Classes | |
class | seqan3::bi_fm_index< text_t, index_traits_t > |
The SeqAn Bidirectional FM Index. More... | |
interface | seqan3::bi_fm_index_concept |
Concept for bidirectional FM indices. More... | |
struct | seqan3::bi_fm_index_default_traits |
The default Bidirectional FM Index Configuration. More... | |
class | seqan3::bi_fm_index_iterator< index_t > |
The SeqAn Bidirectional FM Index Iterator. More... | |
interface | seqan3::bi_fm_index_iterator_concept |
Concept for bidirectional FM index iterators. More... | |
interface | seqan3::bi_fm_index_traits_concept |
Concept for bidirectional FM Index traits. More... | |
class | seqan3::fm_index< text_t, fm_index_traits > |
The SeqAn FM Index. More... | |
interface | seqan3::fm_index_concept |
Concept for unidirectional FM indices. More... | |
struct | seqan3::fm_index_default_traits |
The default FM Index Configuration. More... | |
class | seqan3::fm_index_iterator< index_t > |
The SeqAn FM Index Iterator. More... | |
interface | seqan3::fm_index_iterator_concept |
Concept for unidirectional FM index iterators. More... | |
interface | seqan3::fm_index_traits_concept |
Concept for unidirectional FM Index traits. More... | |
Requirements for seqan3::fm_index_traits_concept | |
The SDSL index must support the following interface to work with SeqAn3. | |
typename t::sdsl_index_type | seqan3::fm_index_traits_concept::sdsl_index_type |
Declares the type of the underlying SDSL index. Must satisfy the seqan3::detail::sdsl_index_concept. | |
Requirements for seqan3::fm_index_concept | |
You can expect these member types and member functions on all types that satisfy seqan3::fm_index_concept. | |
typename t::text_type | seqan3::fm_index_concept::text_type |
Type of the indexed text. | |
typename t::char_type | seqan3::fm_index_concept::char_type |
Type of the underlying character of text_type. | |
typename t::size_type | seqan3::fm_index_concept::size_type |
Type for representing the size of the indexed text. | |
typename t::iterator_type | seqan3::fm_index_concept::iterator_type |
Type of the unidirectional FM index iterator. More... | |
Requirements for seqan3::fm_index_iterator_concept | |
You can expect these member types and member functions on all types that satisfy seqan3::fm_index_iterator_concept. | |
typename t::index_type | seqan3::fm_index_iterator_concept::index_type |
Type of the underlying SeqAn FM index (not the underlying SDSL index). | |
typename t::size_type | seqan3::fm_index_iterator_concept::size_type |
Type for representing the size of the indexed text. More... | |
Requirements for seqan3::bi_fm_index_traits_concept | |
The bidirectional FM index traits must provide the following types: | |
typename t::fm_index_traits | seqan3::bi_fm_index_traits_concept::fm_index_traits |
Declares the type of the underlying unidirectional FM index on the original text. Must satisfy seqan3::fm_index_traits_concept. | |
typename t::rev_fm_index_traits | seqan3::bi_fm_index_traits_concept::rev_fm_index_traits |
Declares the type of the underlying unidirectional FM index on the reversed text. Must satisfy seqan3::fm_index_traits_concept. | |
Requirements for seqan3::bi_fm_index_concept | |
You can expect these member types and member functions on all types that satisfy seqan3::bi_fm_index_concept. | |
typename t::iterator_type | seqan3::bi_fm_index_concept::iterator_type |
Type of the bidirectional FM index iterator. | |
typename t::fwd_iterator_type | seqan3::bi_fm_index_concept::fwd_iterator_type |
Type of the unidirectional FM index iterator based on the unidirectional FM index on the original text. | |
typename t::rev_iterator_type | seqan3::bi_fm_index_concept::rev_iterator_type |
Type of the unidirectional FM index iterator based on the unidirectional FM index on the reversed text. More... | |
Requirements for seqan3::bi_fm_index_iterator_concept | |
You can expect these member types and member functions on all types that satisfy seqan3::fm_index_iterator_concept. | |
typename t::index_type | seqan3::bi_fm_index_iterator_concept::index_type |
Type of the underlying SeqAn FM index (not the underlying SDSL index). | |
typename t::size_type | seqan3::bi_fm_index_iterator_concept::size_type |
Type for representing the size of the indexed text. More... | |
FM indices are text indices similar to suffix trees or suffix arrays which are based on the Burrow Wheeler transform and a sampled suffix array. FM indices are significantly smaller in space without sacrificing speed. They also allow for adjusting the speed respectively space by choosing the underlying data structures accordingly or modyfing the sampling rate of the sampled suffix array.
The FM indices are based on the SDSL 3 (succinct data structure library). You are able to specify the underlying implementation of the SDSL to adjust it to your needs as well as choose one of the preconfigured indices that are suitable for common applications in sequence analysis.
For technical reasons you can currently only build indices over a seqan3::alphabet_concept if its seqan3::alphabet_size is smaller or equal 256.
You can choose between unidirectional and bidirectional FM indices (which can be thought of suffix trees and affix trees, i.e. a combination of suffix and prefix trees being able to search a pattern from left to right, right to left and character by character in any arbitrary order). Roughly speaking bidirectional FM indices are more powerful for approximate string matching at the cost of a higher space consumption
Index Iterators are lightweight objects, i.e. they are cheap to copy.
Note that although the SeqAn3 index iterators are called "iterators", they don't model any of the standard library iterator concepts, not even std::Iterator.
typename t::iterator_type iterator_type |
Type of the unidirectional FM index iterator.
typename t::rev_iterator_type rev_iterator_type |
Type of the unidirectional FM index iterator based on the unidirectional FM index on the reversed text.