Detailed description

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

Definition at line 662 of file qgram.h.

#include <qgram.h>

Inheritance diagram for nvbio::QGramSetIndexDevice:

Public Types
typedef device_tag	system_tag

typedef QGramIndexCore < device_tag, uint64, uint32, uint2 >	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, uint2 >
typedef device_tag	system_tag

typedef uint64	qgram_type

typedef uint32	index_type

typedef uint2	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 , uint2 * >	plain_view_type

typedef QGramIndexViewCore < const uint64 , const uint32 , const uint2 * >	const_plain_view_type

Public Methods
template<typename string_set_type >
void	build (const uint32 q, const uint32 symbol_sz, const string_set_type string_set, const uint32 qlut=0)

template<typename string_set_type , typename seed_functor >
void	build (const uint32 q, const uint32 symbol_sz, const string_set_type string_set, const seed_functor seeder, const uint32 qlut=0)

template<typename SystemTag >
QGramSetIndexDevice &	operator= (const QGramIndexCore< SystemTag, uint64, uint32, uint2 > &src)

Public Methods inherited from nvbio::QGramIndexCore< device_tag, uint64, uint32, uint2 >
	QGramIndexCore ()

uint64	used_host_memory () const

uint64	used_device_memory () const

Additional Inherited Members
Public Members inherited from nvbio::QGramIndexCore< device_tag, uint64, uint32, uint2 >
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

typedef core_type::const_plain_view_type nvbio::QGramSetIndexDevice::const_plain_view_type

Definition at line 678 of file qgram.h.

typedef core_type::coord_type nvbio::QGramSetIndexDevice::coord_type

Definition at line 676 of file qgram.h.

typedef core_type::coord_vector_type nvbio::QGramSetIndexDevice::coord_vector_type

Definition at line 674 of file qgram.h.

typedef QGramIndexCore< device_tag, uint64, uint32, uint2> nvbio::QGramSetIndexDevice::core_type

Definition at line 670 of file qgram.h.

typedef core_type::index_vector_type nvbio::QGramSetIndexDevice::index_vector_type

Definition at line 673 of file qgram.h.

typedef core_type::plain_view_type nvbio::QGramSetIndexDevice::plain_view_type

Definition at line 677 of file qgram.h.

typedef core_type::qgram_type nvbio::QGramSetIndexDevice::qgram_type

Definition at line 675 of file qgram.h.

typedef core_type::qgram_vector_type nvbio::QGramSetIndexDevice::qgram_vector_type

Definition at line 672 of file qgram.h.

typedef device_tag nvbio::QGramSetIndexDevice::system_tag

Definition at line 664 of file qgram.h.

Member Function Documentation

template<typename string_set_type >

void nvbio::QGramSetIndexDevice::build	(	const uint32	q,
		const uint32	symbol_sz,
		const string_set_type	string_set,
		const uint32	qlut = `0`
	)

build a q-gram index from a given string-set T

Template Parameters

string_set_type the string-set type

Parameters

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

Definition at line 319 of file qgram_inl.h.

template<typename string_set_type , typename seed_functor >

void nvbio::QGramSetIndexDevice::build	(	const uint32	q,
		const uint32	symbol_sz,
		const string_set_type	string_set,
		const seed_functor	seeder,
		const uint32	qlut = `0`
	)

build a q-gram index from a given string-set T using a Seeding Functor

Template Parameters

string_set_type	the string-set type
seed_functor	the Seeding Functor type

Parameters

q	the q parameter
symbol_sz	the size of the symbols, in bits
string_set	the string-set
seeder	the seeding functor
qlut	the number of symbols to include in the LUT (of size O( A^qlut )) used to accelerate q-gram searches

Definition at line 195 of file qgram_inl.h.

template<typename SystemTag >

QGramSetIndexDevice & nvbio::QGramSetIndexDevice::operator= ( const QGramIndexCore< SystemTag, uint64, uint32, uint2 > & src)

copy operator

Definition at line 389 of file qgram_inl.h.

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

E:/git/nvbio/nvbio/qgram/qgram.h
E:/git/nvbio/nvbio/qgram/qgram_inl.h

Detailed description

Public Types

Public Methods

Additional Inherited Members

Member Typedef Documentation

Member Function Documentation