Detailed description

Basic FM-index interface.

This class holds pointers to data that is typically going to be allocated/loaded/deallocated by inheriting classes. The idea is that accessing this basic information is fast and requires no virtual function calls.

Definition at line 84 of file fmindex.h.

#include <fmindex.h>

Inheritance diagram for nvbio::io::FMIndexDataCore:

Public Types
typedef const uint32 *	bwt_occ_type

typedef const uint32 *	count_table_type

typedef SSA_index_multiple_context < SA_INT, const uint32 * >	ssa_type

Public Methods
	FMIndexDataCore ()

uint32	flags () const
	return loading flags More...

uint32	length () const
	return sequence length More...

uint32	primary () const
	return the primary key More...

uint32	rprimary () const
	return the reverse primary key More...

bool	has_ssa () const
	return whether the sampled suffix array is present More...

bool	has_rssa () const
	return whether the reverse sampled suffix array is present More...

const uint32 *	bwt_occ () const
	return the BWT stream More...

const uint32 *	rbwt_occ () const
	return the reverse BWT stream More...

const uint32 *	count_table () const
	return the count table More...

uint32	bwt_occ_words () const
	return the number of sequence words More...

uint32	sa_words () const
	return the number of SA words More...

ssa_type	ssa () const

ssa_type	rssa () const

const uint32 *	L2 () const
	return the L2 table More...

Public Members
uint32	m_flags

uint32	m_seq_length

uint32	m_bwt_occ_words

uint32	m_sa_words

uint32	m_primary

uint32	m_rprimary

uint32 *	m_L2

uint32 *	m_bwt_occ

uint32 *	m_rbwt_occ

uint32 *	m_count_table

ssa_type	m_ssa

ssa_type	m_rssa

Static Public Members
static const uint32	FORWARD = 0x02

static const uint32	REVERSE = 0x04

static const uint32	SA = 0x10

static const uint32	BWT_BITS = 2u

static const bool	BWT_BIG_ENDIAN = true

static const uint32	BWT_SYMBOLS_PER_WORD = (8*sizeof(uint32))/BWT_BITS

static const uint32	OCC_INT = 64

static const uint32	SA_INT = 16

Member Typedef Documentation

typedef const uint32* nvbio::io::FMIndexDataCore::bwt_occ_type

Definition at line 97 of file fmindex.h.

typedef const uint32* nvbio::io::FMIndexDataCore::count_table_type

Definition at line 98 of file fmindex.h.

typedef SSA_index_multiple_context< SA_INT, const uint32*> nvbio::io::FMIndexDataCore::ssa_type

empty constructor

Definition at line 102 of file fmindex.h.

Constructor & Destructor Documentation

nvbio::io::FMIndexDataCore::FMIndexDataCore ( )

inline

Definition at line 106 of file fmindex.h.

Member Function Documentation

const uint32* nvbio::io::FMIndexDataCore::bwt_occ ( ) const

inline

return the BWT stream

Definition at line 125 of file fmindex.h.

uint32 nvbio::io::FMIndexDataCore::bwt_occ_words ( ) const

inline

return the number of sequence words

Definition at line 128 of file fmindex.h.

const uint32* nvbio::io::FMIndexDataCore::count_table ( ) const

inline

return the count table

Definition at line 127 of file fmindex.h.

uint32 nvbio::io::FMIndexDataCore::flags ( ) const

inline

return loading flags

Definition at line 119 of file fmindex.h.

bool nvbio::io::FMIndexDataCore::has_rssa ( ) const

inline

return whether the reverse sampled suffix array is present

Definition at line 124 of file fmindex.h.

bool nvbio::io::FMIndexDataCore::has_ssa ( ) const

inline

return whether the sampled suffix array is present

Definition at line 123 of file fmindex.h.

const uint32* nvbio::io::FMIndexDataCore::L2 ( ) const

inline

return the L2 table

Definition at line 132 of file fmindex.h.

uint32 nvbio::io::FMIndexDataCore::length ( ) const

inline

return sequence length

Definition at line 120 of file fmindex.h.

uint32 nvbio::io::FMIndexDataCore::primary ( ) const

inline

return the primary key

Definition at line 121 of file fmindex.h.

const uint32* nvbio::io::FMIndexDataCore::rbwt_occ ( ) const

inline

return the reverse BWT stream

Definition at line 126 of file fmindex.h.

uint32 nvbio::io::FMIndexDataCore::rprimary ( ) const

inline

return the reverse primary key

Definition at line 122 of file fmindex.h.

ssa_type nvbio::io::FMIndexDataCore::rssa ( ) const

inline

Definition at line 131 of file fmindex.h.

uint32 nvbio::io::FMIndexDataCore::sa_words ( ) const

inline

return the number of SA words

Definition at line 129 of file fmindex.h.

ssa_type nvbio::io::FMIndexDataCore::ssa ( ) const

inline

Definition at line 130 of file fmindex.h.

Member Data Documentation

const bool nvbio::io::FMIndexDataCore::BWT_BIG_ENDIAN = true

static

Definition at line 91 of file fmindex.h.

const uint32 nvbio::io::FMIndexDataCore::BWT_BITS = 2u

static

Definition at line 90 of file fmindex.h.

const uint32 nvbio::io::FMIndexDataCore::BWT_SYMBOLS_PER_WORD = (8*sizeof(uint32))/BWT_BITS

static

Definition at line 92 of file fmindex.h.

const uint32 nvbio::io::FMIndexDataCore::FORWARD = 0x02

static

Definition at line 86 of file fmindex.h.

uint32* nvbio::io::FMIndexDataCore::m_bwt_occ

Definition at line 143 of file fmindex.h.

uint32 nvbio::io::FMIndexDataCore::m_bwt_occ_words

Definition at line 137 of file fmindex.h.

uint32* nvbio::io::FMIndexDataCore::m_count_table

Definition at line 145 of file fmindex.h.

uint32 nvbio::io::FMIndexDataCore::m_flags

Definition at line 135 of file fmindex.h.

uint32* nvbio::io::FMIndexDataCore::m_L2

Definition at line 142 of file fmindex.h.

uint32 nvbio::io::FMIndexDataCore::m_primary

Definition at line 139 of file fmindex.h.

uint32* nvbio::io::FMIndexDataCore::m_rbwt_occ

Definition at line 144 of file fmindex.h.

uint32 nvbio::io::FMIndexDataCore::m_rprimary

Definition at line 140 of file fmindex.h.

ssa_type nvbio::io::FMIndexDataCore::m_rssa

Definition at line 147 of file fmindex.h.

uint32 nvbio::io::FMIndexDataCore::m_sa_words

Definition at line 138 of file fmindex.h.

uint32 nvbio::io::FMIndexDataCore::m_seq_length

Definition at line 136 of file fmindex.h.

ssa_type nvbio::io::FMIndexDataCore::m_ssa

Definition at line 146 of file fmindex.h.

const uint32 nvbio::io::FMIndexDataCore::OCC_INT = 64

static

Definition at line 94 of file fmindex.h.

const uint32 nvbio::io::FMIndexDataCore::REVERSE = 0x04

static

Definition at line 87 of file fmindex.h.

const uint32 nvbio::io::FMIndexDataCore::SA = 0x10

static

Definition at line 88 of file fmindex.h.

const uint32 nvbio::io::FMIndexDataCore::SA_INT = 16

static

Definition at line 95 of file fmindex.h.

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

E:/git/nvbio/nvbio/io/fmindex/fmindex.h

Detailed description

Public Types

Public Methods

Public Members

Static Public Members

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation