CNgAligner::~CNgAligner ( )
virtual

Definition at line 72 of file ngalign.cpp.

◆ CNgAligner() [2/2]

CNgAligner::CNgAligner ( const CNgAligner )
private

Member Function Documentation

◆ AddAligner()

void CNgAligner::AddAligner ( IAlignmentFactory Aligner)

◆ AddFilter()

void CNgAligner::AddFilter ( IAlignmentFilter Filter)

◆ AddScorer()

void CNgAligner::AddScorer ( IAlignmentScorer Scorer)

◆ Align()

TAlignSetRef CNgAligner::Align ( )

◆ operator=()

CNgAligner& CNgAligner::operator= ( const CNgAligner )
private

◆ SetQuery()

void CNgAligner::SetQuery ( ISequenceSet Set)

◆ SetSubject()

void CNgAligner::SetSubject ( ISequenceSet Set)

◆ x_Align_Impl()

TAlignSetRef CNgAligner::x_Align_Impl ( )
protectedvirtual

Member Data Documentation

◆ m_Aligners

TFactories CNgAligner::m_Aligners
private

Definition at line 97 of file ngalign.hpp.

Referenced by AddAligner(), and x_Align_Impl().

◆ m_AllowDupes

bool CNgAligner::m_AllowDupes
private

Definition at line 87 of file ngalign.hpp.

Referenced by x_Align_Impl().

◆ m_Filters

TFilters CNgAligner::m_Filters
private

Definition at line 96 of file ngalign.hpp.

Referenced by AddFilter(), and x_Align_Impl().

◆ m_GenColl

CRef<objects::CGC_Assembly> CNgAligner::m_GenColl
private

Definition at line 88 of file ngalign.hpp.

Referenced by x_Align_Impl().

◆ m_Query

CIRef<ISequenceSet> CNgAligner::m_Query
private

Definition at line 90 of file ngalign.hpp.

Referenced by SetQuery(), and x_Align_Impl().

◆ m_Scope

CRef<objects::CScope> CNgAligner::m_Scope
private

Definition at line 86 of file ngalign.hpp.

Referenced by x_Align_Impl().

◆ m_Scorers

TScorers CNgAligner::m_Scorers
private

Definition at line 98 of file ngalign.hpp.

Referenced by AddScorer(), and x_Align_Impl().

◆ m_Subject

CIRef<ISequenceSet> CNgAligner::m_Subject
private

Definition at line 91 of file ngalign.hpp.

Referenced by SetSubject(), and x_Align_Impl().


The documentation for this class was generated from the following files:
Modified on Tue Jun 18 13:40:32 2024 by modify_doxy.py rev. 669887