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< uint32 >	d_indices
thrust::device_vector< word_type >	d_radices
thrust::device_vector< uint32 >	d_buckets
thrust::device_vector< uint8 >	d_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.

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

• E:/git/nvbio/nvbio/sufsort/sufsort_priv.h