CGenbankIdResolve Class Reference

Search Toolkit Book for CGenbankIdResolve

#include <objtools/writers/genbank_id_resolve.hpp>

Collaboration diagram for CGenbankIdResolve:

Public Member Functions
	~CGenbankIdResolve ()
void	SetThrowOnUnresolvedGi (bool doThrow)
void	SetLabelType (CSeq_id::ELabelType labelType)
bool	GetBestId (CSeq_id_Handle, CScope &, string &)
bool	GetBestId (const CMappedFeat &, string &)
bool	GetBestId (const CSeq_loc &, string &)

Static Public Member Functions
static CGenbankIdResolve &	Get ()

Private Member Functions
	CGenbankIdResolve ()
CScope &	xGetDefaultScope ()

Private Attributes
CRef< CScope >	mpDefaultScope
bool	mThrowOnUnresolvedGi
CSeq_id::ELabelType	mLabelType

Detailed Description

Definition at line 47 of file genbank_id_resolve.hpp.

Constructor & Destructor Documentation

~CGenbankIdResolve()

CGenbankIdResolve::~CGenbankIdResolve

(

)

Definition at line 50 of file genbank_id_resolve.cpp.

CGenbankIdResolve()

CGenbankIdResolve::CGenbankIdResolve ( )

private

Definition at line 43 of file genbank_id_resolve.cpp.

Member Function Documentation

Get()

CGenbankIdResolve & CGenbankIdResolve::Get ( void  )

static

Definition at line 56 of file genbank_id_resolve.cpp.

Referenced by CBedFeatureRecord::AssignLocation(), CAlnWriter::CAlnWriter(), CAlnWriter::GetBestId(), CWriteUtil::GetBestId(), CGffIdGenerator::GetGffSourceId(), CBedFeatureRecord::SetLocation(), CVcfWriter::x_WriteFeatureChrom(), CGff2Writer::xAssignFeatureAttributeProduct(), CGff2Writer::xAssignFeatureAttributeProteinId(), CGff3Writer::xAssignFeatureAttributeTranscriptId(), CGtfWriter::xAssignFeatureAttributeTranscriptId(), CGff2Writer::xAssignFeatureSeqId(), CGff3Writer::xAssignSourceSeqId(), CGffIdGenerator::xExtractFeatureLocation(), CPslRecord::xInitializeSequenceInfo(), CAnnotWriterApp::xSetupIdResolving(), CWiggleWriter::xTableGetChromName(), CGff3Writer::xWriteFeatureProtein(), CGff3Writer::xWriteRecord(), CGff3Writer::xWriteSequenceHeader(), CWiggleWriter::xWriteSingleGraphFixedStep(), CWiggleWriter::xWriteTableBedStyle(), CWiggleWriter::xWriteTableFixedStep(), and CWiggleWriter::xWriteTableVariableStep().

GetBestId() [1/3]

bool CGenbankIdResolve::GetBestId	(	const CMappedFeat &	mf,
		string &	best_id
	)

Definition at line 95 of file genbank_id_resolve.cpp.

References GetBestId(), GetIdHandle(), CMappedFeat::GetLocation(), CMappedFeat::GetLocationId(), and CSeq_feat_Handle::GetScope().

GetBestId() [2/3]

bool CGenbankIdResolve::GetBestId	(	const CSeq_loc &	loc,
		string &	best_id
	)

Definition at line 110 of file genbank_id_resolve.cpp.

References GetBestId(), CSeq_id_Handle::GetHandle(), CSeq_loc::GetId(), NCBI_THROW, and xGetDefaultScope().

GetBestId() [3/3]

bool CGenbankIdResolve::GetBestId	(	CSeq_id_Handle	idh,
		CScope &	scope,
		string &	best_id
	)

Definition at line 64 of file genbank_id_resolve.cpp.

References eGetId_Best, CSeq_id_Handle::GetGi(), GetId(), CSeq_id::GetLabel(), CSeq_id_Handle::GetSeqId(), CSeq_id_Handle::IsGi(), mLabelType, mThrowOnUnresolvedGi, NCBI_THROW, and NStr::NumericToString().

Referenced by CBedFeatureRecord::AssignLocation(), GetBestId(), CAlnWriter::GetBestId(), CWriteUtil::GetBestId(), CGffIdGenerator::GetGffSourceId(), CVcfWriter::x_WriteFeatureChrom(), CGff3Writer::xAssignSourceSeqId(), CPslRecord::xInitializeSequenceInfo(), CWiggleWriter::xTableGetChromName(), CGff3Writer::xWriteFeatureProtein(), CWiggleWriter::xWriteSingleGraphFixedStep(), CWiggleWriter::xWriteTableBedStyle(), CWiggleWriter::xWriteTableFixedStep(), and CWiggleWriter::xWriteTableVariableStep().

SetLabelType()

void CGenbankIdResolve::SetLabelType ( CSeq_id::ELabelType  labelType )

inline

Definition at line 61 of file genbank_id_resolve.hpp.

References mLabelType.

Referenced by CAlnWriter::CAlnWriter().

SetThrowOnUnresolvedGi()

void CGenbankIdResolve::SetThrowOnUnresolvedGi ( bool  doThrow )

inline

Definition at line 57 of file genbank_id_resolve.hpp.

References mThrowOnUnresolvedGi.

Referenced by CAnnotWriterApp::xSetupIdResolving().

xGetDefaultScope()

CScope & CGenbankIdResolve::xGetDefaultScope ( )

private

Definition at line 127 of file genbank_id_resolve.cpp.

References CScope::AddDefaults(), CObjectManager::GetInstance(), mpDefaultScope, and CRef< C, Locker >::Reset().

Referenced by GetBestId().

Member Data Documentation

mLabelType

CSeq_id::ELabelType CGenbankIdResolve::mLabelType

private

Definition at line 89 of file genbank_id_resolve.hpp.

Referenced by GetBestId(), and SetLabelType().

mpDefaultScope

CRef<CScope> CGenbankIdResolve::mpDefaultScope

private

Definition at line 87 of file genbank_id_resolve.hpp.

Referenced by xGetDefaultScope().

mThrowOnUnresolvedGi

bool CGenbankIdResolve::mThrowOnUnresolvedGi

private

Definition at line 88 of file genbank_id_resolve.hpp.

Referenced by GetBestId(), and SetThrowOnUnresolvedGi().

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

• include/objtools/writers/genbank_id_resolve.hpp
• src/objtools/writers/genbank_id_resolve.cpp