NCBI C++ ToolKit
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CIgBlastnApp::CIgWorker Class Reference

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#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...
 
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 Attributes

const CArgsthm_args
 
CRef< CIgBlastnAppArgsthm_CmdLineArgs
 
CFastMutexthm_Mutex_Input
 
CFastMutexthm_Mutex_Output
 
CFastMutexthm_Mutex_Notify
 
CFastMutexthm_Mutex_Global
 
IG_ResultsMapthm_all_results
 
intthm_max_batch
 
CRef< CIgBlastArgsthm_ig_args
 
CRef< CBlastOptionsHandlethm_opts_hndl
 
CRef< CLocalDbAdapterthm_blastdb
 
CRef< CBlastInputthm_input
 
intthm_run_thread_count
 
CSemaphorethm_new_batch_done
 
int thm_tid
 
CStopWatch thm_sw
 
boolthm_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< Uint8TCounter
 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 CThreadGetCurrentThread (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

◆ 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:
Modified on Wed Feb 28 07:14:00 2024 by modify_doxy.py rev. 669887