NCBI C++ ToolKit
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CGff2Writer Class Reference

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CWriterBase implementation that formats Genbank objects as plain GFF files. More...

#include <objtools/writers/gff_writer.hpp>

+ Inheritance diagram for CGff2Writer:
+ Collaboration diagram for CGff2Writer:

Public Types

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

 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 ()
 

Protected Member Functions

virtual bool xAssignFeature (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)
 
virtual bool xAssignFeatureBasic (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)
 
virtual bool xAssignFeatureType (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)
 
virtual bool xAssignFeatureSeqId (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)
 
virtual bool xAssignFeatureMethod (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)
 
virtual bool xAssignFeatureEndpoints (CGffFeatureRecord &record, CGffFeatureContext &, const CMappedFeat &mapped_feat)
 
virtual bool xAssignFeatureScore (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)
 
virtual bool xAssignFeatureStrand (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)
 
virtual bool xAssignFeaturePhase (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)
 
virtual bool xAssignFeatureAttributes (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)
 
virtual bool xAssignFeatureAttributesFormatIndependent (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)
 
virtual bool xAssignFeatureAttributesFormatSpecific (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)
 
virtual bool xAssignFeatureAttributesQualifiers (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)
 
virtual bool xAssignFeatureAttributesGene (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)
 
virtual bool xAssignFeatureAttributeDbxref (CGffFeatureRecord &, CGffFeatureContext &, const string &label, const CMappedFeat &)
 
virtual bool xAssignFeatureAttributeDbxref (CGffFeatureRecord &, CGffFeatureContext &, const CMappedFeat &)
 
virtual bool xAssignFeatureAttributeNote (CGffFeatureRecord &, CGffFeatureContext &, 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 x_WriteSeqAnnotHandle (CSeq_annot_Handle)
 
virtual bool x_WriteBioseqHandle (CBioseq_Handle)
 
virtual bool xWriteFeature (CGffFeatureContext &, const CMappedFeat &)
 
bool xWriteFeature (CFeat_CI feat_it) override
 
virtual bool xWriteAllChildren (CGffFeatureContext &, const CMappedFeat &)
 
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...
 

Static Protected Member Functions

static bool IsTranscriptType (const CMappedFeat &)
 
static bool HasAccaptableTranscriptParent (CGffFeatureContext &, const CMappedFeat &)
 
static bool xIntervalsNeedPartNumbers (const list< CRef< CSeq_interval >> &)
 

Protected Attributes

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...
 
- Private Member Functions inherited from CFeatWriter
virtual ~CFeatWriter (void)=default
 
bool WriteFeatures (CFeat_CI &first)
 

Detailed Description

CWriterBase implementation that formats Genbank objects as plain GFF files.

GFF (or GFF2) is a predecessor of GTF, GFF3, GVF and probably half a dozen other dialects in use today. GFF files consist of feature records, with each feature record consisting of nine columns. There is some agreed upon meaning of the first eight columns and on the general grammer of the column contents. Beyond that, there has never been a universally agreed upon defintion of the format (probably the prime reason the format is deprecated now). For the purpose of this implementation, GFF is taken to be the greatest common denominator between GTF and GFF3 (and this GVF). Those other writers then derive from this one, adding their own bits and pieces to complete the format renderer.

Definition at line 57 of file gff_writer.hpp.

Member Enumeration Documentation

◆ TFlags

Enumerator
fSoQuirks 
fGenerateMissingTranscripts 
fGff2WriterLast 

Definition at line 62 of file gff_writer.hpp.

Constructor & Destructor Documentation

◆ CGff2Writer() [1/2]

CGff2Writer::CGff2Writer ( CScope scope,
CNcbiOstream ostr,
unsigned int  flags = fNormal 
)

Constructor.

Parameters
scopescope to be used for ID reference resolution (it's OK to create one on the fly).
ostrstream objects should be written to.
flagsany output customization flags.

Definition at line 59 of file gff_writer.cpp.

References m_pScope, and CRef< C, Locker >::Reset().

◆ CGff2Writer() [2/2]

CGff2Writer::CGff2Writer ( CNcbiOstream ostr,
unsigned int  uFlags = fNormal 
)

Constructor.

Scopeless version. A scope will be allocated internally.

Parameters
ostrstream objects should be written to.
flagsany output customization flags.

Definition at line 72 of file gff_writer.cpp.

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

◆ ~CGff2Writer()

CGff2Writer::~CGff2Writer ( )
virtual

Definition at line 85 of file gff_writer.cpp.

Member Function Documentation

◆ HasAccaptableTranscriptParent()

bool CGff2Writer::HasAccaptableTranscriptParent ( CGffFeatureContext context,
const CMappedFeat mf 
)
staticprotected

◆ IsTranscriptType()

bool CGff2Writer::IsTranscriptType ( const CMappedFeat mf)
staticprotected

◆ WriteAlign()

bool CGff2Writer::WriteAlign ( const CSeq_align align,
const string asmblyName = "",
const string asmblyAccession = "" 
)
overridevirtual

Write a Seq-align object.

Calling this function on a general GFF2 writer (as opposed to GFF3 or another more specialized format will fail because GFF2 at this general level does not address alignments; you will need at least a GFF3 writer for that.

Parameters
alignSeq-align object to be rendered
asmblyNameoptional assembly name to use for the file header
asmblyAccessionoptional assembly accession to use for the file header

Reimplemented from CWriterBase.

Definition at line 311 of file gff_writer.cpp.

References x_WriteAlign(), and x_WriteAssemblyInfo().

Referenced by CGtfExportJob::Run().

◆ WriteAnnot()

bool CGff2Writer::WriteAnnot ( const CSeq_annot annot,
const string asmblyName = "",
const string asmblyAccession = "" 
)
overridevirtual

Convenience function to render a "naked" Seq-annot.

Makes use of the internal scope.

Parameters
annotSeq-annot object to be rendered
asmblyNameoptional assembly name to use for the file header
asmblyAccessionoptional assembly accession to use for the file header

Reimplemented from CWriterBase.

Definition at line 91 of file gff_writer.cpp.

References x_WriteAnnot(), and x_WriteAssemblyInfo().

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

◆ WriteBioseqHandle()

bool CGff2Writer::WriteBioseqHandle ( CBioseq_Handle  bsh,
const string asmblyName = "",
const string asmblyAccession = "" 
)
overridevirtual

Write Bioseq contained in given handle Essentially, will write all features that live on the given Bioseq.

Parameters
bshBioseq handle to be processed
asmblyNameoptional assembly name to use for the file header
asmblyAccessionoptional assembly accession to use for the file header

Reimplemented from CWriterBase.

Definition at line 192 of file gff_writer.cpp.

References x_WriteAssemblyInfo(), and x_WriteBioseqHandle().

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

◆ WriteFooter() [1/2]

bool CGff2Writer::WriteFooter ( )
overridevirtual

Write a trailer marking the end of a parsing context.

Reimplemented from CWriterBase.

Definition at line 346 of file gff_writer.cpp.

References CWriterBase::m_Os.

Referenced by CGffExportJob::Run(), CGtfExportJob::Run(), sRunTest(), sUpdateCase(), WriteFooter(), and CProjectFileWriter::x_WriteGtf().

◆ WriteFooter() [2/2]

virtual bool CGff2Writer::WriteFooter ( const CSeq_annot )
inlinevirtual

Definition at line 107 of file gff_writer.hpp.

References WriteFooter().

◆ WriteHeader() [1/2]

bool CGff2Writer::WriteHeader ( void  )
overridevirtual

Write a file header identifying the file content as GFF version 2.

Reimplemented from CWriterBase.

Reimplemented in CGvfWriter, and CGtfWriter.

Definition at line 335 of file gff_writer.cpp.

References m_bHeaderWritten, and CWriterBase::m_Os.

Referenced by WriteHeader(), CGff3Writer::WriteHeader(), and CGtfWriter::WriteHeader().

◆ WriteHeader() [2/2]

bool CGff2Writer::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 CGtfWriter, and CGvfWriter.

Definition at line 100 of file gff_writer.hpp.

References WriteHeader().

◆ WriteSeqAnnotHandle()

bool CGff2Writer::WriteSeqAnnotHandle ( CSeq_annot_Handle  sah,
const string asmblyName = "",
const string asmblyAccession = "" 
)
overridevirtual

Write Seq-annot contained in given handle Essentially, write out embedded feature table.

Other annotation types are not supported in the generic GFF2 writer(i.e. there will be a header and nothing else.

Parameters
sahSeq-annot handle to be processed
asmblyNameoptional assembly name to use for the file header
asmblyAccessionoptional assembly accession to use for the file header

Reimplemented from CWriterBase.

Definition at line 246 of file gff_writer.cpp.

References x_WriteAssemblyInfo(), and x_WriteSeqAnnotHandle().

Referenced by CProjectFileWriter::x_WriteGtf().

◆ WriteSeqEntryHandle()

bool CGff2Writer::WriteSeqEntryHandle ( CSeq_entry_Handle  seh,
const string asmblyName = "",
const string asmblyAccession = "" 
)
overridevirtual

Write Seq-entry contained in a given handle.

Essentially, will iterate through all contained Bioseq objects and process those, with some special processing for nuc-prot sets.

Parameters
sehSeq-entry handle to be processed
asmblyNameoptional assembly name to use for the file header
asmblyAccessionoptional assembly accession to use for the file header

Reimplemented from CWriterBase.

Definition at line 118 of file gff_writer.cpp.

References x_WriteAssemblyInfo(), and x_WriteSeqEntryHandle().

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

◆ x_WriteAlign()

bool CGff2Writer::x_WriteAlign ( const CSeq_align align)
protectedvirtual

Definition at line 327 of file gff_writer.cpp.

Referenced by WriteAlign(), and x_WriteSeqAnnotHandle().

◆ x_WriteAnnot()

bool CGff2Writer::x_WriteAnnot ( const CSeq_annot annot)
protectedvirtual

◆ x_WriteAssemblyInfo()

bool CGff2Writer::x_WriteAssemblyInfo ( const string strName,
const string strAccession 
)
protectedvirtual

◆ x_WriteBioseqHandle()

bool CGff2Writer::x_WriteBioseqHandle ( CBioseq_Handle  bsh)
protectedvirtual

Reimplemented in CGtfWriter, and CGff3Writer.

Definition at line 208 of file gff_writer.cpp.

References fc, CWriterBase::GetRange(), CWriterBase::SetAnnotSelector(), and xWriteFeature().

Referenced by WriteBioseqHandle(), and x_WriteSeqEntryHandle().

◆ x_WriteSeqAnnotHandle()

bool CGff2Writer::x_WriteSeqAnnotHandle ( CSeq_annot_Handle  sah)
protectedvirtual

◆ x_WriteSeqEntryHandle()

bool CGff2Writer::x_WriteSeqEntryHandle ( CSeq_entry_Handle  seh)
protectedvirtual

◆ x_WriteSequenceHeader() [1/2]

virtual bool CGff2Writer::x_WriteSequenceHeader ( CBioseq_Handle  )
inlineprotectedvirtual

Definition at line 352 of file gff_writer.hpp.

Referenced by x_WriteSeqEntryHandle().

◆ x_WriteSequenceHeader() [2/2]

virtual bool CGff2Writer::x_WriteSequenceHeader ( CSeq_id_Handle  )
inlineprotectedvirtual

Definition at line 355 of file gff_writer.hpp.

◆ xAssignFeature()

bool CGff2Writer::xAssignFeature ( CGffFeatureRecord record,
CGffFeatureContext fc,
const CMappedFeat mf 
)
protectedvirtual

◆ xAssignFeatureAttributeCodeBreak()

bool CGff2Writer::xAssignFeatureAttributeCodeBreak ( CGffFeatureRecord record,
CGffFeatureContext ,
const CMappedFeat mf 
)
protected

◆ xAssignFeatureAttributeDbxref() [1/2]

virtual bool CGff2Writer::xAssignFeatureAttributeDbxref ( CGffFeatureRecord ,
CGffFeatureContext ,
const CMappedFeat  
)
inlineprotectedvirtual

Reimplemented in CGtfWriter, and CGff3Writer.

Definition at line 262 of file gff_writer.hpp.

◆ xAssignFeatureAttributeDbxref() [2/2]

bool CGff2Writer::xAssignFeatureAttributeDbxref ( CGffFeatureRecord record,
CGffFeatureContext fc,
const string label,
const CMappedFeat mf 
)
protectedvirtual

◆ xAssignFeatureAttributeEcNumbers()

bool CGff2Writer::xAssignFeatureAttributeEcNumbers ( CGffFeatureRecord record,
CGffFeatureContext ,
const CMappedFeat mf 
)
protected

◆ xAssignFeatureAttributeException()

bool CGff2Writer::xAssignFeatureAttributeException ( CGffFeatureRecord record,
CGffFeatureContext ,
const CMappedFeat mf 
)
protected

◆ xAssignFeatureAttributeExonNumber()

bool CGff2Writer::xAssignFeatureAttributeExonNumber ( CGffFeatureRecord record,
CGffFeatureContext ,
const CMappedFeat mf 
)
protected

◆ xAssignFeatureAttributeExperiment()

bool CGff2Writer::xAssignFeatureAttributeExperiment ( CGffFeatureRecord record,
CGffFeatureContext ,
const CMappedFeat mf 
)
protected

◆ xAssignFeatureAttributeFunction()

bool CGff2Writer::xAssignFeatureAttributeFunction ( CGffFeatureRecord record,
CGffFeatureContext ,
const CMappedFeat mf 
)
protected

◆ xAssignFeatureAttributeGeneBiotype()

bool CGff2Writer::xAssignFeatureAttributeGeneBiotype ( CGffFeatureRecord record,
CGffFeatureContext fc,
const CMappedFeat mf 
)
protected

◆ xAssignFeatureAttributeIsOrdered()

bool CGff2Writer::xAssignFeatureAttributeIsOrdered ( CGffFeatureRecord record,
CGffFeatureContext ,
const CMappedFeat mf 
)
protected

◆ xAssignFeatureAttributeMapLoc()

bool CGff2Writer::xAssignFeatureAttributeMapLoc ( CGffFeatureRecord record,
CGffFeatureContext ,
const CMappedFeat mf 
)
protected

◆ xAssignFeatureAttributeModelEvidence()

bool CGff2Writer::xAssignFeatureAttributeModelEvidence ( CGffFeatureRecord record,
CGffFeatureContext ,
const CMappedFeat mf 
)
protected

◆ xAssignFeatureAttributeNote()

virtual bool CGff2Writer::xAssignFeatureAttributeNote ( CGffFeatureRecord ,
CGffFeatureContext ,
const CMappedFeat  
)
inlineprotectedvirtual

Reimplemented in CGtfWriter, and CGff3Writer.

Definition at line 267 of file gff_writer.hpp.

Referenced by xAssignFeatureAttributesFormatIndependent().

◆ xAssignFeatureAttributeOldLocusTag()

bool CGff2Writer::xAssignFeatureAttributeOldLocusTag ( CGffFeatureRecord record,
CGffFeatureContext ,
const CMappedFeat mf 
)
protected

◆ xAssignFeatureAttributePartial()

bool CGff2Writer::xAssignFeatureAttributePartial ( CGffFeatureRecord record,
CGffFeatureContext fc,
const CMappedFeat mf 
)
protectedvirtual

◆ xAssignFeatureAttributeProduct()

bool CGff2Writer::xAssignFeatureAttributeProduct ( CGffFeatureRecord record,
CGffFeatureContext ,
const CMappedFeat mf 
)
protectedvirtual

◆ xAssignFeatureAttributeProteinId()

bool CGff2Writer::xAssignFeatureAttributeProteinId ( CGffFeatureRecord record,
CGffFeatureContext fc,
const CMappedFeat mf 
)
protectedvirtual

◆ xAssignFeatureAttributePseudo()

bool CGff2Writer::xAssignFeatureAttributePseudo ( CGffFeatureRecord record,
CGffFeatureContext fc,
const CMappedFeat mf 
)
protectedvirtual

◆ xAssignFeatureAttributePseudoGene()

bool CGff2Writer::xAssignFeatureAttributePseudoGene ( CGffFeatureRecord record,
CGffFeatureContext fc,
const CMappedFeat mf 
)
protected

◆ xAssignFeatureAttributeRibosomalSlippage()

bool CGff2Writer::xAssignFeatureAttributeRibosomalSlippage ( CGffFeatureRecord record,
CGffFeatureContext fc,
const CMappedFeat mf 
)
protectedvirtual

◆ xAssignFeatureAttributeRptFamily()

bool CGff2Writer::xAssignFeatureAttributeRptFamily ( CGffFeatureRecord record,
CGffFeatureContext ,
const CMappedFeat mf 
)
protected

◆ xAssignFeatureAttributes()

bool CGff2Writer::xAssignFeatureAttributes ( CGffFeatureRecord record,
CGffFeatureContext fc,
const CMappedFeat mf 
)
protectedvirtual

◆ xAssignFeatureAttributesFormatIndependent()

bool CGff2Writer::xAssignFeatureAttributesFormatIndependent ( CGffFeatureRecord record,
CGffFeatureContext fc,
const CMappedFeat mf 
)
protectedvirtual

◆ xAssignFeatureAttributesFormatSpecific()

bool CGff2Writer::xAssignFeatureAttributesFormatSpecific ( CGffFeatureRecord record,
CGffFeatureContext fc,
const CMappedFeat mf 
)
protectedvirtual

Reimplemented in CGtfWriter, and CGff3Writer.

Definition at line 572 of file gff_writer.cpp.

Referenced by xAssignFeatureAttributes().

◆ xAssignFeatureAttributesGene()

bool CGff2Writer::xAssignFeatureAttributesGene ( CGffFeatureRecord record,
CGffFeatureContext fc,
const CMappedFeat mf 
)
protectedvirtual

◆ xAssignFeatureAttributesGoMarkup()

bool CGff2Writer::xAssignFeatureAttributesGoMarkup ( CGffFeatureRecord record,
CGffFeatureContext ,
const CMappedFeat mf 
)
protected

◆ xAssignFeatureAttributesQualifiers()

virtual bool CGff2Writer::xAssignFeatureAttributesQualifiers ( CGffFeatureRecord ,
CGffFeatureContext ,
const CMappedFeat  
)
inlineprotectedvirtual

Reimplemented in CGtfWriter, and CGff3Writer.

Definition at line 247 of file gff_writer.hpp.

Referenced by xAssignFeatureAttributesFormatIndependent().

◆ xAssignFeatureAttributeTranslationTable()

bool CGff2Writer::xAssignFeatureAttributeTranslationTable ( CGffFeatureRecord record,
CGffFeatureContext ,
const CMappedFeat mf 
)
protectedvirtual

◆ xAssignFeatureBasic()

bool CGff2Writer::xAssignFeatureBasic ( CGffFeatureRecord record,
CGffFeatureContext fc,
const CMappedFeat mf 
)
protectedvirtual

◆ xAssignFeatureEndpoints()

bool CGff2Writer::xAssignFeatureEndpoints ( CGffFeatureRecord record,
CGffFeatureContext fc,
const CMappedFeat mapped_feat 
)
protectedvirtual

◆ xAssignFeatureMethod()

bool CGff2Writer::xAssignFeatureMethod ( CGffFeatureRecord record,
CGffFeatureContext ,
const CMappedFeat mf 
)
protectedvirtual

Reimplemented in CGvfWriter, CGtfWriter, and CGff3Writer.

Definition at line 487 of file gff_writer.cpp.

References CGffBaseRecord::SetMethod().

Referenced by xAssignFeatureBasic().

◆ xAssignFeaturePhase()

bool CGff2Writer::xAssignFeaturePhase ( CGffFeatureRecord record,
CGffFeatureContext fc,
const CMappedFeat mf 
)
protectedvirtual

Reimplemented in CGff3Writer.

Definition at line 453 of file gff_writer.cpp.

Referenced by xAssignFeatureBasic().

◆ xAssignFeatureScore()

bool CGff2Writer::xAssignFeatureScore ( CGffFeatureRecord record,
CGffFeatureContext fc,
const CMappedFeat mf 
)
protectedvirtual

◆ xAssignFeatureSeqId()

bool CGff2Writer::xAssignFeatureSeqId ( CGffFeatureRecord record,
CGffFeatureContext fc,
const CMappedFeat mf 
)
protectedvirtual

◆ xAssignFeatureStrand()

bool CGff2Writer::xAssignFeatureStrand ( CGffFeatureRecord record,
CGffFeatureContext fc,
const CMappedFeat mf 
)
protectedvirtual

Reimplemented in CGff3Writer.

Definition at line 474 of file gff_writer.cpp.

References eNa_strand_plus, CMappedFeat::GetLocation(), location, and CGffBaseRecord::SetStrand().

Referenced by xAssignFeatureBasic().

◆ xAssignFeatureType()

bool CGff2Writer::xAssignFeatureType ( CGffFeatureRecord record,
CGffFeatureContext fc,
const CMappedFeat mf 
)
protectedvirtual

Reimplemented in CGvfWriter, CGtfWriter, and CGff3Writer.

Definition at line 463 of file gff_writer.cpp.

References CGffBaseRecord::SetType().

Referenced by xAssignFeatureBasic().

◆ xGenerateMissingTranscript()

CMappedFeat CGff2Writer::xGenerateMissingTranscript ( CGffFeatureContext context,
const CMappedFeat mf 
)
protected

◆ xGeneratingMissingTranscripts()

virtual bool CGff2Writer::xGeneratingMissingTranscripts ( ) const
inlineprotectedvirtual

Definition at line 386 of file gff_writer.hpp.

References fGenerateMissingTranscripts, and CWriterBase::m_uFlags.

Referenced by xGenerateMissingTranscript().

◆ xIntervalsNeedPartNumbers()

bool CGff2Writer::xIntervalsNeedPartNumbers ( const list< CRef< CSeq_interval >> &  sublocs)
staticprotected

◆ xWriteAllChildren()

bool CGff2Writer::xWriteAllChildren ( CGffFeatureContext fc,
const CMappedFeat mf 
)
protectedvirtual

Reimplemented in CGff3Writer.

Definition at line 226 of file gff_writer.cpp.

References fc, and xWriteFeature().

Referenced by CGtfWriter::x_WriteBioseqHandle().

◆ xWriteFeature() [1/2]

bool CGff2Writer::xWriteFeature ( CFeat_CI  feat_it)
overrideprotectedvirtual

Reimplemented from CFeatWriter.

Definition at line 299 of file gff_writer.cpp.

References fc, CSeq_feat_Handle::GetAnnot(), and xWriteFeature().

◆ xWriteFeature() [2/2]

bool CGff2Writer::xWriteFeature ( CGffFeatureContext context,
const CMappedFeat mf 
)
protectedvirtual

Member Data Documentation

◆ m_bHeaderWritten

bool CGff2Writer::m_bHeaderWritten
protected

◆ m_pScope

CRef<CScope> CGff2Writer::m_pScope
protected

The documentation for this class was generated from the following files:
Modified on Tue Jul 23 17:53:56 2024 by modify_doxy.py rev. 669887