structured_rna.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 <iostream>
#include <optional>
#include <string>
#include <utility>

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

namespace seqan3
{

template <NucleotideAlphabet sequence_alphabet_t, RnaStructureAlphabet structure_alphabet_t>
    requires WritableAlphabet<sequence_alphabet_t> && WritableAlphabet<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

    SEQAN3_DOXYGEN_ONLY(( constexpr structured_rna(component_type const alph) noexcept {} ))
    SEQAN3_DOXYGEN_ONLY(( constexpr structured_rna(indirect_component_type const alph) noexcept {} ))
    SEQAN3_DOXYGEN_ONLY(( constexpr structured_rna & operator=(component_type const alph) noexcept {} ))
    SEQAN3_DOXYGEN_ONLY(( constexpr structured_rna & operator=(indirect_component_type const alph) noexcept {} ))

    // Inherit operators from base
    using base_type::operator=;
    using base_type::operator==;
    using base_type::operator!=;
    using base_type::operator>=;
    using base_type::operator<=;
    using base_type::operator<;
    using base_type::operator>;

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

    structured_rna & assign_char_strictly(char_type const c)
    {
        seqan3::assign_char_strictly_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