nvbio::FMIndexFilter< host_tag, fm_index_type > Struct Template Reference

Detailed description

template< typename fm_index_type>
struct nvbio::FMIndexFilter< host_tag, fm_index_type >

This class implements a FM-index filter which can be used to find and filter matches between an arbitrary string-set and an FM-index.

The filter will return an ordered set of (index-pos,string-id) pairs, where string-id is the index into the string-set and index-pos is an index into the FM-index.

Template Parameters

fm_index_type

the type of the fm-index

Definition at line 75 of file filter.h.

#include <filter.h>

Inheritance diagram for nvbio::FMIndexFilter< host_tag, fm_index_type >:

Public Types
typedef host_tag	system_tag
	the backend system More...
typedef fm_index_type	index_type
	the index type More...
typedef index_type::index_type	coord_type
	the coordinate type of the fm-index, uint32|uint64|uint32_2|uint64_2 More...
typedef vector_type < coord_type, 2 >::type	range_type
	ranges are either uint32_2 or uint64_2; More...
typedef vector_type < coord_type, hit_dim >::type	hit_type
	hits are either uint2 or uint4 More...

Public Methods
template<typename string_set_type >
uint64	rank (const fm_index_type &index, const string_set_type &string_set)
template<typename hits_iterator >
void	locate (const uint64 begin, const uint64 end, hits_iterator hits)
uint64	n_hits () const
const range_type *	ranges () const
const uint64 *	ranks () const

Public Members
uint32	m_n_queries
index_type	m_index
uint64	m_n_occurrences
thrust::host_vector< range_type >	m_ranges
thrust::host_vector< uint64 >	m_slots

Static Public Members
static const uint32	coord_dim = vector_traits<coord_type>::DIM
static const uint32	hit_dim = coord_dim*2
	hits are either uint2 or uint4 More...

Member Typedef Documentation

template<typename fm_index_type >

typedef index_type::index_type nvbio::FMIndexFilter< host_tag, fm_index_type >::coord_type

the coordinate type of the fm-index, uint32|uint64|uint32_2|uint64_2

Definition at line 80 of file filter.h.

template<typename fm_index_type >

typedef vector_type<coord_type,hit_dim>::type nvbio::FMIndexFilter< host_tag, fm_index_type >::hit_type

hits are either uint2 or uint4

Definition at line 86 of file filter.h.

template<typename fm_index_type >

typedef fm_index_type nvbio::FMIndexFilter< host_tag, fm_index_type >::index_type

the index type

Definition at line 78 of file filter.h.

template<typename fm_index_type >

typedef vector_type<coord_type,2>::type nvbio::FMIndexFilter< host_tag, fm_index_type >::range_type

ranges are either uint32_2 or uint64_2;

Definition at line 83 of file filter.h.

template<typename fm_index_type >

typedef host_tag nvbio::FMIndexFilter< host_tag, fm_index_type >::system_tag

the backend system

Definition at line 77 of file filter.h.

Member Function Documentation

template<typename fm_index_type >

template<typename hits_iterator >

void nvbio::FMIndexFilter< host_tag, fm_index_type >::locate	(	const uint64	begin,
		const uint64	end,
		hits_iterator	hits
	)

enumerate all hits in a given range

Template Parameters

hits_iterator

a hit_type iterator

Parameters

begin	the beginning of the hits sequence to locate, in [0,n_hits)
end	the end of the hits sequence to locate, in [0,n_hits]

Definition at line 238 of file filter_inl.h.

template<typename fm_index_type >

uint64 nvbio::FMIndexFilter< host_tag, fm_index_type >::n_hits ( ) const

inline

return the number of hits from the last rank query

Definition at line 115 of file filter.h.

template<typename fm_index_type >

const range_type* nvbio::FMIndexFilter< host_tag, fm_index_type >::ranges ( ) const

inline

return the individual ranges of the ranked queries

Definition at line 119 of file filter.h.

template<typename fm_index_type >

template<typename string_set_type >

uint64 nvbio::FMIndexFilter< host_tag, fm_index_type >::rank	(	const fm_index_type &	index,
		const string_set_type &	string_set
	)

enact the filter on an FM-index and a string-set

Parameters

index	the FM-index
string-set	the query string-set

Returns

the total number of hits

Definition at line 202 of file filter_inl.h.

template<typename fm_index_type >

const uint64* nvbio::FMIndexFilter< host_tag, fm_index_type >::ranks ( ) const

inline

return the global ranks of the output hits (i.e. the range [ranks[i], ranks[i+1]) identifies the position of the hits corresponding to the i-th query in the locate output)

Definition at line 124 of file filter.h.

Member Data Documentation

template<typename fm_index_type >

const uint32 nvbio::FMIndexFilter< host_tag, fm_index_type >::coord_dim = vector_traits<coord_type>::DIM

static

Definition at line 81 of file filter.h.

template<typename fm_index_type >

const uint32 nvbio::FMIndexFilter< host_tag, fm_index_type >::hit_dim = coord_dim*2

static

hits are either uint2 or uint4

Definition at line 85 of file filter.h.

template<typename fm_index_type >

index_type nvbio::FMIndexFilter< host_tag, fm_index_type >::m_index

Definition at line 127 of file filter.h.

template<typename fm_index_type >

uint64 nvbio::FMIndexFilter< host_tag, fm_index_type >::m_n_occurrences

Definition at line 128 of file filter.h.

template<typename fm_index_type >

uint32 nvbio::FMIndexFilter< host_tag, fm_index_type >::m_n_queries

Definition at line 126 of file filter.h.

template<typename fm_index_type >

thrust::host_vector<range_type> nvbio::FMIndexFilter< host_tag, fm_index_type >::m_ranges

Definition at line 129 of file filter.h.

template<typename fm_index_type >

thrust::host_vector<uint64> nvbio::FMIndexFilter< host_tag, fm_index_type >::m_slots

Definition at line 130 of file filter.h.

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

• E:/git/nvbio/nvbio/fmindex/filter.h
• E:/git/nvbio/nvbio/fmindex/filter_inl.h