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CGffBaseRecord Class Reference

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#include <objtools/writers/gff_base_record.hpp>

+ Inheritance diagram for CGffBaseRecord:
+ Collaboration diagram for CGffBaseRecord:

Public Types

typedef map< string, vector< string > > TAttributes
 
typedef TAttributes::iterator TAttrIt
 
typedef TAttributes::const_iterator TAttrCit
 
typedef map< string, stringTScores
 
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 CAtomicCounter TCounter
 Counter type is CAtomiCounter. More...
 
typedef TCounter::TValue TCount
 Alias for value type of counter. More...
 

Public Member Functions

 CGffBaseRecord (const string &id="")
 
 CGffBaseRecord (const CGffBaseRecord &)
 
virtual ~CGffBaseRecord ()
 
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 SetRecordId (const string &)
 
void SetParent (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 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_locGetLocation () 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
 

Protected Member Functions

string xEscapedValue (const string &, const string &) const
 
string xEscapedString (const string &) const
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Protected Attributes

CRef< CSeq_locm_pLoc
 
string mSeqId
 
string mType
 
string mMethod
 
unsigned int mSeqStart
 
unsigned int mSeqStop
 
string mScore
 
string mStrand
 
string mPhase
 
TAttributes mAttributes
 
TScores mExtraScores
 
string mRecordId
 
string mParent
 

Static Protected Attributes

static const char * ATTR_SEPARATOR = ";"
 

Additional Inherited Members

- Static Public Member Functions inherited from CObject
static NCBI_NORETURN void ThrowNullPointerException (void)
 Define method to throw null pointer exception. More...
 
static NCBI_NORETURN 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...
 

Detailed Description

Definition at line 44 of file gff_base_record.hpp.

Member Typedef Documentation

Definition at line 51 of file gff_base_record.hpp.

Definition at line 49 of file gff_base_record.hpp.

Definition at line 50 of file gff_base_record.hpp.

Definition at line 55 of file gff_base_record.hpp.

Definition at line 54 of file gff_base_record.hpp.

Definition at line 53 of file gff_base_record.hpp.

Constructor & Destructor Documentation

CGffBaseRecord::CGffBaseRecord ( const string id = "")

Definition at line 49 of file gff_base_record.cpp.

References SetRecordId().

CGffBaseRecord::CGffBaseRecord ( const CGffBaseRecord other)
CGffBaseRecord::~CGffBaseRecord ( )
virtual

Definition at line 90 of file gff_base_record.cpp.

Member Function Documentation

bool CGffBaseRecord::AddAttribute ( const string key,
const string value 
)
bool CGffBaseRecord::AddAttributes ( const string key,
const vector< string > &  values 
)
bool CGffBaseRecord::CanGetLocation ( void  ) const
inline

Definition at line 114 of file gff_base_record.hpp.

References m_pLoc.

Referenced by CGff3Writer::xWriteRecord().

bool CGffBaseRecord::DropAttributes ( const string attr)
bool CGffBaseRecord::GetAttributes ( const string key,
vector< string > &  value 
) const
const CSeq_loc& CGffBaseRecord::GetLocation ( void  ) const
inline

Definition at line 115 of file gff_base_record.hpp.

References m_pLoc.

Referenced by CGff3Writer::xWriteRecord().

bool CGffBaseRecord::SetAttribute ( const string key,
const string value 
)

Definition at line 124 of file gff_base_record.cpp.

References AddAttribute(), DropAttributes(), mParent, mRecordId, and value.

Referenced by CGffAlignRecord::FinalizeMatches(), CGffFeatureRecord::SetLocation(), CGff3FlybaseWriter::xAssignAlignmentDensegTarget(), CGff3Writer::xAssignAlignmentDensegTarget(), CGff3FlybaseWriter::xAssignAlignmentSplicedTarget(), CGff3Writer::xAssignAlignmentSplicedTarget(), CGff3FlybaseWriter::xAssignDefline(), CGff3Writer::xAssignFeatureAttributeEcNumbers(), CGff3Writer::xAssignFeatureAttributeException(), CGff3Writer::xAssignFeatureAttributeExonNumber(), CGff3Writer::xAssignFeatureAttributeExperiment(), CGff3Writer::xAssignFeatureAttributeFunction(), CGff3Writer::xAssignFeatureAttributeGbKey(), CGff3Writer::xAssignFeatureAttributeGene(), CGff3Writer::xAssignFeatureAttributeGeneBiotype(), CGff3Writer::xAssignFeatureAttributeGeneDesc(), CGff3Writer::xAssignFeatureAttributeIsOrdered(), CGff3Writer::xAssignFeatureAttributeLocusTag(), CGff3Writer::xAssignFeatureAttributeMapLoc(), CGff3Writer::xAssignFeatureAttributeModelEvidence(), CGff3Writer::xAssignFeatureAttributeName(), CGff3Writer::xAssignFeatureAttributeNcrnaClass(), CGff3Writer::xAssignFeatureAttributeNote(), CGff3Writer::xAssignFeatureAttributeOldLocusTag(), CGff3Writer::xAssignFeatureAttributePartial(), CGff3Writer::xAssignFeatureAttributeProduct(), CGff3Writer::xAssignFeatureAttributeProteinId(), CGff3Writer::xAssignFeatureAttributePseudo(), CGff3Writer::xAssignFeatureAttributePseudoGene(), CGff3Writer::xAssignFeatureAttributeRptFamily(), CGff3Writer::xAssignFeatureAttributesGoMarkup(), CGff3Writer::xAssignFeatureAttributesQualifiers(), CGff3Writer::xAssignFeatureAttributeTranscriptId(), CGff3Writer::xAssignFeatureAttributeTranslationTable(), CGff3Writer::xAssignFeatureEndpoints(), CGff3Writer::xAssignSourceAttributeGbKey(), CGff3Writer::xAssignSourceAttributeGenome(), CGff3Writer::xAssignSourceAttributeIsCircular(), CGff3Writer::xAssignSourceAttributeMolType(), CGff3Writer::xAssignSourceAttributeName(), CGff3Writer::xAssignSourceAttributesOrgMod(), CGff3Writer::xAssignSourceAttributesSubSource(), CGff3FlybaseWriter::xAssignTaxid(), CGff3Writer::xWriteFeatureCDJVSegment(), CGff3Writer::xWriteFeatureRecords(), and CGff3Writer::xWriteFeatureRna().

bool CGffBaseRecord::SetAttributes ( const string key,
const vector< string > &  values 
)
void CGffBaseRecord::SetLocation ( unsigned int  seqStart,
unsigned int  seqStop,
ENa_strand  seqStrand = objects::eNa_strand_unknown 
)
void CGffBaseRecord::SetMethod ( const string method)
void CGffBaseRecord::SetParent ( const string parent)
void CGffBaseRecord::SetPhase ( unsigned int  phase)
void CGffBaseRecord::SetRecordId ( const string recordId)
void CGffBaseRecord::SetScore ( const CScore score)
void CGffBaseRecord::SetSeqId ( const string seqId)
void CGffBaseRecord::SetStrand ( ENa_strand  seqStrand)
void CGffBaseRecord::SetType ( const string type)
string CGffBaseRecord::StrAttributes ( ) const
virtual
string CGffBaseRecord::StrMethod ( ) const
virtual

Definition at line 253 of file gff_base_record.cpp.

References mMethod, and xEscapedString().

Referenced by CGff3Writer::xWriteRecord().

string CGffBaseRecord::StrPhase ( ) const
virtual

Definition at line 397 of file gff_base_record.cpp.

References mPhase.

Referenced by CGff3Writer::xWriteRecord().

string CGffBaseRecord::StrScore ( ) const
virtual

Definition at line 369 of file gff_base_record.cpp.

References mScore.

Referenced by CGff3Writer::xWriteRecord().

string CGffBaseRecord::StrSeqId ( ) const
virtual
string CGffBaseRecord::StrSeqStart ( ) const
virtual

Definition at line 376 of file gff_base_record.cpp.

References mSeqStart, and NStr::UIntToString().

Referenced by CGff3Writer::xWriteRecord().

string CGffBaseRecord::StrSeqStop ( ) const
virtual

Definition at line 383 of file gff_base_record.cpp.

References mSeqStop, and NStr::UIntToString().

Referenced by CGff3Writer::xWriteRecord().

string CGffBaseRecord::StrStrand ( ) const
virtual

Definition at line 390 of file gff_base_record.cpp.

References mStrand.

Referenced by CGff3Writer::xWriteRecord().

string CGffBaseRecord::StrType ( ) const
virtual

Definition at line 260 of file gff_base_record.cpp.

References mType, and xEscapedString().

Referenced by CGff3Writer::xWriteRecord().

string CGffBaseRecord::xEscapedString ( const string str) const
protected

Definition at line 517 of file gff_base_record.cpp.

References str().

Referenced by StrAttributes(), StrMethod(), StrSeqId(), and StrType().

string CGffBaseRecord::xEscapedValue ( const string key,
const string value 
) const
protected

Member Data Documentation

const char * CGffBaseRecord::ATTR_SEPARATOR = ";"
staticprotected

Definition at line 125 of file gff_base_record.hpp.

Referenced by StrAttributes().

CRef<CSeq_loc> CGffBaseRecord::m_pLoc
protected
TAttributes CGffBaseRecord::mAttributes
protected
TScores CGffBaseRecord::mExtraScores
protected

Definition at line 137 of file gff_base_record.hpp.

Referenced by SetScore(), and StrAttributes().

string CGffBaseRecord::mMethod
protected

Definition at line 130 of file gff_base_record.hpp.

Referenced by SetMethod(), and StrMethod().

string CGffBaseRecord::mParent
protected

Definition at line 139 of file gff_base_record.hpp.

Referenced by AddAttribute(), SetAttribute(), SetParent(), and StrAttributes().

string CGffBaseRecord::mPhase
protected

Definition at line 135 of file gff_base_record.hpp.

Referenced by SetPhase(), and StrPhase().

string CGffBaseRecord::mRecordId
protected

Definition at line 138 of file gff_base_record.hpp.

Referenced by AddAttribute(), SetAttribute(), SetRecordId(), and StrAttributes().

string CGffBaseRecord::mScore
protected

Definition at line 133 of file gff_base_record.hpp.

Referenced by SetScore(), and StrScore().

string CGffBaseRecord::mSeqId
protected

Definition at line 128 of file gff_base_record.hpp.

Referenced by SetSeqId(), and StrSeqId().

unsigned int CGffBaseRecord::mSeqStart
protected

Definition at line 131 of file gff_base_record.hpp.

Referenced by CGffFeatureRecord::SetLocation(), SetLocation(), and StrSeqStart().

unsigned int CGffBaseRecord::mSeqStop
protected

Definition at line 132 of file gff_base_record.hpp.

Referenced by CGffFeatureRecord::SetLocation(), SetLocation(), and StrSeqStop().

string CGffBaseRecord::mStrand
protected

Definition at line 134 of file gff_base_record.hpp.

Referenced by SetStrand(), and StrStrand().

string CGffBaseRecord::mType
protected

Definition at line 129 of file gff_base_record.hpp.

Referenced by SetType(), and StrType().


The documentation for this class was generated from the following files:
Modified on Tue Sep 19 16:28:48 2017 by modify_doxy.py rev. 546573