edit_distance_algorithm.hpp

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// -----------------------------------------------------------------------------------------------------
// 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/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
{
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>
    constexpr auto operator()(indexed_sequence_pairs_t && indexed_sequence_pairs)
    {
        using indexed_sequence_pair_t = std::ranges::range_value_t<indexed_sequence_pairs_t>; // The value type.
        using sequence_pair_t = std::tuple_element_t<0, indexed_sequence_pair_t>; // The sequence pair type.
        using sequence1_t = std::remove_reference_t<std::tuple_element_t<0, sequence_pair_t>>;
        using sequence2_t = std::remove_reference_t<std::tuple_element_t<1, sequence_pair_t>>;
        using alignment_result_value_t = typename align_result_selector<sequence1_t, sequence2_t, config_t>::type;
 
        using std::get;
 
        std::vector<alignment_result<alignment_result_value_t>> result_vector{};  // Stores the results.
        for (auto && [sequence_pair, index] : indexed_sequence_pairs)
            result_vector.push_back(compute_single_pair(index, get<0>(sequence_pair), get<1>(sequence_pair)));
 
        return result_vector;
    }
private:
 
    template <std::ranges::forward_range first_range_t, std::ranges::forward_range second_range_t>
    constexpr auto compute_single_pair(size_t const idx, first_range_t && first_range, second_range_t && second_range)
    {
        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{}};
        return algo(idx);
    }
 
    std::shared_ptr<remove_cvref_t<config_t>> cfg_ptr{};
};
 
} // namespace seqan3::detail