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

Inheritance diagram for CWriteDB_File:

Collaboration diagram for CWriteDB_File:

Public Member Functions
	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

Static Public Member Functions
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)

Protected Types
typedef ofstream	TFile
	Underlying 'output file' type used here. More...

Protected Member Functions
Uint8	x_DefaultByteLimit ()
	The default value for max_file_size. More...

virtual void	x_Flush ()=0
	This should flush any unwritten data to disk. 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
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...

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 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...

Detailed Description

CWriteDB_IndexFile class.

This manufactures blast database index files from input data.

Definition at line 57 of file writedb_files.hpp.

Member Typedef Documentation

◆ TFile

typedef ofstream CWriteDB_File::TFile

protected

Underlying 'output file' type used here.

Definition at line 167 of file writedb_files.hpp.

Constructor & Destructor Documentation

◆ CWriteDB_File()

CWriteDB_File::CWriteDB_File	(	const string &	basename,
		const string &	extension,
		int	index,
		Uint8	max_file_size,
		bool	always_create
	)

Constructor.

The filename is constructed from basename, extension, and index, but might be changed if the RenameSingle() method is called. If zero is specified for maximum file size, a default size is provided by this class. The maximum file size is not enforced by this class, instead each derived class must do its own enforcement.

Parameters

basename	Database base name, shared by all files. [in]
extension	File name extension for this file. [in]
index	Volume index used in filename. [in]
max_file_size	File size limit (in bytes). [in]
always_create	If true the file will be created now. [in]

Definition at line 158 of file writedb_files.cpp.

References _ASSERT, Create(), m_MaxFileSize, m_Nul, m_Offset, m_UseIndex, x_DefaultByteLimit(), and x_MakeFileName().

Member Function Documentation

◆ Close()

void CWriteDB_File::Close ( void )

Close the file, flushing any remaining data to disk.

Definition at line 259 of file writedb_files.cpp.

References m_Created, m_RealFile, and x_Flush().

Referenced by CWriteDB_GiMask::AddGiMask(), CWriteDB_Isam::Close(), CWriteDB_Column::Close(), CWriteDB_GiMask::Close(), CWriteDB_Volume::Close(), and CWriteDB_OidList::Close().

◆ Create()

void CWriteDB_File::Create ( void )

Create and open the file.

This method must be called before the first time that data is written to the file. If the constructor is passed 'true' for always_create, this method will be called during construction. It is an error to call this method more than once (including via the constructor) or to not call it but to call Write. The rationale for making this explicit is to permit some files to be created optionally, such as ISAM files, which should only be created if the corresponding ID types are found.

Definition at line 197 of file writedb_files.cpp.

References _ASSERT, m_Created, m_Fname, m_RealFile, and out().

Referenced by CWriteDB_GiMaskOffset::AddGIs(), CWriteDB_GiMaskIndex::AddGIs(), CWriteDB_File(), CWriteDB_ColumnData::WriteBlob(), CWriteDB_GiMaskData::WriteMask(), CWriteDB_OidList::x_CreateMaskFile(), CWriteDB_IsamIndex::x_Flush(), CWriteDB_ColumnData::x_Flush(), CWriteDB_ColumnIndex::x_Flush(), and CWriteDB_GiIndex::x_Flush().

◆ GetFilename()

const string& CWriteDB_File::GetFilename ( void ) const

inline

Get the current filename for this file.

The filename is returned. The data returned by this method reflects changes made by RenameSingle(), so it is probably best to call it after that method has been called (if it will be called).

Returns: The filename.

Definition at line 157 of file writedb_files.hpp.

References m_Fname.

Referenced by CWriteDB_Isam::ListFiles(), CWriteDB_GiMask::ListFiles(), CWriteDB_Volume::ListFiles(), CWriteDB_Column::ListFiles(), and CWriteDB_Volume::RenameFileIndex().

◆ MakeShortName()

string CWriteDB_File::MakeShortName	(	const string &	base,
		int	index
	)

static

Construct the short name for a volume.

Volume names consist of the database base name, ".", and the volume index in decimal. The volume index is normally two digits, but if more than 100 volumes are needed, the filename will use three or more index digits as needed.

Parameters

base	Base name to use.
index	Volume index.

Returns: A short name.

Definition at line 235 of file writedb_files.cpp.

Referenced by CWriteDB_Volume::CWriteDB_Volume(), CMakeProfileDBApp::x_InitRPSDbInfo(), and x_MakeFileName().

◆ RenameFileIndex()

void CWriteDB_File::RenameFileIndex ( unsigned int num_digits )

virtual

Definition at line 279 of file writedb_files.cpp.

References _ASSERT, CDirEntry::fRF_Overwrite, i, log10(), m_BaseName, m_Extension, m_Fname, m_Index, and CDirEntry::Rename().

Referenced by CWriteDB_Isam::RenameFileIndex(), CWriteDB_Column::RenameFileIndex(), and CWriteDB_Volume::RenameFileIndex().

◆ RenameSingle()

void CWriteDB_File::RenameSingle ( )

virtual

Rename this file, disincluding the volume index.

Definition at line 267 of file writedb_files.cpp.

References _ASSERT, CDirEntry::fRF_Overwrite, m_Fname, m_UseIndex, CDirEntry::Rename(), and x_MakeFileName().

Referenced by CWriteDB_GiMask::Close(), CWriteDB_Isam::RenameSingle(), CWriteDB_Column::RenameSingle(), and CWriteDB_Volume::RenameSingle().

◆ Write() [1/2]

unsigned int CWriteDB_File::Write	(	const char *	data,
		int	length
	)

Definition at line 224 of file writedb_files.cpp.

References _ASSERT, data, m_Created, m_Offset, and m_RealFile.

◆ Write() [2/2]

unsigned int CWriteDB_File::Write ( const CTempString & data )

Write contents of a string to the file.

Parameters

data	Data to write.

Returns: File offset after write.

Definition at line 204 of file writedb_files.cpp.

References _ASSERT, data, m_Created, m_Offset, and m_RealFile.

Referenced by CWriteDB_GiMaskOffset::AddGIs(), CWriteDB_GiMaskIndex::AddGIs(), CWriteDB_HeaderFile::AddSequence(), CWriteDB_SequenceFile::AddSequence(), CWriteDB_ColumnData::WriteBlob(), CWriteDB_GiMaskData::WriteMask(), WriteWithNull(), CWriteDB_GiMaskIndex::x_BuildHeaderFields(), CWriteDB_OidList::x_CreateMaskFile(), CWriteDB_ColumnIndex::x_Flush(), and CWriteDB_IsamIndex::x_FlushStringIndex().

◆ WriteInt4()

unsigned int CWriteDB_File::WriteInt4 ( int data )

inline

Write an Int4 (in bigendian order) to the file.

Parameters

data	String to write.

Returns: File offset after write.

Definition at line 103 of file writedb_files.hpp.

References data, m_Offset, m_RealFile, and s_WriteInt4().

Referenced by CWriteDB_OidList::x_CreateMaskFile(), CWriteDB_GiIndex::x_Flush(), CWriteDB_IsamIndex::x_FlushNumericIndex(), CWriteDB_IsamIndex::x_FlushStringIndex(), and CWriteDB_IsamIndex::x_WriteHeader().

◆ WriteInt8()

unsigned int CWriteDB_File::WriteInt8 ( Int8 data )

inline

Write an Int8 (in bigendian order) to the file.

Parameters

data	String to write.

Returns: File offset after write.

Definition at line 113 of file writedb_files.hpp.

References data, m_Offset, m_RealFile, and s_WriteInt8BE().

Referenced by CWriteDB_IsamIndex::x_FlushNumericIndex().

◆ WriteWithNull()

unsigned int CWriteDB_File::WriteWithNull ( const CTempString & data )

inline

Write contents of a string to the file, appending a NUL.

Parameters

data	String to write.

Returns: File offset after write.

Definition at line 123 of file writedb_files.hpp.

References data, m_Nul, and Write().

Referenced by CWriteDB_SequenceFile::AddSequence(), and CWriteDB_SequenceFile::CWriteDB_SequenceFile().

◆ x_DefaultByteLimit()

Uint8 CWriteDB_File::x_DefaultByteLimit ( )

inlineprotected

The default value for max_file_size.

Returns: The max file size used if otherwise unspecified.

Definition at line 174 of file writedb_files.hpp.

Referenced by CWriteDB_File().

◆ x_Flush()

virtual void CWriteDB_File::x_Flush ( )

protectedpure virtual

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.

Implemented in CWriteDB_OidList, CWriteDB_GiIndex, CWriteDB_GiMaskOffset, CWriteDB_GiMaskData, CWriteDB_ColumnIndex, CWriteDB_ColumnData, CWriteDB_FileAutoFlush, CWriteDB_IsamData, CWriteDB_IsamIndex, CWriteDB_SequenceFile, CWriteDB_HeaderFile, and CWriteDB_IndexFile.

Referenced by Close().

◆ x_MakeFileName()

void CWriteDB_File::x_MakeFileName ( )

protected

Build the filename for this file.

Definition at line 247 of file writedb_files.cpp.

References m_BaseName, m_Extension, m_Fname, m_Index, m_UseIndex, and MakeShortName().

Referenced by CWriteDB_File(), and RenameSingle().

Member Data Documentation

◆ m_BaseName

string CWriteDB_File::m_BaseName

protected

Database base name for all files.

Definition at line 194 of file writedb_files.hpp.

Referenced by RenameFileIndex(), x_MakeFileName(), and CWriteDB_IndexFile::x_MakeLmdbName().

◆ m_Created

bool CWriteDB_File::m_Created

protected

True if the file has already been opened.

Definition at line 164 of file writedb_files.hpp.

Referenced by CWriteDB_GiMaskOffset::AddGIs(), CWriteDB_GiMaskIndex::AddGIs(), Close(), Create(), CWriteDB_IsamIndex::Empty(), Write(), CWriteDB_ColumnData::WriteBlob(), CWriteDB_GiMaskData::WriteMask(), CWriteDB_IndexFile::x_Flush(), CWriteDB_ColumnData::x_Flush(), and CWriteDB_ColumnIndex::x_Flush().

◆ m_Extension

string CWriteDB_File::m_Extension

protected

File extension for this file.

Definition at line 195 of file writedb_files.hpp.

Referenced by RenameFileIndex(), and x_MakeFileName().

◆ m_Fname

string CWriteDB_File::m_Fname

protected

Current filename for output file.

Definition at line 203 of file writedb_files.hpp.

Referenced by Create(), GetFilename(), RenameFileIndex(), RenameSingle(), and x_MakeFileName().

◆ m_Index

int CWriteDB_File::m_Index

protected

Volume index.

Definition at line 196 of file writedb_files.hpp.

Referenced by RenameFileIndex(), CWriteDB_IndexFile::x_Flush(), and x_MakeFileName().

◆ m_MaxFileSize

Uint8 CWriteDB_File::m_MaxFileSize

protected

Maximum file size in bytes.

Definition at line 198 of file writedb_files.hpp.

Referenced by CWriteDB_IndexFile::CanFit(), CWriteDB_ColumnIndex::CanFit(), CWriteDB_IsamIndex::CanFit(), CWriteDB_GiMaskData::CanFit(), CWriteDB_HeaderFile::CanFit(), CWriteDB_ColumnData::CanFit(), CWriteDB_SequenceFile::CanFit(), and CWriteDB_File().

◆ m_Nul

string CWriteDB_File::m_Nul

protected

For convenience, a string containing one NUL character.

Definition at line 170 of file writedb_files.hpp.

Referenced by CWriteDB_File(), WriteWithNull(), and CWriteDB_IndexFile::x_Flush().

◆ m_Offset

unsigned int CWriteDB_File::m_Offset

protected

Stream position.

Definition at line 197 of file writedb_files.hpp.

Referenced by CWriteDB_SequenceFile::CanFit(), CWriteDB_File(), Write(), WriteInt4(), and WriteInt8().

◆ m_RealFile

TFile CWriteDB_File::m_RealFile

protected

Actual stream implementing the output file.

Definition at line 204 of file writedb_files.hpp.

Referenced by Close(), Create(), Write(), WriteInt4(), WriteInt8(), and CWriteDB_IndexFile::x_Flush().

◆ m_UseIndex

bool CWriteDB_File::m_UseIndex

protected

True if filenames should use volume index.

Definition at line 202 of file writedb_files.hpp.

Referenced by CWriteDB_File(), RenameSingle(), and x_MakeFileName().

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

include/objtools/blast/seqdb_writer/writedb_files.hpp
src/objtools/blast/seqdb_writer/writedb_files.cpp

Public Member Functions

Static Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TFile

Constructor & Destructor Documentation

◆ CWriteDB_File()

Member Function Documentation

◆ Close()

◆ Create()

◆ GetFilename()

◆ MakeShortName()

◆ RenameFileIndex()

◆ RenameSingle()

◆ Write() [1/2]

◆ Write() [2/2]

◆ WriteInt4()

◆ WriteInt8()

◆ WriteWithNull()

◆ x_DefaultByteLimit()

◆ x_Flush()

◆ x_MakeFileName()

Member Data Documentation

◆ m_BaseName

◆ m_Created

◆ m_Extension

◆ m_Fname

◆ m_Index

◆ m_MaxFileSize

◆ m_Nul

◆ m_Offset

◆ m_RealFile

◆ m_UseIndex