rna5.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/dna5.hpp>
#include <bio/alphabet/nucleotide/nucleotide_base.hpp>
 
// ------------------------------------------------------------------
// rna5
// ------------------------------------------------------------------
 
namespace bio::alphabet
{
 
class rna5 : public nucleotide_base<rna5, 5>
{
private:
    using base_t = nucleotide_base<rna5, 5>;
 
    friend base_t;
    friend base_t::base_t;
 
public:
    constexpr rna5() noexcept                         = default; 
    constexpr rna5(rna5 const &) noexcept             = default; 
    constexpr rna5(rna5 &&) noexcept                  = default; 
    constexpr rna5 & operator=(rna5 const &) noexcept = default; 
    constexpr rna5 & operator=(rna5 &&) noexcept      = default; 
    ~rna5() noexcept                                  = default; 
 
    using base_t::base_t;
 
    constexpr rna5(dna5 const & r) noexcept { assign_rank(r.to_rank()); }
 
protected:
 
    static constexpr std::array<char_type, alphabet_size> rank_to_char{'A', 'C', 'G', 'N', 'U'};
 
    static constexpr std::array<rank_type, 256> char_to_rank = dna5::char_to_rank;
 
    static const std::array<rna5, alphabet_size> complement_table;
};
 
} // namespace bio::alphabet
 
// ------------------------------------------------------------------
// literals
// ------------------------------------------------------------------
 
namespace bio::alphabet
{
 
inline namespace literals
{
 
consteval rna5 operator""_rna5(char const c)
{
    if (!char_is_valid_for<rna5>(c))
        throw std::invalid_argument{"Illegal character in character literal."};
 
    return rna5{}.assign_char(c);
}
 
template <meta::detail::literal_buffer_string str>
constexpr std::vector<rna5> operator""_rna5()
{
    return detail::string_literal<str, rna5>();
}
 
} // namespace literals
 
} // namespace bio::alphabet
 
// ------------------------------------------------------------------
// rna5 (deferred definition)
// ------------------------------------------------------------------
 
namespace bio::alphabet
{
 
constexpr std::array<rna5, rna5::alphabet_size> rna5::complement_table{
  'U'_rna5, // complement of 'A'_rna5
  'G'_rna5, // complement of 'C'_rna5
  'C'_rna5, // complement of 'G'_rna5
  'N'_rna5, // complement of 'N'_rna5
  'A'_rna5  // complement of 'U'_rna5
};
 
} // namespace bio::alphabet