NCBI C++ ToolKit
Public Member Functions | Protected Member Functions | Private Member Functions | Private Attributes | List of all members
CBlastAsyncFormatThread Class Reference

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...
 
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
 

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 &)
 
CBlastAsyncFormatThreadoperator= (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< 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...
 

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
batchNumberorders how the results are printed. Numbering starts at zero and missing values not allowed.
resultsdata 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(), 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:
Modified on Fri Jan 05 07:24:37 2024 by modify_doxy.py rev. 669887