rna15.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/dna15.hpp>
#include <seqan3/alphabet/nucleotide/nucleotide_base.hpp>

// ------------------------------------------------------------------
// rna15
// ------------------------------------------------------------------

namespace seqan3
{

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 char_type rank_to_char[alphabet_size]
    {
        '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;
};

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

using rna15_vector = std::vector<rna15>;

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

constexpr rna15 operator""_rna15(char const c) noexcept
{
    return rna15{}.assign_char(c);
}

inline rna15_vector operator""_rna15(char const * s, std::size_t n)
{
    rna15_vector r;
    r.resize(n);

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

    return r;
}

// ------------------------------------------------------------------
// rna15 (deferred definition)
// ------------------------------------------------------------------

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 seqan3