Search Toolkit Book for CGff3FeatureRecord
#include <objtools/writers/gff3_writer.hpp>
Inheritance diagram for CGff3FeatureRecord:
Collaboration diagram for CGff3FeatureRecord:
Public Member Functions | |
| CGff3FeatureRecord () | |
| CGff3FeatureRecord (const CGff3FeatureRecord &rhs) | |
| void | SetRecordId (const string &recordId) |
| void | SetParent (const string &parent) |
| string | Id () const |
| string | Parent () const |
| string | StrAttributes () const |
| Public Member Functions inherited from CGffFeatureRecord | |
| CGffFeatureRecord (const string &id="") | |
| CGffFeatureRecord (const CGffFeatureRecord &other) | |
| virtual | ~CGffFeatureRecord () |
| void | InitLocation (const CSeq_loc &) |
| void | SetLocation (const CSeq_interval &, unsigned int, unsigned int=0) |
| void | SetEndpoints (unsigned int start, unsigned int stop, ENa_strand strand) |
| const CSeq_loc & | Location () const |
| void | SetGbKeyFrom (CMappedFeat) |
| Public Member Functions inherited from CGffBaseRecord | |
| CGffBaseRecord (const string &id="") | |
| CGffBaseRecord (const CGffBaseRecord &) | |
| virtual | ~CGffBaseRecord () |
| const TAttributes & | Attributes () const |
| bool | AddAttribute (const string &, const string &) |
| bool | AddAttributes (const string &, const vector< string > &) |
| bool | SetAttribute (const string &, const string &) |
| bool | SetAttributes (const string &, const vector< string > &) |
| bool | GetAttributes (const string &, vector< string > &) const |
| bool | DropAttributes (const string &) |
| void | SetSeqId (const string &) |
| void | SetMethod (const string &) |
| void | SetType (const string &) |
| void | SetLocation (unsigned int, unsigned int, ENa_strand=objects::eNa_strand_unknown) |
| void | SetStrand (ENa_strand) |
| void | SetScore (const CScore &) |
| void | SetScore (const std::string &) |
| void | SetPhase (unsigned int) |
| virtual string | StrSeqId () const |
| virtual string | StrMethod () const |
| virtual string | StrType () const |
| virtual string | StrSeqStart () const |
| virtual string | StrSeqStop () const |
| virtual string | StrStrand () const |
| virtual string | StrScore () const |
| virtual string | StrPhase () const |
| bool | CanGetLocation () const |
| const CSeq_loc & | GetLocation () const |
| unsigned int | SeqStart () const |
| unsigned int | SeqStop () const |
| objects::ENa_strand | SeqStrand () const |
| Public Member Functions inherited from CObject | |
| CObject (void) | |
| Constructor. More... | |
| CObject (const CObject &src) | |
| Copy constructor. More... | |
| virtual | ~CObject (void) |
| Destructor. More... | |
| CObject & | operator= (const CObject &src) THROWS_NONE |
| Assignment operator. More... | |
| bool | CanBeDeleted (void) const THROWS_NONE |
| Check if object can be deleted. More... | |
| bool | IsAllocatedInPool (void) const THROWS_NONE |
| Check if object is allocated in memory pool (not system heap) More... | |
| bool | Referenced (void) const THROWS_NONE |
| Check if object is referenced. More... | |
| bool | ReferencedOnlyOnce (void) const THROWS_NONE |
| Check if object is referenced only once. More... | |
| void | AddReference (void) const |
| Add reference to object. More... | |
| void | RemoveReference (void) const |
| Remove reference to object. More... | |
| void | ReleaseReference (void) const |
| Remove reference without deleting object. More... | |
| virtual void | DoNotDeleteThisObject (void) |
| Mark this object as not allocated in heap – do not delete this object. More... | |
| virtual void | DoDeleteThisObject (void) |
| Mark this object as allocated in heap – object can be deleted. More... | |
| void * | operator new (size_t size) |
| Define new operator for memory allocation. More... | |
| void * | operator new[] (size_t size) |
| Define new[] operator for 'array' memory allocation. More... | |
| void | operator delete (void *ptr) |
| Define delete operator for memory deallocation. More... | |
| void | operator delete[] (void *ptr) |
| Define delete[] operator for memory deallocation. More... | |
| void * | operator new (size_t size, void *place) |
| Define new operator. More... | |
| void | operator delete (void *ptr, void *place) |
| Define delete operator. More... | |
| void * | operator new (size_t size, CObjectMemoryPool *place) |
| Define new operator using memory pool. More... | |
| void | operator delete (void *ptr, CObjectMemoryPool *place) |
| Define delete operator. More... | |
| virtual void | DebugDump (CDebugDumpContext ddc, unsigned int depth) const |
| Define method for dumping debug information. More... | |
| Public Member Functions inherited from CDebugDumpable | |
| CDebugDumpable (void) | |
| virtual | ~CDebugDumpable (void) |
| void | DebugDumpText (ostream &out, const string &bundle, unsigned int depth) const |
| void | DebugDumpFormat (CDebugDumpFormatter &ddf, const string &bundle, unsigned int depth) const |
| void | DumpToConsole (void) const |
Protected Attributes | |
| string | mRecordId |
| string | mParent |
| Protected Attributes inherited from CGffBaseRecord | |
| CRef< CSeq_loc > | m_pLoc |
| string | mSeqId |
| string | mType |
| string | mMethod |
| unsigned int | mSeqStart |
| unsigned int | mSeqStop |
| string | mScore |
| string | mStrand |
| optional< int > | mPhase |
| TAttributes | mAttributes |
| TScores | mExtraScores |
Additional Inherited Members | |
| Public Types inherited from CGffBaseRecord | |
| typedef map< string, vector< string > > | TAttributes |
| typedef TAttributes::iterator | TAttrIt |
| typedef TAttributes::const_iterator | TAttrCit |
| typedef map< string, string > | TScores |
| typedef TScores::iterator | TScoreIt |
| typedef TScores::const_iterator | TScoreCit |
| Public Types inherited from CObject | |
| enum | EAllocFillMode { eAllocFillNone = 1 , eAllocFillZero , eAllocFillPattern } |
| Control filling of newly allocated memory. More... | |
| typedef CObjectCounterLocker | TLockerType |
| Default locker type for CRef. More... | |
| typedef atomic< Uint8 > | TCounter |
| Counter type is CAtomiCounter. More... | |
| typedef Uint8 | TCount |
| Alias for value type of counter. More... | |
| Static Public Member Functions inherited from CObject | |
| static NCBI_XNCBI_EXPORT void | ThrowNullPointerException (void) |
| Define method to throw null pointer exception. More... | |
| static NCBI_XNCBI_EXPORT void | ThrowNullPointerException (const type_info &type) |
| static EAllocFillMode | GetAllocFillMode (void) |
| static void | SetAllocFillMode (EAllocFillMode mode) |
| static void | SetAllocFillMode (const string &value) |
| Set mode from configuration parameter value. More... | |
| Static Public Member Functions inherited from CDebugDumpable | |
| static void | EnableDebugDump (bool on) |
| Static Public Attributes inherited from CObject | |
| static const TCount | eCounterBitsCanBeDeleted = 1 << 0 |
| Define possible object states. More... | |
| static const TCount | eCounterBitsInPlainHeap = 1 << 1 |
| Heap signature was found. More... | |
| static const TCount | eCounterBitsPlaceMask |
| Mask for 'in heap' state flags. More... | |
| static const int | eCounterStep = 1 << 2 |
| Skip over the "in heap" bits. More... | |
| static const TCount | eCounterValid = TCount(1) << (sizeof(TCount) * 8 - 2) |
| Minimal value for valid objects (reference counter is zero) Must be a single bit value. More... | |
| static const TCount | eCounterStateMask |
| Valid object, and object in heap. More... | |
| Protected Member Functions inherited from CGffBaseRecord | |
| const string & | xEscapedValue (const string &key, const string &value) const |
| const string & | xEscapedString (const string &value) const |
| Protected Member Functions inherited from CObject | |
| virtual void | DeleteThis (void) |
| Virtual method "deleting" this object. More... | |
| Static Protected Attributes inherited from CGffBaseRecord | |
| static const char * | ATTR_SEPARATOR = ";" |
Detailed Description
Definition at line 88 of file gff3_writer.hpp.
Constructor & Destructor Documentation
◆ CGff3FeatureRecord() [1/2]
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inline |
Definition at line 93 of file gff3_writer.hpp.
◆ CGff3FeatureRecord() [2/2]
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inline |
Definition at line 97 of file gff3_writer.hpp.
Member Function Documentation
◆ Id()
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inline |
Definition at line 105 of file gff3_writer.hpp.
References mRecordId.
Referenced by CGff3Writer::xWriteFeatureCDJVSegment(), CGff3Writer::xWriteFeatureCds(), CGff3Writer::xWriteFeatureRna(), CGff3Writer::xWriteFeatureTrna(), and CGff3Writer::xWriteNucleotideFeatureTransSpliced().
◆ Parent()
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inline |
Definition at line 106 of file gff3_writer.hpp.
References mParent.
◆ SetParent()
Definition at line 103 of file gff3_writer.hpp.
References mParent.
Referenced by CGff3Writer::xAssignFeatureAttributeParentCds(), CGff3Writer::xAssignFeatureAttributeParentGene(), CGff3Writer::xAssignFeatureAttributeParentMrna(), CGff3Writer::xAssignFeatureAttributeParentpreRNA(), CGff3Writer::xAssignFeatureAttributeParentRegion(), CGff3Writer::xAssignFeatureAttributeParentVDJsegmentCregion(), CGff3Writer::xAssignFeatureAttributesQualifiers(), CGff3Writer::xWriteFeatureCDJVSegment(), CGff3Writer::xWriteFeatureCds(), CGff3Writer::xWriteFeatureRna(), CGff3Writer::xWriteFeatureTrna(), and CGff3Writer::xWriteNucleotideFeatureTransSpliced().
◆ SetRecordId()
Definition at line 101 of file gff3_writer.hpp.
References mRecordId.
Referenced by CGff3Writer::xAssignFeatureAttributeID(), CGff3Writer::xAssignFeatureAttributesQualifiers(), CGff3Writer::xWriteFeatureCDJVSegment(), CGff3Writer::xWriteFeatureCds(), CGff3Writer::xWriteFeatureRna(), CGff3Writer::xWriteFeatureTrna(), and CGff3Writer::xWriteNucleotideFeatureTransSpliced().
◆ StrAttributes()
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inlinevirtual |
Reimplemented from CGffBaseRecord.
Definition at line 108 of file gff3_writer.hpp.
References CGffBaseRecord::ATTR_SEPARATOR, attributes, mParent, mRecordId, CGffBaseRecord::StrAttributes(), and CGffBaseRecord::xEscapedString().
Member Data Documentation
◆ mParent
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protected |
Definition at line 133 of file gff3_writer.hpp.
Referenced by Parent(), SetParent(), and StrAttributes().
◆ mRecordId
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protected |
Definition at line 132 of file gff3_writer.hpp.
Referenced by Id(), SetRecordId(), and StrAttributes().
The documentation for this class was generated from the following file:
- include/objtools/writers/gff3_writer.hpp
