aa27.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 aa27 : public aminoacid_base<aa27, 27>
{
private:
    using base_t = aminoacid_base<aa27, 27>;
 
    friend base_t;
    friend base_t::base_t;
 
public:
    constexpr aa27() noexcept                         = default; 
    constexpr aa27(aa27 const &) noexcept             = default; 
    constexpr aa27(aa27 &&) noexcept                  = default; 
    constexpr aa27 & operator=(aa27 const &) noexcept = default; 
    constexpr aa27 & operator=(aa27 &&) noexcept      = default; 
    ~aa27() noexcept                                  = default; 
 
    using base_t::base_t;
 
protected:
    static constexpr std::array<char_type, alphabet_size> rank_to_char{'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I',
                                                                       'J', 'K', 'L', 'M', 'N', 'O', 'P', 'Q', 'R',
                                                                       'S', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z', '*'};
 
    static constexpr std::array<rank_type, 256> char_to_rank = []() constexpr
    {
        std::array<rank_type, 256> ret{};
 
        // initialize with UNKNOWN
        ret.fill(23); // value of 'X'
 
        // 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;
        }
 
        return ret;
    }();
};
 
} // namespace bio::alphabet
 
// ------------------------------------------------------------------
// literals
// ------------------------------------------------------------------
 
namespace bio::alphabet
{
 
inline namespace literals
{
 
consteval aa27 operator""_aa27(char const c)
{
    if (!char_is_valid_for<aa27>(c))
        throw std::invalid_argument{"Illegal character in character literal."};
 
    return aa27{}.assign_char(c);
}
 
template <meta::detail::literal_buffer_string str>
constexpr std::vector<aa27> operator""_aa27()
{
    return detail::string_literal<str, aa27>();
}
 
} // namespace literals
 
} // namespace bio::alphabet