nvbio::QGroupIndexDevice Struct Reference

Detailed description

A device-side q-group index (see Q-Group Index Module)

Definition at line 200 of file qgroup.h.

#include <qgroup.h>

Public Types
typedef device_tag	system_tag
typedef thrust::device_vector < uint32 >	vector_type
typedef uint32	coord_type
typedef QGroupIndexView	view_type

Public Methods
template<typename string_type >
void	build (const uint32 q, const uint32 symbol_sz, const uint32 string_len, const string_type string)
uint64	used_host_memory () const
uint64	used_device_memory () 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

typedef uint32 nvbio::QGroupIndexDevice::coord_type

Definition at line 207 of file qgroup.h.

typedef device_tag nvbio::QGroupIndexDevice::system_tag

Definition at line 204 of file qgroup.h.

typedef thrust::device_vector<uint32> nvbio::QGroupIndexDevice::vector_type

Definition at line 206 of file qgroup.h.

typedef QGroupIndexView nvbio::QGroupIndexDevice::view_type

Definition at line 208 of file qgroup.h.

Member Function Documentation

template<typename string_type >

void nvbio::QGroupIndexDevice::build	(	const uint32	q,
		const uint32	symbol_sz,
		const uint32	string_len,
		const string_type	string
	)

build a q-group index from a given string T; the amount of storage required is basically O( A^q + |T|*32 ) bits, where A is the alphabet size.

Template Parameters

string_type

the string iterator type

Parameters

q	the q parameter
symbol_sz	the size of the symbols, in bits
string_len	the size of the string
string	the string iterator

Definition at line 178 of file qgroup_inl.h.

uint64 nvbio::QGroupIndexDevice::used_device_memory ( ) const

inline

return the amount of device memory used

Definition at line 233 of file qgroup.h.

uint64 nvbio::QGroupIndexDevice::used_host_memory ( ) const

inline

return the amount of device memory used

Definition at line 229 of file qgroup.h.

Member Data Documentation

vector_type nvbio::QGroupIndexDevice::I

Definition at line 245 of file qgroup.h.

uint32 nvbio::QGroupIndexDevice::n_qgrams

Definition at line 243 of file qgroup.h.

uint32 nvbio::QGroupIndexDevice::n_unique_qgrams

Definition at line 244 of file qgroup.h.

vector_type nvbio::QGroupIndexDevice::P

Definition at line 248 of file qgroup.h.

uint32 nvbio::QGroupIndexDevice::Q

Definition at line 241 of file qgroup.h.

vector_type nvbio::QGroupIndexDevice::S

Definition at line 246 of file qgroup.h.

vector_type nvbio::QGroupIndexDevice::SS

Definition at line 247 of file qgroup.h.

uint32 nvbio::QGroupIndexDevice::symbol_size

Definition at line 242 of file qgroup.h.

const uint32 nvbio::QGroupIndexDevice::WORD_SIZE = 32

static

Definition at line 202 of file qgroup.h.

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

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