qgram.h File Reference

#include <nvbio/basic/types.h>
#include <nvbio/basic/numbers.h>
#include <nvbio/basic/algorithms.h>
#include <nvbio/basic/cuda/primitives.h>
#include <nvbio/basic/thrust_view.h>
#include <nvbio/basic/exceptions.h>
#include <nvbio/basic/iterator.h>
#include <nvbio/basic/vector.h>
#include <nvbio/strings/seeds.h>
#include <thrust/host_vector.h>
#include <thrust/device_vector.h>
#include <thrust/sort.h>
#include <thrust/for_each.h>
#include <thrust/binary_search.h>
#include <thrust/iterator/constant_iterator.h>
#include <thrust/iterator/counting_iterator.h>
#include <nvbio/qgram/qgram_inl.h>

Go to the source code of this file.

Classes
struct	nvbio::QGramIndexViewCore< QGramVectorType, IndexVectorType, CoordVectorType >
struct	nvbio::QGramIndexCore< SystemTag, QGramType, IndexType, CoordType >
struct	nvbio::QGramIndexHost
struct	nvbio::QGramIndexDevice
struct	nvbio::QGramSetIndexHost
struct	nvbio::QGramSetIndexDevice
struct	nvbio::plain_view_subtype< QGramIndexHost >
struct	nvbio::plain_view_subtype< QGramIndexDevice >
struct	nvbio::plain_view_subtype< const QGramIndexHost >
struct	nvbio::plain_view_subtype< const QGramIndexDevice >
struct	nvbio::plain_view_subtype< QGramSetIndexHost >
struct	nvbio::plain_view_subtype< QGramSetIndexDevice >
struct	nvbio::plain_view_subtype< const QGramSetIndexHost >
struct	nvbio::plain_view_subtype< const QGramSetIndexDevice >
struct	nvbio::qgram_locate_functor< qgram_index_type >
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 >

Namespaces
	nvbio
	Define a vector_view POD type and plain_view() for std::vector.

Typedefs
typedef QGramIndexViewCore < uint64 *, uint32 *, uint32 * >	nvbio::QGramIndexView
typedef QGramIndexViewCore < uint64 *, uint32 *, uint2 * >	nvbio::QGramSetIndexView
typedef QGramIndexViewCore < const uint64 *, const uint32 *, const uint32 * >	nvbio::ConstQGramIndexView
typedef QGramIndexViewCore < const uint64 *, const uint32 *, const uint2 * >	nvbio::ConstQGramSetIndexView

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)
template<typename SystemTag , typename QT , typename IT , typename CT >
QGramIndexViewCore< QT, IT, CT >	nvbio::plain_view (const QGramIndexViewCore< QT, IT, CT > qgram)
template<typename SystemTag , typename QT , typename IT , typename CT >
QGramIndexViewCore< QT *, IT *, CT * >	nvbio::plain_view (QGramIndexCore< SystemTag, QT, IT, CT > &qgram)
template<typename SystemTag , typename QT , typename IT , typename CT >
QGramIndexViewCore< const QT *, const IT *, const CT * >	nvbio::plain_view (const QGramIndexCore< SystemTag, QT, IT, CT > &qgram)