nvbio::io::SequenceDataMMAP Struct Reference

Detailed description

A concrete SequenceData storage implementation in system mapped memory

Definition at line 81 of file sequence_mmap.h.

#include <sequence_mmap.h>

Inheritance diagram for nvbio::io::SequenceDataMMAP:

Public Types
typedef SequenceDataView	plain_view_type
typedef ConstSequenceDataView	const_plain_view_type
Public Types inherited from nvbio::io::SequenceData
typedef SequenceDataView	plain_view_type
typedef ConstSequenceDataView	const_plain_view_type

Public Methods
	SequenceDataMMAP ()
bool	load (const char *name)
	operator plain_view_type ()
	operator const_plain_view_type () const
Public Methods inherited from nvbio::io::SequenceData
virtual	~SequenceData ()
Public Methods inherited from nvbio::io::SequenceDataInfo
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE	SequenceDataInfo ()
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE Alphabet	alphabet () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	size () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	bps () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	words () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	qs () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	name_stream_len () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE bool	has_qualities () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	max_sequence_len () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	min_sequence_len () const
NVBIO_HOST_DEVICE NVBIO_FORCEINLINE uint32	avg_sequence_len () const

Public Members
uint32 *	m_sequence_ptr
uint32 *	m_sequence_index_ptr
char *	m_qual_ptr
char *	m_name_ptr
uint32 *	m_name_index_ptr
MappedFile	m_info_file
	internal memory-mapped info object server More...
MappedFile	m_sequence_file
	internal memory-mapped genome object server More...
MappedFile	m_sequence_index_file
	internal memory-mapped forward occurrence table object server More...
MappedFile	m_qual_file
	internal memory-mapped reverse occurrence table object server More...
MappedFile	m_name_file
	internal memory-mapped forward BWT object server More...
MappedFile	m_name_index_file
	internal memory-mapped reverse BWT object server More...

Member Typedef Documentation

typedef ConstSequenceDataView nvbio::io::SequenceDataMMAP::const_plain_view_type

Definition at line 84 of file sequence_mmap.h.

typedef SequenceDataView nvbio::io::SequenceDataMMAP::plain_view_type

Definition at line 83 of file sequence_mmap.h.

Constructor & Destructor Documentation

nvbio::io::SequenceDataMMAP::SequenceDataMMAP ( )

inline

constructor

Definition at line 88 of file sequence_mmap.h.

Member Function Documentation

bool nvbio::io::SequenceDataMMAP::load

(

const char *

name)

load from a memory mapped object

Parameters

name	memory mapped object name

Definition at line 66 of file sequence_mmap.cpp.

nvbio::io::SequenceDataMMAP::operator const_plain_view_type ( ) const

inlinevirtual

convert to a const plain_view

Reimplemented from nvbio::io::SequenceData.

Definition at line 116 of file sequence_mmap.h.

nvbio::io::SequenceDataMMAP::operator plain_view_type ( )

inlinevirtual

convert to a plain_view

Reimplemented from nvbio::io::SequenceData.

Definition at line 104 of file sequence_mmap.h.

Member Data Documentation

MappedFile nvbio::io::SequenceDataMMAP::m_info_file

internal memory-mapped info object server

Definition at line 133 of file sequence_mmap.h.

MappedFile nvbio::io::SequenceDataMMAP::m_name_file

internal memory-mapped forward BWT object server

Definition at line 137 of file sequence_mmap.h.

MappedFile nvbio::io::SequenceDataMMAP::m_name_index_file

internal memory-mapped reverse BWT object server

Definition at line 138 of file sequence_mmap.h.

uint32* nvbio::io::SequenceDataMMAP::m_name_index_ptr

Definition at line 131 of file sequence_mmap.h.

char* nvbio::io::SequenceDataMMAP::m_name_ptr

Definition at line 130 of file sequence_mmap.h.

MappedFile nvbio::io::SequenceDataMMAP::m_qual_file

internal memory-mapped reverse occurrence table object server

Definition at line 136 of file sequence_mmap.h.

char* nvbio::io::SequenceDataMMAP::m_qual_ptr

Definition at line 129 of file sequence_mmap.h.

MappedFile nvbio::io::SequenceDataMMAP::m_sequence_file

internal memory-mapped genome object server

Definition at line 134 of file sequence_mmap.h.

MappedFile nvbio::io::SequenceDataMMAP::m_sequence_index_file

internal memory-mapped forward occurrence table object server

Definition at line 135 of file sequence_mmap.h.

uint32* nvbio::io::SequenceDataMMAP::m_sequence_index_ptr

Definition at line 128 of file sequence_mmap.h.

uint32* nvbio::io::SequenceDataMMAP::m_sequence_ptr

Definition at line 127 of file sequence_mmap.h.

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

• E:/git/nvbio/nvbio/io/sequence/sequence_mmap.h
• E:/git/nvbio/nvbio/io/sequence/sequence_mmap.cpp