CWriteDB_OidList Class Reference

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

Inheritance diagram for CWriteDB_OidList:

Collaboration diagram for CWriteDB_OidList:

Public Member Functions
	CWriteDB_OidList (const string &dbname, bool protein, int index, Uint8 max_fsize, EOidMaskType mask_type)
	~CWriteDB_OidList ()
void	AddOid (int oid)
void	Close (int total_oids)
	Total num of oids in db or vol. More...
Public Member Functions inherited from CWriteDB_File
	CWriteDB_File (const string &basename, const string &extension, int index, Uint8 max_file_size, bool always_create)
	Constructor. More...
void	Create ()
	Create and open the file. More...
unsigned int	Write (const CTempString &data)
	Write contents of a string to the file. More...
unsigned int	Write (const char *data, int length)
unsigned int	WriteInt4 (int data)
	Write an Int4 (in bigendian order) to the file. More...
unsigned int	WriteInt8 (Int8 data)
	Write an Int8 (in bigendian order) to the file. More...
unsigned int	WriteWithNull (const CTempString &data)
	Write contents of a string to the file, appending a NUL. More...
void	Close ()
	Close the file, flushing any remaining data to disk. More...
virtual void	RenameSingle ()
	Rename this file, disincluding the volume index. More...
virtual void	RenameFileIndex (unsigned int num_digits)
const string &	GetFilename () const
	Get the current filename for this file. 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
void	x_Flush ()
	This should flush any unwritten data to disk. More...
void	x_CreateBitMap (int num_oids)
void	x_CreateMaskFile ()

Private Attributes
EOidMaskType	m_Type
vector< uint32_t >	m_OidList
int	m_TotalOids
uint8_t *	m_Map
size_t	m_MapSize

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 CWriteDB_File
static string	MakeShortName (const string &base, int index)
	Construct the short name for a volume. 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 Types inherited from CWriteDB_File
typedef ofstream	TFile
	Underlying 'output file' type used here. More...
Protected Member Functions inherited from CWriteDB_File
Uint8	x_DefaultByteLimit ()
	The default value for max_file_size. More...
void	x_MakeFileName ()
	Build the filename for this file. More...
Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...
Protected Attributes inherited from CWriteDB_File
bool	m_Created
	True if the file has already been opened. More...
string	m_Nul
	For convenience, a string containing one NUL character. More...
string	m_BaseName
	Database base name for all files. More...
string	m_Extension
	File extension for this file. More...
int	m_Index
	Volume index. More...
unsigned int	m_Offset
	Stream position. More...
Uint8	m_MaxFileSize
	Maximum file size in bytes. More...
bool	m_UseIndex
	True if filenames should use volume index. More...
string	m_Fname
	Current filename for output file. More...
TFile	m_RealFile
	Actual stream implementing the output file. More...

Detailed Description

Definition at line 100 of file writedb_volume.hpp.

Constructor & Destructor Documentation

CWriteDB_OidList()

CWriteDB_OidList::CWriteDB_OidList	(	const string &	dbname,
		bool	protein,
		int	index,
		Uint8	max_fsize,
		EOidMaskType	mask_type
	)

Definition at line 572 of file writedb_volume.cpp.

~CWriteDB_OidList()

CWriteDB_OidList::~CWriteDB_OidList ( )

inline

Definition at line 109 of file writedb_volume.hpp.

References m_Map.

Member Function Documentation

AddOid()

void CWriteDB_OidList::AddOid ( int  oid )

inline

Definition at line 115 of file writedb_volume.hpp.

References m_OidList.

Referenced by CWriteDB_Volume::WriteSequence().

Close()

void CWriteDB_OidList::Close ( int  total_oids )

inline

Total num of oids in db or vol.

Definition at line 119 of file writedb_volume.hpp.

References CWriteDB_File::Close(), and m_TotalOids.

Referenced by CWriteDB_Volume::Close().

x_CreateBitMap()

void CWriteDB_OidList::x_CreateBitMap ( int  num_oids )

private

Definition at line 580 of file writedb_volume.cpp.

References fExcludeModel, ITERATE, m_Map, m_MapSize, m_OidList, m_Type, mask, NCBI_THROW, NULL, offset, and uint8_t.

Referenced by x_Flush().

x_CreateMaskFile()

void CWriteDB_OidList::x_CreateMaskFile ( )

private

Definition at line 630 of file writedb_volume.cpp.

References CWriteDB_File::Create(), m_Map, m_MapSize, m_TotalOids, CWriteDB_File::Write(), and CWriteDB_File::WriteInt4().

Referenced by x_Flush().

x_Flush()

void CWriteDB_OidList::x_Flush ( )

privatevirtual

This should flush any unwritten data to disk.

This method must be implemented by derived classes to flush any unwritten data to disk. In the cases of sequence and header files, it will normally do nothing, because such files are written as the data is available. For index (pin/nin) and ISAM files, this method does most of the disk I/O.

Implements CWriteDB_File.

Definition at line 639 of file writedb_volume.cpp.

References Info(), LOG_POST, m_OidList, m_TotalOids, m_Type, x_CreateBitMap(), and x_CreateMaskFile().

Member Data Documentation

m_Map

uint8_t* CWriteDB_OidList::m_Map

private

Definition at line 131 of file writedb_volume.hpp.

Referenced by x_CreateBitMap(), x_CreateMaskFile(), and ~CWriteDB_OidList().

m_MapSize

size_t CWriteDB_OidList::m_MapSize

private

Definition at line 132 of file writedb_volume.hpp.

Referenced by x_CreateBitMap(), and x_CreateMaskFile().

m_OidList

vector<uint32_t> CWriteDB_OidList::m_OidList

private

Definition at line 129 of file writedb_volume.hpp.

Referenced by AddOid(), x_CreateBitMap(), and x_Flush().

m_TotalOids

int CWriteDB_OidList::m_TotalOids

private

Definition at line 130 of file writedb_volume.hpp.

Referenced by Close(), x_CreateMaskFile(), and x_Flush().

m_Type

EOidMaskType CWriteDB_OidList::m_Type

private

Definition at line 128 of file writedb_volume.hpp.

Referenced by x_CreateBitMap(), and x_Flush().

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

• src/objtools/blast/seqdb_writer/writedb_volume.hpp
• src/objtools/blast/seqdb_writer/writedb_volume.cpp