Search Toolkit Book for CWriteDB_ColumnBuilder

Builder for BlastDb format column files. More...

#include <objtools/blast/seqdb_writer/writedb.hpp>

Inheritance diagram for CWriteDB_ColumnBuilder:

Collaboration diagram for CWriteDB_ColumnBuilder:

Public Member Functions
	CWriteDB_ColumnBuilder (const string &title, const string &basename, char file_id='a')
	Construct a BlastDb format column. More...

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

	~CWriteDB_ColumnBuilder ()
	Destructor. More...

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

void	Close ()
	Complete and close the column files. More...

void	ListFiles (vector< string > &files) const
	List Filenames. 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 Member Functions
	CWriteDB_ColumnBuilder (const CWriteDB_ColumnBuilder &)
	Prevent the copy constructor. More...

CWriteDB_ColumnBuilder &	operator= (CWriteDB_ColumnBuilder &)
	Prevent copy assignment. More...

Private Attributes
class CWriteDB_Column *	m_Impl
	Implementation object. More...

Additional Inherited Members
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...

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

Builder for BlastDb format column files.

This class supports construction of BlastDb format column files outside of BlastDb volumes. To build column files as part of a volume, use CWriteDB's column related methods. This class is an interface to the column file construction functionality, but is intended for data not associated with specific BlastDb volumes. Columns built with CWriteDB::CreateColumn participate in WriteDB's other volume-oriented policies such as volume breaking to enforce file size limits, and compatibility with component file naming conventions for CWriteDB and CSeqDB.

Definition at line 540 of file writedb.hpp.

Constructor & Destructor Documentation

◆ CWriteDB_ColumnBuilder() [1/2]

CWriteDB_ColumnBuilder::CWriteDB_ColumnBuilder	(	const string &	title,
		const string &	basename,
		char	file_id = `'a'`
	)

Construct a BlastDb format column.

The `title' string names this column, and can be used to uniquely identify it in cases where the file name must be chosen arbitrarily. This version chooses file extensions using a basic pattern (<name>.x?[ab]) designed to not conflict with columns created by WriteDB as part of a volume. The file_id character must be alphanumeric.

Parameters

title	Internal name of this column.
basename	Column filename (minus extension).
file_id	Identifier for this column.

Definition at line 370 of file writedb_column.cpp.

References _ASSERT, basename, isalnum(), and m_Impl.

◆ ~CWriteDB_ColumnBuilder()

CWriteDB_ColumnBuilder::~CWriteDB_ColumnBuilder ( )

Destructor.

Definition at line 395 of file writedb_column.cpp.

References m_Impl.

◆ CWriteDB_ColumnBuilder() [2/2]

CWriteDB_ColumnBuilder::CWriteDB_ColumnBuilder ( const CWriteDB_ColumnBuilder & )

private

Prevent the copy constructor.

Member Function Documentation

◆ AddBlob()

void CWriteDB_ColumnBuilder::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 405 of file writedb_column.cpp.

References CWriteDB_Column::AddBlob(), and m_Impl.

◆ AddMetaData()

void CWriteDB_ColumnBuilder::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 410 of file writedb_column.cpp.

References CWriteDB_Column::AddMetaData(), ncbi::grid::netcache::search::fields::key, m_Impl, and value.

◆ Close()

void CWriteDB_ColumnBuilder::Close ( void )

Complete and close the column files.

Definition at line 415 of file writedb_column.cpp.

References CWriteDB_Column::Close(), m_Impl, and CWriteDB_Column::RenameSingle().

◆ ListFiles()

void CWriteDB_ColumnBuilder::ListFiles ( vector< string > & files ) 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.

Parameters

files The list of files created for this column.

Definition at line 400 of file writedb_column.cpp.

References CWriteDB_Column::ListFiles(), and m_Impl.

Referenced by s_WrapUpColumn().

◆ operator=()

CWriteDB_ColumnBuilder& CWriteDB_ColumnBuilder::operator= ( CWriteDB_ColumnBuilder & )

private

Prevent copy assignment.

Member Data Documentation

◆ m_Impl

class CWriteDB_Column* CWriteDB_ColumnBuilder::m_Impl

private

Implementation object.

Definition at line 605 of file writedb.hpp.

Referenced by AddBlob(), AddMetaData(), Close(), CWriteDB_ColumnBuilder(), ListFiles(), and ~CWriteDB_ColumnBuilder().

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

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

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CWriteDB_ColumnBuilder() [1/2]

◆ ~CWriteDB_ColumnBuilder()

◆ CWriteDB_ColumnBuilder() [2/2]

Member Function Documentation

◆ AddBlob()

◆ AddMetaData()

◆ Close()

◆ ListFiles()

◆ operator=()

Member Data Documentation

◆ m_Impl