rna4.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/dna4.hpp>
#include <seqan3/alphabet/nucleotide/nucleotide_base.hpp>

// ------------------------------------------------------------------
// rna4
// ------------------------------------------------------------------

namespace seqan3
{

class rna4 : public nucleotide_base<rna4, 4>
{
private:
    using base_t = nucleotide_base<rna4, 4>;

    friend base_t;
    friend base_t::base_t;

public:
    constexpr rna4()                          noexcept = default; 
    constexpr rna4(rna4 const &)              noexcept = default; 
    constexpr rna4(rna4 &&)                   noexcept = default; 
    constexpr rna4 & operator=(rna4 const &)  noexcept = default; 
    constexpr rna4 & operator=(rna4 &&)       noexcept = default; 
    ~rna4()                                   noexcept = default; 

    using base_t::base_t;

    constexpr rna4(dna4 const & r) noexcept
    {
        assign_rank(r.to_rank());
    }

protected:

    static constexpr char_type rank_to_char[alphabet_size]
    {
        'A',
        'C',
        'G',
        'U'
    };

    static constexpr std::array<rank_type, 256> char_to_rank = dna4::char_to_rank;

    static const std::array<rna4, alphabet_size> complement_table;
};

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

using rna4_vector = std::vector<rna4>;

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

constexpr rna4 operator""_rna4(char const c) noexcept
{
    return rna4{}.assign_char(c);
}

inline rna4_vector operator""_rna4(char const * s, std::size_t n)
{
    rna4_vector r;
    r.resize(n);

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

    return r;
}

// ------------------------------------------------------------------
// rna4 (deferred definition)
// ------------------------------------------------------------------

constexpr std::array<rna4, rna4::alphabet_size> rna4::complement_table
{
    'U'_rna4,    // complement of 'A'_rna4
    'G'_rna4,    // complement of 'C'_rna4
    'C'_rna4,    // complement of 'G'_rna4
    'A'_rna4     // complement of 'U'_rna4
};

} // namespace seqan3