Search Toolkit Book for CWGSDb_Impl::SSeqTableCursor

Inheritance diagram for CWGSDb_Impl::SSeqTableCursor:

Collaboration diagram for CWGSDb_Impl::SSeqTableCursor:

Public Types
typedef pair< TVDBRowId, TVDBRowId >	row_range_t

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
	SSeqTableCursor (const CVDBTable &table)

	DECLARE_VDB_COLUMN_AS (NCBI_gi, GI)

	DECLARE_VDB_COLUMN_AS_STRING (ACCESSION)

	DECLARE_VDB_COLUMN_AS (uint32_t, ACC_VERSION)

	DECLARE_VDB_COLUMN_AS_STRING (CONTIG_NAME)

	DECLARE_VDB_COLUMN_AS_STRING (NAME)

	DECLARE_VDB_COLUMN_AS_STRING (TITLE)

	DECLARE_VDB_COLUMN_AS_STRING (LABEL)

	DECLARE_VDB_COLUMN_AS (INSDC_coord_zero, READ_START)

	DECLARE_VDB_COLUMN_AS (INSDC_coord_len, READ_LEN)

	DECLARE_VDB_COLUMN_AS (INSDC_coord_zero, TRIM_START)

	DECLARE_VDB_COLUMN_AS (INSDC_coord_len, TRIM_LEN)

	DECLARE_VDB_COLUMN_AS_STRING (DESCR)

	DECLARE_VDB_COLUMN_AS_STRING (NUC_PROT_DESCR)

	DECLARE_VDB_COLUMN_AS_STRING (ANNOT)

	DECLARE_VDB_COLUMN_AS (NCBI_gb_state, GB_STATE)

	DECLARE_VDB_COLUMN_AS_STRING (PUBLIC_COMMENT)

	DECLARE_VDB_COLUMN_AS (INSDC_coord_zero, GAP_START)

	DECLARE_VDB_COLUMN_AS (INSDC_coord_len, GAP_LEN)

	DECLARE_VDB_COLUMN_AS (NCBI_WGS_component_props, GAP_PROPS)

	DECLARE_VDB_COLUMN_AS (NCBI_WGS_gap_linkage, GAP_LINKAGE)

	DECLARE_VDB_COLUMN_AS (INSDC_quality_phred, QUALITY)

	DECLARE_VDB_COLUMN_AS (bool, CIRCULAR)

	DECLARE_VDB_COLUMN_AS (NCBI_WGS_hash, HASH)

	DECLARE_VDB_COLUMN_AS (TVDBRowId, FEAT_ROW_START)

	DECLARE_VDB_COLUMN_AS (TVDBRowId, FEAT_ROW_END)

	DECLARE_VDB_COLUMN_AS (TVDBRowId, FEAT_PRODUCT_ROW_ID)

	DECLARE_VDB_COLUMN_AS (row_range_t, CONTIG_NAME_ROW_RANGE)

	DECLARE_VDB_COLUMN_AS (Uint1, AMBIGUITY_MASK)

	DECLARE_VDB_COLUMN_AS (INSDC_coord_zero, AMBIGUITY_POS)

	DECLARE_VDB_COLUMN_AS (INSDC_4na_bin, AMBIGUITY_4NA)

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

Public Attributes
CVDBCursor	m_Cursor

CVDBColumnBits< 2 >	m_READ_2na

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...

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

Detailed Description

Definition at line 486 of file wgsread.cpp.

Member Typedef Documentation

◆ row_range_t

typedef pair<TVDBRowId, TVDBRowId> CWGSDb_Impl::SSeqTableCursor::row_range_t

Definition at line 517 of file wgsread.cpp.

Constructor & Destructor Documentation

◆ SSeqTableCursor()

CWGSDb_Impl::SSeqTableCursor::SSeqTableCursor ( const CVDBTable & table )

explicit

Definition at line 547 of file wgsread.cpp.

References m_Cursor, s_UseAmbiguity4na(), s_UseAmbiguityMask(), and s_UseGapInfo().

Member Function Documentation

◆ DECLARE_VDB_COLUMN_AS() [1/21]

CWGSDb_Impl::SSeqTableCursor::DECLARE_VDB_COLUMN_AS	(	bool	,
		CIRCULAR
	)

◆ DECLARE_VDB_COLUMN_AS() [2/21]

CWGSDb_Impl::SSeqTableCursor::DECLARE_VDB_COLUMN_AS	(	INSDC_4na_bin	,
		AMBIGUITY_4NA
	)

◆ DECLARE_VDB_COLUMN_AS() [3/21]

CWGSDb_Impl::SSeqTableCursor::DECLARE_VDB_COLUMN_AS	(	INSDC_coord_len	,
		GAP_LEN
	)

◆ DECLARE_VDB_COLUMN_AS() [4/21]

CWGSDb_Impl::SSeqTableCursor::DECLARE_VDB_COLUMN_AS	(	INSDC_coord_len	,
		READ_LEN
	)

◆ DECLARE_VDB_COLUMN_AS() [5/21]

CWGSDb_Impl::SSeqTableCursor::DECLARE_VDB_COLUMN_AS	(	INSDC_coord_len	,
		TRIM_LEN
	)

◆ DECLARE_VDB_COLUMN_AS() [6/21]

CWGSDb_Impl::SSeqTableCursor::DECLARE_VDB_COLUMN_AS	(	INSDC_coord_zero	,
		AMBIGUITY_POS
	)

◆ DECLARE_VDB_COLUMN_AS() [7/21]

CWGSDb_Impl::SSeqTableCursor::DECLARE_VDB_COLUMN_AS	(	INSDC_coord_zero	,
		GAP_START
	)

◆ DECLARE_VDB_COLUMN_AS() [8/21]

CWGSDb_Impl::SSeqTableCursor::DECLARE_VDB_COLUMN_AS	(	INSDC_coord_zero	,
		READ_START
	)

◆ DECLARE_VDB_COLUMN_AS() [9/21]

CWGSDb_Impl::SSeqTableCursor::DECLARE_VDB_COLUMN_AS	(	INSDC_coord_zero	,
		TRIM_START
	)

◆ DECLARE_VDB_COLUMN_AS() [10/21]

CWGSDb_Impl::SSeqTableCursor::DECLARE_VDB_COLUMN_AS	(	INSDC_quality_phred	,
		QUALITY
	)

◆ DECLARE_VDB_COLUMN_AS() [11/21]

CWGSDb_Impl::SSeqTableCursor::DECLARE_VDB_COLUMN_AS	(	NCBI_gb_state	,
		GB_STATE
	)

◆ DECLARE_VDB_COLUMN_AS() [12/21]

CWGSDb_Impl::SSeqTableCursor::DECLARE_VDB_COLUMN_AS	(	NCBI_gi	,
		GI
	)

◆ DECLARE_VDB_COLUMN_AS() [13/21]

CWGSDb_Impl::SSeqTableCursor::DECLARE_VDB_COLUMN_AS	(	NCBI_WGS_component_props	,
		GAP_PROPS
	)

◆ DECLARE_VDB_COLUMN_AS() [14/21]

CWGSDb_Impl::SSeqTableCursor::DECLARE_VDB_COLUMN_AS	(	NCBI_WGS_gap_linkage	,
		GAP_LINKAGE
	)

◆ DECLARE_VDB_COLUMN_AS() [15/21]

CWGSDb_Impl::SSeqTableCursor::DECLARE_VDB_COLUMN_AS	(	NCBI_WGS_hash	,
		HASH
	)

◆ DECLARE_VDB_COLUMN_AS() [16/21]

CWGSDb_Impl::SSeqTableCursor::DECLARE_VDB_COLUMN_AS	(	row_range_t	,
		CONTIG_NAME_ROW_RANGE
	)

◆ DECLARE_VDB_COLUMN_AS() [17/21]

CWGSDb_Impl::SSeqTableCursor::DECLARE_VDB_COLUMN_AS	(	TVDBRowId	,
		FEAT_PRODUCT_ROW_ID
	)

◆ DECLARE_VDB_COLUMN_AS() [18/21]

CWGSDb_Impl::SSeqTableCursor::DECLARE_VDB_COLUMN_AS	(	TVDBRowId	,
		FEAT_ROW_END
	)

◆ DECLARE_VDB_COLUMN_AS() [19/21]

CWGSDb_Impl::SSeqTableCursor::DECLARE_VDB_COLUMN_AS	(	TVDBRowId	,
		FEAT_ROW_START
	)

◆ DECLARE_VDB_COLUMN_AS() [20/21]

CWGSDb_Impl::SSeqTableCursor::DECLARE_VDB_COLUMN_AS	(	Uint1	,
		AMBIGUITY_MASK
	)

◆ DECLARE_VDB_COLUMN_AS() [21/21]

CWGSDb_Impl::SSeqTableCursor::DECLARE_VDB_COLUMN_AS	(	uint32_t	,
		ACC_VERSION
	)

◆ DECLARE_VDB_COLUMN_AS_STRING() [1/9]

CWGSDb_Impl::SSeqTableCursor::DECLARE_VDB_COLUMN_AS_STRING ( ACCESSION )

◆ DECLARE_VDB_COLUMN_AS_STRING() [2/9]

CWGSDb_Impl::SSeqTableCursor::DECLARE_VDB_COLUMN_AS_STRING ( ANNOT )

◆ DECLARE_VDB_COLUMN_AS_STRING() [3/9]

CWGSDb_Impl::SSeqTableCursor::DECLARE_VDB_COLUMN_AS_STRING ( CONTIG_NAME )

◆ DECLARE_VDB_COLUMN_AS_STRING() [4/9]

CWGSDb_Impl::SSeqTableCursor::DECLARE_VDB_COLUMN_AS_STRING ( DESCR )

◆ DECLARE_VDB_COLUMN_AS_STRING() [5/9]

CWGSDb_Impl::SSeqTableCursor::DECLARE_VDB_COLUMN_AS_STRING ( LABEL )

◆ DECLARE_VDB_COLUMN_AS_STRING() [6/9]

CWGSDb_Impl::SSeqTableCursor::DECLARE_VDB_COLUMN_AS_STRING ( NAME )

◆ DECLARE_VDB_COLUMN_AS_STRING() [7/9]

CWGSDb_Impl::SSeqTableCursor::DECLARE_VDB_COLUMN_AS_STRING ( NUC_PROT_DESCR )

◆ DECLARE_VDB_COLUMN_AS_STRING() [8/9]

CWGSDb_Impl::SSeqTableCursor::DECLARE_VDB_COLUMN_AS_STRING ( PUBLIC_COMMENT )

◆ DECLARE_VDB_COLUMN_AS_STRING() [9/9]

CWGSDb_Impl::SSeqTableCursor::DECLARE_VDB_COLUMN_AS_STRING ( TITLE )

Member Data Documentation

◆ m_Cursor

CVDBCursor CWGSDb_Impl::SSeqTableCursor::m_Cursor

Definition at line 489 of file wgsread.cpp.

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

◆ m_READ_2na

CVDBColumnBits<2> CWGSDb_Impl::SSeqTableCursor::m_READ_2na

Definition at line 519 of file wgsread.cpp.

Referenced by CWGSDb_Impl::SAmbiguityInfo::Get2na().

The documentation for this struct was generated from the following file:

src/sra/readers/sra/wgsread.cpp

Public Types

Public Member Functions

Public Attributes

Additional Inherited Members