Detailed description

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

A context class to perform suffix bucketing for all suffixes of a string-set

Template Parameters

SYMBOL_SIZE	the size of the symbols, in bits
N_BITS	the number of bits used for bucketing
DOLLAR_BITS	the number of bits used for encoding whether and where a dollar occurrs in the first N_BITS
bucket_type	the word type used to encode buckets, i.e the first N_BITS of each suffix

Definition at line 54 of file sufsort_bucketing.h.

#include <sufsort_bucketing.h>

Public Methods
	DeviceCoreSetSuffixBucketer (mgpu::ContextPtr _mgpu)

void	clear_timers ()

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
SetSuffixFlattener< SYMBOL_SIZE >	suffixes

thrust::device_vector< uint32 >	d_indices

thrust::device_vector < bucket_type >	d_radices

thrust::device_vector< uint32 >	d_buckets

thrust::device_vector< uint2 >	d_output

thrust::host_vector< bucket_type >	h_radices

thrust::host_vector< uint2 >	h_suffixes

uint32	n_collected

uint32	max_suffix_len

float	d_setup_time

float	d_flatten_time

float	d_count_sort_time

float	d_collect_sort_time

float	d_filter_time

float	d_remap_time

float	d_max_time

float	d_search_time

float	d_copy_time

mgpu::ContextPtr	m_mgpu

Constructor & Destructor Documentation

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS, typename bucket_type = uint32>

nvbio::priv::DeviceCoreSetSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS, bucket_type >::DeviceCoreSetSuffixBucketer ( mgpu::ContextPtr _mgpu)

inline

constructor

Definition at line 58 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::DeviceCoreSetSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS, bucket_type >::allocated_device_memory ( ) const

inline

return the amount of used device memory

Definition at line 313 of file sufsort_bucketing.h.

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS, typename bucket_type = uint32>

uint64 nvbio::priv::DeviceCoreSetSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS, bucket_type >::allocated_host_memory ( ) const

inline

return the amount of used device memory

Definition at line 325 of file sufsort_bucketing.h.

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS, typename bucket_type = uint32>

void nvbio::priv::DeviceCoreSetSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS, bucket_type >::clear_timers ( )

inline

clear internal timers

Definition at line 73 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::DeviceCoreSetSuffixBucketer< 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 165 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::DeviceCoreSetSuffixBucketer< 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 91 of file sufsort_bucketing.h.

Member Data Documentation

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS, typename bucket_type = uint32>

thrust::device_vector<uint32> nvbio::priv::DeviceCoreSetSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS, bucket_type >::d_buckets

Definition at line 337 of file sufsort_bucketing.h.

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS, typename bucket_type = uint32>

float nvbio::priv::DeviceCoreSetSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS, bucket_type >::d_collect_sort_time

Definition at line 347 of file sufsort_bucketing.h.

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS, typename bucket_type = uint32>

float nvbio::priv::DeviceCoreSetSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS, bucket_type >::d_copy_time

Definition at line 352 of file sufsort_bucketing.h.

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS, typename bucket_type = uint32>

float nvbio::priv::DeviceCoreSetSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS, bucket_type >::d_count_sort_time

Definition at line 346 of file sufsort_bucketing.h.

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS, typename bucket_type = uint32>

float nvbio::priv::DeviceCoreSetSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS, bucket_type >::d_filter_time

Definition at line 348 of file sufsort_bucketing.h.

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS, typename bucket_type = uint32>

float nvbio::priv::DeviceCoreSetSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS, bucket_type >::d_flatten_time

Definition at line 345 of file sufsort_bucketing.h.

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS, typename bucket_type = uint32>

thrust::device_vector<uint32> nvbio::priv::DeviceCoreSetSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS, bucket_type >::d_indices

Definition at line 335 of file sufsort_bucketing.h.

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS, typename bucket_type = uint32>

float nvbio::priv::DeviceCoreSetSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS, bucket_type >::d_max_time

Definition at line 350 of file sufsort_bucketing.h.

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS, typename bucket_type = uint32>

thrust::device_vector<uint2> nvbio::priv::DeviceCoreSetSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS, bucket_type >::d_output

Definition at line 338 of file sufsort_bucketing.h.

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS, typename bucket_type = uint32>

thrust::device_vector<bucket_type> nvbio::priv::DeviceCoreSetSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS, bucket_type >::d_radices

Definition at line 336 of file sufsort_bucketing.h.

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS, typename bucket_type = uint32>

float nvbio::priv::DeviceCoreSetSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS, bucket_type >::d_remap_time

Definition at line 349 of file sufsort_bucketing.h.

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS, typename bucket_type = uint32>

float nvbio::priv::DeviceCoreSetSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS, bucket_type >::d_search_time

Definition at line 351 of file sufsort_bucketing.h.

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS, typename bucket_type = uint32>

float nvbio::priv::DeviceCoreSetSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS, bucket_type >::d_setup_time

Definition at line 344 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::DeviceCoreSetSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS, bucket_type >::h_radices

Definition at line 339 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::DeviceCoreSetSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS, bucket_type >::h_suffixes

Definition at line 340 of file sufsort_bucketing.h.

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS, typename bucket_type = uint32>

mgpu::ContextPtr nvbio::priv::DeviceCoreSetSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS, bucket_type >::m_mgpu

Definition at line 353 of file sufsort_bucketing.h.

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS, typename bucket_type = uint32>

uint32 nvbio::priv::DeviceCoreSetSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS, bucket_type >::max_suffix_len

Definition at line 342 of file sufsort_bucketing.h.

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS, typename bucket_type = uint32>

uint32 nvbio::priv::DeviceCoreSetSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS, bucket_type >::n_collected

Definition at line 341 of file sufsort_bucketing.h.

template<uint32 SYMBOL_SIZE, uint32 N_BITS, uint32 DOLLAR_BITS, typename bucket_type = uint32>

SetSuffixFlattener<SYMBOL_SIZE> nvbio::priv::DeviceCoreSetSuffixBucketer< SYMBOL_SIZE, N_BITS, DOLLAR_BITS, bucket_type >::suffixes

Definition at line 334 of file sufsort_bucketing.h.

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

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

Detailed description

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

Public Methods

Public Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

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