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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
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

Definition at line 207 of file qgroup.h.

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.

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_typethe string iterator type
qthe q parameter
symbol_szthe size of the symbols, in bits
string_lenthe size of the string
stringthe string iterator

Definition at line 178 of file qgroup_inl.h.

uint64 nvbio::QGroupIndexDevice::used_device_memory ( ) const

return the amount of device memory used

Definition at line 233 of file qgroup.h.

uint64 nvbio::QGroupIndexDevice::used_host_memory ( ) const

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

Definition at line 202 of file qgroup.h.

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