Detailed description

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

Definition at line 636 of file qgram.h.

#include <qgram.h>

Inheritance diagram for nvbio::QGramSetIndexHost:

Public Types
typedef host_tag	system_tag

typedef QGramIndexCore < host_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< host_tag, uint64, uint32, uint2 >
typedef host_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 SystemTag >
QGramSetIndexHost &	operator= (const QGramIndexCore< SystemTag, uint64, uint32, uint2 > &src)

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

uint64	used_host_memory () const

uint64	used_device_memory () const

Additional Inherited Members
Public Members inherited from nvbio::QGramIndexCore< host_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...