76 sdsl::sa_order_sa_sampling<>,
78 sdsl_wt_index_type::alphabet_type>;
120 template <std::ranges::range text_t>
123 detail::fm_index_validator::validate<alphabet_t, text_layout_mode_>(text);
152 template <
typename bi_fm_index_t>
173 template <std::ranges::range text_t>
241 return !(*
this == rhs);
287 template <cereal_archive archive_t>
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.
fm_index_type fwd_fm
Underlying FM index for the original text.
Definition: bi_fm_index.hpp:96
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. Cursor is pointing ...
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
typename sdsl_index_type::alphabet_type::char_type sdsl_char_type
The type of the reduced alphabet type. (The reduced alphabet might be smaller than the original alpha...
Definition: bi_fm_index.hpp:83
sdsl_index_type_ sdsl_index_type
The type of the underlying SDSL index for the original text.
Definition: bi_fm_index.hpp:70
rev_fm_index_type rev_fm
Underlying FM index for the reversed text.
Definition: bi_fm_index.hpp:99
typename sdsl_index_type::alphabet_type::sigma_type sdsl_sigma_type
The type of the alphabet size of the underlying SDSL index.
Definition: bi_fm_index.hpp:86
void construct(text_t &&text)
Constructs the index given a range. The range cannot be an rvalue (i.e. a temporary object) and has t...
Definition: bi_fm_index.hpp:121
sdsl::csa_wt< sdsl_wt_index_type::wavelet_tree_type, 10 '000 '000, 10 '000 '000, sdsl::sa_order_sa_sampling<>, sdsl::isa_sampling<>, sdsl_wt_index_type::alphabet_type > rev_sdsl_index_type
The type of the underlying SDSL index for the reversed text.
Definition: bi_fm_index.hpp:78
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:461
alphabet_t alphabet_type
The type of the underlying character of the indexed text.
Definition: fm_index.hpp:381
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:82
sdsl_wt_index_type default_sdsl_index_type
The default FM Index Configuration.
Definition: fm_index.hpp:151
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.