Search Toolkit Book for CBlastAsyncFormatThread

Run as separate thread and format results. More...

#include <algo/blast/format/blast_async_format.hpp>

Inheritance diagram for CBlastAsyncFormatThread:

Collaboration diagram for CBlastAsyncFormatThread:

Public Member Functions
	CBlastAsyncFormatThread ()

void	QueueResults (int batchNumber, vector< SFormatResultValues > results)
	Queue results for printing. More...

void	Finalize ()
	Close queue for printing. No calls to QueueResults allowed after this. More...

void	Join ()
	Calls Finalize (if not already called) then CThread::Join(); Should only be called if QueueResults will no longer be called. More...

Public Member Functions inherited from CThread
	CThread (void)
	Constructor. More...

bool	Run (TRunMode flags=fRunDefault)
	Run the thread. More...

void	Detach (void)
	Inform the thread that user does not need to wait for its termination. More...

void	Join (void **exit_data=0)
	Wait for the thread termination. More...

bool	Discard (void)
	If the thread has not been Run() yet, then schedule the thread object for destruction, and return TRUE. More...

bool	IsTerminated (void) const
	Check if the thread has been terminated. More...

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

Protected Member Functions
virtual	~CBlastAsyncFormatThread (void)

virtual void *	Main (void)
	Derived (user-created) class must provide a real thread function. More...

Protected Member Functions inherited from CThread
virtual void	OnExit (void)
	Override this to execute finalization code. More...

virtual	~CThread (void)
	To be called only internally! NOTE: destructor of the derived (user-provided) class should be declared "protected", too! More...

TThreadHandle	GetThreadHandle ()

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

Private Member Functions
	CBlastAsyncFormatThread (const CBlastAsyncFormatThread &)

CBlastAsyncFormatThread &	operator= (const CBlastAsyncFormatThread &)

Private Attributes
std::map< int, vector< SFormatResultValues > >	m_ResultsMap

bool	m_Done

CSemaphore	m_Semaphore

Additional Inherited Members
Public Types inherited from CThread
enum	ERunMode { fRunDefault = 0x00 , fRunDetached = 0x01 , fRunBound = 0x10 , fRunUnbound = 0x20 , fRunNice = 0x40 , fRunAllowST = 0x100 , fRunCloneRequestContext = 0x200 }
	Which mode should the thread run in. More...

typedef int	TRunMode
	Bitwise OR'd flags for thread creation passed to Run(). More...

typedef unsigned int	TID
	Get ID of current thread. More...

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 CThread
static void	Exit (void *exit_data)
	Cancel current thread. More...

static TID	GetSelf (void)

static bool	IsMain (void)

static CThread *	GetCurrentThread (void)
	Get current CThread object (or NULL, if main thread) More...

static void	GetSystemID (TThreadSystemID *id)
	Get system ID of the current thread - for internal use only. More...

static unsigned int	GetThreadsCount ()
	Get total amount of threads This amount does not contain main thread. More...

static void	SetCurrentThreadName (const CTempString &)
	Set name for the current thread. More...

static void	InitializeMainThreadId (void)
	Initialize main thread's TID. More...

static bool	IsAppExiting (void)
	Check if the application is exiting (entered the destructor). More...

static void	SetWaitForAllThreadsTimeout (const CTimeout &timeout)
	Set timeout for stopping all threads on application exit. 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

Run as separate thread and format results.

Definition at line 63 of file blast_async_format.hpp.

Constructor & Destructor Documentation

◆ CBlastAsyncFormatThread() [1/2]

CBlastAsyncFormatThread::CBlastAsyncFormatThread ( )

inline

Definition at line 66 of file blast_async_format.hpp.

◆ ~CBlastAsyncFormatThread()

CBlastAsyncFormatThread::~CBlastAsyncFormatThread ( void )

protectedvirtual

Definition at line 45 of file blast_async_format.cpp.

◆ CBlastAsyncFormatThread() [2/2]

CBlastAsyncFormatThread::CBlastAsyncFormatThread ( const CBlastAsyncFormatThread & )

private

Member Function Documentation

◆ Finalize()

void CBlastAsyncFormatThread::Finalize ( )

Close queue for printing. No calls to QueueResults allowed after this.

Definition at line 68 of file blast_async_format.cpp.

References blastProcessGuard, CFastMutex::Lock(), m_Done, m_Semaphore, CSemaphore::Post(), and CFastMutex::Unlock().

Referenced by BOOST_AUTO_TEST_CASE(), and Join().

◆ Join()

void CBlastAsyncFormatThread::Join ( )

Calls Finalize (if not already called) then CThread::Join(); Should only be called if QueueResults will no longer be called.

Definition at line 77 of file blast_async_format.cpp.

References Finalize(), CThread::Join(), and m_Done.

Referenced by BOOST_AUTO_TEST_CASE(), and CBlastKmerApplication::Run().

◆ Main()

void * CBlastAsyncFormatThread::Main ( void )

protectedvirtual

Derived (user-created) class must provide a real thread function.

Implements CThread.

Definition at line 86 of file blast_async_format.cpp.

References blastProcessGuard, ITERATE, CFastMutex::Lock(), m_Done, m_ResultsMap, m_Semaphore, NULL, CSemaphore::Post(), result, CFastMutex::Unlock(), and CSemaphore::Wait().

◆ operator=()

CBlastAsyncFormatThread& CBlastAsyncFormatThread::operator= ( const CBlastAsyncFormatThread & )

private

◆ QueueResults()

void CBlastAsyncFormatThread::QueueResults	(	int	batchNumber,
		vector< SFormatResultValues >	results
	)

Queue results for printing.

Will throw if called after call to Finalize or if a duplicate batchNumber is entered. Batch numbers should start at zero and increase. Missing numbers NOT allowed.

Parameters

batchNumber	orders how the results are printed. Numbering starts at zero and missing values not allowed.
results	data needed for formatting

Definition at line 50 of file blast_async_format.cpp.

References blastProcessGuard, eUnknown, CFastMutex::Lock(), m_Done, m_ResultsMap, m_Semaphore, NCBI_THROW, NStr::NumericToString(), CSemaphore::Post(), results, and CFastMutex::Unlock().

Referenced by BOOST_AUTO_TEST_CASE(), and CBlastKmerThread::Main().

Member Data Documentation

◆ m_Done

bool CBlastAsyncFormatThread::m_Done

private

Definition at line 99 of file blast_async_format.hpp.

Referenced by Finalize(), Join(), Main(), and QueueResults().

◆ m_ResultsMap

std::map<int, vector<SFormatResultValues> > CBlastAsyncFormatThread::m_ResultsMap

private

Definition at line 97 of file blast_async_format.hpp.

Referenced by Main(), and QueueResults().

◆ m_Semaphore

CSemaphore CBlastAsyncFormatThread::m_Semaphore

private

Definition at line 101 of file blast_async_format.hpp.

Referenced by Finalize(), Main(), and QueueResults().

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

include/algo/blast/format/blast_async_format.hpp
src/algo/blast/format/blast_async_format.cpp

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CBlastAsyncFormatThread() [1/2]

◆ ~CBlastAsyncFormatThread()

◆ CBlastAsyncFormatThread() [2/2]

Member Function Documentation

◆ Finalize()

◆ Join()

◆ Main()

◆ operator=()

◆ QueueResults()

Member Data Documentation

◆ m_Done

◆ m_ResultsMap

◆ m_Semaphore