NVBIO: nvbio::InfixSetCore< SequenceType, InfixIterator, 4u > Struct Template Reference

Detailed description

template< typename SequenceType, typename InfixIterator>
struct nvbio::InfixSetCore< SequenceType, InfixIterator, 4u >

Represent a set of infixes of a string-set

Template Parameters

SequenceType	the string or string-set type
InfixIterator	the infix iterator type - value_type can be uint4 or uint64_4

Definition at line 381 of file infix.h.

#include <infix.h>

Public Types
typedef SequenceType	sequence_type

typedef InfixIterator	infix_iterator

typedef sequence_type::string_type	base_string_type

typedef std::iterator_traits < InfixIterator >::value_type	coord_type

typedef Infix < base_string_type, coord_type >	string_type

Public Methods
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE	InfixSetCore ()

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

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	size () const

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE string_type	operator[] (const uint32 i) const

Public Members
uint32	m_size

sequence_type	m_sequence

infix_iterator	m_infixes

Member Typedef Documentation

template<typename SequenceType , typename InfixIterator >

typedef sequence_type::string_type nvbio::InfixSetCore< SequenceType, InfixIterator, 4u >::base_string_type

Definition at line 386 of file infix.h.

template<typename SequenceType , typename InfixIterator >

typedef std::iterator_traits<InfixIterator>::value_type nvbio::InfixSetCore< SequenceType, InfixIterator, 4u >::coord_type

Definition at line 387 of file infix.h.

template<typename SequenceType , typename InfixIterator >

typedef InfixIterator nvbio::InfixSetCore< SequenceType, InfixIterator, 4u >::infix_iterator

Definition at line 384 of file infix.h.

template<typename SequenceType , typename InfixIterator >

typedef SequenceType nvbio::InfixSetCore< SequenceType, InfixIterator, 4u >::sequence_type

Definition at line 383 of file infix.h.

template<typename SequenceType , typename InfixIterator >

typedef Infix<base_string_type, coord_type> nvbio::InfixSetCore< SequenceType, InfixIterator, 4u >::string_type

Definition at line 388 of file infix.h.

Constructor & Destructor Documentation

template<typename SequenceType , typename InfixIterator >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE nvbio::InfixSetCore< SequenceType, InfixIterator, 4u >::InfixSetCore ( )

inline

constructor

Definition at line 393 of file infix.h.

template<typename SequenceType , typename InfixIterator >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE nvbio::InfixSetCore< SequenceType, InfixIterator, 4u >::InfixSetCore	(	const uint32	size,
		const sequence_type	sequence,
		const infix_iterator	infixes
	)

inline

constructor

Definition at line 398 of file infix.h.

Member Function Documentation

template<typename SequenceType , typename InfixIterator >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE string_type nvbio::InfixSetCore< SequenceType, InfixIterator, 4u >::operator[] ( const uint32 i) const

inline

indexing operator: access the i-th string

Definition at line 414 of file infix.h.

template<typename SequenceType , typename InfixIterator >

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::InfixSetCore< SequenceType, InfixIterator, 4u >::size ( void ) const

inline

set size

Definition at line 409 of file infix.h.

Member Data Documentation

template<typename SequenceType , typename InfixIterator >

infix_iterator nvbio::InfixSetCore< SequenceType, InfixIterator, 4u >::m_infixes

Definition at line 422 of file infix.h.

template<typename SequenceType , typename InfixIterator >

sequence_type nvbio::InfixSetCore< SequenceType, InfixIterator, 4u >::m_sequence

Definition at line 421 of file infix.h.

template<typename SequenceType , typename InfixIterator >

uint32 nvbio::InfixSetCore< SequenceType, InfixIterator, 4u >::m_size

Definition at line 420 of file infix.h.

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

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