aa10murphy.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/aminoacid/aminoacid_base.hpp>
#include <bio/alphabet/aminoacid/concept.hpp>
#include <bio/alphabet/detail/to_lower.hpp>
 
namespace bio::alphabet
{
 
class aa10murphy : public aminoacid_base<aa10murphy, 10>
{
private:
    using base_t = aminoacid_base<aa10murphy, 10>;
 
    friend base_t;
    friend base_t::base_t;
 
public:
    constexpr aa10murphy() noexcept                               = default; 
    constexpr aa10murphy(aa10murphy const &) noexcept             = default; 
    constexpr aa10murphy(aa10murphy &&) noexcept                  = default; 
    constexpr aa10murphy & operator=(aa10murphy const &) noexcept = default; 
    constexpr aa10murphy & operator=(aa10murphy &&) noexcept      = default; 
    ~aa10murphy() noexcept                                        = default; 
 
    using base_t::base_t;
 
protected:
    static constexpr std::array<char_type, alphabet_size> rank_to_char{
      'A',
      'B',
      'C',
      'F',
      'G',
      'H',
      'I',
      'K',
      'P',
      'S',
    };
 
    static constexpr std::array<rank_type, 256> char_to_rank = []() constexpr
    {
        std::array<rank_type, 256> ret{};
 
        // initialize with UNKNOWN
        ret.fill(9); // value of 'S', because that appears most frequently
 
        // reverse mapping for characters and their lowercase
        for (rank_type rnk = 0u; rnk < alphabet_size; ++rnk)
        {
            ret[static_cast<rank_type>(rank_to_char[rnk])]                   = rnk;
            ret[static_cast<rank_type>(detail::to_lower(rank_to_char[rnk]))] = rnk;
        }
 
        ret['D'] = ret['B'];
        ret['d'] = ret['B']; // Convert D to B (either D/N).
        ret['E'] = ret['B'];
        ret['e'] = ret['B']; // Convert E to B (either D/N).
        ret['J'] = ret['I'];
        ret['j'] = ret['I']; // Convert J (either I/L) to I.
        ret['L'] = ret['I'];
        ret['l'] = ret['I']; // Convert L to I.
        ret['M'] = ret['I'];
        ret['m'] = ret['I']; // Convert M to I.
        ret['N'] = ret['B'];
        ret['n'] = ret['B']; // Convert N to B (either D/N).
        ret['O'] = ret['K'];
        ret['o'] = ret['K']; // Convert Pyrrolysine to K.
        ret['Q'] = ret['B'];
        ret['q'] = ret['B']; // Convert Q to B (either D/N).
        ret['R'] = ret['K'];
        ret['r'] = ret['K']; // Convert R to K.
        ret['T'] = ret['S'];
        ret['t'] = ret['S']; // Convert T to S.
        ret['U'] = ret['C'];
        ret['u'] = ret['C']; // Convert Selenocysteine to C.
        ret['V'] = ret['I'];
        ret['v'] = ret['I']; // Convert V to I.
        ret['W'] = ret['F'];
        ret['w'] = ret['F']; // Convert W to F.
        ret['X'] = ret['S'];
        ret['x'] = ret['S']; // Convert unknown amino acids to Serine.
        ret['Y'] = ret['F'];
        ret['y'] = ret['F']; // Convert Y to F.
        ret['Z'] = ret['B'];
        ret['z'] = ret['B']; // Convert Z (either E/Q) to B (either D/N).
        ret['*'] = ret
          ['F']; // The most common stop codon is UGA. This is most similar to a Tryptophan which in this alphabet gets converted to Phenylalanine.
        return ret;
    }();
};
 
} // namespace bio::alphabet
 
// ------------------------------------------------------------------
// literals
// ------------------------------------------------------------------
 
namespace bio::alphabet
{
 
inline namespace literals
{
 
consteval aa10murphy operator""_aa10murphy(char const c)
{
    if (!char_is_valid_for<aa10murphy>(c))
        throw std::invalid_argument{"Illegal character in character literal."};
 
    return aa10murphy{}.assign_char(c);
}
 
template <meta::detail::literal_buffer_string str>
constexpr std::vector<aa10murphy> operator""_aa10murphy()
{
    return detail::string_literal<str, aa10murphy>();
}
 
} // namespace literals
 
} // namespace bio::alphabet