nucleotide_base.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/alphabet/alphabet_base.hpp>
#include <seqan3/alphabet/detail/convert.hpp>
#include <seqan3/alphabet/nucleotide/concept.hpp>
#include <seqan3/core/char_operations/transform.hpp>

namespace seqan3
{

template <typename derived_type, auto size>
class nucleotide_base : public alphabet_base<derived_type, size, char>
{
private:
    using base_t = alphabet_base<derived_type, size, char>;

    constexpr nucleotide_base()                                    noexcept = default; 
    constexpr nucleotide_base(nucleotide_base const &)             noexcept = default; 
    constexpr nucleotide_base(nucleotide_base &&)                  noexcept = default; 
    constexpr nucleotide_base & operator=(nucleotide_base const &) noexcept = default; 
    constexpr nucleotide_base & operator=(nucleotide_base &&)      noexcept = default; 
    ~nucleotide_base()                                             noexcept = default; 

    friend derived_type;

protected:
    // Import from base:
    using typename base_t::char_type;
    using typename base_t::rank_type;

public:
    using base_t::alphabet_size;
    using base_t::to_rank;

    // This constructor needs to be public, because constructor templates are not inherited otherwise
    template <typename other_nucl_type>
        requires !std::Same<nucleotide_base, other_nucl_type> &&
                 !std::Same<derived_type, other_nucl_type> &&
                 NucleotideAlphabet<other_nucl_type>
    explicit constexpr nucleotide_base(other_nucl_type const & other) noexcept
    {
        using seqan3::to_rank;
        static_cast<derived_type &>(*this) =
            detail::convert_through_char_representation<derived_type, other_nucl_type>[to_rank(other)];
    }

    constexpr derived_type complement() const noexcept
    {
        return derived_type::complement_table[to_rank()];
    }

    static constexpr bool char_is_valid(char_type const c) noexcept
    {
        return valid_char_table[static_cast<uint8_t>(c)];
    }

private:
    static constexpr std::array<bool, 256> valid_char_table
    {
        [] () constexpr
        {
            // init with false
            std::array<bool, 256> ret{};

            // the original valid chars and their lower cases
            for (uint8_t c : derived_type::rank_to_char)
            {
                ret[         c ] = true;
                ret[to_lower(c)] = true;
            }

            // U and T shall be accepted for all
            ret['U'] = true;
            ret['T'] = true;
            ret['u'] = true;
            ret['t'] = true;

            return ret;
        }()
    };
};

} // namespace seqan3