NVBIO: nvbio::PrefixSet< SequenceType, PrefixIterator > Struct Template Reference

Detailed description

template< typename SequenceType, typename PrefixIterator>
struct nvbio::PrefixSet< SequenceType, PrefixIterator >

: Represent a set of prefixes of a string or string-set. An PrefixSet is a String Set.

: For a string T[0,...,n-1], a prefix is a substring T[0,j). An PrefixSet 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 prefix ending coordinate. These coordinates must be of type string_set_prefix_coord_type or long_string_set_prefix_coord_type.

Template Parameters

SequenceType	the string or string-set type
PrefixIterator	the prefix iterator type - value_type can be string_prefix_coord_type for strings, string_set_prefix_coord_type for string-sets

Definition at line 439 of file prefix.h.

#include <prefix.h>

Inheritance diagram for nvbio::PrefixSet< SequenceType, PrefixIterator >:

Public Types
typedef PrefixSetCore < SequenceType, PrefixIterator, vector_traits< typename std::iterator_traits < PrefixIterator >::value_type > ::DIM >	base_type

typedef SequenceType	sequence_type
	the underlying sequence type More...

typedef PrefixIterator	prefix_iterator
	the underlingy prefix iterator type More...

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

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

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

typedef StringSetIterator < PrefixSet< SequenceType, InfixIterator > >	iterator
	the iterator type More...

typedef StringSetIterator < PrefixSet< SequenceType, InfixIterator > >	const_iterator
	the const_iterator type More...

Public Methods
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE	PrefixSet ()

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE	PrefixSet (const uint32 size, const sequence_type sequence, const prefix_iterator prefixes)

const_iterator	begin () const

const_iterator	end () const

iterator	begin ()

iterator	end ()

Member Typedef Documentation

template<typename SequenceType , typename PrefixIterator >

typedef PrefixSetCore< SequenceType, PrefixIterator, vector_traits<typename std::iterator_traits<PrefixIterator>::value_type>::DIM> nvbio::PrefixSet< SequenceType, PrefixIterator >::base_type

Definition at line 447 of file prefix.h.

template<typename SequenceType , typename PrefixIterator >

typedef StringSetIterator< PrefixSet<SequenceType,InfixIterator> > nvbio::PrefixSet< SequenceType, PrefixIterator >::const_iterator

the const_iterator type

Definition at line 457 of file prefix.h.

template<typename SequenceType , typename PrefixIterator >

typedef base_type::coord_type nvbio::PrefixSet< SequenceType, PrefixIterator >::coord_type

the prefix coordinates type

Definition at line 453 of file prefix.h.

template<typename SequenceType , typename PrefixIterator >

typedef StringSetIterator< PrefixSet<SequenceType,InfixIterator> > nvbio::PrefixSet< SequenceType, PrefixIterator >::iterator

the iterator type

Definition at line 456 of file prefix.h.

template<typename SequenceType , typename PrefixIterator >

typedef PrefixIterator nvbio::PrefixSet< SequenceType, PrefixIterator >::prefix_iterator

the underlingy prefix iterator type

Definition at line 450 of file prefix.h.

template<typename SequenceType , typename PrefixIterator >

typedef SequenceType nvbio::PrefixSet< SequenceType, PrefixIterator >::sequence_type

the underlying sequence type

Definition at line 449 of file prefix.h.

template<typename SequenceType , typename PrefixIterator >

typedef base_type::string_type nvbio::PrefixSet< SequenceType, PrefixIterator >::string_type

the prefix string type

Definition at line 454 of file prefix.h.

template<typename SequenceType , typename PrefixIterator >

typedef iterator_system<PrefixIterator>::type nvbio::PrefixSet< SequenceType, PrefixIterator >::system_tag

the system tag

Definition at line 451 of file prefix.h.

Constructor & Destructor Documentation

template<typename SequenceType , typename PrefixIterator >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE nvbio::PrefixSet< SequenceType, PrefixIterator >::PrefixSet ( )

inline

constructor

Definition at line 462 of file prefix.h.

template<typename SequenceType , typename PrefixIterator >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE nvbio::PrefixSet< SequenceType, PrefixIterator >::PrefixSet	(	const uint32	size,
		const sequence_type	sequence,
		const prefix_iterator	prefixes
	)

inline

constructor

Definition at line 467 of file prefix.h.

Member Function Documentation

template<typename SequenceType , typename PrefixIterator >

const_iterator nvbio::PrefixSet< SequenceType, PrefixIterator >::begin ( void ) const

inline

begin iterator

Definition at line 475 of file prefix.h.

template<typename SequenceType , typename PrefixIterator >

iterator nvbio::PrefixSet< SequenceType, PrefixIterator >::begin ( void )

inline

begin iterator

Definition at line 483 of file prefix.h.

template<typename SequenceType , typename PrefixIterator >

const_iterator nvbio::PrefixSet< SequenceType, PrefixIterator >::end ( void ) const

inline

begin iterator

Definition at line 479 of file prefix.h.

template<typename SequenceType , typename PrefixIterator >

iterator nvbio::PrefixSet< SequenceType, PrefixIterator >::end ( void )

inline

begin iterator

Definition at line 487 of file prefix.h.

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

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