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

Inheritance diagram for CSeqDBSeqFile:

Collaboration diagram for CSeqDBSeqFile:

Public Types
typedef CSeqDBAtlas::TIndx	TIndx
	Type which spans possible file offsets. More...

Public Types inherited from CSeqDBExtFile
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
	CSeqDBSeqFile (CSeqDBAtlas &atlas, const string &dbname, char prot_nucl)
	Constructor. More...

virtual	~CSeqDBSeqFile ()
	Destructor. More...

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

const char *	GetFileDataPtr (TIndx start) const
	Get a pointer into the file contents. More...

Public Member Functions inherited from CSeqDBExtFile
	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

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 CSeqDBExtFile
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 inherited from CSeqDBExtFile
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...

Detailed Description

Sequence data file.

This is the .psq or .nsq file; it provides the raw sequence data, and for nucleotide sequences, ambiguity data. For nucleotide sequences, the last byte will contain a two bit marker with a number from 0-3, which indicates how much of the rest of that byte is filled with base information (0-3 bases, which is 0-6 bits). For ambiguous regions, the sequence data is normally randomized in this file, to reduce the number of accidental false positives during the search. The ambiguity data encodes the location of, and actual data for, those regions.

Definition at line 748 of file seqdbfile.hpp.

Member Typedef Documentation

◆ TIndx

typedef CSeqDBAtlas::TIndx CSeqDBSeqFile::TIndx

Type which spans possible file offsets.

Definition at line 751 of file seqdbfile.hpp.

Constructor & Destructor Documentation

◆ CSeqDBSeqFile()

CSeqDBSeqFile::CSeqDBSeqFile	(	CSeqDBAtlas &	atlas,
		const string &	dbname,
		char	prot_nucl
	)

inline

Constructor.

This builds an object which provides access to the sequence data file for a volume. This file is simply a concatenation of all the sequence data for the database sequences. In a protein file, these are just the database sequences seperated by NUL bytes. In a nucleotide volume, the packed data for each sequence is followed by ambiguity data for that sequence (if any such data exists).

Parameters

atlas	The memory management layer object.
dbname	The name of the database volume.
prot_nucl	The sequence data type.
locked	The lock holder object for this thread.

Definition at line 771 of file seqdbfile.hpp.

◆ ~CSeqDBSeqFile()

virtual CSeqDBSeqFile::~CSeqDBSeqFile ( )

inlinevirtual

Destructor.

Definition at line 779 of file seqdbfile.hpp.

Member Function Documentation

◆ GetFileDataPtr()

const char* CSeqDBSeqFile::GetFileDataPtr ( TIndx start ) const

inline

Get a pointer into the file contents.

Copy the sequence 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. If the user will take ownership of the memory region hold, the keep argument should be specified as true.

Parameters

start	The starting offset for the first byte to read.
end	The offset for the first byte after the area to read.
keep	True if an extra hold should be acquired on the data.
hold	Specify true to get a request-duration hold.
locked	The lock holder object for this thread.

Returns: A pointer into the file data.

Definition at line 822 of file seqdbfile.hpp.

References CSeqDBFileMemMap::GetFileDataPtr(), and CSeqDBExtFile::m_Lease.

Referenced by CSeqDBVol::GetRawSeqAndAmbig(), CSeqDBVol::x_GetAmbChar(), and CSeqDBVol::x_GetSequence().

◆ ReadBytes()

void CSeqDBSeqFile::ReadBytes	(	char *	buf,
		TIndx	start,
		TIndx	end
	)		const

inline

Read part of the file into a buffer.

Copy the sequence 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 795 of file seqdbfile.hpp.

References buf, and CSeqDBExtFile::x_ReadBytes().

Referenced by CSeqDBVol::GetSeqLengthExact().

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

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

Public Types

Public Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ TIndx

Constructor & Destructor Documentation

◆ CSeqDBSeqFile()

◆ ~CSeqDBSeqFile()

Member Function Documentation

◆ GetFileDataPtr()

◆ ReadBytes()