#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< 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 ()

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 ()

ICanceled *	x_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< CAppJobError >	m_Error

CRef< CObject >	m_Result

string	m_Desc
	Job description or name. More...

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...

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

Definition at line 227 of file seqgraphic_job.hpp.

References m_GraphLevel.

Referenced by CSGSeqGraphJob::x_Execute(), CSGFeatureJob::x_Execute(), and CSGSeqGraphJob::x_LoadGraphFromCoverageGraph().

◆ GetScope()

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

inline

CSGAnnotJob inline methods.

Definition at line 219 of file seqgraphic_job.hpp.

References m_Handle.

Referenced by CSGAlignmentJob::x_CreateFeatGlyph(), CSGSeqGraphJob::x_Execute(), CSGAlignmentJob::x_LoadAlignmentFeats(), and CBatchFeatJob::x_LoadFeatProducts().

◆ 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

Definition at line 176 of file seqgraphic_job.cpp.

References CSeq_graph_Base::C_Graph::e_Byte, CSeq_graph_Base::C_Graph::e_Int, CSeq_graph_Base::C_Graph::e_Real, map_checker< Container >::end(), map_checker< Container >::find(), CMappedGraph::GetAnnot(), CSeqUtils::GetAnnotComment(), CSeq_graph_Base::C_Graph::GetByte(), CRange_Base::GetFrom(), CMappedGraph::GetGraph(), CSeq_graph_Base::C_Graph::GetInt(), CSeq_annot_Handle::GetName(), CSeq_graph_Base::C_Graph::GetReal(), CRange_Base::GetTo(), CSeqUtils::GetUnnamedAnnot(), map_checker< Container >::insert(), CSeq_annot_Handle::IsNamed(), CSGAnnotJob::SGraphObject::m_Map, CSGAnnotJob::SGraphObject::m_Max, CSGAnnotJob::SGraphObject::m_Min, m_Range, CSeq_graph_Base::C_Graph::Which(), x_AddGraphToMap(), x_GetGraphName(), and x_PercentileButNotMax().

Referenced by x_CreateHistFromGraph().

◆ 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

Definition at line 155 of file seqgraphic_job.cpp.

References SAnnotSelector::AddNamedAnnots(), CombineWithZoomLevel(), CSeq_annot_Base::C_Data::e_Graph, IAppJob::eFailed, SAnnotSelector::GetNamedAnnotAccessions(), SAnnotSelector::IncludeNamedAnnotAccession(), SAnnotSelector::IsIncludedAnyNamedAnnotAccession(), ITERATE, m_Sel, SAnnotSelector::ResetAnnotsNames(), SAnnotSelector::SetAnnotType(), CSeqGraphicJob::SetTaskName(), and x_CreateHistFromGraph().

Referenced by CSGFeatureJob::x_CreateFeatHistFromGraph(), and CSGSeqGraphJob::x_LoadGraphFromCoverageGraph().

◆ 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

target sequence

Definition at line 201 of file seqgraphic_job.hpp.

Referenced by GetScope(), CSGFeatureJob::x_CalcIntervals(), CSGAlignStatJob::x_CollectAlignStats(), CSGFeatureJob::x_CreateFeature1(), x_CreateHistFromGraph(), CSGAlignStatJob::x_CreatePileUpGraphs(), CSnpJob::x_Execute(), CSGAlignStatJob::x_Execute(), CSGSeqGraphJob::x_Execute(), CBinsJob::x_Execute(), CEpigenomicsJob::x_Execute(), CSGFeatureJob::x_Execute(), CGeneModelFeatJob::x_Execute(), CSGSegmentSmearJob::x_Execute(), CVcfFeatureJob::x_Execute(), CBinsJob::x_FetchGraphs(), CSnpJob::x_FetchGraphs(), CSGAlignmentJob::x_GetAlignments(), CSGAlignmentJob::x_GetAlignSmear(), CSGSegmentSmearJob::x_GetCacheKey(), CHapmapJob::x_Load(), CLDBlockJob::x_Load(), CSGAlignmentJob::x_LoadAlignments(), CSGAlignStatJob::x_LoadAlignments(), CSGSegmentSmearJob::x_LoadFromDeltaSeqs(), CSGSegmentSmearJob::x_LoadFromNA(), CSGSegmentSmearJob::x_LoadGaps(), CSGSeqGraphJob::x_LoadSeqTable(), CSnpJob::x_PreFetchFtable(), CBinsJob::x_PreFetchFtable(), and CGeneModelFeatJob::x_ProcessLandMarkFeatures().

◆ m_Range

TSeqRange CSGAnnotJob::m_Range

protected

target range

Definition at line 203 of file seqgraphic_job.hpp.

Referenced by x_AddGraphObject(), x_AddGraphToMap(), CSGFeatureJob::x_CreateFeatHist(), CSGFeatureJob::x_CreateFeatSmear(), x_CreateHistFromGraph(), CSGAlignStatJob::x_CreatePileUpGraphs(), CSnpJob::x_Execute(), CSGAlignStatJob::x_Execute(), CSGSeqGraphJob::x_Execute(), CBinsJob::x_Execute(), CEpigenomicsJob::x_Execute(), CSGFeatureJob::x_Execute(), CGeneModelFeatJob::x_Execute(), CVcfFeatureJob::x_Execute(), CBinsJob::x_FetchGraphs(), CSnpJob::x_FetchGraphs(), CSGAlignmentJob::x_GetAlignments(), CSGAlignmentJob::x_GetAlignSmear(), CHapmapJob::x_Load(), CLDBlockJob::x_Load(), CSGAlignmentJob::x_LoadAlignmentFeats(), CSGAlignmentJob::x_LoadAlignments(), CSGAlignStatJob::x_LoadAlignments(), CBatchFeatJob::x_LoadFeatProducts(), CSGSegmentSmearJob::x_LoadFromDeltaSeqs(), CSGSegmentSmearJob::x_LoadFromNA(), CSGSegmentSmearJob::x_LoadFromNetCache(), CLDBlockJob::x_LoadFtable(), CSGSegmentSmearJob::x_LoadGaps(), CSGSeqGraphJob::x_LoadSeqTable(), CSnpJob::x_MakeHistogramFromFtable(), CBinsJob::x_PreFetchFtable(), CSGFeatureJob::x_ProcessCachedBigBed(), CSGFeatureJob::x_ProcessCachedVcfTabix(), and CGeneModelFeatJob::x_ProcessLandMarkFeatures().

◆ m_Sel

objects::SAnnotSelector CSGAnnotJob::m_Sel

protected

our annotation selector

Definition at line 202 of file seqgraphic_job.hpp.

Referenced by CSGSegmentSmearJob::CSGSegmentSmearJob(), CEpigenomicsJob::x_Execute(), CSGFeatureJob::x_Execute(), CGeneModelFeatJob::x_Execute(), CVcfFeatureJob::x_Execute(), CSGAlignmentJob::x_GetCoverageGraph(), CHapmapJob::x_Load(), CSGAlignmentJob::x_LoadAlignmentFeats(), CSGAlignmentJob::x_LoadAlignments(), CSGAlignStatJob::x_LoadAlignments(), x_LoadCoverageGraph(), CSGSegmentSmearJob::x_LoadFromNA(), CSGSeqGraphJob::x_LoadGraph(), CSGSeqGraphJob::x_LoadSeqTable(), CSGFeatureJob::x_ProcessCachedBigBed(), and CSGFeatureJob::x_ProcessCachedVcfTabix().

The documentation for this class was generated from the following files:

include/gui/widgets/seq_graphic/seqgraphic_job.hpp
src/gui/widgets/seq_graphic/seqgraphic_job.cpp

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CSGAnnotJob()

Member Function Documentation

◆ GetGraphLevel()

◆ GetScope()

◆ SetGraphLevel()

◆ x_AddGraphObject()

◆ x_AddGraphToMap() [1/2]

◆ x_AddGraphToMap() [2/2]

◆ x_CreateHistFromGraph()

◆ x_GetGraphName()

◆ x_LoadCoverageGraph()

◆ x_PercentileButNotMax()

Member Data Documentation

◆ m_GraphLevel

◆ m_Handle

◆ m_Range

◆ m_Sel