Search Toolkit Book for CWriteDB_Column

#include "writedb_column.hpp"
(Private to src/objtools/blast/seqdb_writer.)

Inheritance diagram for CWriteDB_Column:

Collaboration diagram for CWriteDB_Column:

Public Types
typedef map< string, string >	TColumnMeta
	Type used for database column meta-data. 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
	CWriteDB_Column (const string &dbname, const string &extn1, const string &extn2, int index, const string &title, const TColumnMeta &meta, Uint8 max_file_size)
	Construct WriteDB style database column. More...

void	AddByteOrder (const string &dbname, const string &extn, int index, Uint8 max_file_size)
	Add support for multiple byte order. More...

	~CWriteDB_Column ()
	Destructor. More...

void	RenameSingle ()
	Rename files to single-volume names. More...

void	RenameFileIndex (unsigned int num_digits)

void	Close ()
	Flush data to disk and close all associated files. More...

bool	CanFit (int bytes) const
	Tests whether there is room for a given blob. More...

void	ListFiles (vector< string > &files, bool skip_empty) const
	List Filenames. More...

void	AddBlob (const CBlastDbBlob &blob)
	Add a blob to the column. More...

void	AddBlob (const CBlastDbBlob &blob, const CBlastDbBlob &blob2)

void	AddMetaData (const string &key, const string &value)
	Add meta data to the column. 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

Private Attributes
CRef< CWriteDB_ColumnIndex >	m_IFile
	Index file, contains meta data and samples of the key/oid pairs. More...

CRef< CWriteDB_ColumnData >	m_DFile
	Data file, contains one record for each key/oid pair, in big and small endian. More...

bool	m_UseBothByteOrder
	Support for multiple byte order. More...

CRef< CWriteDB_ColumnData >	m_DFile2

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

CWriteDB_Column class.

This manages construction of a WriteDB column, which maps OIDs to blob data.

Definition at line 224 of file writedb_column.hpp.

Member Typedef Documentation

◆ TColumnMeta

typedef map<string, string> CWriteDB_Column::TColumnMeta

Type used for database column meta-data.

Definition at line 227 of file writedb_column.hpp.

Constructor & Destructor Documentation

◆ CWriteDB_Column()

CWriteDB_Column::CWriteDB_Column	(	const string &	dbname,
		const string &	extn1,
		const string &	extn2,
		int	index,
		const string &	title,
		const TColumnMeta &	meta,
		Uint8	max_file_size
	)

Construct WriteDB style database column.

Parameters

dbname	Base of filename.
extn1	Extension used for index file.
extn2	Extension used for data file in big endian.
index	Volume index.
title	Title of this column.
meta	User-defined meta data for this file.

Definition at line 45 of file writedb_column.cpp.

References dbname(), m_DFile, m_IFile, and CRef< C, Locker >::Reset().

◆ ~CWriteDB_Column()

CWriteDB_Column::~CWriteDB_Column ( )

Destructor.

Definition at line 80 of file writedb_column.cpp.

Member Function Documentation

◆ AddBlob() [1/2]

void CWriteDB_Column::AddBlob ( const CBlastDbBlob & blob )

Add a blob to the column.

The data described by `blob' is added to the column. If the blob is empty, no data is stored but the OID is incremented.

Parameters

blob	The blob to add to the column.

Definition at line 93 of file writedb_column.cpp.

References m_DFile, m_IFile, CWriteDB_ColumnData::WriteBlob(), and CWriteDB_ColumnIndex::WriteBlobIndex().

Referenced by CWriteDB_ColumnBuilder::AddBlob(), and AddBlob().

◆ AddBlob() [2/2]

void CWriteDB_Column::AddBlob	(	const CBlastDbBlob &	blob,
		const CBlastDbBlob &	blob2
	)

Definition at line 103 of file writedb_column.cpp.

References AddBlob(), m_DFile2, m_UseBothByteOrder, and CWriteDB_ColumnData::WriteBlob().

◆ AddByteOrder()

void CWriteDB_Column::AddByteOrder	(	const string &	dbname,
		const string &	extn,
		int	index,
		Uint8	max_file_size
	)

Add support for multiple byte order.

Parameters

dbname	Base of filename.
extn	Extension used for index file.
index	Volume index.

Definition at line 68 of file writedb_column.cpp.

References dbname(), m_DFile2, m_UseBothByteOrder, and CRef< C, Locker >::Reset().

◆ AddMetaData()

void CWriteDB_Column::AddMetaData	(	const string &	key,
		const string &	value
	)

Add meta data to the column.

In addition to normal blob data, database columns can store a `dictionary' of user-defined metadata in key/value form. This method adds one such key/value pair to the column. Specifying a key a second time causes replacement of the previous value. Using this mechanism to store large amounts of data may have a negative impact on performance.

Parameters

key	Key string.
value	Value string.

Definition at line 135 of file writedb_column.cpp.

References CWriteDB_ColumnIndex::AddMetaData(), ncbi::grid::netcache::search::fields::key, m_IFile, and rapidjson::value.

Referenced by CWriteDB_ColumnBuilder::AddMetaData().

◆ CanFit()

bool CWriteDB_Column::CanFit ( int bytes ) const

Tests whether there is room for a given blob.

Parameters

bytes Size of the blob that would be added.

Returns: Returns true if the IDs can fit into the volume.

Definition at line 116 of file writedb_column.cpp.

References CWriteDB_ColumnIndex::CanFit(), CWriteDB_ColumnData::CanFit(), m_DFile, m_IFile, and ncbi::grid::netcache::search::fields::size.

◆ Close()

void CWriteDB_Column::Close ( void )

Flush data to disk and close all associated files.

Definition at line 109 of file writedb_column.cpp.

References CWriteDB_File::Close(), m_DFile, m_DFile2, m_IFile, and m_UseBothByteOrder.

Referenced by CWriteDB_ColumnBuilder::Close().

◆ ListFiles()

void CWriteDB_Column::ListFiles	(	vector< string > &	files,
		bool	skip_empty
	)		const

List Filenames.

Returns a list of the files constructed by this class; the returned list may not be complete until Close() has been called. The list is not cleared; instead names are appended to existing contents.

Parameters

files The set of resolved database path names.

Definition at line 84 of file writedb_column.cpp.

References CWriteDB_ColumnData::Empty(), CWriteDB_File::GetFilename(), m_DFile, m_DFile2, m_IFile, and m_UseBothByteOrder.

Referenced by CWriteDB_ColumnBuilder::ListFiles().

◆ RenameFileIndex()

void CWriteDB_Column::RenameFileIndex ( unsigned int num_digits )

Definition at line 128 of file writedb_column.cpp.

References m_DFile, m_DFile2, m_IFile, m_UseBothByteOrder, and CWriteDB_File::RenameFileIndex().

◆ RenameSingle()

void CWriteDB_Column::RenameSingle ( )

Rename files to single-volume names.

When volume component files are generated by WriteDB, the names include a volume index. This method renames the files to names that do not include the volume index. This method should not be called until after Close() is called.

Definition at line 121 of file writedb_column.cpp.

References m_DFile, m_DFile2, m_IFile, m_UseBothByteOrder, and CWriteDB_File::RenameSingle().

Referenced by CWriteDB_ColumnBuilder::Close().

Member Data Documentation

◆ m_DFile

CRef<CWriteDB_ColumnData> CWriteDB_Column::m_DFile

private

Data file, contains one record for each key/oid pair, in big and small endian.

Definition at line 313 of file writedb_column.hpp.

Referenced by AddBlob(), CanFit(), Close(), CWriteDB_Column(), ListFiles(), RenameFileIndex(), and RenameSingle().

◆ m_DFile2

CRef<CWriteDB_ColumnData> CWriteDB_Column::m_DFile2

private

Definition at line 317 of file writedb_column.hpp.

Referenced by AddBlob(), AddByteOrder(), Close(), ListFiles(), RenameFileIndex(), and RenameSingle().

◆ m_IFile

CRef<CWriteDB_ColumnIndex> CWriteDB_Column::m_IFile

private

Index file, contains meta data and samples of the key/oid pairs.

Definition at line 310 of file writedb_column.hpp.

Referenced by AddBlob(), AddMetaData(), CanFit(), Close(), CWriteDB_Column(), ListFiles(), RenameFileIndex(), and RenameSingle().

◆ m_UseBothByteOrder

bool CWriteDB_Column::m_UseBothByteOrder

private

Support for multiple byte order.

Definition at line 316 of file writedb_column.hpp.

Referenced by AddBlob(), AddByteOrder(), Close(), ListFiles(), RenameFileIndex(), and RenameSingle().

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

src/objtools/blast/seqdb_writer/writedb_column.hpp
src/objtools/blast/seqdb_writer/writedb_column.cpp

Public Types

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TColumnMeta

Constructor & Destructor Documentation

◆ CWriteDB_Column()

◆ ~CWriteDB_Column()

Member Function Documentation

◆ AddBlob() [1/2]

◆ AddBlob() [2/2]

◆ AddByteOrder()

◆ AddMetaData()

◆ CanFit()

◆ Close()

◆ ListFiles()

◆ RenameFileIndex()

◆ RenameSingle()

Member Data Documentation

◆ m_DFile

◆ m_DFile2

◆ m_IFile

◆ m_UseBothByteOrder