Search Toolkit Book for CWriteDB_GiMaskData

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

Inheritance diagram for CWriteDB_GiMaskData:

Collaboration diagram for CWriteDB_GiMaskData:

Public Types
typedef vector< pair< TSeqPos, TSeqPos > >	TPairVector

typedef pair< int, int >	TOffset

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_GiMaskData (const string &maskname, const string &extn, int index, Uint8 max_file_size, bool le=false)
	Constructor for an gimask data file. More...

	~CWriteDB_GiMaskData ()
	Destructor. More...

void	WriteMask (const TPairVector &mask)
	Write a new data blob. More...

int	GetIndex () const
	Get current index. More...

TOffset	GetOffset () const
	Get current index/offset pair. More...

bool	CanFit (int num_masks) const
	Tests whether there is room for another batch. 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 ()
	Flush any stored data. More...

Private Attributes
Uint8	m_DataLength
	Length of data written so far. More...

bool	m_UseLE
	Use little endian? More...

int	m_Index
	Current index. More...

Additional Inherited Members
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

CWriteDB_GiMaskData class.

Manufacture gi based mask data files from input data.

Definition at line 56 of file writedb_gimask.hpp.

Member Typedef Documentation

◆ TOffset

typedef pair<int, int> CWriteDB_GiMaskData::TOffset

Definition at line 59 of file writedb_gimask.hpp.

◆ TPairVector

typedef vector< pair<TSeqPos, TSeqPos> > CWriteDB_GiMaskData::TPairVector

Definition at line 58 of file writedb_gimask.hpp.

Constructor & Destructor Documentation

◆ CWriteDB_GiMaskData()

CWriteDB_GiMaskData::CWriteDB_GiMaskData	(	const string &	maskname,
		const string &	extn,
		int	index,
		Uint8	max_file_size,
		bool	le = `false`
	)

Constructor for an gimask data file.

Parameters

maskname	Database name (same for all volumes).
extn	File extension to use for index file.
max_file_size	Maximum size of any generated file in bytes.
le	Use little endian format

Definition at line 279 of file writedb_gimask.cpp.

◆ ~CWriteDB_GiMaskData()

CWriteDB_GiMaskData::~CWriteDB_GiMaskData ( )

inline

Destructor.

Definition at line 74 of file writedb_gimask.hpp.

Member Function Documentation

◆ CanFit()

bool CWriteDB_GiMaskData::CanFit ( int num_masks ) const

inline

Tests whether there is room for another batch.

Parameters

the	number of masks to be added. [in]

Returns: Return TRUE if masks can fit into the volume.

Definition at line 96 of file writedb_gimask.hpp.

References m_DataLength, and CWriteDB_File::m_MaxFileSize.

Referenced by CWriteDB_GiMask::AddGiMask().

◆ GetIndex()

int CWriteDB_GiMaskData::GetIndex ( void ) const

inline

Get current index.

Definition at line 81 of file writedb_gimask.hpp.

References m_Index.

Referenced by CWriteDB_GiMask::AddGiMask(), and CWriteDB_GiMask::Close().

◆ GetOffset()

TOffset CWriteDB_GiMaskData::GetOffset ( void ) const

inline

Get current index/offset pair.

Returns: The current volume index and offset in byte

Definition at line 88 of file writedb_gimask.hpp.

References m_DataLength, and m_Index.

Referenced by CWriteDB_GiMask::AddGiMask().

◆ WriteMask()

void CWriteDB_GiMaskData::WriteMask ( const TPairVector & mask )

Write a new data blob.

Parameters

mask	Mask data to write.

Definition at line 290 of file writedb_gimask.cpp.

References CWriteDB_File::Create(), data, ITERATE, CWriteDB_File::m_Created, m_DataLength, m_UseLE, mask, compile_time_bits::range(), and CWriteDB_File::Write().

Referenced by CWriteDB_GiMask::AddGiMask().

◆ x_Flush()

void CWriteDB_GiMaskData::x_Flush ( void )

inlineprivatevirtual

Flush any stored data.

Implements CWriteDB_File.

Definition at line 112 of file writedb_gimask.hpp.

Member Data Documentation

◆ m_DataLength

Uint8 CWriteDB_GiMaskData::m_DataLength

private

Length of data written so far.

Definition at line 103 of file writedb_gimask.hpp.

Referenced by CanFit(), GetOffset(), and WriteMask().

◆ m_Index

int CWriteDB_GiMaskData::m_Index

private

Current index.

Definition at line 109 of file writedb_gimask.hpp.

Referenced by GetIndex(), and GetOffset().

◆ m_UseLE

bool CWriteDB_GiMaskData::m_UseLE

private

Use little endian?

Definition at line 106 of file writedb_gimask.hpp.

Referenced by WriteMask().

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

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

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TOffset

◆ TPairVector

Constructor & Destructor Documentation

◆ CWriteDB_GiMaskData()

◆ ~CWriteDB_GiMaskData()

Member Function Documentation

◆ CanFit()

◆ GetIndex()

◆ GetOffset()

◆ WriteMask()

◆ x_Flush()

Member Data Documentation

◆ m_DataLength

◆ m_Index

◆ m_UseLE