Search Toolkit Book for CVDBGraphDb_Impl

#include <sra/readers/sra/graphread.hpp>

Inheritance diagram for CVDBGraphDb_Impl:

Collaboration diagram for CVDBGraphDb_Impl:

Classes
struct	SGraphTableCursor

struct	SSeqInfo

Public Member Functions
	CVDBGraphDb_Impl (CVDBMgr &mgr, CTempString path, ELookupType lookup_type=eLookupDefault)

virtual	~CVDBGraphDb_Impl (void)

bool	HasMidZoomGraphs (void)

bool	LookupIsInVDB () const

bool	LookupIsInMemory () 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

Static Public Member Functions
static bool	LookupIsInMemory (ELookupType lookup_type)

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 Types
typedef list< SSeqInfo >	TSeqInfoList

typedef map< CSeq_id_Handle, TSeqInfoList::iterator >	TSeqInfoMapBySeq_id

typedef map< TVDBRowId, TSeqInfoList::iterator >	TSeqInfoMapByFirstRow

Protected Member Functions
const string &	GetPath (void) const

const TSeqInfoList &	GetSeqInfoList (void) const

const TSeqInfoMapBySeq_id &	GetSeqInfoMapBySeq_id (void) const

const CVDBTable &	GraphTable (void)

CRef< SGraphTableCursor >	Graph (void)

void	Put (CRef< SGraphTableCursor > &curs)

SSeqInfo	GetSeqInfoAtRow (TVDBRowId row)

SSeqInfo	GetSeqInfo (const CSeq_id_Handle &seq_id)

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

Friends
class	CVDBGraphSeqIterator

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...

Public Types inherited from SVDBGraphDb_Base
enum	ELookupType { eLookupDefault , eLookupInMemory , eLookupInVDB }

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 62 of file graphread.hpp.

Member Typedef Documentation

◆ TSeqInfoList

typedef list<SSeqInfo> CVDBGraphDb_Impl::TSeqInfoList

protected

Definition at line 131 of file graphread.hpp.

◆ TSeqInfoMapByFirstRow

typedef map<TVDBRowId, TSeqInfoList::iterator> CVDBGraphDb_Impl::TSeqInfoMapByFirstRow

protected

Definition at line 133 of file graphread.hpp.

◆ TSeqInfoMapBySeq_id

typedef map<CSeq_id_Handle, TSeqInfoList::iterator> CVDBGraphDb_Impl::TSeqInfoMapBySeq_id

protected

Definition at line 132 of file graphread.hpp.

Constructor & Destructor Documentation

◆ CVDBGraphDb_Impl()

CVDBGraphDb_Impl::CVDBGraphDb_Impl	(	CVDBMgr &	mgr,
		CTempString	path,
		ELookupType	lookup_type = `eLookupDefault`
	)

◆ ~CVDBGraphDb_Impl()

CVDBGraphDb_Impl::~CVDBGraphDb_Impl ( void )

virtual

Definition at line 203 of file graphread.cpp.

Member Function Documentation

◆ GetPath()

const string& CVDBGraphDb_Impl::GetPath ( void ) const

inlineprotected

Definition at line 111 of file graphread.hpp.

References m_Path.

◆ GetSeqInfo()

CVDBGraphDb_Impl::SSeqInfo CVDBGraphDb_Impl::GetSeqInfo ( const CSeq_id_Handle & seq_id )

protected

◆ GetSeqInfoAtRow()

CVDBGraphDb_Impl::SSeqInfo CVDBGraphDb_Impl::GetSeqInfoAtRow ( TVDBRowId row )

protected

Definition at line 229 of file graphread.cpp.

References _ASSERT, CVDBValue::eMissing_Allow, ctll::empty(), map_checker< Container >::end(), map_checker< Container >::find(), CVDBTableIndex::Find(), CSeq_id_Handle::GetHandle(), Graph(), info, m_LookupIndex, m_SeqInfoMutex, m_SeqMapByFirstRow, Put(), and compile_time_bits::range().

Referenced by CVDBGraphSeqIterator::CVDBGraphSeqIterator().

◆ GetSeqInfoList()

const TSeqInfoList& CVDBGraphDb_Impl::GetSeqInfoList ( void ) const

inlineprotected

Definition at line 135 of file graphread.hpp.

References m_SeqList.

◆ GetSeqInfoMapBySeq_id()

const TSeqInfoMapBySeq_id& CVDBGraphDb_Impl::GetSeqInfoMapBySeq_id ( void ) const

inlineprotected

Definition at line 138 of file graphread.hpp.

References m_SeqMapBySeq_id.

◆ Graph()

CRef< CVDBGraphDb_Impl::SGraphTableCursor > CVDBGraphDb_Impl::Graph ( void )

protected

Definition at line 208 of file graphread.cpp.

References GraphTable(), and m_Graph.

Referenced by CVDBGraphDb_Impl(), GetSeqInfo(), GetSeqInfoAtRow(), and HasMidZoomGraphs().

◆ GraphTable()

const CVDBTable& CVDBGraphDb_Impl::GraphTable ( void )

inlineprotected

Definition at line 143 of file graphread.hpp.

References m_GraphTable.

Referenced by CVDBGraphDb_Impl(), and Graph().

◆ HasMidZoomGraphs()

bool CVDBGraphDb_Impl::HasMidZoomGraphs ( void )

Definition at line 219 of file graphread.cpp.

References Graph(), and Put().

◆ LookupIsInMemory() [1/2]

bool CVDBGraphDb_Impl::LookupIsInMemory ( ) const

inline

Definition at line 75 of file graphread.hpp.

References m_LookupIndex.

Referenced by CVDBGraphDb_Impl().

◆ LookupIsInMemory() [2/2]

bool CVDBGraphDb_Impl::LookupIsInMemory ( ELookupType lookup_type )

static

Definition at line 64 of file graphread.cpp.

References SVDBGraphDb_Base::eLookupDefault, SVDBGraphDb_Base::eLookupInMemory, and NCBI_PARAM_TYPE.

◆ LookupIsInVDB()

bool CVDBGraphDb_Impl::LookupIsInVDB ( ) const

inline

Definition at line 71 of file graphread.hpp.

References m_LookupIndex.

◆ Put()

void CVDBGraphDb_Impl::Put ( CRef< SGraphTableCursor > & curs )

inlineprotected

Definition at line 149 of file graphread.hpp.

References m_Graph.

Referenced by CVDBGraphDb_Impl(), CVDBGraphSeqIterator::GetAnnot(), GetSeqInfo(), GetSeqInfoAtRow(), HasMidZoomGraphs(), and CVDBGraphSeqIterator::SeqTableIsSmaller().

Friends And Related Function Documentation

◆ CVDBGraphSeqIterator

friend class CVDBGraphSeqIterator

friend

Definition at line 82 of file graphread.hpp.

Member Data Documentation

◆ m_Graph

CVDBObjectCache<SGraphTableCursor> CVDBGraphDb_Impl::m_Graph

private

Definition at line 163 of file graphread.hpp.

Referenced by Graph(), and Put().

◆ m_GraphTable

CVDBTable CVDBGraphDb_Impl::m_GraphTable

private

Definition at line 160 of file graphread.hpp.

Referenced by CVDBGraphDb_Impl(), and GraphTable().

◆ m_LookupIndex

CVDBTableIndex CVDBGraphDb_Impl::m_LookupIndex

private

Definition at line 161 of file graphread.hpp.

Referenced by CVDBGraphDb_Impl(), GetSeqInfo(), GetSeqInfoAtRow(), LookupIsInMemory(), and LookupIsInVDB().

◆ m_Mgr

CVDBMgr CVDBGraphDb_Impl::m_Mgr

private

Definition at line 157 of file graphread.hpp.

◆ m_Path

string CVDBGraphDb_Impl::m_Path

private

Definition at line 158 of file graphread.hpp.

Referenced by GetPath().

◆ m_SeqInfoMutex

CMutex CVDBGraphDb_Impl::m_SeqInfoMutex

private

Definition at line 165 of file graphread.hpp.

Referenced by GetSeqInfo(), and GetSeqInfoAtRow().

◆ m_SeqList

TSeqInfoList CVDBGraphDb_Impl::m_SeqList

private

Definition at line 166 of file graphread.hpp.

Referenced by CVDBGraphDb_Impl(), and GetSeqInfoList().

◆ m_SeqMapByFirstRow

TSeqInfoMapByFirstRow CVDBGraphDb_Impl::m_SeqMapByFirstRow

private

Definition at line 168 of file graphread.hpp.

Referenced by CVDBGraphDb_Impl(), and GetSeqInfoAtRow().

◆ m_SeqMapBySeq_id

TSeqInfoMapBySeq_id CVDBGraphDb_Impl::m_SeqMapBySeq_id

private

Definition at line 167 of file graphread.hpp.

Referenced by CVDBGraphDb_Impl(), GetSeqInfo(), and GetSeqInfoMapBySeq_id().

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

include/sra/readers/sra/graphread.hpp
src/sra/readers/sra/graphread.cpp

Private Attributes
CVDBMgr	m_Mgr

string	m_Path

CVDBTable	m_GraphTable

CVDBTableIndex	m_LookupIndex

CVDBObjectCache< SGraphTableCursor >	m_Graph

CMutex	m_SeqInfoMutex

TSeqInfoList	m_SeqList

TSeqInfoMapBySeq_id	m_SeqMapBySeq_id

TSeqInfoMapByFirstRow	m_SeqMapByFirstRow

Classes

Public Member Functions

Static Public Member Functions

Protected Types

Protected Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TSeqInfoList

◆ TSeqInfoMapByFirstRow

◆ TSeqInfoMapBySeq_id

Constructor & Destructor Documentation

◆ CVDBGraphDb_Impl()

◆ ~CVDBGraphDb_Impl()

Member Function Documentation

◆ GetPath()

◆ GetSeqInfo()

◆ GetSeqInfoAtRow()

◆ GetSeqInfoList()

◆ GetSeqInfoMapBySeq_id()

◆ Graph()

◆ GraphTable()

◆ HasMidZoomGraphs()

◆ LookupIsInMemory() [1/2]

◆ LookupIsInMemory() [2/2]

◆ LookupIsInVDB()

◆ Put()

Friends And Related Function Documentation

◆ CVDBGraphSeqIterator

Member Data Documentation

◆ m_Graph

◆ m_GraphTable

◆ m_LookupIndex

◆ m_Mgr

◆ m_Path

◆ m_SeqInfoMutex

◆ m_SeqList

◆ m_SeqMapByFirstRow

◆ m_SeqMapBySeq_id