nvbio::StridedPackedStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator > Struct Template Reference

Detailed description

template< typename StreamIterator, typename SymbolType, uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename LengthIterator>
struct nvbio::StridedPackedStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator >

A collection of packed strings stored in strided vectors of words. i.e. if the stride is n, the i-th string s_i is stored in the words w(i + 0), w(i + n), w(i + 2n), ...

s0	s1	s2	...
w(0 + 0)	w(1 + 0)	w(2 + 0)	...
w(0 + n)	w(1 + n)	w(2 + n)	...
w(0 + 2n)	w(1 + 2n)	w(2 + 2n)	...

This representation can be convenient for kernels where the i-th thread (modulo the grid-size) operates on the i-th string and the character accesses are in-sync, as in this case all the memory accesses will be coalesced.

Note that the number of words must be at least n times the number of words needed to store the longest string in the set.

Definition at line 734 of file string_set.h.

#include <string_set.h>

Public Types
typedef strided_packed_string_set_tag	string_set_tag
typedef SymbolType	symbol_type
typedef StreamIterator	stream_iterator
typedef strided_iterator < StreamIterator >	strided_stream_iterator
typedef PackedStream < strided_stream_iterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T >	packed_stream_type
typedef packed_stream_type::iterator	packed_stream_iterator
typedef vector_view < packed_stream_type >	string_type
typedef LengthIterator	length_iterator
typedef iterator_system < StreamIterator >::type	system_tag

Public Methods
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE	StridedPackedStringSet ()
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE	StridedPackedStringSet (const uint32 size, const uint32 stride, const StreamIterator stream, const LengthIterator lengths)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	size () const
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	stride () const
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE string_type	operator[] (const uint32 i) const
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE stream_iterator	base_stream () const
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE length_iterator	lengths () const

Static Public Members
static const uint32	SYMBOL_SIZE = SYMBOL_SIZE_T
static const bool	BIG_ENDIAN = BIG_ENDIAN_T

Member Typedef Documentation

template<typename StreamIterator, typename SymbolType, uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename LengthIterator>

typedef LengthIterator nvbio::StridedPackedStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator >::length_iterator

Definition at line 744 of file string_set.h.

template<typename StreamIterator, typename SymbolType, uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename LengthIterator>

typedef packed_stream_type::iterator nvbio::StridedPackedStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator >::packed_stream_iterator

Definition at line 742 of file string_set.h.

template<typename StreamIterator, typename SymbolType, uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename LengthIterator>

typedef PackedStream<strided_stream_iterator,SymbolType,SYMBOL_SIZE_T,BIG_ENDIAN_T> nvbio::StridedPackedStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator >::packed_stream_type

Definition at line 741 of file string_set.h.

template<typename StreamIterator, typename SymbolType, uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename LengthIterator>

typedef StreamIterator nvbio::StridedPackedStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator >::stream_iterator

Definition at line 739 of file string_set.h.

template<typename StreamIterator, typename SymbolType, uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename LengthIterator>

typedef strided_iterator<StreamIterator> nvbio::StridedPackedStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator >::strided_stream_iterator

Definition at line 740 of file string_set.h.

template<typename StreamIterator, typename SymbolType, uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename LengthIterator>

typedef strided_packed_string_set_tag nvbio::StridedPackedStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator >::string_set_tag

Definition at line 736 of file string_set.h.

template<typename StreamIterator, typename SymbolType, uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename LengthIterator>

typedef vector_view<packed_stream_type> nvbio::StridedPackedStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator >::string_type

Definition at line 743 of file string_set.h.

template<typename StreamIterator, typename SymbolType, uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename LengthIterator>

typedef SymbolType nvbio::StridedPackedStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator >::symbol_type

Definition at line 737 of file string_set.h.

template<typename StreamIterator, typename SymbolType, uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename LengthIterator>

typedef iterator_system<StreamIterator>::type nvbio::StridedPackedStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator >::system_tag

Definition at line 745 of file string_set.h.

Constructor & Destructor Documentation

template<typename StreamIterator, typename SymbolType, uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename LengthIterator>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE nvbio::StridedPackedStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator >::StridedPackedStringSet ( )

inline

default constructor

Definition at line 753 of file string_set.h.

template<typename StreamIterator, typename SymbolType, uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename LengthIterator>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE nvbio::StridedPackedStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator >::StridedPackedStringSet ( const uint32  size, const uint32  stride, const StreamIterator  stream, const LengthIterator  lengths  )

inline

constructor

Parameters

size	set size
stride	set stride
string	flat string iterator
lengths	string lengths

Definition at line 763 of file string_set.h.

Member Function Documentation

template<typename StreamIterator, typename SymbolType, uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename LengthIterator>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE stream_iterator nvbio::StridedPackedStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator >::base_stream ( ) const

inline

return the base string

Definition at line 801 of file string_set.h.

template<typename StreamIterator, typename SymbolType, uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename LengthIterator>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE length_iterator nvbio::StridedPackedStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator >::lengths ( ) const

inline

return the length vector

Definition at line 806 of file string_set.h.

template<typename StreamIterator, typename SymbolType, uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename LengthIterator>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE string_type nvbio::StridedPackedStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator >::operator[] ( const uint32  i) const

inline

indexing operator: access the i-th string

Definition at line 786 of file string_set.h.

template<typename StreamIterator, typename SymbolType, uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename LengthIterator>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::StridedPackedStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator >::size ( void  ) const

inline

set size

Definition at line 776 of file string_set.h.

template<typename StreamIterator, typename SymbolType, uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename LengthIterator>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::StridedPackedStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator >::stride ( ) const

inline

stride

Definition at line 781 of file string_set.h.

Member Data Documentation

template<typename StreamIterator, typename SymbolType, uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename LengthIterator>

const bool nvbio::StridedPackedStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator >::BIG_ENDIAN = BIG_ENDIAN_T

static

Definition at line 748 of file string_set.h.

template<typename StreamIterator, typename SymbolType, uint32 SYMBOL_SIZE_T, bool BIG_ENDIAN_T, typename LengthIterator>

const uint32 nvbio::StridedPackedStringSet< StreamIterator, SymbolType, SYMBOL_SIZE_T, BIG_ENDIAN_T, LengthIterator >::SYMBOL_SIZE = SYMBOL_SIZE_T

static

Definition at line 747 of file string_set.h.

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

• E:/git/nvbio/nvbio/strings/string_set.h