Database component file. More...

#include <objtools/blast/seqdb_reader/impl/seqdbfile.hpp>

Inheritance diagram for CSeqDBExtFile:

Collaboration diagram for CSeqDBExtFile:

Public Types
typedef CSeqDBAtlas::TIndx	TIndx
	Type which spans possible file offsets. 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
	CSeqDBExtFile (CSeqDBAtlas &atlas, const string &dbfilename, char prot_nucl)
	Constructor. More...

virtual	~CSeqDBExtFile ()
	Destructor. More...

void	UnLease ()
	Release memory held in the atlas layer by this object. 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

Protected Member Functions
void	x_ReadBytes (char *buf, TIndx start, TIndx end) const
	Read part of the file into a buffer. More...

template<class T >
TIndx	x_ReadSwapped (CSeqDBFileMemMap &lease, TIndx offset, T *value)
	Read a numerical object from the file. More...

char	x_GetSeqType () const
	Get the volume's sequence data type. More...

void	x_SetFileType (char prot_nucl)
	Sets the sequence data type. More...

Protected Member Functions inherited from CObject
virtual void	DeleteThis (void)
	Virtual method "deleting" this object. More...

Protected Attributes
CSeqDBAtlas &	m_Atlas
	The memory layer management object. More...

string	m_FileName
	The name of this file. More...

char	m_ProtNucl
	Either 'p' for protein or 'n' for nucleotide. More...

CSeqDBFileMemMap	m_Lease
	A memory lease used by this file. More...

CSeqDBRawFile	m_File
	The raw file object. 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...

Detailed Description

Database component file.

This represents any database component file with an extension like "pxx" or "nxx". This finds the correct type (protein or nucleotide) if that is unknown, and computes the filename based on a filename template like "path/to/file/basename.-in".

This also provides a 'protected' interface to the specific db files, and defines a few useful methods.

Definition at line 258 of file seqdbfile.hpp.

Member Typedef Documentation

◆ TIndx

typedef CSeqDBAtlas::TIndx CSeqDBExtFile::TIndx

Type which spans possible file offsets.

Definition at line 261 of file seqdbfile.hpp.

Constructor & Destructor Documentation

◆ CSeqDBExtFile()

CSeqDBExtFile::CSeqDBExtFile	(	CSeqDBAtlas &	atlas,
		const string &	dbfilename,
		char	prot_nucl
	)

Constructor.

This builds an object which has a few properties required by most or all database volume component files. This object keeps a lease on the file from the first access until instructed not to, moving and expanding that lease to cover incoming requests. By keeping a lease, lookups, file opens, and other expensive operations are usually avoided on subsequent calls. This object also provides some methods to read data in a byte swapped or direct way.

Parameters

atlas	The memory management layer object.
dbfilename	The name of the managed file.
prot_nucl	The sequence data type.
locked	The lock holder object for this thread.

Definition at line 106 of file seqdbfile.cpp.

References CSeqDBFileMemMap::Init(), m_File, m_FileName, m_Lease, NCBI_THROW, CSeqDBRawFile::Open(), string, and x_SetFileType().

◆ ~CSeqDBExtFile()

virtual CSeqDBExtFile::~CSeqDBExtFile ( )

inlinevirtual

Destructor.

Definition at line 287 of file seqdbfile.hpp.

Member Function Documentation

◆ UnLease()

void CSeqDBExtFile::UnLease ( )

inline

Release memory held in the atlas layer by this object.

Definition at line 293 of file seqdbfile.hpp.

References CSeqDBFileMemMap::Clear(), and m_Lease.

Referenced by CSeqDBVol::UnLease().

◆ x_GetSeqType()

char CSeqDBExtFile::x_GetSeqType ( ) const

inlineprotected

Get the volume's sequence data type.

This object knows which type of sequence data it deals with - this method returns that information.

Returns: The type of sequence data in use.

Definition at line 353 of file seqdbfile.hpp.

References m_ProtNucl.

Referenced by CSeqDBIdxFile::CSeqDBIdxFile(), CSeqDBIdxFile::GetAmbStartEnd(), CSeqDBIdxFile::GetSeqStartEnd(), CSeqDBIdxFile::GetSeqType(), and CSeqDBIdxFile::x_GetAmb().

◆ x_ReadBytes()

void CSeqDBExtFile::x_ReadBytes	(	char *	buf,
		TIndx	start,
		TIndx	end
	)		const

inlineprotected

Read part of the file into a buffer.

Copy the file data from offsets start to end into the array at buf, which is assumed to already have been allocated. This method assumes the atlas lock is held.

Parameters

buf	The destination for the data to be read.
start	The starting offset for the first byte to read.
end	The offset for the first byte after the area to read.

Definition at line 312 of file seqdbfile.hpp.

References buf, m_File, m_Lease, and CSeqDBRawFile::ReadBytes().

Referenced by CSeqDBSeqFile::ReadBytes(), and CSeqDBHdrFile::ReadBytes().

◆ x_ReadSwapped()

template<class T >

TIndx CSeqDBExtFile::x_ReadSwapped	(	CSeqDBFileMemMap &	lease,
		TIndx	offset,
		T *	value
	)

inlineprotected

Read a numerical object from the file.

Given a pointer to an object in memory, this reads a numerical value for it from the file. The data in the file is assumed to be in network byte order, and the user version in the local default byte order (host order). The offset of the data is provided, and the size of the object is taken as sizeof(T).

Parameters

lease	A memory lease object to use for the read.
offset	The starting offset of the object in the file.
value	A pointer to the object.
locked	The lock holder object for this thread.

Returns: The offset of the first byte after the object.

Definition at line 338 of file seqdbfile.hpp.

References m_File, offset, CSeqDBRawFile::ReadSwapped(), and value.

Referenced by CSeqDBIdxFile::CSeqDBIdxFile().

◆ x_SetFileType()

void CSeqDBExtFile::x_SetFileType ( char prot_nucl )

inlineprotected

Sets the sequence data type.

The sequence data will be set as protein or nucleotide. An exception is thrown if an invalid type is provided. The first character of the file extension will be modified to reflect the sequence data type.

Parameters

prot_nucl Either 'p' or 'n' for protein or nucleotide.

Definition at line 387 of file seqdbfile.hpp.

References _ASSERT, m_FileName, m_ProtNucl, and NCBI_THROW.

Referenced by CSeqDBExtFile().

Member Data Documentation

◆ m_Atlas

CSeqDBAtlas& CSeqDBExtFile::m_Atlas

protected

The memory layer management object.

Definition at line 372 of file seqdbfile.hpp.

◆ m_File

CSeqDBRawFile CSeqDBExtFile::m_File

protected

The raw file object.

Definition at line 384 of file seqdbfile.hpp.

Referenced by CSeqDBExtFile(), x_ReadBytes(), and x_ReadSwapped().

◆ m_FileName

string CSeqDBExtFile::m_FileName

protected

The name of this file.

Definition at line 375 of file seqdbfile.hpp.

Referenced by CSeqDBExtFile(), CSeqDBIdxFile::x_GetAmb(), CSeqDBIdxFile::x_GetHdr(), CSeqDBIdxFile::x_GetSeq(), and x_SetFileType().

◆ m_Lease

CSeqDBFileMemMap CSeqDBExtFile::m_Lease

mutableprotected

A memory lease used by this file.

Definition at line 381 of file seqdbfile.hpp.

Referenced by CSeqDBExtFile(), CSeqDBIdxFile::CSeqDBIdxFile(), CSeqDBIdxFile::GetAmbStartEnd(), CSeqDBSeqFile::GetFileDataPtr(), CSeqDBHdrFile::GetFileDataPtr(), CSeqDBIdxFile::GetHdrStartEnd(), CSeqDBIdxFile::GetSeqStart(), CSeqDBIdxFile::GetSeqStartEnd(), UnLease(), and x_ReadBytes().

◆ m_ProtNucl

char CSeqDBExtFile::m_ProtNucl

protected

Either 'p' for protein or 'n' for nucleotide.

Definition at line 378 of file seqdbfile.hpp.

Referenced by x_GetSeqType(), and x_SetFileType().

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

include/objtools/blast/seqdb_reader/impl/seqdbfile.hpp
src/objtools/blast/seqdb_reader/seqdbfile.cpp

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TIndx

Constructor & Destructor Documentation

◆ CSeqDBExtFile()

◆ ~CSeqDBExtFile()

Member Function Documentation

◆ UnLease()

◆ x_GetSeqType()

◆ x_ReadBytes()

◆ x_ReadSwapped()

◆ x_SetFileType()

Member Data Documentation

◆ m_Atlas

◆ m_File

◆ m_FileName

◆ m_Lease

◆ m_ProtNucl