CGffFeatureContext Class Reference

Search Toolkit Book for CGffFeatureContext

#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
CGffFeatureContext &	operator= (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

Definition at line 51 of file feature_context.hpp.

References xAssignSequenceHasBioSource(), and xAssignSequenceIsGenomicRecord().

CGffFeatureContext() [3/3]

CGffFeatureContext::CGffFeatureContext ( const CGffFeatureContext &  other )

inline

Definition at line 66 of file feature_context.hpp.

References xAssignSequenceHasBioSource(), and xAssignSequenceIsGenomicRecord().

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(), CGff2Writer::HasAccaptableTranscriptParent(), CGff2Writer::xGenerateMissingTranscript(), CGtfWriter::xGenericGeneId(), and CGtfWriter::xWriteRecordsCds().

FindBestGeneParent()

CMappedFeat CGffFeatureContext::FindBestGeneParent

(

const CMappedFeat &

mf

)

Definition at line 770 of file write_util.cpp.

References CSeqFeatData::eSubtype_mobile_element, CSeqFeatData::eSubtype_mRNA, GetBestGeneForFeat(), GetBestGeneForMrna(), CSeq_feat_Handle::GetFeatSubtype(), m_ft, m_mfLastIn, and m_mfLastOut.

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

Definition at line 729 of file write_util.cpp.

References CSeq_descr_Base::CanGet(), CSeq_descr_Base::Get(), CBioseq_Handle::GetDescr(), CBioseq_set_Handle::GetDescr(), CBioseq_Handle::GetParentBioseq_set(), CBioseq_Handle::IsSetDescr(), CBioseq_set_Handle::IsSetDescr(), CSeqdesc_Base::IsSource(), m_bSequenceHasBioSource, and m_bsh.

Referenced by CGffFeatureContext().

xAssignSequenceIsGenomicRecord()

void CGffFeatureContext::xAssignSequenceIsGenomicRecord ( )

protected

Definition at line 694 of file write_util.cpp.

References CSeq_descr_Base::CanGet(), CMolInfo_Base::eBiomol_cRNA, CMolInfo_Base::eBiomol_genomic, CSeq_descr_Base::Get(), CMolInfo_Base::GetBiomol(), CBioseq_Handle::GetDescr(), CSeqdesc_Base::GetMolinfo(), CSeqdesc_Base::IsMolinfo(), CMolInfo_Base::IsSetBiomol(), CBioseq_Handle::IsSetDescr(), m_bSequenceIsGenomicRecord, and m_bsh.

Referenced by CGffFeatureContext().

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

Definition at line 95 of file feature_context.hpp.

Referenced by BioseqHandle(), xAssignSequenceHasBioSource(), and xAssignSequenceIsGenomicRecord().

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().

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The documentation for this class was generated from the following files:

• include/objtools/writers/feature_context.hpp
• src/objtools/writers/write_util.cpp