Detailed description

template< typename string_set_type, uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>
struct nvbio::priv::DeviceStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >

Definition at line 1820 of file sufsort_priv.h.

#include <sufsort_priv.h>

Public Methods
	DeviceStringSetRadices ()

	DeviceStringSetRadices (const string_set_type string_set)

uint32	num_words (const uint32 max_string_len) const

uint64	needed_device_memory (const uint32 n_suffixes) const

void	reserve (const uint32 n_suffixes, const uint32 slice_size)

void	set (const string_set_type string_set)

void	init (const uint32 n_suffixes, const uint2 _h_suffixes, const uint2 _d_suffixes)

void	init_slice (const uint32 n_indices, const uint32 *d_indices, const uint32 word_block_begin, const uint32 word_block_end)

void	extract (const uint32 n_indices, const uint32 d_indices, const uint32 word_idx, const uint32 word_block_begin, const uint32 word_block_end, uint32 d_radices) const

void	dollar_bwt (const uint32 begin, const uint32 end, uint8 *h_bwt)

void	bwt (const uint32 n_suffixes, const uint32 d_indices, uint8 h_bwt, uint8 *d_bwt)

uint64	allocated_device_memory () const

uint64	allocated_host_memory () const

Public Members
string_set_type	m_string_set

thrust::device_ptr< const uint2 >	d_suffixes

thrust::device_vector< uint8 >	d_symbols

Constructor & Destructor Documentation

template<typename string_set_type, uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>

nvbio::priv::DeviceStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >::DeviceStringSetRadices ( )

inline

Definition at line 1822 of file sufsort_priv.h.

template<typename string_set_type, uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>

nvbio::priv::DeviceStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >::DeviceStringSetRadices ( const string_set_type string_set)

inline

Definition at line 1823 of file sufsort_priv.h.

Member Function Documentation

template<typename string_set_type, uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>

uint64 nvbio::priv::DeviceStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >::allocated_device_memory ( ) const

inline

return the amount of used device memory

Definition at line 1973 of file sufsort_priv.h.

template<typename string_set_type, uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>

uint64 nvbio::priv::DeviceStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >::allocated_host_memory ( ) const

inline

return the amount of used device memory

Definition at line 1980 of file sufsort_priv.h.

template<typename string_set_type, uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>

void nvbio::priv::DeviceStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >::bwt	(	const uint32	n_suffixes,
		const uint32 *	d_indices,
		uint8 *	h_bwt,
		uint8 *	d_bwt
	)

inline

extract the bwt of the given block

Definition at line 1930 of file sufsort_priv.h.

template<typename string_set_type, uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>

void nvbio::priv::DeviceStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >::dollar_bwt	(	const uint32	begin,
		const uint32	end,
		uint8 *	h_bwt
	)

inline

extract the bwt of the given block

Definition at line 1905 of file sufsort_priv.h.

template<typename string_set_type, uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>

void nvbio::priv::DeviceStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >::extract	(	const uint32	n_indices,
		const uint32 *	d_indices,
		const uint32	word_idx,
		const uint32	word_block_begin,
		const uint32	word_block_end,
		uint32 *	d_radices
	)		const

inline

extract the radices corresponding to a given word of the given suffixes

Parameters

n_indices	the input number of suffixes
d_indices	a device vector of the indices to extract
word_idx	the word index to extract
word_begin	the beginning of the current slice range
word_idx	the end of the current slice range
d_radices	the destination device array to hold the output

Definition at line 1876 of file sufsort_priv.h.

template<typename string_set_type, uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>

void nvbio::priv::DeviceStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >::init	(	const uint32	n_suffixes,
		const uint2 *	_h_suffixes,
		const uint2 *	_d_suffixes
	)

inline

initialize the suffixes to extract

Definition at line 1854 of file sufsort_priv.h.

template<typename string_set_type, uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>

void nvbio::priv::DeviceStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >::init_slice	(	const uint32	n_indices,
		const uint32 *	d_indices,
		const uint32	word_block_begin,
		const uint32	word_block_end
	)

inline

initialize extraction of a slice of words

Definition at line 1861 of file sufsort_priv.h.

template<typename string_set_type, uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>

uint64 nvbio::priv::DeviceStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >::needed_device_memory ( const uint32 n_suffixes) const

inline

needed amount of device storage

Definition at line 1836 of file sufsort_priv.h.

template<typename string_set_type, uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>

uint32 nvbio::priv::DeviceStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >::num_words ( const uint32 max_string_len) const

inline

return the number of words needed to represent a given string length

Definition at line 1827 of file sufsort_priv.h.

template<typename string_set_type, uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>

void nvbio::priv::DeviceStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >::reserve	(	const uint32	n_suffixes,
		const uint32	slice_size
	)

inline

reserve any temporary space for the given amount of suffixes

Definition at line 1843 of file sufsort_priv.h.

template<typename string_set_type, uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>

void nvbio::priv::DeviceStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >::set ( const string_set_type string_set)

inline

set string set

Definition at line 1850 of file sufsort_priv.h.

Member Data Documentation

template<typename string_set_type, uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>

thrust::device_ptr<const uint2> nvbio::priv::DeviceStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >::d_suffixes

Definition at line 1986 of file sufsort_priv.h.

template<typename string_set_type, uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>

thrust::device_vector<uint8> nvbio::priv::DeviceStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >::d_symbols

Definition at line 1987 of file sufsort_priv.h.

template<typename string_set_type, uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>

string_set_type nvbio::priv::DeviceStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >::m_string_set

Definition at line 1985 of file sufsort_priv.h.

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

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

Detailed description

template< typename string_set_type, uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS> struct nvbio::priv::DeviceStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >

Public Methods

Public Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

template< typename string_set_type, uint32 SYMBOL_SIZE, uint32 DOLLAR_BITS, uint32 WORD_BITS>
struct nvbio::priv::DeviceStringSetRadices< string_set_type, SYMBOL_SIZE, DOLLAR_BITS, WORD_BITS >