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 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 | ~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< CBlastxNodeArgs > | 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 |
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 |
||
| ) |
Definition at line 50 of file blastx_node.cpp.
References CBlastNode::eInitialized, CBlastNodeMsg::eRunRequest, input(), m_CmdLineArgs, m_Input, CRef< C, Locker >::Reset(), CBlastNode::SendMsg(), and CBlastNode::SetState().
◆ ~CBlastxNode()
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protectedvirtual |
Definition at line 72 of file blastx_node.cpp.
References m_CmdLineArgs, and CRef< C, Locker >::Reset().
Member Function Documentation
◆ GetBlastResults()
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virtual |
Implements CBlastNode.
Definition at line 61 of file blastx_node.cpp.
References CBlastNode::eDone, CBlastxNodeArgs::GetOutputStrStream(), CBlastNode::GetState(), CBlastNode::GetStatus(), and m_CmdLineArgs.
◆ Main()
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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, results, 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
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private |
Definition at line 56 of file blastx_node.hpp.
Referenced by CBlastxNode(), GetBlastResults(), Main(), and ~CBlastxNode().
◆ m_Input
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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:
- src/app/blast/blastx_node.hpp
- src/app/blast/blastx_node.cpp
