nucleotide_scoring_scheme.hpp

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// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2019, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2019, 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 <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>;
public:
    //NOTE(h-2): unfortunately these are not inherited in the documentation
    SEQAN3_DOXYGEN_ONLY(( constexpr nucleotide_scoring_scheme() noexcept {} ))
    SEQAN3_DOXYGEN_ONLY((
      template <Arithmetic score_arg_t>
      constexpr nucleotide_scoring_scheme(match_score<score_arg_t> const ms, mismatch_score<score_arg_t> const mms) {}
    ))
    SEQAN3_DOXYGEN_ONLY(( constexpr nucleotide_scoring_scheme(matrix_type const & _matrix) noexcept {} ))

    using base_t::base_t;
};

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