nvbio::SparseStringSet< StringIterator, RangeIterator > Struct Template Reference

Detailed description

template< typename StringIterator, typename RangeIterator>
struct nvbio::SparseStringSet< StringIterator, RangeIterator >

A sparse collection of strings that are stored as ranges of a larger string, and their starting points and end points are given by a range vector.

Template Parameters

StringIterator	base string support
RangeIterator	an iterator definining a set of ranges, whose value_type must be uint2.

Assume you have a large packed-DNA genome and have identified a few isolated regions of importance that you want to analyze. With the following container you can easily represent them:

void analyze_regions(
    const thrust::device_vector<uint32>& genome_storage,
    const thrust::device_vector<uint2>&  regions)
{
    typedef PackedStream<const uint32*, uint8, 2u, true>        packed_iterator;
    typedef const uint2*                                        ranges_iterator;
    typedef SparseStringSet<packed_iterator, ranges_iterator>   sparse_string_set;

    packed_iterator packed_stream( plain_view( genome_storage ) );

    // build the string set
    sparse_string_set string_set(
        regions.size(),
        packed_stream,
        plain_view( regions ) );

    // work with the string set
    ...
}

Definition at line 613 of file string_set.h.

#include <string_set.h>

Public Types
typedef sparse_string_set_tag	string_set_tag
typedef std::iterator_traits < StringIterator >::value_type	symbol_type
typedef vector_view < StringIterator >	string_type
typedef StringIterator	symbol_iterator
typedef RangeIterator	range_iterator
typedef iterator_system < StringIterator >::type	system_tag
typedef StringSetIterator < SparseStringSet < StringIterator, RangeIterator > >	iterator
typedef StringSetIterator < SparseStringSet < StringIterator, RangeIterator > >	const_iterator

Public Methods
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE	SparseStringSet ()
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE	SparseStringSet (const uint32 size, const StringIterator string, const RangeIterator ranges)
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32	size () const
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE string_type	operator[] (const uint32 i) const
const_iterator	begin () const
const_iterator	end () const
iterator	begin ()
iterator	end ()
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE symbol_iterator	base_string () const
NVBIO_FORCEINLINE NVBIO_HOST_DEVICE range_iterator	ranges () const

Related Functions
(Note that these are not member functions.)
template<typename StringIterator , typename RangeIterator >
SparseStringSet < StringIterator, RangeIterator >	make_sparse_string_set (const uint32 size, const StringIterator string, const RangeIterator offsets)

Member Typedef Documentation

template<typename StringIterator, typename RangeIterator>

typedef StringSetIterator< SparseStringSet<StringIterator,RangeIterator> > nvbio::SparseStringSet< StringIterator, RangeIterator >::const_iterator

Definition at line 623 of file string_set.h.

template<typename StringIterator, typename RangeIterator>

typedef StringSetIterator< SparseStringSet<StringIterator,RangeIterator> > nvbio::SparseStringSet< StringIterator, RangeIterator >::iterator

Definition at line 622 of file string_set.h.

template<typename StringIterator, typename RangeIterator>

typedef RangeIterator nvbio::SparseStringSet< StringIterator, RangeIterator >::range_iterator

Definition at line 619 of file string_set.h.

template<typename StringIterator, typename RangeIterator>

typedef sparse_string_set_tag nvbio::SparseStringSet< StringIterator, RangeIterator >::string_set_tag

Definition at line 615 of file string_set.h.

template<typename StringIterator, typename RangeIterator>

typedef vector_view<StringIterator> nvbio::SparseStringSet< StringIterator, RangeIterator >::string_type

Definition at line 617 of file string_set.h.

template<typename StringIterator, typename RangeIterator>

typedef StringIterator nvbio::SparseStringSet< StringIterator, RangeIterator >::symbol_iterator

Definition at line 618 of file string_set.h.

template<typename StringIterator, typename RangeIterator>

typedef std::iterator_traits<StringIterator>::value_type nvbio::SparseStringSet< StringIterator, RangeIterator >::symbol_type

Definition at line 616 of file string_set.h.

template<typename StringIterator, typename RangeIterator>

typedef iterator_system<StringIterator>::type nvbio::SparseStringSet< StringIterator, RangeIterator >::system_tag

Definition at line 620 of file string_set.h.

Constructor & Destructor Documentation

template<typename StringIterator, typename RangeIterator>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE nvbio::SparseStringSet< StringIterator, RangeIterator >::SparseStringSet ( )

inline

default constructor

Definition at line 628 of file string_set.h.

template<typename StringIterator, typename RangeIterator>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE nvbio::SparseStringSet< StringIterator, RangeIterator >::SparseStringSet ( const uint32  size, const StringIterator  string, const RangeIterator  ranges  )

inline

constructor

Parameters

size	set size
string	flat string iterator
ranges	string ranges in the flat string array

Definition at line 637 of file string_set.h.

Member Function Documentation

template<typename StringIterator, typename RangeIterator>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE symbol_iterator nvbio::SparseStringSet< StringIterator, RangeIterator >::base_string ( ) const

inline

return the base string

Definition at line 681 of file string_set.h.

template<typename StringIterator, typename RangeIterator>

const_iterator nvbio::SparseStringSet< StringIterator, RangeIterator >::begin ( void  ) const

inline

begin iterator

Definition at line 664 of file string_set.h.

template<typename StringIterator, typename RangeIterator>

iterator nvbio::SparseStringSet< StringIterator, RangeIterator >::begin ( void  )

inline

begin iterator

Definition at line 672 of file string_set.h.

template<typename StringIterator, typename RangeIterator>

const_iterator nvbio::SparseStringSet< StringIterator, RangeIterator >::end ( void  ) const

inline

begin iterator

Definition at line 668 of file string_set.h.

template<typename StringIterator, typename RangeIterator>

iterator nvbio::SparseStringSet< StringIterator, RangeIterator >::end ( void  )

inline

begin iterator

Definition at line 676 of file string_set.h.

template<typename StringIterator, typename RangeIterator>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE string_type nvbio::SparseStringSet< StringIterator, RangeIterator >::operator[] ( const uint32  i) const

inline

indexing operator: access the i-th string

Definition at line 653 of file string_set.h.

template<typename StringIterator, typename RangeIterator>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE range_iterator nvbio::SparseStringSet< StringIterator, RangeIterator >::ranges ( ) const

inline

return the offset vector

Definition at line 686 of file string_set.h.

template<typename StringIterator, typename RangeIterator>

NVBIO_FORCEINLINE NVBIO_HOST_DEVICE uint32 nvbio::SparseStringSet< StringIterator, RangeIterator >::size ( void  ) const

inline

set size

Definition at line 648 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