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CFastaIdHandler Class Reference

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#include <objtools/readers/fasta_reader_utils.hpp>

+ Inheritance diagram for CFastaIdHandler:
+ Collaboration diagram for CFastaIdHandler:

Public Member Functions

 CFastaIdHandler (void)
 
void SetGenerator (CSeqIdGenerator &generator)
 
CSeqIdGeneratorSetGenerator (void)
 
const CSeqIdGeneratorGetGenerator (void) const
 
virtual CRef< CSeq_idGenerateID (bool unique_id)
 
virtual CRef< CSeq_idGenerateID (const string &defline, bool unique_id=true)
 
void ClearIdCache (void)
 
bool CacheIdHandle (CSeq_id_Handle idh)
 
- 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 Types

using TIdHandleCache = set< CSeq_id_Handle >
 

Protected Member Functions

bool x_IsUniqueIdHandle (CSeq_id_Handle idh)
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Protected Attributes

CRef< CSeqIdGeneratormp_IdGenerator
 
TIdHandleCache m_PreviousIdHandles
 

Additional Inherited Members

- 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...
 

Detailed Description

Definition at line 188 of file fasta_reader_utils.hpp.

Member Typedef Documentation

◆ TIdHandleCache

Definition at line 225 of file fasta_reader_utils.hpp.

Constructor & Destructor Documentation

◆ CFastaIdHandler()

CFastaIdHandler::CFastaIdHandler ( void  )
inline

Definition at line 191 of file fasta_reader_utils.hpp.

Member Function Documentation

◆ CacheIdHandle()

bool CFastaIdHandler::CacheIdHandle ( CSeq_id_Handle  idh)
inline

◆ ClearIdCache()

void CFastaIdHandler::ClearIdCache ( void  )
inline

◆ GenerateID() [1/2]

CRef< CSeq_id > CFastaIdHandler::GenerateID ( bool  unique_id)
virtual

Definition at line 439 of file fasta_reader_utils.cpp.

Referenced by CFastaReader::GenerateID().

◆ GenerateID() [2/2]

CRef< CSeq_id > CFastaIdHandler::GenerateID ( const string defline,
bool  unique_id = true 
)
virtual

◆ GetGenerator()

const CSeqIdGenerator& CFastaIdHandler::GetGenerator ( void  ) const
inline

Definition at line 201 of file fasta_reader_utils.hpp.

References mp_IdGenerator.

Referenced by CFastaReader::GetIDGenerator().

◆ SetGenerator() [1/2]

void CFastaIdHandler::SetGenerator ( CSeqIdGenerator generator)
inline

Definition at line 193 of file fasta_reader_utils.hpp.

References mp_IdGenerator, and CRef< C, Locker >::Reset().

Referenced by CFastaReader::SetIDGenerator().

◆ SetGenerator() [2/2]

CSeqIdGenerator& CFastaIdHandler::SetGenerator ( void  )
inline

Definition at line 197 of file fasta_reader_utils.hpp.

References mp_IdGenerator.

◆ x_IsUniqueIdHandle()

bool CFastaIdHandler::x_IsUniqueIdHandle ( CSeq_id_Handle  idh)
inlineprotected

Member Data Documentation

◆ m_PreviousIdHandles

TIdHandleCache CFastaIdHandler::m_PreviousIdHandles
protected

Definition at line 227 of file fasta_reader_utils.hpp.

Referenced by CacheIdHandle(), ClearIdCache(), and x_IsUniqueIdHandle().

◆ mp_IdGenerator

CRef<CSeqIdGenerator> CFastaIdHandler::mp_IdGenerator
protected

Definition at line 226 of file fasta_reader_utils.hpp.

Referenced by GenerateID(), GetGenerator(), and SetGenerator().


The documentation for this class was generated from the following files:
Modified on Fri Dec 01 04:43:03 2023 by modify_doxy.py rev. 669887