NVBIO: nvbio::StringBWTHandler< string_type, output_iterator > Struct Template Reference

Detailed description

template< typename string_type, typename output_iterator>
struct nvbio::StringBWTHandler< string_type, output_iterator >

a utility StringSuffixHandler to compute the BWT of the sorted suffixes

Definition at line 312 of file sufsort_utils.h.

#include <sufsort_utils.h>

Public Types
typedef string_type::index_type	index_type

Public Methods
	StringBWTHandler (const index_type _string_len, const string_type _string, output_iterator _output)

void	process_batch (const uint32 n_suffixes, const uint32 *d_suffixes)

void	process_scattered (const uint32 n_suffixes, const uint32 d_suffixes, const uint32 d_slots)

void	remove_dollar ()

Public Members
const index_type	string_len

const string_type	string

uint32	primary

uint32	n_output

output_iterator	output

thrust::device_vector< uint8 >	d_block_bwt

Static Public Members
static const uint32	NULL_PRIMARY = uint32(-1)

Member Typedef Documentation

template<typename string_type, typename output_iterator>

typedef string_type::index_type nvbio::StringBWTHandler< string_type, output_iterator >::index_type

Definition at line 314 of file sufsort_utils.h.

Constructor & Destructor Documentation

template<typename string_type, typename output_iterator>

nvbio::StringBWTHandler< string_type, output_iterator >::StringBWTHandler	(	const index_type	_string_len,
		const string_type	_string,
		output_iterator	_output
	)

inline

Definition at line 320 of file sufsort_utils.h.

Member Function Documentation

template<typename string_type, typename output_iterator>

void nvbio::StringBWTHandler< string_type, output_iterator >::process_batch	(	const uint32	n_suffixes,
		const uint32 *	d_suffixes
	)

inline

Definition at line 336 of file sufsort_utils.h.

template<typename string_type, typename output_iterator>

void nvbio::StringBWTHandler< string_type, output_iterator >::process_scattered	(	const uint32	n_suffixes,
		const uint32 *	d_suffixes,
		const uint32 *	d_slots
	)

inline

Definition at line 374 of file sufsort_utils.h.

template<typename string_type, typename output_iterator>

void nvbio::StringBWTHandler< string_type, output_iterator >::remove_dollar ( )

inline

Definition at line 412 of file sufsort_utils.h.

Member Data Documentation

template<typename string_type, typename output_iterator>

thrust::device_vector<uint8> nvbio::StringBWTHandler< string_type, output_iterator >::d_block_bwt

Definition at line 444 of file sufsort_utils.h.

template<typename string_type, typename output_iterator>

uint32 nvbio::StringBWTHandler< string_type, output_iterator >::n_output

Definition at line 442 of file sufsort_utils.h.

template<typename string_type, typename output_iterator>

const uint32 nvbio::StringBWTHandler< string_type, output_iterator >::NULL_PRIMARY = uint32(-1)

static

Definition at line 316 of file sufsort_utils.h.

template<typename string_type, typename output_iterator>

output_iterator nvbio::StringBWTHandler< string_type, output_iterator >::output

Definition at line 443 of file sufsort_utils.h.

template<typename string_type, typename output_iterator>

uint32 nvbio::StringBWTHandler< string_type, output_iterator >::primary

Definition at line 441 of file sufsort_utils.h.

template<typename string_type, typename output_iterator>

const string_type nvbio::StringBWTHandler< string_type, output_iterator >::string

Definition at line 440 of file sufsort_utils.h.

template<typename string_type, typename output_iterator>

const index_type nvbio::StringBWTHandler< string_type, output_iterator >::string_len

Definition at line 439 of file sufsort_utils.h.

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

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