Search Toolkit Book for CKalignToolJob
#include <gui/packages/pkg_alignment/kalign_tool_job.hpp>
Inheritance diagram for CKalignToolJob:
Collaboration diagram for CKalignToolJob:
Public Member Functions | |
| CKalignToolJob (const CKalignToolParams ¶ms) | |
| CKalignToolJob. More... | |
| Public Member Functions inherited from CMSAToolJob | |
| CMSAToolJob (const wxString &tool_name) | |
| CMSAToolJob. More... | |
| virtual | ~CMSAToolJob () |
| Public Member Functions inherited from CDataLoadingAppJob | |
| CDataLoadingAppJob () | |
| constructor for derived classes More... | |
| virtual | ~CDataLoadingAppJob () |
| const CSelectProjectOptions::TData & | GetData () const |
| const objects::CScope & | GetScope () const |
| virtual void | GetHTMLResults (wxString &, wxString &) |
| void | AddProjectItem (objects::CProjectItem &item) |
| void | AddProjectItem (objects::CProjectItem &item, objects::CLoaderDescriptor &loader) |
| void | AddDataLoader (objects::CLoaderDescriptor &loader) |
| void | ClearItems () |
| virtual EJobState | Run () |
| Function that does all the useful work, called by the Engine. More... | |
| virtual CRef< CObject > | GetResult () |
| Returns the Job Result. More... | |
| virtual CConstIRef< IAppJobProgress > | GetProgress () |
| implement Run() in derived classes, make sure that exceptions are handled and m_StopRequested flag is respected. More... | |
| Public Member Functions inherited from CAppJob | |
| CAppJob (const string &descr="AppJob") | |
| CAppJob. More... | |
| virtual CConstIRef< IAppJobError > | GetError () override |
| Returns IAppJobError object describing internal error that caused the Job to fail. More... | |
| virtual string | GetDescr () const override |
| Returns a human readable description of the Job (optional) More... | |
| Public Member Functions inherited from CJobCancelable | |
| CJobCancelable () | |
| void | SetDataLocker (ILocker *locker) |
| virtual void | RequestCancel () override |
| RequestCancel() is called to notify the Job that it shall exit Run() function ASAP. More... | |
| virtual bool | IsCanceled () const override |
| 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 |
| Public Member Functions inherited from IAppJob | |
| virtual | ~IAppJob () |
Protected Member Functions | |
| virtual wxString | x_GetCommandLine (const wxString &input, const wxString &output, bool is_nucleotide) |
| Returns the command line, that will be used to execute the third-party tool. More... | |
| virtual TConstScopedObjects & | x_GetObjects () |
| Returns the sequences that will be aligned. More... | |
| Protected Member Functions inherited from CMSAToolJob | |
| virtual bool | BeforeRun () |
| Function will be called on the main thread before execution of Run Should not do any lengthy work returns true to continue job execution on worker thread false to quit execution with status - failed. More... | |
| virtual void | x_CreateProjectItems () |
| override this function in derived classes and populate m_Items. More... | |
| virtual void | x_AddTreeProjectItem (const string &title, const string &comment) |
| virtual wxString | x_GetWorkingDirectory () const |
| Returns the directory where to execute the msa tool. More... | |
| Protected Member Functions inherited from CDataLoadingAppJob | |
| virtual void | x_ResetState () |
| prepares job for execution by clearing state variables More... | |
| virtual void | x_Run () |
| void | x_SetTextResult (const string &result) |
| Protected Member Functions inherited from CAppJob | |
| virtual void | x_SetStatusText (const string &text) |
| Protected Member Functions inherited from CJobCancelable | |
| CLockerGuard | x_GetGuard () |
| ICanceled * | x_GetICanceled () |
| Protected Member Functions inherited from CObject | |
| virtual void | DeleteThis (void) |
| Virtual method "deleting" this object. More... | |
Private Attributes | |
| CKalignToolParams | m_Params |
Additional Inherited Members | |
| Public Types inherited from CMSAToolJob | |
| typedef pair< CConstRef< objects::CSeq_loc >, CRef< objects::CScope > > | TLocPair |
| typedef map< string, TLocPair > | TIdMap |
| typedef map< objects::CSeq_id_Handle, bool > | TSeqTypeMap |
| 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... | |
| Public Types inherited from IAppJob | |
| enum | EJobState { eInvalid , eRunning , eCompleted , eFailed , eCanceled , eSuspended } |
| Job states (describe FSM) 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 CMSAToolJob | |
| wxString | m_TmpIn |
| wxString | m_TmpOut |
| wxString | m_TmpTreeOut |
| long | m_PId |
| TIdMap | m_IdMap |
| to make the alignment as robust as possible, we assign every sequence a unique identifer independeont of its existing identifiers this map allows us to convert back at the end More... | |
| TSeqTypeMap | m_SeqTypes |
| objects::CMappingRanges | m_Ranges |
| wxString | m_CmdLine |
| wxString | m_ToolName |
| Protected Attributes inherited from CDataLoadingAppJob | |
| string | m_TextResult |
| CRef< objects::CScope > | m_Scope |
| Protected Attributes inherited from CAppJob | |
| CFastMutex | m_Mutex |
| string | m_Descr |
| mutex to sync our internals More... | |
| string | m_Status |
| Current status of the Job. More... | |
| CRef< CAppJobError > | m_Error |
Detailed Description
Definition at line 50 of file kalign_tool_job.hpp.
The documentation for this class was generated from the following files:
- include/gui/packages/pkg_alignment/kalign_tool_job.hpp
- src/gui/packages/pkg_alignment/kalign_tool_job.cpp
