edit_distance_algorithm.hpp

Go to the documentation of this file.

// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2020, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2020, Knut Reinert & MPI für molekulare Genetik
// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
// shipped with this file and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md
// -----------------------------------------------------------------------------------------------------
 
#pragma once
 
#include <tuple>
 
#include <seqan3/alignment/configuration/align_config_edit.hpp>
#include <seqan3/alignment/pairwise/detail/concept.hpp>
#include <seqan3/alignment/pairwise/edit_distance_unbanded.hpp>
 
namespace seqan3::detail
{
 
template <typename config_t, typename traits_t>
class edit_distance_algorithm
{
private:
    using configuration_traits_type = alignment_configuration_traits<config_t>;
    using alignment_result_type = typename configuration_traits_type::alignment_result_type;
 
    static_assert(!std::same_as<alignment_result_type, empty_type>, "Alignment result type was not configured.");
 
public:
    constexpr edit_distance_algorithm() = default;                                            
    constexpr edit_distance_algorithm(edit_distance_algorithm const &) = default;             
    constexpr edit_distance_algorithm(edit_distance_algorithm &&) = default;                  
    constexpr edit_distance_algorithm & operator=(edit_distance_algorithm const &) = default; 
    constexpr edit_distance_algorithm & operator=(edit_distance_algorithm &&) = default;      
    ~edit_distance_algorithm() = default;                                                     
 
    constexpr edit_distance_algorithm(config_t const & cfg) : cfg_ptr{new config_t(cfg)}
    {}
 
    template <indexed_sequence_pair_range indexed_sequence_pairs_t, typename callback_t>
        requires std::invocable<callback_t, alignment_result_type>
    constexpr void operator()(indexed_sequence_pairs_t && indexed_sequence_pairs, callback_t && callback)
    {
        using std::get;
 
        for (auto && [sequence_pair, index] : indexed_sequence_pairs)
            compute_single_pair(index,
                                get<0>(sequence_pair),
                                get<1>(sequence_pair),
                                std::forward<callback_t>(callback));
    }
private:
 
    template <std::ranges::forward_range first_range_t, std::ranges::forward_range second_range_t, typename callback_t>
    constexpr void compute_single_pair(size_t const idx,
                                       first_range_t && first_range,
                                       second_range_t && second_range,
                                       callback_t && callback)
    {
        using edit_traits = default_edit_distance_trait_type<first_range_t,
                                                             second_range_t,
                                                             config_t,
                                                             typename traits_t::is_semi_global_type>;
        edit_distance_unbanded algo{first_range, second_range, *cfg_ptr, edit_traits{}};
        algo(idx, callback);
    }
 
    std::shared_ptr<std::remove_cvref_t<config_t>> cfg_ptr{};
};
 
} // namespace seqan3::detail