nucleotide_base.hpp

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// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2022 deCODE Genetics
// 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/biocpp/biocpp-core/blob/main/LICENSE.md
// -----------------------------------------------------------------------------------------------------
 
#pragma once
 
#include <bio/alphabet/base.hpp>
#include <bio/alphabet/detail/convert.hpp>
#include <bio/alphabet/detail/to_lower.hpp>
#include <bio/alphabet/nucleotide/concept.hpp>
 
namespace bio::alphabet
{
 
template <typename derived_type, auto size>
class nucleotide_base : public base<derived_type, size, char>
{
private:
    using base_t = 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 <meta::different_from<derived_type> other_nucl_type>
        requires nucleotide<other_nucl_type>
    explicit constexpr nucleotide_base(other_nucl_type const & other) noexcept
    {
        static_cast<derived_type &>(*this) =
          detail::convert_through_char_representation<derived_type, other_nucl_type>[bio::alphabet::to_rank(other)];
    }
 
    constexpr derived_type complement() const noexcept
        requires(requires(derived_type d) { d.complement_table; })
    {
        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
    {
        static_assert(sizeof(char_type) == 1, "This table is unusable for char types larger than 1 byte.");
 
        // init with false
        std::array<bool, 256> ret{};
 
        // the original valid chars and their lower cases
        for (char_type c : derived_type::rank_to_char)
        {
            ret[c]                   = true;
            ret[detail::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;
    }();
 
    friend constexpr derived_type tag_invoke(custom::complement, derived_type const a) noexcept
    {
        return a.complement();
    }
};
 
} // namespace bio::alphabet