fm_index.hpp File Reference

Provides the unidirectional seqan3::fm_index. More...

#include <algorithm>
#include <filesystem>
#include <ranges>
#include <seqan3/alphabet/views/to_rank.hpp>
#include <seqan3/contrib/sdsl-lite.hpp>
#include <seqan3/core/range/type_traits.hpp>
#include <seqan3/search/fm_index/concept.hpp>
#include <seqan3/search/fm_index/detail/fm_index_cursor.hpp>
#include <seqan3/search/fm_index/fm_index_cursor.hpp>

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Classes
class	seqan3::fm_index< alphabet_t, text_layout_mode_, sdsl_index_type_ >
	The SeqAn FM Index. More...
struct	seqan3::detail::fm_index_validator
	Class used to validate the requirements on the input text of the fm_index. More...
class	seqan3::detail::reverse_fm_index< alphabet_t, text_layout_mode, sdsl_index_type >
	An FM Index specialisation that handles reversing the given text. More...

Namespaces
namespace	seqan3
	The main SeqAn3 namespace.
namespace	seqan3::detail
	The internal SeqAn3 namespace.

Typedefs
using	seqan3::default_sdsl_index_type = sdsl_wt_index_type
	The default FM Index Configuration.
using	seqan3::sdsl_wt_index_type = seqan3::contrib::sdsl::csa_wt< seqan3::contrib::sdsl::wt_blcd< seqan3::contrib::sdsl::bit_vector, seqan3::contrib::sdsl::rank_support_v<>, seqan3::contrib::sdsl::select_support_scan<>, seqan3::contrib::sdsl::select_support_scan< 0 > >, 16, 10 '000 '000, seqan3::contrib::sdsl::sa_order_sa_sampling<>, seqan3::contrib::sdsl::isa_sampling<>, seqan3::contrib::sdsl::plain_byte_alphabet >
	The FM Index Configuration using a Wavelet Tree.

Functions
Template argument type deduction guides
template<std::ranges::range text_t>
	seqan3::fm_index (text_t &&) -> fm_index< range_innermost_value_t< text_t >, text_layout
	Deduces the alphabet and dimensions of the text.

Detailed Description

Provides the unidirectional seqan3::fm_index.

Author

Christopher Pockrandt <christopher.pockrandt AT fu-berlin.de>