NCBI C++ ToolKit
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CBlastNode Class Referenceabstract

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#include <algo/blast/api/blast_node.hpp>

+ Inheritance diagram for CBlastNode:
+ Collaboration diagram for CBlastNode:

Public Types

enum  EState { eInitialized , eRunning , eError , eDone }
 
- 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...
 

Public Member Functions

 CBlastNode (int node_num, const CNcbiArguments &ncbi_args, const CArgs &args, CBlastAppDiagHandler &bah, int query_index, int num_queries, CBlastNodeMailbox *mailbox)
 
virtual int GetBlastResults (CNcbiOstream &os)=0
 
int GetNodeNum ()
 
EState GetState ()
 
int GetStatus ()
 
const CArgsGetArgs ()
 
CBlastAppDiagHandlerGetDiagHandler ()
 
const CNcbiArgumentsGetArguments ()
 
void SendMsg (CBlastNodeMsg::EMsgType msg_type, void *ptr=NULL)
 
stringGetNodeIdStr ()
 
int GetNumOfQueries ()
 
int GetQueriesLength ()
 
- 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 ~CBlastNode (void)
 
virtual void * Main (void)=0
 Derived (user-created) class must provide a real thread function. More...
 
void SetState (EState state)
 
void SetStatus (int status)
 
void SetQueriesLength (int l)
 
void SetDataLoaderPrefix ()
 
- 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...
 

Protected Attributes

int m_NodeNum
 

Private Attributes

const CNcbiArgumentsm_NcbiArgs
 
const CArgsm_Args
 
CBlastAppDiagHandlerm_Bah
 
int m_QueryIndex
 
int m_NumOfQueries
 
string m_NodeIdStr
 
CRef< CBlastNodeMailboxm_Mailbox
 
EState m_State
 
int m_Status
 
int m_QueriesLength
 
string m_DataLoaderPrefix
 

Additional Inherited Members

- 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

Definition at line 86 of file blast_node.hpp.

Member Enumeration Documentation

◆ EState

Enumerator
eInitialized 
eRunning 
eError 
eDone 

Definition at line 89 of file blast_node.hpp.

Constructor & Destructor Documentation

◆ CBlastNode()

CBlastNode::CBlastNode ( int  node_num,
const CNcbiArguments ncbi_args,
const CArgs args,
CBlastAppDiagHandler bah,
int  query_index,
int  num_queries,
CBlastNodeMailbox mailbox 
)

◆ ~CBlastNode()

CBlastNode::~CBlastNode ( void  )
protectedvirtual

Member Function Documentation

◆ GetArgs()

const CArgs& CBlastNode::GetArgs ( )
inline

◆ GetArguments()

const CNcbiArguments& CBlastNode::GetArguments ( )
inline

◆ GetBlastResults()

virtual int CBlastNode::GetBlastResults ( CNcbiOstream os)
pure virtual

◆ GetDiagHandler()

CBlastAppDiagHandler& CBlastNode::GetDiagHandler ( )
inline

◆ GetNodeIdStr()

string& CBlastNode::GetNodeIdStr ( )
inline

◆ GetNodeNum()

int CBlastNode::GetNodeNum ( )
inline

◆ GetNumOfQueries()

int CBlastNode::GetNumOfQueries ( )
inline

Definition at line 107 of file blast_node.hpp.

References m_NumOfQueries.

◆ GetQueriesLength()

int CBlastNode::GetQueriesLength ( )
inline

Definition at line 108 of file blast_node.hpp.

References m_QueriesLength.

◆ GetState()

EState CBlastNode::GetState ( )
inline

◆ GetStatus()

int CBlastNode::GetStatus ( )
inline

◆ Main()

virtual void* CBlastNode::Main ( void  )
protectedpure virtual

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

Implements CThread.

Implemented in CTblastnNode, CRPSTBlastnNode, CRPSBlastNode, CBlastxNode, CBlastpNode, and CBlastnNode.

◆ SendMsg()

void CBlastNode::SendMsg ( CBlastNodeMsg::EMsgType  msg_type,
void *  ptr = NULL 
)

◆ SetDataLoaderPrefix()

void CBlastNode::SetDataLoaderPrefix ( )
protected

◆ SetQueriesLength()

void CBlastNode::SetQueriesLength ( int  l)
inlineprotected

◆ SetState()

void CBlastNode::SetState ( EState  state)
inlineprotected

◆ SetStatus()

void CBlastNode::SetStatus ( int  status)
inlineprotected

Member Data Documentation

◆ m_Args

const CArgs& CBlastNode::m_Args
private

Definition at line 119 of file blast_node.hpp.

Referenced by GetArgs().

◆ m_Bah

CBlastAppDiagHandler& CBlastNode::m_Bah
private

Definition at line 120 of file blast_node.hpp.

Referenced by GetDiagHandler().

◆ m_DataLoaderPrefix

string CBlastNode::m_DataLoaderPrefix
private

Definition at line 128 of file blast_node.hpp.

Referenced by SetDataLoaderPrefix(), and ~CBlastNode().

◆ m_Mailbox

CRef<CBlastNodeMailbox> CBlastNode::m_Mailbox
private

Definition at line 124 of file blast_node.hpp.

Referenced by CBlastNode(), SendMsg(), and ~CBlastNode().

◆ m_NcbiArgs

const CNcbiArguments& CBlastNode::m_NcbiArgs
private

Definition at line 118 of file blast_node.hpp.

Referenced by GetArguments().

◆ m_NodeIdStr

string CBlastNode::m_NodeIdStr
private

Definition at line 123 of file blast_node.hpp.

Referenced by CBlastNode(), and GetNodeIdStr().

◆ m_NodeNum

int CBlastNode::m_NodeNum
protected

Definition at line 116 of file blast_node.hpp.

Referenced by GetNodeNum().

◆ m_NumOfQueries

int CBlastNode::m_NumOfQueries
private

Definition at line 122 of file blast_node.hpp.

Referenced by GetNumOfQueries().

◆ m_QueriesLength

int CBlastNode::m_QueriesLength
private

Definition at line 127 of file blast_node.hpp.

Referenced by GetQueriesLength(), and SetQueriesLength().

◆ m_QueryIndex

int CBlastNode::m_QueryIndex
private

Definition at line 121 of file blast_node.hpp.

◆ m_State

EState CBlastNode::m_State
private

Definition at line 125 of file blast_node.hpp.

Referenced by GetState(), and SetState().

◆ m_Status

int CBlastNode::m_Status
private

Definition at line 126 of file blast_node.hpp.

Referenced by GetStatus(), and SetStatus().


The documentation for this class was generated from the following files:
Modified on Sun Jul 21 04:15:01 2024 by modify_doxy.py rev. 669887