NCBI C++ ToolKit
Public Member Functions | Private Member Functions | Private Attributes | List of all members
CBlastInputOMF Class Reference

Search Toolkit Book for CBlastInputOMF

#include <algo/blast/blastinput/blast_input.hpp>

+ Inheritance diagram for CBlastInputOMF:
+ Collaboration diagram for CBlastInputOMF:

Public Member Functions

 CBlastInputOMF (CBlastInputSourceOMF *source, TSeqPos batch_size)
 
void GetNextSeqBatch (CBioseq_set &bioseq_set)
 
CRef< CBioseq_setGetNextSeqBatch (void)
 
void SetBatchSize (TSeqPos num)
 
TSeqPos GetBatchSize (void) const
 
void SetMaxBatchNumSeqs (TSeqPos num)
 
TSeqPos GetMaxBatchNumSeqs (void) const
 
bool End (void)
 
Int8 GetNumSeqsProcessed () const
 
Int8 GetTotalLengthProcessed () 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
 

Private Member Functions

 CBlastInputOMF (const CBlastInputOMF &rhs)
 
CBlastInputOMFoperator= (const CBlastInputOMF &rhs)
 

Private Attributes

CBlastInputSourceOMFm_Source
 
TSeqPos m_BatchSize
 
TSeqPos m_MaxNumSequences
 
CRef< CBioseq_setm_BioseqSet
 
Int8 m_NumSeqs
 
Int8 m_TotalLength
 

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

Detailed Description

Definition at line 441 of file blast_input.hpp.

Constructor & Destructor Documentation

◆ CBlastInputOMF() [1/2]

CBlastInputOMF::CBlastInputOMF ( CBlastInputSourceOMF source,
TSeqPos  batch_size 
)

Definition at line 294 of file blast_input.cpp.

◆ CBlastInputOMF() [2/2]

CBlastInputOMF::CBlastInputOMF ( const CBlastInputOMF rhs)
private

Member Function Documentation

◆ End()

bool CBlastInputOMF::End ( void  )
inline

Definition at line 456 of file blast_input.hpp.

References CBlastInputSourceOMF::End(), and m_Source.

Referenced by CMagicBlastThread::Main().

◆ GetBatchSize()

TSeqPos CBlastInputOMF::GetBatchSize ( void  ) const
inline

Definition at line 451 of file blast_input.hpp.

References m_BatchSize.

◆ GetMaxBatchNumSeqs()

TSeqPos CBlastInputOMF::GetMaxBatchNumSeqs ( void  ) const
inline

Definition at line 454 of file blast_input.hpp.

References m_MaxNumSequences.

◆ GetNextSeqBatch() [1/2]

void CBlastInputOMF::GetNextSeqBatch ( CBioseq_set bioseq_set)

◆ GetNextSeqBatch() [2/2]

CRef< CBioseq_set > CBlastInputOMF::GetNextSeqBatch ( void  )

Definition at line 326 of file blast_input.cpp.

◆ GetNumSeqsProcessed()

Int8 CBlastInputOMF::GetNumSeqsProcessed ( ) const
inline

Definition at line 458 of file blast_input.hpp.

References m_NumSeqs.

◆ GetTotalLengthProcessed()

Int8 CBlastInputOMF::GetTotalLengthProcessed ( ) const
inline

Definition at line 459 of file blast_input.hpp.

References m_TotalLength.

◆ operator=()

CBlastInputOMF& CBlastInputOMF::operator= ( const CBlastInputOMF rhs)
private

◆ SetBatchSize()

void CBlastInputOMF::SetBatchSize ( TSeqPos  num)
inline

Definition at line 450 of file blast_input.hpp.

References m_BatchSize.

◆ SetMaxBatchNumSeqs()

void CBlastInputOMF::SetMaxBatchNumSeqs ( TSeqPos  num)
inline

Definition at line 453 of file blast_input.hpp.

References m_MaxNumSequences.

Member Data Documentation

◆ m_BatchSize

TSeqPos CBlastInputOMF::m_BatchSize
private

Definition at line 466 of file blast_input.hpp.

Referenced by GetBatchSize(), GetNextSeqBatch(), and SetBatchSize().

◆ m_BioseqSet

CRef<CBioseq_set> CBlastInputOMF::m_BioseqSet
private

Definition at line 468 of file blast_input.hpp.

◆ m_MaxNumSequences

TSeqPos CBlastInputOMF::m_MaxNumSequences
private

Definition at line 467 of file blast_input.hpp.

Referenced by GetMaxBatchNumSeqs(), GetNextSeqBatch(), and SetMaxBatchNumSeqs().

◆ m_NumSeqs

Int8 CBlastInputOMF::m_NumSeqs
private

Definition at line 471 of file blast_input.hpp.

Referenced by GetNextSeqBatch(), and GetNumSeqsProcessed().

◆ m_Source

CBlastInputSourceOMF* CBlastInputOMF::m_Source
private

Definition at line 465 of file blast_input.hpp.

Referenced by End(), and GetNextSeqBatch().

◆ m_TotalLength

Int8 CBlastInputOMF::m_TotalLength
private

Definition at line 474 of file blast_input.hpp.

Referenced by GetNextSeqBatch(), and GetTotalLengthProcessed().


The documentation for this class was generated from the following files:
Modified on Tue Jun 11 09:21:59 2024 by modify_doxy.py rev. 669887