19 #include <sdsl/suffix_trees.hpp>
29 namespace seqan3::detail
34 struct fm_index_validator
50 template <semialphabet alphabet_t, text_layout text_layout_mode_, std::ranges::range text_t>
51 static void validate(text_t && text)
55 static_assert(std::ranges::bidirectional_range<text_t>,
"The text must model bidirectional_range.");
56 static_assert(std::convertible_to<range_innermost_value_t<text_t>, alphabet_t>,
57 "The alphabet of the text collection must be convertible to the alphabet of the index.");
58 static_assert(range_dimension_v<text_t> == 1,
"The input cannot be a text collection.");
60 if (std::ranges::empty(text))
65 static_assert(std::ranges::bidirectional_range<text_t>,
66 "The text collection must model bidirectional_range.");
67 static_assert(std::ranges::bidirectional_range<std::ranges::range_reference_t<text_t>>,
68 "The elements of the text collection must model bidirectional_range.");
69 static_assert(std::convertible_to<range_innermost_value_t<text_t>, alphabet_t>,
70 "The alphabet of the text collection must be convertible to the alphabet of the index.");
71 static_assert(range_dimension_v<text_t> == 2,
"The input must be a text collection.");
73 if (std::ranges::empty(text))
76 static_assert(
alphabet_size<range_innermost_value_t<text_t>> <= 256,
"The alphabet is too big.");
86 template <
typename index_t>
87 class fm_index_cursor;
89 template <
typename index_t>
90 class bi_fm_index_cursor;
96 detail::sdsl_index sdsl_index_type_>
97 class reverse_fm_index;
137 sdsl::csa_wt<sdsl::wt_blcd<sdsl::bit_vector,
138 sdsl::rank_support_v<>,
139 sdsl::select_support_scan<>,
140 sdsl::select_support_scan<0>>,
143 sdsl::sa_order_sa_sampling<>,
144 sdsl::isa_sampling<>,
145 sdsl::plain_byte_alphabet>;
200 using sdsl_index_type = sdsl_index_type_;
204 using sdsl_char_type =
typename sdsl_index_type::alphabet_type::char_type;
206 using sdsl_sigma_type =
typename sdsl_index_type::alphabet_type::sigma_type;
209 friend class detail::reverse_fm_index<alphabet_t, text_layout_mode_, sdsl_index_type_>;
212 sdsl_index_type index;
215 sdsl::sd_vector<> text_begin;
217 sdsl::select_support_sd<1> text_begin_ss;
219 sdsl::rank_support_sd<1> text_begin_rs;
240 template <std::ranges::range text_t>
244 void construct(text_t && text)
246 detail::fm_index_validator::validate<alphabet_t, text_layout_mode_>(text);
248 constexpr
auto sigma = alphabet_size<alphabet_t>;
255 sdsl::int_vector<8> tmp_text(std::ranges::distance(text));
261 if constexpr (sigma == 256)
265 "character alphabets the last one/two values are reserved"
266 "(single sequence/collection).");
270 | std::views::reverse,
271 std::ranges::begin(tmp_text));
273 sdsl::construct_im(index, tmp_text, 0);
282 template <std::ranges::range text_t>
286 void construct(text_t && text,
bool reverse =
false)
288 detail::fm_index_validator::validate<alphabet_t, text_layout_mode_>(text);
292 for (
auto && t : text)
293 text_sizes.
push_back(std::ranges::distance(t));
295 size_t const number_of_texts{text_sizes.
size()};
300 if (number_of_texts == text_size)
303 constexpr
auto sigma = alphabet_size<alphabet_t>;
308 sdsl::sd_vector_builder builder(text_size, number_of_texts);
309 size_t prefix_sum{0};
311 for (
auto &&
size : text_sizes)
313 builder.set(prefix_sum);
314 prefix_sum +=
size + 1;
317 text_begin = sdsl::sd_vector<>(builder);
318 text_begin_ss = sdsl::select_support_sd<1>(&text_begin);
319 text_begin_rs = sdsl::rank_support_sd<1>(&text_begin);
322 sdsl::int_vector<8> tmp_text(text_size - (number_of_texts > 1));
324 constexpr uint8_t delimiter = sigma >= 255 ? 255 : sigma + 1;
332 if constexpr (sigma >= 255)
336 " for full character alphabets the last one/"
337 "two values are reserved (single sequence/"
343 | views::join(delimiter),
344 std::ranges::begin(tmp_text));
349 if (number_of_texts == 1)
350 tmp_text.back() = delimiter;
352 std::ranges::reverse(tmp_text);
359 if (number_of_texts == 1)
361 std::ranges::reverse(tmp_text.begin(), tmp_text.end() - 1);
362 tmp_text.back() = delimiter;
366 std::ranges::reverse(tmp_text);
370 sdsl::construct_im(index, tmp_text, 0);
388 template <
typename bi_fm_index_t>
391 template <
typename fm_index_t>
394 template <
typename fm_index_t>
395 friend class detail::fm_index_cursor_node;
404 index{rhs.index}, text_begin{rhs.text_begin}, text_begin_ss{rhs.text_begin_ss}, text_begin_rs{rhs.text_begin_rs}
406 text_begin_ss.set_vector(&text_begin);
407 text_begin_rs.set_vector(&text_begin);
412 index{
std::
move(rhs.index)}, text_begin{
std::
move(rhs.text_begin)},text_begin_ss{
std::
move(rhs.text_begin_ss)},
413 text_begin_rs{
std::
move(rhs.text_begin_rs)}
415 text_begin_ss.set_vector(&text_begin);
416 text_begin_rs.set_vector(&text_begin);
424 text_begin_ss =
std::move(rhs.text_begin_ss);
425 text_begin_rs =
std::move(rhs.text_begin_rs);
427 text_begin_ss.set_vector(&text_begin);
428 text_begin_rs.set_vector(&text_begin);
443 template <std::ranges::b
idirectional_range text_t>
446 construct(std::forward<text_t>(text));
496 return (index == rhs.index) && (text_begin == rhs.text_begin);
512 return !(*
this == rhs);
541 template <cereal_archive archive_t>
542 void CEREAL_SERIALIZE_FUNCTION_NAME(archive_t & archive)
546 archive(text_begin_ss);
547 text_begin_ss.set_vector(&text_begin);
548 archive(text_begin_rs);
549 text_begin_rs.set_vector(&text_begin);
551 auto sigma = alphabet_size<alphabet_t>;
553 if (sigma != alphabet_size<alphabet_t>)
556 " but it is being read into an fm_index with an alphabet of size " +
565 (tmp ?
"text collection" :
"single text") +
566 " but it is being read into an fm_index expecting a " +
578 template <std::ranges::range text_t>
585 namespace seqan3::detail
603 class reverse_fm_index :
public fm_index<alphabet_t, text_layout_mode, sdsl_index_type>
607 template <std::ranges::range text_t>
608 void construct_(text_t && text)
612 auto reverse_text = text | std::views::reverse;
613 this->construct(reverse_text);
617 auto reverse_text = text | views::deep{std::views::reverse} | std::views::reverse;
618 this->construct(reverse_text,
true);
626 template <std::ranges::b
idirectional_range text_t>
627 explicit reverse_fm_index(text_t && text)
629 construct_(std::forward<text_t>(text));
Adaptations of algorithms from the Ranges TS.
Provides seqan3::views::to_rank.
The SeqAn Bidirectional FM Index Cursor.
Definition: bi_fm_index_cursor.hpp:58
The SeqAn FM Index Cursor.
Definition: fm_index_cursor.hpp:90
The SeqAn FM Index.
Definition: fm_index.hpp:194
fm_index()=default
Defaulted.
static constexpr text_layout text_layout_mode
Indicates whether index is built over a collection.
Definition: fm_index.hpp:375
cursor_type cursor() const noexcept
Returns a seqan3::fm_index_cursor on the index that can be used for searching.
Definition: fm_index.hpp:529
size_type size() const noexcept
Returns the length of the indexed text including sentinel characters.
Definition: fm_index.hpp:461
bool operator!=(fm_index const &rhs) const noexcept
Compares two indices.
Definition: fm_index.hpp:510
bool empty() const noexcept
Checks whether the index is empty.
Definition: fm_index.hpp:477
bool operator==(fm_index const &rhs) const noexcept
Compares two indices.
Definition: fm_index.hpp:493
fm_index & operator=(fm_index rhs)
When copy/move assigning, also update internal data structures.
Definition: fm_index.hpp:420
~fm_index()=default
Defaulted.
alphabet_t alphabet_type
The type of the underlying character of the indexed text.
Definition: fm_index.hpp:381
fm_index(fm_index &&rhs)
When move constructing, also update internal data structures.
Definition: fm_index.hpp:411
typename sdsl_index_type::size_type size_type
Type for representing positions in the indexed text.
Definition: fm_index.hpp:383
fm_index(text_t &&text)
Constructor that immediately constructs the index given a range. The range cannot be empty.
Definition: fm_index.hpp:444
fm_index(fm_index const &rhs)
When copy constructing, also update internal data structures.
Definition: fm_index.hpp:403
Provides various transformation traits used by the range module.
Provides the internal representation of a node of the seqan3::fm_index_cursor.
This header includes C++17 filesystem support and imports it into namespace std::filesystem (independ...
Provides the seqan3::fm_index_cursor for searching in the unidirectional seqan3::fm_index.
constexpr auto alphabet_size
A type trait that holds the size of a (semi-)alphabet.
Definition: concept.hpp:858
text_layout
The possible text layouts (single, collection) the seqan3::fm_index and seqan3::bi_fm_index can suppo...
Definition: concept.hpp:82
sdsl_wt_index_type default_sdsl_index_type
The default FM Index Configuration.
Definition: fm_index.hpp:151
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:145
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:579
@ single
The text is a single range.
Definition: concept.hpp:84
@ collection
The text is a range of ranges.
Definition: concept.hpp:86
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:434
auto const to_rank
A view that calls seqan3::to_rank() on each element in the input range.
Definition: to_rank.hpp:71
auto const move
A view that turns lvalue-references into rvalue-references.
Definition: move.hpp:70
The basis for seqan3::alphabet, but requires only rank interface (not char).
Provides seqan3::views::join.
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
SeqAn specific customisations in the standard namespace.
Adaptations of concepts from the Ranges TS.
Provides the concept for seqan3::detail::sdsl_index.
Provides seqan3::views::to.