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

Search Toolkit Book for CSplignJob

CSplignJob. More...

+ Inheritance diagram for CSplignJob:
+ Collaboration diagram for CSplignJob:

Public Member Functions

 CSplignJob (const CSplignParams &params, const TConstScopedObjects &genomic, const TConstScopedObjects &cdna)
 CSplignJob. More...
 
- Public Member Functions inherited from CDataLoadingAppJob
 CDataLoadingAppJob ()
 constructor for derived classes More...
 
virtual ~CDataLoadingAppJob ()
 
const CSelectProjectOptions::TDataGetData () 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< CObjectGetResult ()
 Returns the Job Result. More...
 
virtual CConstIRef< IAppJobProgressGetProgress ()
 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< IAppJobErrorGetError () 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...
 
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
 
- 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...
 

Static Public Member Functions

static bool s_SplignInterruptCallback (CNWAligner::SProgressInfo *prog)
 
static Boolean s_BlastInterruptCallback (SBlastProgress *prog)
 
- 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)
 

Protected Member Functions

virtual void x_CreateProjectItems ()
 override this function in derived classes and populate m_Items. 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 ()
 
ICanceledx_GetICanceled ()
 
- Protected Member Functions inherited from CObject
virtual void DeleteThis (void)
 Virtual method "deleting" this object. More...
 

Protected Attributes

CSplignParams m_Params
 
TConstScopedObjects m_Genomic
 
TConstScopedObjects m_cDNA
 
- 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< CAppJobErrorm_Error
 

Additional Inherited Members

- 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...
 
- Public Types inherited from IAppJob
enum  EJobState {
  eInvalid , eRunning , eCompleted , eFailed ,
  eCanceled , eSuspended
}
 Job states (describe FSM) More...
 
- 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...
 

Detailed Description

CSplignJob.

Definition at line 199 of file splign_tool.cpp.

Constructor & Destructor Documentation

◆ CSplignJob()

CSplignJob::CSplignJob ( const CSplignParams params,
const TConstScopedObjects genomic,
const TConstScopedObjects cdna 
)

CSplignJob.

Definition at line 318 of file splign_tool.cpp.

References CAppJob::m_Descr.

Member Function Documentation

◆ s_BlastInterruptCallback()

Boolean CSplignJob::s_BlastInterruptCallback ( SBlastProgress prog)
static

Definition at line 229 of file splign_tool.cpp.

References FALSE, CJobCancelable::IsCanceled(), prog, and TRUE.

Referenced by x_CreateProjectItems().

◆ s_SplignInterruptCallback()

bool CSplignJob::s_SplignInterruptCallback ( CNWAligner::SProgressInfo prog)
static

Definition at line 217 of file splign_tool.cpp.

References CJobCancelable::IsCanceled(), and prog.

Referenced by x_CreateProjectItems().

◆ x_CreateProjectItems()

void CSplignJob::x_CreateProjectItems ( )
protectedvirtual

override this function in derived classes and populate m_Items.

If data loaders are needed, they should be created here too.

Implements CDataLoadingAppJob.

Definition at line 326 of file splign_tool.cpp.

References CDataLoadingAppJob::AddProjectItem(), CSplignFormatter::AsSeqAlignSet(), CurrentTime(), CSplignFormatter::eAF_SplicedSegWithParts, CLabel::eDefault, eMegablast, CSeq_align_set_Base::Get(), CSplignParams::GetCDNAStrand(), CSplignParams::GetCompPenalty(), CSplignParams::GetDiscType(), CSplignParams::GetEndGapDetect(), GetId(), CLabel::GetLabel(), CSplignParams::GetMaxGenomicExtent(), CSplignParams::GetMaxIntron(), CSplignParams::GetMinCompIdentity(), CSplignParams::GetMinExonIdentity(), CSplignParams::GetPolyADetect(), CJobCancelable::IsCanceled(), CSeq_align_set::IsEmpty(), ITERATE, label, m_cDNA, m_Genomic, m_Params, max(), NON_CONST_ITERATE, CSplign::PreserveScope(), CRef< C, Locker >::Reset(), CBl2Seq::Run(), CSplign::Run(), s_BlastInterruptCallback(), CSplign::s_CreateDefaultAligner(), s_SplignInterruptCallback(), CSeq_align_set_Base::Set(), CSplign::SetAligner(), CSplign::SetCompartmentPenalty(), CSeq_annot::SetCreateDate(), CSeq_annot_Base::SetData(), CSplign::SetEndGapDetection(), CBl2Seq::SetInterruptCallback(), CProjectItem_Base::SetItem(), CProjectItem_Base::SetLabel(), CSplign::SetMaxGenomicExtent(), CSplign::SetMaxIntron(), CSplign::SetMinCompartmentIdentity(), CSplign::SetMinExonIdentity(), CSplign::SetMinSingletonIdentity(), CSeq_annot::SetNameDesc(), CSplign::SetPolyaDetection(), CSplign::SetScope(), CSplignFormatter::SetSeqIds(), CSplign::SetStrand(), and str().

Member Data Documentation

◆ m_cDNA

TConstScopedObjects CSplignJob::m_cDNA
protected

Definition at line 214 of file splign_tool.cpp.

Referenced by x_CreateProjectItems().

◆ m_Genomic

TConstScopedObjects CSplignJob::m_Genomic
protected

Definition at line 213 of file splign_tool.cpp.

Referenced by x_CreateProjectItems().

◆ m_Params

CSplignParams CSplignJob::m_Params
protected

Definition at line 212 of file splign_tool.cpp.

Referenced by x_CreateProjectItems().


The documentation for this class was generated from the following file:
Modified on Mon Feb 26 03:59:40 2024 by modify_doxy.py rev. 669887