dna4.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 <vector>
 
#include <bio/alphabet/nucleotide/nucleotide_base.hpp>
 
// ------------------------------------------------------------------
// dna4
// ------------------------------------------------------------------
 
namespace bio::alphabet
{
 
class rna4;
 
class dna4 : public nucleotide_base<dna4, 4>
{
private:
    using base_t = nucleotide_base<dna4, 4>;
 
    friend base_t;
    friend base_t::base_t;
    friend rna4;
 
public:
    constexpr dna4() noexcept                         = default; 
    constexpr dna4(dna4 const &) noexcept             = default; 
    constexpr dna4(dna4 &&) noexcept                  = default; 
    constexpr dna4 & operator=(dna4 const &) noexcept = default; 
    constexpr dna4 & operator=(dna4 &&) noexcept      = default; 
    ~dna4() noexcept                                  = default; 
 
    using base_t::base_t;
 
    template <std::same_as<rna4> t> // Accept incomplete type
    constexpr dna4(t const & r) noexcept
    {
        assign_rank(r.to_rank());
    }
 
    constexpr dna4 complement() const noexcept { return dna4{}.assign_rank(to_rank() ^ 0b11); }
 
protected:
 
    static constexpr std::array<char_type, alphabet_size> rank_to_char{'A', 'C', 'G', 'T'};
 
    static constexpr std::array<rank_type, 256> char_to_rank = []() constexpr
    {
        std::array<rank_type, 256> ret{};
 
        // reverse mapping for characters and their lowercase
        for (size_t rnk = 0u; rnk < alphabet_size; ++rnk)
        {
            ret[rank_to_char[rnk]]                   = rnk;
            ret[detail::to_lower(rank_to_char[rnk])] = rnk;
        }
 
        // set U equal to T
        ret['U'] = ret['T'];
        ret['u'] = ret['t'];
 
        // iupac characters get special treatment, because there is no N
        ret['R'] = ret['A'];
        ret['r'] = ret['A']; // or G
        ret['Y'] = ret['C'];
        ret['y'] = ret['C']; // or T
        ret['S'] = ret['C'];
        ret['s'] = ret['C']; // or G
        ret['W'] = ret['A'];
        ret['w'] = ret['A']; // or T
        ret['K'] = ret['G'];
        ret['k'] = ret['G']; // or T
        ret['M'] = ret['A'];
        ret['m'] = ret['A']; // or T
        ret['B'] = ret['C'];
        ret['b'] = ret['C']; // or G or T
        ret['D'] = ret['A'];
        ret['d'] = ret['A']; // or G or T
        ret['H'] = ret['A'];
        ret['h'] = ret['A']; // or C or T
        ret['V'] = ret['A'];
        ret['v'] = ret['A']; // or C or G
 
        return ret;
    }();
};
 
} // namespace bio::alphabet
 
// ------------------------------------------------------------------
// literals
// ------------------------------------------------------------------
 
namespace bio::alphabet
{
 
inline namespace literals
{
 
consteval dna4 operator""_dna4(char const c)
{
    if (!char_is_valid_for<dna4>(c))
        throw std::invalid_argument{"Illegal character in character literal."};
 
    return dna4{}.assign_char(c);
}
 
template <meta::detail::literal_buffer_string str>
constexpr std::vector<dna4> operator""_dna4()
{
    return detail::string_literal<str, dna4>();
}
 
} // namespace literals
 
} // namespace bio::alphabet