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NCBI C++ ToolKit: CWriterBase Class Reference

Search Toolkit Book for CWriterBase

Defines and provides stubs for a general interface to a variety of file formatters. More...

#include <objtools/writers/writer.hpp>

virtual  ~CWriterBase ()   virtual bool  WriteAnnot (const CSeq_annot &, const string &="", const string &="")   Write a raw Seq-annot to the internal output stream. More...
  virtual bool  WriteAlign (const CSeq_align &, const string &="", const string &="")   Write a raw Seq-align to the internal output stream. More...
  virtual bool  WriteSeqEntryHandle (CSeq_entry_Handle, const string &="", const string &="")   Write a Seq-entry handle to the internal output stream. More...
  virtual bool  WriteBioseqHandle (CBioseq_Handle, const string &="", const string &="")   Write a Bioseq handle to the internal output stream. More...
  virtual bool  WriteSeqAnnotHandle (CSeq_annot_Handle, const string &="", const string &="")   Write a Seq-annot handle to the internal output stream. More...
  virtual bool  WriteHeader ()   Write a file header. More...
  virtual bool  WriteHeader (const CSeq_annot &)   Write a file header, using annotation information. More...
  virtual bool  WriteFooter ()   Write a file trailer. More...
  void  SetMessageListener (CWriterListener *pMessageListener)   virtual void  PutMessage (const CWriterMessage &message)   virtual SAnnotSelector &  SetAnnotSelector (void)   SAnnotSelector &  GetAnnotSelector (void)   virtual CRange< TSeqPos > &  SetRange (void)   virtual const CRange< TSeqPos > &  GetRange (void) const   CGenbankIdResolve &  SetIdResolve (void)   bool  GetBestId (CSeq_id_Handle idh, CScope &scope, string &best_id) const   bool  GetBestId (const CMappedFeat &mf, string &best_id) const     CObject (void)   Constructor. More...
    CObject (const CObject &src)   Copy constructor. More...
  virtual  ~CObject (void)   Destructor. More...
  CObject &  operator= (const CObject &src) THROWS_NONE   Assignment operator. More...
  bool  CanBeDeleted (void) const THROWS_NONE   Check if object can be deleted. More...
  bool  IsAllocatedInPool (void) const THROWS_NONE   Check if object is allocated in memory pool (not system heap) More...
  bool  Referenced (void) const THROWS_NONE   Check if object is referenced. More...
  bool  ReferencedOnlyOnce (void) const THROWS_NONE   Check if object is referenced only once. More...
  void  AddReference (void) const   Add reference to object. More...
  void  RemoveReference (void) const   Remove reference to object. More...
  void  ReleaseReference (void) const   Remove reference without deleting object. More...
  virtual void  DoNotDeleteThisObject (void)   Mark this object as not allocated in heap – do not delete this object. More...
  virtual void  DoDeleteThisObject (void)   Mark this object as allocated in heap – object can be deleted. More...
  void *  operator new (size_t size)   Define new operator for memory allocation. More...
  void *  operator new[] (size_t size)   Define new[] operator for 'array' memory allocation. More...
  void  operator delete (void *ptr)   Define delete operator for memory deallocation. More...
  void  operator delete[] (void *ptr)   Define delete[] operator for memory deallocation. More...
  void *  operator new (size_t size, void *place)   Define new operator. More...
  void  operator delete (void *ptr, void *place)   Define delete operator. More...
  void *  operator new (size_t size, CObjectMemoryPool *place)   Define new operator using memory pool. More...
  void  operator delete (void *ptr, CObjectMemoryPool *place)   Define delete operator. More...
  virtual void  DebugDump (CDebugDumpContext ddc, unsigned int depth) const   Define method for dumping debug information. More...
    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     CInterruptable ()   virtual  ~CInterruptable ()   void  SetCanceler (ICanceled *pCanceller)   bool  IsCanceled () const   virtual  ~ICanceled ()  

Defines and provides stubs for a general interface to a variety of file formatters.

These writers take Genbank object in raw or handle form, and render them to an output stream in their respective formats.

Definition at line 78 of file writer.hpp.

◆ TFlags

Customization flags that are relevant to all CWriterBase derived writers.

Enumerator fNormal  fDebugOutput  fWriterBaseLast 

Definition at line 85 of file writer.hpp.

◆ CWriterBase() ◆ ~CWriterBase() virtual CWriterBase::~CWriterBase ( ) inlinevirtual

Definition at line 98 of file writer.hpp.

◆ GetAnnotSelector() ◆ GetBestId() [1/2] ◆ GetBestId() [2/2]

Definition at line 56 of file writer.cpp.

References mpIdResolve.

Referenced by CAlnWriter::GetBestId(), CVcfWriter::x_WriteFeatureChrom(), CGff2Writer::xAssignFeatureAttributeProduct(), CGff2Writer::xAssignFeatureAttributeProteinId(), CGff3Writer::xAssignFeatureAttributeTranscriptId(), CGtfWriter::xAssignFeatureAttributeTranscriptId(), CGff2Writer::xAssignFeatureSeqId(), CGff3Writer::xAssignSourceSeqId(), CWiggleWriter::xTableGetChromName(), CGff3Writer::xWriteRecord(), CWiggleWriter::xWriteSingleGraphFixedStep(), CWiggleWriter::xWriteTableBedStyle(), CWiggleWriter::xWriteTableFixedStep(), and CWiggleWriter::xWriteTableVariableStep().

◆ GetRange()

Definition at line 257 of file writer.hpp.

References m_Range.

Referenced by CGff2Writer::x_WriteBioseqHandle(), CGff3Writer::x_WriteBioseqHandle(), CGtfWriter::x_WriteBioseqHandle(), CVcfWriter::x_WriteData(), CGff3Writer::xAssignFeature(), CGff2Writer::xAssignFeatureAttributeCodeBreak(), CGff2Writer::xAssignFeatureAttributePartial(), CGff2Writer::xAssignFeatureAttributeProduct(), CGff3Writer::xWriteFeatureCds(), CGff3Writer::xWriteNucleotideFeature(), CGff3Writer::xWriteNucleotideSequence(), CGff3Writer::xWriteProteinFeature(), and CGff3Writer::xWriteProteinSequence().

◆ PutMessage() ◆ SetAnnotSelector()

Reimplemented in CVcfWriter.

Definition at line 241 of file writer.hpp.

References SAnnotSelector::eSortOrder_Normal, and m_Selector.

Referenced by GetAnnotSelector(), CVcfWriter::SetAnnotSelector(), CGff2Writer::x_WriteBioseqHandle(), CGff3Writer::x_WriteBioseqHandle(), CGtfWriter::x_WriteBioseqHandle(), CGff2Writer::x_WriteSeqAnnotHandle(), CGvfWriter::x_WriteSeqAnnotHandle(), CAnnotWriterApp::xInitWriter(), CGff3Writer::xSetJunkFilteringAnnotSelector(), CGff3Writer::xWriteNucleotideSequence(), CGff3Writer::xWriteProteinSequence(), and CBedWriter::xWriteTrackedAnnot().

◆ SetIdResolve() ◆ SetMessageListener() void CWriterBase::SetMessageListener ( CWriterListener *  pMessageListener ) inline ◆ SetRange() ◆ WriteAlign()

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
align the Seq-align object to be written. name parameter describing the object. Handling will be format specific. descr parameter describing the object. Handling will be format specific.

Reimplemented in CPslWriter, CAlnWriter, CGff2Writer, and CGff3Writer.

Definition at line 130 of file writer.hpp.

Referenced by CAnnotWriterApp::xProcessInputObject().

◆ WriteAnnot() ◆ WriteBioseqHandle()

Write a Bioseq handle 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
bsh the Bioseq handle to be written. name parameter describing the object. Handling will be format specific. descr parameter describing the object. Handling will be format specific.

Reimplemented in CGff2Writer.

Definition at line 168 of file writer.hpp.

Referenced by CAnnotWriterApp::xProcessBioseqHandle().

◆ WriteFooter() virtual bool CWriterBase::WriteFooter ( ) inlinevirtual ◆ WriteHeader() [1/2] virtual bool CWriterBase::WriteHeader ( void  ) inlinevirtual ◆ WriteHeader() [2/2] ◆ WriteSeqAnnotHandle()

Write a Seq-annot handle 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
sah the Seq-annot handle to be written. name parameter describing the object. Handling will be format specific. descr parameter describing the object. Handling will be format specific.

Reimplemented in CGff2Writer.

Definition at line 187 of file writer.hpp.

◆ WriteSeqEntryHandle()

Write a Seq-entry handle 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
seh the Seq-entry handle to be written. name parameter describing the object. Handling will be format specific. descr parameter describing the object. Handling will be format specific.

Reimplemented in CGff2Writer, and CBedWriter.

Definition at line 149 of file writer.hpp.

Referenced by sRunTest(), sUpdateCase(), and CAnnotWriterApp::xProcessInputObject().

◆ m_Os

Definition at line 271 of file writer.hpp.

Referenced by CPslWriter::WriteAlign(), CUCSCRegionWriter::WriteAnnot(), CBedGraphWriter::WriteAnnot(), CBedWriter::WriteAnnot(), CAlnWriter::WriteContiguous(), CGff3Writer::WriteFooter(), CWiggleWriter::WriteFooter(), CGff3Writer::WriteHeader(), CGff2Writer::WriteHeader(), CGtfWriter::WriteHeader(), CGvfWriter::WriteHeader(), CBedWriter::WriteSeqEntryHandle(), CGff2Writer::x_WriteAssemblyInfo(), CVcfWriter::x_WriteFeature(), CVcfWriter::x_WriteFeatureAlt(), CVcfWriter::x_WriteFeatureChrom(), CVcfWriter::x_WriteFeatureFilter(), CVcfWriter::x_WriteFeatureGenotypeData(), CVcfWriter::x_WriteFeatureId(), CVcfWriter::x_WriteFeatureInfo(), CVcfWriter::x_WriteFeaturePos(), CVcfWriter::x_WriteFeatureQual(), CVcfWriter::x_WriteFeatureRef(), CVcfWriter::x_WriteHeader(), CVcfWriter::x_WriteMeta(), CVcfWriter::x_WriteMetaCreateNew(), CGff3Writer::xWriteAlignment(), CBedGraphWriter::xWriteAnnotSeqTable(), CWiggleWriter::xWriteDefaultTrackLine(), CBedWriter::xWriteFeaturesThreeFeatData(), CBedWriter::xWriteFeaturesTracked(), CGff3Writer::xWriteRecord(), CGvfWriter::xWriteRecord(), CGtfWriter::xWriteRecord(), CGff3Writer::xWriteSequenceHeader(), CBedGraphWriter::xWriteSingleFeature(), CBedGraphWriter::xWriteSingleGraphByte(), CWiggleWriter::xWriteSingleGraphFixedStep(), CBedGraphWriter::xWriteSingleGraphInt(), CBedGraphWriter::xWriteSingleGraphReal(), CWiggleWriter::xWriteSingleGraphRecordsByte(), CWiggleWriter::xWriteSingleGraphRecordsInt(), CWiggleWriter::xWriteSingleGraphRecordsReal(), CWiggleWriter::xWriteTableBedStyle(), CWiggleWriter::xWriteTableFixedStep(), CWiggleWriter::xWriteTableVariableStep(), and CWiggleWriter::xWriteTrackLine().

◆ m_Range ◆ m_Selector ◆ m_uFlags unsigned int CWriterBase::m_uFlags protected ◆ mpIdResolve ◆ mpMessageListener

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

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