Search Toolkit Book for CSGDataSourceContext

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

Inheritance diagram for CSGDataSourceContext:

Collaboration diagram for CSGDataSourceContext:

Public Types
typedef map< string, CWeakIRef< ISGDataSource > >	TDSRegistry

typedef CIRef< ISGDataSourceType >	TDataSourceTypeRef

typedef vector< TDataSourceTypeRef >	TDataSourceTypeVec

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 INonAsnDataRegistry
using	TDataBlob = INonAsnTrackData::TDataBlob

Public Member Functions
	CSGDataSourceContext ()

virtual	~CSGDataSourceContext ()

ISGDataSouceContext interface implementation.
virtual CIRef< ISGDataSource >	GetDS (const string &type, SConstScopedObject &object)
	Get a seqgraphic data source instance of the specified type. More...

virtual void	ClearCache ()
	clear the cache if any. More...

INonAsnDataRegistry interface implementation.
virtual void	AddNonAsnData (const INonAsnTrackData &data)

virtual void	RemoveNonAsnData (const INonAsnTrackData &data)

virtual bool	HasNonAsnData (const string &annot_name) const

virtual const TDataBlob &	GetNonAsnDataBlob (const string &annot_name) const

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 ISGDataSourceContext
virtual	~ISGDataSourceContext ()

Public Member Functions inherited from INonAsnDataRegistry
virtual	~INonAsnDataRegistry ()

Private Types
using	TBlobsMap = map< string, const TDataBlob * >

Private Member Functions
	CSGDataSourceContext (const CSGDataSourceContext &)
	prohibited copy constructor and assignment operator. More...

CSGDataSourceContext &	operator= (const CSGDataSourceContext &)

Private Attributes
TDataSourceTypeVec	m_DataSourceTypes
	All the registered data source types. More...

TDSRegistry	m_DataSources
	The cached data source instances. More...

CFastMutex	m_Mutex
	make sure data source context is thread-safe More...

TBlobsMap	m_NonAsnDataBlobs

std::mutex	m_NonAsnDataBlobsMutex

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

Detailed Description

Definition at line 74 of file seqgraphic_ds_manager.hpp.

Member Typedef Documentation

◆ TBlobsMap

using CSGDataSourceContext::TBlobsMap = map<string, const TDataBlob*>

private

Definition at line 116 of file seqgraphic_ds_manager.hpp.

◆ TDataSourceTypeRef

typedef CIRef<ISGDataSourceType> CSGDataSourceContext::TDataSourceTypeRef

Definition at line 81 of file seqgraphic_ds_manager.hpp.

◆ TDataSourceTypeVec

typedef vector<TDataSourceTypeRef> CSGDataSourceContext::TDataSourceTypeVec

Definition at line 82 of file seqgraphic_ds_manager.hpp.

◆ TDSRegistry

typedef map< string, CWeakIRef<ISGDataSource> > CSGDataSourceContext::TDSRegistry

Definition at line 80 of file seqgraphic_ds_manager.hpp.

Constructor & Destructor Documentation

◆ CSGDataSourceContext() [1/2]

CSGDataSourceContext::CSGDataSourceContext ( )

Definition at line 40 of file seqgraphic_ds_manager.cpp.

References EXT_POINT__SEQGRAPHIC_DATA_SOURCE_TYPE, GetExtensionAsInterface(), and m_DataSourceTypes.

◆ ~CSGDataSourceContext()

CSGDataSourceContext::~CSGDataSourceContext ( )

virtual

Definition at line 96 of file seqgraphic_ds_manager.cpp.

◆ CSGDataSourceContext() [2/2]

CSGDataSourceContext::CSGDataSourceContext ( const CSGDataSourceContext & )

private

prohibited copy constructor and assignment operator.

Member Function Documentation

◆ AddNonAsnData()

void CSGDataSourceContext::AddNonAsnData ( const INonAsnTrackData & data )

virtual

Implements INonAsnDataRegistry.

Definition at line 114 of file seqgraphic_ds_manager.cpp.

References INonAsnTrackData::GetAnnots(), INonAsnTrackData::GetBlob(), m_NonAsnDataBlobs, and m_NonAsnDataBlobsMutex.

◆ ClearCache()

void CSGDataSourceContext::ClearCache ( )

virtual

clear the cache if any.

Implements ISGDataSourceContext.

Definition at line 101 of file seqgraphic_ds_manager.cpp.

References map_checker< Container >::clear(), m_DataSources, m_Mutex, m_NonAsnDataBlobs, and m_NonAsnDataBlobsMutex.

◆ GetDS()

CIRef< ISGDataSource > CSGDataSourceContext::GetDS	(	const string &	type,
		SConstScopedObject &	object
	)

virtual

Get a seqgraphic data source instance of the specified type.

If a datasource is not sharable, it will just create one based on the input object. If a datasource is sharable, it will return a cached instance if there is a cached one. Otherwise, a new instance will get created, cached and returned. TODO, preferably, the context should be able to distinguish different objects in addition to the types.

Implements ISGDataSourceContext.

Definition at line 48 of file seqgraphic_ds_manager.cpp.

References ISGDataSourceType::CreateDS(), map_checker< Container >::end(), map_checker< Container >::erase(), map_checker< Container >::find(), CRef< C, Locker >::GetPointer(), CRef< C, Locker >::GetPointerOrNull(), i, CRef< C, Locker >::IsNull(), ISGDataSourceType::IsSharable(), m_DataSources, m_DataSourceTypes, m_Mutex, NCBI_THROW, CRef< C, Locker >::Reset(), INonAsnDataSource::SetNonAsnDataRegistry(), and type.

◆ GetNonAsnDataBlob()

const INonAsnDataRegistry::TDataBlob & CSGDataSourceContext::GetNonAsnDataBlob ( const string & annot_name ) const

virtual

Implements INonAsnDataRegistry.

Definition at line 136 of file seqgraphic_ds_manager.cpp.

References m_NonAsnDataBlobs, and m_NonAsnDataBlobsMutex.

◆ HasNonAsnData()

bool CSGDataSourceContext::HasNonAsnData ( const string & annot_name ) const

virtual

Implements INonAsnDataRegistry.

Definition at line 130 of file seqgraphic_ds_manager.cpp.

References m_NonAsnDataBlobs, and m_NonAsnDataBlobsMutex.

◆ operator=()

CSGDataSourceContext& CSGDataSourceContext::operator= ( const CSGDataSourceContext & )

private

◆ RemoveNonAsnData()

void CSGDataSourceContext::RemoveNonAsnData ( const INonAsnTrackData & data )

virtual

Implements INonAsnDataRegistry.

Definition at line 120 of file seqgraphic_ds_manager.cpp.

References map_checker< Container >::end(), map_checker< Container >::erase(), CVcfHistogram::EraseCachePerAnnotation(), map_checker< Container >::find(), INonAsnTrackData::GetAnnots(), m_NonAsnDataBlobs, and m_NonAsnDataBlobsMutex.

Member Data Documentation

◆ m_DataSources

TDSRegistry CSGDataSourceContext::m_DataSources

private

The cached data source instances.

Definition at line 113 of file seqgraphic_ds_manager.hpp.

Referenced by ClearCache(), and GetDS().

◆ m_DataSourceTypes

TDataSourceTypeVec CSGDataSourceContext::m_DataSourceTypes

private

All the registered data source types.

Definition at line 112 of file seqgraphic_ds_manager.hpp.

Referenced by CSGDataSourceContext(), and GetDS().

◆ m_Mutex

CFastMutex CSGDataSourceContext::m_Mutex

private

make sure data source context is thread-safe

Definition at line 114 of file seqgraphic_ds_manager.hpp.

Referenced by ClearCache(), and GetDS().

◆ m_NonAsnDataBlobs

TBlobsMap CSGDataSourceContext::m_NonAsnDataBlobs

private

Definition at line 118 of file seqgraphic_ds_manager.hpp.

Referenced by AddNonAsnData(), ClearCache(), GetNonAsnDataBlob(), HasNonAsnData(), and RemoveNonAsnData().

◆ m_NonAsnDataBlobsMutex

std::mutex CSGDataSourceContext::m_NonAsnDataBlobsMutex

mutableprivate

Definition at line 119 of file seqgraphic_ds_manager.hpp.

Referenced by AddNonAsnData(), ClearCache(), GetNonAsnDataBlob(), HasNonAsnData(), and RemoveNonAsnData().

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

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

Public Types

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TBlobsMap

◆ TDataSourceTypeRef

◆ TDataSourceTypeVec

◆ TDSRegistry

Constructor & Destructor Documentation

◆ CSGDataSourceContext() [1/2]

◆ ~CSGDataSourceContext()

◆ CSGDataSourceContext() [2/2]

Member Function Documentation

◆ AddNonAsnData()

◆ ClearCache()

◆ GetDS()

◆ GetNonAsnDataBlob()

◆ HasNonAsnData()

◆ operator=()

◆ RemoveNonAsnData()

Member Data Documentation

◆ m_DataSources

◆ m_DataSourceTypes

◆ m_Mutex

◆ m_NonAsnDataBlobs

◆ m_NonAsnDataBlobsMutex