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_set >	GetNextSeqBatch (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...

CObject &	operator= (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)

CBlastInputOMF &	operator= (const CBlastInputOMF &rhs)

Private Attributes
CBlastInputSourceOMF *	m_Source

TSeqPos	m_BatchSize

TSeqPos	m_MaxNumSequences

CRef< CBioseq_set >	m_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< Uint8 >	TCounter
	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 )

Definition at line 306 of file blast_input.cpp.

References CBlastInputSourceOMF::End(), CBlastInputSourceOMF::GetNextSequence(), CBioseq_set_Base::GetSeq_set(), m_BatchSize, m_MaxNumSequences, m_NumSeqs, m_Source, m_TotalLength, and CBioseq_set_Base::SetSeq_set().

Referenced by CMagicBlastThread::Main().

◆ 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:

include/algo/blast/blastinput/blast_input.hpp
src/algo/blast/blastinput/blast_input.cpp

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CBlastInputOMF() [1/2]

◆ CBlastInputOMF() [2/2]

Member Function Documentation

◆ End()

◆ GetBatchSize()

◆ GetMaxBatchNumSeqs()

◆ GetNextSeqBatch() [1/2]

◆ GetNextSeqBatch() [2/2]

◆ GetNumSeqsProcessed()

◆ GetTotalLengthProcessed()

◆ operator=()

◆ SetBatchSize()

◆ SetMaxBatchNumSeqs()

Member Data Documentation

◆ m_BatchSize

◆ m_BioseqSet

◆ m_MaxNumSequences

◆ m_NumSeqs

◆ m_Source

◆ m_TotalLength