alphabet_proxy.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 <concepts>
 
#include <seqan3/alphabet/alphabet_base.hpp>
#include <seqan3/alphabet/detail/concept.hpp>
#include <seqan3/alphabet/nucleotide/concept.hpp>
#include <seqan3/alphabet/quality/concept.hpp>
#include <seqan3/core/detail/template_inspection.hpp>
#include <seqan3/utility/concept.hpp>
#include <seqan3/utility/type_traits/basic.hpp>
 
namespace seqan3
{
 
template <typename derived_type, writable_semialphabet alphabet_type>
    requires std::regular<alphabet_type>
class alphabet_proxy :
    public std::conditional_t<std::is_class_v<alphabet_type>,
                              alphabet_type,
                              alphabet_base<derived_type,
                                            alphabet_size<alphabet_type>,
                                            detail::valid_template_spec_or_t<void, alphabet_char_t, alphabet_type>>>
{
private:
    using base_t =
        std::conditional_t<std::is_class_v<alphabet_type>,
                           alphabet_type,              // inherit from emulated type if possible
                           alphabet_base<derived_type, // else: alphabet_base
                                         alphabet_size<alphabet_type>,
                                         detail::valid_template_spec_or_t<void, alphabet_char_t, alphabet_type>>>;
 
    friend base_t;
 
    using char_type = detail::valid_template_spec_or_t<char, alphabet_char_t, alphabet_type>;
 
    using phred_type = detail::valid_template_spec_or_t<int8_t, alphabet_phred_t, alphabet_type>;
 
private:
    constexpr alphabet_proxy() noexcept = default;                          
    constexpr alphabet_proxy(alphabet_proxy const &) = default;             
    constexpr alphabet_proxy(alphabet_proxy &&) = default;                  
    constexpr alphabet_proxy & operator=(alphabet_proxy const &) = default; 
    constexpr alphabet_proxy & operator=(alphabet_proxy &&) = default;      
    ~alphabet_proxy() = default;                                            
 
    constexpr alphabet_proxy(alphabet_type const a) noexcept
        requires std::is_class_v<alphabet_type>
        : base_t{a}
    {}
    constexpr alphabet_proxy(alphabet_type const a) noexcept {…}
 
    constexpr alphabet_proxy(alphabet_type const a) noexcept
        requires (!std::is_class_v<alphabet_type>)
        : base_t{}
    {
        base_t::assign_rank(seqan3::to_rank(a));
    }
    constexpr alphabet_proxy(alphabet_type const a) noexcept {…}
 
    constexpr derived_type & operator=(alphabet_type const & c) noexcept
    {
        if constexpr (std::is_class_v<alphabet_type>)
            seqan3::assign_rank_to(seqan3::to_rank(c), static_cast<alphabet_type &>(*this));
        else
            base_t::assign_rank(seqan3::to_rank(c));
 
        static_cast<derived_type &>(*this).on_update(); // <- this invokes the actual proxy behaviour!
        return static_cast<derived_type &>(*this);
    }
    constexpr derived_type & operator=(alphabet_type const & c) noexcept {…}
 
    template <typename indirect_assignable_type>
    constexpr derived_type & operator=(indirect_assignable_type const & c) noexcept
        requires weakly_assignable_from<alphabet_type, indirect_assignable_type>
    {
        alphabet_type a{};
        a = c;
        return operator=(a);
    }
    constexpr derived_type & operator=(indirect_assignable_type const & c) noexcept {…}
 
    friend derived_type;
 
public:
    static constexpr auto alphabet_size = seqan3::alphabet_size<alphabet_type>;
 
    constexpr derived_type & assign_rank(alphabet_rank_t<alphabet_type> const r) noexcept
    {
        alphabet_type tmp{};
        assign_rank_to(r, tmp);
        return operator=(tmp);
    }
    constexpr derived_type & assign_rank(alphabet_rank_t<alphabet_type> const r) noexcept {…}
 
    constexpr derived_type & assign_char(char_type const c) noexcept
        requires writable_alphabet<alphabet_type>
    {
        alphabet_type tmp{};
        assign_char_to(c, tmp);
        return operator=(tmp);
    }
    constexpr derived_type & assign_char(char_type const c) noexcept {…}
 
    constexpr derived_type & assign_phred(phred_type const c) noexcept
        requires writable_quality_alphabet<alphabet_type>
    {
        alphabet_type tmp{};
        assign_phred_to(c, tmp);
        return operator=(tmp);
    }
    constexpr derived_type & assign_phred(phred_type const c) noexcept {…}
 
    constexpr operator alphabet_type() const noexcept
    {
        if constexpr (std::is_class_v<alphabet_type>)
            return *this;
        else
            return assign_rank_to(base_t::to_rank(), alphabet_type{});
 
        /* Instead of static_cast'ing to the alphabet_type which also considers the constructors of the alphabet_type,
         * we explicitly invoke this operator in various places.
         * This prevents errors associated with using alphabet_type's constructors.
         *
         * This is one of error cases:
         * The tuple composite seqan3::qualified returns a component_proxy which inherits from alphabet_proxy_base.
         * The qualified alphabet itself inherits from phred_base.
         * Now when accessing get<1>(seq_qual_alph) we want to call to_phred at some point because we want the quality,
         * therefore the to_phred function from alphabet_proxy is called, but this function did a static_cast to the
         * derived type which is calling the constructor from phred_base. Unfortunately now, the generic phred_base
         * constructor uses `assign_phred_to(to_phred(other), static_cast<derived_type &>(*this))`; (here) which again
         * tries to call to_phred of the alphabet_proxy => infinite loop :boom:
         */
    }
    constexpr operator alphabet_type() const noexcept {…}
 
    template <typename other_t>
        requires (!std::is_class_v<alphabet_type>) && std::convertible_to<alphabet_type, other_t>
    constexpr operator other_t() const noexcept
    {
        return operator alphabet_type();
    }
    constexpr operator other_t() const noexcept {…}
 
    constexpr auto to_rank() const noexcept
    {
        return seqan3::to_rank(operator alphabet_type());
    }
    constexpr auto to_rank() const noexcept {…}
 
    constexpr auto to_char() const noexcept
        requires alphabet<alphabet_type>
    {
        return seqan3::to_char(operator alphabet_type());
    }
    constexpr auto to_char() const noexcept {…}
 
    constexpr auto to_phred() const noexcept
        requires quality_alphabet<alphabet_type>
    {
        return seqan3::to_phred(operator alphabet_type());
    }
    constexpr auto to_phred() const noexcept {…}
 
    constexpr alphabet_type complement() const noexcept
        requires nucleotide_alphabet<alphabet_type>
    {
        return seqan3::complement(operator alphabet_type());
    }
    constexpr alphabet_type complement() const noexcept {…}
 
    static constexpr bool char_is_valid(char_type const c) noexcept
        requires writable_alphabet<alphabet_type>
    {
        return char_is_valid_for<alphabet_type>(c);
    }
    static constexpr bool char_is_valid(char_type const c) noexcept {…}
 
private:
    template <typename t>
    static constexpr bool is_alphabet_comparable_with =
        !std::is_same_v<derived_type, t> && detail::weakly_equality_comparable_with<alphabet_type, t>;
 
public:
    template <typename t>
    friend constexpr auto operator==(derived_type const lhs,
                                     t const rhs) noexcept -> std::enable_if_t<is_alphabet_comparable_with<t>, bool>
    {
        return (lhs.operator alphabet_type() == rhs);
    }
    friend constexpr auto operator==(derived_type const lhs, {…};
 
    template <typename t>
    friend constexpr auto
    operator==(t const lhs, derived_type const rhs) noexcept -> std::enable_if_t<is_alphabet_comparable_with<t>, bool>
    {
        return (rhs == lhs);
    }
    operator==(t const lhs, derived_type const rhs) noexcept -> std::enable_if_t<is_alphabet_comparable_with<t>, bool> {…};
 
    template <typename t>
    friend constexpr auto operator!=(derived_type const lhs,
                                     t const rhs) noexcept -> std::enable_if_t<is_alphabet_comparable_with<t>, bool>
    {
        return !(lhs == rhs);
    }
    friend constexpr auto operator!=(derived_type const lhs, {…};
 
    template <typename t>
    friend constexpr auto
    operator!=(t const lhs, derived_type const rhs) noexcept -> std::enable_if_t<is_alphabet_comparable_with<t>, bool>
    {
        return (rhs != lhs);
    }
    operator!=(t const lhs, derived_type const rhs) noexcept -> std::enable_if_t<is_alphabet_comparable_with<t>, bool> {…};
};
class alphabet_proxy : {…};
 
} // namespace seqan3