Detailed description

A device-side q-gram index for strings (see Q-Gram Index Module)

Definition at line 591 of file qgram.h.

#include <qgram.h>

Inheritance diagram for nvbio::QGramIndexDevice:

Public Types
typedef device_tag	system_tag

typedef QGramIndexCore < device_tag, uint64, uint32, uint32 >	core_type

typedef core_type::qgram_vector_type	qgram_vector_type

typedef core_type::index_vector_type	index_vector_type

typedef core_type::coord_vector_type	coord_vector_type

typedef core_type::qgram_type	qgram_type

typedef core_type::coord_type	coord_type

typedef core_type::plain_view_type	plain_view_type

typedef core_type::const_plain_view_type	const_plain_view_type

Public Types inherited from nvbio::QGramIndexCore< device_tag, uint64, uint32, uint32 >
typedef device_tag	system_tag

typedef uint64	qgram_type

typedef uint32	index_type

typedef uint32	coord_type

typedef nvbio::vector < system_tag, qgram_type >	qgram_vector_type

typedef nvbio::vector < system_tag, index_type >	index_vector_type

typedef nvbio::vector < system_tag, coord_type >	coord_vector_type

typedef QGramIndexViewCore < uint64 , uint32 , uint32 * >	plain_view_type

typedef QGramIndexViewCore < const uint64 , const uint32 , const uint32 * >	const_plain_view_type

Public Methods
template<typename string_type >
void	build (const uint32 q, const uint32 symbol_sz, const uint32 string_len, const string_type string, const uint32 qlut=0)

template<typename SystemTag >
QGramIndexDevice &	operator= (const QGramIndexCore< SystemTag, uint64, uint32, uint32 > &src)

Public Methods inherited from nvbio::QGramIndexCore< device_tag, uint64, uint32, uint32 >
	QGramIndexCore ()

uint64	used_host_memory () const

uint64	used_device_memory () const

Additional Inherited Members
Public Members inherited from nvbio::QGramIndexCore< device_tag, uint64, uint32, uint32 >
uint32	Q
	the q-gram size More...

uint32	symbol_size
	symbol size More...

uint32	n_qgrams
	the number of q-grams in the original string More...

uint32	n_unique_qgrams
	the number of unique q-grams in the original string More...

qgram_vector_type	qgrams
	the sorted list of unique q-grams More...

index_vector_type	slots
	slots[i] stores the first occurrence of q-grams[i] in index More...

coord_vector_type	index
	the list of occurrences of all (partially-sorted) q-grams in the original string More...

uint32	QL
	the number of LUT symbols More...

uint32	QLS
	the number of leading bits of a q-gram to lookup in the LUT More...

index_vector_type	lut
	a LUT used to accelerate q-gram searches More...

Member Typedef Documentation

Definition at line 607 of file qgram.h.

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Definition at line 603 of file qgram.h.

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Definition at line 602 of file qgram.h.

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Definition at line 604 of file qgram.h.

Definition at line 601 of file qgram.h.

Definition at line 593 of file qgram.h.

template<typename string_type >

void nvbio::QGramIndexDevice::build	(	const uint32	q,
		const uint32	symbol_sz,
		const uint32	string_len,
		const string_type	string,
		const uint32	qlut = `0`
	)

build a q-gram index from a given string T

Template Parameters

string_type the string iterator type

Parameters

q	the q parameter
symbol_sz	the size of the symbols, in bits
string_len	the size of the string
string	the string iterator
qlut	the number of symbols to include in the LUT (of size O( A^qlut )) used to accelerate q-gram searches

Definition at line 39 of file qgram_inl.h.

template<typename SystemTag >

QGramIndexDevice & nvbio::QGramIndexDevice::operator= ( const QGramIndexCore< SystemTag, uint64, uint32, uint32 > & src)

copy operator

Definition at line 354 of file qgram_inl.h.

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