NCBI C++ ToolKit
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Search Toolkit Book for CGffFeatureRecord
#include <objtools/writers/gff_feature_record.hpp>
Public Member Functions | |
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) |
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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 |
virtual string | StrAttributes () const |
bool | CanGetLocation () const |
const CSeq_loc & | GetLocation () const |
unsigned int | SeqStart () const |
unsigned int | SeqStop () const |
objects::ENa_strand | SeqStrand () const |
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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... | |
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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 |
Additional Inherited Members | |
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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 |
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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... | |
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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... | |
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static void | EnableDebugDump (bool on) |
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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... | |
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const string & | xEscapedValue (const string &key, const string &value) const |
const string & | xEscapedString (const string &value) const |
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virtual void | DeleteThis (void) |
Virtual method "deleting" this object. More... | |
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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 |
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static const char * | ATTR_SEPARATOR = ";" |
Definition at line 43 of file gff_feature_record.hpp.
Definition at line 41 of file gff_feature_record.cpp.
CGffFeatureRecord::CGffFeatureRecord | ( | const CGffFeatureRecord & | other | ) |
Definition at line 48 of file gff_feature_record.cpp.
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virtual |
Definition at line 54 of file gff_feature_record.cpp.
Definition at line 59 of file gff_feature_record.cpp.
References CSeq_loc::Assign(), CGffBaseRecord::m_pLoc, and CRef< C, Locker >::Reset().
Referenced by CGff3Writer::xAssignFeature().
Definition at line 64 of file gff_feature_record.hpp.
References CGffBaseRecord::m_pLoc.
Referenced by SetLocation(), CGff3Writer::xAssignFeatureEndpoints(), CGff3Writer::xWriteFeatureCDJVSegment(), CGff3Writer::xWriteFeatureCds(), CGff3Writer::xWriteFeatureGene(), CGff3Writer::xWriteFeatureRecords(), CGff3Writer::xWriteFeatureRna(), CGff3Writer::xWriteFeatureTrna(), and CGff3Writer::xWriteNucleotideFeatureTransSpliced().
void CGffFeatureRecord::SetEndpoints | ( | unsigned int | start, |
unsigned int | stop, | ||
ENa_strand | strand | ||
) |
Definition at line 68 of file gff_feature_record.cpp.
References CGffBaseRecord::SetLocation().
Referenced by CGff2Writer::xAssignFeatureEndpoints(), and CGff3Writer::xWriteNucleotideFeatureTransSpliced().
void CGffFeatureRecord::SetGbKeyFrom | ( | CMappedFeat | mf | ) |
Definition at line 123 of file gff_feature_record.cpp.
References CSeq_feat_Handle::GetData(), CSeqFeatData::GetKey(), and CGffBaseRecord::SetAttribute().
Referenced by CGff2Writer::xAssignFeatureAttributesFormatIndependent().
void CGffFeatureRecord::SetLocation | ( | const CSeq_interval & | interval, |
unsigned int | wrapSize, | ||
unsigned int | wrapPoint = 0 |
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) |
Definition at line 78 of file gff_feature_record.cpp.
References CSeq_interval_Base::CanGetFrom(), CSeq_interval_Base::CanGetTo(), eExtreme_Biological, eExtreme_Positional, eNa_strand_minus, CSeq_interval_Base::GetFrom(), CSeq_loc::GetStart(), CSeq_loc::GetStop(), GetStrand(), CSeq_interval_Base::GetStrand(), CSeq_interval_Base::GetTo(), NStr::IntToString(), CSeq_interval_Base::IsSetStrand(), Location(), CGffBaseRecord::m_pLoc, max(), min(), CGffBaseRecord::mSeqStart, CGffBaseRecord::mSeqStop, CRef< C, Locker >::Reset(), CGffBaseRecord::SetAttribute(), CSeq_loc::SetInt(), and CGffBaseRecord::SetStrand().
Referenced by CGff3Writer::xWriteFeatureCDJVSegment(), CGff3Writer::xWriteFeatureCds(), CGff3Writer::xWriteFeatureProtein(), CGff3Writer::xWriteFeatureRna(), CGff3Writer::xWriteFeatureTrna(), and CGff3Writer::xWriteNucleotideFeatureTransSpliced().