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

Inheritance diagram for CVDBValue:

Collaboration diagram for CVDBValue:

Classes
struct	SRef

struct	SSaveRef

Public Types
enum	EMissing { eMissing_Throw , eMissing_Allow }

Public Member Functions
	CVDBValue (void)

	CVDBValue (const CVDBCursor &cursor, const CVDBColumn &column)

	CVDBValue (const CVDBCursor &cursor, TVDBRowId row, const CVDBColumn &column, EMissing missing=eMissing_Throw)

	CVDBValue (const SRef &ref)

	CVDBValue (const CVDBCursor &cursor, const char *param_name, const CTempString &param_value, const CVDBColumn &column)

bool	empty (void) const

size_t	size (void) const

CNcbiOstream &	PrintFullName (CNcbiOstream &out) const

Protected Member Functions
void	x_Get (const CVDBCursor &cursor, const CVDBColumn &column)

void	x_Get (const CVDBCursor &cursor, TVDBRowId row, const CVDBColumn &column, EMissing missing=eMissing_Throw)

void	x_ReportIndexOutOfBounds (size_t index) const

void	x_ReportNotOneValue (void) const

void	x_CheckIndex (size_t index) const

void	x_CheckRange (size_t pos, size_t len) const

void	x_CheckOneValue (void) const

Protected Attributes
SSaveRef	m_Ref

const void *	m_Data

uint32_t	m_ElemCount

Detailed Description

Definition at line 607 of file vdbread.hpp.

Member Enumeration Documentation

◆ EMissing

enum CVDBValue::EMissing

Enumerator
eMissing_Throw
eMissing_Allow

Definition at line 610 of file vdbread.hpp.

Constructor & Destructor Documentation

◆ CVDBValue() [1/5]

CVDBValue::CVDBValue ( void )

inline

Definition at line 648 of file vdbread.hpp.

◆ CVDBValue() [2/5]

CVDBValue::CVDBValue	(	const CVDBCursor &	cursor,
		const CVDBColumn &	column
	)

inline

Definition at line 653 of file vdbread.hpp.

References column, and x_Get().

◆ CVDBValue() [3/5]

CVDBValue::CVDBValue	(	const CVDBCursor &	cursor,
		TVDBRowId	row,
		const CVDBColumn &	column,
		EMissing	missing = `eMissing_Throw`
	)

inline

Definition at line 659 of file vdbread.hpp.

References column, and x_Get().

◆ CVDBValue() [4/5]

CVDBValue::CVDBValue ( const SRef & ref )

inlineexplicit

Definition at line 666 of file vdbread.hpp.

References CVDBValue::SRef::column, CVDBValue::SRef::cursor, CVDBValue::SRef::row, and x_Get().

◆ CVDBValue() [5/5]

CVDBValue::CVDBValue	(	const CVDBCursor &	cursor,
		const char *	param_name,
		const CTempString &	param_value,
		const CVDBColumn &	column
	)

inline

Definition at line 672 of file vdbread.hpp.

References column, CVDBCursor::SetParam(), and x_Get().

Member Function Documentation

◆ empty()

bool CVDBValue::empty ( void ) const

inline

Definition at line 682 of file vdbread.hpp.

References m_ElemCount.

Referenced by CCSraRefSeqIterator::GetAlnOverStarts(), CWGSProteinIterator::GetBestProductFeatRowId(), CWGSSeqIterator::GetGi(), CWGSProteinIterator::GetGi(), CWGSSeqIterator::GetLocFeatRowIdRange(), CWGSScaffoldIterator::GetLocFeatRowIdRange(), CWGSProteinIterator::GetLocFeatRowIdRange(), CCSraAlignIterator::GetMatchAlign(), CWGSProteinIterator::GetProductFeatRowId(), CWGSFeatureIterator::GetProductRowId(), CWGSDb_Impl::GetProtAccRowId(), CWGSScaffoldIterator::GetSeq_inst(), CWGSSeqIterator::x_CreateBioseq(), CWGSProteinIterator::x_CreateBioseq(), and CWGSSeqIterator::x_CreateEntry().

◆ PrintFullName()

CNcbiOstream& CVDBValue::PrintFullName ( CNcbiOstream & out ) const

inline

Definition at line 691 of file vdbread.hpp.

References m_Ref, out(), and CVDBValue::SSaveRef::PrintFullName().

Referenced by operator<<().

◆ size()

size_t CVDBValue::size ( void ) const

inline

Definition at line 686 of file vdbread.hpp.

References m_ElemCount.

Referenced by CVDBValueFor< char >::end(), CCSraRefSeqIterator::GetAlnOverStarts(), CWGSProteinIterator::GetBestProductFeatRowId(), CCSraRefSeqIterator::GetEstimatedNumberOfAlignments(), CCSraAlignIterator::GetMatchAlign(), CCSraShortReadIterator::GetMateCount(), CWGSDb_Impl::GetProtAccRowId(), CWGSScaffoldIterator::GetSeq_inst(), CWGSScaffoldIterator::GetSeqLength(), CCSraAlignIterator::MakeFullMismatch(), CVDBStringValue::operator CTempString(), sx_Assign(), CVDBStringValue::Value(), CWGSDb_Impl::SAmbiguityInfo::x_Calculate4na(), CWGSDb_Impl::SAmbiguityInfo::x_CalculateAmbiguityMask(), x_CheckIndex(), x_CheckOneValue(), x_CheckRange(), CVDBValueFor4Bits::x_CheckRange(), CVDBValueFor2Bits::x_CheckRange(), x_CollectCoverageGraph(), CVDBGraphSeqIterator::x_MakeGraph(), x_ReportIndexOutOfBounds(), CVDBValueFor4Bits::x_ReportIndexOutOfBounds(), CVDBValueFor2Bits::x_ReportIndexOutOfBounds(), x_ReportNotOneValue(), and CCSraAlignIterator::x_Settle().

◆ x_CheckIndex()

void CVDBValue::x_CheckIndex ( size_t index ) const

inlineprotected

Definition at line 706 of file vdbread.hpp.

References size(), and x_ReportIndexOutOfBounds().

Referenced by CVDBValueFor< char >::operator[]().

◆ x_CheckOneValue()

void CVDBValue::x_CheckOneValue ( void ) const

inlineprotected

Definition at line 713 of file vdbread.hpp.

References size(), and x_ReportNotOneValue().

Referenced by CVDBValueFor< char >::Value().

◆ x_CheckRange()

void CVDBValue::x_CheckRange	(	size_t	pos,
		size_t	len
	)		const

protected

Definition at line 1770 of file vdbread.cpp.

References len, NCBI_THROW2_FMT, and size().

Referenced by CVDBValueFor4Bits::substr(), CVDBValueFor2Bits::substr(), and CVDBValueFor< char >::substr().

◆ x_Get() [1/2]

void CVDBValue::x_Get	(	const CVDBCursor &	cursor,
		const CVDBColumn &	column
	)

protected

Definition at line 1628 of file vdbread.cpp.

References CHECK_VDB_TIMEOUT_FMT, column, DECLARE_SDK_GET_GUARD, i, Info(), LOG_POST, m_Data, m_ElemCount, m_Ref, NCBI_THROW2_FMT, NStr::PrintableString(), s_GetDebugLevel(), and CVDBValue::SSaveRef::Set().

Referenced by CVDBValue().

◆ x_Get() [2/2]

void CVDBValue::x_Get	(	const CVDBCursor &	cursor,
		TVDBRowId	row,
		const CVDBColumn &	column,
		EMissing	missing = `eMissing_Throw`
	)

protected

Definition at line 1684 of file vdbread.cpp.

References CHECK_VDB_TIMEOUT_FMT, column, DECLARE_SDK_GET_GUARD, eMissing_Throw, i, Info(), LOG_POST, m_Data, m_ElemCount, m_Ref, NCBI_THROW2_FMT, NStr::PrintableString(), s_GetDebugLevel(), and CVDBValue::SSaveRef::Set().

◆ x_ReportIndexOutOfBounds()

void CVDBValue::x_ReportIndexOutOfBounds ( size_t index ) const

protected

Definition at line 1748 of file vdbread.cpp.

References NCBI_THROW2_FMT, and size().

Referenced by x_CheckIndex().

◆ x_ReportNotOneValue()

void CVDBValue::x_ReportNotOneValue ( void ) const

protected

Definition at line 1759 of file vdbread.cpp.

References NCBI_THROW2_FMT, and size().

Referenced by x_CheckOneValue().

Member Data Documentation

◆ m_Data

const void* CVDBValue::m_Data

protected

Definition at line 721 of file vdbread.hpp.

Referenced by CVDBValueFor< char >::data(), CVDBStringValue::data(), and x_Get().

◆ m_ElemCount

uint32_t CVDBValue::m_ElemCount

protected

Definition at line 722 of file vdbread.hpp.

Referenced by empty(), size(), x_Get(), CVDBValueFor4Bits::x_Get(), and CVDBValueFor2Bits::x_Get().

◆ m_Ref

SSaveRef CVDBValue::m_Ref

protected

Definition at line 720 of file vdbread.hpp.

Referenced by PrintFullName(), CVDBValueFor4Bits::substr(), CVDBValueFor2Bits::substr(), x_Get(), CVDBValueFor4Bits::x_Get(), and CVDBValueFor2Bits::x_Get().

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

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

Classes

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Member Enumeration Documentation

◆ EMissing

Constructor & Destructor Documentation

◆ CVDBValue() [1/5]

◆ CVDBValue() [2/5]

◆ CVDBValue() [3/5]

◆ CVDBValue() [4/5]

◆ CVDBValue() [5/5]

Member Function Documentation

◆ empty()

◆ PrintFullName()

◆ size()

◆ x_CheckIndex()

◆ x_CheckOneValue()

◆ x_CheckRange()

◆ x_Get() [1/2]

◆ x_Get() [2/2]

◆ x_ReportIndexOutOfBounds()

◆ x_ReportNotOneValue()

Member Data Documentation

◆ m_Data

◆ m_ElemCount

◆ m_Ref