Search Toolkit Book for CHapmapJob
Inheritance diagram for CHapmapJob:
Collaboration diagram for CHapmapJob:
Classes | |
| struct | SParams |
Public Member Functions | |
| CHapmapJob (const CBioseq_Handle &handle, const TSeqRange &range, const SParams ¶ms) | |
| virtual EJobState | x_Execute () |
| method truly doing the job. More... | |
| Public Member Functions inherited from CSGAnnotJob | |
| CSGAnnotJob (const string &desc, objects::CBioseq_Handle handle, const objects::SAnnotSelector &sel, const TSeqRange &range) | |
| CSGAnnotJob. More... | |
| void | SetGraphLevel (int level) |
| int | GetGraphLevel () const |
| objects::CScope & | GetScope (void) const |
| CSGAnnotJob inline methods. More... | |
| template<typename TGraphType > | |
| void | x_AddGraphToMap (CDensityMap< float > &the_map, const CMappedGraph &gr, const TGraphType &graph, double &g_max, double &g_min, bool fixed_scale) |
| Public Member Functions inherited from CSeqGraphicJob | |
| CSeqGraphicJob (const string &desc=kEmptyStr) | |
| CSeqGraphicJob. More... | |
| virtual | ~CSeqGraphicJob () |
| void | SetToken (TJobToken token) |
| CSeqGraphicJob inline methods. More... | |
| virtual EJobState | Run () |
| Function that does all the useful work, called by the Engine. More... | |
| virtual CConstIRef< IAppJobProgress > | GetProgress () |
| return progress object, the function shall be synchronized internally. More... | |
| virtual CRef< CObject > | GetResult () |
| Returns the Job Result. More... | |
| virtual CConstIRef< IAppJobError > | GetError () |
| Returns IAppJobError object describing internal error that caused the Job to fail. More... | |
| virtual string | GetDescr () const |
| Returns a human readable description of the Job (optional) More... | |
| virtual void | SetTaskName (const string &name) |
| virtual void | SetTaskCompleted (int completed) |
| set total finished task number. More... | |
| virtual void | AddTaskCompleted (int delta) |
| set to add newly finished task number. More... | |
| virtual void | SetTaskTotal (int total) |
| virtual bool | StopRequested () const |
| 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 () |
| 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... | |
| Public Member Functions inherited from ISeqTaskProgressCallback | |
| virtual | ~ISeqTaskProgressCallback () |
Private Member Functions | |
| EJobState | x_Load (CSeqGlyph::TObjects *) |
Private Attributes | |
| SParams | m_Params |
Additional Inherited Members | |
| Public Types inherited from CSeqGraphicJob | |
| typedef int | TJobToken |
| typedef map< string, string > | TAnnotNameTitleMap |
| List of annotations with the corresponding titles. 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... | |
| 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 Member Functions inherited from CSGAnnotJob | |
| IAppJob::EJobState | x_LoadCoverageGraph (CSeqGlyph::TObjects &glyphs, int level, TModelUnit window, const string &title, bool fixed_scale, const TAxisLimits &y_limits) |
| IAppJob::EJobState | x_CreateHistFromGraph (CSeqGlyph::TObjects &glyphs, const objects::SAnnotSelector &sel, TModelUnit window, bool fixed_scale, const TAxisLimits &y_limits) |
| template<typename TGraphType > | |
| void | x_AddGraphToMap (CDensityMap< float > &the_map, const objects::CMappedGraph &gr, const TGraphType &graph, double &g_max, double &g_min, bool fixed_scale) |
| void | x_AddGraphObject (map< string, SGraphObject > &d_maps, const objects::CMappedGraph &gr, TModelUnit window, bool fixed_scale) |
| string | x_GetGraphName (const objects::CMappedGraph &gr) const |
| Get a name for a graph. More... | |
| bool | x_PercentileButNotMax (const objects::CMappedGraph &gr) const |
| Check the graph type. More... | |
| 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... | |
| Protected Attributes inherited from CSGAnnotJob | |
| objects::CBioseq_Handle | m_Handle |
| target sequence More... | |
| objects::SAnnotSelector | m_Sel |
| our annotation selector More... | |
| TSeqRange | m_Range |
| target range More... | |
| int | m_GraphLevel |
| coverate graph level More... | |
| Protected Attributes inherited from CSeqGraphicJob | |
| TJobToken | m_Token |
| Job token recognizable by job listener. More... | |
| CRef< CAppJobError > | m_Error |
| CRef< CObject > | m_Result |
| string | m_Desc |
| Job description or name. More... | |
Detailed Description
Definition at line 58 of file hapmap_ds.cpp.
Constructor & Destructor Documentation
◆ CHapmapJob()
|
inline |
Definition at line 71 of file hapmap_ds.cpp.
Member Function Documentation
◆ x_Execute()
|
virtual |
method truly doing the job.
Implements CSeqGraphicJob.
Definition at line 85 of file hapmap_ds.cpp.
References IAppJob::eCompleted, IAppJob::eFailed, CException::GetMsg(), CSeqGraphicJob::m_Error, CSeqGraphicJob::m_Result, CRef< C, Locker >::Reset(), result, CException::what(), and x_Load().
◆ x_Load()
|
private |
Definition at line 112 of file hapmap_ds.cpp.
References CHapmapJob::SParams::bAdaptiveSelector, data, CHapmapJob::SParams::depth, CSeq_annot_Base::C_Data::e_Graph, CSeq_annot_Base::C_Data::e_Seq_table, IAppJob::eCompleted, CSeqFeatData::eSubtype_any, fabs, CRange_Base::GetFrom(), CSeq_annot_Handle::GetSeq_tableNumRows(), CRange_Base::GetTo(), CSeqUtils::IsNAA(), CSGAnnotJob::m_Handle, m_Params, CSGAnnotJob::m_Range, CSGAnnotJob::m_Sel, CHapmapJob::SParams::name, row, CHapmapJob::SParams::scale, CHistogramGlyph::SetAnnotName(), CSeqUtils::SetResolveDepth(), CTableFieldHandle_Base::TryGet(), and rapidjson::value.
Referenced by x_Execute().
Member Data Documentation
◆ m_Params
|
private |
Definition at line 82 of file hapmap_ds.cpp.
Referenced by x_Load().
The documentation for this class was generated from the following file:
- src/gui/packages/pkg_snp/hapmap/hapmap_ds.cpp
