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nvbio::priv::HostStringSetRadices< 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::HostStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >

Definition at line 1546 of file sufsort_priv.h.

#include <sufsort_priv.h>

Public Methods

 HostStringSetRadices (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 block_size)
 
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
 
const uint2 * m_suffixes
 
thrust::device_ptr< const uint2 > d_suffixes
 
thrust::device_vector< uint2 > d_active_suffixes
 
thrust::device_vector< uint8 > d_symbols
 
thrust::host_vector< uint2 > h_active_suffixes
 
thrust::host_vector< uint8 > h_symbols
 
thrust::host_vector< uint32 > m_block
 

Constructor & Destructor Documentation

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

Definition at line 1548 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::HostStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >::allocated_device_memory ( ) const
inline

return the amount of used device memory

Definition at line 1789 of file sufsort_priv.h.

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

return the amount of used device memory

Definition at line 1798 of file sufsort_priv.h.

template<typename string_set_type , uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>
void nvbio::priv::HostStringSetRadices< 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 1702 of file sufsort_priv.h.

template<typename string_set_type , uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>
void nvbio::priv::HostStringSetRadices< 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 1684 of file sufsort_priv.h.

template<typename string_set_type , uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>
void nvbio::priv::HostStringSetRadices< 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 1659 of file sufsort_priv.h.

template<typename string_set_type , uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>
void nvbio::priv::HostStringSetRadices< 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 1588 of file sufsort_priv.h.

template<typename string_set_type , uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>
void nvbio::priv::HostStringSetRadices< 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 1596 of file sufsort_priv.h.

template<typename string_set_type , uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>
uint64 nvbio::priv::HostStringSetRadices< 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 1561 of file sufsort_priv.h.

template<typename string_set_type , uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>
uint32 nvbio::priv::HostStringSetRadices< 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 1552 of file sufsort_priv.h.

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

reserve any temporary space for the given amount of suffixes

Definition at line 1569 of file sufsort_priv.h.

Member Data Documentation

template<typename string_set_type , uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>
thrust::device_vector<uint2> nvbio::priv::HostStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >::d_active_suffixes

Definition at line 1809 of file sufsort_priv.h.

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

Definition at line 1808 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::HostStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >::d_symbols

Definition at line 1810 of file sufsort_priv.h.

template<typename string_set_type , uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>
thrust::host_vector<uint2> nvbio::priv::HostStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >::h_active_suffixes

Definition at line 1811 of file sufsort_priv.h.

template<typename string_set_type , uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>
thrust::host_vector<uint8> nvbio::priv::HostStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >::h_symbols

Definition at line 1812 of file sufsort_priv.h.

template<typename string_set_type , uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>
thrust::host_vector<uint32> nvbio::priv::HostStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >::m_block

Definition at line 1813 of file sufsort_priv.h.

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

Definition at line 1806 of file sufsort_priv.h.

template<typename string_set_type , uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>
const uint2* nvbio::priv::HostStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >::m_suffixes

Definition at line 1807 of file sufsort_priv.h.

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