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 157 of file fmindex.h.

#include <fmindex.h>

Inheritance diagram for nvbio::io::FMIndexData:

Public Types
typedef const uint4 *	bwt_occ_type

typedef deinterleaved_iterator < 2, 0, bwt_occ_type >	bwt_type

typedef deinterleaved_iterator < 2, 1, bwt_occ_type >	occ_type

typedef const uint32 *	count_table_type

typedef SSA_index_multiple < SA_INT >	ssa_storage_type

typedef PackedStream< bwt_type, uint8, BWT_BITS, BWT_BIG_ENDIAN >	bwt_stream_type

typedef rank_dictionary < BWT_BITS, FMIndexDataCore::OCC_INT, bwt_stream_type, occ_type, count_table_type >	rank_dict_type

typedef fm_index < rank_dict_type, ssa_type >	fm_index_type

typedef fm_index < rank_dict_type, null_type >	partial_fm_index_type

Public Types inherited from nvbio::io::FMIndexDataCore
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
	FMIndexData ()
	empty constructor More...

virtual	~FMIndexData ()
	virtual destructor More...

occ_type	occ_iterator () const

occ_type	rocc_iterator () const

bwt_type	bwt_iterator () const

bwt_type	rbwt_iterator () const

ssa_type	ssa_iterator () const

ssa_type	rssa_iterator () const

count_table_type	count_table_iterator () const

rank_dict_type	rank_dict () const

rank_dict_type	rrank_dict () const

fm_index_type	index () const

fm_index_type	rindex () const

partial_fm_index_type	partial_index () const

partial_fm_index_type	rpartial_index () const

Public Methods inherited from nvbio::io::FMIndexDataCore
	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...

Additional Inherited Members
Public Members inherited from nvbio::io::FMIndexDataCore
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 inherited from nvbio::io::FMIndexDataCore
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 uint4* nvbio::io::FMIndexData::bwt_occ_type

Definition at line 159 of file fmindex.h.

typedef PackedStream<bwt_type,uint8,BWT_BITS,BWT_BIG_ENDIAN> nvbio::io::FMIndexData::bwt_stream_type

Definition at line 165 of file fmindex.h.

typedef deinterleaved_iterator<2,0,bwt_occ_type> nvbio::io::FMIndexData::bwt_type

Definition at line 160 of file fmindex.h.

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

Definition at line 163 of file fmindex.h.

typedef fm_index<rank_dict_type, ssa_type> nvbio::io::FMIndexData::fm_index_type

Definition at line 174 of file fmindex.h.

typedef deinterleaved_iterator<2,1,bwt_occ_type> nvbio::io::FMIndexData::occ_type

Definition at line 161 of file fmindex.h.

typedef fm_index<rank_dict_type, null_type> nvbio::io::FMIndexData::partial_fm_index_type

Definition at line 175 of file fmindex.h.

typedef rank_dictionary< BWT_BITS, FMIndexDataCore::OCC_INT, bwt_stream_type, occ_type, count_table_type> nvbio::io::FMIndexData::rank_dict_type

Definition at line 172 of file fmindex.h.

typedef SSA_index_multiple<SA_INT> nvbio::io::FMIndexData::ssa_storage_type

Definition at line 164 of file fmindex.h.

Constructor & Destructor Documentation

nvbio::io::FMIndexData::FMIndexData ( )

empty constructor

virtual nvbio::io::FMIndexData::~FMIndexData ( )

inlinevirtual

virtual destructor

Definition at line 178 of file fmindex.h.

Member Function Documentation

bwt_type nvbio::io::FMIndexData::bwt_iterator ( ) const

inline

Definition at line 185 of file fmindex.h.

count_table_type nvbio::io::FMIndexData::count_table_iterator ( ) const

inline

Definition at line 191 of file fmindex.h.

fm_index_type nvbio::io::FMIndexData::index ( ) const

inline

Definition at line 196 of file fmindex.h.

occ_type nvbio::io::FMIndexData::occ_iterator ( ) const

inline

iterators access

Definition at line 182 of file fmindex.h.

partial_fm_index_type nvbio::io::FMIndexData::partial_index ( ) const

inline

Definition at line 199 of file fmindex.h.

rank_dict_type nvbio::io::FMIndexData::rank_dict ( ) const

inline

Definition at line 193 of file fmindex.h.

bwt_type nvbio::io::FMIndexData::rbwt_iterator ( ) const

inline

Definition at line 186 of file fmindex.h.

fm_index_type nvbio::io::FMIndexData::rindex ( ) const

inline

Definition at line 197 of file fmindex.h.

occ_type nvbio::io::FMIndexData::rocc_iterator ( ) const

inline

Definition at line 183 of file fmindex.h.

partial_fm_index_type nvbio::io::FMIndexData::rpartial_index ( ) const

inline

Definition at line 200 of file fmindex.h.

rank_dict_type nvbio::io::FMIndexData::rrank_dict ( ) const

inline

Definition at line 194 of file fmindex.h.

ssa_type nvbio::io::FMIndexData::rssa_iterator ( ) const

inline

Definition at line 189 of file fmindex.h.

ssa_type nvbio::io::FMIndexData::ssa_iterator ( ) const

inline

Definition at line 188 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

Additional Inherited Members

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation