NVBIO: nvbio::QGroupIndexViewCore< index_iterator > Struct Template Reference

Detailed description

template< typename index_iterator>
struct nvbio::QGroupIndexViewCore< index_iterator >

A plain view of a q-group index (see Q-Group Index Module)

Definition at line 81 of file qgroup.h.

#include <qgroup.h>

Public Types
typedef index_iterator	vector_type

typedef uint32	coord_type

typedef QGroupIndexViewCore < index_iterator >	plain_view_type

typedef QGroupIndexViewCore < index_iterator >	const_plain_view_type

typedef uint64	argument_type

typedef uint2	result_type

Public Methods
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE	QGroupIndexViewCore (const uint32 _Q=0, const uint32 _symbol_size=0, const uint32 _n_qgrams=0, const uint32 _n_unique_qgrams=0, vector_type _I=NULL, vector_type _S=NULL, vector_type _SS=NULL, vector_type _P=NULL)

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint2	range (const uint64 g) const

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint2	operator() (const uint64 g) const

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	locate (const uint32 i) const

Public Members
uint32	Q

uint32	symbol_size

uint32	n_qgrams

uint32	n_unique_qgrams

vector_type	I

vector_type	S

vector_type	SS

vector_type	P

Static Public Members
static const uint32	WORD_SIZE = 32

Member Typedef Documentation

template<typename index_iterator >

typedef uint64 nvbio::QGroupIndexViewCore< index_iterator >::argument_type

Definition at line 94 of file qgroup.h.

template<typename index_iterator >

typedef QGroupIndexViewCore<index_iterator> nvbio::QGroupIndexViewCore< index_iterator >::const_plain_view_type

Definition at line 91 of file qgroup.h.

template<typename index_iterator >

typedef uint32 nvbio::QGroupIndexViewCore< index_iterator >::coord_type

Definition at line 87 of file qgroup.h.

template<typename index_iterator >

typedef QGroupIndexViewCore<index_iterator> nvbio::QGroupIndexViewCore< index_iterator >::plain_view_type

Definition at line 90 of file qgroup.h.

template<typename index_iterator >

typedef uint2 nvbio::QGroupIndexViewCore< index_iterator >::result_type

Definition at line 95 of file qgroup.h.

template<typename index_iterator >

typedef index_iterator nvbio::QGroupIndexViewCore< index_iterator >::vector_type

Definition at line 86 of file qgroup.h.

Constructor & Destructor Documentation

template<typename index_iterator >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE nvbio::QGroupIndexViewCore< index_iterator >::QGroupIndexViewCore	(	const uint32	_Q = `0`,
		const uint32	_symbol_size = `0`,
		const uint32	_n_qgrams = `0`,
		const uint32	_n_unique_qgrams = `0`,
		vector_type	_I = `NULL`,
		vector_type	_S = `NULL`,
		vector_type	_SS = `NULL`,
		vector_type	_P = `NULL`
	)

inline

constructor

Definition at line 100 of file qgroup.h.

Member Function Documentation

template<typename index_iterator >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::QGroupIndexViewCore< index_iterator >::locate ( const uint32 i) const

inline

locate a given occurrence of a q-gram

Definition at line 146 of file qgroup.h.

template<typename index_iterator >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint2 nvbio::QGroupIndexViewCore< index_iterator >::operator() ( const uint64 g) const

inline

functor operator

Definition at line 141 of file qgroup.h.

template<typename index_iterator >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint2 nvbio::QGroupIndexViewCore< index_iterator >::range ( const uint64 g) const

inline

return the slots of P corresponding to the given qgram g

Definition at line 121 of file qgroup.h.

Member Data Documentation

template<typename index_iterator >

vector_type nvbio::QGroupIndexViewCore< index_iterator >::I

Definition at line 153 of file qgroup.h.

template<typename index_iterator >

uint32 nvbio::QGroupIndexViewCore< index_iterator >::n_qgrams

Definition at line 151 of file qgroup.h.

template<typename index_iterator >

uint32 nvbio::QGroupIndexViewCore< index_iterator >::n_unique_qgrams

Definition at line 152 of file qgroup.h.

template<typename index_iterator >

vector_type nvbio::QGroupIndexViewCore< index_iterator >::P

Definition at line 156 of file qgroup.h.

template<typename index_iterator >

uint32 nvbio::QGroupIndexViewCore< index_iterator >::Q

Definition at line 149 of file qgroup.h.

template<typename index_iterator >

vector_type nvbio::QGroupIndexViewCore< index_iterator >::S

Definition at line 154 of file qgroup.h.

template<typename index_iterator >

vector_type nvbio::QGroupIndexViewCore< index_iterator >::SS

Definition at line 155 of file qgroup.h.

template<typename index_iterator >

uint32 nvbio::QGroupIndexViewCore< index_iterator >::symbol_size

Definition at line 150 of file qgroup.h.

template<typename index_iterator >

const uint32 nvbio::QGroupIndexViewCore< index_iterator >::WORD_SIZE = 32

static

Definition at line 83 of file qgroup.h.

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

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