rna15.hpp

Go to the documentation of this file.

// -----------------------------------------------------------------------------------------------------
// 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/dna15.hpp>
#include <bio/alphabet/nucleotide/nucleotide_base.hpp>
 
// ------------------------------------------------------------------
// rna15
// ------------------------------------------------------------------
 
namespace bio::alphabet
{
 
class rna15 : public nucleotide_base<rna15, 15>
{
private:
    using base_t = nucleotide_base<rna15, 15>;
 
    friend base_t;
    friend base_t::base_t;
 
public:
    constexpr rna15() noexcept                          = default; 
    constexpr rna15(rna15 const &) noexcept             = default; 
    constexpr rna15(rna15 &&) noexcept                  = default; 
    constexpr rna15 & operator=(rna15 const &) noexcept = default; 
    constexpr rna15 & operator=(rna15 &&) noexcept      = default; 
    ~rna15() noexcept                                   = default; 
 
    using base_t::base_t;
 
    constexpr rna15(dna15 const & r) noexcept { assign_rank(r.to_rank()); }
 
protected:
 
    static constexpr std::array<char_type, alphabet_size>
      rank_to_char{'A', 'B', 'C', 'D', 'G', 'H', 'K', 'M', 'N', 'R', 'S', 'U', 'V', 'W', 'Y'};
 
    static constexpr std::array<rank_type, 256> char_to_rank = dna15::char_to_rank;
 
    static const std::array<rna15, alphabet_size> complement_table;
};
 
} // namespace bio::alphabet
 
// ------------------------------------------------------------------
// literals
// ------------------------------------------------------------------
 
namespace bio::alphabet
{
 
inline namespace literals
{
 
consteval rna15 operator""_rna15(char const c)
{
    if (!char_is_valid_for<rna15>(c))
        throw std::invalid_argument{"Illegal character in character literal."};
 
    return rna15{}.assign_char(c);
}
 
template <meta::detail::literal_buffer_string str>
constexpr std::vector<rna15> operator""_rna15()
{
    return detail::string_literal<str, rna15>();
}
 
} // namespace literals
 
} // namespace bio::alphabet
 
// ------------------------------------------------------------------
// rna15 (deferred definition)
// ------------------------------------------------------------------
 
namespace bio::alphabet
{
 
constexpr std::array<rna15, rna15::alphabet_size> rna15::complement_table{
  'U'_rna15, // complement of 'A'_rna15
  'V'_rna15, // complement of 'B'_rna15
  'G'_rna15, // complement of 'C'_rna15
  'H'_rna15, // complement of 'D'_rna15
  'C'_rna15, // complement of 'G'_rna15
  'D'_rna15, // complement of 'H'_rna15
  'M'_rna15, // complement of 'K'_rna15
  'K'_rna15, // complement of 'M'_rna15
  'N'_rna15, // complement of 'N'_rna15
  'Y'_rna15, // complement of 'R'_rna15
  'S'_rna15, // complement of 'S'_rna15
  'A'_rna15, // complement of 'U'_rna15
  'B'_rna15, // complement of 'V'_rna15
  'W'_rna15, // complement of 'W'_rna15
  'R'_rna15  // complement of 'Y'_rna15
};
 
} // namespace bio::alphabet