Q-Gram Module

Detailed Description

This module contains a series of classes and functions to operate on q-grams and q-gram indices. It implements the following data-structures:

• the Q-Group Index
• the Q-Gram Index
• the Q-Gram Filter

It also defines convenience functions to generate q-grams extracted out of strings and string-sets (see Seeding):

• generate_qgrams()

Modules
	Q-Gram Index Module
	Q-Group Index Module

Classes
struct	nvbio::QGramFilter< system_tag, qgram_index_type, query_iterator, index_iterator >
struct	nvbio::QGramFilter< host_tag, qgram_index_type, query_iterator, index_iterator >
struct	nvbio::QGramFilter< device_tag, qgram_index_type, query_iterator, index_iterator >
struct	nvbio::QGramFilterHost< qgram_index_type, query_iterator, index_iterator >
struct	nvbio::QGramFilterDevice< qgram_index_type, query_iterator, index_iterator >
struct	nvbio::string_qgram_functor< string_type >
struct	nvbio::string_set_qgram_functor< string_set_type >
struct	nvbio::string_qgram_search_functor< qgram_index_type, string_type >

Functions
template<typename string_type , typename index_iterator , typename qgram_iterator >
void	nvbio::generate_qgrams (const uint32 q, const uint32 symbol_size, const uint32 string_len, const string_type string, const uint32 n_qgrams, const index_iterator indices, qgram_iterator qgrams)
template<typename string_set_type , typename index_iterator , typename qgram_iterator >
void	nvbio::generate_qgrams (const uint32 q, const uint32 symbol_size, const string_set_type string_set, const uint32 n_qgrams, const index_iterator indices, qgram_iterator qgrams)

Function Documentation

template<typename string_type , typename index_iterator , typename qgram_iterator >

void nvbio::generate_qgrams	(	const uint32	q,
		const uint32	symbol_size,
		const uint32	string_len,
		const string_type	string,
		const uint32	n_qgrams,
		const index_iterator	indices,
		qgram_iterator	qgrams
	)

generate the q-grams corresponding to a list of q-gram coordinates

Template Parameters

string_type	a string iterator
index_iterator	a q-gram coordinate iterator
qgram_iterator	a q-gram iterator

Parameters

q	the q-gram length
symbol_size	the symbol size, in bits
string_len	the input string length
string	the input string
n_qgrams	the number of q-grams to generate
indices	the input q-gram coordinates
indices	the output q-grams

Definition at line 418 of file qgram_inl.h.

template<typename string_set_type , typename index_iterator , typename qgram_iterator >

void nvbio::generate_qgrams	(	const uint32	q,
		const uint32	symbol_size,
		const string_set_type	string_set,
		const uint32	n_qgrams,
		const index_iterator	indices,
		qgram_iterator	qgrams
	)

generate the q-grams corresponding to a list of q-gram coordinates

Template Parameters

string_type	a string iterator
index_iterator	a q-gram coordinate iterator
qgram_iterator	a q-gram iterator

Parameters

q	the q-gram length
symbol_size	the symbol size, in bits
string_set	the input string-set
n_qgrams	the number of q-grams to generate
indices	the input q-gram coordinates
indices	the output q-grams

Definition at line 448 of file qgram_inl.h.