#include <objtools/writers/gvf_writer.hpp>

Inheritance diagram for CGvfWriter:

Collaboration diagram for CGvfWriter:

Public Member Functions
	CGvfWriter (CScope &, CNcbiOstream &, unsigned int=fNormal)

	CGvfWriter (CNcbiOstream &, unsigned int=fNormal)

virtual	~CGvfWriter ()

bool	WriteHeader () override
	Write a file header. More...

bool	WriteHeader (const CSeq_annot &) override
	Write a file header, using annotation information. More...

Public Member Functions inherited from CGff3Writer
	CGff3Writer (CScope &, CNcbiOstream &, unsigned int=fNormal, bool sortAlignments=false)

	CGff3Writer (CNcbiOstream &, unsigned int=fNormal, bool sortAlignments=false)

virtual	~CGff3Writer ()=default

void	SetDefaultMethod (const string &defaultMethod)

void	SetBioseqHandle (CBioseq_Handle bsh)

bool	WriteAlign (const CSeq_align &, const string &asmblyName="", const string &asmblyAccession="") override
	Write a raw Seq-align to the internal output stream. More...

Public Member Functions inherited from CGff2Writer
	CGff2Writer (CScope &scope, CNcbiOstream &ostr, unsigned int flags=fNormal)
	Constructor. More...

	CGff2Writer (CNcbiOstream &, unsigned int=fNormal)
	Constructor. More...

virtual	~CGff2Writer ()

bool	WriteFooter () override
	Write a trailer marking the end of a parsing context. More...

virtual bool	WriteFooter (const CSeq_annot &)

bool	WriteAnnot (const CSeq_annot &annot, const string &asmblyName="", const string &asmblyAccession="") override
	Convenience function to render a "naked" Seq-annot. More...

bool	WriteAlign (const CSeq_align &, const string &asmblyName="", const string &asmblyAccession="") override
	Write a Seq-align object. More...

bool	WriteSeqEntryHandle (CSeq_entry_Handle seh, const string &asmblyName="", const string &asmblyAccession="") override
	Write Seq-entry contained in a given handle. More...

bool	WriteBioseqHandle (CBioseq_Handle bsh, const string &asmblyName="", const string &asmblyAccession="") override
	Write Bioseq contained in given handle Essentially, will write all features that live on the given Bioseq. More...

bool	WriteSeqAnnotHandle (CSeq_annot_Handle sah, const string &asmblyName="", const string &asmblyAccession="") override
	Write Seq-annot contained in given handle Essentially, write out embedded feature table. More...

Public Member Functions inherited from CWriterBase
virtual	~CWriterBase ()

void	SetMessageListener (CWriterListener *pMessageListener)

virtual void	PutMessage (const CWriterMessage &message)

virtual SAnnotSelector &	SetAnnotSelector (void)

SAnnotSelector &	GetAnnotSelector (void)

virtual CRange< TSeqPos > &	SetRange (void)

virtual const CRange< TSeqPos > &	GetRange (void) const

Public Member Functions inherited from CObject
	CObject (void)
	Constructor. More...

	CObject (const CObject &src)
	Copy constructor. More...

virtual	~CObject (void)
	Destructor. More...

CObject &	operator= (const CObject &src) THROWS_NONE
	Assignment operator. More...

bool	CanBeDeleted (void) const THROWS_NONE
	Check if object can be deleted. More...

bool	IsAllocatedInPool (void) const THROWS_NONE
	Check if object is allocated in memory pool (not system heap) More...

bool	Referenced (void) const THROWS_NONE
	Check if object is referenced. More...

bool	ReferencedOnlyOnce (void) const THROWS_NONE
	Check if object is referenced only once. More...

void	AddReference (void) const
	Add reference to object. More...

void	RemoveReference (void) const
	Remove reference to object. More...

void	ReleaseReference (void) const
	Remove reference without deleting object. More...

virtual void	DoNotDeleteThisObject (void)
	Mark this object as not allocated in heap – do not delete this object. More...

virtual void	DoDeleteThisObject (void)
	Mark this object as allocated in heap – object can be deleted. More...

void *	operator new (size_t size)
	Define new operator for memory allocation. More...

void *	operator new[] (size_t size)
	Define new[] operator for 'array' memory allocation. More...

void	operator delete (void *ptr)
	Define delete operator for memory deallocation. More...

void	operator delete[] (void *ptr)
	Define delete[] operator for memory deallocation. More...

void *	operator new (size_t size, void *place)
	Define new operator. More...

void	operator delete (void ptr, void place)
	Define delete operator. More...

void *	operator new (size_t size, CObjectMemoryPool *place)
	Define new operator using memory pool. More...

void	operator delete (void ptr, CObjectMemoryPool place)
	Define delete operator. More...

virtual void	DebugDump (CDebugDumpContext ddc, unsigned int depth) const
	Define method for dumping debug information. More...

Public Member Functions inherited from CDebugDumpable
	CDebugDumpable (void)

virtual	~CDebugDumpable (void)

void	DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const

void	DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const

void	DumpToConsole (void) const

Public Member Functions inherited from CInterruptable
	CInterruptable ()

virtual	~CInterruptable ()

void	SetCanceler (ICanceled *pCanceller)

bool	IsCanceled () const

Public Member Functions inherited from ICanceled
virtual	~ICanceled ()

Public Member Functions inherited from CAlignWriter
virtual	~CAlignWriter (void)=default

bool	WriteAlignments (CAlign_CI first)

Protected Member Functions
bool	x_WriteSeqAnnotHandle (CSeq_annot_Handle) override

bool	xWriteFeature (CGffFeatureContext &, const CMappedFeat &) override

bool	xWriteRecord (const CGffBaseRecord &) override

virtual bool	xWriteFeatureVariationRef (CGffFeatureContext &, const CMappedFeat &)

bool	xAssignFeatureAttributes (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &) override

bool	xAssignFeatureType (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &) override

bool	xAssignFeatureMethod (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &) override

Protected Member Functions inherited from CGff3Writer
bool	x_WriteBioseqHandle (CBioseq_Handle) override

virtual bool	x_WriteFeatureContext (CGffFeatureContext &)

virtual bool	xPassesFilterByViewMode (CBioseq_Handle)

virtual SAnnotSelector &	xSetJunkFilteringAnnotSelector ()

bool	xWriteAlign (const CSeq_align &, const string &="") override

virtual bool	xWriteAlignDenseg (const CSeq_align &, const string &="")

virtual bool	xWriteAlignSpliced (const CSeq_align &, const string &="")

virtual bool	xWriteAlignDisc (const CSeq_align &, const string &="")

virtual bool	xWriteSequenceHeader (CBioseq_Handle)

virtual bool	xWriteSource (CBioseq_Handle)

bool	xWriteFeature (CFeat_CI feat_it) override

virtual bool	xWriteSequence (CBioseq_Handle)

virtual bool	xWriteNucleotideSequence (CBioseq_Handle)

virtual bool	xWriteProteinSequence (CBioseq_Handle)

virtual bool	xWriteNucleotideFeature (CGffFeatureContext &, const CMappedFeat &)

virtual bool	xWriteNucleotideFeatureTransSpliced (CGffFeatureContext &, const CMappedFeat &)

virtual bool	xWriteProteinFeature (CGffFeatureContext &, const CMappedFeat &)

virtual bool	xWriteFeatureGene (CGffFeatureContext &, const CMappedFeat &)

virtual bool	xWriteFeatureRna (CGffFeatureContext &, const CMappedFeat &)

virtual bool	xWriteFeatureCds (CGffFeatureContext &, const CMappedFeat &)

virtual bool	xWriteFeatureGeneric (CGffFeatureContext &, const CMappedFeat &)

virtual bool	xWriteFeatureProtein (CGffFeatureContext &, const CMappedFeat &, const CMappedFeat &)

virtual bool	xWriteFeatureTrna (CGffFeatureContext &, const CMappedFeat &)

virtual bool	xWriteFeatureCDJVSegment (CGffFeatureContext &, const CMappedFeat &)

bool	xWriteAllChildren (CGffFeatureContext &, const CMappedFeat &) override

void	xWriteAlignment (const CGffAlignRecord &record)

virtual bool	xWriteFeatureRecords (const CGffFeatureRecord &, const CSeq_loc &, unsigned int)

bool	xSplicedSegHasProteinProd (const CSpliced_seg &spliced)

bool	xAssignAlignment (CGffFeatureRecord &)

virtual bool	xAssignAlignmentScores (CGffAlignRecord &, const CSeq_align &)

bool	xAssignAlignmentDenseg (CGffAlignRecord &, const CAlnMap &, unsigned int)

virtual bool	xAssignAlignmentDensegSeqId (CGffAlignRecord &, const CAlnMap &, unsigned int)

bool	xAssignAlignmentDensegType (CGffAlignRecord &, const CAlnMap &, unsigned int)

bool	xAssignAlignmentDensegMethod (CGffAlignRecord &, const CAlnMap &, unsigned int)

virtual bool	xAssignAlignmentDensegScores (CGffAlignRecord &, const CAlnMap &, unsigned int)

virtual bool	xAssignAlignmentDensegTarget (CGffAlignRecord &, const CAlnMap &, unsigned int)

bool	xAssignAlignmentDensegGap (CGffAlignRecord &, const CAlnMap &, unsigned int)

virtual bool	xAssignAlignmentDensegLocation (CGffAlignRecord &, const CAlnMap &, unsigned int)

bool	xAssignAlignmentSpliced (CGffAlignRecord &, const CSpliced_seg &, const CSpliced_exon &)

virtual bool	xAssignAlignmentSplicedTarget (CGffAlignRecord &, const CSpliced_seg &, const CSpliced_exon &)

bool	xAssignAlignmentSplicedPhase (CGffAlignRecord &, const CSpliced_seg &, const CSpliced_exon &)

bool	xAssignAlignmentSplicedAttributes (CGffAlignRecord &, const CSpliced_seg &, const CSpliced_exon &)

virtual bool	xAssignAlignmentSplicedGap (CGffAlignRecord &, const CSpliced_seg &, const CSpliced_exon &)

virtual bool	xAssignAlignmentSplicedScores (CGffAlignRecord &, const CSpliced_seg &, const CSpliced_exon &)

virtual bool	xAssignAlignmentSplicedLocation (CGffAlignRecord &, const CSpliced_seg &, const CSpliced_exon &)

bool	xAssignAlignmentSplicedType (CGffAlignRecord &, const CSpliced_seg &, const CSpliced_exon &)

bool	xAssignAlignmentSplicedMethod (CGffAlignRecord &, const CSpliced_seg &, const CSpliced_exon &)

virtual bool	xAssignAlignmentSplicedSeqId (CGffAlignRecord &, const CSpliced_seg &, const CSpliced_exon &)

virtual void	x_SortAlignments (TAlignCache &alignCache, CScope &scope)

bool	xAssignSource (CGff3SourceRecord &, CBioseq_Handle)

bool	xAssignSourceType (CGff3SourceRecord &)

bool	xAssignSourceSeqId (CGff3SourceRecord &, CBioseq_Handle)

bool	xAssignSourceMethod (CGff3SourceRecord &, CBioseq_Handle)

bool	xAssignSourceEndpoints (CGff3SourceRecord &, CBioseq_Handle)

bool	xAssignSourceAttributes (CGff3SourceRecord &, CBioseq_Handle)

bool	xAssignSourceAttributeGbKey (CGff3SourceRecord &)

bool	xAssignSourceAttributeMolType (CGff3SourceRecord &, CBioseq_Handle)

bool	xAssignSourceAttributeIsCircular (CGff3SourceRecord &, CBioseq_Handle)

bool	xAssignSourceAttributesBioSource (CGff3SourceRecord &, CBioseq_Handle)

bool	xAssignSourceAttributeGenome (CGff3SourceRecord &, const CBioSource &)

bool	xAssignSourceAttributeName (CGff3SourceRecord &, const CBioSource &)

bool	xAssignSourceAttributeDbxref (CGff3SourceRecord &, const CBioSource &)

bool	xAssignSourceAttributesOrgMod (CGff3SourceRecord &, const CBioSource &)

bool	xAssignSourceAttributesSubSource (CGff3SourceRecord &, const CBioSource &)

bool	xAssignFeature (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &) override

bool	xAssignFeatureEndpoints (CGffFeatureRecord &record, CGffFeatureContext &, const CMappedFeat &mapped_feat) override

bool	xAssignFeatureStrand (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &) override

bool	xAssignFeaturePhase (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &) override

bool	xAssignFeatureAttributesFormatIndependent (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &) override

bool	xAssignFeatureAttributesFormatSpecific (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &) override

bool	xAssignFeatureAttributeParent (CGff3FeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

bool	xAssignFeatureAttributeID (CGff3FeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

virtual bool	xAssignFeatureAttributeParentMrna (CGff3FeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

virtual bool	xAssignFeatureAttributeParentCds (CGff3FeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

virtual bool	xAssignFeatureAttributeParentpreRNA (CGff3FeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

virtual bool	xAssignFeatureAttributeParentVDJsegmentCregion (CGff3FeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

virtual bool	xAssignFeatureAttributeParentGene (CGff3FeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

virtual bool	xAssignFeatureAttributeParentRegion (CGff3FeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

bool	xAssignFeatureAttributeDbxref (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &) override

bool	xAssignFeatureAttributeName (CGffFeatureRecord &, const CMappedFeat &)

bool	xAssignFeatureAttributeNote (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &) override

bool	xAssignFeatureAttributeNcrnaClass (CGffFeatureRecord &, const CMappedFeat &)

bool	xAssignFeatureAttributeTranscriptId (CGffFeatureRecord &, const CMappedFeat &)

bool	xAssignFeatureAttributesQualifiers (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &) override

string	xNextAlignId ()

Protected Member Functions inherited from CGff2Writer
virtual bool	xAssignFeatureBasic (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

virtual bool	xAssignFeatureSeqId (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

virtual bool	xAssignFeatureScore (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

virtual bool	xAssignFeatureAttributesGene (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

virtual bool	xAssignFeatureAttributeDbxref (CGffFeatureRecord &, CGffFeatureContext &, const string &label, const CMappedFeat &)

virtual bool	xAssignFeatureAttributeProduct (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

virtual bool	xAssignFeatureAttributeProteinId (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

virtual bool	xAssignFeatureAttributeRibosomalSlippage (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

virtual bool	xAssignFeatureAttributeTranslationTable (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

virtual bool	xAssignFeatureAttributePartial (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

virtual bool	xAssignFeatureAttributePseudo (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

bool	xAssignFeatureAttributeCodeBreak (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

bool	xAssignFeatureAttributeOldLocusTag (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

bool	xAssignFeatureAttributeGeneBiotype (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

bool	xAssignFeatureAttributeMapLoc (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

bool	xAssignFeatureAttributeException (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

bool	xAssignFeatureAttributeExperiment (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

bool	xAssignFeatureAttributeModelEvidence (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

bool	xAssignFeatureAttributeRptFamily (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

bool	xAssignFeatureAttributePseudoGene (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

bool	xAssignFeatureAttributeIsOrdered (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

bool	xAssignFeatureAttributeFunction (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

bool	xAssignFeatureAttributesGoMarkup (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

bool	xAssignFeatureAttributeEcNumbers (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

bool	xAssignFeatureAttributeExonNumber (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)

virtual bool	x_WriteSequenceHeader (CBioseq_Handle)

virtual bool	x_WriteSequenceHeader (CSeq_id_Handle)

virtual bool	x_WriteAnnot (const CSeq_annot &)

virtual bool	x_WriteAlign (const CSeq_align &)

virtual bool	x_WriteSeqEntryHandle (CSeq_entry_Handle)

bool	xWriteFeature (CFeat_CI feat_it) override

virtual bool	x_WriteAssemblyInfo (const string &, const string &)

virtual bool	xGeneratingMissingTranscripts () const

CMappedFeat	xGenerateMissingTranscript (CGffFeatureContext &, const CMappedFeat &)

Protected Member Functions inherited from CWriterBase
	CWriterBase (CNcbiOstream &ostr, unsigned int uFlags=0)

Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Additional Inherited Members
Public Types inherited from CGff3Writer
enum	TFlags { fExtraQuals = (fGff2WriterLast << 1) , fMicroIntrons = (fGff2WriterLast << 2) , fExcludeNucs = (fGff2WriterLast << 3) , fIncludeProts = (fGff2WriterLast << 4) , fGff3WriterLast = fIncludeProts }

Public Types inherited from CGff2Writer
enum	TFlags { fSoQuirks = (fWriterBaseLast << 1) , fGenerateMissingTranscripts = (fWriterBaseLast << 2) , fGff2WriterLast = fSoQuirks }

Public Types inherited from CWriterBase
enum	TFlags { fNormal = 0 , fDebugOutput = (1<<0) , fWriterBaseLast = fDebugOutput }
	Customization flags that are relevant to all CWriterBase derived writers. More...

Public Types inherited from CObject
enum	EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern }
	Control filling of newly allocated memory. More...

typedef CObjectCounterLocker	TLockerType
	Default locker type for CRef. More...

typedef atomic< Uint8 >	TCounter
	Counter type is CAtomiCounter. More...

typedef Uint8	TCount
	Alias for value type of counter. More...

Static Public Member Functions inherited from CObject
static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (void)
	Define method to throw null pointer exception. More...

static NCBI_XNCBI_EXPORT void	ThrowNullPointerException (const type_info &type)

static EAllocFillMode	GetAllocFillMode (void)

static void	SetAllocFillMode (EAllocFillMode mode)

static void	SetAllocFillMode (const string &value)
	Set mode from configuration parameter value. More...

Static Public Member Functions inherited from CDebugDumpable
static void	EnableDebugDump (bool on)

Static Public Attributes inherited from CObject
static const TCount	eCounterBitsCanBeDeleted = 1 << 0
	Define possible object states. More...

static const TCount	eCounterBitsInPlainHeap = 1 << 1
	Heap signature was found. More...

static const TCount	eCounterBitsPlaceMask
	Mask for 'in heap' state flags. More...

static const int	eCounterStep = 1 << 2
	Skip over the "in heap" bits. More...

static const TCount	eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2)
	Minimal value for valid objects (reference counter is zero) Must be a single bit value. More...

static const TCount	eCounterStateMask
	Valid object, and object in heap. More...

Protected Types inherited from CGff3Writer
typedef list< pair< CConstRef< CSeq_align >, string > >	TAlignCache

using	TFeatureMap = map< CMappedFeat, CRef< CGff3FeatureRecord > >

using	TGeneMapNew = TFeatureMap

using	TMrnaMapNew = TFeatureMap

using	TCdsMapNew = TFeatureMap

using	TRegionMapNew = TFeatureMap

Static Protected Member Functions inherited from CGff2Writer
static bool	IsTranscriptType (const CMappedFeat &)

static bool	HasAccaptableTranscriptParent (CGffFeatureContext &, const CMappedFeat &)

static bool	xIntervalsNeedPartNumbers (const list< CRef< CSeq_interval >> &)

Protected Attributes inherited from CGff3Writer
unsigned int	m_uRecordId

string	m_sDefaultMethod

TGeneMapNew	m_GeneMapNew

TMrnaMapNew	m_MrnaMapNew

TMrnaMapNew	m_CdsMapNew

TFeatureMap	m_PrernaMapNew

TFeatureMap	m_VDJsegmentCregionMapNew

TRegionMapNew	m_RegionMapNew

bool	m_SortAlignments

unsigned int	m_uPendingGeneId

unsigned int	m_uPendingMrnaId

unsigned int	m_uPendingTrnaId

unsigned int	m_uPendingCdsId

unsigned int	m_uPendingGenericId

unsigned int	m_uPendingAlignId

CGffIdGenerator	m_idGenerator

CBioseq_Handle	m_BioseqHandle

Protected Attributes inherited from CGff2Writer
CRef< CScope >	m_pScope

bool	m_bHeaderWritten

Protected Attributes inherited from CWriterBase
CNcbiOstream &	m_Os

unsigned int	m_uFlags

unique_ptr< SAnnotSelector >	m_Selector

CRange< TSeqPos >	m_Range

CWriterListener *	mpMessageListener

Protected Attributes inherited from CInterruptable
ICanceled *	mpCancelled

Detailed Description

Definition at line 44 of file gvf_writer.hpp.

Constructor & Destructor Documentation

◆ CGvfWriter() [1/2]

CGvfWriter::CGvfWriter	(	CScope &	scope,
		CNcbiOstream &	ostr,
		unsigned int	uFlags = `fNormal`
	)

Definition at line 44 of file gvf_writer.cpp.

References CGff3Writer::m_uPendingGeneId, CGff3Writer::m_uPendingMrnaId, and CGff3Writer::m_uRecordId.

◆ CGvfWriter() [2/2]

CGvfWriter::CGvfWriter	(	CNcbiOstream &	ostr,
		unsigned int	uFlags = `fNormal`
	)

Definition at line 57 of file gvf_writer.cpp.

References CGff3Writer::m_uPendingGeneId, CGff3Writer::m_uPendingMrnaId, and CGff3Writer::m_uRecordId.

◆ ~CGvfWriter()

CGvfWriter::~CGvfWriter ( )

virtual

Definition at line 69 of file gvf_writer.cpp.

Member Function Documentation

◆ WriteHeader() [1/2]

bool CGvfWriter::WriteHeader ( void )

overridevirtual

Write a file header.

Header syntax and rules depend on the file format. This do-nothing implementation should therefore be re-implemented in format specific subclasses.

Reimplemented from CGff3Writer.

Definition at line 132 of file gvf_writer.cpp.

References CGff2Writer::m_bHeaderWritten, and CWriterBase::m_Os.

Referenced by WriteHeader().

◆ WriteHeader() [2/2]

bool CGvfWriter::WriteHeader ( const CSeq_annot & )

overridevirtual

Write a file header, using annotation information.

Header syntax and rules depend on the file format. This do-nothing implementation should therefore be re-implemented in format specific subclasses.

Reimplemented from CGff3Writer.

Definition at line 75 of file gvf_writer.cpp.

References data, CAnnot_descr_Base::Get(), CUser_object_Base::GetData(), CSeq_annot_Base::GetDesc(), CAnnot_descr_Base::IsSet(), CSeq_annot_Base::IsSetDesc(), ncbi::grid::netcache::search::fields::key, CWriterBase::m_Os, rapidjson::value, and WriteHeader().

◆ x_WriteSeqAnnotHandle()

bool CGvfWriter::x_WriteSeqAnnotHandle ( CSeq_annot_Handle sah )

overrideprotectedvirtual

Reimplemented from CGff3Writer.

Definition at line 225 of file gvf_writer.cpp.

References CSeq_annot_Handle::GetCompleteSeq_annot(), CWriterBase::SetAnnotSelector(), and xWriteFeature().

◆ xAssignFeatureAttributes()

bool CGvfWriter::xAssignFeatureAttributes	(	CGffFeatureRecord &	rec,
		CGffFeatureContext &	,
		const CMappedFeat &	mf
	)

overrideprotectedvirtual

Reimplemented from CGff2Writer.

Definition at line 245 of file gvf_writer.cpp.

References set< Key, Compare >::end(), set< Key, Compare >::find(), CSeq_feat_Handle::GetQual(), isupper(), ncbi::grid::netcache::search::fields::key, CGffBaseRecord::SetAttribute(), NStr::ToLower(), and rapidjson::value.

◆ xAssignFeatureMethod()

bool CGvfWriter::xAssignFeatureMethod	(	CGffFeatureRecord &	record,
		CGffFeatureContext &	fc,
		const CMappedFeat &	mf
	)

overrideprotectedvirtual

Reimplemented from CGff3Writer.

Definition at line 196 of file gvf_writer.cpp.

References CGvfWriteRecord::AssignSource().

◆ xAssignFeatureType()

bool CGvfWriter::xAssignFeatureType	(	CGffFeatureRecord &	record,
		CGffFeatureContext &	fc,
		const CMappedFeat &	mf
	)

overrideprotectedvirtual

Reimplemented from CGff3Writer.

Definition at line 184 of file gvf_writer.cpp.

References CGvfWriteRecord::AssignType().

◆ xWriteFeature()

bool CGvfWriter::xWriteFeature	(	CGffFeatureContext &	fc,
		const CMappedFeat &	mf
	)

overrideprotectedvirtual

Reimplemented from CGff2Writer.

Definition at line 144 of file gvf_writer.cpp.

References CSeqFeatData::eSubtype_variation_ref, CSeq_feat_Handle::GetFeatSubtype(), and xWriteFeatureVariationRef().

Referenced by x_WriteSeqAnnotHandle().

◆ xWriteFeatureVariationRef()

bool CGvfWriter::xWriteFeatureVariationRef	(	CGffFeatureContext &	fc,
		const CMappedFeat &	mf
	)

protectedvirtual

Definition at line 160 of file gvf_writer.cpp.

References CInterruptable::IsCanceled(), NCBI_THROW, CGff3Writer::xAssignFeature(), and xWriteRecord().

Referenced by xWriteFeature().

◆ xWriteRecord()

bool CGvfWriter::xWriteRecord ( const CGffBaseRecord & pRecord )

overrideprotectedvirtual

Reimplemented from CGff3Writer.

Definition at line 208 of file gvf_writer.cpp.

References CWriterBase::m_Os, CGffBaseRecord::StrAttributes(), CGffBaseRecord::StrMethod(), CGffBaseRecord::StrPhase(), CGffBaseRecord::StrScore(), CGffBaseRecord::StrSeqId(), CGffBaseRecord::StrSeqStart(), CGffBaseRecord::StrSeqStop(), CGffBaseRecord::StrStrand(), and CGffBaseRecord::StrType().

Referenced by xWriteFeatureVariationRef().

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

include/objtools/writers/gvf_writer.hpp
src/objtools/writers/gvf_writer.cpp

Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CGvfWriter() [1/2]

◆ CGvfWriter() [2/2]

◆ ~CGvfWriter()

Member Function Documentation

◆ WriteHeader() [1/2]

◆ WriteHeader() [2/2]

◆ x_WriteSeqAnnotHandle()

◆ xAssignFeatureAttributes()

◆ xAssignFeatureMethod()

◆ xAssignFeatureType()

◆ xWriteFeature()

◆ xWriteFeatureVariationRef()

◆ xWriteRecord()