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nvbio::priv::DeviceStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS > Struct Template Reference

Detailed description

template< typename string_set_type, uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>
struct nvbio::priv::DeviceStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >

Definition at line 1820 of file sufsort_priv.h.

#include <sufsort_priv.h>

Public Methods

 DeviceStringSetRadices ()
 
 DeviceStringSetRadices (const string_set_type string_set)
 
uint32 num_words (const uint32 max_string_len) const
 
uint64 needed_device_memory (const uint32 n_suffixes) const
 
void reserve (const uint32 n_suffixes, const uint32 slice_size)
 
void set (const string_set_type string_set)
 
void init (const uint32 n_suffixes, const uint2 *_h_suffixes, const uint2 *_d_suffixes)
 
void init_slice (const uint32 n_indices, const uint32 *d_indices, const uint32 word_block_begin, const uint32 word_block_end)
 
void extract (const uint32 n_indices, const uint32 *d_indices, const uint32 word_idx, const uint32 word_block_begin, const uint32 word_block_end, uint32 *d_radices) const
 
void dollar_bwt (const uint32 begin, const uint32 end, uint8 *h_bwt)
 
void bwt (const uint32 n_suffixes, const uint32 *d_indices, uint8 *h_bwt, uint8 *d_bwt)
 
uint64 allocated_device_memory () const
 
uint64 allocated_host_memory () const
 

Public Members

string_set_type m_string_set
 
thrust::device_ptr< const uint2 > d_suffixes
 
thrust::device_vector< uint8d_symbols
 

Constructor & Destructor Documentation

template<typename string_set_type, uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>
nvbio::priv::DeviceStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >::DeviceStringSetRadices ( )
inline

Definition at line 1822 of file sufsort_priv.h.

template<typename string_set_type, uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>
nvbio::priv::DeviceStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >::DeviceStringSetRadices ( const string_set_type  string_set)
inline

Definition at line 1823 of file sufsort_priv.h.

Member Function Documentation

template<typename string_set_type, uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>
uint64 nvbio::priv::DeviceStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >::allocated_device_memory ( ) const
inline

return the amount of used device memory

Definition at line 1973 of file sufsort_priv.h.

template<typename string_set_type, uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>
uint64 nvbio::priv::DeviceStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >::allocated_host_memory ( ) const
inline

return the amount of used device memory

Definition at line 1980 of file sufsort_priv.h.

template<typename string_set_type, uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>
void nvbio::priv::DeviceStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >::bwt ( const uint32  n_suffixes,
const uint32 d_indices,
uint8 h_bwt,
uint8 d_bwt 
)
inline

extract the bwt of the given block

Definition at line 1930 of file sufsort_priv.h.

template<typename string_set_type, uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>
void nvbio::priv::DeviceStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >::dollar_bwt ( const uint32  begin,
const uint32  end,
uint8 h_bwt 
)
inline

extract the bwt of the given block

Definition at line 1905 of file sufsort_priv.h.

template<typename string_set_type, uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>
void nvbio::priv::DeviceStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >::extract ( const uint32  n_indices,
const uint32 d_indices,
const uint32  word_idx,
const uint32  word_block_begin,
const uint32  word_block_end,
uint32 d_radices 
) const
inline

extract the radices corresponding to a given word of the given suffixes

Parameters
n_indicesthe input number of suffixes
d_indicesa device vector of the indices to extract
word_idxthe word index to extract
word_beginthe beginning of the current slice range
word_idxthe end of the current slice range
d_radicesthe destination device array to hold the output

Definition at line 1876 of file sufsort_priv.h.

template<typename string_set_type, uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>
void nvbio::priv::DeviceStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >::init ( const uint32  n_suffixes,
const uint2 *  _h_suffixes,
const uint2 *  _d_suffixes 
)
inline

initialize the suffixes to extract

Definition at line 1854 of file sufsort_priv.h.

template<typename string_set_type, uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>
void nvbio::priv::DeviceStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >::init_slice ( const uint32  n_indices,
const uint32 d_indices,
const uint32  word_block_begin,
const uint32  word_block_end 
)
inline

initialize extraction of a slice of words

Definition at line 1861 of file sufsort_priv.h.

template<typename string_set_type, uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>
uint64 nvbio::priv::DeviceStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >::needed_device_memory ( const uint32  n_suffixes) const
inline

needed amount of device storage

Definition at line 1836 of file sufsort_priv.h.

template<typename string_set_type, uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>
uint32 nvbio::priv::DeviceStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >::num_words ( const uint32  max_string_len) const
inline

return the number of words needed to represent a given string length

Definition at line 1827 of file sufsort_priv.h.

template<typename string_set_type, uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>
void nvbio::priv::DeviceStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >::reserve ( const uint32  n_suffixes,
const uint32  slice_size 
)
inline

reserve any temporary space for the given amount of suffixes

Definition at line 1843 of file sufsort_priv.h.

template<typename string_set_type, uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>
void nvbio::priv::DeviceStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >::set ( const string_set_type  string_set)
inline

set string set

Definition at line 1850 of file sufsort_priv.h.

Member Data Documentation

template<typename string_set_type, uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>
thrust::device_ptr<const uint2> nvbio::priv::DeviceStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >::d_suffixes

Definition at line 1986 of file sufsort_priv.h.

template<typename string_set_type, uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>
thrust::device_vector<uint8> nvbio::priv::DeviceStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >::d_symbols

Definition at line 1987 of file sufsort_priv.h.

template<typename string_set_type, uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>
string_set_type nvbio::priv::DeviceStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >::m_string_set

Definition at line 1985 of file sufsort_priv.h.


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