rna4.hpp

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// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: BSD-3-Clause

 
#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;

    template <std::same_as<dna4> t>
    constexpr rna4(t const & r) noexcept
    {
        assign_rank(r.to_rank());
    }

 
private:
    static constexpr char_type rank_to_char_table[alphabet_size]{'A', 'C', 'G', 'U'};

    static constexpr rank_type rank_complement(rank_type const rank)
    {
        return dna4::rank_complement(rank);
    }

    static constexpr char_type rank_to_char(rank_type const rank)
    {
        return rank_to_char_table[rank];
    }

    static constexpr rank_type char_to_rank(char_type const chr)
    {
        return dna4::char_to_rank(chr);
    }
};
 
// ------------------------------------------------------------------
// containers
// ------------------------------------------------------------------

using rna4_vector = std::vector<rna4>;
 
// ------------------------------------------------------------------
// literals
// ------------------------------------------------------------------
inline namespace literals
{


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

SEQAN3_WORKAROUND_LITERAL 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;
}
 
} // namespace literals
 
} // namespace seqan3