70 using sdsl_index_type = sdsl_index_type_;
73 using rev_sdsl_index_type = sdsl::csa_wt<sdsl_wt_index_type::wavelet_tree_type,
76 sdsl::sa_order_sa_sampling<>,
78 sdsl_wt_index_type::alphabet_type>;
83 using sdsl_char_type =
typename sdsl_index_type::alphabet_type::char_type;
86 using sdsl_sigma_type =
typename sdsl_index_type::alphabet_type::sigma_type;
92 using rev_fm_index_type = detail::reverse_fm_index<alphabet_t, text_layout_mode_, rev_sdsl_index_type>;
99 rev_fm_index_type rev_fm;
120 template <std::ranges::range text_t>
121 void construct(text_t && text)
123 detail::fm_index_validator::validate<alphabet_t, text_layout_mode_>(text);
126 rev_fm = rev_fm_index_type{text};
152 template <
typename bi_fm_index_t>
173 template <std::ranges::range text_t>
176 construct(std::forward<text_t>(text));
193 return fwd_fm.
size();
241 return !(*
this == rhs);
287 template <cereal_archive archive_t>
288 void CEREAL_SERIALIZE_FUNCTION_NAME(archive_t & archive)
300 template <std::ranges::range text_t>
Provides the seqan3::bi_fm_index_cursor for searching in the bidirectional seqan3::bi_fm_index.
The SeqAn Bidirectional FM Index Cursor.
Definition: bi_fm_index_cursor.hpp:58
The SeqAn Bidirectional FM Index.
Definition: bi_fm_index.hpp:64
bi_fm_index(text_t &&text)
Constructor that immediately constructs the index given a range. The range cannot be empty.
Definition: bi_fm_index.hpp:174
bi_fm_index & operator=(bi_fm_index const &)=default
Defaulted.
bi_fm_index(bi_fm_index &&)=default
Defaulted.
bi_fm_index()=default
Defaulted.
fwd_cursor_type fwd_cursor() const noexcept
Returns a unidirectional seqan3::fm_index_cursor on the original text of the bidirectional index that...
Definition: bi_fm_index.hpp:275
bool operator==(bi_fm_index const &rhs) const noexcept
Compares two indices.
Definition: bi_fm_index.hpp:223
bool operator!=(bi_fm_index const &rhs) const noexcept
Compares two indices.
Definition: bi_fm_index.hpp:239
static constexpr text_layout text_layout_mode
Indicates whether index is built over a collection.
Definition: bi_fm_index.hpp:131
cursor_type cursor() const noexcept
Returns a seqan3::bi_fm_index_cursor on the index that can be used for searching.
Definition: bi_fm_index.hpp:258
typename sdsl_index_type::size_type size_type
Type for representing positions in the indexed text.
Definition: bi_fm_index.hpp:139
bi_fm_index & operator=(bi_fm_index &&)=default
Defaulted.
bool empty() const noexcept
Checks whether the index is empty.
Definition: bi_fm_index.hpp:207
bi_fm_index(bi_fm_index const &)=default
Defaulted.
typename fm_index_type::alphabet_type alphabet_type
The type of the underlying character of the indexed text.
Definition: bi_fm_index.hpp:137
size_type size() const noexcept
Returns the length of the indexed text including sentinel characters.
Definition: bi_fm_index.hpp:191
~bi_fm_index()=default
Defaulted.
The SeqAn FM Index Cursor.
Definition: fm_index_cursor.hpp:90
size_type size() const noexcept
Returns the length of the indexed text including sentinel characters.
Definition: fm_index.hpp:460
alphabet_t alphabet_type
The type of the underlying character of the indexed text.
Definition: fm_index.hpp:380
Provides various transformation traits used by the range module.
This header includes C++17 filesystem support and imports it into namespace std::filesystem (independ...
Provides the unidirectional seqan3::fm_index.
text_layout
The possible text layouts (single, collection) the seqan3::fm_index and seqan3::bi_fm_index can suppo...
Definition: concept.hpp:81
sdsl_wt_index_type default_sdsl_index_type
The default FM Index Configuration.
Definition: fm_index.hpp:150
bi_fm_index(text_t &&) -> bi_fm_index< range_innermost_value_t< text_t >, text_layout
Deduces the dimensions of the text.
Definition: bi_fm_index.hpp:301
The basis for seqan3::alphabet, but requires only rank interface (not char).
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
Adaptations of concepts from the Ranges TS.