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

Inheritance diagram for CGraphCache< TData >:

Collaboration diagram for CGraphCache< TData >:

Public Member Functions
virtual	~CGraphCache ()

void	Stop ()

CRef< TData >	GetCachedData (const string &data_key)
	Retrieves TData from in-memory cache. More...

CRef< TData >	GetData (const string &data_key)
	Retrieves TData from in-memory cache or if not found calls TData::Init to initialize new TData instance. More...

void	RemoveData (const string &data_key)
	Removes Data from in-memory cache. More...

void	SaveData (CRef< TData > data)
	Clones TData, puts it into Save Queue for asynchroneous storage operation. More...

void	EnableICache (bool value)

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

Static Public Member Functions
static CGraphCache &	GetInstance ()

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)

Private Types
using	TDataKey = string

Private Member Functions
	CGraphCache ()

	CGraphCache (const CGraphCache &)=delete

CGraphCache &	operator= (const CGraphCache &)=delete

void	x_Run (CRef< CRequestContext > context)

Private Attributes
mutex	m_Lock
	Saving Queue and Cache lock. More...

queue< CRef< TData > >	m_Queue
	Saving Queue for storage operations. More...

bool	m_HasICache = false
	Flag indicates if data should be saved into ICache. More...

map< TDataKey, CRef< TData > >	m_Cache
	in-memory data cache More...

TGraphCachePool	m_Storage
	ICache pool. More...

condition_variable	m_CV
	wake-up signal for save requests More...

thread	m_Thread
	background thread for save processing More...

atomic< bool >	m_StopRequested {false}
	flag to stop the backround thread More...

Friends
class	CSafeStatic_Allocator< CGraphCache >

Additional Inherited Members
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...

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

template<class TData>
class CGraphCache< TData >

CGraphCache –.

in-memeory cache for graph data Provides concurrent access and asynchroneous storage operation for TData

TData is expected to provide: Init() - method to be called to initialize data Save() - method to serialize data

ICache storage is not used by default the caller needs to invoke EnableICache() to enable it

if ICache is enabled GraphCache start a backround thread (m_Thread) on first save request The consecutive save request sends a copy of data to m_Queue for asynchroneous Save.

Definition at line 93 of file graph_cache.hpp.

Member Typedef Documentation

◆ TDataKey

template<class TData >

using CGraphCache< TData >::TDataKey = string

private

Definition at line 232 of file graph_cache.hpp.

Constructor & Destructor Documentation

◆ ~CGraphCache()

template<class TData >

virtual CGraphCache< TData >::~CGraphCache ( )

inlinevirtual

Definition at line 103 of file graph_cache.hpp.

References ERR_POST, Error(), and CGraphCache< TData >::Stop().

◆ CGraphCache() [1/2]

template<class TData >

CGraphCache< TData >::CGraphCache ( )

inlineprivate

Definition at line 196 of file graph_cache.hpp.

◆ CGraphCache() [2/2]

template<class TData >

CGraphCache< TData >::CGraphCache ( const CGraphCache< TData > & )

privatedelete

Member Function Documentation

◆ EnableICache()

template<class TData >

void CGraphCache< TData >::EnableICache ( bool value )

inline

Definition at line 192 of file graph_cache.hpp.

References CGraphCache< TData >::m_HasICache, and value.

Referenced by CSGAlignmentDS::EnablePileUpCache().

◆ GetCachedData()

template<class TData >

CRef<TData> CGraphCache< TData >::GetCachedData ( const string & data_key )

inline

Retrieves TData from in-memory cache.

Parameters

data_key memory access key generated by TData

Returns: instance of TData or NULL if there are no cached data

Definition at line 124 of file graph_cache.hpp.

References CGraphCache< TData >::m_Cache, and CGraphCache< TData >::m_Lock.

Referenced by CSGAlignmentDS::IsGraphCached(), CVcfFeatureJob::x_Execute(), and CSGFeatureJob::x_ProcessCachedVcfTabix().

◆ GetData()

template<class TData >

CRef<TData> CGraphCache< TData >::GetData ( const string & data_key )

inline

Retrieves TData from in-memory cache or if not found calls TData::Init to initialize new TData instance.

Parameters

data_key memory access key generated by TData

Returns: instance of TData or NULL if there are no cached data and TData does not have ICache

Definition at line 140 of file graph_cache.hpp.

References CGraphCache< TData >::m_Cache, CGraphCache< TData >::m_HasICache, CGraphCache< TData >::m_Lock, CGraphCache< TData >::m_Storage, and Ref().

Referenced by CSGAlignmentDS::CanShowRange(), CSGAlignmentDS::GetGraphCost(), CSGAlignmentDS::IsRangeCached(), CSGAlignStatJob::x_Execute(), CSGSeqGraphJob::x_Execute(), CVcfFeatureJob::x_Execute(), and CSGFeatureJob::x_ProcessCachedBigBed().

◆ GetInstance()

template<class TData >

static CGraphCache& CGraphCache< TData >::GetInstance ( void )

inlinestatic

Definition at line 97 of file graph_cache.hpp.

References CSafeStatic< T, Callbacks >::Get().

Referenced by CSGAlignmentDS::CanShowRange(), CSGAlignmentDS::ClearCache(), CSGAlignmentDS::EnablePileUpCache(), CVcfHistogram::EraseCachePerAnnotation(), CSGAlignmentDS::GetGraphCost(), CSGAlignmentDS::IsGraphCached(), CSGAlignmentDS::IsRangeCached(), CSGAlignStatJob::x_Execute(), CSGSeqGraphJob::x_Execute(), CVcfFeatureJob::x_Execute(), CWigGraph::x_FetchData(), CSGFeatureJob::x_ProcessCachedBigBed(), and CSGFeatureJob::x_ProcessCachedVcfTabix().

◆ operator=()

template<class TData >

CGraphCache& CGraphCache< TData >::operator= ( const CGraphCache< TData > & )

privatedelete

◆ RemoveData()

template<class TData >

void CGraphCache< TData >::RemoveData ( const string & data_key )

inline

Removes Data from in-memory cache.

Parameters

data_key memory access key generated by TData

Definition at line 161 of file graph_cache.hpp.

References map_checker< Container >::end(), map_checker< Container >::erase(), map_checker< Container >::find(), CGraphCache< TData >::m_Cache, and CGraphCache< TData >::m_Lock.

Referenced by CSGAlignmentDS::ClearCache(), and CSGAlignStatJob::x_Execute().

◆ SaveData()

template<class TData >

void CGraphCache< TData >::SaveData ( CRef< TData > data )

inline

Clones TData, puts it into Save Queue for asynchroneous storage operation.

Parameters

data	Instance of TData

Definition at line 173 of file graph_cache.hpp.

References CDiagContext::GetRequestContext(), CGraphCache< TData >::m_CV, CGraphCache< TData >::m_HasICache, CGraphCache< TData >::m_Lock, CGraphCache< TData >::m_Queue, CGraphCache< TData >::m_Thread, and CGraphCache< TData >::x_Run().

Referenced by CSGAlignStatJob::x_Execute(), CVcfFeatureJob::x_Execute(), and CWigGraph::x_FetchData().

◆ Stop()

template<class TData >

void CGraphCache< TData >::Stop ( void )

inline

Definition at line 111 of file graph_cache.hpp.

References CGraphCache< TData >::m_CV, CGraphCache< TData >::m_StopRequested, and CGraphCache< TData >::m_Thread.

Referenced by CGraphCache< TData >::~CGraphCache().

◆ x_Run()

template<class TData >

void CGraphCache< TData >::x_Run ( CRef< CRequestContext > context )

inlineprivate

Definition at line 205 of file graph_cache.hpp.

References CGraphCache< TData >::m_CV, CGraphCache< TData >::m_Lock, CGraphCache< TData >::m_Queue, CGraphCache< TData >::m_StopRequested, CGraphCache< TData >::m_Storage, and CDiagContext::SetRequestContext().

Referenced by CGraphCache< TData >::SaveData().

Friends And Related Function Documentation

◆ CSafeStatic_Allocator< CGraphCache >

template<class TData >

friend class CSafeStatic_Allocator< CGraphCache >

friend

Definition at line 196 of file graph_cache.hpp.

Member Data Documentation

◆ m_Cache

template<class TData >

map<TDataKey, CRef<TData> > CGraphCache< TData >::m_Cache

private

in-memory data cache

Definition at line 233 of file graph_cache.hpp.

Referenced by CGraphCache< TData >::GetCachedData(), CGraphCache< TData >::GetData(), and CGraphCache< TData >::RemoveData().

◆ m_CV

template<class TData >

condition_variable CGraphCache< TData >::m_CV

private

wake-up signal for save requests

Definition at line 237 of file graph_cache.hpp.

Referenced by CGraphCache< TData >::SaveData(), CGraphCache< TData >::Stop(), and CGraphCache< TData >::x_Run().

◆ m_HasICache

template<class TData >

bool CGraphCache< TData >::m_HasICache = false

private

Flag indicates if data should be saved into ICache.

Definition at line 230 of file graph_cache.hpp.

Referenced by CGraphCache< TData >::EnableICache(), CGraphCache< TData >::GetData(), and CGraphCache< TData >::SaveData().

◆ m_Lock

template<class TData >

mutex CGraphCache< TData >::m_Lock

private

Saving Queue and Cache lock.

Definition at line 226 of file graph_cache.hpp.

Referenced by CGraphCache< TData >::GetCachedData(), CGraphCache< TData >::GetData(), CGraphCache< TData >::RemoveData(), CGraphCache< TData >::SaveData(), and CGraphCache< TData >::x_Run().

◆ m_Queue

template<class TData >

queue<CRef<TData> > CGraphCache< TData >::m_Queue

private

Saving Queue for storage operations.

Definition at line 228 of file graph_cache.hpp.

Referenced by CGraphCache< TData >::SaveData(), and CGraphCache< TData >::x_Run().

◆ m_StopRequested

template<class TData >

atomic<bool> CGraphCache< TData >::m_StopRequested {false}

private

flag to stop the backround thread

Definition at line 239 of file graph_cache.hpp.

Referenced by CGraphCache< TData >::Stop(), and CGraphCache< TData >::x_Run().

◆ m_Storage

template<class TData >

TGraphCachePool CGraphCache< TData >::m_Storage

private

ICache pool.

Definition at line 235 of file graph_cache.hpp.

Referenced by CGraphCache< TData >::GetData(), and CGraphCache< TData >::x_Run().

◆ m_Thread

template<class TData >

thread CGraphCache< TData >::m_Thread

private

background thread for save processing

Definition at line 238 of file graph_cache.hpp.

Referenced by CGraphCache< TData >::SaveData(), and CGraphCache< TData >::Stop().

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

include/gui/widgets/seq_graphic/graph_cache.hpp

Public Member Functions

Static Public Member Functions

Private Types

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

template<class TData> class CGraphCache< TData >

Member Typedef Documentation

◆ TDataKey

Constructor & Destructor Documentation

◆ ~CGraphCache()

◆ CGraphCache() [1/2]

◆ CGraphCache() [2/2]

Member Function Documentation

◆ EnableICache()

◆ GetCachedData()

◆ GetData()

◆ GetInstance()

◆ operator=()

◆ RemoveData()

◆ SaveData()

◆ Stop()

◆ x_Run()

Friends And Related Function Documentation

◆ CSafeStatic_Allocator< CGraphCache >

Member Data Documentation

◆ m_Cache

◆ m_CV

◆ m_HasICache

◆ m_Lock

◆ m_Queue

◆ m_StopRequested

◆ m_Storage

◆ m_Thread

template<class TData>
class CGraphCache< TData >