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

Inheritance diagram for CSGFeatureDS:

Collaboration diagram for CSGFeatureDS:

Public Member Functions
	CSGFeatureDS (objects::CScope &scope, const objects::CSeq_id &id)
	CSGFeatureDS. More...

virtual void	LoadFeatures (objects::SAnnotSelector &sel, const TSeqRange &range, TModelUnit window, TJobToken token=-1, int max_feat=-1, ELinkedFeatDisplay LinkedFeatDisplay=ELinkedFeatDisplay::eLFD_Default, const string &extra_filter="")

virtual void	LoadFeatures (const TSeqRange &range, TModelUnit window, TJobToken token, const TFeatBatchJobRequests &requests)

void	CalcFeatHistogram (const CSeqGlyph::TObjects &objs, const TSeqRange &range, TModelUnit window, TJobToken token=-1)

void	LoadGeneModelFeatures (objects::SAnnotSelector &lm_feat_sel, objects::SAnnotSelector &m_feat_sel, TJobToken lm_token, TJobToken main_token, bool landmark_feat, const TSeqRange &range, TModelUnit window, const CRef< CGeneModelConfig > &conf)
	load features for gene model. More...

void	GetAnnotNames (objects::SAnnotSelector &sel, const TSeqRange &range, TAnnotNameTitleMap &names) const

void	GetAnnotNames_var (objects::SAnnotSelector &sel, const TSeqRange &range, TAnnotNameTitleMap &names) const

vector< string >	GetFilters (const string &annot_name, const TSeqRange &range) const

void	SetFilter (const string &filter)
	CSGFeatureDS inline method. More...

const string &	GetFilter () const

void	SetSortBy (const string &sortby)

const string &	GetSortBy () const

void	SetGraphCacheKey (const string &graph_cache_key)

void	SetRemoteDataType (const string &data_type)

bool	IsBigBed () const

bool	IsVcfTabix () const

Public Member Functions inherited from CSGGenBankDS
	CSGGenBankDS (objects::CScope &scope, const objects::CSeq_id &id)

virtual	~CSGGenBankDS ()

bool	IsRefSeq () const

void	SetDepth (int depth)
	Set the annotation selector resolving depth. More...

int	GetDepth () const

void	SetAdaptive (bool flag)

bool	GetAdaptive () const

objects::CBioseq_Handle &	GetBioseqHandle (void)
	Get the underlying bioseq handle. More...

const objects::CBioseq_Handle &	GetBioseqHandle (void) const

objects::CScope &	GetScope (void) const
	Get the scope from the handle. More...

void	SetJobListener (CEventHandler *listener)
	Set JobDispatcher listener. More...

virtual void	ClearJobID (TJobID job_id)

bool	IsJobNeeded (TJobID job_id) const

virtual bool	AllJobsFinished () const

virtual void	DeleteAllJobs ()
	Remove waiting jobs from queue or cancel the unfinished jobs. More...

void	SetCoordMapper (ICoordMapper *mapper)

void	SetGraphLevels (const string &annot)

Public Member Functions inherited from CObjectEx
	CObjectEx (void)

virtual	~CObjectEx (void)

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 CWeakObject
	CWeakObject (void)

virtual	~CWeakObject (void)

CPtrToObjectProxy *	GetPtrProxy (void) const
	Get pointer to proxy object containing pointer to this object. More...

Public Member Functions inherited from ISGDataSource
virtual	~ISGDataSource ()

Private Attributes
string	m_Filter

string	m_SortBy

string	m_GraphCacheKey

string	m_RmtDataType

Additional Inherited Members
Public Types inherited from CSGGenBankDS
typedef CAppJobDispatcher::TJobID	TJobID

typedef int	TJobToken

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 ISGDataSource
typedef map< string, string >	TAnnotNameTitleMap
	List of annotations with the corresponding titles. More...

Static Public Member Functions inherited from CSGDataSource
static void	SetBackgroundJob (bool flag)

static bool	IsBackgroundJob ()

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...

Protected Types inherited from CSGGenBankDS
typedef set< int >	TGraphLevels

Protected Member Functions inherited from CSGGenBankDS
void	x_ForegroundJob (IAppJob &job)

TJobID	x_BackgroundJob (IAppJob &job, int report_period, const string &pool)
	Jobs on thread pool. More...

TJobID	x_LaunchJob (IAppJob &job, int report_period=1, const string &pool="ObjManagerEngine")
	Launch either a background or foreground job. More...

Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Protected Member Functions inherited from CWeakObject
void	CleanWeakRefs (void) const
	Method cleaning all CWeakRefs referencing at this moment to the object After calling to this method all existing CWeakRefs referencing to the object will return NULL, so it effectively will be equal to deleting the object. More...

Protected Attributes inherited from CSGGenBankDS
objects::CBioseq_Handle	m_Handle

CEventHandler *	m_JobListener
	our listener to JobDispatcher events More...

vector< TJobID >	m_ActiveJobs
	all currently active jobs for this DS More...

int	m_Depth
	annotation resolving depth More...

bool	m_Adaptive
	adaptive/exact annot selector More...

CIRef< ICoordMapper >	m_Mapper
	coordinate mapper between mapped features coord. and sequence coord. More...

TGraphLevels	m_GraphLevels
	Existing coverage graph levels. More...

Static Protected Attributes inherited from CSGDataSource
static bool	m_Background = true

Detailed Description

CSGFeatureDS.

Definition at line 48 of file feature_ds.hpp.

Constructor & Destructor Documentation

◆ CSGFeatureDS()

CSGFeatureDS::CSGFeatureDS	(	objects::CScope &	scope,
		const objects::CSeq_id &	id
	)

CSGFeatureDS.

Definition at line 438 of file feature_ds.cpp.

Member Function Documentation

◆ CalcFeatHistogram()

void CSGFeatureDS::CalcFeatHistogram	(	const CSeqGlyph::TObjects &	objs,
		const TSeqRange &	range,
		TModelUnit	window,
		TJobToken	token = `-1`
	)

Definition at line 508 of file feature_ds.cpp.

References compile_time_bits::range(), and CSGGenBankDS::x_LaunchJob().

◆ GetAnnotNames()

void CSGFeatureDS::GetAnnotNames	(	objects::SAnnotSelector &	sel,
		const TSeqRange &	range,
		TAnnotNameTitleMap &	names
	)		const

Definition at line 519 of file feature_ds.cpp.

References CSGFeatureJob::GetAnnotNames(), CSGGenBankDS::m_Adaptive, CSGGenBankDS::m_Depth, CSGGenBankDS::m_Handle, names, compile_time_bits::range(), and CSeqUtils::SetResolveDepth().

Referenced by CFeatureTrackFactory::CreateTracks(), and CGeneModelFactory::CreateTracks().

◆ GetAnnotNames_var()

void CSGFeatureDS::GetAnnotNames_var	(	objects::SAnnotSelector &	sel,
		const TSeqRange &	range,
		TAnnotNameTitleMap &	names
	)		const

Definition at line 528 of file feature_ds.cpp.

References CSGFeatureJob::GetAnnotNames_var(), CSGGenBankDS::m_Adaptive, CSGGenBankDS::m_Depth, CSGGenBankDS::m_Handle, names, compile_time_bits::range(), and CSeqUtils::SetResolveDepth().

Referenced by CVarTrackFactory::CreateTracks().

◆ GetFilter()

const string & CSGFeatureDS::GetFilter ( void ) const

inline

Definition at line 180 of file feature_ds.hpp.

References m_Filter.

Referenced by CFeatureTrack::GenerateAsn1().

◆ GetFilters()

vector< string > CSGFeatureDS::GetFilters	(	const string &	annot_name,
		const TSeqRange &	range
	)		const

Definition at line 537 of file feature_ds.cpp.

References CSeqUtils::GetAnnotSelector(), CGeneModelFeatJob::GetFilters(), m_Filter, CSGGenBankDS::m_Handle, compile_time_bits::range(), and CSeqUtils::SetAnnot().

Referenced by CGeneModelFactory::x_CreateTracksWithFilters().

◆ GetSortBy()

const string & CSGFeatureDS::GetSortBy ( ) const

inline

Definition at line 188 of file feature_ds.hpp.

References m_SortBy.

◆ IsBigBed()

bool CSGFeatureDS::IsBigBed ( ) const

inline

Definition at line 204 of file feature_ds.hpp.

References NStr::EqualNocase(), and m_RmtDataType.

Referenced by LoadFeatures(), and CFeatureTrack::x_AddFeaturesLayout().

◆ IsVcfTabix()

bool CSGFeatureDS::IsVcfTabix ( ) const

inline

Definition at line 210 of file feature_ds.hpp.

References NStr::EqualNocase(), and m_RmtDataType.

Referenced by LoadFeatures().

◆ LoadFeatures() [1/2]

void CSGFeatureDS::LoadFeatures	(	const TSeqRange &	range,
		TModelUnit	window,
		TJobToken	token,
		const TFeatBatchJobRequests &	requests
	)

virtual

Reimplemented in CVcfFeatureDS.

Definition at line 469 of file feature_ds.cpp.

References CGraphUtils::GetNearestLevel(), IsBigBed(), IsVcfTabix(), m_GraphCacheKey, CSGGenBankDS::m_GraphLevels, CSGGenBankDS::m_Handle, compile_time_bits::range(), and CSGGenBankDS::x_LaunchJob().

◆ LoadFeatures() [2/2]

virtual void CSGFeatureDS::LoadFeatures	(	objects::SAnnotSelector &	sel,
		const TSeqRange &	range,
		TModelUnit	window,
		TJobToken	token = `-1`,
		int	max_feat = `-1`,
		ELinkedFeatDisplay	LinkedFeatDisplay = `ELinkedFeatDisplay::eLFD_Default`,
		const string &	extra_filter = `""`
	)

virtual

Reimplemented in CVcfFeatureDS.

Referenced by CGeneModelTrack::x_AddMainFeaturesLayout(), CFeatureTrack::x_LoadFeatures(), and CIntronTrack::x_LoadFeatures().

◆ LoadGeneModelFeatures()

void CSGFeatureDS::LoadGeneModelFeatures	(	objects::SAnnotSelector &	lm_feat_sel,
		objects::SAnnotSelector &	m_feat_sel,
		TJobToken	lm_token,
		TJobToken	main_token,
		bool	landmark_feat,
		const TSeqRange &	range,
		TModelUnit	window,
		const CRef< CGeneModelConfig > &	conf
	)

load features for gene model.

This method will either load landmark features or all main features based on both overview flag and number of genes presented given the range. The main features include genes, Rnas, CDSs, and exons.

Parameters

lm_feat_sel	annot selector for loading landmark features (genes)
m_feat_sel	annot selector for loading main features.
lm_token	token for loading landmark features job.
main_token	token for loading main features job.
style	the merging style for RNA and cds features.
landmark_feat	show landmark features if suitable.
min_overview_feat	minimal feature number to be in overview model.
range	the data range.
window	the window scale bases per pixel for creating densitymap.
max_feat	the maximum features allowed.