nvbio::SparseSymbolSet Struct Reference

Detailed description

A data structure to hold a sparse subset of symbols from a larger set/string

Definition at line 201 of file paged_text.h.

#include <paged_text.h>

Public Methods
	SparseSymbolSet ()
uint32	size () const
void	reserve (const uint64 n, const uint32 n_special)
void	set (const uint64 range, const uint32 n_special, const uint32 *p, const uint32 *id)
void	insert (const uint64 range, const uint32 n_block, const uint64 *g, const uint32 n_special, const uint32 *p_special, const uint64 *g_special, const uint32 *id_special)
void	set_range (const uint64 n)
uint32	rank (const uint64 i) const
const uint64 *	pos () const
const uint64 *	ids () const

Public Members
uint64	m_n
uint32	m_n_special
nvbio::vector< host_tag, uint64 >	m_pos
nvbio::vector< host_tag, uint64 >	m_new_pos
nvbio::vector< host_tag, uint64 >	m_id
nvbio::vector< host_tag, uint64 >	m_new_id
nvbio::vector< host_tag, uint32 >	m_buckets

Static Public Members
static const uint32	LOG_BUCKET_SIZE = 20u
static const uint32	BUCKET_SIZE = 1u << LOG_BUCKET_SIZE

Constructor & Destructor Documentation

nvbio::SparseSymbolSet::SparseSymbolSet ( )

inline

constructor

Parameters

c	the special symbol recorded into this set

Definition at line 210 of file paged_text.h.

Member Function Documentation

const uint64* nvbio::SparseSymbolSet::ids ( ) const

inline

Definition at line 277 of file paged_text.h.

void nvbio::SparseSymbolSet::insert	(	const uint64	range,
		const uint32	n_block,
		const uint64 *	g,
		const uint32	n_special,
		const uint32 *	p_special,
		const uint64 *	g_special,
		const uint32 *	id_special
	)

simulates the insertion of a set of n_block symbols at positions g in a string, n_special of which are special and will be recorded in this set. Note that the actual symbols in the block don't need to be known, but in order to adjust the positions of the previously inserted symbols we need to know all their insertion positions, for the entire block, not just for the special symbols.

Parameters

range	total number of symbols in the virtual string
n_block	total number of inserted symbols
g	insertion positions for the entire block
n_special	number of symbols in the block which are special
p_special	the positions of the special symbols in the block
g_special	the insertion positions of the special symbols
id_special	the ids associated to the special symbols
n_special	number of symbols in c which are special

Definition at line 236 of file paged_text.cpp.

const uint64* nvbio::SparseSymbolSet::pos ( ) const

inline

Definition at line 276 of file paged_text.h.

uint32 nvbio::SparseSymbolSet::rank ( const uint64  i) const

inline

find how many special symbols there are in the range [0,i] (inclusive)

Definition at line 260 of file paged_text.h.

void nvbio::SparseSymbolSet::reserve	(	const uint64	n,
		const uint32	n_special
	)

reserve enough storage for n special symbols

Definition at line 202 of file paged_text.cpp.

void nvbio::SparseSymbolSet::set	(	const uint64	range,
		const uint32	n_special,
		const uint32 *	p,
		const uint32 *	id
	)

set the initial set of symbols

Parameters

range	total number of symbols in the virtual string
n_special	number of symbols in the block which are special
p_special	the positions of the special symbols in the block
g_special	the insertion positions of the special symbols

Definition at line 213 of file paged_text.cpp.

void nvbio::SparseSymbolSet::set_range

(

const uint64

n)

extend the range of string indices

Definition at line 281 of file paged_text.cpp.

uint32 nvbio::SparseSymbolSet::size ( void  ) const

inline

return the number of special symbols collected so far

Definition at line 214 of file paged_text.h.

Member Data Documentation

const uint32 nvbio::SparseSymbolSet::BUCKET_SIZE = 1u << LOG_BUCKET_SIZE

static

Definition at line 204 of file paged_text.h.

const uint32 nvbio::SparseSymbolSet::LOG_BUCKET_SIZE = 20u

static

Definition at line 203 of file paged_text.h.

nvbio::vector<host_tag,uint32> nvbio::SparseSymbolSet::m_buckets

Definition at line 285 of file paged_text.h.

nvbio::vector<host_tag,uint64> nvbio::SparseSymbolSet::m_id

Definition at line 283 of file paged_text.h.

uint64 nvbio::SparseSymbolSet::m_n

Definition at line 279 of file paged_text.h.

uint32 nvbio::SparseSymbolSet::m_n_special

Definition at line 280 of file paged_text.h.

nvbio::vector<host_tag,uint64> nvbio::SparseSymbolSet::m_new_id

Definition at line 284 of file paged_text.h.

nvbio::vector<host_tag,uint64> nvbio::SparseSymbolSet::m_new_pos

Definition at line 282 of file paged_text.h.

nvbio::vector<host_tag,uint64> nvbio::SparseSymbolSet::m_pos

Definition at line 281 of file paged_text.h.

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

• E:/git/nvbio/nvbio/fmindex/paged_text.h
• E:/git/nvbio/nvbio/fmindex/paged_text.cpp