nucleotide_scoring_scheme.hpp

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// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: BSD-3-Clause

 
#pragma once
 
#include <seqan3/alignment/scoring/scoring_scheme_base.hpp>
#include <seqan3/alphabet/nucleotide/dna15.hpp>
 
namespace seqan3
{

template <arithmetic score_type = int8_t>
class nucleotide_scoring_scheme : public scoring_scheme_base<nucleotide_scoring_scheme<score_type>, dna15, score_type>
{
private:
    using base_t = scoring_scheme_base<nucleotide_scoring_scheme, dna15, score_type>;

    friend base_t;
 
public:
    using typename base_t::matrix_type;

    constexpr nucleotide_scoring_scheme() noexcept = default;
    template <arithmetic score_arg_t>
    constexpr nucleotide_scoring_scheme(match_score<score_arg_t> const ms, mismatch_score<score_arg_t> const mms) :
        base_t{ms, mms}
    {}

    constexpr nucleotide_scoring_scheme(matrix_type const & matrix) noexcept : base_t{matrix}
    {}

};


nucleotide_scoring_scheme() -> nucleotide_scoring_scheme<int8_t>;

template <arithmetic score_arg_type>
nucleotide_scoring_scheme(match_score<score_arg_type>,
                          mismatch_score<score_arg_type>) -> nucleotide_scoring_scheme<int8_t>;

template <arithmetic score_arg_type>
nucleotide_scoring_scheme(std::array<std::array<score_arg_type, 15>, 15>) -> nucleotide_scoring_scheme<score_arg_type>;
 
} // namespace seqan3