NCBI C++ ToolKit
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CGff3Writer Class Reference

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#include <objtools/writers/gff3_writer.hpp>

+ Inheritance diagram for CGff3Writer:
+ Collaboration diagram for CGff3Writer:

Public Types

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...
 

Public Member Functions

 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 WriteHeader () override
 Write a file header. More...
 
bool WriteHeader (const CSeq_annot &annot) override
 Write a file header, using annotation information. More...
 
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 WriteHeader () override
 Write a file header identifying the file content as GFF version 2. More...
 
bool WriteHeader (const CSeq_annot &) override
 Write a file header, using annotation information. More...
 
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 Types

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
 

Protected Member Functions

bool x_WriteBioseqHandle (CBioseq_Handle) override
 
bool x_WriteSeqAnnotHandle (CSeq_annot_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
 
virtual bool xWriteRecord (const CGffBaseRecord &)
 
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 xAssignFeatureType (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &) override
 
bool xAssignFeatureMethod (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 xAssignFeatureAttributes (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)
 
virtual bool xWriteFeature (CGffFeatureContext &, const CMappedFeat &)
 
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...
 

Protected Attributes

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
 

Additional Inherited Members

- 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...
 
- 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 >> &)
 

Detailed Description

Definition at line 139 of file gff3_writer.hpp.

Member Typedef Documentation

◆ TAlignCache

typedef list<pair<CConstRef<CSeq_align>, string> > CGff3Writer::TAlignCache
protected

Definition at line 179 of file gff3_writer.hpp.

◆ TCdsMapNew

Definition at line 507 of file gff3_writer.hpp.

◆ TFeatureMap

Definition at line 499 of file gff3_writer.hpp.

◆ TGeneMapNew

Definition at line 501 of file gff3_writer.hpp.

◆ TMrnaMapNew

Definition at line 504 of file gff3_writer.hpp.

◆ TRegionMapNew

Definition at line 514 of file gff3_writer.hpp.

Member Enumeration Documentation

◆ TFlags

Enumerator
fExtraQuals 
fMicroIntrons 
fExcludeNucs 
fIncludeProts 
fGff3WriterLast 

Definition at line 144 of file gff3_writer.hpp.

Constructor & Destructor Documentation

◆ CGff3Writer() [1/2]

CGff3Writer::CGff3Writer ( CScope scope,
CNcbiOstream ostr,
unsigned int  uFlags = fNormal,
bool  sortAlignments = false 
)

◆ CGff3Writer() [2/2]

CGff3Writer::CGff3Writer ( CNcbiOstream ostr,
unsigned int  uFlags = fNormal,
bool  sortAlignments = false 
)

◆ ~CGff3Writer()

virtual CGff3Writer::~CGff3Writer ( )
virtualdefault

Member Function Documentation

◆ SetBioseqHandle()

void CGff3Writer::SetBioseqHandle ( CBioseq_Handle  bsh)

Definition at line 284 of file gff3_writer.cpp.

References m_BioseqHandle.

◆ SetDefaultMethod()

void CGff3Writer::SetDefaultMethod ( const string defaultMethod)
inline

Definition at line 166 of file gff3_writer.hpp.

References m_sDefaultMethod.

Referenced by CAnnotWriterApp::xInitWriter().

◆ WriteAlign()

bool CGff3Writer::WriteAlign ( const CSeq_align ,
const string = "",
const string = "" 
)
overridevirtual

Write a raw Seq-align to the internal output stream.

This implementation will just generate an error and then exit. It should be re-implemented in format specific subclasses.

Parameters
alignthe Seq-align object to be written.
nameparameter describing the object. Handling will be format specific.
descrparameter describing the object. Handling will be format specific.

Reimplemented from CWriterBase.

Definition at line 293 of file gff3_writer.cpp.

References CException::GetMsg(), NCBI_THROW, CSeq_align::Validate(), CGff2Writer::x_WriteAssemblyInfo(), and xWriteAlign().

Referenced by CGffExportJob::Run(), sRunTest(), and sUpdateCase().

◆ WriteHeader() [1/2]

bool CGff3Writer::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 CWriterBase.

Reimplemented in CGvfWriter.

Definition at line 1072 of file gff3_writer.cpp.

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

Referenced by CGffExportJob::Run(), sRunTest(), and sUpdateCase().

◆ WriteHeader() [2/2]

bool CGff3Writer::WriteHeader ( const CSeq_annot )
inlineoverridevirtual

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 CWriterBase.

Reimplemented in CGvfWriter.

Definition at line 171 of file gff3_writer.hpp.

References CGff2Writer::WriteHeader().

◆ x_SortAlignments()

void CGff3Writer::x_SortAlignments ( TAlignCache alignCache,
CScope scope 
)
protectedvirtual

Definition at line 1196 of file gff3_writer.cpp.

Referenced by x_WriteBioseqHandle().

◆ x_WriteBioseqHandle()

bool CGff3Writer::x_WriteBioseqHandle ( CBioseq_Handle  bsh)
overrideprotectedvirtual

◆ x_WriteFeatureContext()

bool CGff3Writer::x_WriteFeatureContext ( CGffFeatureContext fc)
protectedvirtual

◆ x_WriteSeqAnnotHandle()

bool CGff3Writer::x_WriteSeqAnnotHandle ( CSeq_annot_Handle  sah)
overrideprotectedvirtual

◆ xAssignAlignment()

bool CGff3Writer::xAssignAlignment ( CGffFeatureRecord )
protected

◆ xAssignAlignmentDenseg()

bool CGff3Writer::xAssignAlignmentDenseg ( CGffAlignRecord record,
const CAlnMap alnMap,
unsigned int  srcRow 
)
protected

◆ xAssignAlignmentDensegGap()

bool CGff3Writer::xAssignAlignmentDensegGap ( CGffAlignRecord record,
const CAlnMap alnMap,
unsigned int  srcRow 
)
protected

◆ xAssignAlignmentDensegLocation()

bool CGff3Writer::xAssignAlignmentDensegLocation ( CGffAlignRecord record,
const CAlnMap alnMap,
unsigned int  srcRow 
)
protectedvirtual

◆ xAssignAlignmentDensegMethod()

bool CGff3Writer::xAssignAlignmentDensegMethod ( CGffAlignRecord record,
const CAlnMap alnMap,
unsigned int  srcRow 
)
protected

◆ xAssignAlignmentDensegScores()

bool CGff3Writer::xAssignAlignmentDensegScores ( CGffAlignRecord record,
const CAlnMap alnMap,
unsigned int  srcRow 
)
protectedvirtual

◆ xAssignAlignmentDensegSeqId()

bool CGff3Writer::xAssignAlignmentDensegSeqId ( CGffAlignRecord record,
const CAlnMap alnMap,
unsigned int  srcRow 
)
protectedvirtual

◆ xAssignAlignmentDensegTarget()

bool CGff3Writer::xAssignAlignmentDensegTarget ( CGffAlignRecord record,
const CAlnMap alnMap,
unsigned int  srcRow 
)
protectedvirtual

◆ xAssignAlignmentDensegType()

bool CGff3Writer::xAssignAlignmentDensegType ( CGffAlignRecord record,
const CAlnMap alnMap,
unsigned int  srcRow 
)
protected

◆ xAssignAlignmentScores()

bool CGff3Writer::xAssignAlignmentScores ( CGffAlignRecord record,
const CSeq_align align 
)
protectedvirtual

◆ xAssignAlignmentSpliced()

bool CGff3Writer::xAssignAlignmentSpliced ( CGffAlignRecord record,
const CSpliced_seg spliced,
const CSpliced_exon exon 
)
protected

◆ xAssignAlignmentSplicedAttributes()

bool CGff3Writer::xAssignAlignmentSplicedAttributes ( CGffAlignRecord record,
const CSpliced_seg spliced,
const CSpliced_exon exon 
)
protected

Definition at line 456 of file gff3_writer.cpp.

Referenced by xAssignAlignmentSpliced().

◆ xAssignAlignmentSplicedGap()

bool CGff3Writer::xAssignAlignmentSplicedGap ( CGffAlignRecord record,
const CSpliced_seg spliced,
const CSpliced_exon exon 
)
protectedvirtual

◆ xAssignAlignmentSplicedLocation()

bool CGff3Writer::xAssignAlignmentSplicedLocation ( CGffAlignRecord record,
const CSpliced_seg spliced,
const CSpliced_exon exon 
)
protectedvirtual

◆ xAssignAlignmentSplicedMethod()

bool CGff3Writer::xAssignAlignmentSplicedMethod ( CGffAlignRecord record,
const CSpliced_seg spliced,
const CSpliced_exon exon 
)
protected

◆ xAssignAlignmentSplicedPhase()

bool CGff3Writer::xAssignAlignmentSplicedPhase ( CGffAlignRecord record,
const CSpliced_seg spliced,
const CSpliced_exon exon 
)
protected

Definition at line 445 of file gff3_writer.cpp.

Referenced by xAssignAlignmentSpliced().

◆ xAssignAlignmentSplicedScores()

bool CGff3Writer::xAssignAlignmentSplicedScores ( CGffAlignRecord record,
const CSpliced_seg spliced,
const CSpliced_exon exon 
)
protectedvirtual

◆ xAssignAlignmentSplicedSeqId()

bool CGff3Writer::xAssignAlignmentSplicedSeqId ( CGffAlignRecord record,
const CSpliced_seg spliced,
const CSpliced_exon exon 
)
protectedvirtual

◆ xAssignAlignmentSplicedTarget()

bool CGff3Writer::xAssignAlignmentSplicedTarget ( CGffAlignRecord record,
const CSpliced_seg spliced,
const CSpliced_exon exon 
)
protectedvirtual

◆ xAssignAlignmentSplicedType()

bool CGff3Writer::xAssignAlignmentSplicedType ( CGffAlignRecord record,
const CSpliced_seg spliced,
const CSpliced_exon exon 
)
protected

◆ xAssignFeature()

bool CGff3Writer::xAssignFeature ( CGffFeatureRecord record,
CGffFeatureContext fc,
const CMappedFeat mf 
)
overrideprotectedvirtual

◆ xAssignFeatureAttributeDbxref()

bool CGff3Writer::xAssignFeatureAttributeDbxref ( CGffFeatureRecord record,
CGffFeatureContext fc,
const CMappedFeat mf 
)
overrideprotectedvirtual

Reimplemented from CGff2Writer.

Definition at line 1865 of file gff3_writer.cpp.

References fc, and CGff2Writer::xAssignFeatureAttributeDbxref().

◆ xAssignFeatureAttributeID()

bool CGff3Writer::xAssignFeatureAttributeID ( CGff3FeatureRecord record,
CGffFeatureContext fc,
const CMappedFeat mf 
)
protected

◆ xAssignFeatureAttributeName()

bool CGff3Writer::xAssignFeatureAttributeName ( CGffFeatureRecord record,
const CMappedFeat mf 
)
protected

◆ xAssignFeatureAttributeNcrnaClass()

bool CGff3Writer::xAssignFeatureAttributeNcrnaClass ( CGffFeatureRecord record,
const CMappedFeat mf 
)
protected

◆ xAssignFeatureAttributeNote()

bool CGff3Writer::xAssignFeatureAttributeNote ( CGffFeatureRecord record,
CGffFeatureContext ,
const CMappedFeat mf 
)
overrideprotectedvirtual

◆ xAssignFeatureAttributeParent()

bool CGff3Writer::xAssignFeatureAttributeParent ( CGff3FeatureRecord record,
CGffFeatureContext fc,
const CMappedFeat mf 
)
protected

Definition at line 2083 of file gff3_writer.cpp.

References CSeqFeatData_Base::e_Rna, CSeqFeatData::eSubtype_3UTR, CSeqFeatData::eSubtype_5UTR, CSeqFeatData::eSubtype_C_region, CSeqFeatData::eSubtype_cdregion, CSeqFeatData::eSubtype_D_segment, CSeqFeatData::eSubtype_exon, CSeqFeatData::eSubtype_intron, CSeqFeatData::eSubtype_J_segment, CSeqFeatData::eSubtype_mat_peptide, CSeqFeatData::eSubtype_mat_peptide_aa, CSeqFeatData::eSubtype_misc_feature, CSeqFeatData::eSubtype_misc_recomb, CSeqFeatData::eSubtype_misc_structure, CSeqFeatData::eSubtype_mobile_element, CSeqFeatData::eSubtype_mRNA, CSeqFeatData::eSubtype_N_region, CSeqFeatData::eSubtype_ncRNA, CSeqFeatData::eSubtype_polyA_site, CSeqFeatData::eSubtype_propeptide, CSeqFeatData::eSubtype_protein_bind, CSeqFeatData::eSubtype_regulatory, CSeqFeatData::eSubtype_rep_origin, CSeqFeatData::eSubtype_repeat_region, CSeqFeatData::eSubtype_S_region, CSeqFeatData::eSubtype_sig_peptide, CSeqFeatData::eSubtype_sig_peptide_aa, CSeqFeatData::eSubtype_stem_loop, CSeqFeatData::eSubtype_transit_peptide, CSeqFeatData::eSubtype_transit_peptide_aa, CSeqFeatData::eSubtype_V_region, CSeqFeatData::eSubtype_V_segment, fc, CSeq_feat_Handle::GetFeatSubtype(), CSeq_feat_Handle::GetFeatType(), xAssignFeatureAttributeParentCds(), xAssignFeatureAttributeParentGene(), xAssignFeatureAttributeParentMrna(), xAssignFeatureAttributeParentpreRNA(), xAssignFeatureAttributeParentRegion(), and xAssignFeatureAttributeParentVDJsegmentCregion().

Referenced by xAssignFeatureAttributesFormatSpecific().

◆ xAssignFeatureAttributeParentCds()

bool CGff3Writer::xAssignFeatureAttributeParentCds ( CGff3FeatureRecord record,
CGffFeatureContext fc,
const CMappedFeat mf 
)
protectedvirtual

◆ xAssignFeatureAttributeParentGene()

bool CGff3Writer::xAssignFeatureAttributeParentGene ( CGff3FeatureRecord record,
CGffFeatureContext fc,
const CMappedFeat mf 
)
protectedvirtual

◆ xAssignFeatureAttributeParentMrna()

bool CGff3Writer::xAssignFeatureAttributeParentMrna ( CGff3FeatureRecord record,
CGffFeatureContext fc,
const CMappedFeat mf 
)
protectedvirtual

◆ xAssignFeatureAttributeParentpreRNA()

bool CGff3Writer::xAssignFeatureAttributeParentpreRNA ( CGff3FeatureRecord record,
CGffFeatureContext fc,
const CMappedFeat mf 
)
protectedvirtual

◆ xAssignFeatureAttributeParentRegion()

bool CGff3Writer::xAssignFeatureAttributeParentRegion ( CGff3FeatureRecord record,
CGffFeatureContext fc,
const CMappedFeat mf 
)
protectedvirtual

◆ xAssignFeatureAttributeParentVDJsegmentCregion()

bool CGff3Writer::xAssignFeatureAttributeParentVDJsegmentCregion ( CGff3FeatureRecord record,
CGffFeatureContext fc,
const CMappedFeat mf 
)
protectedvirtual

◆ xAssignFeatureAttributesFormatIndependent()

bool CGff3Writer::xAssignFeatureAttributesFormatIndependent ( CGffFeatureRecord record,
CGffFeatureContext fc,
const CMappedFeat mf 
)
overrideprotectedvirtual

◆ xAssignFeatureAttributesFormatSpecific()

bool CGff3Writer::xAssignFeatureAttributesFormatSpecific ( CGffFeatureRecord rec,
CGffFeatureContext fc,
const CMappedFeat mf 
)
overrideprotectedvirtual

◆ xAssignFeatureAttributesQualifiers()

bool CGff3Writer::xAssignFeatureAttributesQualifiers ( CGffFeatureRecord rec,
CGffFeatureContext ,
const CMappedFeat mf 
)
overrideprotectedvirtual

◆ xAssignFeatureAttributeTranscriptId()

bool CGff3Writer::xAssignFeatureAttributeTranscriptId ( CGffFeatureRecord record,
const CMappedFeat mf 
)
protected

◆ xAssignFeatureEndpoints()

bool CGff3Writer::xAssignFeatureEndpoints ( CGffFeatureRecord record,
CGffFeatureContext fc,
const CMappedFeat mapped_feat 
)
overrideprotectedvirtual

◆ xAssignFeatureMethod()

bool CGff3Writer::xAssignFeatureMethod ( CGffFeatureRecord record,
CGffFeatureContext fc,
const CMappedFeat mf 
)
overrideprotectedvirtual

◆ xAssignFeaturePhase()

bool CGff3Writer::xAssignFeaturePhase ( CGffFeatureRecord record,
CGffFeatureContext fc,
const CMappedFeat mf 
)
overrideprotectedvirtual

◆ xAssignFeatureStrand()

bool CGff3Writer::xAssignFeatureStrand ( CGffFeatureRecord record,
CGffFeatureContext fc,
const CMappedFeat mf 
)
overrideprotectedvirtual

Reimplemented from CGff2Writer.

Definition at line 1811 of file gff3_writer.cpp.

References CMappedFeat::GetLocation(), CSeq_loc::GetStrand(), and CGffBaseRecord::SetStrand().

◆ xAssignFeatureType()

bool CGff3Writer::xAssignFeatureType ( CGffFeatureRecord record,
CGffFeatureContext fc,
const CMappedFeat mf 
)
overrideprotectedvirtual

Reimplemented from CGff2Writer.

Reimplemented in CGvfWriter.

Definition at line 1647 of file gff3_writer.cpp.

References CSoMap::FeatureToSoType(), CMappedFeat::GetOriginalFeature(), and CGffBaseRecord::SetType().

◆ xAssignSource()

bool CGff3Writer::xAssignSource ( CGff3SourceRecord record,
CBioseq_Handle  bsh 
)
protected

◆ xAssignSourceAttributeDbxref()

bool CGff3Writer::xAssignSourceAttributeDbxref ( CGff3SourceRecord record,
const CBioSource bioSrc 
)
protected

◆ xAssignSourceAttributeGbKey()

bool CGff3Writer::xAssignSourceAttributeGbKey ( CGff3SourceRecord record)
protected

Definition at line 2380 of file gff3_writer.cpp.

References CGffBaseRecord::SetAttribute().

Referenced by xAssignSourceAttributes().

◆ xAssignSourceAttributeGenome()

bool CGff3Writer::xAssignSourceAttributeGenome ( CGff3SourceRecord record,
const CBioSource bioSrc 
)
protected

◆ xAssignSourceAttributeIsCircular()

bool CGff3Writer::xAssignSourceAttributeIsCircular ( CGff3SourceRecord record,
CBioseq_Handle  bsh 
)
protected

◆ xAssignSourceAttributeMolType()

bool CGff3Writer::xAssignSourceAttributeMolType ( CGff3SourceRecord record,
CBioseq_Handle  bsh 
)
protected

Definition at line 2389 of file gff3_writer.cpp.

References CWriteUtil::GetBiomol(), and CGffBaseRecord::SetAttribute().

Referenced by xAssignSourceAttributes().

◆ xAssignSourceAttributeName()

bool CGff3Writer::xAssignSourceAttributeName ( CGff3SourceRecord record,
const CBioSource bioSrc 
)
protected

◆ xAssignSourceAttributes()

bool CGff3Writer::xAssignSourceAttributes ( CGff3SourceRecord record,
CBioseq_Handle  bsh 
)
protected

◆ xAssignSourceAttributesBioSource()

bool CGff3Writer::xAssignSourceAttributesBioSource ( CGff3SourceRecord record,
CBioseq_Handle  bsh 
)
protected

◆ xAssignSourceAttributesOrgMod()

bool CGff3Writer::xAssignSourceAttributesOrgMod ( CGff3SourceRecord record,
const CBioSource bioSrc 
)
protected

◆ xAssignSourceAttributesSubSource()

bool CGff3Writer::xAssignSourceAttributesSubSource ( CGff3SourceRecord record,
const CBioSource bioSrc 
)
protected

◆ xAssignSourceEndpoints()

bool CGff3Writer::xAssignSourceEndpoints ( CGff3SourceRecord record,
CBioseq_Handle  bsh 
)
protected

◆ xAssignSourceMethod()

bool CGff3Writer::xAssignSourceMethod ( CGff3SourceRecord record,
CBioseq_Handle  bsh 
)
protected

Definition at line 2335 of file gff3_writer.cpp.

References CWriteUtil::GetIdType(), and CGffBaseRecord::SetMethod().

Referenced by xAssignSource().

◆ xAssignSourceSeqId()

bool CGff3Writer::xAssignSourceSeqId ( CGff3SourceRecord record,
CBioseq_Handle  bsh 
)
protected

◆ xAssignSourceType()

bool CGff3Writer::xAssignSourceType ( CGff3SourceRecord record)
protected

Definition at line 2288 of file gff3_writer.cpp.

References CGffBaseRecord::SetType().

Referenced by xAssignSource().

◆ xNextAlignId()

string CGff3Writer::xNextAlignId ( )
protected

Definition at line 3088 of file gff3_writer.cpp.

References m_uPendingAlignId, string, and NStr::UIntToString().

Referenced by xWriteAlign().

◆ xPassesFilterByViewMode()

bool CGff3Writer::xPassesFilterByViewMode ( CBioseq_Handle  bsh)
protectedvirtual

◆ xSetJunkFilteringAnnotSelector()

SAnnotSelector & CGff3Writer::xSetJunkFilteringAnnotSelector ( void  )
protectedvirtual

◆ xSplicedSegHasProteinProd()

bool CGff3Writer::xSplicedSegHasProteinProd ( const CSpliced_seg spliced)
protected

◆ xWriteAlign()

bool CGff3Writer::xWriteAlign ( const CSeq_align align,
const string alignId = "" 
)
overrideprotectedvirtual

◆ xWriteAlignDenseg()

bool CGff3Writer::xWriteAlignDenseg ( const CSeq_align align,
const string alignId = "" 
)
protectedvirtual

◆ xWriteAlignDisc()

bool CGff3Writer::xWriteAlignDisc ( const CSeq_align align,
const string alignId = "" 
)
protectedvirtual

◆ xWriteAlignment()

void CGff3Writer::xWriteAlignment ( const CGffAlignRecord record)
protected

◆ xWriteAlignSpliced()

bool CGff3Writer::xWriteAlignSpliced ( const CSeq_align align,
const string alignId = "" 
)
protectedvirtual

◆ xWriteAllChildren()

bool CGff3Writer::xWriteAllChildren ( CGffFeatureContext fc,
const CMappedFeat mf 
)
overrideprotectedvirtual

Reimplemented from CGff2Writer.

Definition at line 1316 of file gff3_writer.cpp.

References fc, and xWriteNucleotideFeature().

Referenced by x_WriteFeatureContext().

◆ xWriteFeature()

bool CGff3Writer::xWriteFeature ( CFeat_CI  feat_it)
overrideprotectedvirtual

Reimplemented from CFeatWriter.

Definition at line 1353 of file gff3_writer.cpp.

References fc, CAnnotTypes_CI::GetAnnot(), m_BioseqHandle, and xWriteNucleotideFeature().

◆ xWriteFeatureCDJVSegment()

bool CGff3Writer::xWriteFeatureCDJVSegment ( CGffFeatureContext fc,
const CMappedFeat mf 
)
protectedvirtual

◆ xWriteFeatureCds()

bool CGff3Writer::xWriteFeatureCds ( CGffFeatureContext fc,
const CMappedFeat mf 
)
protectedvirtual

◆ xWriteFeatureGene()

bool CGff3Writer::xWriteFeatureGene ( CGffFeatureContext fc,
const CMappedFeat mf 
)
protectedvirtual

◆ xWriteFeatureGeneric()

bool CGff3Writer::xWriteFeatureGeneric ( CGffFeatureContext fc,
const CMappedFeat mf 
)
protectedvirtual

◆ xWriteFeatureProtein()

bool CGff3Writer::xWriteFeatureProtein ( CGffFeatureContext fc,
const CMappedFeat cds,
const CMappedFeat protein 
)
protectedvirtual

◆ xWriteFeatureRecords()

bool CGff3Writer::xWriteFeatureRecords ( const CGffFeatureRecord record,
const CSeq_loc location,
unsigned int  seqLength 
)
protectedvirtual

◆ xWriteFeatureRna()

bool CGff3Writer::xWriteFeatureRna ( CGffFeatureContext fc,
const CMappedFeat mf 
)
protectedvirtual

◆ xWriteFeatureTrna()

bool CGff3Writer::xWriteFeatureTrna ( CGffFeatureContext fc,
const CMappedFeat mf 
)
protectedvirtual

◆ xWriteNucleotideFeature()

bool CGff3Writer::xWriteNucleotideFeature ( CGffFeatureContext fc,
const CMappedFeat mf 
)
protectedvirtual

◆ xWriteNucleotideFeatureTransSpliced()

bool CGff3Writer::xWriteNucleotideFeatureTransSpliced ( CGffFeatureContext fc,
const CMappedFeat mf 
)
protectedvirtual

◆ xWriteNucleotideSequence()

bool CGff3Writer::xWriteNucleotideSequence ( CBioseq_Handle  bsh)
protectedvirtual

◆ xWriteProteinFeature()

bool CGff3Writer::xWriteProteinFeature ( CGffFeatureContext fc,
const CMappedFeat mf 
)
protectedvirtual

◆ xWriteProteinSequence()

bool CGff3Writer::xWriteProteinSequence ( CBioseq_Handle  bsh)
protectedvirtual

◆ xWriteRecord()

bool CGff3Writer::xWriteRecord ( const CGffBaseRecord record)
protectedvirtual

◆ xWriteSequence()

bool CGff3Writer::xWriteSequence ( CBioseq_Handle  bsh)
protectedvirtual

◆ xWriteSequenceHeader()

bool CGff3Writer::xWriteSequenceHeader ( CBioseq_Handle  bsh)
protectedvirtual

◆ xWriteSource()

bool CGff3Writer::xWriteSource ( CBioseq_Handle  bsh)
protectedvirtual

Member Data Documentation

◆ m_BioseqHandle

CBioseq_Handle CGff3Writer::m_BioseqHandle
protected

Definition at line 527 of file gff3_writer.hpp.

Referenced by SetBioseqHandle(), and xWriteFeature().

◆ m_CdsMapNew

TMrnaMapNew CGff3Writer::m_CdsMapNew
protected

Definition at line 508 of file gff3_writer.hpp.

Referenced by xAssignFeatureAttributeParentCds().

◆ m_GeneMapNew

TGeneMapNew CGff3Writer::m_GeneMapNew
protected

Definition at line 502 of file gff3_writer.hpp.

Referenced by xAssignFeatureAttributeParentGene(), and xWriteFeatureGene().

◆ m_idGenerator

CGffIdGenerator CGff3Writer::m_idGenerator
protected

◆ m_MrnaMapNew

TMrnaMapNew CGff3Writer::m_MrnaMapNew
protected

◆ m_PrernaMapNew

TFeatureMap CGff3Writer::m_PrernaMapNew
protected

Definition at line 510 of file gff3_writer.hpp.

Referenced by xAssignFeatureAttributeParentpreRNA(), and xWriteFeatureRna().

◆ m_RegionMapNew

TRegionMapNew CGff3Writer::m_RegionMapNew
protected

Definition at line 515 of file gff3_writer.hpp.

Referenced by xAssignFeatureAttributeParentRegion().

◆ m_sDefaultMethod

string CGff3Writer::m_sDefaultMethod
protected

◆ m_SortAlignments

bool CGff3Writer::m_SortAlignments
protected

Definition at line 518 of file gff3_writer.hpp.

Referenced by x_WriteBioseqHandle().

◆ m_uPendingAlignId

unsigned int CGff3Writer::m_uPendingAlignId
protected

Definition at line 524 of file gff3_writer.hpp.

Referenced by CGff3Writer(), and xNextAlignId().

◆ m_uPendingCdsId

unsigned int CGff3Writer::m_uPendingCdsId
protected

Definition at line 522 of file gff3_writer.hpp.

Referenced by CGff3Writer().

◆ m_uPendingGeneId

unsigned int CGff3Writer::m_uPendingGeneId
protected

Definition at line 519 of file gff3_writer.hpp.

Referenced by CGff3Writer(), and CGvfWriter::CGvfWriter().

◆ m_uPendingGenericId

unsigned int CGff3Writer::m_uPendingGenericId
protected

Definition at line 523 of file gff3_writer.hpp.

Referenced by CGff3Writer().

◆ m_uPendingMrnaId

unsigned int CGff3Writer::m_uPendingMrnaId
protected

Definition at line 520 of file gff3_writer.hpp.

Referenced by CGff3Writer(), and CGvfWriter::CGvfWriter().

◆ m_uPendingTrnaId

unsigned int CGff3Writer::m_uPendingTrnaId
protected

Definition at line 521 of file gff3_writer.hpp.

Referenced by CGff3Writer().

◆ m_uRecordId

unsigned int CGff3Writer::m_uRecordId
protected

Definition at line 496 of file gff3_writer.hpp.

Referenced by CGff3Writer(), and CGvfWriter::CGvfWriter().

◆ m_VDJsegmentCregionMapNew

TFeatureMap CGff3Writer::m_VDJsegmentCregionMapNew
protected

The documentation for this class was generated from the following files:
Modified on Wed Apr 17 13:09:09 2024 by modify_doxy.py rev. 669887