rna5.hpp

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// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2019, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2019, 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/seqan/seqan3/blob/master/LICENSE.md
// -----------------------------------------------------------------------------------------------------

#pragma once

#include <vector>

#include <seqan3/alphabet/nucleotide/dna5.hpp>
#include <seqan3/alphabet/nucleotide/nucleotide_base.hpp>

// ------------------------------------------------------------------
// rna5
// ------------------------------------------------------------------

namespace seqan3
{

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 char_type rank_to_char[alphabet_size]
    {
        '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;
};

// ------------------------------------------------------------------
// containers
// ------------------------------------------------------------------

using rna5_vector = std::vector<rna5>;

// ------------------------------------------------------------------
// literals
// ------------------------------------------------------------------

constexpr rna5 operator""_rna5(char const c) noexcept
{
    return rna5{}.assign_char(c);
}

inline rna5_vector operator""_rna5(char const * s, std::size_t n)
{
    rna5_vector r;
    r.resize(n);

    for (size_t i = 0; i < n; ++i)
        r[i].assign_char(s[i]);

    return r;
}

// ------------------------------------------------------------------
// rna5 (deferred definition)
// ------------------------------------------------------------------

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 seqan3