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

Detailed description

template< uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS, typename bucket_type = uint32>
struct nvbio::priv::HostCoreSetSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS, bucket_type >

A context class to perform suffix bucketing for all suffixes of a string-set, using a host core

Definition at line 629 of file sufsort_bucketing.h.

#include <sufsort_bucketing.h>

Public Methods

 HostCoreSetSuffixBucketer ()
 
void clear_timers ()
 
void count_init ()
 
template<typename string_set_type >
uint64 count (const string_set_type &string_set)
 
template<typename string_set_type , typename bucketmap_iterator >
uint32 collect (const string_set_type &string_set, const uint32 bucket_begin, const uint32 bucket_end, const uint32 string_offset, const bucketmap_iterator bucketmap)
 
uint64 allocated_device_memory () const
 
uint64 allocated_host_memory () const
 

Public Members

thrust::host_vector< uint32h_buckets
 
thrust::host_vector< bucket_type > h_radices
 
thrust::host_vector< uint2 > h_suffixes
 
uint32 n_suffixes
 
uint32 n_collected
 
uint32 max_suffix_len
 

Constructor & Destructor Documentation

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS, typename bucket_type = uint32>
nvbio::priv::HostCoreSetSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS, bucket_type >::HostCoreSetSuffixBucketer ( )
inline

constructor

Definition at line 633 of file sufsort_bucketing.h.

Member Function Documentation

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS, typename bucket_type = uint32>
uint64 nvbio::priv::HostCoreSetSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS, bucket_type >::allocated_device_memory ( ) const
inline

return the amount of used device memory

Definition at line 760 of file sufsort_bucketing.h.

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS, typename bucket_type = uint32>
uint64 nvbio::priv::HostCoreSetSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS, bucket_type >::allocated_host_memory ( ) const
inline

return the amount of used device memory

Definition at line 764 of file sufsort_bucketing.h.

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS, typename bucket_type = uint32>
void nvbio::priv::HostCoreSetSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS, bucket_type >::clear_timers ( )
inline

clear internal timers

Definition at line 637 of file sufsort_bucketing.h.

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS, typename bucket_type = uint32>
template<typename string_set_type , typename bucketmap_iterator >
uint32 nvbio::priv::HostCoreSetSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS, bucket_type >::collect ( const string_set_type &  string_set,
const uint32  bucket_begin,
const uint32  bucket_end,
const uint32  string_offset,
const bucketmap_iterator  bucketmap 
)
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 702 of file sufsort_bucketing.h.

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS, typename bucket_type = uint32>
template<typename string_set_type >
uint64 nvbio::priv::HostCoreSetSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS, bucket_type >::count ( const string_set_type &  string_set)
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 661 of file sufsort_bucketing.h.

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS, typename bucket_type = uint32>
void nvbio::priv::HostCoreSetSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS, bucket_type >::count_init ( )
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 642 of file sufsort_bucketing.h.

Member Data Documentation

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS, typename bucket_type = uint32>
thrust::host_vector<uint32> nvbio::priv::HostCoreSetSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS, bucket_type >::h_buckets

Definition at line 773 of file sufsort_bucketing.h.

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS, typename bucket_type = uint32>
thrust::host_vector<bucket_type> nvbio::priv::HostCoreSetSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS, bucket_type >::h_radices

Definition at line 774 of file sufsort_bucketing.h.

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS, typename bucket_type = uint32>
thrust::host_vector<uint2> nvbio::priv::HostCoreSetSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS, bucket_type >::h_suffixes

Definition at line 775 of file sufsort_bucketing.h.

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS, typename bucket_type = uint32>
uint32 nvbio::priv::HostCoreSetSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS, bucket_type >::max_suffix_len

Definition at line 778 of file sufsort_bucketing.h.

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS, typename bucket_type = uint32>
uint32 nvbio::priv::HostCoreSetSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS, bucket_type >::n_collected

Definition at line 777 of file sufsort_bucketing.h.

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS, typename bucket_type = uint32>
uint32 nvbio::priv::HostCoreSetSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS, bucket_type >::n_suffixes

Definition at line 776 of file sufsort_bucketing.h.


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