nvbio::priv::SetSuffixFlattener< SYMBOL_SIZE > Struct Template Reference

Detailed description

template< uint32 SYMBOL_SIZE>
struct nvbio::priv::SetSuffixFlattener< SYMBOL_SIZE >

A helper class allowing to "flatten" the suffixes in a given string-set, i.e. to extract all of them word-by-word in a flattened array.

Definition at line 1031 of file sufsort_priv.h.

#include <sufsort_priv.h>

Public Methods
	SetSuffixFlattener (mgpu::ContextPtr _mgpu)
void	clear_timers ()
void	reserve (const uint32 n_strings, const uint32 n_suffixes)
uint64	needed_device_memory (const uint32 n_strings, const uint32 n_suffixes) const
template<typename string_set_type >
void	set (const string_set_type &string_set, const bool empty_suffixes=true)
template<uint32 BITS, uint32 DOLLAR_BITS, typename string_set_type , typename index_iterator , typename radix_iterator >
void	flatten (const string_set_type &string_set, const uint32 word_idx, const Bits< BITS, DOLLAR_BITS > word_bits, const index_iterator indices, radix_iterator radices)
template<typename string_set_type >
uint32	max_length (const string_set_type &string_set, const bool empty_suffixes=true)
template<typename string_set_type , typename index_iterator >
uint32	max_length (const string_set_type &string_set, const index_iterator indices_begin, const index_iterator indices_end)
uint64	allocated_device_memory () const

Public Members
uint32	n_suffixes
	number of suffixes in the string set More...
thrust::device_vector< uint32 >	cum_lengths
	cumulative string lengths More...
thrust::device_vector< uint32 >	string_ids
thrust::device_vector< uint8 >	temp_storage
float	d_scan_time
float	d_search_time
mgpu::ContextPtr	m_mgpu

Constructor & Destructor Documentation

template<uint32 SYMBOL_SIZE>

nvbio::priv::SetSuffixFlattener< SYMBOL_SIZE >::SetSuffixFlattener ( mgpu::ContextPtr  _mgpu)

inline

Definition at line 1033 of file sufsort_priv.h.

Member Function Documentation

template<uint32 SYMBOL_SIZE>

uint64 nvbio::priv::SetSuffixFlattener< SYMBOL_SIZE >::allocated_device_memory ( ) const

inline

return the amount of used device memory

Definition at line 1169 of file sufsort_priv.h.

template<uint32 SYMBOL_SIZE>

void nvbio::priv::SetSuffixFlattener< SYMBOL_SIZE >::clear_timers ( )

inline

clear internal timers

Definition at line 1040 of file sufsort_priv.h.

template<uint32 SYMBOL_SIZE>

template<uint32 BITS, uint32 DOLLAR_BITS, typename string_set_type , typename index_iterator , typename radix_iterator >

void nvbio::priv::SetSuffixFlattener< SYMBOL_SIZE >::flatten ( const string_set_type &  string_set, const uint32  word_idx, const Bits< BITS, DOLLAR_BITS >  word_bits, const index_iterator  indices, radix_iterator  radices  )

inline

extract the given radix of all suffixes

Definition at line 1111 of file sufsort_priv.h.

template<uint32 SYMBOL_SIZE>

template<typename string_set_type >

uint32 nvbio::priv::SetSuffixFlattener< SYMBOL_SIZE >::max_length ( const string_set_type &  string_set, const bool  empty_suffixes = true  )

inline

compute the maximum suffix length among the specified range

Definition at line 1134 of file sufsort_priv.h.

template<uint32 SYMBOL_SIZE>

template<typename string_set_type , typename index_iterator >

uint32 nvbio::priv::SetSuffixFlattener< SYMBOL_SIZE >::max_length ( const string_set_type &  string_set, const index_iterator  indices_begin, const index_iterator  indices_end  )

inline

compute the maximum suffix length among the specified range

Definition at line 1150 of file sufsort_priv.h.

template<uint32 SYMBOL_SIZE>

uint64 nvbio::priv::SetSuffixFlattener< SYMBOL_SIZE >::needed_device_memory ( const uint32  n_strings, const uint32  n_suffixes  ) const

inline

return the amount of device memory needed

Definition at line 1056 of file sufsort_priv.h.

template<uint32 SYMBOL_SIZE>

void nvbio::priv::SetSuffixFlattener< SYMBOL_SIZE >::reserve ( const uint32  n_strings, const uint32  n_suffixes  )

inline

reserve storage

Definition at line 1048 of file sufsort_priv.h.

template<uint32 SYMBOL_SIZE>

template<typename string_set_type >

void nvbio::priv::SetSuffixFlattener< SYMBOL_SIZE >::set ( const string_set_type &  string_set, const bool  empty_suffixes = true  )

inline

initialize this flattener, building the auxiliary data-structures needed to extract the radices

Definition at line 1065 of file sufsort_priv.h.

Member Data Documentation

template<uint32 SYMBOL_SIZE>

thrust::device_vector<uint32> nvbio::priv::SetSuffixFlattener< SYMBOL_SIZE >::cum_lengths

cumulative string lengths

Definition at line 1178 of file sufsort_priv.h.

template<uint32 SYMBOL_SIZE>

float nvbio::priv::SetSuffixFlattener< SYMBOL_SIZE >::d_scan_time

Definition at line 1185 of file sufsort_priv.h.

template<uint32 SYMBOL_SIZE>

float nvbio::priv::SetSuffixFlattener< SYMBOL_SIZE >::d_search_time

Definition at line 1186 of file sufsort_priv.h.

template<uint32 SYMBOL_SIZE>

mgpu::ContextPtr nvbio::priv::SetSuffixFlattener< SYMBOL_SIZE >::m_mgpu

Definition at line 1187 of file sufsort_priv.h.

template<uint32 SYMBOL_SIZE>

uint32 nvbio::priv::SetSuffixFlattener< SYMBOL_SIZE >::n_suffixes

number of suffixes in the string set

Definition at line 1177 of file sufsort_priv.h.

template<uint32 SYMBOL_SIZE>

thrust::device_vector<uint32> nvbio::priv::SetSuffixFlattener< SYMBOL_SIZE >::string_ids

a vector containing the string index corresponding to each flattened suffixes; i.e. if the set contains 3 strings of length (3, 2, 5), the string ids will be the vector (0,0,0,1,1,2,2,2,2,2).

Definition at line 1179 of file sufsort_priv.h.

template<uint32 SYMBOL_SIZE>

thrust::device_vector<uint8> nvbio::priv::SetSuffixFlattener< SYMBOL_SIZE >::temp_storage

Definition at line 1183 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