Search Toolkit Book for CWriteDB_SequenceFile

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

Inheritance diagram for CWriteDB_SequenceFile:

Collaboration diagram for CWriteDB_SequenceFile:

Public Member Functions
	CWriteDB_SequenceFile (const string &dbname, bool protein, int index, Uint8 max_file_size, Uint8 max_letters)
	Constructor. More...

bool	CanFit (int size, int letters)
	Returns true if the specified amount of data would fit. More...

void	AddSequence (const string &sequence, unsigned int &offset, int length)
	Add a protein sequence to this file. More...

void	AddSequence (const string &sequence, const string &ambig, unsigned int &off_seq, unsigned int &off_amb, int length)
	Add a nucleotide sequence to this file. 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
virtual void	x_Flush ()
	Flush unwritten data to the output file. More...

Private Attributes
Uint8	m_Letters
	Letters of sequence data added so far. More...

Uint8	m_BaseLimit
	Limit on letters of sequence data. More...

bool	m_Protein
	True if this is a protein database. 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 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 396 of file writedb_files.hpp.

Constructor & Destructor Documentation

◆ CWriteDB_SequenceFile()

CWriteDB_SequenceFile::CWriteDB_SequenceFile	(	const string &	dbname,
		bool	protein,
		int	index,
		Uint8	max_file_size,
		Uint8	max_letters
	)

Constructor.

Parameters

dbname	Database base name.
protein	True for protein volumes.
index	Index of this volume.
max_file_size	Maximum file size in bytes (or zero).
max_letter	Maximum sequence letters per volume (or zero).

Definition at line 463 of file writedb_files.cpp.

References CWriteDB_File::WriteWithNull().

Member Function Documentation

◆ AddSequence() [1/2]

void CWriteDB_SequenceFile::AddSequence	(	const string &	sequence,
		const string &	ambig,
		unsigned int &	off_seq,
		unsigned int &	off_amb,
		int	length
	)

inline

Add a nucleotide sequence to this file.

This method should only be called in the nucleotide case.

Parameters

sequence	Packed sequence data. [in]
ambig	Packed ambiguity data. [in]
off_seq	Offset of the end of the sequence data. [out]
off_amb	Offset of the end of the ambiguity data. [out]
length	Length of the sequence in letters. [in]

Definition at line 463 of file writedb_files.hpp.

References _ASSERT, ambig(), m_Letters, m_Protein, and CWriteDB_File::Write().

◆ AddSequence() [2/2]

void CWriteDB_SequenceFile::AddSequence	(	const string &	sequence,
		unsigned int &	offset,
		int	length
	)

inline

Add a protein sequence to this file.

This method should only be called in the protein case.

Parameters

sequence	Packed sequence data. [in]
offset	Offset of the end of the sequence data. [out]
length	Length of the sequence in letters. [in]

Definition at line 443 of file writedb_files.hpp.

References _ASSERT, m_Letters, m_Protein, offset, and CWriteDB_File::WriteWithNull().

Referenced by CWriteDB_Volume::WriteSequence().

◆ CanFit()

bool CWriteDB_SequenceFile::CanFit	(	int	size,
		int	letters
	)

inline

Returns true if the specified amount of data would fit.

If the specified amount of data (in bytes) would fit in the file without exceeding the max_file_size, and the specified number of letters would fit without exceeding the maximum letters limit, this method returns true.

Parameters

size	Size of new data in bytes.
letters	Number of sequence letters in new data.

Definition at line 419 of file writedb_files.hpp.

References _ASSERT, m_BaseLimit, m_Letters, CWriteDB_File::m_MaxFileSize, CWriteDB_File::m_Offset, and ncbi::grid::netcache::search::fields::size.

Referenced by CWriteDB_Volume::WriteSequence().

◆ x_Flush()

virtual void CWriteDB_SequenceFile::x_Flush ( void )

inlineprivatevirtual

Flush unwritten data to the output file.

Implements CWriteDB_File.

Definition at line 479 of file writedb_files.hpp.

Member Data Documentation

◆ m_BaseLimit

Uint8 CWriteDB_SequenceFile::m_BaseLimit

private

Limit on letters of sequence data.

Definition at line 486 of file writedb_files.hpp.

Referenced by CanFit().

◆ m_Letters

Uint8 CWriteDB_SequenceFile::m_Letters

private

Letters of sequence data added so far.

Definition at line 485 of file writedb_files.hpp.

Referenced by AddSequence(), and CanFit().

◆ m_Protein

bool CWriteDB_SequenceFile::m_Protein

private

True if this is a protein database.

Definition at line 488 of file writedb_files.hpp.

Referenced by AddSequence().

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

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ CWriteDB_SequenceFile()

Member Function Documentation

◆ AddSequence() [1/2]

◆ AddSequence() [2/2]

◆ CanFit()

◆ x_Flush()

Member Data Documentation

◆ m_BaseLimit

◆ m_Letters

◆ m_Protein