Detailed description

template< typename fm_index_type>
struct nvbio::MEMFilterHost< fm_index_type >

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

: The filter is designed to:

first find and rank the suffix array ranges containing occurrences of all MEMs, expressed as a series of lists of (SA-begin, SA-end,string-begin,string-end) tuples: there is one such list for each string in the set, and the entries are stored contiguously in a single vector;
and then enumerate each individual occurrence of a MEM within the lists, as a set of (index-pos,string-id,string-begin,string-end) tuples.

Template Parameters

fm_index_type the type of the fm-index

Definition at line 473 of file mem.h.

#include <mem.h>

Inheritance diagram for nvbio::MEMFilterHost< fm_index_type >:

Additional Inherited Members
Public Types inherited from nvbio::MEMFilter< host_tag, fm_index_type >
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 More...

typedef MEMRange< coord_type >	rank_type
	rank coordinates are either uint32_4 or uint64_4 More...

typedef MEMHit< coord_type >	mem_type
	MEM coordinates are either uint32_4 or uint64_4. More...

typedef mem_type	hit_type
	MEM coordinates are either uint32_4 or uint64_4. More...

Public Methods inherited from nvbio::MEMFilter< host_tag, fm_index_type >
template<typename string_set_type >
uint64	rank (const fm_index_type &f_index, const fm_index_type &r_index, const string_set_type &string_set, const uint32 min_intv=1u, const uint32 max_intv=uint32(-1), const uint32 min_span=1u, const uint32 split_len=uint32(-1), const uint32 split_width=uint32(-1))

uint32	first_hit (const uint32 string_id) const

template<typename mems_iterator >
void	locate (const uint64 begin, const uint64 end, mems_iterator mems)

uint64	n_hits () const

uint64	n_mems () const

uint64	n_ranges () const

Public Members inherited from nvbio::MEMFilter< host_tag, fm_index_type >
uint32	m_n_queries

index_type	m_f_index

index_type	m_r_index

uint64	m_n_occurrences

HostVectorArray< rank_type >	m_mem_ranges

thrust::host_vector< uint64 >	m_slots

Static Public Members inherited from nvbio::MEMFilter< host_tag, fm_index_type >
static const uint32	coord_dim = vector_traits<coord_type>::DIM

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

E:/git/nvbio/nvbio/fmindex/mem.h

Detailed description

template< typename fm_index_type> struct nvbio::MEMFilterHost< fm_index_type >

Additional Inherited Members

template< typename fm_index_type>
struct nvbio::MEMFilterHost< fm_index_type >