Search Toolkit Book for CWriteDB_GiMask

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

Inheritance diagram for CWriteDB_GiMask:

Collaboration diagram for CWriteDB_GiMask:

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

typedef pair< int, int >	TOffset

typedef vector< pair< TGi, TOffset > >	TGiOffset

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_GiMask (const string &maskname, const string &desc, Uint8 max_file_size)
	Construct WriteDB style database gimask. More...

	~CWriteDB_GiMask ()
	Destructor. More...

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

void	ListFiles (vector< string > &files) const
	List Filenames. More...

const string &	GetName () const
	Get Mask Name. More...

void	AddGiMask (const vector< TGi > &GIs, const TPairVector &masks)
	Add a mask data for a sequence represented by a set of GIs. 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
string	m_MaskName

Uint8	m_MaxFileSize

CRef< CWriteDB_GiMaskData >	m_DFile
	Data file. More...

CRef< CWriteDB_GiMaskData >	m_DFile_LE

CRef< CWriteDB_GiMaskOffset >	m_OFile
	Offset file. More...

CRef< CWriteDB_GiMaskOffset >	m_OFile_LE

CRef< CWriteDB_GiMaskIndex >	m_IFile
	Index file. More...

CRef< CWriteDB_GiMaskIndex >	m_IFile_LE

TGiOffset	m_GiOffset
	Sorted list of (GI, offset) pairs. 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_GiMask class.

This manages construction of WriteDB gi mask files.

Definition at line 218 of file writedb_gimask.hpp.

Member Typedef Documentation

◆ TGiOffset

typedef vector< pair<TGi, TOffset> > CWriteDB_GiMask::TGiOffset

Definition at line 222 of file writedb_gimask.hpp.

◆ TOffset

typedef pair<int, int> CWriteDB_GiMask::TOffset

Definition at line 221 of file writedb_gimask.hpp.

◆ TPairVector

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

Definition at line 220 of file writedb_gimask.hpp.

Constructor & Destructor Documentation

◆ CWriteDB_GiMask()

CWriteDB_GiMask::CWriteDB_GiMask	(	const string &	maskname,
		const string &	desc,
		Uint8	max_file_size
	)

Construct WriteDB style database gimask.

Parameters

maskname	Name of the mask data
desc	Description of this mask.

Definition at line 46 of file writedb_gimask.cpp.

◆ ~CWriteDB_GiMask()

CWriteDB_GiMask::~CWriteDB_GiMask ( )

inline

Destructor.

Definition at line 232 of file writedb_gimask.hpp.

Member Function Documentation

◆ AddGiMask()

void CWriteDB_GiMask::AddGiMask	(	const vector< TGi > &	GIs,
		const TPairVector &	masks
	)

Add a mask data for a sequence represented by a set of GIs.

Parameters

GIs	The GIs of the sequence
masks	The masks represented as ranges

Definition at line 70 of file writedb_gimask.cpp.

References CWriteDB_GiMaskData::CanFit(), CWriteDB_File::Close(), CWriteDB_GiMaskData::GetIndex(), CWriteDB_GiMaskData::GetOffset(), ITERATE, m_DFile, m_DFile_LE, m_GiOffset, m_MaskName, m_MaxFileSize, mask, offset, CRef< C, Locker >::Reset(), and CWriteDB_GiMaskData::WriteMask().

◆ Close()

void CWriteDB_GiMask::Close ( void )

Flush data to disk and close all associated files.

Definition at line 90 of file writedb_gimask.cpp.

References CWriteDB_GiMaskOffset::AddGIs(), CWriteDB_GiMaskIndex::AddGIs(), CWriteDB_File::Close(), CWriteDB_GiMaskData::GetIndex(), m_DFile, m_DFile_LE, m_GiOffset, m_IFile, m_IFile_LE, m_MaskName, m_OFile, m_OFile_LE, CWriteDB_File::RenameSingle(), and ct::sort().

◆ GetName()

const string& CWriteDB_GiMask::GetName ( void ) const

inline

Get Mask Name.

Returns the name of the mask

Definition at line 251 of file writedb_gimask.hpp.

References m_MaskName.

◆ ListFiles()

void CWriteDB_GiMask::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.

Definition at line 59 of file writedb_gimask.cpp.

References CWriteDB_File::GetFilename(), m_DFile, m_DFile_LE, m_GiOffset, m_IFile, m_IFile_LE, m_OFile, and m_OFile_LE.

Member Data Documentation

◆ m_DFile

CRef<CWriteDB_GiMaskData> CWriteDB_GiMask::m_DFile

private

Data file.

Definition at line 267 of file writedb_gimask.hpp.

Referenced by AddGiMask(), Close(), and ListFiles().

◆ m_DFile_LE

CRef<CWriteDB_GiMaskData> CWriteDB_GiMask::m_DFile_LE

private

Definition at line 268 of file writedb_gimask.hpp.

Referenced by AddGiMask(), Close(), and ListFiles().

◆ m_GiOffset

TGiOffset CWriteDB_GiMask::m_GiOffset

private

Sorted list of (GI, offset) pairs.

Definition at line 279 of file writedb_gimask.hpp.

Referenced by AddGiMask(), Close(), and ListFiles().

◆ m_IFile

CRef<CWriteDB_GiMaskIndex> CWriteDB_GiMask::m_IFile

private

Index file.

Definition at line 275 of file writedb_gimask.hpp.

Referenced by Close(), and ListFiles().

◆ m_IFile_LE

CRef<CWriteDB_GiMaskIndex> CWriteDB_GiMask::m_IFile_LE

private

Definition at line 276 of file writedb_gimask.hpp.

Referenced by Close(), and ListFiles().

◆ m_MaskName

string CWriteDB_GiMask::m_MaskName

private

Definition at line 263 of file writedb_gimask.hpp.

Referenced by AddGiMask(), Close(), and GetName().

◆ m_MaxFileSize

Uint8 CWriteDB_GiMask::m_MaxFileSize

private

Definition at line 264 of file writedb_gimask.hpp.

Referenced by AddGiMask().

◆ m_OFile

CRef<CWriteDB_GiMaskOffset> CWriteDB_GiMask::m_OFile

private

Offset file.

Definition at line 271 of file writedb_gimask.hpp.

Referenced by Close(), and ListFiles().

◆ m_OFile_LE

CRef<CWriteDB_GiMaskOffset> CWriteDB_GiMask::m_OFile_LE

private

Definition at line 272 of file writedb_gimask.hpp.

Referenced by Close(), and ListFiles().

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 Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TGiOffset

◆ TOffset

◆ TPairVector

Constructor & Destructor Documentation

◆ CWriteDB_GiMask()

◆ ~CWriteDB_GiMask()

Member Function Documentation

◆ AddGiMask()

◆ Close()

◆ GetName()

◆ ListFiles()

Member Data Documentation

◆ m_DFile

◆ m_DFile_LE

◆ m_GiOffset

◆ m_IFile

◆ m_IFile_LE

◆ m_MaskName

◆ m_MaxFileSize

◆ m_OFile

◆ m_OFile_LE