CSNPDb_Impl Class Reference

Search Toolkit Book for CSNPDb_Impl

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

Inheritance diagram for CSNPDb_Impl:

Collaboration diagram for CSNPDb_Impl:

Classes
struct	SExtraTableCursor
struct	SFeatTableCursor
struct	SGraphTableCursor
struct	SPageTableCursor
struct	SSeqInfo
struct	SSeqTableCursor
struct	STrackInfo
struct	STrackTableCursor

Public Types
typedef vector< SSeqInfo >	TSeqInfoList
typedef map< CSeq_id_Handle, size_t >	TSeqInfoMapBySeq_id
typedef vector< STrackInfo >	TTrackInfoList
typedef map< string, size_t >	TTrackInfoMapByName
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 SSNPDb_Defs
enum	ESearchMode { eSearchByOverlap , eSearchByStart }
enum	EFeatSubtype {   eFeatSubtype_unknown = 0 , eFeatSubtype_identity = 1 , eFeatSubtype_inversion = 2 , eFeatSubtype_single_nucleotide_variation = 3 ,   eFeatSubtype_multi_nucleotide_variation = 4 , eFeatSubtype_deletion_insertion = 5 , eFeatSubtype_deletion = 6 , eFeatSubtype_insertion = 7 ,   eFeatSubtype_str = 8 }
enum	EFeatSubtypeChar {   eFeatSubtypeChar_unknown = 'U' , eFeatSubtypeChar_identity = '-' , eFeatSubtypeChar_inversion = 'V' , eFeatSubtypeChar_single_nucleotide_variation = 'S' ,   eFeatSubtypeChar_multi_nucleotide_variation = 'M' , eFeatSubtypeChar_deletion_insertion = 'L' , eFeatSubtypeChar_deletion = 'D' , eFeatSubtypeChar_insertion = 'I' ,   eFeatSubtypeChar_str = 'R' }
typedef Uint8	TFilter
typedef int	TSplitVersion
typedef int	TChunkId

Public Member Functions
	CSNPDb_Impl (CVDBMgr &mgr, CTempString path_or_acc)
virtual	~CSNPDb_Impl (void)
const string &	GetDbPath (void) const
const TSeqInfoList &	GetSeqInfoList (void) const
const TSeqInfoMapBySeq_id &	GetSeqInfoMapBySeq_id (void) const
const TTrackInfoList &	GetTrackInfoList (void) const
const TTrackInfoMapByName &	GetTrackInfoMapByName (void) const
TTrackInfoList::const_iterator	FindTrack (const string &name) const
TSeqInfoList::const_iterator	FindSeq (const string &accession, int version)
TSeqInfoList::const_iterator	FindSeq (const CSeq_id_Handle &seq_id)
TSeqPos	GetPageSize (void) const
TSeqPos	GetOverviewZoom (void) const
TSeqPos	GetCoverageZoom (void) 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

Protected Member Functions
const CVDBTable &	SeqTable (void)
const CVDBTable &	GraphTable (void)
const CVDBTable &	PageTable (void)
const CVDBTable &	FeatTable (void)
const CVDBTable &	ExtraTable (void)
CRef< SSeqTableCursor >	Seq (TVDBRowId row=0)
void	Put (CRef< SSeqTableCursor > &curs, TVDBRowId row=0)
CRef< SGraphTableCursor >	Graph (TVDBRowId row=0)
void	Put (CRef< SGraphTableCursor > &curs, TVDBRowId row=0)
CRef< SPageTableCursor >	Page (TVDBRowId row=0)
void	Put (CRef< SPageTableCursor > &curs, TVDBRowId row=0)
CRef< SFeatTableCursor >	Feat (TVDBRowId row=0)
void	Put (CRef< SFeatTableCursor > &curs, TVDBRowId row=0)
CRef< SExtraTableCursor >	Extra (TVDBRowId row=0)
void	Put (CRef< SExtraTableCursor > &curs, TVDBRowId row=0)
size_t	x_GetSeqVDBIndex (TSeqInfoList::const_iterator seq) const
size_t	x_GetTrackVDBIndex (TTrackInfoList::const_iterator track) const
TVDBRowId	x_GetSeqVDBRowId (TSeqInfoList::const_iterator seq) const
TVDBRowId	x_GetTrackVDBRowId (TTrackInfoList::const_iterator track) const
void	x_Update (TSeqInfoList::const_iterator seq)
CRange< TVDBRowId >	x_GetPageVDBRowRange (TSeqInfoList::const_iterator seq)
TVDBRowId	x_GetGraphVDBRowId (TSeqInfoList::const_iterator seq, TTrackInfoList::const_iterator track)
Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Private Types
typedef map< TVDBRowId, TVDBRowId >	TSeq2PageMap

Private Attributes
CVDBMgr	m_Mgr
string	m_DbPath
CVDB	m_Db
CVDBTable	m_SeqTable
CVDBTable	m_GraphTable
CVDBTable	m_PageTable
CVDBTable	m_FeatTable
CVDBTable	m_ExtraTable
CVDBObjectCache< SSeqTableCursor >	m_Seq
CVDBTableIndex	m_SeqAccIndex
CVDBObjectCache< SGraphTableCursor >	m_Graph
CVDBObjectCache< SPageTableCursor >	m_Page
CVDBObjectCache< SFeatTableCursor >	m_Feat
CVDBObjectCache< SExtraTableCursor >	m_Extra
TSeqInfoList	m_SeqList
TSeqInfoMapBySeq_id	m_SeqMapBySeq_id
TSeq2PageMap	m_Seq2PageMap
TTrackInfoList	m_TrackList
TTrackInfoMapByName	m_TrackMapByName
CMutex	m_Mutex

Friends
class	CSNPDbTrackIterator
class	CSNPDbSeqIterator
class	CSNPDbPageIterator
class	CSNPDbGraphIterator
class	CSNPDbFeatIterator

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 180 of file snpread.hpp.

Member Typedef Documentation

TSeq2PageMap

typedef map<TVDBRowId, TVDBRowId> CSNPDb_Impl::TSeq2PageMap

private

Definition at line 361 of file snpread.hpp.

TSeqInfoList

typedef vector<SSeqInfo> CSNPDb_Impl::TSeqInfoList

Definition at line 222 of file snpread.hpp.

TSeqInfoMapBySeq_id

typedef map<CSeq_id_Handle, size_t> CSNPDb_Impl::TSeqInfoMapBySeq_id

Definition at line 223 of file snpread.hpp.

TTrackInfoList

typedef vector<STrackInfo> CSNPDb_Impl::TTrackInfoList

Definition at line 230 of file snpread.hpp.

TTrackInfoMapByName

typedef map<string, size_t> CSNPDb_Impl::TTrackInfoMapByName

Definition at line 231 of file snpread.hpp.

Constructor & Destructor Documentation

CSNPDb_Impl()

CSNPDb_Impl::CSNPDb_Impl	(	CVDBMgr &	mgr,
		CTempString	path_or_acc
	)

Definition at line 316 of file snpread.cpp.

References CSraException::eNotFoundDb, CSraException::GetErrCode(), CSeq_id_Handle::GetHandle(), CVDBCursor::GetMaxRowId(), CSraException::GetRC(), CSNPDb_Impl::SSeqInfo::SPageSet::GetRowIdEnd(), CSNPDb_Impl::SSeqInfo::SPageSet::GetSeqPosEnd(), i, info, kPageSize, kPreloadSeqList, CSNPDb_Impl::STrackTableCursor::m_Cursor, m_Db, m_ExtraTable, m_FeatTable, m_GraphTable, m_Mgr, CSNPDb_Impl::SSeqInfo::SPageSet::m_PageCount, m_PageTable, CSNPDb_Impl::SSeqInfo::SPageSet::m_RowId, m_SeqAccIndex, m_SeqList, m_SeqMapBySeq_id, CSNPDb_Impl::SSeqInfo::SPageSet::m_SeqPos, m_SeqTable, m_TrackList, m_TrackMapByName, NCBI_THROW2_FMT, Page(), Put(), row, Seq(), table, and NStr::TrimSuffixInPlace().

~CSNPDb_Impl()

CSNPDb_Impl::~CSNPDb_Impl ( void  )

virtual

Definition at line 447 of file snpread.cpp.

Member Function Documentation

Extra()

CRef< CSNPDb_Impl::SExtraTableCursor > CSNPDb_Impl::Extra ( TVDBRowId  row = 0 )

protected

Definition at line 274 of file snpread.cpp.

References ExtraTable(), m_Extra, row, and table.

Referenced by CSNPDbFeatIterator::GetExtraRange().

ExtraTable()

const CVDBTable& CSNPDb_Impl::ExtraTable ( void  )

inlineprotected

Definition at line 295 of file snpread.hpp.

References m_ExtraTable.

Referenced by Extra().

Feat()

CRef< CSNPDb_Impl::SFeatTableCursor > CSNPDb_Impl::Feat ( TVDBRowId  row = 0 )

protected

Definition at line 264 of file snpread.cpp.

References FeatTable(), m_Feat, and row.

Referenced by CSNPDbFeatIterator::x_InitPage().

FeatTable()

const CVDBTable& CSNPDb_Impl::FeatTable ( void  )

inlineprotected

Definition at line 291 of file snpread.hpp.

References m_FeatTable.

Referenced by Feat().

FindSeq() [1/2]

CSNPDb_Impl::TSeqInfoList::const_iterator CSNPDb_Impl::FindSeq

(

const CSeq_id_Handle &

seq_id

)

Definition at line 514 of file snpread.cpp.

References map_checker< Container >::end(), map_checker< Container >::find(), FindSeq(), CSeq_id_Handle::GetSeqId(), CSeq_id::GetTextseq_Id(), m_SeqList, and m_SeqMapBySeq_id.

FindSeq() [2/2]

CSNPDb_Impl::TSeqInfoList::const_iterator CSNPDb_Impl::FindSeq	(	const string &	accession,
		int	version
	)

Definition at line 484 of file snpread.cpp.

References CVDBTableIndex::Find(), m_SeqAccIndex, m_SeqList, NStr::NumericToString(), compile_time_bits::range(), NStr::ToUpper(), dtl::version, and x_Update().

Referenced by FindSeq().

FindTrack()

CSNPDb_Impl::TTrackInfoList::const_iterator CSNPDb_Impl::FindTrack

(

const string &

name

)

const

Definition at line 471 of file snpread.cpp.

References map_checker< Container >::end(), map_checker< Container >::find(), m_TrackList, and m_TrackMapByName.

GetCoverageZoom()

TSeqPos CSNPDb_Impl::GetCoverageZoom

(

void

)

const

Definition at line 464 of file snpread.cpp.

References kCoverageZoom.

Referenced by CSNPDb::GetCoverageZoom(), and CSNPDbSeqIterator::GetCoverageZoom().

GetDbPath()

const string& CSNPDb_Impl::GetDbPath ( void  ) const

inline

Definition at line 233 of file snpread.hpp.

References m_DbPath.

Referenced by CSNPBlobId::CSNPBlobId(), x_GetGraphVDBRowId(), and x_GetPageVDBRowRange().

GetOverviewZoom()

TSeqPos CSNPDb_Impl::GetOverviewZoom

(

void

)

const

Definition at line 458 of file snpread.cpp.

References kOverviewZoom.

Referenced by CSNPDb::GetOverviewZoom(), and CSNPDbSeqIterator::GetOverviewZoom().

GetPageSize()

TSeqPos CSNPDb_Impl::GetPageSize

(

void

)

const

Definition at line 452 of file snpread.cpp.

References kPageSize.

Referenced by CSNPDbSeqIterator::GetPageSize(), CSNPDbPageIterator::GetPageSize(), and CSNPDbGraphIterator::GetPageSize().

GetSeqInfoList()

const TSeqInfoList& CSNPDb_Impl::GetSeqInfoList ( void  ) const

inline

Definition at line 237 of file snpread.hpp.

References m_SeqList.

Referenced by CSNPDbSeqIterator::GetList(), x_GetGraphVDBRowId(), x_GetPageVDBRowRange(), and x_GetSeqVDBIndex().

GetSeqInfoMapBySeq_id()

const TSeqInfoMapBySeq_id& CSNPDb_Impl::GetSeqInfoMapBySeq_id ( void  ) const

inline

Definition at line 240 of file snpread.hpp.

References m_SeqMapBySeq_id.

GetTrackInfoList()

const TTrackInfoList& CSNPDb_Impl::GetTrackInfoList ( void  ) const

inline

Definition at line 244 of file snpread.hpp.

References m_TrackList.

Referenced by CSNPDbTrackIterator::GetList(), CSNPDb::GetTrackCount(), x_GetGraphVDBRowId(), and x_GetTrackVDBIndex().

GetTrackInfoMapByName()

const TTrackInfoMapByName& CSNPDb_Impl::GetTrackInfoMapByName ( void  ) const

inline

Definition at line 247 of file snpread.hpp.

References m_TrackMapByName.

Graph()

CRef< CSNPDb_Impl::SGraphTableCursor > CSNPDb_Impl::Graph ( TVDBRowId  row = 0 )

protected

Definition at line 244 of file snpread.cpp.

References GraphTable(), m_Graph, and row.

Referenced by CSNPDbGraphIterator::Select(), and CSNPDbFeatIterator::x_SetFilter().

GraphTable()

const CVDBTable& CSNPDb_Impl::GraphTable ( void  )

inlineprotected

Definition at line 283 of file snpread.hpp.

References m_GraphTable.

Referenced by Graph().

Page()

CRef< CSNPDb_Impl::SPageTableCursor > CSNPDb_Impl::Page ( TVDBRowId  row = 0 )

protected

Definition at line 254 of file snpread.cpp.

References m_Page, PageTable(), and row.

Referenced by CSNPDb_Impl(), CSNPDbSeqIterator::GetSNPCount(), CSNPDbPageIterator::Select(), and x_Update().

PageTable()

const CVDBTable& CSNPDb_Impl::PageTable ( void  )

inlineprotected

Definition at line 287 of file snpread.hpp.

References m_PageTable.

Referenced by Page().

Put() [1/5]

void CSNPDb_Impl::Put ( CRef< SExtraTableCursor > &  curs, TVDBRowId  row = 0  )

protected

Definition at line 310 of file snpread.cpp.

References m_Extra, and row.

Put() [2/5]

void CSNPDb_Impl::Put ( CRef< SFeatTableCursor > &  curs, TVDBRowId  row = 0  )

protected

Definition at line 304 of file snpread.cpp.

References m_Feat, and row.

Put() [3/5]

void CSNPDb_Impl::Put ( CRef< SGraphTableCursor > &  curs, TVDBRowId  row = 0  )

protected

Definition at line 292 of file snpread.cpp.

References m_Graph, and row.

Put() [4/5]

void CSNPDb_Impl::Put ( CRef< SPageTableCursor > &  curs, TVDBRowId  row = 0  )

protected

Definition at line 298 of file snpread.cpp.

References m_Page, and row.

Put() [5/5]

void CSNPDb_Impl::Put ( CRef< SSeqTableCursor > &  curs, TVDBRowId  row = 0  )

protected

Definition at line 286 of file snpread.cpp.

References m_Seq, and row.

Referenced by CSNPDb_Impl(), CSNPDbSeqIterator::GetSNPCount(), CSNPDbPageIterator::Reset(), CSNPDbGraphIterator::Reset(), CSNPDbFeatIterator::Reset(), and x_Update().

Seq()

CRef< CSNPDb_Impl::SSeqTableCursor > CSNPDb_Impl::Seq ( TVDBRowId  row = 0 )

protected

Definition at line 234 of file snpread.cpp.

References m_Seq, row, and SeqTable().

Referenced by CSNPDb_Impl(), and x_Update().

SeqTable()

const CVDBTable& CSNPDb_Impl::SeqTable ( void  )

inlineprotected

Definition at line 279 of file snpread.hpp.

References m_SeqTable.

Referenced by Seq().

x_GetGraphVDBRowId()

TVDBRowId CSNPDb_Impl::x_GetGraphVDBRowId ( TSeqInfoList::const_iterator  seq, TTrackInfoList::const_iterator  track  )

protected

Definition at line 651 of file snpread.cpp.

References GetDbPath(), GetSeqInfoList(), GetTrackInfoList(), kPageSize, len, and NCBI_THROW_FMT.

Referenced by CSNPDbSeqIterator::GetGraphVDBRowId(), and CSNPDbFeatIterator::x_SetFilter().

x_GetPageVDBRowRange()

CRange< TVDBRowId > CSNPDb_Impl::x_GetPageVDBRowRange ( TSeqInfoList::const_iterator  seq )

protected

Definition at line 639 of file snpread.cpp.

References GetDbPath(), GetSeqInfoList(), and NCBI_THROW_FMT.

Referenced by CSNPDbSeqIterator::GetPageVDBRowRange().

x_GetSeqVDBIndex()

size_t CSNPDb_Impl::x_GetSeqVDBIndex ( TSeqInfoList::const_iterator  seq ) const

inlineprotected

Definition at line 324 of file snpread.hpp.

References GetSeqInfoList().

Referenced by CSNPDbSeqIterator::GetVDBSeqIndex(), and x_GetSeqVDBRowId().

x_GetSeqVDBRowId()

TVDBRowId CSNPDb_Impl::x_GetSeqVDBRowId ( TSeqInfoList::const_iterator  seq ) const

inlineprotected

Definition at line 330 of file snpread.hpp.

References x_GetSeqVDBIndex().

Referenced by CSNPDbSeqIterator::GetVDBRowId(), and CSNPDbPageIterator::x_GetSeqVDBRowId().

x_GetTrackVDBIndex()

size_t CSNPDb_Impl::x_GetTrackVDBIndex ( TTrackInfoList::const_iterator  track ) const

inlineprotected

Definition at line 327 of file snpread.hpp.

References GetTrackInfoList().

Referenced by CSNPDbTrackIterator::GetVDBTrackIndex(), and x_GetTrackVDBRowId().

x_GetTrackVDBRowId()

TVDBRowId CSNPDb_Impl::x_GetTrackVDBRowId ( TTrackInfoList::const_iterator  track ) const

inlineprotected

Definition at line 333 of file snpread.hpp.

References x_GetTrackVDBIndex().

Referenced by CSNPDbTrackIterator::GetVDBRowId(), and CSNPDbPageIterator::x_GetTrackVDBRowId().

x_Update()

void CSNPDb_Impl::x_Update ( TSeqInfoList::const_iterator  seq )

protected

Definition at line 537 of file snpread.cpp.

References _ASSERT, map_checker< Container >::begin(), map_checker< Container >::end(), CSeq_id_Handle::GetHandle(), CSNPDb_Impl::SSeqInfo::SPageSet::GetRowIdEnd(), CSNPDb_Impl::SSeqInfo::SPageSet::GetSeqPosEnd(), info, kPageSize, map_checker< Container >::lower_bound(), m_Mutex, CSNPDb_Impl::SSeqInfo::SPageSet::m_PageCount, CSNPDb_Impl::SSeqInfo::SPageSet::m_RowId, m_Seq2PageMap, m_SeqList, CSNPDb_Impl::SSeqInfo::SPageSet::m_SeqPos, m_TrackList, Page(), Put(), row, and Seq().

Referenced by CSNPDbSeqIterator::CSNPDbSeqIterator(), FindSeq(), and CSNPDbSeqIterator::operator++().

Friends And Related Function Documentation

CSNPDbFeatIterator

friend class CSNPDbFeatIterator

friend

Definition at line 264 of file snpread.hpp.

CSNPDbGraphIterator

friend class CSNPDbGraphIterator

friend

Definition at line 263 of file snpread.hpp.

CSNPDbPageIterator

friend class CSNPDbPageIterator

friend

Definition at line 262 of file snpread.hpp.

CSNPDbSeqIterator

friend class CSNPDbSeqIterator

friend

Definition at line 261 of file snpread.hpp.

CSNPDbTrackIterator

friend class CSNPDbTrackIterator

friend

Definition at line 260 of file snpread.hpp.

Member Data Documentation

m_Db

CVDB CSNPDb_Impl::m_Db

private

Definition at line 345 of file snpread.hpp.

Referenced by CSNPDb_Impl().

m_DbPath

string CSNPDb_Impl::m_DbPath

private

Definition at line 344 of file snpread.hpp.

Referenced by GetDbPath().

m_Extra

CVDBObjectCache<SExtraTableCursor> CSNPDb_Impl::m_Extra

private

Definition at line 357 of file snpread.hpp.

Referenced by Extra(), and Put().

m_ExtraTable

CVDBTable CSNPDb_Impl::m_ExtraTable

private

Definition at line 350 of file snpread.hpp.

Referenced by CSNPDb_Impl(), and ExtraTable().

m_Feat

CVDBObjectCache<SFeatTableCursor> CSNPDb_Impl::m_Feat

private

Definition at line 356 of file snpread.hpp.

Referenced by Feat(), and Put().

m_FeatTable

CVDBTable CSNPDb_Impl::m_FeatTable

private

Definition at line 349 of file snpread.hpp.

Referenced by CSNPDb_Impl(), and FeatTable().

m_Graph

CVDBObjectCache<SGraphTableCursor> CSNPDb_Impl::m_Graph

private

Definition at line 354 of file snpread.hpp.

Referenced by Graph(), and Put().

m_GraphTable

CVDBTable CSNPDb_Impl::m_GraphTable

private

Definition at line 347 of file snpread.hpp.

Referenced by CSNPDb_Impl(), and GraphTable().

m_Mgr

CVDBMgr CSNPDb_Impl::m_Mgr

private

Definition at line 343 of file snpread.hpp.

Referenced by CSNPDb_Impl().

m_Mutex

CMutex CSNPDb_Impl::m_Mutex

private

Definition at line 366 of file snpread.hpp.

Referenced by x_Update().

m_Page

CVDBObjectCache<SPageTableCursor> CSNPDb_Impl::m_Page

private

Definition at line 355 of file snpread.hpp.

Referenced by Page(), and Put().

m_PageTable

CVDBTable CSNPDb_Impl::m_PageTable

private

Definition at line 348 of file snpread.hpp.

Referenced by CSNPDb_Impl(), and PageTable().

m_Seq

CVDBObjectCache<SSeqTableCursor> CSNPDb_Impl::m_Seq

private

Definition at line 352 of file snpread.hpp.

Referenced by Put(), and Seq().

m_Seq2PageMap

TSeq2PageMap CSNPDb_Impl::m_Seq2PageMap

private

Definition at line 362 of file snpread.hpp.

Referenced by x_Update().

m_SeqAccIndex

CVDBTableIndex CSNPDb_Impl::m_SeqAccIndex

private

Definition at line 353 of file snpread.hpp.

Referenced by CSNPDb_Impl(), and FindSeq().

m_SeqList

TSeqInfoList CSNPDb_Impl::m_SeqList

private

Definition at line 359 of file snpread.hpp.

Referenced by CSNPDb_Impl(), FindSeq(), GetSeqInfoList(), and x_Update().

m_SeqMapBySeq_id

TSeqInfoMapBySeq_id CSNPDb_Impl::m_SeqMapBySeq_id

private

Definition at line 360 of file snpread.hpp.

Referenced by CSNPDb_Impl(), FindSeq(), and GetSeqInfoMapBySeq_id().

m_SeqTable

CVDBTable CSNPDb_Impl::m_SeqTable

private

Definition at line 346 of file snpread.hpp.

Referenced by CSNPDb_Impl(), and SeqTable().

m_TrackList

TTrackInfoList CSNPDb_Impl::m_TrackList

private

Definition at line 364 of file snpread.hpp.

Referenced by CSNPDb_Impl(), FindTrack(), GetTrackInfoList(), and x_Update().

m_TrackMapByName

TTrackInfoMapByName CSNPDb_Impl::m_TrackMapByName

private

Definition at line 365 of file snpread.hpp.

Referenced by CSNPDb_Impl(), FindTrack(), and GetTrackInfoMapByName().

---

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

• include/sra/readers/sra/snpread.hpp
• src/sra/readers/sra/snpread.cpp