structured_aa.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 <string>
#include <utility>

#include <seqan3/alphabet/aminoacid/all.hpp>
#include <seqan3/alphabet/composite/alphabet_tuple_base.hpp>
#include <seqan3/alphabet/concept.hpp>
#include <seqan3/alphabet/structure/dssp9.hpp>

namespace seqan3
{

template <WritableAlphabet sequence_alphabet_t = aa27, WritableAlphabet structure_alphabet_t = dssp9>
    requires (!std::is_reference_v<sequence_alphabet_t>) && (!std::is_reference_v<structure_alphabet_t>)
class structured_aa :
    public alphabet_tuple_base<structured_aa<sequence_alphabet_t, structure_alphabet_t>,
                                 sequence_alphabet_t, structure_alphabet_t>
{
private:
    using base_type = alphabet_tuple_base<structured_aa<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_aa()                                    noexcept = default; 
    constexpr structured_aa(structured_aa const &)               noexcept = default; 
    constexpr structured_aa(structured_aa &&)                    noexcept = default; 
    constexpr structured_aa & operator =(structured_aa const &)  noexcept = default; 
    constexpr structured_aa & operator =(structured_aa &&)       noexcept = default; 
    ~structured_aa()                                             noexcept = default; 

    using base_type::base_type; // Inherit non-default constructors


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

    // 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_aa & 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));
    }

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

template <typename sequence_alphabet_type, typename structure_alphabet_type>
structured_aa(sequence_alphabet_type &&, structure_alphabet_type &&)
    -> structured_aa<std::decay_t<sequence_alphabet_type>, std::decay_t<structure_alphabet_type>>;

} // namespace seqan3