NCBI C++ ToolKit
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CGffFeatureContext Class Reference

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#include <objtools/writers/feature_context.hpp>

+ Collaboration diagram for CGffFeatureContext:

Public Member Functions

 CGffFeatureContext ()
 
 CGffFeatureContext (const CFeat_CI &feat_iter, CBioseq_Handle bsh=CBioseq_Handle(), CSeq_annot_Handle sah=CSeq_annot_Handle())
 
 CGffFeatureContext (const CGffFeatureContext &other)
 
feature::CFeatTree & FeatTree ()
 
CBioseq_Handle BioseqHandle () const
 
CSeq_annot_Handle AnnotHandle () const
 
CMappedFeat FindBestGeneParent (const CMappedFeat &mf)
 
bool IsSequenceGenomicRecord () const
 
bool HasSequenceBioSource () const
 
bool ShouldInheritPseudo () const
 
void AssignShouldInheritPseudo (bool shouldInheritPseudo)
 

Protected Member Functions

void xAssignSequenceHasBioSource ()
 
void xAssignSequenceIsGenomicRecord ()
 

Protected Attributes

feature::CFeatTree m_ft
 
CMappedFeat m_mfLastIn
 
CMappedFeat m_mfLastOut
 
CBioseq_Handle m_bsh
 
CSeq_annot_Handle m_sah
 
bool m_bSequenceHasBioSource
 
bool m_bSequenceIsGenomicRecord
 
bool mShouldInheritPseudo
 

Private Member Functions

CGffFeatureContextoperator= (const CGffFeatureContext &)
 

Detailed Description

Definition at line 44 of file feature_context.hpp.

Constructor & Destructor Documentation

◆ CGffFeatureContext() [1/3]

CGffFeatureContext::CGffFeatureContext ( )
inline

Definition at line 48 of file feature_context.hpp.

◆ CGffFeatureContext() [2/3]

CGffFeatureContext::CGffFeatureContext ( const CFeat_CI feat_iter,
CBioseq_Handle  bsh = CBioseq_Handle(),
CSeq_annot_Handle  sah = CSeq_annot_Handle() 
)
inline

◆ CGffFeatureContext() [3/3]

CGffFeatureContext::CGffFeatureContext ( const CGffFeatureContext other)
inline

Member Function Documentation

◆ AnnotHandle()

CSeq_annot_Handle CGffFeatureContext::AnnotHandle ( ) const
inline

Definition at line 81 of file feature_context.hpp.

References m_sah.

◆ AssignShouldInheritPseudo()

void CGffFeatureContext::AssignShouldInheritPseudo ( bool  shouldInheritPseudo)
inline

Definition at line 88 of file feature_context.hpp.

References mShouldInheritPseudo.

◆ BioseqHandle()

CBioseq_Handle CGffFeatureContext::BioseqHandle ( ) const
inline

Definition at line 80 of file feature_context.hpp.

References m_bsh.

◆ FeatTree()

feature::CFeatTree& CGffFeatureContext::FeatTree ( )
inline

Definition at line 79 of file feature_context.hpp.

References m_ft.

Referenced by CGtfRecord::FeatTree().

◆ FindBestGeneParent()

CMappedFeat CGffFeatureContext::FindBestGeneParent ( const CMappedFeat mf)

◆ HasSequenceBioSource()

bool CGffFeatureContext::HasSequenceBioSource ( ) const
inline

Definition at line 85 of file feature_context.hpp.

References m_bSequenceHasBioSource.

◆ IsSequenceGenomicRecord()

bool CGffFeatureContext::IsSequenceGenomicRecord ( ) const
inline

Definition at line 84 of file feature_context.hpp.

References m_bSequenceIsGenomicRecord.

◆ operator=()

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

◆ ShouldInheritPseudo()

bool CGffFeatureContext::ShouldInheritPseudo ( ) const
inline

Definition at line 87 of file feature_context.hpp.

References mShouldInheritPseudo.

◆ xAssignSequenceHasBioSource()

void CGffFeatureContext::xAssignSequenceHasBioSource ( )
protected

◆ xAssignSequenceIsGenomicRecord()

void CGffFeatureContext::xAssignSequenceIsGenomicRecord ( )
protected

Member Data Documentation

◆ m_bSequenceHasBioSource

bool CGffFeatureContext::m_bSequenceHasBioSource
protected

Definition at line 97 of file feature_context.hpp.

Referenced by HasSequenceBioSource(), and xAssignSequenceHasBioSource().

◆ m_bSequenceIsGenomicRecord

bool CGffFeatureContext::m_bSequenceIsGenomicRecord
protected

Definition at line 98 of file feature_context.hpp.

Referenced by IsSequenceGenomicRecord(), and xAssignSequenceIsGenomicRecord().

◆ m_bsh

CBioseq_Handle CGffFeatureContext::m_bsh
protected

◆ m_ft

feature::CFeatTree CGffFeatureContext::m_ft
protected

Definition at line 93 of file feature_context.hpp.

Referenced by FeatTree(), and FindBestGeneParent().

◆ m_mfLastIn

CMappedFeat CGffFeatureContext::m_mfLastIn
protected

Definition at line 94 of file feature_context.hpp.

Referenced by FindBestGeneParent().

◆ m_mfLastOut

CMappedFeat CGffFeatureContext::m_mfLastOut
protected

Definition at line 94 of file feature_context.hpp.

Referenced by FindBestGeneParent().

◆ m_sah

CSeq_annot_Handle CGffFeatureContext::m_sah
protected

Definition at line 96 of file feature_context.hpp.

Referenced by AnnotHandle().

◆ mShouldInheritPseudo

bool CGffFeatureContext::mShouldInheritPseudo
protected

Definition at line 99 of file feature_context.hpp.

Referenced by AssignShouldInheritPseudo(), and ShouldInheritPseudo().


The documentation for this class was generated from the following files:
Modified on Mon May 27 04:37:28 2024 by modify_doxy.py rev. 669887