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

Inheritance diagram for CWriteDB_Isam:

Collaboration diagram for CWriteDB_Isam:

Public Types
typedef EWriteDBIsamType	EIsamType
	Type of identifier stored in this ISAM index. More...

typedef vector< CRef< CSeq_id > >	TIdList
	Type used for lists of sequence identifiers. More...

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_Isam (EIsamType itype, const string &dbname, bool protein, int index, Uint8 max_file_size, bool sparse)
	Constructor for an ISAM index file. More...

	~CWriteDB_Isam ()
	Destructor. More...

void	AddIds (int oid, const TIdList &ids)
	Add sequence IDs to the index file. More...

void	AddPig (int oid, int pig)
	Set PIG for a protein sequence. More...

void	AddHash (int oid, int hash)
	Set a sequence's hash value. More...

void	RenameSingle ()
	Rename files to single-volume names. More...

void	RenameFileIndex (unsigned int num_digits)

void	Close ()
	Flush data to disk and close all associated files. More...

bool	CanFit (int num)
	Tests whether there is room for a given number of IDs. 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 Attributes
CRef< CWriteDB_IsamIndex >	m_IFile
	Index file, contains meta data and samples of the key/oid pairs. More...

CRef< CWriteDB_IsamData >	m_DFile
	Data file, contains one record for each key/oid pair. More...

Additional Inherited Members
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

CWriteDB_Isam class.

This manufactures isam indices.

Definition at line 401 of file writedb_isam.hpp.

Member Typedef Documentation

◆ EIsamType

typedef EWriteDBIsamType CWriteDB_Isam::EIsamType

Type of identifier stored in this ISAM index.

Definition at line 404 of file writedb_isam.hpp.

◆ TIdList

typedef vector< CRef<CSeq_id> > CWriteDB_Isam::TIdList

Type used for lists of sequence identifiers.

Definition at line 407 of file writedb_isam.hpp.

Constructor & Destructor Documentation

◆ CWriteDB_Isam()

CWriteDB_Isam::CWriteDB_Isam	(	EIsamType	itype,
		const string &	dbname,
		bool	protein,
		int	index,
		Uint8	max_file_size,
		bool	sparse
	)

Constructor for an ISAM index file.

Parameters

itype	Type (GI, PIG, or string). [in]
dbname	Database name (same for all volumes). [in]
protein	True for protein, false for nucleotide. [in]
index	Index of the associated volume. [in]
max_file_size	Maximum size of any generated file in bytes. [in]
sparse	Set to true if sparse mode should be used. [in]

Definition at line 98 of file writedb_isam.cpp.

References dbname(), m_DFile, m_IFile, and CRef< C, Locker >::Reset().

◆ ~CWriteDB_Isam()

CWriteDB_Isam::~CWriteDB_Isam ( )

Destructor.

Definition at line 120 of file writedb_isam.cpp.

Member Function Documentation

◆ AddHash()

void CWriteDB_Isam::AddHash	(	int	oid,
		int	hash
	)

Set a sequence's hash value.

The sequence hash is a hash of a sequence. This adds that hash for the purpose of building an ISAM file mapping hash values to OIDs.

Parameters

oid	OID of the sequence. [in]
hash	Sequence hash for this sequence. [in]

Definition at line 139 of file writedb_isam.cpp.

References CWriteDB_IsamIndex::AddHash(), and m_IFile.

Referenced by CWriteDB_Volume::WriteSequence().

◆ AddIds()

void CWriteDB_Isam::AddIds	(	int	oid,
		const TIdList &	ids
	)

Add sequence IDs to the index file.

If this is a GI index, GIs are collected and added to an internal list. If this is a string index, various strings are constructed from the identifiers and added to a sorting class. How many and what kind of strings are indexed depends on whether the "sparse" flag is specified.

Parameters

oid	OID of the sequence. [in]
ids	List of sequence identifiers. [in]

Definition at line 129 of file writedb_isam.cpp.

References CWriteDB_IsamIndex::AddIds(), and m_IFile.

Referenced by CWriteDB_Volume::WriteSequence().

◆ AddPig()

void CWriteDB_Isam::AddPig	(	int	oid,
		int	pig
	)

Set PIG for a protein sequence.

The PIG identifier corresponds to a specific string of protein residues rather than to a single defline or GI, and as such is not treated as a true sequence identifier. Each PIG will be associated with one OID in a non-redundant protein database.

Parameters

oid	OID of the sequence. [in]
pig	PIG identifier for this sequence. [in]

Definition at line 134 of file writedb_isam.cpp.

References CWriteDB_IsamIndex::AddPig(), and m_IFile.

Referenced by CWriteDB_Volume::WriteSequence().

◆ CanFit()

bool CWriteDB_Isam::CanFit ( int num )

Tests whether there is room for a given number of IDs.

This returns true if the specified number of identifiers can be added to this volume without overflowing the maximum file size. For strings, the estimating technique used is very rough (to avoid excess computation) and will tend to return false several disk blocks before the ISAM file actually reaches the maximum file size. This is done for performance reasons.

Parameters

num	Number of IDs that would be added. [in]

Returns: Returns true if the IDs can fit into the volume.

Definition at line 124 of file writedb_isam.cpp.

References CWriteDB_IsamIndex::CanFit(), and m_IFile.

Referenced by CWriteDB_Volume::WriteSequence().

◆ Close()

void CWriteDB_Isam::Close ( void )

Flush data to disk and close all associated files.

Definition at line 144 of file writedb_isam.cpp.

References CWriteDB_File::Close(), m_DFile, and m_IFile.

Referenced by CWriteDB_Volume::Close().

◆ ListFiles()

void CWriteDB_Isam::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. The list is not cleared; instead names are appended to existing contents.

Parameters

files The set of resolved database path names. [out]

Definition at line 819 of file writedb_isam.cpp.

References CWriteDB_IsamIndex::Empty(), CWriteDB_File::GetFilename(), m_DFile, and m_IFile.

Referenced by CWriteDB_Volume::ListFiles().

◆ RenameFileIndex()

void CWriteDB_Isam::RenameFileIndex ( unsigned int num_digits )

Definition at line 160 of file writedb_isam.cpp.

References m_DFile, m_IFile, and CWriteDB_File::RenameFileIndex().

Referenced by CWriteDB_Volume::RenameFileIndex().

◆ RenameSingle()

void CWriteDB_Isam::RenameSingle ( )

Rename files to single-volume names.

When volume component files are generated by WriteDB, the names include a volume index. This method renames the files to names that do not include the volume index. This method should not be called until after Close() is called.

Definition at line 154 of file writedb_isam.cpp.

References m_DFile, m_IFile, and CWriteDB_File::RenameSingle().

Referenced by CWriteDB_Volume::RenameSingle().

Member Data Documentation

◆ m_DFile

CRef<CWriteDB_IsamData> CWriteDB_Isam::m_DFile

private

Data file, contains one record for each key/oid pair.

Definition at line 505 of file writedb_isam.hpp.

Referenced by Close(), CWriteDB_Isam(), ListFiles(), RenameFileIndex(), and RenameSingle().

◆ m_IFile

CRef<CWriteDB_IsamIndex> CWriteDB_Isam::m_IFile

private

Index file, contains meta data and samples of the key/oid pairs.

Definition at line 502 of file writedb_isam.hpp.

Referenced by AddHash(), AddIds(), AddPig(), CanFit(), Close(), CWriteDB_Isam(), ListFiles(), RenameFileIndex(), and RenameSingle().

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

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

Public Types

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ EIsamType

◆ TIdList

Constructor & Destructor Documentation

◆ CWriteDB_Isam()

◆ ~CWriteDB_Isam()

Member Function Documentation

◆ AddHash()

◆ AddIds()

◆ AddPig()

◆ CanFit()

◆ Close()

◆ ListFiles()

◆ RenameFileIndex()

◆ RenameSingle()

Member Data Documentation

◆ m_DFile

◆ m_IFile