structured_aa.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 <seqan3/alphabet/aminoacid/aa27.hpp>
#include <seqan3/alphabet/composite/alphabet_tuple_base.hpp>
#include <seqan3/alphabet/concept.hpp>
#include <seqan3/alphabet/structure/dssp9.hpp>
 
namespace seqan3
{
 
template <writable_alphabet sequence_alphabet_t = aa27, writable_alphabet 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
 
#if SEQAN3_DOXYGEN_ONLY(1) 0
    template <typename component_type>
    constexpr structured_aa(component_type const alph)
    {}
    constexpr structured_aa(component_type const alph) {…}
 
    template <typename indirect_component_type>
    constexpr structured_aa(indirect_component_type const alph)
    {}
    constexpr structured_aa(indirect_component_type const alph) {…}
 
    template <typename component_type>
    constexpr structured_aa & operator=(component_type const alph)
    {}
    constexpr structured_aa & operator=(component_type const alph) {…}
 
    template <typename indirect_component_type>
    constexpr structured_aa & operator=(indirect_component_type const alph)
    {}
    constexpr structured_aa & operator=(indirect_component_type const alph) {…}
#endif
 
    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 structured_aa & assign_char(char_type const c) noexcept {…}
 
    constexpr char_type to_char() const noexcept
    {
        return seqan3::to_char(get<0>(*this));
    }
    constexpr char_type to_char() const noexcept {…}
 
    static constexpr bool char_is_valid(char_type const c) noexcept
    {
        return char_is_valid_for<sequence_alphabet_type>(c);
    }
    static constexpr bool char_is_valid(char_type const c) noexcept {…}
};
class structured_aa : {…};
 
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