NCBI C++ ToolKit
|
Search Toolkit Book for CBlastnNode
#include "blastn_node.hpp"
(Private to src/app/blast
.)
Public Member Functions | |
CBlastnNode (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 CArgs & | GetArgs () |
CBlastAppDiagHandler & | GetDiagHandler () |
const CNcbiArguments & | GetArguments () |
void | SendMsg (CBlastNodeMsg::EMsgType msg_type, void *ptr=NULL) |
string & | GetNodeIdStr () |
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... | |
CObject & | operator= (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 | ~CBlastnNode (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< CBlastnNodeArgs > | m_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< Uint8 > | TCounter |
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 CThread * | GetCurrentThread (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 |
Definition at line 43 of file blastn_node.hpp.
CBlastnNode::CBlastnNode | ( | int | check_num, |
const CNcbiArguments & | ncbi_args, | ||
const CArgs & | args, | ||
CBlastAppDiagHandler & | bah, | ||
string & | input, | ||
int | query_index, | ||
int | num_queries, | ||
CBlastNodeMailbox * | mailbox = NULL |
||
) |
Definition at line 50 of file blastn_node.cpp.
References CBlastNode::eInitialized, CBlastNodeMsg::eRunRequest, input(), m_CmdLineArgs, m_Input, CRef< C, Locker >::Reset(), CBlastNode::SendMsg(), and CBlastNode::SetState().
|
protectedvirtual |
Definition at line 72 of file blastn_node.cpp.
References m_CmdLineArgs, and CRef< C, Locker >::Reset().
|
virtual |
Implements CBlastNode.
Definition at line 61 of file blastn_node.cpp.
References CBlastNode::eDone, CBlastnNodeArgs::GetOutputStrStream(), CBlastNode::GetState(), CBlastNode::GetStatus(), and m_CmdLineArgs.
|
protectedvirtual |
Derived (user-created) class must provide a real thread function.
Implements CBlastNode.
Definition at line 78 of file blastn_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(), CBatchSizeMixer::GetBatchSize(), CBlastAppArgs::GetBlastDatabaseArgs(), CBlastAppArgs::GetClientId(), GetCmdlineArgs(), CFormattingArgs::GetCustomDelimiter(), CFormattingArgs::GetCustomOutputFormatSpec(), CBlastOptions::GetDbGeneticCode(), CBlastFormat::GetDbTotalLength(), CBlastNode::GetDiagHandler(), CLocalDbAdapter::GetFilteringAlgorithm(), CFormattingArgs::GetFormattedOutputChoice(), CBlastAppArgs::GetFormattingArgs(), CFormattingArgs::GetHitsSortOption(), CFormattingArgs::GetHspsSortOption(), CBlastnNodeArgs::GetInputStream(), CFormattingArgs::GetLineLength(), CBlastOptions::GetMatrixName(), CBlastOptions::GetMBIndexLoaded(), CBlastAppDiagHandler::GetMessages(), CBlastNode::GetNodeIdStr(), CBlastNode::GetNodeNum(), CFormattingArgs::GetNumAlignments(), CFormattingArgs::GetNumDescriptions(), CLocalBlast::GetNumExtensions(), CBlastOptionsHandle::GetOptions(), CBlastnNodeArgs::GetOutputStream(), CQueryOptionsArgs::GetParseDeflines(), CBlastOptions::GetProgram(), CBlastnNodeArgs::GetQueryBatchSize(), CBlastOptions::GetQueryGeneticCode(), CBlastAppArgs::GetQueryOptionsArgs(), CQueryOptionsArgs::GetRange(), CRemoteBlast::GetResultSet(), CQueryOptionsArgs::GetStrand(), GetSubjectFile(), CBlastOptions::GetSumStatisticsMode(), CBlastAppArgs::GetTask(), CBlastOptions::GetUseIndex(), CSetupFactory::InitializeMegablastDbIndex(), InitializeQueryDataLoaderConfiguration(), InitializeRemoteBlast(), InitializeSubject(), input(), NStr::IntToString(), IsIStreamEmpty(), ITERATE, kArgOutput, m_CmdLineArgs, 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, results, CLocalBlast::Run(), SaveSearchStrategy(), CBlastNode::SendMsg(), CBlastFormat::SetBaseFile(), CBlastFormat::SetCustomDelimiter(), CBlastNode::SetDataLoaderPrefix(), SetDiagPostPrefix(), CBlastFormat::SetHitsSortOption(), CBlastFormat::SetHspsSortOption(), CBlastFormat::SetLineLength(), CThreadable::SetNumberOfThreads(), CBlastOptionsHandle::SetOptions(), CBlastAppArgs::SetOptions(), CBlastAppArgs::SetOptionsForSavedStrategy(), CBlastNode::SetQueriesLength(), CBlastFormat::SetQueryRange(), CBlastNode::SetState(), CBlastNode::SetStatus(), CBatchSizeMixer::SetTargetHits(), CFormattingArgs::ShowGis(), SplitQuery_GetChunkSize(), CQueryOptionsArgs::UseLowercaseMasks(), UseXInclude(), Warning(), and CBlastFormat::WriteArchive().
|
private |
Definition at line 56 of file blastn_node.hpp.
Referenced by CBlastnNode(), GetBlastResults(), Main(), and ~CBlastnNode().
|
private |
Definition at line 55 of file blastn_node.hpp.
Referenced by CBlastnNode().