Search Toolkit Book for CIgBlastnApp::CIgWorker

#include "igblastn.hpp"
(Private to src/app/igblast.)

Inheritance diagram for CIgBlastnApp::CIgWorker:

Collaboration diagram for CIgBlastnApp::CIgWorker:

Public Member Functions
	CIgWorker (const CArgs &args, CRef< CIgBlastnAppArgs > cmd_line_args, CFastMutex &mx_input, CFastMutex &mx_output, CFastMutex &mx_notify, CFastMutex &mx_global, IG_ResultsMap &resmap, int &maxbatch, CRef< CIgBlastArgs > igargs, CRef< CBlastOptionsHandle > opts_hndl, CRef< CLocalDbAdapter > blastdb, CRef< CBlastInput > user_input, int &th_count, CSemaphore &batct_notify, bool &any_started)

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

virtual void	OnExit (void)
	Override this to execute finalization code. 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

Private Attributes
const CArgs &	thm_args

CRef< CIgBlastnAppArgs >	thm_CmdLineArgs

CFastMutex &	thm_Mutex_Input

CFastMutex &	thm_Mutex_Output

CFastMutex &	thm_Mutex_Notify

CFastMutex &	thm_Mutex_Global

IG_ResultsMap &	thm_all_results

int &	thm_max_batch

CRef< CIgBlastArgs >	thm_ig_args

CRef< CBlastOptionsHandle >	thm_opts_hndl

CRef< CLocalDbAdapter >	thm_blastdb

CRef< CBlastInput >	thm_input

int &	thm_run_thread_count

CSemaphore &	thm_new_batch_done

int	thm_tid

CStopWatch	thm_sw

bool &	thm_any_started

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...

Protected Member Functions inherited from CThread
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...

Detailed Description

Definition at line 65 of file igblastn.hpp.

Constructor & Destructor Documentation

◆ CIgWorker()

CIgBlastnApp::CIgWorker::CIgWorker	(	const CArgs &	args,
		CRef< CIgBlastnAppArgs >	cmd_line_args,
		CFastMutex &	mx_input,
		CFastMutex &	mx_output,
		CFastMutex &	mx_notify,
		CFastMutex &	mx_global,
		IG_ResultsMap &	resmap,
		int &	maxbatch,
		CRef< CIgBlastArgs >	igargs,
		CRef< CBlastOptionsHandle >	opts_hndl,
		CRef< CLocalDbAdapter >	blastdb,
		CRef< CBlastInput >	user_input,
		int &	th_count,
		CSemaphore &	batct_notify,
		bool &	any_started
	)

inline

Definition at line 67 of file igblastn.hpp.

Member Function Documentation

◆ Main()

void * CIgBlastnApp::CIgWorker::Main ( void )

virtual

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

Implements CThread.

Definition at line 65 of file igblastn_app.cpp.

References _ASSERT, CIgBlastArgs::AddIgSequenceScope(), eDPF_ErrCodeExplanation, CRef< C, Locker >::Empty(), CBlastInput::End(), CSignal::eSignal_SEGV, CBlastAppArgs::ExecuteRemotely(), CBlastAppArgs::GetBlastDatabaseArgs(), CBlastDatabaseArgs::GetDatabaseName(), CIgBlastnAppArgs::GetIgBlastArgs(), CIgBlastArgs::GetIgBlastOptions(), CObjectManager::GetInstance(), CBlastInput::GetNextSeqBatch(), CBlastDatabaseArgs::GetSearchDatabase(), CThread::GetSelf(), CBlastDatabaseArgs::GetSubjects(), InitializeSubject(), kEmptyStr, CIgBlastOptions::m_Db, msg(), NcbiEmptyString, NULL, CSemaphore::Post(), query, CSignal::Raise(), CRef< C, Locker >::Reset(), results, CIgBlast::Run(), CIgBlast::SetNumberOfThreads(), CBlastAppArgs::SetOptions(), CStopWatch::Start(), thm_all_results, thm_any_started, thm_args, thm_CmdLineArgs, thm_input, thm_max_batch, thm_Mutex_Global, thm_Mutex_Input, thm_Mutex_Notify, thm_Mutex_Output, thm_new_batch_done, thm_run_thread_count, thm_sw, thm_tid, and CStackTrace::Write().

◆ OnExit()

void CIgBlastnApp::CIgWorker::OnExit ( void )

virtual

Override this to execute finalization code.

Unlike destructor, this code will be executed before thread termination and as a part of the thread.

Reimplemented from CThread.

Definition at line 203 of file igblastn_app.cpp.

Member Data Documentation

◆ thm_all_results

IG_ResultsMap& CIgBlastnApp::CIgWorker::thm_all_results

private

Definition at line 108 of file igblastn.hpp.

Referenced by Main().

◆ thm_any_started

bool& CIgBlastnApp::CIgWorker::thm_any_started

private

Definition at line 118 of file igblastn.hpp.

Referenced by Main().

◆ thm_args

const CArgs& CIgBlastnApp::CIgWorker::thm_args

private

Definition at line 102 of file igblastn.hpp.

Referenced by Main().

◆ thm_blastdb

CRef<CLocalDbAdapter> CIgBlastnApp::CIgWorker::thm_blastdb

private

Definition at line 112 of file igblastn.hpp.

◆ thm_CmdLineArgs

CRef<CIgBlastnAppArgs> CIgBlastnApp::CIgWorker::thm_CmdLineArgs

private

Definition at line 103 of file igblastn.hpp.

Referenced by Main().

◆ thm_ig_args

CRef<CIgBlastArgs> CIgBlastnApp::CIgWorker::thm_ig_args

private

Definition at line 110 of file igblastn.hpp.

◆ thm_input

CRef<CBlastInput> CIgBlastnApp::CIgWorker::thm_input

private

Definition at line 113 of file igblastn.hpp.

Referenced by Main().

◆ thm_max_batch

int& CIgBlastnApp::CIgWorker::thm_max_batch

private

Definition at line 109 of file igblastn.hpp.

Referenced by Main().

◆ thm_Mutex_Global

CFastMutex& CIgBlastnApp::CIgWorker::thm_Mutex_Global

private

Definition at line 107 of file igblastn.hpp.

Referenced by Main().

◆ thm_Mutex_Input

CFastMutex& CIgBlastnApp::CIgWorker::thm_Mutex_Input

private

Definition at line 104 of file igblastn.hpp.

Referenced by Main().

◆ thm_Mutex_Notify

CFastMutex& CIgBlastnApp::CIgWorker::thm_Mutex_Notify

private

Definition at line 106 of file igblastn.hpp.

Referenced by Main().

◆ thm_Mutex_Output

CFastMutex& CIgBlastnApp::CIgWorker::thm_Mutex_Output

private

Definition at line 105 of file igblastn.hpp.

Referenced by Main().

◆ thm_new_batch_done

CSemaphore& CIgBlastnApp::CIgWorker::thm_new_batch_done

private

Definition at line 115 of file igblastn.hpp.

Referenced by Main().

◆ thm_opts_hndl

CRef<CBlastOptionsHandle> CIgBlastnApp::CIgWorker::thm_opts_hndl

private

Definition at line 111 of file igblastn.hpp.

◆ thm_run_thread_count

int& CIgBlastnApp::CIgWorker::thm_run_thread_count

private

Definition at line 114 of file igblastn.hpp.

Referenced by Main().

◆ thm_sw

CStopWatch CIgBlastnApp::CIgWorker::thm_sw

private

Definition at line 117 of file igblastn.hpp.

Referenced by Main().

◆ thm_tid

int CIgBlastnApp::CIgWorker::thm_tid

private

Definition at line 116 of file igblastn.hpp.

Referenced by Main().

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

src/app/igblast/igblastn.hpp
src/app/igblast/igblastn_app.cpp

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CIgWorker()

Member Function Documentation

◆ Main()

◆ OnExit()

Member Data Documentation

◆ thm_all_results

◆ thm_any_started

◆ thm_args

◆ thm_blastdb

◆ thm_CmdLineArgs

◆ thm_ig_args

◆ thm_input

◆ thm_max_batch

◆ thm_Mutex_Global

◆ thm_Mutex_Input

◆ thm_Mutex_Notify

◆ thm_Mutex_Output

◆ thm_new_batch_done

◆ thm_opts_hndl

◆ thm_run_thread_count

◆ thm_sw

◆ thm_tid