structured_rna.hpp

Go to the documentation of this file.

// 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 <seqan3/alphabet/composite/alphabet_tuple_base.hpp>
#include <seqan3/alphabet/nucleotide/concept.hpp>
#include <seqan3/alphabet/structure/concept.hpp>
 
namespace seqan3
{

template <nucleotide_alphabet sequence_alphabet_t, rna_structure_alphabet structure_alphabet_t>
    requires writable_alphabet<sequence_alphabet_t> && writable_alphabet<structure_alphabet_t>
class structured_rna :
    public alphabet_tuple_base<structured_rna<sequence_alphabet_t, structure_alphabet_t>,
                               sequence_alphabet_t,
                               structure_alphabet_t>
{
private:
    using base_type = alphabet_tuple_base<structured_rna<sequence_alphabet_t, structure_alphabet_t>,
                                          sequence_alphabet_t,
                                          structure_alphabet_t>;
 
public:
    using sequence_alphabet_type = sequence_alphabet_t;
    using structure_alphabet_type = structure_alphabet_t;

    using char_type = alphabet_char_t<sequence_alphabet_type>;

    constexpr structured_rna() noexcept = default;                                   
    constexpr structured_rna(structured_rna const &) noexcept = default;             
    constexpr structured_rna(structured_rna &&) noexcept = default;                  
    constexpr structured_rna & operator=(structured_rna const &) noexcept = default; 
    constexpr structured_rna & operator=(structured_rna &&) noexcept = default;      
    ~structured_rna() noexcept = default;                                            
 
    using base_type::base_type; // Inherit non-default constructors
 
#if SEQAN3_DOXYGEN_ONLY(1) 0
    constexpr structured_rna(component_type const alph) noexcept
    {}

    constexpr structured_rna(indirect_component_type const alph) noexcept
    {}

    constexpr structured_rna & operator=(component_type const alph) noexcept
    {}

    constexpr structured_rna & operator=(indirect_component_type const alph) noexcept
    {}
#endif // SEQAN3_DOXYGEN_ONLY
 
    // Inherit operators from base
    using base_type::operator=;


    constexpr structured_rna & assign_char(char_type const c) noexcept
    {
        seqan3::assign_char_to(c, get<0>(*this));
        return *this;
    }



    constexpr char_type to_char() const noexcept
    {
        return seqan3::to_char(get<0>(*this));
    }

    constexpr structured_rna complement() const noexcept
    {
        return structured_rna{get<0>(*this).complement(), get<1>(*this)};
    }


    static constexpr bool char_is_valid(char_type const c) noexcept
    {
        return char_is_valid_for<sequence_alphabet_type>(c);
    }


    constexpr bool is_pair_open() const noexcept
    {
        return get<1>(*this).is_pair_open();
    };

    constexpr bool is_pair_close() const noexcept
    {
        return get<1>(*this).is_pair_close();
    };

    constexpr bool is_unpaired() const noexcept
    {
        return get<1>(*this).is_unpaired();
    };

    static constexpr uint8_t max_pseudoknot_depth{structure_alphabet_t::max_pseudoknot_depth};

    constexpr std::optional<uint8_t> pseudoknot_id() const noexcept
    {
        return get<1>(*this).pseudoknot_id();
    };

};

template <typename sequence_alphabet_type, typename structure_alphabet_type>
structured_rna(sequence_alphabet_type &&, structure_alphabet_type &&)
    -> structured_rna<std::decay_t<sequence_alphabet_type>, std::decay_t<structure_alphabet_type>>;
 
} // namespace seqan3