19#include <sdsl/suffix_trees.hpp>
49 return lhs.begin_position == rhs.begin_position && lhs.end_position == rhs.end_position;
85template <
typename index_t>
129 template <
typename _index_t>
145 assert(l <= r && r < csa.size());
150 if constexpr(!std::same_as<index_alphabet_type, sdsl::plain_byte_alphabet>)
152 cc = csa.char2comp[c];
153 if (cc == 0 && c > 0)
158 if (l == 0 && r + 1 == csa.size())
161 _r = csa.C[cc + 1] - 1;
166 _l = c_begin + csa.bwt.rank(l, c);
167 _r = c_begin + csa.bwt.rank(r + 1, c) - 1;
174 assert(r + 1 - l >= 0);
198 node({0, _index.index.size() - 1, 0, 0}),
199 sigma(_index.index.sigma - index_t::text_layout_mode)
201 assert(_index.index.size() != 0);
219 assert(
index !=
nullptr);
224 return node == rhs.node;
241 assert(
index !=
nullptr);
243 return !(*
this == rhs);
267 assert(
index !=
nullptr);
299 template <
typename char_t>
301 requires std::convertible_to<char_t, index_alphabet_type>
305 assert(
index !=
nullptr);
326 template <
typename char_type>
328 requires detail::is_char_adaptation_v<char_type>
351 template <std::ranges::range seq_t>
354 static_assert(std::ranges::forward_range<seq_t>,
"The query must model forward_range.");
356 "The alphabet of the sequence must be convertible to the alphabet of the index.");
358 assert(
index !=
nullptr);
366 for (
auto it = std::ranges::begin(
seq); it != std::ranges::end(
seq); ++len, ++it)
475 assert(
index !=
nullptr);
500 assert(
index !=
nullptr);
523 template <std::ranges::range text_t>
529 static_assert(std::ranges::input_range<text_t>,
"The text must model input_range.");
530 static_assert(range_dimension_v<text_t> == 1,
"The input cannot be a text collection.");
532 "The alphabet types of the given text and index differ.");
533 assert(
index !=
nullptr);
540 template <std::ranges::range text_t>
546 static_assert(std::ranges::input_range<text_t>,
"The text collection must model input_range.");
547 static_assert(range_dimension_v<text_t> == 2,
"The input must be a text collection.");
549 "The alphabet types of the given text and index differ.");
550 assert(
index !=
nullptr);
562 size_type const start_location =
index->text_begin_ss.select(rank);
564 size_type const query_begin = location - start_location;
583 assert(
index !=
nullptr);
604 assert(
index !=
nullptr);
622 assert(
index !=
nullptr);
630 size_type sequence_position = loc -
index->text_begin_ss.select(sequence_rank);
653 assert(
index !=
nullptr);
668 assert(
index !=
nullptr);
673 auto loc = _offset -
index->index[sa_pos];
675 size_type sequence_position = loc -
index->text_begin_ss.select(sequence_rank);
687 template <cereal_archive archive_t>
Core alphabet concept and free function/type trait wrappers.
Provides alphabet adaptations for standard char types.
The SeqAn Bidirectional FM Index Cursor.
Definition: bi_fm_index_cursor.hpp:55
The SeqAn FM Index Cursor.
Definition: fm_index_cursor.hpp:87
bool extend_right(seq_t &&seq) noexcept
Tries to extend the query by seq to the right.
Definition: fm_index_cursor.hpp:352
locate_result_type locate() const
Locates the occurrences of the searched query in the text.
Definition: fm_index_cursor.hpp:599
bool extend_right(char_t const c) noexcept
Tries to extend the query by the character c to the right.
Definition: fm_index_cursor.hpp:303
auto path_label(text_t &&text) const noexcept
Returns the searched query.
Definition: fm_index_cursor.hpp:524
bool cycle_back() noexcept
Tries to replace the rightmost character of the query by the next lexicographically larger character ...
Definition: fm_index_cursor.hpp:413
size_type parent_rb
Right suffix array interval of the parent node. Needed for cycle_back().
Definition: fm_index_cursor.hpp:123
bool operator!=(fm_index_cursor const &rhs) const noexcept
Compares two cursors.
Definition: fm_index_cursor.hpp:239
bool backward_search(sdsl_index_type const &csa, sdsl_char_type const c, size_type &l, size_type &r) const noexcept
Optimized backward search without alphabet mapping.
Definition: fm_index_cursor.hpp:140
seqan3::suffix_array_interval suffix_array_interval() const noexcept
Returns the half-open suffix array interval.
Definition: fm_index_cursor.hpp:473
typename index_type::sdsl_char_type sdsl_char_type
Type of the representation of characters in the underlying SDSL index.
Definition: fm_index_cursor.hpp:105
bool operator==(fm_index_cursor const &rhs) const noexcept
Compares two cursors.
Definition: fm_index_cursor.hpp:217
size_type count() const noexcept
Counts the number of occurrences of the searched query in the text.
Definition: fm_index_cursor.hpp:581
size_type last_rank() const noexcept
Outputs the rightmost rank.
Definition: fm_index_cursor.hpp:450
bool extend_right() noexcept
Tries to extend the query by the smallest possible character to the right such that the query is foun...
Definition: fm_index_cursor.hpp:263
typename index_t::alphabet_type index_alphabet_type
Alphabet type of the index.
Definition: fm_index_cursor.hpp:111
node_type node
Underlying index from the SDSL.
Definition: fm_index_cursor.hpp:125
size_type offset() const noexcept
Helper function to recompute text positions since the indexed text is reversed.
Definition: fm_index_cursor.hpp:133
size_type query_length() const noexcept
Returns the length of the searched query. Returns the depth of the cursor node in the implicit suffi...
Definition: fm_index_cursor.hpp:498
index_t index_type
Type of the index.
Definition: fm_index_cursor.hpp:93
typename index_type::size_type size_type
Type for representing positions in the indexed text.
Definition: fm_index_cursor.hpp:95
typename index_type::sdsl_sigma_type sdsl_sigma_type
Type of the alphabet size in the underlying SDSL index.
Definition: fm_index_cursor.hpp:109
typename index_t::sdsl_index_type sdsl_index_type
Type of the SDSL index.
Definition: fm_index_cursor.hpp:107
auto lazy_locate() const
Locates the occurrences of the searched query in the text on demand, i.e. a std::ranges::view is retu...
Definition: fm_index_cursor.hpp:648
bool extend_right(char_type const *cstring) noexcept
This is an overloaded member function, provided for convenience. It differs from the above function o...
Definition: fm_index_cursor.hpp:330
sdsl_sigma_type sigma
Alphabet size of the index without delimiters.
Definition: fm_index_cursor.hpp:127
size_type parent_lb
Left suffix array interval of the parent node. Needed for cycle_back().
Definition: fm_index_cursor.hpp:121
index_type const * index
Underlying FM index.
Definition: fm_index_cursor.hpp:119
fm_index_cursor() noexcept=default
Default constructor. Accessing member functions on a default constructed object is undefined behavior...
Provides various transformation traits used by the range module.
Provides the internal representation of a node of the seqan3::fm_index_cursor.
T emplace_back(T... args)
constexpr auto to_rank
Return the rank representation of a (semi-)alphabet object.
Definition: concept.hpp:155
@ seq
The "sequence", usually a range of nucleotides or amino acids.
text_layout
The possible text layouts (single, collection) the seqan3::fm_index and seqan3::bi_fm_index can suppo...
Definition: concept.hpp:72
@ single
The text is a single range.
Definition: concept.hpp:74
@ collection
The text is a range of ranges.
Definition: concept.hpp:76
constexpr simd_t iota(typename simd_traits< simd_t >::scalar_type const offset)
Fills a seqan3::simd::simd_type vector with the scalar values offset, offset+1, offset+2,...
Definition: algorithm.hpp:312
decltype(detail::transform< trait_t >(list_t{})) transform
Apply a transformation trait to every type in the list and return a seqan3::type_list of the results.
Definition: traits.hpp:495
constexpr auto slice
A view adaptor that returns a half-open interval on the underlying range.
Definition: slice.hpp:183
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
The <ranges> header from C++20's standard library.
Provides the concept for seqan3::detail::sdsl_index.
Provides seqan3::views::slice.
Internal representation of the node of an FM index cursor.
Definition: fm_index_cursor.hpp:30
size_type rb
Right suffix array bound.
Definition: fm_index_cursor.hpp:41
sdsl_char_type last_char
Label of the last edge moved down. Needed for cycle_back().
Definition: fm_index_cursor.hpp:45
size_type depth
Depth of the node in the suffix tree, i.e. length of the searched query.
Definition: fm_index_cursor.hpp:43
size_type lb
Left suffix array bound.
Definition: fm_index_cursor.hpp:39
The underlying suffix array interval.
Definition: fm_index_cursor.hpp:33
size_t end_position
The exclusive end position of the interval ("right boundary").
Definition: fm_index_cursor.hpp:37
size_t begin_position
The begin position of the interval ("left boundary").
Definition: fm_index_cursor.hpp:35
friend bool operator==(suffix_array_interval const &lhs, suffix_array_interval const &rhs) noexcept
Test for equality.
Definition: fm_index_cursor.hpp:47
friend bool operator!=(suffix_array_interval const &lhs, suffix_array_interval const &rhs) noexcept
Test for inequality.
Definition: fm_index_cursor.hpp:57