NCBI C++ ToolKit
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CGffAlignmentRecord Class Reference

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#include <objtools/writers/gff3_alignment_data.hpp>

+ Inheritance diagram for CGffAlignmentRecord:
+ Collaboration diagram for CGffAlignmentRecord:

Public Member Functions

 CGffAlignmentRecord (unsigned int uFlags=0, unsigned int uRecordId=0)
 
virtual ~CGffAlignmentRecord ()
 
virtual void SetMatchType (const CSeq_id &, const CSeq_id &)
 
void SetScore (const CScore &)
 
string StrAttributes () const
 
- Public Member Functions inherited from CGffWriteRecord
 CGffWriteRecord (CGffFeatureContext &fc, const string &id="")
 
virtual ~CGffWriteRecord ()
 
bool CorrectType (const string &strType)
 
virtual string StrStructibutes () 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_locLocation () const
 
void SetGbKeyFrom (CMappedFeat)
 
- Public Member Functions inherited from CGffBaseRecord
 CGffBaseRecord (const string &id="")
 
 CGffBaseRecord (const CGffBaseRecord &)
 
virtual ~CGffBaseRecord ()
 
const TAttributesAttributes () 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_locGetLocation () 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...
 
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 Attributes

unsigned int m_uFlags
 
string mIdAttribute
 
string m_strAlignment
 
string m_strOtherScores
 
bool m_bIsTrivial
 
- Protected Attributes inherited from CGffWriteRecord
CGffFeatureContextm_fc
 
- Protected Attributes inherited from CGffBaseRecord
CRef< CSeq_locm_pLoc
 
string mSeqId
 
string mType
 
string mMethod
 
unsigned int mSeqStart
 
unsigned int mSeqStop
 
string mScore
 
string mStrand
 
optional< intmPhase
 
TAttributes mAttributes
 
TScores mExtraScores
 

Static Protected Attributes

static CGffFeatureContext sDummyContext
 
- Static Protected Attributes inherited from CGffWriteRecord
static const char * ATTR_SEPARATOR = "; "
 
- Static Protected Attributes inherited from CGffBaseRecord
static const char * ATTR_SEPARATOR = ";"
 

Additional Inherited Members

- Public Types inherited from CGffWriteRecord
typedef map< string, vector< string > > TAttributes
 
typedef TAttributes::iterator TAttrIt
 
typedef TAttributes::const_iterator TAttrCit
 
- Public Types inherited from CGffBaseRecord
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 atomic< Uint8TCounter
 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 stringxEscapedValue (const string &key, const string &value) const
 
const stringxEscapedString (const string &value) const
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Detailed Description

Definition at line 45 of file gff3_alignment_data.hpp.

Constructor & Destructor Documentation

◆ CGffAlignmentRecord()

CGffAlignmentRecord::CGffAlignmentRecord ( unsigned int  uFlags = 0,
unsigned int  uRecordId = 0 
)
inline

◆ ~CGffAlignmentRecord()

virtual CGffAlignmentRecord::~CGffAlignmentRecord ( )
inlinevirtual

Definition at line 61 of file gff3_alignment_data.hpp.

Member Function Documentation

◆ SetMatchType()

void CGffAlignmentRecord::SetMatchType ( const CSeq_id source,
const CSeq_id target 
)
virtual

◆ SetScore()

void CGffAlignmentRecord::SetScore ( const CScore score)

◆ StrAttributes()

string CGffAlignmentRecord::StrAttributes ( ) const
virtual

Reimplemented from CGffBaseRecord.

Definition at line 55 of file gff3_alignment_data.cpp.

References m_bIsTrivial, m_strAlignment, m_strOtherScores, mIdAttribute, and str().

Member Data Documentation

◆ m_bIsTrivial

bool CGffAlignmentRecord::m_bIsTrivial
protected

Definition at line 79 of file gff3_alignment_data.hpp.

Referenced by StrAttributes().

◆ m_strAlignment

string CGffAlignmentRecord::m_strAlignment
protected

Definition at line 76 of file gff3_alignment_data.hpp.

Referenced by StrAttributes().

◆ m_strOtherScores

string CGffAlignmentRecord::m_strOtherScores
protected

Definition at line 77 of file gff3_alignment_data.hpp.

Referenced by SetScore(), and StrAttributes().

◆ m_uFlags

unsigned int CGffAlignmentRecord::m_uFlags
protected

Definition at line 74 of file gff3_alignment_data.hpp.

◆ mIdAttribute

string CGffAlignmentRecord::mIdAttribute
protected

Definition at line 75 of file gff3_alignment_data.hpp.

Referenced by CGffAlignmentRecord(), and StrAttributes().

◆ sDummyContext

CGffFeatureContext CGffAlignmentRecord::sDummyContext
staticprotected

Definition at line 73 of file gff3_alignment_data.hpp.


The documentation for this class was generated from the following files:
Modified on Tue Feb 27 05:57:04 2024 by modify_doxy.py rev. 669887