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nvbio::priv::StringSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS > Struct Template Reference

Detailed description

template< uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS>
struct nvbio::priv::StringSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS >

A context class to perform suffix bucketing

Definition at line 1340 of file sufsort_priv.h.

#include <sufsort_priv.h>

Public Types

typedef uint32 word_type
 

Public Methods

 StringSuffixBucketer ()
 
template<typename suffix_iterator , typename string_type >
void count (const uint32 n_suffixes, const suffix_iterator suffixes, const uint32 string_length, const string_type &string)
 
template<typename suffix_iterator , typename string_type , typename bucketmap_iterator , typename output_iterator >
uint32 collect (const uint32 n_suffixes, const suffix_iterator suffixes, const uint64 string_length, const string_type &string, const uint32 bucket_begin, const uint32 bucket_end, const bucketmap_iterator bucketmap, output_iterator output_radices, output_iterator output_indices)
 

Public Members

thrust::device_vector< uint32d_indices
 
thrust::device_vector< word_typed_radices
 
thrust::device_vector< uint32d_buckets
 
thrust::device_vector< uint8d_temp_storage
 
float d_setup_time
 
float d_flatten_time
 
float d_count_sort_time
 
float d_collect_sort_time
 
float d_remap_time
 
float d_copy_time
 
float d_filter_time
 

Member Typedef Documentation

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS>
typedef uint32 nvbio::priv::StringSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS >::word_type

Definition at line 1342 of file sufsort_priv.h.

Constructor & Destructor Documentation

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS>
nvbio::priv::StringSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS >::StringSuffixBucketer ( )
inline

Definition at line 1344 of file sufsort_priv.h.

Member Function Documentation

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS>
template<typename suffix_iterator , typename string_type , typename bucketmap_iterator , typename output_iterator >
uint32 nvbio::priv::StringSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS >::collect ( const uint32  n_suffixes,
const suffix_iterator  suffixes,
const uint64  string_length,
const string_type &  string,
const uint32  bucket_begin,
const uint32  bucket_end,
const bucketmap_iterator  bucketmap,
output_iterator  output_radices,
output_iterator  output_indices 
)
inline

collect the suffixes falling in a given set of buckets, where the buckets are defined by the first n_bits of the suffix

Definition at line 1418 of file sufsort_priv.h.

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS>
template<typename suffix_iterator , typename string_type >
void nvbio::priv::StringSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS >::count ( const uint32  n_suffixes,
const suffix_iterator  suffixes,
const uint32  string_length,
const string_type &  string 
)
inline

count the number of suffixes falling in each bucket, where the buckets are defined by the first n_bits of the suffix

Definition at line 1350 of file sufsort_priv.h.

Member Data Documentation

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS>
thrust::device_vector<uint32> nvbio::priv::StringSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS >::d_buckets

Definition at line 1531 of file sufsort_priv.h.

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS>
float nvbio::priv::StringSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS >::d_collect_sort_time

Definition at line 1536 of file sufsort_priv.h.

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS>
float nvbio::priv::StringSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS >::d_copy_time

Definition at line 1538 of file sufsort_priv.h.

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS>
float nvbio::priv::StringSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS >::d_count_sort_time

Definition at line 1535 of file sufsort_priv.h.

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS>
float nvbio::priv::StringSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS >::d_filter_time

Definition at line 1539 of file sufsort_priv.h.

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS>
float nvbio::priv::StringSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS >::d_flatten_time

Definition at line 1534 of file sufsort_priv.h.

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS>
thrust::device_vector<uint32> nvbio::priv::StringSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS >::d_indices

Definition at line 1529 of file sufsort_priv.h.

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS>
thrust::device_vector<word_type> nvbio::priv::StringSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS >::d_radices

Definition at line 1530 of file sufsort_priv.h.

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS>
float nvbio::priv::StringSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS >::d_remap_time

Definition at line 1537 of file sufsort_priv.h.

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS>
float nvbio::priv::StringSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS >::d_setup_time

Definition at line 1533 of file sufsort_priv.h.

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS>
thrust::device_vector<uint8> nvbio::priv::StringSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS >::d_temp_storage

Definition at line 1532 of file sufsort_priv.h.


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