CBGZFStream Class Reference

Search Toolkit Book for CBGZFStream

#include <sra/readers/bam/bgzf.hpp>

Collaboration diagram for CBGZFStream:

Public Member Functions
	CBGZFStream ()
	CBGZFStream (CBGZFFile &file)
	~CBGZFStream ()
void	Close ()
void	Open (CBGZFFile &file)
CBGZFBlock::TDataSize	GetBlockDataSize () const
CBGZFBlock::TFileBlockPos	GetBlockFilePos () const
CBGZFBlock::TFileBlockPos	GetNextBlockFilePos () const
bool	HaveBytesInBlock () const
CBGZFPos	GetPos () const
CBGZFPos	GetNextBlockPos () const
CBGZFPos	GetSeekPos () const
CBGZFPos	GetEndPos () const
void	Seek (CBGZFPos pos, CBGZFPos end_pos=CBGZFPos::GetInvalid())
size_t	GetNextAvailableBytes ()
bool	HaveNextAvailableBytes ()
bool	HaveNextDataBlock ()
size_t	Read (char *buf, size_t count)
const char *	Read (size_t count)

Private Member Functions
bool	x_NextBlock ()
const char *	x_Read (CBGZFPos::TFileBlockPos file_pos, size_t size, char *buffer)
bool	x_ReadBlock (CBGZFPos::TFileBlockPos file_pos)

Private Attributes
CRef< CBGZFFile >	m_File
CPagedFile::TPage	m_Page
CBGZFFile::TBlock	m_Block
CBGZFPos::TByteOffset	m_ReadPos
CSimpleBufferT< char >	m_InReadBuffer
CSimpleBufferT< char >	m_OutReadBuffer
CBGZFPos	m_EndPos

Detailed Description

Definition at line 366 of file bgzf.hpp.

Constructor & Destructor Documentation

CBGZFStream() [1/2]

CBGZFStream::CBGZFStream

(

)

Definition at line 417 of file bgzf.cpp.

CBGZFStream() [2/2]

CBGZFStream::CBGZFStream ( CBGZFFile &  file )

explicit

Definition at line 424 of file bgzf.cpp.

References file, and Open().

~CBGZFStream()

CBGZFStream::~CBGZFStream

(

)

Definition at line 433 of file bgzf.cpp.

Member Function Documentation

Close()

void CBGZFStream::Close

(

void

)

Definition at line 438 of file bgzf.cpp.

References m_Block, m_File, m_Page, CCacheWithLock< Key, Value, Less >::CLock::Reset(), CBinaryRangeCacheWithLock< Position, Value >::CLock::Reset(), and CRef< C, Locker >::Reset().

Referenced by Open().

GetBlockDataSize()

CBGZFBlock::TDataSize CBGZFStream::GetBlockDataSize ( ) const

inline

Definition at line 377 of file bgzf.hpp.

References m_Block.

Referenced by GetNextAvailableBytes(), HaveBytesInBlock(), and Seek().

GetBlockFilePos()

CBGZFBlock::TFileBlockPos CBGZFStream::GetBlockFilePos ( ) const

inline

Definition at line 381 of file bgzf.hpp.

References m_Block.

Referenced by GetPos().

GetEndPos()

CBGZFPos CBGZFStream::GetEndPos ( ) const

inline

Definition at line 411 of file bgzf.hpp.

References m_EndPos.

GetNextAvailableBytes()

size_t CBGZFStream::GetNextAvailableBytes

(

)

Definition at line 653 of file bgzf.cpp.

References GetBlockDataSize(), m_ReadPos, and x_NextBlock().

Referenced by Read().

GetNextBlockFilePos()

CBGZFBlock::TFileBlockPos CBGZFStream::GetNextBlockFilePos ( ) const

inline

Definition at line 385 of file bgzf.hpp.

References m_Block.

Referenced by GetNextBlockPos(), HaveNextDataBlock(), and x_NextBlock().

GetNextBlockPos()

CBGZFPos CBGZFStream::GetNextBlockPos ( ) const

inline

Definition at line 398 of file bgzf.hpp.

References GetNextBlockFilePos().

Referenced by GetSeekPos().

GetPos()

CBGZFPos CBGZFStream::GetPos ( void  ) const

inline

Definition at line 394 of file bgzf.hpp.

References GetBlockFilePos(), and m_ReadPos.

Referenced by GetSeekPos(), HaveNextAvailableBytes(), and Seek().

GetSeekPos()

CBGZFPos CBGZFStream::GetSeekPos ( ) const

inline

Definition at line 402 of file bgzf.hpp.

References GetNextBlockPos(), GetPos(), and HaveBytesInBlock().

Referenced by CBamHeader::Read().

HaveBytesInBlock()

bool CBGZFStream::HaveBytesInBlock ( ) const

inline

Definition at line 389 of file bgzf.hpp.

References GetBlockDataSize(), and m_ReadPos.

Referenced by GetSeekPos(), HaveNextAvailableBytes(), HaveNextDataBlock(), and Seek().

HaveNextAvailableBytes()

bool CBGZFStream::HaveNextAvailableBytes ( )

inline

Definition at line 421 of file bgzf.hpp.

References GetPos(), HaveBytesInBlock(), HaveNextDataBlock(), and m_EndPos.

Referenced by CBamRawAlignIterator::x_NextAnnot().

HaveNextDataBlock()

bool CBGZFStream::HaveNextDataBlock

(

)

Definition at line 663 of file bgzf.cpp.

References _ASSERT, GetNextBlockFilePos(), HaveBytesInBlock(), m_EndPos, and x_NextBlock().

Referenced by HaveNextAvailableBytes().

Open()

void CBGZFStream::Open

(

CBGZFFile &

file

)

Definition at line 446 of file bgzf.cpp.

References Close(), file, CBGZFPos::GetInvalid(), m_EndPos, m_File, and CRef< C, Locker >::Reset().

Referenced by CBGZFStream().

Read() [1/2]

size_t CBGZFStream::Read	(	char *	buf,
		size_t	count
	)

Definition at line 678 of file bgzf.cpp.

References _ASSERT, buf, count, GetNextAvailableBytes(), m_Block, m_ReadPos, and min().

Read() [2/2]

const char * CBGZFStream::Read

(

size_t

count

)

Definition at line 690 of file bgzf.cpp.

References _ASSERT, cnt, count, CSimpleBufferT< T, ResizeStrategy >::data(), GetNextAvailableBytes(), CBGZFBlock::kMaxDataSize, m_Block, m_OutReadBuffer, m_ReadPos, min(), and s_Reserve().

Seek()

void CBGZFStream::Seek	(	CBGZFPos	pos,
		CBGZFPos	end_pos = CBGZFPos::GetInvalid()
	)

Definition at line 462 of file bgzf.cpp.

References CBGZFFile::GetBlock(), GetBlockDataSize(), CBGZFPos::GetByteOffset(), CBGZFPos::GetFileBlockPos(), GetPos(), HaveBytesInBlock(), m_Block, m_EndPos, m_File, m_InReadBuffer, m_Page, m_ReadPos, and NCBI_THROW_FMT.

Referenced by CBamRawAlignIterator::x_UpdateRange().

x_NextBlock()

bool CBGZFStream::x_NextBlock ( )

private

Definition at line 454 of file bgzf.cpp.

References CBGZFFile::GetBlock(), GetNextBlockFilePos(), m_Block, m_File, m_InReadBuffer, m_Page, and m_ReadPos.

Referenced by GetNextAvailableBytes(), and HaveNextDataBlock().

x_Read()

const char* CBGZFStream::x_Read ( CBGZFPos::TFileBlockPos  file_pos, size_t  size, char *  buffer  )

private

x_ReadBlock()

bool CBGZFStream::x_ReadBlock ( CBGZFPos::TFileBlockPos  file_pos )

private

Member Data Documentation

m_Block

CBGZFFile::TBlock CBGZFStream::m_Block

private

Definition at line 450 of file bgzf.hpp.

Referenced by Close(), GetBlockDataSize(), GetBlockFilePos(), GetNextBlockFilePos(), Read(), Seek(), and x_NextBlock().

m_EndPos

CBGZFPos CBGZFStream::m_EndPos

private

Definition at line 454 of file bgzf.hpp.

Referenced by GetEndPos(), HaveNextAvailableBytes(), HaveNextDataBlock(), Open(), and Seek().

m_File

CRef<CBGZFFile> CBGZFStream::m_File

private

Definition at line 448 of file bgzf.hpp.

Referenced by Close(), Open(), Seek(), and x_NextBlock().

m_InReadBuffer

CSimpleBufferT<char> CBGZFStream::m_InReadBuffer

private

Definition at line 452 of file bgzf.hpp.

Referenced by Seek(), and x_NextBlock().

m_OutReadBuffer

CSimpleBufferT<char> CBGZFStream::m_OutReadBuffer

private

Definition at line 453 of file bgzf.hpp.

Referenced by Read().

m_Page

CPagedFile::TPage CBGZFStream::m_Page

private

Definition at line 449 of file bgzf.hpp.

Referenced by Close(), Seek(), and x_NextBlock().

m_ReadPos

CBGZFPos::TByteOffset CBGZFStream::m_ReadPos

private

Definition at line 451 of file bgzf.hpp.

Referenced by GetNextAvailableBytes(), GetPos(), HaveBytesInBlock(), Read(), Seek(), and x_NextBlock().

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

• include/sra/readers/bam/bgzf.hpp
• src/sra/readers/bam/bgzf.cpp