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CSGSegmentMapJob Class Reference

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CSGSegmentMapJob declaration. More...

+ Inheritance diagram for CSGSegmentMapJob:
+ Collaboration diagram for CSGSegmentMapJob:

Public Member Functions

 CSGSegmentMapJob (const string &desc, objects::CBioseq_Handle handle, const TSeqRange &range, int depth, int cutoff, TJobToken token)
 CSGSegmentMapJob implementation. More...
 
- 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< IAppJobProgressGetProgress ()
 return progress object, the function shall be synchronized internally. More...
 
virtual CRef< CObjectGetResult ()
 Returns the Job Result. More...
 
virtual CConstIRef< IAppJobErrorGetError ()
 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...
 
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...
 
- Public Member Functions inherited from ISeqTaskProgressCallback
virtual ~ISeqTaskProgressCallback ()
 

Static Public Member Functions

static int GetSegmentMapLevels (const objects::CBioseq_Handle &handle, const TSeqRange &range)
 
static bool HasSegmentMap (const objects::CBioseq_Handle &Handle, int level, const TSeqRange &range)
 
- 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 EJobState x_Execute ()
 method truly doing the job. More...
 
- 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...
 

Private Member Functions

bool x_AdaptiveDepth () const
 
IAppJob::EJobState x_MergeSeqSegments (CSegmentGlyph::TSeqMapList &seg_maps, CSeqGlyph::TObjects &objs)
 merge equal segment maps into one map. More...
 

Private Attributes

objects::CBioseq_Handle m_Handle
 target sequence More...
 
TSeqRange m_Range
 target range More...
 
int m_Depth
 Resolve depth for selector. More...
 
int m_Cutoff
 limit of number of segments we want to show. More...
 

Additional Inherited Members

- Public Types inherited from CSeqGraphicJob
typedef int TJobToken
 
typedef map< string, stringTAnnotNameTitleMap
 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< 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...
 
- Protected Attributes inherited from CSeqGraphicJob
TJobToken m_Token
 Job token recognizable by job listener. More...
 
CRef< CAppJobErrorm_Error
 
CRef< CObjectm_Result
 
string m_Desc
 Job description or name. More...
 

Detailed Description

CSGSegmentMapJob declaration.

Definition at line 62 of file segment_map_ds.cpp.

Constructor & Destructor Documentation

◆ CSGSegmentMapJob()

CSGSegmentMapJob::CSGSegmentMapJob ( const string desc,
objects::CBioseq_Handle  handle,
const TSeqRange range,
int  depth,
int  cutoff,
TJobToken  token 
)

CSGSegmentMapJob implementation.

Definition at line 333 of file segment_map_ds.cpp.

References CSeqGraphicJob::SetToken().

Member Function Documentation

◆ GetSegmentMapLevels()

int CSGSegmentMapJob::GetSegmentMapLevels ( const objects::CBioseq_Handle &  handle,
const TSeqRange range 
)
static

◆ HasSegmentMap()

bool CSGSegmentMapJob::HasSegmentMap ( const objects::CBioseq_Handle &  Handle,
int  level,
const TSeqRange range 
)
static

◆ x_AdaptiveDepth()

bool CSGSegmentMapJob::x_AdaptiveDepth ( ) const
inlineprivate

Definition at line 78 of file segment_map_ds.cpp.

References m_Depth.

Referenced by x_Execute().

◆ x_Execute()

IAppJob::EJobState CSGSegmentMapJob::x_Execute ( )
protectedvirtual

◆ x_MergeSeqSegments()

IAppJob::EJobState CSGSegmentMapJob::x_MergeSeqSegments ( CSegmentGlyph::TSeqMapList seg_maps,
CSeqGlyph::TObjects objs 
)
private

Member Data Documentation

◆ m_Cutoff

int CSGSegmentMapJob::m_Cutoff
private

limit of number of segments we want to show.

<=0 means there is no limit.

Definition at line 97 of file segment_map_ds.cpp.

Referenced by x_Execute().

◆ m_Depth

int CSGSegmentMapJob::m_Depth
private

Resolve depth for selector.

Valid numbers include: -1: adaptive, 0: first level, 1: second Depending on the sequence currently shown, first level may be the scaffolds (chromosome) or the compoments (config)

Definition at line 93 of file segment_map_ds.cpp.

Referenced by x_AdaptiveDepth(), and x_Execute().

◆ m_Handle

objects::CBioseq_Handle CSGSegmentMapJob::m_Handle
private

target sequence

Definition at line 86 of file segment_map_ds.cpp.

Referenced by x_Execute().

◆ m_Range

TSeqRange CSGSegmentMapJob::m_Range
private

target range

Definition at line 87 of file segment_map_ds.cpp.

Referenced by x_Execute().


The documentation for this class was generated from the following file:
Modified on Thu May 23 12:30:59 2024 by modify_doxy.py rev. 669887