19#include <sdsl/suffix_trees.hpp>
27namespace seqan3::detail
32struct fm_index_validator
48 template <semialphabet alphabet_t, text_layout text_layout_mode_, std::ranges::range text_t>
49 static void validate(text_t && text)
53 static_assert(std::ranges::bidirectional_range<text_t>,
"The text must model bidirectional_range.");
54 static_assert(std::convertible_to<range_innermost_value_t<text_t>, alphabet_t>,
55 "The alphabet of the text collection must be convertible to the alphabet of the index.");
56 static_assert(range_dimension_v<text_t> == 1,
"The input cannot be a text collection.");
58 if (std::ranges::empty(text))
63 static_assert(std::ranges::bidirectional_range<text_t>,
64 "The text collection must model bidirectional_range.");
65 static_assert(std::ranges::bidirectional_range<std::ranges::range_reference_t<text_t>>,
66 "The elements of the text collection must model bidirectional_range.");
67 static_assert(std::convertible_to<range_innermost_value_t<text_t>, alphabet_t>,
68 "The alphabet of the text collection must be convertible to the alphabet of the index.");
69 static_assert(range_dimension_v<text_t> == 2,
"The input must be a text collection.");
71 if (std::ranges::empty(text))
74 static_assert(alphabet_size<range_innermost_value_t<text_t>> <= 256,
"The alphabet is too big.");
84template <
typename index_t>
87template <
typename index_t>
88class bi_fm_index_cursor;
94 detail::sdsl_index sdsl_index_type_>
95class reverse_fm_index;
132 sdsl::csa_wt<sdsl::wt_blcd<sdsl::bit_vector,
133 sdsl::rank_support_v<>,
134 sdsl::select_support_scan<>,
135 sdsl::select_support_scan<0>>,
138 sdsl::sa_order_sa_sampling<>,
139 sdsl::isa_sampling<>,
140 sdsl::plain_byte_alphabet>;
197 using sdsl_index_type = sdsl_index_type_;
201 using sdsl_char_type =
typename sdsl_index_type::alphabet_type::char_type;
203 using sdsl_sigma_type =
typename sdsl_index_type::alphabet_type::sigma_type;
206 friend class detail::reverse_fm_index<alphabet_t, text_layout_mode_, sdsl_index_type_>;
209 sdsl_index_type index;
212 sdsl::sd_vector<> text_begin;
214 sdsl::select_support_sd<1> text_begin_ss;
216 sdsl::rank_support_sd<1> text_begin_rs;
219 template <
typename output_it_t,
typename sequence_t>
220 static output_it_t copy_sequence_ranks_shifted_by_one(output_it_t output_it, sequence_t &&
sequence)
222 constexpr size_t sigma = alphabet_size<alphabet_t>;
225 constexpr auto warn_if_rank_out_of_range = [](uint8_t
const rank)
227 if (rank >= max_sigma - 1)
229 "character alphabets the last one/two values are reserved"
230 "(single sequence/collection).");
236 if constexpr (sigma >= max_sigma)
237 warn_if_rank_out_of_range(rank);
261 template <std::ranges::range text_t>
265 void construct(text_t && text)
267 detail::fm_index_validator::validate<alphabet_t, text_layout_mode_>(text);
274 sdsl::int_vector<8> tmp_text(std::ranges::distance(text));
277 copy_sequence_ranks_shifted_by_one(std::ranges::begin(tmp_text), text | std::views::reverse);
279 sdsl::construct_im(index, tmp_text, 0);
288 template <std::ranges::range text_t>
292 void construct(text_t && text,
bool reverse =
false)
294 detail::fm_index_validator::validate<alphabet_t, text_layout_mode_>(text);
298 for (
auto && t : text)
299 text_sizes.
push_back(std::ranges::distance(t));
301 size_t const number_of_texts{text_sizes.
size()};
306 if (number_of_texts == text_size)
309 constexpr auto sigma = alphabet_size<alphabet_t>;
314 sdsl::sd_vector_builder builder(text_size, number_of_texts);
315 size_t prefix_sum{0};
317 for (
auto &&
size : text_sizes)
319 builder.set(prefix_sum);
320 prefix_sum +=
size + 1;
323 text_begin = sdsl::sd_vector<>(builder);
324 text_begin_ss = sdsl::select_support_sd<1>(&text_begin);
325 text_begin_rs = sdsl::rank_support_sd<1>(&text_begin);
328 sdsl::int_vector<8> tmp_text(text_size - (number_of_texts > 1));
330 constexpr uint8_t delimiter = sigma >= 255 ? 255 : sigma + 1;
332 auto copy_join_with = [](
auto output_it,
auto &&
collection)
335 auto collection_it = std::ranges::begin(
collection);
336 auto const collection_sentinel = std::ranges::end(
collection);
337 if (collection_it == collection_sentinel)
340 output_it = copy_sequence_ranks_shifted_by_one(output_it, *collection_it);
343 for (; collection_it != collection_sentinel; ++collection_it)
345 *output_it = delimiter;
347 output_it = copy_sequence_ranks_shifted_by_one(output_it, *collection_it);
352 copy_join_with(std::ranges::begin(tmp_text), text);
357 if (number_of_texts == 1)
358 tmp_text.back() = delimiter;
360 std::ranges::reverse(tmp_text);
367 if (number_of_texts == 1)
369 std::ranges::reverse(tmp_text.begin(), tmp_text.end() - 1);
370 tmp_text.back() = delimiter;
374 std::ranges::reverse(tmp_text);
378 sdsl::construct_im(index, tmp_text, 0);
396 template <
typename bi_fm_index_t>
399 template <
typename fm_index_t>
402 template <
typename fm_index_t>
403 friend class detail::fm_index_cursor_node;
412 index{rhs.index}, text_begin{rhs.text_begin}, text_begin_ss{rhs.text_begin_ss}, text_begin_rs{rhs.text_begin_rs}
414 text_begin_ss.set_vector(&text_begin);
415 text_begin_rs.set_vector(&text_begin);
420 index{
std::move(rhs.index)}, text_begin{
std::move(rhs.text_begin)},text_begin_ss{
std::move(rhs.text_begin_ss)},
421 text_begin_rs{
std::move(rhs.text_begin_rs)}
423 text_begin_ss.set_vector(&text_begin);
424 text_begin_rs.set_vector(&text_begin);
430 index = std::move(rhs.index);
431 text_begin = std::move(rhs.text_begin);
432 text_begin_ss = std::move(rhs.text_begin_ss);
433 text_begin_rs = std::move(rhs.text_begin_rs);
435 text_begin_ss.set_vector(&text_begin);
436 text_begin_rs.set_vector(&text_begin);
451 template <std::ranges::b
idirectional_range text_t>
454 construct(std::forward<text_t>(text));
504 return (index == rhs.index) && (text_begin == rhs.text_begin);
520 return !(*
this == rhs);
549 template <cereal_archive archive_t>
550 void CEREAL_SERIALIZE_FUNCTION_NAME(archive_t & archive)
554 archive(text_begin_ss);
555 text_begin_ss.set_vector(&text_begin);
556 archive(text_begin_rs);
557 text_begin_rs.set_vector(&text_begin);
559 auto sigma = alphabet_size<alphabet_t>;
561 if (sigma != alphabet_size<alphabet_t>)
564 " but it is being read into an fm_index with an alphabet of size " +
573 (tmp ?
"text collection" :
"single text") +
574 " but it is being read into an fm_index expecting a " +
586template <std::ranges::range text_t>
591namespace seqan3::detail
610class reverse_fm_index :
public fm_index<alphabet_t, text_layout_mode, sdsl_index_type>
614 template <std::ranges::range text_t>
615 void construct_(text_t && text)
619 auto reverse_text = text | std::views::reverse;
620 this->construct(reverse_text);
624 auto reverse_text = text | views::deep{std::views::reverse} | std::views::reverse;
625 this->construct(reverse_text,
true);
633 template <std::ranges::b
idirectional_range text_t>
634 explicit reverse_fm_index(text_t && text)
636 construct_(std::forward<text_t>(text));
The SeqAn Bidirectional FM Index Cursor.
Definition: bi_fm_index_cursor.hpp:55
The SeqAn FM Index Cursor.
Definition: fm_index_cursor.hpp:87
The SeqAn FM Index.
Definition: fm_index.hpp:191
fm_index & operator=(fm_index rhs)
When copy/move assigning, also update internal data structures.
Definition: fm_index.hpp:428
fm_index()=default
Defaulted.
static constexpr text_layout text_layout_mode
Indicates whether index is built over a collection.
Definition: fm_index.hpp:383
cursor_type cursor() const noexcept
Returns a seqan3::fm_index_cursor on the index that can be used for searching. .
Definition: fm_index.hpp:537
size_type size() const noexcept
Returns the length of the indexed text including sentinel characters.
Definition: fm_index.hpp:469
bool operator!=(fm_index const &rhs) const noexcept
Compares two indices.
Definition: fm_index.hpp:518
bool empty() const noexcept
Checks whether the index is empty.
Definition: fm_index.hpp:485
bool operator==(fm_index const &rhs) const noexcept
Compares two indices.
Definition: fm_index.hpp:501
~fm_index()=default
Defaulted.
alphabet_t alphabet_type
The type of the underlying character of the indexed text.
Definition: fm_index.hpp:389
fm_index(fm_index &&rhs)
When move constructing, also update internal data structures.
Definition: fm_index.hpp:419
typename sdsl_index_type::size_type size_type
Type for representing positions in the indexed text.
Definition: fm_index.hpp:391
fm_index(text_t &&text)
Constructor that immediately constructs the index given a range. The range cannot be empty.
Definition: fm_index.hpp:452
fm_index(fm_index const &rhs)
When copy constructing, also update internal data structures.
Definition: fm_index.hpp:411
Provides various transformation traits used by the range module.
Provides the internal representation of a node of the seqan3::fm_index_cursor.
Provides the seqan3::fm_index_cursor for searching in the unidirectional seqan3::fm_index.
constexpr auto to_rank
Return the rank representation of a (semi-)alphabet object.
Definition: concept.hpp:154
text_layout
The possible text layouts (single, collection) the seqan3::fm_index and seqan3::bi_fm_index can suppo...
Definition: concept.hpp:72
sdsl_wt_index_type default_sdsl_index_type
The default FM Index Configuration.
Definition: fm_index.hpp:147
sdsl::csa_wt< sdsl::wt_blcd< sdsl::bit_vector, sdsl::rank_support_v<>, sdsl::select_support_scan<>, sdsl::select_support_scan< 0 > >, 16, 10 '000 '000, sdsl::sa_order_sa_sampling<>, sdsl::isa_sampling<>, sdsl::plain_byte_alphabet > sdsl_wt_index_type
The FM Index Configuration using a Wavelet Tree.
Definition: fm_index.hpp:140
@ single
The text is a single range.
Definition: concept.hpp:74
@ collection
The text is a range of ranges.
Definition: concept.hpp:76
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
The basis for seqan3::alphabet, but requires only rank interface (not char).
The generic concept for a (biological) sequence.
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
fm_index(text_t &&) -> fm_index< range_innermost_value_t< text_t >, text_layout
Deduces the alphabet and dimensions of the text.
Definition: fm_index.hpp:587
SeqAn specific customisations in the standard namespace.
The <ranges> header from C++20's standard library.
Provides the concept for seqan3::detail::sdsl_index.
Provides seqan3::views::to_rank.