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< uint32 >	h_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:

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