Search Toolkit Book for CLocalRPSBlast

#include <algo/blast/api/rpsblast_local.hpp>

Inheritance diagram for CLocalRPSBlast:

Collaboration diagram for CLocalRPSBlast:

Public Member Functions
	CLocalRPSBlast (CRef< CBlastQueryVector > query_vector, const string &db, CRef< CBlastOptionsHandle > options, unsigned int num_of_threads=kAutoThreadedSearch)

CRef< CSearchResultSet >	Run ()

	~CLocalRPSBlast ()

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
	CLocalRPSBlast (const CLocalRPSBlast &)

CLocalRPSBlast &	operator= (const CLocalRPSBlast &)

CRef< CSearchResultSet >	RunThreadedSearch ()

void	x_AdjustDbSize (void)

Private Attributes
unsigned int	m_num_of_threads

const string	m_db_name

CRef< CBlastOptionsHandle >	m_opt_handle

CRef< CBlastQueryVector >	m_query_vector

unsigned int	m_num_of_dbs

vector< string >	m_rps_databases

Static Private Attributes
static const int	kDisableThreadedSearch = 1

static const int	kAutoThreadedSearch = 0

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 41 of file rpsblast_local.hpp.

Constructor & Destructor Documentation

◆ CLocalRPSBlast() [1/2]

CLocalRPSBlast::CLocalRPSBlast ( const CLocalRPSBlast & )

private

◆ CLocalRPSBlast() [2/2]

CLocalRPSBlast::CLocalRPSBlast	(	CRef< CBlastQueryVector >	query_vector,
		const string &	db,
		CRef< CBlastOptionsHandle >	options,
		unsigned int	num_of_threads = `kAutoThreadedSearch`
	)

Definition at line 331 of file rpsblast_local.cpp.

◆ ~CLocalRPSBlast()

CLocalRPSBlast::~CLocalRPSBlast ( )

inline

Definition at line 93 of file rpsblast_local.hpp.

Member Function Documentation

◆ operator=()

CLocalRPSBlast& CLocalRPSBlast::operator= ( const CLocalRPSBlast & )

private

◆ Run()

CRef< CSearchResultSet > CLocalRPSBlast::Run ( void )

Definition at line 374 of file rpsblast_local.cpp.

Referenced by CRPSBlastNode::Main(), CRPSTBlastnNode::Main(), CRPSBlastApp::x_RunMTBySplitDB(), and CRPSTBlastnApp::x_RunMTBySplitDB().

◆ RunThreadedSearch()

CRef< CSearchResultSet > CLocalRPSBlast::RunThreadedSearch ( void )

private

Definition at line 409 of file rpsblast_local.cpp.

◆ x_AdjustDbSize()

void CLocalRPSBlast::x_AdjustDbSize ( void )

private

Definition at line 349 of file rpsblast_local.cpp.

Member Data Documentation

◆ kAutoThreadedSearch

const int CLocalRPSBlast::kAutoThreadedSearch = 0

staticprivate

Definition at line 59 of file rpsblast_local.hpp.

◆ kDisableThreadedSearch

const int CLocalRPSBlast::kDisableThreadedSearch = 1

staticprivate

Definition at line 58 of file rpsblast_local.hpp.

◆ m_db_name

const string CLocalRPSBlast::m_db_name

private

Definition at line 53 of file rpsblast_local.hpp.

◆ m_num_of_dbs

unsigned int CLocalRPSBlast::m_num_of_dbs

private

Definition at line 56 of file rpsblast_local.hpp.

◆ m_num_of_threads

unsigned int CLocalRPSBlast::m_num_of_threads

private

Definition at line 52 of file rpsblast_local.hpp.

◆ m_opt_handle

CRef<CBlastOptionsHandle> CLocalRPSBlast::m_opt_handle

private

Definition at line 54 of file rpsblast_local.hpp.

◆ m_query_vector

CRef<CBlastQueryVector> CLocalRPSBlast::m_query_vector

private

Definition at line 55 of file rpsblast_local.hpp.

◆ m_rps_databases

vector<string> CLocalRPSBlast::m_rps_databases

private

Definition at line 57 of file rpsblast_local.hpp.

The documentation for this class was generated from the following files:

include/algo/blast/api/rpsblast_local.hpp
src/algo/blast/api/rpsblast_local.cpp

Public Member Functions

Private Member Functions

Private Attributes

Static Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CLocalRPSBlast() [1/2]

◆ CLocalRPSBlast() [2/2]

◆ ~CLocalRPSBlast()

Member Function Documentation

◆ operator=()

◆ Run()

◆ RunThreadedSearch()

◆ x_AdjustDbSize()

Member Data Documentation

◆ kAutoThreadedSearch

◆ kDisableThreadedSearch

◆ m_db_name

◆ m_num_of_dbs

◆ m_num_of_threads

◆ m_opt_handle

◆ m_query_vector

◆ m_rps_databases