`Blob' Class for SeqDB (and WriteDB). More...

#include <objtools/blast/seqdb_reader/seqdbblob.hpp>

Inheritance diagram for CBlastDbBlob:

Collaboration diagram for CBlastDbBlob:

Public Types
enum	EStringFormat { eNone , eNUL , eSize4 , eSizeVar }
	String termination style. More...

enum	EPadding { eSimple , eString }
	Padding style. More...

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
	CBlastDbBlob (int size=0)
	Create a new object, reserving 'size' bytes for writing. More...

	CBlastDbBlob (CTempString data, bool copy)
	Create a readable object containing the specified data. More...

CTempString	Str () const
	Get blob contents as a CTempString. More...

int	Size () const
	Get size of blob contents. More...

void	Clear ()
	Clear all owned data and reference an empty string. More...

void	ReferTo (CTempString data)
	Refer to an existing memory area. More...

void	ReferTo (CTempString data, CRef< CObject > lifetime)
	Refer to an existing memory area. More...

Int8	ReadVarInt ()
	Read a variable length integer from the blob. More...

Int8	ReadVarInt (int offset) const
	Read a variable length integer from the blob. More...

int	ReadInt1 ()
	Read a 1 byte integer at the pointer (and move the pointer). More...

int	ReadInt1 (int offset) const
	Read a 1 byte integer from the given offset. More...

int	ReadInt2 ()
	Read a 2 byte integer at the pointer (and move the pointer). More...

int	ReadInt2 (int offset) const
	Read a 2 byte integer from the given offset. More...

Int4	ReadInt4 ()
	Read a 4 byte integer at the pointer (and move the pointer). More...

Int4	ReadInt4 (int offset) const
	Read a 4 byte integer from the given offset. More...

Int8	ReadInt8 ()
	Read an 8 byte integer at the pointer (and move the pointer). More...

Int8	ReadInt8 (int offset) const
	Read an 8 byte integer from the given offset. More...

void	SeekRead (int offset)
	Move the read pointer to a specific location. More...

int	WriteVarInt (Int8 x)
	Write a variable length integer to the blob. More...

int	WriteVarInt (Int8 x, int offset)
	Write a variable length integer to the blob. More...

void	WriteInt1 (int x)
	Write a 1 byte integer to the blob. More...

void	WriteInt1_LE (int x)

void	WriteInt1 (int x, int offset)
	Write a 1 byte integer to the blob. More...

void	WriteInt1_LE (int x, int offset)

void	WriteInt2 (int x)
	Write a 1 byte integer to the blob. More...

void	WriteInt2_LE (int x)

void	WriteInt2 (int x, int offset)
	Write a 1 byte integer to the blob. More...

void	WriteInt2_LE (int x, int offset)

void	WriteInt4 (Int4 x)
	Write a 4 byte integer to the blob. More...

void	WriteInt4_LE (Int4 x)

void	WriteInt4 (Int4 x, int offset)
	Write a 4 byte integer into the blob at a given offset. More...

void	WriteInt4_LE (Int4 x, int offset)

void	WriteInt8 (Int8 x)
	Write an 8 byte integer to the blob. More...

void	WriteInt8_LE (Int8 x)

void	WriteInt8 (Int8 x, int offset)
	Write an 8 byte integer into the blob at a given offset. More...

void	WriteInt8_LE (Int8 x, int offset)

void	SeekWrite (int offset)
	Seek write pointer to a specific location. More...

CTempString	ReadString (EStringFormat fmt)
	Read string data from the blob (moving the read pointer). More...

CTempString	ReadString (EStringFormat fmt, int offset) const
	Read string data from the blob at a given offset. More...

int	WriteString (CTempString str, EStringFormat fmt)
	Write string data to the blob. More...

int	WriteString (CTempString str, EStringFormat fmt, int offset)
	Write string data to the blob at a specific offset. More...

void	WritePadBytes (int align, EPadding fmt)
	Align the offset by writing pad bytes. More...

void	SkipPadBytes (int align, EPadding fmt)
	Align the offset by skipping bytes. More...

const char *	ReadRaw (int size)
	Read raw data (moving the read pointer). More...

void	WriteRaw (const char *begin, int size)
	Write raw data to the blob (moving the write pointer). More...

void	WriteRaw (const char *begin, int size, int offset)
	Write raw data to the blob at the given offset. More...

int	GetWriteOffset () const
	Get the current write pointer offset. More...

int	GetReadOffset () const
	Get the current read pointer offset. More...

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 int	VarIntSize (Int8 x)
	Compute bytes used for a variable length integer. More...

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)

Private Member Functions
void	x_Copy (int total)
	Copy referenced data to owned data. More...

void	x_Reserve (int size)
	Write raw bytes as a CTempString. More...

void	x_WriteRaw (const char ptr, int size, int offsetp)
	Write raw bytes as ptr + size at a given offset. More...

const char *	x_ReadRaw (int size, int *offsetp) const
	Read raw bytes from a given offset. More...

int	x_WriteVarInt (Int8 x, int *offsetp)
	Write a variable length integer into the buffer. More...

Int8	x_ReadVarInt (int *offsetp) const
	Read a variable length integer from the buffer. More...

int	x_WriteString (CTempString str, EStringFormat fmt, int *offsetp)
	Write string data to the blob. More...

CTempString	x_ReadString (EStringFormat fmt, int *offsetp) const
	Read string data from the blob. More...

template<typename TValue , int TBytes>
TValue	x_ReadIntFixed (int *offsetp) const
	Read a fixed length integer. More...

template<typename TValue , int TBytes>
void	x_WriteIntFixed (TValue x, int *offsetp)
	Write a fixed length integer in big endian. More...

template<typename TValue , int TBytes>
void	x_WriteIntFixed_LE (TValue x, int *offsetp)
	Write a fixed length integer in small endian. More...

Private Attributes
bool	m_Owner
	True if this object owns the target data. More...

int	m_ReadOffset
	The `read pointer' for stream-like access. More...

int	m_WriteOffset
	The `write pointer' for stream-like access. More...

vector< char >	m_DataHere
	Data owned by this object. More...

CTempString	m_DataRef
	Non-owned data (only used for `read' streams). More...

CRef< CObject >	m_Lifetime
	Lifetime maintenance object for referenced data. More...

Additional Inherited Members
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

`Blob' Class for SeqDB (and WriteDB).

This manages serialization and deserialization of binary data of unspecified size and format, known in RDBMS jargon as `blob' data. The primary goals here are to standardize the encoding of data types and to optimize performance. Read and write operations are handled by the same class. For both read and write operations, random and stream access are supported.

Definition at line 56 of file seqdbblob.hpp.

Member Enumeration Documentation

◆ EPadding

enum CBlastDbBlob::EPadding

Padding style.

Enumerator
eSimple	Just write NUL bytes until aligned.
eString	Pad using NUL terminated string of '#' bytes.

Definition at line 270 of file seqdbblob.hpp.

◆ EStringFormat

enum CBlastDbBlob::EStringFormat

String termination style.

Enumerator
eNone	Write the string as-is.
eNUL	Write a NUL terminated string.
eSize4	Write string length as Int4, then string data.
eSizeVar	Write string length as VarInt, then string data.

Definition at line 233 of file seqdbblob.hpp.

Constructor & Destructor Documentation

◆ CBlastDbBlob() [1/2]

CBlastDbBlob::CBlastDbBlob ( int size = 0 )

Create a new object, reserving 'size' bytes for writing.

Parameters

size	This many bytes will be reserved for writing.

Definition at line 40 of file seqdbblob.cpp.

References m_DataHere, and ncbi::grid::netcache::search::fields::size.

◆ CBlastDbBlob() [2/2]

CBlastDbBlob::CBlastDbBlob	(	CTempString	data,
		bool	copy
	)

Create a readable object containing the specified data.

If `copy' is specified as false, only a reference to the data will be kept, and write operations are illegal. If `copy' is specified as true, the data is copied into an internal buffer, and both read and write operations are legal.

Parameters

data	The data to refer to.
copy	Specify true to copy the data to a buffer.

Definition at line 48 of file seqdbblob.cpp.

References data, m_DataHere, m_DataRef, and m_Owner.

Member Function Documentation

◆ Clear()

void CBlastDbBlob::Clear ( void )

Clear all owned data and reference an empty string.

Definition at line 58 of file seqdbblob.cpp.

References m_DataHere, m_DataRef, m_Lifetime, m_Owner, m_ReadOffset, m_WriteOffset, and CRef< C, Locker >::Reset().

Referenced by CWriteDB_GiMaskOffset::AddGIs(), CBuildDatabase::AddSequences(), CSeqDB_ColumnReader::GetBlob(), CSeqDBImpl::GetColumnBlob(), and CWriteDB_Impl::SetMaskData().

◆ GetReadOffset()

int CBlastDbBlob::GetReadOffset ( ) const

Get the current read pointer offset.

Returns: The offset at which the next read would occur.

Definition at line 557 of file seqdbblob.cpp.

References m_ReadOffset.

Referenced by s_ReadRanges(), CSeqDBColumn::x_ReadFields(), and CSeqDBColumn::x_ReadMetaData().

◆ GetWriteOffset()

int CBlastDbBlob::GetWriteOffset ( ) const

Get the current write pointer offset.

Returns: The offset at which the next write would occur.

Definition at line 552 of file seqdbblob.cpp.

References m_WriteOffset.

Referenced by CWriteDB_GiMaskIndex::x_BuildHeaderFields(), CWriteDB_ColumnIndex::x_BuildHeaderStrings(), and CWriteDB_ColumnIndex::x_BuildMetaData().

◆ ReadInt1() [1/2]

int CBlastDbBlob::ReadInt1 ( )

Read a 1 byte integer at the pointer (and move the pointer).

Definition at line 119 of file seqdbblob.cpp.

References m_ReadOffset.

◆ ReadInt1() [2/2]

int CBlastDbBlob::ReadInt1 ( int offset ) const

Read a 1 byte integer from the given offset.

Parameters

off	The offset from which to read the integer.

Returns: The 1 byte value read from the data.

Definition at line 124 of file seqdbblob.cpp.

References offset.

◆ ReadInt2() [1/2]

int CBlastDbBlob::ReadInt2 ( )

Read a 2 byte integer at the pointer (and move the pointer).

Definition at line 129 of file seqdbblob.cpp.

References m_ReadOffset.

◆ ReadInt2() [2/2]

int CBlastDbBlob::ReadInt2 ( int offset ) const

Read a 2 byte integer from the given offset.

Parameters

off	The offset from which to read the integer.

Returns: The 2 byte value read from the data.

Definition at line 134 of file seqdbblob.cpp.

References offset.

◆ ReadInt4() [1/2]

Int4 CBlastDbBlob::ReadInt4 ( )

Read a 4 byte integer at the pointer (and move the pointer).

Definition at line 139 of file seqdbblob.cpp.

References m_ReadOffset.

Referenced by SReadInt4::Read(), CSeqDBColumn::x_ReadFields(), and CSeqDBGiMask::x_ReadFields().

◆ ReadInt4() [2/2]

Int4 CBlastDbBlob::ReadInt4 ( int offset ) const

Read a 4 byte integer from the given offset.

Parameters

off	The offset from which to read the integer.

Returns: The four byte value read from the data.

Definition at line 144 of file seqdbblob.cpp.

References offset.

◆ ReadInt8() [1/2]

Int8 CBlastDbBlob::ReadInt8 ( )

Read an 8 byte integer at the pointer (and move the pointer).

Definition at line 149 of file seqdbblob.cpp.

References m_ReadOffset.

Referenced by CSeqDBColumn::x_ReadFields().

◆ ReadInt8() [2/2]

Int8 CBlastDbBlob::ReadInt8 ( int offset ) const

Read an 8 byte integer from the given offset.

Parameters

off	The offset from which to read the integer.

Returns: The eight byte value read from the data.

Definition at line 154 of file seqdbblob.cpp.

References offset.

◆ ReadRaw()

const char * CBlastDbBlob::ReadRaw ( int size )

Read raw data (moving the read pointer).

Parameters

size	Number of bytes to move the pointer.

Definition at line 416 of file seqdbblob.cpp.

References m_ReadOffset, ncbi::grid::netcache::search::fields::size, and x_ReadRaw().

Referenced by SReadInt4::Read().

◆ ReadString() [1/2]

CTempString CBlastDbBlob::ReadString ( EStringFormat fmt )

Read string data from the blob (moving the read pointer).

Parameters

str	The string to read.
fmt	String termination criteria.

Returns: The number of bytes read.

Definition at line 159 of file seqdbblob.cpp.

References m_ReadOffset, and x_ReadString().

Referenced by SkipPadBytes(), CSeqDBColumn::x_ReadFields(), CSeqDBGiMask::x_ReadFields(), and CSeqDBColumn::x_ReadMetaData().

◆ ReadString() [2/2]

CTempString CBlastDbBlob::ReadString	(	EStringFormat	fmt,
		int	offset
	)		const

Read string data from the blob at a given offset.

Parameters

str	The string to read.
fmt	String termination criteria.
offset	The offset to read from.

Returns: The number of bytes read.

Definition at line 164 of file seqdbblob.cpp.

References offset, and x_ReadString().

◆ ReadVarInt() [1/2]

Int8 CBlastDbBlob::ReadVarInt ( )

Read a variable length integer from the blob.

Parameters

x	The integer to read.

Returns: The number of bytes read.

Definition at line 82 of file seqdbblob.cpp.

References m_ReadOffset, and x_ReadVarInt().

Referenced by CSeqDBColumn::x_ReadMetaData().

◆ ReadVarInt() [2/2]

Int8 CBlastDbBlob::ReadVarInt ( int offset ) const

Read a variable length integer from the blob.

Parameters

x	The integer to read.
offset	The offset to read the integer at.

Returns: The number of bytes read.

Definition at line 87 of file seqdbblob.cpp.

References offset, and x_ReadVarInt().

◆ ReferTo() [1/2]

void CBlastDbBlob::ReferTo ( CTempString data )

Refer to an existing memory area.

This method causes this blob to refer to an existing area of memory without copying it. The caller should guarantee that the referenced data is valid until past the last read of the data. If such a guarantee is not possible, then Clear() and WriteRaw() can be substituted (at the cost of an additional copy operation). Alternately, the two-argument ReferTo() operation can be used to provides `lifetime' management.

Parameters

data	Specifies the referenced memory region.

Definition at line 68 of file seqdbblob.cpp.

References data, m_DataRef, m_Lifetime, m_Owner, and CRef< C, Locker >::Reset().

Referenced by CSeqDBGiMask::s_GetFileRange(), and CSeqDBColumn::x_GetFileRange().

◆ ReferTo() [2/2]

void CBlastDbBlob::ReferTo	(	CTempString	data,
		CRef< CObject >	lifetime
	)

Refer to an existing memory area.

This method causes this blob to refer to an existing area of memory without copying it. This version allows the caller to specify a CObject that maintains the lifetime of the memory region. This object will keep a reference to the CObject as long as it references the specified memory region, after which the CObject should be released. The specified CObject should be allocated on the heap.

Parameters

data	Specifies the referenced memory region.
lifetime	The lifetime management object.

Definition at line 75 of file seqdbblob.cpp.

References data, m_DataRef, m_Lifetime, and m_Owner.

◆ SeekRead()

void CBlastDbBlob::SeekRead ( int offset )

Move the read pointer to a specific location.

Parameters

offset The new read offset.

Definition at line 547 of file seqdbblob.cpp.

References m_ReadOffset, and offset.

Referenced by s_ReadRanges().

◆ SeekWrite()

void CBlastDbBlob::SeekWrite ( int offset )

Seek write pointer to a specific location.

Parameters

offset The new write offset.

Definition at line 542 of file seqdbblob.cpp.

References m_WriteOffset, and offset.

Referenced by CWriteDB_ColumnIndex::x_BuildHeaderFields().

◆ Size()

int CBlastDbBlob::Size ( void ) const

Get size of blob contents.

Definition at line 518 of file seqdbblob.cpp.

References m_DataHere, m_DataRef, m_Owner, and CTempString::size().

Referenced by CSeqDBColumn::GetBlob(), CSeqDBImpl::GetMaskData(), CWriteDB_ColumnData::WriteBlob(), and CWriteDB_ColumnIndex::WriteBlobIndex().

◆ SkipPadBytes()

void CBlastDbBlob::SkipPadBytes	(	int	align,
		EPadding	fmt
	)

Align the offset by skipping bytes.

This works just like WritePadBytes, but verifies that the pad bytes exist and have the correct values, and skips over them, rather than writing them. If fmt is eString, the alignment value is ignored.

Parameters

align	Pad to a multiple of this size.
fmt	String termination criteria.

Definition at line 590 of file seqdbblob.cpp.

References _ASSERT, eNUL, eSimple, eString, i, int, m_ReadOffset, ReadString(), SEQDB_FILE_ASSERT, tmp, and x_ReadRaw().

Referenced by CSeqDBColumn::x_ReadMetaData().

◆ Str()

CTempString CBlastDbBlob::Str ( ) const

Get blob contents as a CTempString.

Definition at line 526 of file seqdbblob.cpp.

References m_DataHere, m_DataRef, m_Owner, and CTempString::size().

Referenced by CWriteDB_GiMaskOffset::AddGIs(), CWriteDB_GiMaskIndex::AddGIs(), BOOST_AUTO_TEST_CASE(), CWriteDB_ColumnData::WriteBlob(), CWriteDB_GiMaskIndex::x_BuildHeaderFields(), CWriteDB_ColumnIndex::x_Flush(), x_ReadRaw(), x_ReadString(), and x_ReadVarInt().

◆ VarIntSize()

int CBlastDbBlob::VarIntSize ( Int8 x )

static

Compute bytes used for a variable length integer.

Parameters

x	The integer value.

Returns: The number of bytes that would be written.

Definition at line 285 of file seqdbblob.cpp.

Referenced by CWriteDB_ColumnIndex::AddMetaData().

◆ WriteInt1() [1/2]

void CBlastDbBlob::WriteInt1 ( int x )

Write a 1 byte integer to the blob.

Parameters

x	The integer to write.

Definition at line 303 of file seqdbblob.cpp.

References NULL.

◆ WriteInt1() [2/2]

void CBlastDbBlob::WriteInt1	(	int	x,
		int	offset
	)

Write a 1 byte integer to the blob.

Parameters

x	The integer to write.
offset	The offset to write the integer at.

Definition at line 308 of file seqdbblob.cpp.

References offset.

◆ WriteInt1_LE() [1/2]

void CBlastDbBlob::WriteInt1_LE ( int x )

Definition at line 343 of file seqdbblob.cpp.

References NULL.

◆ WriteInt1_LE() [2/2]

void CBlastDbBlob::WriteInt1_LE	(	int	x,
		int	offset
	)

Definition at line 348 of file seqdbblob.cpp.

References offset.

◆ WriteInt2() [1/2]

void CBlastDbBlob::WriteInt2 ( int x )

Write a 1 byte integer to the blob.

Parameters

x	The integer to write.

Definition at line 313 of file seqdbblob.cpp.

References NULL.

◆ WriteInt2() [2/2]

void CBlastDbBlob::WriteInt2	(	int	x,
		int	offset
	)

Write a 1 byte integer to the blob.

Parameters

x	The integer to write.
offset	The offset to write the integer at.

Definition at line 318 of file seqdbblob.cpp.

References offset.

◆ WriteInt2_LE() [1/2]

void CBlastDbBlob::WriteInt2_LE ( int x )

Definition at line 353 of file seqdbblob.cpp.

References NULL.

◆ WriteInt2_LE() [2/2]

void CBlastDbBlob::WriteInt2_LE	(	int	x,
		int	offset
	)

Definition at line 358 of file seqdbblob.cpp.

References offset.

◆ WriteInt4() [1/2]

void CBlastDbBlob::WriteInt4 ( Int4 x )

Write a 4 byte integer to the blob.

Parameters

x	The integer to write.

Definition at line 323 of file seqdbblob.cpp.

References NULL.

Referenced by CWriteDB_GiMaskOffset::AddGIs(), CWriteDB_GiMaskIndex::AddGIs(), CWriteDB_Impl::SetMaskData(), CWriteDB_ColumnIndex::WriteBlobIndex(), CWriteDB_ColumnIndex::x_BuildHeaderFields(), CWriteDB_GiMaskIndex::x_BuildHeaderFields(), and CWriteDB_ColumnIndex::x_BuildHeaderStrings().

◆ WriteInt4() [2/2]

void CBlastDbBlob::WriteInt4	(	Int4	x,
		int	offset
	)

Write a 4 byte integer into the blob at a given offset.

Parameters

x	The integer to write.
offset	The offset to write the integer at.

Definition at line 328 of file seqdbblob.cpp.

References offset.

◆ WriteInt4_LE() [1/2]

void CBlastDbBlob::WriteInt4_LE ( Int4 x )

Definition at line 363 of file seqdbblob.cpp.

References NULL.

Referenced by CWriteDB_GiMaskOffset::AddGIs(), CWriteDB_GiMaskIndex::AddGIs(), and CWriteDB_Impl::SetMaskData().

◆ WriteInt4_LE() [2/2]

void CBlastDbBlob::WriteInt4_LE	(	Int4	x,
		int	offset
	)

Definition at line 368 of file seqdbblob.cpp.

References offset.

◆ WriteInt8() [1/2]

void CBlastDbBlob::WriteInt8 ( Int8 x )

Write an 8 byte integer to the blob.

Parameters

x	The integer to write.

Definition at line 333 of file seqdbblob.cpp.

References NULL.

Referenced by CWriteDB_ColumnIndex::x_BuildHeaderFields().

◆ WriteInt8() [2/2]

void CBlastDbBlob::WriteInt8	(	Int8	x,
		int	offset
	)

Write an 8 byte integer into the blob at a given offset.

Parameters

x	The integer to write.
offset	The offset to write the integer at.

Definition at line 338 of file seqdbblob.cpp.

References offset.

◆ WriteInt8_LE() [1/2]

void CBlastDbBlob::WriteInt8_LE ( Int8 x )

Definition at line 373 of file seqdbblob.cpp.

References NULL.

◆ WriteInt8_LE() [2/2]

void CBlastDbBlob::WriteInt8_LE	(	Int8	x,
		int	offset
	)

Definition at line 378 of file seqdbblob.cpp.

References offset.

◆ WritePadBytes()

void CBlastDbBlob::WritePadBytes	(	int	align,
		EPadding	fmt
	)

Align the offset by writing pad bytes.

One of two padding methods is used. If eSimple is specified, zero or more NUL bytes are written. This uses less overhead but readers of the blob need to know the alignment to read fields found after the padding. If eString is specified, a normal string write is used with eNUL termination and a string that will result in the requested alignment. This is self describing but requires at least one byte.

Parameters

align	Pad to a multiple of this size.
fmt	String termination criteria.

Definition at line 562 of file seqdbblob.cpp.

References _ASSERT, eSimple, i, m_WriteOffset, NULL, pad(), tmp, and x_WriteRaw().

Referenced by CWriteDB_Impl::SetMaskData(), CWriteDB_GiMaskIndex::x_BuildHeaderFields(), and CWriteDB_ColumnIndex::x_BuildHeaderStrings().

◆ WriteRaw() [1/2]

void CBlastDbBlob::WriteRaw	(	const char *	begin,
		int	size
	)

Write raw data to the blob (moving the write pointer).

Parameters

begin	Pointer to the start of the data.
size	Number of bytes to copy.

Definition at line 421 of file seqdbblob.cpp.

References NULL, ncbi::grid::netcache::search::fields::size, and x_WriteRaw().

Referenced by CBuildDatabase::AddSequences().

◆ WriteRaw() [2/2]

void CBlastDbBlob::WriteRaw	(	const char *	begin,
		int	size,
		int	offset
	)

Write raw data to the blob at the given offset.

Parameters

begin	Pointer to the start of the data.
size	Number of bytes to copy.
offset	Location to write data at.

Definition at line 426 of file seqdbblob.cpp.

References offset, ncbi::grid::netcache::search::fields::size, and x_WriteRaw().

◆ WriteString() [1/2]

int CBlastDbBlob::WriteString	(	CTempString	str,
		EStringFormat	fmt
	)

Write string data to the blob.

Parameters

str	The string to write.
fmt	String termination criteria.

Returns: The number of bytes written.

Definition at line 383 of file seqdbblob.cpp.

References NULL, str(), and x_WriteString().

Referenced by BOOST_AUTO_TEST_CASE(), CWriteDB_GiMaskIndex::x_BuildHeaderFields(), CWriteDB_ColumnIndex::x_BuildHeaderStrings(), and CWriteDB_ColumnIndex::x_BuildMetaData().

◆ WriteString() [2/2]

int CBlastDbBlob::WriteString	(	CTempString	str,
		EStringFormat	fmt,
		int	offset
	)

Write string data to the blob at a specific offset.

Parameters

str	The string to write.
fmt	String termination criteria.
offset	The offset to write at.

Returns: The number of bytes written.

Definition at line 388 of file seqdbblob.cpp.

References offset, str(), and x_WriteString().

◆ WriteVarInt() [1/2]

int CBlastDbBlob::WriteVarInt ( Int8 x )

Write a variable length integer to the blob.

Parameters

x	The integer to write.

Returns: The number of bytes written.

Definition at line 243 of file seqdbblob.cpp.

References NULL, and x_WriteVarInt().

Referenced by CWriteDB_ColumnIndex::x_BuildMetaData().

◆ WriteVarInt() [2/2]

int CBlastDbBlob::WriteVarInt	(	Int8	x,
		int	offset
	)

Write a variable length integer to the blob.

Parameters

x	The integer to write.
offset	The offset to write the integer at.

Returns: The number of bytes written.

Definition at line 248 of file seqdbblob.cpp.

References offset, and x_WriteVarInt().

◆ x_Copy()

void CBlastDbBlob::x_Copy ( int total )

private

Copy referenced data to owned data.

This handles the Copy part of Copy On Write. To reduce the allocation count, the `total' parameter can be used to request the total number of bytes needed. If `total' is less than the current size, the current size will be used instead.

Parameters

total Total space needed.

Definition at line 478 of file seqdbblob.cpp.

References _ASSERT, CTempString::data(), m_DataHere, m_DataRef, m_Lifetime, m_Owner, CRef< C, Locker >::Reset(), and CTempString::size().

Referenced by x_Reserve().

◆ x_ReadIntFixed()

template<typename TValue , int TBytes>

TValue CBlastDbBlob::x_ReadIntFixed ( int * offsetp ) const

inlineprivate

Read a fixed length integer.

Parameters

offsetp The offset to read at.

Returns: The value that was read.

Definition at line 389 of file seqdbblob.hpp.

References _ASSERT, buf, and x_ReadRaw().

◆ x_ReadRaw()

const char * CBlastDbBlob::x_ReadRaw	(	int	size,
		int *	offsetp
	)		const

private

Read raw bytes from a given offset.

This method checks that enough bytes exist, updates the read pointer, and returns a pointer to the given data. Unlike with x_WriteRaw, do not use NULL for the read pointer, instead the internal read pointer should be provided if the user did not provide one. This method will throw an exception if there is not enough data.

Parameters

size	Number of bytes needed by caller.
offsetp	Offset from which to read (should not be NULL).

Returns: Pointer to beginning of requested data.

Definition at line 209 of file seqdbblob.cpp.

References _ASSERT, CTempString::data(), NCBI_THROW, ncbi::grid::netcache::search::fields::size, CTempString::size(), and Str().

Referenced by ReadRaw(), SkipPadBytes(), x_ReadIntFixed(), and x_ReadString().

◆ x_ReadString()

CTempString CBlastDbBlob::x_ReadString	(	EStringFormat	fmt,
		int *	offsetp
	)		const

private

Read string data from the blob.

Parameters

fmt	String termination criteria.
offset	The offset to read at (should not be NULL).

Returns: The string that was read.

Definition at line 169 of file seqdbblob.cpp.

References CTempString::data(), eNUL, eSize4, eSizeVar, i, NCBI_THROW, CTempString::size(), Str(), x_ReadRaw(), and x_ReadVarInt().

Referenced by ReadString().

◆ x_ReadVarInt()

Int8 CBlastDbBlob::x_ReadVarInt ( int * offsetp ) const

private

Read a variable length integer from the buffer.

Parameters

offsetp The offset to read at (should not be NULL).

Returns: The integer value.

Definition at line 92 of file seqdbblob.cpp.

References all, i, NCBI_THROW, and Str().

Referenced by ReadVarInt(), and x_ReadString().

◆ x_Reserve()

void CBlastDbBlob::x_Reserve ( int size )

private

Write raw bytes as a CTempString.

Parameters

data	String data to write.

Definition at line 497 of file seqdbblob.cpp.

References m_DataHere, m_Owner, and x_Copy().

Referenced by x_WriteRaw().

◆ x_WriteIntFixed()

template<typename TValue , int TBytes>

void CBlastDbBlob::x_WriteIntFixed	(	TValue	x,
		int *	offsetp
	)

inlineprivate

Write a fixed length integer in big endian.

Parameters

x	The value to write.
offsetp	The offset at which to write.

Definition at line 429 of file seqdbblob.hpp.

References _ASSERT, buf, and x_WriteRaw().

◆ x_WriteIntFixed_LE()

template<typename TValue , int TBytes>

void CBlastDbBlob::x_WriteIntFixed_LE	(	TValue	x,
		int *	offsetp
	)

inlineprivate

Write a fixed length integer in small endian.

Parameters

x	The value to write.
offsetp	The offset at which to write.

Definition at line 458 of file seqdbblob.hpp.

References _ASSERT, buf, and x_WriteRaw().

◆ x_WriteRaw()

void CBlastDbBlob::x_WriteRaw	(	const char *	ptr,
		int	size,
		int *	offsetp
	)

private

Write raw bytes as ptr + size at a given offset.

Parameters

data	String data to write.
size	Number of bytes to write.
offsetp	Offset to write at (NULL means use write pointer).

Definition at line 431 of file seqdbblob.cpp.

References _ASSERT, data, int, len, m_DataHere, m_Owner, m_WriteOffset, min(), NULL, ncbi::grid::netcache::search::fields::size, and x_Reserve().

Referenced by WritePadBytes(), WriteRaw(), x_WriteIntFixed(), x_WriteIntFixed_LE(), x_WriteString(), and x_WriteVarInt().

◆ x_WriteString()

int CBlastDbBlob::x_WriteString	(	CTempString	str,
		EStringFormat	fmt,
		int *	offsetp
	)

private

Write string data to the blob.

Parameters

str	The string to write.
fmt	String termination criteria.
offset	The offset to write at (NULL to use write pointer.)

Returns: The number of bytes written.

Definition at line 393 of file seqdbblob.cpp.

References buf, eNUL, eSize4, eSizeVar, m_WriteOffset, str(), x_WriteRaw(), and x_WriteVarInt().

Referenced by WriteString().

◆ x_WriteVarInt()

int CBlastDbBlob::x_WriteVarInt	(	Int8	x,
		int *	offsetp
	)

private

Write a variable length integer into the buffer.

Parameters

x	The integer to write.
offsetp	The offset to write at (or NULL).

Returns: The number of bytes written.

Definition at line 253 of file seqdbblob.cpp.

References _ASSERT, buf, m_WriteOffset, and x_WriteRaw().

Referenced by WriteVarInt(), and x_WriteString().

Member Data Documentation

◆ m_DataHere

vector<char> CBlastDbBlob::m_DataHere

private

Data owned by this object.

Definition at line 498 of file seqdbblob.hpp.

Referenced by CBlastDbBlob(), Clear(), Size(), Str(), x_Copy(), x_Reserve(), and x_WriteRaw().

◆ m_DataRef

CTempString CBlastDbBlob::m_DataRef

private

Non-owned data (only used for `read' streams).

Definition at line 501 of file seqdbblob.hpp.

Referenced by CBlastDbBlob(), Clear(), ReferTo(), Size(), Str(), and x_Copy().

◆ m_Lifetime

CRef<CObject> CBlastDbBlob::m_Lifetime

private

Lifetime maintenance object for referenced data.

Definition at line 504 of file seqdbblob.hpp.

Referenced by Clear(), ReferTo(), and x_Copy().

◆ m_Owner

bool CBlastDbBlob::m_Owner

private

True if this object owns the target data.

Definition at line 489 of file seqdbblob.hpp.

Referenced by CBlastDbBlob(), Clear(), ReferTo(), Size(), Str(), x_Copy(), x_Reserve(), and x_WriteRaw().

◆ m_ReadOffset

int CBlastDbBlob::m_ReadOffset

private

The `read pointer' for stream-like access.

Definition at line 492 of file seqdbblob.hpp.

Referenced by Clear(), GetReadOffset(), ReadInt1(), ReadInt2(), ReadInt4(), ReadInt8(), ReadRaw(), ReadString(), ReadVarInt(), SeekRead(), and SkipPadBytes().

◆ m_WriteOffset

int CBlastDbBlob::m_WriteOffset

private

The `write pointer' for stream-like access.

Definition at line 495 of file seqdbblob.hpp.

Referenced by Clear(), GetWriteOffset(), SeekWrite(), WritePadBytes(), x_WriteRaw(), x_WriteString(), and x_WriteVarInt().

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

include/objtools/blast/seqdb_reader/seqdbblob.hpp
src/objtools/blast/seqdb_reader/seqdbblob.cpp

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

◆ EPadding

◆ EStringFormat

Constructor & Destructor Documentation

◆ CBlastDbBlob() [1/2]

◆ CBlastDbBlob() [2/2]

Member Function Documentation

◆ Clear()

◆ GetReadOffset()

◆ GetWriteOffset()

◆ ReadInt1() [1/2]

◆ ReadInt1() [2/2]

◆ ReadInt2() [1/2]

◆ ReadInt2() [2/2]

◆ ReadInt4() [1/2]

◆ ReadInt4() [2/2]

◆ ReadInt8() [1/2]

◆ ReadInt8() [2/2]

◆ ReadRaw()

◆ ReadString() [1/2]

◆ ReadString() [2/2]

◆ ReadVarInt() [1/2]

◆ ReadVarInt() [2/2]

◆ ReferTo() [1/2]

◆ ReferTo() [2/2]

◆ SeekRead()

◆ SeekWrite()

◆ Size()

◆ SkipPadBytes()

◆ Str()

◆ VarIntSize()

◆ WriteInt1() [1/2]

◆ WriteInt1() [2/2]

◆ WriteInt1_LE() [1/2]

◆ WriteInt1_LE() [2/2]

◆ WriteInt2() [1/2]

◆ WriteInt2() [2/2]

◆ WriteInt2_LE() [1/2]

◆ WriteInt2_LE() [2/2]

◆ WriteInt4() [1/2]

◆ WriteInt4() [2/2]

◆ WriteInt4_LE() [1/2]

◆ WriteInt4_LE() [2/2]

◆ WriteInt8() [1/2]

◆ WriteInt8() [2/2]

◆ WriteInt8_LE() [1/2]

◆ WriteInt8_LE() [2/2]

◆ WritePadBytes()

◆ WriteRaw() [1/2]

◆ WriteRaw() [2/2]

◆ WriteString() [1/2]

◆ WriteString() [2/2]

◆ WriteVarInt() [1/2]

◆ WriteVarInt() [2/2]

◆ x_Copy()

◆ x_ReadIntFixed()

◆ x_ReadRaw()

◆ x_ReadString()

◆ x_ReadVarInt()

◆ x_Reserve()

◆ x_WriteIntFixed()

◆ x_WriteIntFixed_LE()

◆ x_WriteRaw()

◆ x_WriteString()

◆ x_WriteVarInt()

Member Data Documentation

◆ m_DataHere

◆ m_DataRef

◆ m_Lifetime

◆ m_Owner

◆ m_ReadOffset

◆ m_WriteOffset