NVBIO: nvbio::InfixSet< SequenceType, InfixIterator > Struct Template Reference

Detailed description

template< typename SequenceType, typename InfixIterator>
struct nvbio::InfixSet< SequenceType, InfixIterator >

: Represent a set of infixes of a string or string-set. An InfixSet is a String Set.

: For a string T[0,...,n-1], an infix is a substring T[i,j), with i < j. An InfixSet is hence defined by a string and a collection of ranges { (i_0,j_0), ..., (i_m,j_m) }. These coordinates must be of type string_infix_coord_type or long_string_infix_coord_type.

: For a string-set, an infix is instead defined as a tuple (k,i,j), where k denotes the string index in the set and (i,j) denotes the infix range within the selected string. These coordinates must be of type string_set_infix_coord_type (which for efficiency purposes is a 16-byte aligned uint4) or long_string_set_infix_coord_type.

Template Parameters

SequenceType	the string or string-set type
InfixIterator	the infix iterator type - value_type can be string_infix_coord_type for strings, string_set_infix_coord_type for string-sets

Definition at line 541 of file infix.h.

#include <infix.h>

Inheritance diagram for nvbio::InfixSet< SequenceType, InfixIterator >:

Public Types
typedef InfixSetCore < SequenceType, InfixIterator, vector_traits< typename std::iterator_traits < InfixIterator >::value_type > ::DIM >	base_type

typedef SequenceType	sequence_type
	the underlying sequence type More...

typedef InfixIterator	infix_iterator
	the underlingy infix iterator type More...

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

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

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

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

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

Public Methods
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE	InfixSet ()

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE	InfixSet (const uint32 size, const sequence_type sequence, const infix_iterator infixes)

const_iterator	begin () const

const_iterator	end () const

iterator	begin ()

iterator	end ()

Member Typedef Documentation

template<typename SequenceType , typename InfixIterator >

typedef InfixSetCore< SequenceType, InfixIterator, vector_traits<typename std::iterator_traits<InfixIterator>::value_type>::DIM> nvbio::InfixSet< SequenceType, InfixIterator >::base_type

Definition at line 549 of file infix.h.

template<typename SequenceType , typename InfixIterator >

typedef StringSetIterator< InfixSet<SequenceType,InfixIterator> > nvbio::InfixSet< SequenceType, InfixIterator >::const_iterator

the const_iterator type

Definition at line 559 of file infix.h.

template<typename SequenceType , typename InfixIterator >

typedef base_type::coord_type nvbio::InfixSet< SequenceType, InfixIterator >::coord_type

the infix coordinates type

Definition at line 555 of file infix.h.

template<typename SequenceType , typename InfixIterator >

typedef InfixIterator nvbio::InfixSet< SequenceType, InfixIterator >::infix_iterator

the underlingy infix iterator type

Definition at line 552 of file infix.h.

template<typename SequenceType , typename InfixIterator >

typedef StringSetIterator< InfixSet<SequenceType,InfixIterator> > nvbio::InfixSet< SequenceType, InfixIterator >::iterator

the iterator type

Definition at line 558 of file infix.h.

template<typename SequenceType , typename InfixIterator >

typedef SequenceType nvbio::InfixSet< SequenceType, InfixIterator >::sequence_type

the underlying sequence type

Definition at line 551 of file infix.h.

template<typename SequenceType , typename InfixIterator >

typedef base_type::string_type nvbio::InfixSet< SequenceType, InfixIterator >::string_type

the infix string type

Definition at line 556 of file infix.h.

template<typename SequenceType , typename InfixIterator >

typedef iterator_system<InfixIterator>::type nvbio::InfixSet< SequenceType, InfixIterator >::system_tag

the system tag

Definition at line 553 of file infix.h.

Constructor & Destructor Documentation

template<typename SequenceType , typename InfixIterator >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE nvbio::InfixSet< SequenceType, InfixIterator >::InfixSet ( )

inline

constructor

Definition at line 564 of file infix.h.

template<typename SequenceType , typename InfixIterator >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE nvbio::InfixSet< SequenceType, InfixIterator >::InfixSet	(	const uint32	size,
		const sequence_type	sequence,
		const infix_iterator	infixes
	)

inline

constructor

Definition at line 569 of file infix.h.

Member Function Documentation

template<typename SequenceType , typename InfixIterator >

const_iterator nvbio::InfixSet< SequenceType, InfixIterator >::begin ( void ) const

inline

begin iterator

Definition at line 577 of file infix.h.

template<typename SequenceType , typename InfixIterator >

iterator nvbio::InfixSet< SequenceType, InfixIterator >::begin ( void )

inline

begin iterator

Definition at line 585 of file infix.h.

template<typename SequenceType , typename InfixIterator >

const_iterator nvbio::InfixSet< SequenceType, InfixIterator >::end ( void ) const

inline

begin iterator

Definition at line 581 of file infix.h.

template<typename SequenceType , typename InfixIterator >

iterator nvbio::InfixSet< SequenceType, InfixIterator >::end ( void )

inline

begin iterator

Definition at line 589 of file infix.h.

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

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