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nvbio::cuda::PrefixDoublingSufSort Struct Reference

Detailed description

A sorting enactor for sorting all suffixes of a given string using a modified parallel version of "Faster Suffix Sorting" by Larsson and Sadanake.

Definition at line 51 of file prefix_doubling_sufsort.h.

#include <prefix_doubling_sufsort.h>

Public Methods

 PrefixDoublingSufSort ()
 
template<typename string_type , typename output_iterator >
void sort (const typename stream_traits< string_type >::index_type string_len, const string_type string, output_iterator d_suffixes)
 
void reserve (const uint32 n)
 
void clear ()
 

Public Members

float extract_time
 timing stats More...
 
float gather_time
 timing stats More...
 
float radixsort_time
 timing stats More...
 
float segment_time
 timing stats More...
 
float compact_time
 timing stats More...
 
float inverse_time
 timing stats More...
 

Constructor & Destructor Documentation

nvbio::cuda::PrefixDoublingSufSort::PrefixDoublingSufSort ( )
inline

constructor

Definition at line 55 of file prefix_doubling_sufsort.h.

Member Function Documentation

void nvbio::cuda::PrefixDoublingSufSort::clear ( void  )
inline

free all temporary storage

Definition at line 100 of file prefix_doubling_sufsort.h.

void nvbio::cuda::PrefixDoublingSufSort::reserve ( const uint32  n)
inline

reserve enough storage for sorting n strings/suffixes

Definition at line 80 of file prefix_doubling_sufsort.h.

template<typename string_type , typename output_iterator >
void nvbio::cuda::PrefixDoublingSufSort::sort ( const typename stream_traits< string_type >::index_type  string_len,
const string_type  string,
output_iterator  d_suffixes 
)

Sort all the suffixes of a given string, using a modified parallel version of "Faster Suffix Sorting" by Larsson and Sadanake.

Parameters
string_lenstring length
stringstring iterator
d_suffixesdevice vector of output suffixes

All the other parameters are temporary device buffers

Sort all the suffixes of a given string, using a modified parallel version of "Faster Suffix Sorting" by Larsson and Sadanake.

Parameters
string_lenstring length
stringstring iterator
d_suffixesdevice vector of output suffixes

Definition at line 464 of file prefix_doubling_sufsort.h.

Member Data Documentation

float nvbio::cuda::PrefixDoublingSufSort::compact_time

timing stats

Definition at line 118 of file prefix_doubling_sufsort.h.

float nvbio::cuda::PrefixDoublingSufSort::extract_time

timing stats

Definition at line 114 of file prefix_doubling_sufsort.h.

float nvbio::cuda::PrefixDoublingSufSort::gather_time

timing stats

Definition at line 115 of file prefix_doubling_sufsort.h.

float nvbio::cuda::PrefixDoublingSufSort::inverse_time

timing stats

Definition at line 119 of file prefix_doubling_sufsort.h.

float nvbio::cuda::PrefixDoublingSufSort::radixsort_time

timing stats

Definition at line 116 of file prefix_doubling_sufsort.h.

float nvbio::cuda::PrefixDoublingSufSort::segment_time

timing stats

Definition at line 117 of file prefix_doubling_sufsort.h.


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