NCBI C++ ToolKit
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CGvfWriter Class Reference

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#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 SAnnotSelectorSetAnnotSelector (void)
 
SAnnotSelectorGetAnnotSelector (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...
 
CObjectoperator= (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 SAnnotSelectorxSetJunkFilteringAnnotSelector ()
 
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< Uint8TCounter
 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< CScopem_pScope
 
bool m_bHeaderWritten
 
- Protected Attributes inherited from CWriterBase
CNcbiOstreamm_Os
 
unsigned int m_uFlags
 
unique_ptr< SAnnotSelectorm_Selector
 
CRange< TSeqPosm_Range
 
CWriterListenermpMessageListener
 
- Protected Attributes inherited from CInterruptable
ICanceledmpCancelled
 

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 
)

◆ CGvfWriter() [2/2]

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

◆ ~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 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, value, and WriteHeader().

◆ x_WriteSeqAnnotHandle()

bool CGvfWriter::x_WriteSeqAnnotHandle ( CSeq_annot_Handle  sah)
overrideprotectedvirtual

◆ xAssignFeatureAttributes()

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

◆ 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

◆ xWriteFeatureVariationRef()

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

◆ xWriteRecord()

bool CGvfWriter::xWriteRecord ( const CGffBaseRecord pRecord)
overrideprotectedvirtual

The documentation for this class was generated from the following files:
Modified on Fri Mar 01 10:06:48 2024 by modify_doxy.py rev. 669887