NCBI C++ ToolKit
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CGffAlignRecord Class Reference

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#include <objtools/writers/gff_feature_record.hpp>

+ Inheritance diagram for CGffAlignRecord:
+ Collaboration diagram for CGffAlignRecord:

Public Member Functions

 CGffAlignRecord (const string &id="")
 
void AddInsertion (unsigned int)
 
void AddForwardShift (unsigned int)
 
void AddReverseShift (unsigned int)
 
void AddDeletion (unsigned int)
 
void AddMatch (unsigned int)
 
void FinalizeMatches ()
 
string StrId () const
 
string StrTarget () const
 
string StrGap () const
 
string StrAttributes () const
 
- 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

string mRecordId
 
string mAttrGap
 
bool mGapIsTrivial
 
unsigned int mAccumulatedMatches
 
- 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
 

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, 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...
 
- Static Protected Attributes inherited from CGffBaseRecord
static const char * ATTR_SEPARATOR = ";"
 

Detailed Description

Definition at line 84 of file gff_feature_record.hpp.

Constructor & Destructor Documentation

◆ CGffAlignRecord()

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

Definition at line 131 of file gff_feature_record.cpp.

Member Function Documentation

◆ AddDeletion()

void CGffAlignRecord::AddDeletion ( unsigned int  size)

◆ AddForwardShift()

void CGffAlignRecord::AddForwardShift ( unsigned int  size)

◆ AddInsertion()

void CGffAlignRecord::AddInsertion ( unsigned int  size)

◆ AddMatch()

void CGffAlignRecord::AddMatch ( unsigned int  size)

◆ AddReverseShift()

void CGffAlignRecord::AddReverseShift ( unsigned int  size)

◆ FinalizeMatches()

void CGffAlignRecord::FinalizeMatches ( )

◆ StrAttributes()

string CGffAlignRecord::StrAttributes ( ) const
virtual

◆ StrGap()

string CGffAlignRecord::StrGap ( ) const

Definition at line 142 of file gff_feature_record.cpp.

References mAttrGap.

◆ StrId()

string CGffAlignRecord::StrId ( ) const
inline

Definition at line 111 of file gff_feature_record.hpp.

References mRecordId.

Referenced by CGff3Writer::xWriteAlignment().

◆ StrTarget()

string CGffAlignRecord::StrTarget ( ) const

Member Data Documentation

◆ mAccumulatedMatches

unsigned int CGffAlignRecord::mAccumulatedMatches
protected

Definition at line 120 of file gff_feature_record.hpp.

Referenced by AddMatch(), and FinalizeMatches().

◆ mAttrGap

string CGffAlignRecord::mAttrGap
protected

◆ mGapIsTrivial

bool CGffAlignRecord::mGapIsTrivial
protected

◆ mRecordId

string CGffAlignRecord::mRecordId
protected

Definition at line 117 of file gff_feature_record.hpp.

Referenced by StrAttributes(), and StrId().


The documentation for this class was generated from the following files:
Modified on Tue May 21 10:55:47 2024 by modify_doxy.py rev. 669887