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CSGAnnotJob Class Reference

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#include <gui/widgets/seq_graphic/seqgraphic_job.hpp>

+ Inheritance diagram for CSGAnnotJob:
+ Collaboration diagram for CSGAnnotJob:

Classes

struct  SGraphObject
 
struct  TAxisLimits
 

Public Member Functions

 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< 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 ()
 

Protected Member Functions

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 CSeqGraphicJob
virtual EJobState x_Execute ()=0
 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...
 

Protected Attributes

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< CAppJobErrorm_Error
 
CRef< CObjectm_Result
 
string m_Desc
 Job description or name. 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 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...
 

Detailed Description

Definition at line 115 of file seqgraphic_job.hpp.

Constructor & Destructor Documentation

◆ CSGAnnotJob()

CSGAnnotJob::CSGAnnotJob ( const string desc,
objects::CBioseq_Handle  handle,
const objects::SAnnotSelector &  sel,
const TSeqRange range 
)

CSGAnnotJob.

Definition at line 144 of file seqgraphic_job.cpp.

Member Function Documentation

◆ GetGraphLevel()

int CSGAnnotJob::GetGraphLevel ( ) const
inline

◆ GetScope()

objects::CScope & CSGAnnotJob::GetScope ( void  ) const
inline

◆ SetGraphLevel()

void CSGAnnotJob::SetGraphLevel ( int  level)
inline

Definition at line 223 of file seqgraphic_job.hpp.

References m_GraphLevel.

◆ x_AddGraphObject()

void CSGAnnotJob::x_AddGraphObject ( map< string, SGraphObject > &  d_maps,
const objects::CMappedGraph &  gr,
TModelUnit  window,
bool  fixed_scale 
)
protected

◆ x_AddGraphToMap() [1/2]

template<typename TGraphType >
void CSGAnnotJob::x_AddGraphToMap ( CDensityMap< float > &  the_map,
const CMappedGraph gr,
const TGraphType &  graph,
double &  g_max,
double &  g_min,
bool  fixed_scale 
)

◆ x_AddGraphToMap() [2/2]

template<typename TGraphType >
void CSGAnnotJob::x_AddGraphToMap ( CDensityMap< float > &  the_map,
const objects::CMappedGraph &  gr,
const TGraphType &  graph,
double &  g_max,
double &  g_min,
bool  fixed_scale 
)
protected

Referenced by x_AddGraphObject().

◆ x_CreateHistFromGraph()

IAppJob::EJobState CSGAnnotJob::x_CreateHistFromGraph ( CSeqGlyph::TObjects glyphs,
const objects::SAnnotSelector &  sel,
TModelUnit  window,
bool  fixed_scale,
const TAxisLimits y_limits 
)
protected

◆ x_GetGraphName()

string CSGAnnotJob::x_GetGraphName ( const objects::CMappedGraph &  gr) const
protected

Get a name for a graph.

We should favor title over annotation name.

Definition at line 423 of file seqgraphic_job.cpp.

References CMappedGraph::GetAnnot(), CSeqUtils::GetAnnotName(), CMappedGraph::GetTitle(), CMappedGraph::IsSetTitle(), and kEmptyStr.

Referenced by x_AddGraphObject().

◆ x_LoadCoverageGraph()

IAppJob::EJobState CSGAnnotJob::x_LoadCoverageGraph ( CSeqGlyph::TObjects glyphs,
int  level,
TModelUnit  window,
const string title,
bool  fixed_scale,
const TAxisLimits y_limits 
)
protected

◆ x_PercentileButNotMax()

bool CSGAnnotJob::x_PercentileButNotMax ( const objects::CMappedGraph &  gr) const
protected

Check the graph type.

Returns
true only if the given graph is a percentile graph and not a 100 percentile. A percentile graph is indicated in seq-annot::desc asn as a user-object: Seq-annot ::= { desc { user { type str "AnnotationTrack", data { { label str "StatisticsType", data str "Percentiles" } } } }, And the specific percentile is indicated in seq-graph::comment data graph { { title "Feature density graph", comment "90%", ... } }

Definition at line 438 of file seqgraphic_job.cpp.

References CSeq_annot_Base::CanGetDesc(), CAnnot_descr_Base::Get(), CMappedGraph::GetAnnot(), CMappedGraph::GetComment(), CSeq_annot_Handle::GetCompleteSeq_annot(), CUser_field_Base::GetData(), CSeq_annot_Base::GetDesc(), CUser_field::GetFieldRef(), CUser_field_Base::C_Data::GetStr(), CMappedGraph::IsSetComment(), CUser_field_Base::C_Data::IsStr(), and ITERATE.

Referenced by x_AddGraphObject().

Member Data Documentation

◆ m_GraphLevel

int CSGAnnotJob::m_GraphLevel
protected

coverate graph level

Definition at line 204 of file seqgraphic_job.hpp.

Referenced by GetGraphLevel(), SetGraphLevel(), and CSGSeqGraphJob::x_Execute().

◆ m_Handle

objects::CBioseq_Handle CSGAnnotJob::m_Handle
protected

◆ m_Range

TSeqRange CSGAnnotJob::m_Range
protected

◆ m_Sel

objects::SAnnotSelector CSGAnnotJob::m_Sel
protected

The documentation for this class was generated from the following files:
Modified on Sun Apr 21 03:40:12 2024 by modify_doxy.py rev. 669887