NVBIO: nvbio::SuffixSet< SequenceType, SuffixIterator > Struct Template Reference

Detailed description

template< typename SequenceType, typename SuffixIterator>
struct nvbio::SuffixSet< SequenceType, SuffixIterator >

: Represent a set of suffixes of a string or string-set. A SuffixSet is a String Set.

: For a string T[0,...,n-1], a suffix is a substring T[i,n). A SuffixSet is hence defined by a string and a collection of indices { i_0, ..., i_m }. These coordinates must be of type string_suffix_coord_type or long_string_suffix_coord_type.

: For a string-set, an prefix is instead defined as a pair (k,i), where k denotes the string index in the set and i denotes the suffix starting coordinate. These coordinates must be of type string_set_suffix_coord_type or long_string_set_suffix_coord_type.

Template Parameters

SequenceType	the string or string-set type
SuffixIterator	the suffix iterator type - value_type can be string_suffix_coord_type for strings, string_set_suffix_coord_type

Definition at line 441 of file suffix.h.

#include <suffix.h>

Inheritance diagram for nvbio::SuffixSet< SequenceType, SuffixIterator >:

Public Types
typedef SuffixSetCore < SequenceType, SuffixIterator, vector_traits< typename std::iterator_traits < SuffixIterator >::value_type > ::DIM >	base_type

typedef SequenceType	sequence_type
	the underlying sequence type More...

typedef SuffixIterator	suffix_iterator
	the underlingy suffix iterator type More...

typedef iterator_system < SuffixIterator >::type	system_tag
	the system tag More...

typedef base_type::coord_type	coord_type
	the suffix coordinates type More...

typedef base_type::string_type	string_type
	the suffix string type More...

typedef StringSetIterator < SuffixSet< SequenceType, SuffixIterator > >	iterator
	the iterator type More...

typedef StringSetIterator < SuffixSet< SequenceType, SuffixIterator > >	const_iterator
	the const_iterator type More...

Public Methods
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE	SuffixSet ()

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE	SuffixSet (const uint32 size, const sequence_type sequence, const suffix_iterator suffixes)

const_iterator	begin () const

const_iterator	end () const

iterator	begin ()

iterator	end ()

Member Typedef Documentation

template<typename SequenceType , typename SuffixIterator >

typedef SuffixSetCore< SequenceType, SuffixIterator, vector_traits<typename std::iterator_traits<SuffixIterator>::value_type>::DIM> nvbio::SuffixSet< SequenceType, SuffixIterator >::base_type

Definition at line 449 of file suffix.h.

template<typename SequenceType , typename SuffixIterator >

typedef StringSetIterator< SuffixSet<SequenceType,SuffixIterator> > nvbio::SuffixSet< SequenceType, SuffixIterator >::const_iterator

the const_iterator type

Definition at line 459 of file suffix.h.

template<typename SequenceType , typename SuffixIterator >

typedef base_type::coord_type nvbio::SuffixSet< SequenceType, SuffixIterator >::coord_type

the suffix coordinates type

Definition at line 455 of file suffix.h.

template<typename SequenceType , typename SuffixIterator >

typedef StringSetIterator< SuffixSet<SequenceType,SuffixIterator> > nvbio::SuffixSet< SequenceType, SuffixIterator >::iterator

the iterator type

Definition at line 458 of file suffix.h.

template<typename SequenceType , typename SuffixIterator >

typedef SequenceType nvbio::SuffixSet< SequenceType, SuffixIterator >::sequence_type

the underlying sequence type

Definition at line 451 of file suffix.h.

template<typename SequenceType , typename SuffixIterator >

typedef base_type::string_type nvbio::SuffixSet< SequenceType, SuffixIterator >::string_type

the suffix string type

Definition at line 456 of file suffix.h.

template<typename SequenceType , typename SuffixIterator >

typedef SuffixIterator nvbio::SuffixSet< SequenceType, SuffixIterator >::suffix_iterator

the underlingy suffix iterator type

Definition at line 452 of file suffix.h.

template<typename SequenceType , typename SuffixIterator >

typedef iterator_system<SuffixIterator>::type nvbio::SuffixSet< SequenceType, SuffixIterator >::system_tag

the system tag

Definition at line 453 of file suffix.h.

Constructor & Destructor Documentation

template<typename SequenceType , typename SuffixIterator >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE nvbio::SuffixSet< SequenceType, SuffixIterator >::SuffixSet ( )

inline

constructor

Definition at line 464 of file suffix.h.

template<typename SequenceType , typename SuffixIterator >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE nvbio::SuffixSet< SequenceType, SuffixIterator >::SuffixSet	(	const uint32	size,
		const sequence_type	sequence,
		const suffix_iterator	suffixes
	)

inline

constructor

Definition at line 469 of file suffix.h.

Member Function Documentation

template<typename SequenceType , typename SuffixIterator >

const_iterator nvbio::SuffixSet< SequenceType, SuffixIterator >::begin ( void ) const

inline

begin iterator

Definition at line 477 of file suffix.h.

template<typename SequenceType , typename SuffixIterator >

iterator nvbio::SuffixSet< SequenceType, SuffixIterator >::begin ( void )

inline

begin iterator

Definition at line 485 of file suffix.h.

template<typename SequenceType , typename SuffixIterator >

const_iterator nvbio::SuffixSet< SequenceType, SuffixIterator >::end ( void ) const

inline

begin iterator

Definition at line 481 of file suffix.h.

template<typename SequenceType , typename SuffixIterator >

iterator nvbio::SuffixSet< SequenceType, SuffixIterator >::end ( void )

inline

begin iterator

Definition at line 489 of file suffix.h.

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

E:/git/nvbio/nvbio/strings/suffix.h