Search Toolkit Book for CVDBGraphDataLoader_Impl

#include <sra/data_loaders/vdbgraph/impl/vdbgraphloader_impl.hpp>

Inheritance diagram for CVDBGraphDataLoader_Impl:

Collaboration diagram for CVDBGraphDataLoader_Impl:

Classes
struct	SVDBFileInfo

Public Types
typedef vector< string >	TVDBFiles

typedef CDataLoader::TBlobId	TBlobId

typedef CDataLoader::TTSE_Lock	TTSE_Lock

typedef CDataLoader::TTSE_LockSet	TTSE_LockSet

typedef vector< CAnnotName >	TAnnotNames

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 Member Functions
	CVDBGraphDataLoader_Impl (const TVDBFiles &vdb_files)

	~CVDBGraphDataLoader_Impl (void)

CObjectManager::TPriority	GetDefaultPriority (void) const

TAnnotNames	GetPossibleAnnotNames (void) const

template<class Call >
std::invoke_result< Call >::type	CallWithRetry (Call &&call, const char *name, unsigned retry_count=0)

TBlobId	GetBlobId (const CSeq_id_Handle &idh)

TBlobId	GetBlobIdFromString (const string &str) const

TTSE_Lock	GetBlobById (CDataSource *ds, const TBlobId &blob_id)

TTSE_Lock	GetBlobByIdOnce (CDataSource *ds, const TBlobId &blob_id)

TTSE_LockSet	GetRecords (CDataSource *ds, const CSeq_id_Handle &idh, CDataLoader::EChoice choice)

TTSE_LockSet	GetOrphanAnnotRecords (CDataSource ds, const CSeq_id_Handle &idh, const SAnnotSelector sel, CDataLoader::TProcessedNAs *processed_nas)

TTSE_LockSet	GetOrphanAnnotRecordsOnce (CDataSource ds, const CSeq_id_Handle &idh, const SAnnotSelector sel, CDataLoader::TProcessedNAs *processed_nas)

void	GetChunk (CTSE_Chunk_Info &chunk)

void	GetChunkOnce (CTSE_Chunk_Info &chunk)

CRef< CSeq_entry >	LoadFullEntry (const CVDBGraphBlobId &blob_id)

void	LoadSplitEntry (CTSE_Info &tse, const CVDBGraphBlobId &blob_id)

CRef< SVDBFileInfo >	OpenVDBGraphFile (const string &name)

CRef< SVDBFileInfo >	OpenVDBGraphFileOnce (const string &name)

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

Protected Types
typedef map< string, CRef< SVDBFileInfo > >	TFixedFileMap

typedef limited_size_map< string, CRef< SVDBFileInfo > >	TAutoFileMap

typedef limited_size_map< string, bool >	TMissingFileSet

Protected Member Functions
CRef< SVDBFileInfo >	x_GetFileInfo (const string &name)

CRef< SVDBFileInfo >	x_GetNAFileInfo (const string &na_acc)

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

Protected Attributes
CMutex	m_Mutex

CVDBMgr	m_Mgr

unsigned	m_RetryCount

TFixedFileMap	m_FixedFileMap

TAutoFileMap	m_AutoFileMap

TMissingFileSet	m_MissingFileSet

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...

Detailed Description

Definition at line 49 of file vdbgraphloader_impl.hpp.

Member Typedef Documentation

◆ TAnnotNames

typedef vector<CAnnotName> CVDBGraphDataLoader_Impl::TAnnotNames

Definition at line 62 of file vdbgraphloader_impl.hpp.

◆ TAutoFileMap

typedef limited_size_map<string, CRef<SVDBFileInfo> > CVDBGraphDataLoader_Impl::TAutoFileMap

protected

Definition at line 107 of file vdbgraphloader_impl.hpp.

◆ TBlobId

typedef CDataLoader::TBlobId CVDBGraphDataLoader_Impl::TBlobId

Definition at line 53 of file vdbgraphloader_impl.hpp.

◆ TFixedFileMap

typedef map<string, CRef<SVDBFileInfo> > CVDBGraphDataLoader_Impl::TFixedFileMap

protected

Definition at line 106 of file vdbgraphloader_impl.hpp.

◆ TMissingFileSet

typedef limited_size_map<string, bool> CVDBGraphDataLoader_Impl::TMissingFileSet

protected

Definition at line 108 of file vdbgraphloader_impl.hpp.

◆ TTSE_Lock

typedef CDataLoader::TTSE_Lock CVDBGraphDataLoader_Impl::TTSE_Lock

Definition at line 54 of file vdbgraphloader_impl.hpp.

◆ TTSE_LockSet

typedef CDataLoader::TTSE_LockSet CVDBGraphDataLoader_Impl::TTSE_LockSet

Definition at line 55 of file vdbgraphloader_impl.hpp.

◆ TVDBFiles

typedef vector<string> CVDBGraphDataLoader_Impl::TVDBFiles

Definition at line 52 of file vdbgraphloader_impl.hpp.

Constructor & Destructor Documentation

◆ CVDBGraphDataLoader_Impl()

CVDBGraphDataLoader_Impl::CVDBGraphDataLoader_Impl ( const TVDBFiles & vdb_files )

explicit

Definition at line 239 of file vdbgraphloader_impl.cpp.

References GetDebugLevel(), info, ITERATE, LOG_POST_X, m_FixedFileMap, and OpenVDBGraphFile().

◆ ~CVDBGraphDataLoader_Impl()

CVDBGraphDataLoader_Impl::~CVDBGraphDataLoader_Impl ( void )

Definition at line 254 of file vdbgraphloader_impl.cpp.

Member Function Documentation

◆ CallWithRetry()

template<class Call >

std::invoke_result< Call >::type CVDBGraphDataLoader_Impl::CallWithRetry	(	Call &&	call,
		const char *	name,
		unsigned	retry_count = `0`
	)

Definition at line 261 of file vdbgraphloader_impl.cpp.

References LOG_POST, m_RetryCount, SleepMilliSec(), t, Warning(), and CException::what().

Referenced by GetBlobById(), GetChunk(), GetOrphanAnnotRecords(), and OpenVDBGraphFile().

◆ GetBlobById()

CDataLoader::TTSE_Lock CVDBGraphDataLoader_Impl::GetBlobById	(	CDataSource *	ds,
		const TBlobId &	blob_id
	)

Definition at line 383 of file vdbgraphloader_impl.cpp.

References CallWithRetry(), and GetBlobByIdOnce().

Referenced by CVDBGraphDataLoader::GetBlobById(), and GetOrphanAnnotRecordsOnce().

◆ GetBlobByIdOnce()

CDataLoader::TTSE_Lock CVDBGraphDataLoader_Impl::GetBlobByIdOnce	(	CDataSource *	ds,
		const TBlobId &	blob_id
	)

Definition at line 393 of file vdbgraphloader_impl.cpp.

References CDataSource::GetTSE_LoadLock(), CTSE_LoadLock::IsLoaded(), LoadFullEntry(), LoadSplitEntry(), CTSE_LoadLock::SetLoaded(), and CTSE_Info::SetSeq_entry().

Referenced by GetBlobById().

◆ GetBlobId()

CDataLoader::TBlobId CVDBGraphDataLoader_Impl::GetBlobId ( const CSeq_id_Handle & idh )

Definition at line 368 of file vdbgraphloader_impl.cpp.

Referenced by CVDBGraphDataLoader::GetBlobId().

◆ GetBlobIdFromString()

CDataLoader::TBlobId CVDBGraphDataLoader_Impl::GetBlobIdFromString ( const string & str ) const

Definition at line 376 of file vdbgraphloader_impl.cpp.

References str().

Referenced by CVDBGraphDataLoader::GetBlobIdFromString().

◆ GetChunk()

void CVDBGraphDataLoader_Impl::GetChunk ( CTSE_Chunk_Info & chunk )

Definition at line 598 of file vdbgraphloader_impl.cpp.

References CallWithRetry(), and GetChunkOnce().

Referenced by CVDBGraphDataLoader::GetChunk().

◆ GetChunkOnce()

void CVDBGraphDataLoader_Impl::GetChunkOnce ( CTSE_Chunk_Info & chunk )

◆ GetDefaultPriority()

CObjectManager::TPriority CVDBGraphDataLoader_Impl::GetDefaultPriority ( void ) const

Definition at line 340 of file vdbgraphloader_impl.cpp.

References map_checker< Container >::empty(), CObjectManager::kPriority_Extra, and m_FixedFileMap.

Referenced by CVDBGraphDataLoader::GetDefaultPriority().

◆ GetOrphanAnnotRecords()

CDataLoader::TTSE_LockSet CVDBGraphDataLoader_Impl::GetOrphanAnnotRecords	(	CDataSource *	ds,
		const CSeq_id_Handle &	idh,
		const SAnnotSelector *	sel,
		CDataLoader::TProcessedNAs *	processed_nas
	)

Definition at line 426 of file vdbgraphloader_impl.cpp.

References CallWithRetry(), and GetOrphanAnnotRecordsOnce().

Referenced by CVDBGraphDataLoader::GetOrphanAnnotRecordsNA(), and GetRecords().

◆ GetOrphanAnnotRecordsOnce()

CDataLoader::TTSE_LockSet CVDBGraphDataLoader_Impl::GetOrphanAnnotRecordsOnce	(	CDataSource *	ds,
		const CSeq_id_Handle &	idh,
		const SAnnotSelector *	sel,
		CDataLoader::TProcessedNAs *	processed_nas
	)