CVDBCursor Class Reference

Search Toolkit Book for CVDBCursor

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

Inheritance diagram for CVDBCursor:

Collaboration diagram for CVDBCursor:

Public Member Functions
	CVDBCursor (void)
	CVDBCursor (const CVDBTable &table)
const CVDBTable &	GetTable (void) const
bool	RowIsOpened (void) const
rc_t	OpenRowRc (TVDBRowId row_id)
void	OpenRow (TVDBRowId row_id)
bool	TryOpenRow (TVDBRowId row_id)
void	CloseRow (void)
TVDBRowIdRange	GetRowIdRange (TVDBColumnIdx column=0) const
TVDBRowId	GetMaxRowId (void) const
void	SetParam (const char *name, const CTempString &value) const
uint32_t	GetElementCount (TVDBRowId row, const CVDBColumn &column, uint32_t elem_bits) const
void	ReadElements (TVDBRowId row, const CVDBColumn &column, uint32_t elem_bits, uint32_t start, uint32_t count, void *buffer) const
void	Close (void)
Public Member Functions inherited from CSraRef< const VCursor >
	CSraRef (void)
	CSraRef (const TSelf &ref)
	CSraRef (TSelf &&ref)
	Copy constructor from an existing CRef object,. More...
TSelf &	operator= (const TSelf &ref)
TSelf &	operator= (TSelf &&ref)
	~CSraRef (void)
void	Release (void)
TObject *	GetPointer (void) const
	operator TObject * (void) const
TObject *	operator-> (void) const
TObject &	operator* (void) const

Protected Member Functions
void	Init (const CVDBTable &table)
Protected Member Functions inherited from CSraRef< const VCursor >
	CSraRef (TPointer ptr)
TObject **	x_InitPtr (void)

Private Attributes
CVDBTable	m_Table
bool	m_RowOpened

Additional Inherited Members
Public Types inherited from CSraRef< const VCursor >
typedef const VCursor	TObject
typedef TObject *	TPointer
Protected Types inherited from CSraRef< const VCursor >
typedef CSraRef< const VCursor >	TSelf
typedef CSraRefTraits< const VCursor >	TTraits
Static Protected Member Functions inherited from CSraRef< const VCursor >
static TObject *	s_AddRef (const TSelf &ref)

Detailed Description

Definition at line 372 of file vdbread.hpp.

Constructor & Destructor Documentation

CVDBCursor() [1/2]

CVDBCursor::CVDBCursor ( void  )

inline

Definition at line 376 of file vdbread.hpp.

Referenced by Close().

CVDBCursor() [2/2]

CVDBCursor::CVDBCursor ( const CVDBTable &  table )

inlineexplicit

Definition at line 380 of file vdbread.hpp.

References Init(), and table.

Member Function Documentation

Close()

void CVDBCursor::Close ( void  )

inline

Definition at line 417 of file vdbread.hpp.

References CVDBCursor().

CloseRow()

void CVDBCursor::CloseRow

(

void

)

Definition at line 1338 of file vdbread.cpp.

References m_RowOpened, NCBI_THROW2, and RowIsOpened().

Referenced by OpenRowRc().

GetElementCount()

uint32_t CVDBCursor::GetElementCount	(	TVDBRowId	row,
		const CVDBColumn &	column,
		uint32_t	elem_bits
	)		const

Definition at line 1408 of file vdbread.cpp.

References CHECK_VDB_TIMEOUT_FMT, column, DECLARE_SDK_GET_GUARD, NCBI_THROW2_FMT, and row.

Referenced by CWGSSeqIterator::x_GetQualityArraySize().

GetMaxRowId()

TVDBRowId CVDBCursor::GetMaxRowId

(

void

)

const

Definition at line 1388 of file vdbread.cpp.

References GetRowIdRange(), and compile_time_bits::range().

Referenced by CSNPDb_Impl::CSNPDb_Impl(), CSNPDbFeatIterator::x_InitPage(), and CSNPDbGraphIterator::x_Next().

GetRowIdRange()

TVDBRowIdRange CVDBCursor::GetRowIdRange

(

TVDBColumnIdx

column = 0

)

const

Definition at line 1376 of file vdbread.cpp.

References CHECK_VDB_TIMEOUT_FMT, column, and NCBI_THROW2_FMT.

Referenced by GetMaxRowId(), CVDBColumn::GetRowIdRange(), CWGSFeatureIterator::SelectRowRange(), CWGSProteinIterator::x_Init(), CWGSFeatureIterator::x_Init(), and CWGSGiIterator::x_Init().

GetTable()

const CVDBTable& CVDBCursor::GetTable ( void  ) const

inline

Definition at line 386 of file vdbread.hpp.

References m_Table.

Referenced by operator<<(), and CVDBValue::SSaveRef::Set().

Init()

void CVDBCursor::Init ( const CVDBTable &  table )

protected

Definition at line 1306 of file vdbread.cpp.

References CHECK_VDB_TIMEOUT_FMT, m_Table, NCBI_THROW2, NCBI_THROW2_FMT, table, and CSraRef< const VCursor >::x_InitPtr().

Referenced by CVDBCursor().

OpenRow()

void CVDBCursor::OpenRow

(

TVDBRowId

row_id

)

Definition at line 1366 of file vdbread.cpp.

References CHECK_VDB_TIMEOUT_FMT, NCBI_THROW2_FMT, and OpenRowRc().

OpenRowRc()

rc_t CVDBCursor::OpenRowRc

(

TVDBRowId

row_id

)

Definition at line 1351 of file vdbread.cpp.

References CloseRow(), and m_RowOpened.

Referenced by OpenRow(), and TryOpenRow().

ReadElements()

void CVDBCursor::ReadElements	(	TVDBRowId	row,
		const CVDBColumn &	column,
		uint32_t	elem_bits,
		uint32_t	start,
		uint32_t	count,
		void *	buffer
	)		const

Definition at line 1427 of file vdbread.cpp.

References buffer, CHECK_VDB_TIMEOUT_FMT, column, DECLARE_SDK_GET_GUARD, Info(), LOG_POST, NCBI_THROW2_FMT, NCBI_THROW_FMT, row, and s_GetDebugLevel().

Referenced by CWGSDb_Impl::SAmbiguityInfo::Get2na(), CWGSSeqIterator::GetQualityVec(), and CWGSSeqIterator::x_GetQualityAnnot().

RowIsOpened()

bool CVDBCursor::RowIsOpened ( void  ) const

inline

Definition at line 391 of file vdbread.hpp.

References m_RowOpened.

Referenced by CloseRow().

SetParam()

void CVDBCursor::SetParam	(	const char *	name,
		const CTempString &	value
	)		const

Definition at line 1395 of file vdbread.cpp.

References eNotFound, CSraRef< const VCursor >::GetPointer(), NCBI_THROW2_FMT, and rapidjson::value.

Referenced by CVDBValue::CVDBValue().

TryOpenRow()

bool CVDBCursor::TryOpenRow ( TVDBRowId  row_id )

inline

Definition at line 397 of file vdbread.hpp.

References OpenRowRc().

Member Data Documentation

m_RowOpened

bool CVDBCursor::m_RowOpened

private

Definition at line 426 of file vdbread.hpp.

Referenced by CloseRow(), OpenRowRc(), and RowIsOpened().

m_Table

CVDBTable CVDBCursor::m_Table

private

Definition at line 425 of file vdbread.hpp.

Referenced by GetTable(), and Init().

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

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