NCBI C++ ToolKit
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CBlastKmerThread Class Reference

Search Toolkit Book for CBlastKmerThread

Threading class for BlastKmer searches. More...

#include "kblastthr.hpp"
(Private to src/algo/blast/proteinkmer/demo.)

+ Inheritance diagram for CBlastKmerThread:
+ Collaboration diagram for CBlastKmerThread:

Public Member Functions

 CBlastKmerThread (CBlastInput &input, CRef< CBlastDatabaseArgs > db_args, CRef< CBlastpKmerOptionsHandle > opts_handle, CRef< CFormattingArgs > fmtArgs, CNcbiOstream &outfile, CBlastAsyncFormatThread *formatThr, Boolean believeQuery=false)
 
- 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 ~CBlastKmerThread (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 Attributes

CBlastInputm_Input
 
CRef< CBlastDatabaseArgsm_DbArgs
 
CRef< CBlastpKmerOptionsHandlem_BlastOptsHandle
 
CRef< CFormattingArgsm_FormattingArgs
 
CNcbiOstreamm_OutFile
 
CBlastAsyncFormatThreadm_FormattingThr
 
Boolean m_BelieveQuery
 
CFastMutex m_Guard
 

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

Threading class for BlastKmer searches.

Each thread runs a batch of input sequences through KMER lookup and then through BLAST.

Definition at line 63 of file kblastthr.hpp.

Constructor & Destructor Documentation

◆ CBlastKmerThread()

CBlastKmerThread::CBlastKmerThread ( CBlastInput input,
CRef< CBlastDatabaseArgs db_args,
CRef< CBlastpKmerOptionsHandle opts_handle,
CRef< CFormattingArgs fmtArgs,
CNcbiOstream outfile,
CBlastAsyncFormatThread formatThr,
Boolean  believeQuery = false 
)
inline

Definition at line 66 of file kblastthr.hpp.

◆ ~CBlastKmerThread()

CBlastKmerThread::~CBlastKmerThread ( void  )
protectedvirtual

Definition at line 83 of file kblastthr.cpp.

Member Function Documentation

◆ Main()

void * CBlastKmerThread::Main ( void  )
protectedvirtual

Member Data Documentation

◆ m_BelieveQuery

Boolean CBlastKmerThread::m_BelieveQuery
private

Definition at line 102 of file kblastthr.hpp.

Referenced by Main().

◆ m_BlastOptsHandle

CRef<CBlastpKmerOptionsHandle> CBlastKmerThread::m_BlastOptsHandle
private

Definition at line 94 of file kblastthr.hpp.

Referenced by Main().

◆ m_DbArgs

CRef<CBlastDatabaseArgs> CBlastKmerThread::m_DbArgs
private

Definition at line 92 of file kblastthr.hpp.

Referenced by Main().

◆ m_FormattingArgs

CRef<CFormattingArgs> CBlastKmerThread::m_FormattingArgs
private

Definition at line 96 of file kblastthr.hpp.

Referenced by Main().

◆ m_FormattingThr

CBlastAsyncFormatThread* CBlastKmerThread::m_FormattingThr
private

Definition at line 100 of file kblastthr.hpp.

Referenced by Main().

◆ m_Guard

CFastMutex CBlastKmerThread::m_Guard
private

Definition at line 104 of file kblastthr.hpp.

◆ m_Input

CBlastInput& CBlastKmerThread::m_Input
private

Definition at line 90 of file kblastthr.hpp.

Referenced by Main().

◆ m_OutFile

CNcbiOstream& CBlastKmerThread::m_OutFile
private

Definition at line 98 of file kblastthr.hpp.

Referenced by Main().


The documentation for this class was generated from the following files:
Modified on Sat Feb 24 07:47:59 2024 by modify_doxy.py rev. 669887