nvbio::BWTEContext< SYMBOL_SIZE, BIG_ENDIAN, storage_type, offsets_iterator > Struct Template Reference

Detailed description

template< uint32 SYMBOL_SIZE, bool BIG_ENDIAN, typename storage_type = const uint32*, typename offsets_iterator = const uint64*>
struct nvbio::BWTEContext< SYMBOL_SIZE, BIG_ENDIAN, storage_type, offsets_iterator >

A context for the incremental parallel set-bwte algorithm for computing the BWT of a string-set.

Template Parameters

SYMBOL_SIZE	the size of the symbols, in bits
BIG_ENDIAN	whether the input/output packed streams are big endian
storage_type	the iterator to the input packed stream storage
offsets_iterator	the iterator to the offsets in the concatenated string-set

Definition at line 99 of file bwte.h.

#include <bwte.h>

Public Types
typedef std::iterator_traits < offsets_iterator > ::value_type	index_type
typedef ConcatenatedStringSet < PackedStream< storage_type, uint8, SYMBOL_SIZE, BIG_ENDIAN, index_type >, offsets_iterator >	string_set_type

Public Methods
	BWTEContext (const int device)
uint64	needed_device_memory (const uint32 _max_block_strings, const uint32 _max_block_suffixes) const
void	reserve (const uint32 _max_block_strings, const uint32 _max_block_suffixes)
void	append_block (const uint32 block_begin, const uint32 block_end, const string_set_type string_set, PagedText< SYMBOL_SIZE, BIG_ENDIAN > &BWT_ext, SparseSymbolSet &BWT_ext_dollars, const bool forward)
void	sort_block (const uint32 block_begin, const uint32 block_end, const string_set_type string_set, BWTEBlock &block)
void	merge_block (const uint32 block_begin, const uint32 block_end, const string_set_type string_set, BWTEBlock &block, PagedText< SYMBOL_SIZE, BIG_ENDIAN > &BWT_ext, SparseSymbolSet &BWT_ext_dollars, const bool forward)

Member Typedef Documentation

template<uint32 SYMBOL_SIZE, bool BIG_ENDIAN, typename storage_type = const uint32*, typename offsets_iterator = const uint64*>

typedef std::iterator_traits<offsets_iterator>::value_type nvbio::BWTEContext< SYMBOL_SIZE, BIG_ENDIAN, storage_type, offsets_iterator >::index_type

Definition at line 101 of file bwte.h.

template<uint32 SYMBOL_SIZE, bool BIG_ENDIAN, typename storage_type = const uint32*, typename offsets_iterator = const uint64*>

typedef ConcatenatedStringSet< PackedStream<storage_type,uint8,SYMBOL_SIZE,BIG_ENDIAN,index_type>, offsets_iterator> nvbio::BWTEContext< SYMBOL_SIZE, BIG_ENDIAN, storage_type, offsets_iterator >::string_set_type

Definition at line 104 of file bwte.h.

Constructor & Destructor Documentation

template<uint32 SYMBOL_SIZE, bool BIG_ENDIAN, typename storage_type , typename offsets_iterator >

nvbio::BWTEContext< SYMBOL_SIZE, BIG_ENDIAN, storage_type, offsets_iterator >::BWTEContext

(

const int

device)

constructor

Definition at line 75 of file bwte_inl.h.

Member Function Documentation

template<uint32 SYMBOL_SIZE, bool BIG_ENDIAN, typename storage_type , typename offsets_iterator >

void nvbio::BWTEContext< SYMBOL_SIZE, BIG_ENDIAN, storage_type, offsets_iterator >::append_block	(	const uint32	block_begin,
		const uint32	block_end,
		const string_set_type	string_set,
		PagedText< SYMBOL_SIZE, BIG_ENDIAN > &	BWT_ext,
		SparseSymbolSet &	BWT_ext_dollars,
		const bool	forward
	)

append a new block of strings

Parameters

block_begin	the beginning of the block of strings to encode in the input string-set
block_end	the end of the block of strings to encode in the input string-set
string_set	the input string-set
BWT_ext	the output BWT
BWT_ext_dollars	the output BWT dollars
forward	true if appending the result, false if prepending it

Definition at line 171 of file bwte_inl.h.

template<uint32 SYMBOL_SIZE, bool BIG_ENDIAN, typename storage_type , typename offsets_iterator >

void nvbio::BWTEContext< SYMBOL_SIZE, BIG_ENDIAN, storage_type, offsets_iterator >::merge_block	(	const uint32	block_begin,
		const uint32	block_end,
		const string_set_type	string_set,
		BWTEBlock &	block,
		PagedText< SYMBOL_SIZE, BIG_ENDIAN > &	BWT_ext,
		SparseSymbolSet &	BWT_ext_dollars,
		const bool	forward
	)

Definition at line 194 of file bwte_inl.h.

template<uint32 SYMBOL_SIZE, bool BIG_ENDIAN, typename storage_type , typename offsets_iterator >

uint64 nvbio::BWTEContext< SYMBOL_SIZE, BIG_ENDIAN, storage_type, offsets_iterator >::needed_device_memory	(	const uint32	_max_block_strings,
		const uint32	_max_block_suffixes
	)		const

needed device memory

Definition at line 97 of file bwte_inl.h.

template<uint32 SYMBOL_SIZE, bool BIG_ENDIAN, typename storage_type , typename offsets_iterator >

void nvbio::BWTEContext< SYMBOL_SIZE, BIG_ENDIAN, storage_type, offsets_iterator >::reserve	(	const uint32	_max_block_strings,
		const uint32	_max_block_suffixes
	)

reserve space for a maximum block size

Definition at line 116 of file bwte_inl.h.

template<uint32 SYMBOL_SIZE, bool BIG_ENDIAN, typename storage_type , typename offsets_iterator >

void nvbio::BWTEContext< SYMBOL_SIZE, BIG_ENDIAN, storage_type, offsets_iterator >::sort_block	(	const uint32	block_begin,
		const uint32	block_end,
		const string_set_type	string_set,
		BWTEBlock &	block
	)

Definition at line 290 of file bwte_inl.h.

---

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

• E:/git/nvbio/nvbio/sufsort/bwte.h
• E:/git/nvbio/nvbio/sufsort/bwte_inl.h