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

Collaboration diagram for CSeqDBRawFile:

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

Public Member Functions
	CSeqDBRawFile (CSeqDBAtlas &atlas)
	Constructor. More...

bool	Open (const CSeqDB_Path &name)
	MMap or Open a file. More...

const char *	GetFileDataPtr (CSeqDBFileMemMap &lease, TIndx start, TIndx end) const
	Get a pointer to a section of the file. More...

TIndx	GetFileLength () const
	Get the length of the file. More...

TIndx	ReadSwapped (CSeqDBFileMemMap &lease, TIndx offset, Uint4 *value) const
	Read a four byte numerical object from the file. More...

TIndx	ReadSwapped (CSeqDBFileMemMap &lease, TIndx offset, Uint8 *value) const
	Read an eight byte numerical object from the file. More...

TIndx	ReadSwapped (CSeqDBFileMemMap &lease, TIndx offset, string *value) const
	Read a string object from the file. More...

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

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

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

TIndx	m_Length
	The length of this file. More...

Detailed Description

Raw file.

This is the lowest level of SeqDB file object. It controls basic (byte data) access to the file, isolating higher levels from differences in handling mmapped vs opened files. This has mostly become a thin wrapper around the Atlas functionality.

Definition at line 64 of file seqdbfile.hpp.

Member Typedef Documentation

◆ TIndx

typedef CSeqDBAtlas::TIndx CSeqDBRawFile::TIndx

Type which spans possible file offsets.

Definition at line 67 of file seqdbfile.hpp.

Constructor & Destructor Documentation

◆ CSeqDBRawFile()

CSeqDBRawFile::CSeqDBRawFile ( CSeqDBAtlas & atlas )

inline

Constructor.

Builds a "raw" file object, which is the lowest level of the SeqDB file objects. It provides byte swapping and reading methods, which are implemented via the atlas layer.

Parameters

atlas The memory management layer object.

Definition at line 77 of file seqdbfile.hpp.

Member Function Documentation

◆ GetFileDataPtr()

const char* CSeqDBRawFile::GetFileDataPtr	(	CSeqDBFileMemMap &	lease,
		TIndx	start,
		TIndx	end
	)		const

inline

Get a pointer to a section of the file.

This method insures that the memory lease has a hold that includes the requested section of the file, and returns a pointer to the start offset.

Parameters

lease	The memory lease object for this file.
start	The starting offset for the first byte of the region.
end	The offset for the first byte after the region.
locked	The lock holder object for this thread.

Returns: A pointer to the file data at the start offset.

Definition at line 123 of file seqdbfile.hpp.

References _ASSERT, CSeqDBFileMemMap::GetFileDataPtr(), m_FileName, m_Length, and SEQDB_FILE_ASSERT.

Referenced by CSeqDBGiMask::GetMaskData(), CSeqDBOIDList::x_GetOidMask(), and CSeqDBGiMask::x_ReadFields().

◆ GetFileLength()

TIndx CSeqDBRawFile::GetFileLength ( ) const

inline

Get the length of the file.

The file length is returned as a four byte integer, which is the current maximum size for the blastdb component files.

Returns: The length of the file.

Definition at line 143 of file seqdbfile.hpp.

References m_Length.

Referenced by CSeqDBOIDList::x_GetOidMask(), CSeqDBColumn::x_ReadFields(), and CSeqDBGiMask::x_ReadFields().

◆ Open()

bool CSeqDBRawFile::Open ( const CSeqDB_Path & name )

inline

MMap or Open a file.

This serves to verify the existence of, open, and cache the length of a file.

Parameters

name	The filename to open.
locked	The lock holder object for this thread.

Returns: true if the file was opened successfully.

Definition at line 93 of file seqdbfile.hpp.

References _ASSERT, CSeqDBAtlas::GetFileSizeL(), CSeqDB_Path::GetPathS(), m_Atlas, m_FileName, m_Length, and CSeqDB_Path::Valid().

Referenced by CSeqDBColumn::CSeqDBColumn(), CSeqDBExtFile::CSeqDBExtFile(), CSeqDBOIDList::x_GetOidMask(), and CSeqDBGiMask::x_Open().

◆ ReadBytes()

void CSeqDBRawFile::ReadBytes	(	CSeqDBFileMemMap &	lease,
		char *	buf,
		TIndx	start,
		TIndx	end
	)		const

inline

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

lease	A memory lease object to use for the read.
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 922 of file seqdbfile.hpp.

References buf, CSeqDBFileMemMap::GetFileDataPtr(), and m_FileName.

Referenced by CSeqDBExtFile::x_ReadBytes().

◆ ReadSwapped() [1/3]

TIndx CSeqDBRawFile::ReadSwapped	(	CSeqDBFileMemMap &	lease,
		TIndx	offset,
		string *	value
	)		const

Read a string object from the file.

Given a pointer to a string object, this reads a string value for it from the file. The data in the file is assumed to be a four byte length in network byte order, followed by the bytes of the string. The amount of data is this length + 4.

Parameters

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

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

Definition at line 91 of file seqdbfile.cpp.

References CSeqDBFileMemMap::GetFileDataPtr(), int, len, m_FileName, offset, SeqDB_GetStdOrd(), and rapidjson::value.

◆ ReadSwapped() [2/3]

TIndx CSeqDBRawFile::ReadSwapped	(	CSeqDBFileMemMap &	lease,
		TIndx	offset,
		Uint4 *	value
	)		const

Read a four byte 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 size of the object is taken as sizeof(Uint4).

Parameters

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

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

Definition at line 71 of file seqdbfile.cpp.

References CSeqDBFileMemMap::GetFileDataPtr(), m_FileName, offset, SeqDB_GetStdOrd(), and rapidjson::value.

Referenced by CSeqDBOIDList::x_GetOidMask(), and CSeqDBExtFile::x_ReadSwapped().

◆ ReadSwapped() [3/3]

TIndx CSeqDBRawFile::ReadSwapped	(	CSeqDBFileMemMap &	lease,
		TIndx	offset,
		Uint8 *	value
	)		const

Read an eight byte 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 size of the object is taken as sizeof(Uint8).

Parameters

lease	A memory lease object to use for the read.
offset	The starting offset of the value 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 81 of file seqdbfile.cpp.

References CSeqDBFileMemMap::GetFileDataPtr(), m_FileName, offset, SeqDB_GetBroken(), and rapidjson::value.

Member Data Documentation

◆ m_Atlas

CSeqDBAtlas& CSeqDBRawFile::m_Atlas

private

The memory management layer object.

Definition at line 237 of file seqdbfile.hpp.

Referenced by Open().

◆ m_FileName

string CSeqDBRawFile::m_FileName

private

The name of this file.

Definition at line 240 of file seqdbfile.hpp.

Referenced by GetFileDataPtr(), Open(), ReadBytes(), and ReadSwapped().

◆ m_Length

TIndx CSeqDBRawFile::m_Length

private

The length of this file.

Definition at line 243 of file seqdbfile.hpp.

Referenced by GetFileDataPtr(), GetFileLength(), and Open().

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

Private Attributes

Detailed Description

Member Typedef Documentation

◆ TIndx

Constructor & Destructor Documentation

◆ CSeqDBRawFile()

Member Function Documentation

◆ GetFileDataPtr()

◆ GetFileLength()

◆ Open()

◆ ReadBytes()

◆ ReadSwapped() [1/3]

◆ ReadSwapped() [2/3]

◆ ReadSwapped() [3/3]

Member Data Documentation

◆ m_Atlas

◆ m_FileName

◆ m_Length