nvbio::QGramIndexCore< SystemTag, QGramType, IndexType, CoordType > Struct Template Reference

Detailed description

template< typename SystemTag, typename QGramType, typename IndexType, typename CoordType>
struct nvbio::QGramIndexCore< SystemTag, QGramType, IndexType, CoordType >

The base q-gram index core class (see Q-Gram Index Module)

Definition at line 509 of file qgram.h.

#include <qgram.h>

Public Types
typedef SystemTag	system_tag
typedef QGramType	qgram_type
typedef IndexType	index_type
typedef CoordType	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 < QGramType *, IndexType *, CoordType * >	plain_view_type
typedef QGramIndexViewCore < const QGramType *, const IndexType *, const CoordType * >	const_plain_view_type

Public Methods
	QGramIndexCore ()
uint64	used_host_memory () const
uint64	used_device_memory () const

Public Members
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

template<typename SystemTag, typename QGramType, typename IndexType, typename CoordType>

typedef QGramIndexViewCore<const QGramType*,const IndexType*,const CoordType*> nvbio::QGramIndexCore< SystemTag, QGramType, IndexType, CoordType >::const_plain_view_type

Definition at line 521 of file qgram.h.

template<typename SystemTag, typename QGramType, typename IndexType, typename CoordType>

typedef CoordType nvbio::QGramIndexCore< SystemTag, QGramType, IndexType, CoordType >::coord_type

Definition at line 515 of file qgram.h.

template<typename SystemTag, typename QGramType, typename IndexType, typename CoordType>

typedef nvbio::vector<system_tag,coord_type> nvbio::QGramIndexCore< SystemTag, QGramType, IndexType, CoordType >::coord_vector_type

Definition at line 518 of file qgram.h.

template<typename SystemTag, typename QGramType, typename IndexType, typename CoordType>

typedef IndexType nvbio::QGramIndexCore< SystemTag, QGramType, IndexType, CoordType >::index_type

Definition at line 514 of file qgram.h.

template<typename SystemTag, typename QGramType, typename IndexType, typename CoordType>

typedef nvbio::vector<system_tag,index_type> nvbio::QGramIndexCore< SystemTag, QGramType, IndexType, CoordType >::index_vector_type

Definition at line 517 of file qgram.h.

template<typename SystemTag, typename QGramType, typename IndexType, typename CoordType>

typedef QGramIndexViewCore<QGramType*,IndexType*,CoordType*> nvbio::QGramIndexCore< SystemTag, QGramType, IndexType, CoordType >::plain_view_type

Definition at line 520 of file qgram.h.

template<typename SystemTag, typename QGramType, typename IndexType, typename CoordType>

typedef QGramType nvbio::QGramIndexCore< SystemTag, QGramType, IndexType, CoordType >::qgram_type

Definition at line 513 of file qgram.h.

template<typename SystemTag, typename QGramType, typename IndexType, typename CoordType>

typedef nvbio::vector<system_tag,qgram_type> nvbio::QGramIndexCore< SystemTag, QGramType, IndexType, CoordType >::qgram_vector_type

Definition at line 516 of file qgram.h.

template<typename SystemTag, typename QGramType, typename IndexType, typename CoordType>

typedef SystemTag nvbio::QGramIndexCore< SystemTag, QGramType, IndexType, CoordType >::system_tag

Definition at line 511 of file qgram.h.

Constructor & Destructor Documentation

template<typename SystemTag, typename QGramType, typename IndexType, typename CoordType>

nvbio::QGramIndexCore< SystemTag, QGramType, IndexType, CoordType >::QGramIndexCore ( )

inline

Definition at line 523 of file qgram.h.

Member Function Documentation

template<typename SystemTag, typename QGramType, typename IndexType, typename CoordType>

uint64 nvbio::QGramIndexCore< SystemTag, QGramType, IndexType, CoordType >::used_device_memory ( ) const

inline

return the amount of device memory used

Definition at line 539 of file qgram.h.

template<typename SystemTag, typename QGramType, typename IndexType, typename CoordType>

uint64 nvbio::QGramIndexCore< SystemTag, QGramType, IndexType, CoordType >::used_host_memory ( ) const

inline

return the amount of device memory used

Definition at line 527 of file qgram.h.

Member Data Documentation

template<typename SystemTag, typename QGramType, typename IndexType, typename CoordType>

coord_vector_type nvbio::QGramIndexCore< SystemTag, QGramType, IndexType, CoordType >::index

the list of occurrences of all (partially-sorted) q-grams in the original string

Definition at line 555 of file qgram.h.

template<typename SystemTag, typename QGramType, typename IndexType, typename CoordType>

index_vector_type nvbio::QGramIndexCore< SystemTag, QGramType, IndexType, CoordType >::lut

a LUT used to accelerate q-gram searches

Definition at line 559 of file qgram.h.

template<typename SystemTag, typename QGramType, typename IndexType, typename CoordType>

uint32 nvbio::QGramIndexCore< SystemTag, QGramType, IndexType, CoordType >::n_qgrams

the number of q-grams in the original string

Definition at line 551 of file qgram.h.

template<typename SystemTag, typename QGramType, typename IndexType, typename CoordType>

uint32 nvbio::QGramIndexCore< SystemTag, QGramType, IndexType, CoordType >::n_unique_qgrams

the number of unique q-grams in the original string

Definition at line 552 of file qgram.h.

template<typename SystemTag, typename QGramType, typename IndexType, typename CoordType>

uint32 nvbio::QGramIndexCore< SystemTag, QGramType, IndexType, CoordType >::Q

the q-gram size

Definition at line 549 of file qgram.h.

template<typename SystemTag, typename QGramType, typename IndexType, typename CoordType>

qgram_vector_type nvbio::QGramIndexCore< SystemTag, QGramType, IndexType, CoordType >::qgrams

the sorted list of unique q-grams

Definition at line 553 of file qgram.h.

template<typename SystemTag, typename QGramType, typename IndexType, typename CoordType>

uint32 nvbio::QGramIndexCore< SystemTag, QGramType, IndexType, CoordType >::QL

the number of LUT symbols

Definition at line 557 of file qgram.h.

template<typename SystemTag, typename QGramType, typename IndexType, typename CoordType>

uint32 nvbio::QGramIndexCore< SystemTag, QGramType, IndexType, CoordType >::QLS

the number of leading bits of a q-gram to lookup in the LUT

Definition at line 558 of file qgram.h.

template<typename SystemTag, typename QGramType, typename IndexType, typename CoordType>

index_vector_type nvbio::QGramIndexCore< SystemTag, QGramType, IndexType, CoordType >::slots

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

Definition at line 554 of file qgram.h.

template<typename SystemTag, typename QGramType, typename IndexType, typename CoordType>

uint32 nvbio::QGramIndexCore< SystemTag, QGramType, IndexType, CoordType >::symbol_size

symbol size

Definition at line 550 of file qgram.h.

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

• E:/git/nvbio/nvbio/qgram/qgram.h