Search Toolkit Book for CSGSegmentSmearJob

Inheritance diagram for CSGSegmentSmearJob:

Collaboration diagram for CSGSegmentSmearJob:

Public Member Functions
	CSGSegmentSmearJob (const string &desc, objects::CBioseq_Handle handle, const TSeqRange &range, TModelUnit scale, const string &annot, ICache cache=0, const CSeqVector seq_vec=nullptr)
	CSGSegmentSmearJob implementation. 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 ()

Static Public Member Functions
static void	GetAnnotNames (const objects::CBioseq_Handle &handle, const TSeqRange &range, objects::SAnnotSelector &sel, TAnnotNameTitleMap &annots)

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 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...

Private Member Functions
IAppJob::EJobState	x_LoadFromDeltaSeqs ()

IAppJob::EJobState	x_LoadFromNA ()

IAppJob::EJobState	x_LoadFromNetCache (const string &key)

void	x_WriteToCache (const string &key, const CSegmentSmearGlyph::CSegMap &density_map)

string	x_GetCacheKey () const

bool	x_IsGap (vector< char > is_gaps, int row) const

void	x_LoadGaps ()

Private Attributes
TModelUnit	m_Scale
	bases per pixel More...

string	m_Annot
	annotation storing the segments More...

ICache *	m_Cache
	cache to store segment ranges More...

const CSeqVector *	m_SeqVector

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 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 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

CSGSegmentSmearJob declaration.

Definition at line 103 of file segment_map_ds.cpp.

Constructor & Destructor Documentation

◆ CSGSegmentSmearJob()

CSGSegmentSmearJob::CSGSegmentSmearJob	(	const string &	desc,
		objects::CBioseq_Handle	handle,
		const TSeqRange &	range,
		TModelUnit	scale,
		const string &	annot,
		ICache *	cache = `0`,
		const CSeqVector *	seq_vec = `nullptr`
	)

CSGSegmentSmearJob implementation.

Definition at line 664 of file segment_map_ds.cpp.

References m_Annot, CSGAnnotJob::m_Sel, and CSeqGraphicJob::SetTaskName().

Member Function Documentation

◆ GetAnnotNames()

void CSGSegmentSmearJob::GetAnnotNames	(	const objects::CBioseq_Handle &	handle,
		const TSeqRange &	range,
		objects::SAnnotSelector &	sel,
		TAnnotNameTitleMap &	annots
	)

static

Definition at line 686 of file segment_map_ds.cpp.

References map_checker< Container >::begin(), CSeq_annot_Base::C_Data::e_Seq_table, eNa_strand_unknown, map_checker< Container >::end(), map_checker< Container >::erase(), CAnnotTypes_CI::GetAnnotNames(), CSeqUtils::GetUnnamedAnnot(), COpenRange< TSeqPos >::GetWhole(), map_checker< Container >::insert(), CSeqUtils::IsNAA(), and ITERATE.

Referenced by CSGSegmentMapDS::GetAnnotNames().

◆ x_Execute()

IAppJob::EJobState CSGSegmentSmearJob::x_Execute ( )

protectedvirtual

method truly doing the job.

Implements CSeqGraphicJob.

Definition at line 724 of file segment_map_ds.cpp.

References IAppJob::eFailed, Empty(), CException::GetMsg(), ICache::HasBlobs(), CSeq_id_Base::IsLocal(), ncbi::grid::netcache::search::fields::key, LOG_POST, m_Annot, m_Cache, CSGAnnotJob::m_Handle, Warning(), x_GetCacheKey(), x_LoadFromDeltaSeqs(), x_LoadFromNA(), x_LoadFromNetCache(), and x_LoadGaps().

◆ x_GetCacheKey()

string CSGSegmentSmearJob::x_GetCacheKey ( ) const

private

Definition at line 1001 of file segment_map_ds.cpp.

References CSeq_id::eContent, eGetId_Best, GetId(), CSeq_id::GetLabel(), CSeq_id_Handle::GetSeqId(), and CSGAnnotJob::m_Handle.

Referenced by x_Execute(), x_LoadFromDeltaSeqs(), and x_LoadFromNA().

◆ x_IsGap()

bool CSGSegmentSmearJob::x_IsGap	(	vector< char >	is_gaps,
		int	row
	)		const

inlineprivate

Definition at line 128 of file segment_map_ds.cpp.

References row.

◆ x_LoadFromDeltaSeqs()

IAppJob::EJobState CSGSegmentSmearJob::x_LoadFromDeltaSeqs ( )

private

◆ x_LoadFromNA()

IAppJob::EJobState CSGSegmentSmearJob::x_LoadFromNA ( )

private

Definition at line 860 of file segment_map_ds.cpp.

References CLogPerformance::AddParameter(), CRequestStatus::e200_Ok, IAppJob::eCompleted, IAppJob::eFailed, CSeqTable_column_info_Base::eField_id_location_from, CSeqTable_column_info_Base::eField_id_location_to, CSegmentConfig::eGap, CSeq_table_Base::GetColumns(), CSeq_annot_Handle::GetCompleteSeq_annot(), CSeq_annot_Base::GetData(), CRange_Base::GetFrom(), CSeq_annot_Base::C_Data::GetSeq_table(), CSeq_annot_Handle::GetSeq_tableNumRows(), CRange_Base::GetTo(), ITERATE, m_Cache, CSGAnnotJob::m_Handle, CSGAnnotJob::m_Range, CSeqGraphicJob::m_Result, m_Scale, CSGAnnotJob::m_Sel, NULL, CLogPerformance::Post(), compile_time_bits::range(), CRef< C, Locker >::Reset(), result, row, SGetSeqQuality(), CTableFieldHandle_Base::TryGet(), CSeqTable_column::TryGetBool(), rapidjson::value, x_GetCacheKey(), and x_WriteToCache().

Referenced by x_Execute().

◆ x_LoadFromNetCache()

IAppJob::EJobState CSGSegmentSmearJob::x_LoadFromNetCache ( const string & key )

private

Definition at line 960 of file segment_map_ds.cpp.

References _ASSERT, CLogPerformance::AddParameter(), CRequestStatus::e200_Ok, IAppJob::eCompleted, CRange_Base::GetFrom(), ICache::GetReadStream(), CRange_Base::GetTo(), ncbi::grid::netcache::search::fields::key, m_Cache, CSGAnnotJob::m_Range, CSeqGraphicJob::m_Result, m_Scale, CLogPerformance::Post(), CRef< C, Locker >::Reset(), and result.

Referenced by x_Execute().

◆ x_LoadGaps()

void CSGSegmentSmearJob::x_LoadGaps ( )

private

Definition at line 749 of file segment_map_ds.cpp.

References CSeqVector_CI::GetCurrentSeqMap_CI(), CRange_Base::GetFrom(), CSeqMap_CI::GetPosition(), CRange_Base::GetTo(), CSeqMap_CI::GetType(), m_Cache, CSGAnnotJob::m_Handle, CSGAnnotJob::m_Range, m_SeqVector, and t.

Referenced by x_Execute().

◆ x_WriteToCache()

void CSGSegmentSmearJob::x_WriteToCache	(	const string &	key,
		const CSegmentSmearGlyph::CSegMap &	density_map
	)

private

Definition at line 987 of file segment_map_ds.cpp.

References _ASSERT, CException::GetMsg(), ICache::GetWriteStream(), ncbi::grid::netcache::search::fields::key, LOG_POST, m_Cache, CSegmentSmearGlyph::CSegMap::Serialize(), and Warning().

Referenced by x_LoadFromDeltaSeqs(), and x_LoadFromNA().

Member Data Documentation

◆ m_Annot

string CSGSegmentSmearJob::m_Annot

private

annotation storing the segments

Definition at line 137 of file segment_map_ds.cpp.

Referenced by CSGSegmentSmearJob(), and x_Execute().

◆ m_Cache

ICache* CSGSegmentSmearJob::m_Cache

private

cache to store segment ranges

Definition at line 138 of file segment_map_ds.cpp.

Referenced by x_Execute(), x_LoadFromDeltaSeqs(), x_LoadFromNA(), x_LoadFromNetCache(), x_LoadGaps(), and x_WriteToCache().

◆ m_Scale

TModelUnit CSGSegmentSmearJob::m_Scale

private

bases per pixel

Definition at line 136 of file segment_map_ds.cpp.

Referenced by x_LoadFromDeltaSeqs(), x_LoadFromNA(), and x_LoadFromNetCache().

◆ m_SeqVector

const CSeqVector* CSGSegmentSmearJob::m_SeqVector

private

Definition at line 139 of file segment_map_ds.cpp.

Referenced by x_LoadGaps().

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

src/gui/widgets/seq_graphic/segment_map_ds.cpp

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CSGSegmentSmearJob()

Member Function Documentation

◆ GetAnnotNames()

◆ x_Execute()

◆ x_GetCacheKey()

◆ x_IsGap()

◆ x_LoadFromDeltaSeqs()

◆ x_LoadFromNA()

◆ x_LoadFromNetCache()

◆ x_LoadGaps()

◆ x_WriteToCache()

Member Data Documentation

◆ m_Annot

◆ m_Cache

◆ m_Scale

◆ m_SeqVector