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

Search Toolkit Book for CBlastxNode

#include "blastx_node.hpp"
(Private to src/app/blast.)

+ Inheritance diagram for CBlastxNode:
+ Collaboration diagram for CBlastxNode:

Public Member Functions

 CBlastxNode (int check_num, const CNcbiArguments &ncbi_args, const CArgs &args, CBlastAppDiagHandler &bah, string &input, int query_index, int num_queries, CBlastNodeMailbox *mailbox=NULL)
 
virtual int GetBlastResults (CNcbiOstream &os)
 
- Public Member Functions inherited from CBlastNode
 CBlastNode (int node_num, const CNcbiArguments &ncbi_args, const CArgs &args, CBlastAppDiagHandler &bah, int query_index, int num_queries, CBlastNodeMailbox *mailbox)
 
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 ~CBlastxNode (void)
 
virtual void * Main (void)
 Derived (user-created) class must provide a real thread function. More...
 
- Protected Member Functions inherited from CBlastNode
virtual ~CBlastNode (void)
 
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...
 

Private Attributes

string m_Input
 
CRef< CBlastxNodeArgsm_CmdLineArgs
 

Additional Inherited Members

- Public Types inherited from CBlastNode
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...
 
- 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 Attributes inherited from CBlastNode
int m_NodeNum
 

Detailed Description

Definition at line 43 of file blastx_node.hpp.

Constructor & Destructor Documentation

◆ CBlastxNode()

CBlastxNode::CBlastxNode ( int  check_num,
const CNcbiArguments ncbi_args,
const CArgs args,
CBlastAppDiagHandler bah,
string input,
int  query_index,
int  num_queries,
CBlastNodeMailbox mailbox = NULL 
)

◆ ~CBlastxNode()

CBlastxNode::~CBlastxNode ( void  )
protectedvirtual

Definition at line 72 of file blastx_node.cpp.

References m_CmdLineArgs, and CRef< C, Locker >::Reset().

Member Function Documentation

◆ GetBlastResults()

int CBlastxNode::GetBlastResults ( CNcbiOstream os)
virtual

◆ Main()

void * CBlastxNode::Main ( void  )
protectedvirtual

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

Implements CBlastNode.

Definition at line 78 of file blastx_node.cpp.

References _ASSERT, CFormattingArgs::ArchiveFormatRequested(), BLAST_EXIT_SUCCESS, BlastFormatter_PreFetchSequenceData(), CATCH_ALL, CDebugDumpable::DebugDumpText(), CFormattingArgs::DisplayHtmlOutput(), CBlastAppDiagHandler::DoNotSaveMessages(), CBlastNode::eDone, CBlastNode::eError, CBlastNodeMsg::eErrorExit, CBlastNodeMsg::ePostResult, ERR_POST, CBlastNode::eRunning, CBlastAppArgs::ExecuteRemotely(), CBlastNode::GetArgs(), CBlastNode::GetArguments(), CBlastAppArgs::GetBlastDatabaseArgs(), CBlastAppArgs::GetClientId(), GetCmdlineArgs(), CFormattingArgs::GetCustomDelimiter(), CFormattingArgs::GetCustomOutputFormatSpec(), CBlastOptions::GetDbGeneticCode(), CBlastNode::GetDiagHandler(), CLocalDbAdapter::GetFilteringAlgorithm(), CFormattingArgs::GetFormattedOutputChoice(), CBlastAppArgs::GetFormattingArgs(), CFormattingArgs::GetHitsSortOption(), CFormattingArgs::GetHspsSortOption(), CBlastxNodeArgs::GetInputStream(), CFormattingArgs::GetLineLength(), CBlastOptions::GetMatrixName(), CBlastAppDiagHandler::GetMessages(), CBlastNode::GetNodeIdStr(), CBlastNode::GetNodeNum(), CFormattingArgs::GetNumAlignments(), CFormattingArgs::GetNumDescriptions(), CBlastOptionsHandle::GetOptions(), CBlastxNodeArgs::GetOutputStream(), CQueryOptionsArgs::GetParseDeflines(), CBlastxNodeArgs::GetQueryBatchSize(), CBlastOptions::GetQueryGeneticCode(), CBlastAppArgs::GetQueryOptionsArgs(), CQueryOptionsArgs::GetRange(), CRemoteBlast::GetResultSet(), CQueryOptionsArgs::GetStrand(), GetSubjectFile(), CBlastOptions::GetSumStatisticsMode(), InitializeQueryDataLoaderConfiguration(), InitializeRemoteBlast(), InitializeSubject(), input(), NStr::IntToString(), ITERATE, kArgOutput, m_CmdLineArgs, m_Input, NcbiCerr, NULL, CBlastFormat::PrintEpilog(), CBlastFormat::PrintOneResultSet(), CBlastFormat::PrintProlog(), CBlastAppArgs::ProduceDebugOutput(), CBlastAppArgs::ProduceDebugRemoteOutput(), QueryBatchCleanup(), CQueryOptionsArgs::QueryIsProtein(), RecoverSearchStrategy(), CRef< C, Locker >::Reset(), CBlastAppDiagHandler::ResetMessages(), CBlastFormat::ResetScopeHistory(), result, CLocalBlast::Run(), SaveSearchStrategy(), CBlastNode::SendMsg(), CBlastFormat::SetBaseFile(), CBlastFormat::SetCustomDelimiter(), CBlastNode::SetDataLoaderPrefix(), SetDiagPostPrefix(), CBlastFormat::SetHitsSortOption(), CBlastFormat::SetHspsSortOption(), CBlastFormat::SetLineLength(), CThreadable::SetNumberOfThreads(), CBlastAppArgs::SetOptions(), CBlastAppArgs::SetOptionsForSavedStrategy(), CBlastNode::SetQueriesLength(), CBlastFormat::SetQueryRange(), CBlastNode::SetState(), CBlastNode::SetStatus(), CFormattingArgs::ShowGis(), CQueryOptionsArgs::UseLowercaseMasks(), UseXInclude(), Warning(), and CBlastFormat::WriteArchive().

Member Data Documentation

◆ m_CmdLineArgs

CRef<CBlastxNodeArgs> CBlastxNode::m_CmdLineArgs
private

Definition at line 56 of file blastx_node.hpp.

Referenced by CBlastxNode(), GetBlastResults(), Main(), and ~CBlastxNode().

◆ m_Input

string CBlastxNode::m_Input
private

Definition at line 55 of file blastx_node.hpp.

Referenced by CBlastxNode(), and Main().


The documentation for this class was generated from the following files:
Modified on Wed Feb 21 09:54:20 2024 by modify_doxy.py rev. 669887