alphabet/concept.hpp

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// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: BSD-3-Clause
 
#pragma once
 
#include <type_traits>
 
#include <seqan3/alphabet/exception.hpp>
#include <seqan3/core/concept/cereal.hpp>
#include <seqan3/core/detail/customisation_point.hpp>
#include <seqan3/utility/concept.hpp>
#include <seqan3/utility/detail/type_name_as_string.hpp>
#include <seqan3/utility/type_traits/basic.hpp>
 
// ============================================================================
// forwards
// ============================================================================
 
namespace seqan3::custom
{
 
template <typename t>
struct alphabet
{};
 
template <typename t>
struct alphabet<t const> : alphabet<t>
{};
 
template <typename t>
struct alphabet<t &> : alphabet<t>
{};
 
template <typename t>
struct alphabet<t const &> : alphabet<t>
{};
 
} // namespace seqan3::custom
 
// ============================================================================
// to_rank()
// ============================================================================
 
namespace seqan3::detail::adl_only
{
 
template <typename... args_t>
void to_rank(args_t...) = delete;
 
struct to_rank_cpo : public detail::customisation_point_object<to_rank_cpo, 2>
{
    using base_t = detail::customisation_point_object<to_rank_cpo, 2>;
    using base_t::base_t;
 
    template <typename alphabet_t>
    static constexpr auto SEQAN3_CPO_OVERLOAD(priority_tag<2>, alphabet_t && alphabet)(
        /*return*/ seqan3::custom::alphabet<alphabet_t>::to_rank(std::forward<alphabet_t>(alphabet)) /*;*/
    );
 
    template <typename alphabet_t>
    static constexpr auto SEQAN3_CPO_OVERLOAD(priority_tag<1>, alphabet_t && alphabet)(
        /*return*/ to_rank(std::forward<alphabet_t>(alphabet)) /*;*/
    );
 
    template <typename alphabet_t>
    static constexpr auto SEQAN3_CPO_OVERLOAD(priority_tag<0>, alphabet_t && alphabet)(
        /*return*/ std::forward<alphabet_t>(alphabet).to_rank() /*;*/
    );
};
 
} // namespace seqan3::detail::adl_only
 
namespace seqan3
{
 
inline constexpr auto to_rank = detail::adl_only::to_rank_cpo{};
 
template <typename semi_alphabet_type>
    requires requires {
        { seqan3::to_rank(std::declval<semi_alphabet_type>()) };
    }
using alphabet_rank_t = decltype(seqan3::to_rank(std::declval<semi_alphabet_type>()));
 
} // namespace seqan3
 
// ============================================================================
// assign_rank_to()
// ============================================================================
 
namespace seqan3::detail::adl_only
{
 
template <typename... args_t>
void assign_rank_to(args_t...) = delete;
 
struct assign_rank_to_cpo : public detail::customisation_point_object<assign_rank_to_cpo, 2>
{
    using base_t = detail::customisation_point_object<assign_rank_to_cpo, 2>;
    using base_t::base_t;
 
    template <typename alphabet_t>
    static constexpr auto
    SEQAN3_CPO_OVERLOAD(priority_tag<2>, seqan3::alphabet_rank_t<alphabet_t> const rank, alphabet_t && alphabet)(
        /*return*/ static_cast<alphabet_t>(seqan3::custom::alphabet<alphabet_t>::assign_rank_to(rank, alphabet)) /*;*/
    );
 
    template <typename alphabet_t>
    static constexpr auto
    SEQAN3_CPO_OVERLOAD(priority_tag<1>, seqan3::alphabet_rank_t<alphabet_t> const rank, alphabet_t && alphabet)(
        /*return*/ static_cast<alphabet_t>(assign_rank_to(rank, alphabet)) /*;*/
    );
 
    template <typename alphabet_t> // least priority
    static constexpr auto
    SEQAN3_CPO_OVERLOAD(priority_tag<0>, seqan3::alphabet_rank_t<alphabet_t> const rank, alphabet_t && alphabet)(
        /*return*/ static_cast<alphabet_t>(std::forward<alphabet_t>(alphabet).assign_rank(rank)) /*;*/
    );
};
 
} // namespace seqan3::detail::adl_only
 
namespace seqan3
{
 
inline constexpr auto assign_rank_to = detail::adl_only::assign_rank_to_cpo{};
} // namespace seqan3
 
// ============================================================================
// to_char()
// ============================================================================
 
namespace seqan3::detail::adl_only
{
 
template <typename... args_t>
void to_char(args_t...) = delete;
 
struct to_char_cpo : public detail::customisation_point_object<to_char_cpo, 2>
{
    using base_t = detail::customisation_point_object<to_char_cpo, 2>;
    using base_t::base_t;
 
    template <typename alphabet_t>
    static constexpr auto SEQAN3_CPO_OVERLOAD(priority_tag<2>, alphabet_t && alphabet)(
        /*return*/ seqan3::custom::alphabet<alphabet_t>::to_char(std::forward<alphabet_t>(alphabet)) /*;*/
    );
 
    template <typename alphabet_t>
    static constexpr auto SEQAN3_CPO_OVERLOAD(priority_tag<1>, alphabet_t && alphabet)(
        /*return*/ to_char(std::forward<alphabet_t>(alphabet)) /*;*/
    );
 
    template <typename alphabet_t>
    static constexpr auto SEQAN3_CPO_OVERLOAD(priority_tag<0>, alphabet_t && alphabet)(
        /*return*/ std::forward<alphabet_t>(alphabet).to_char() /*;*/
    );
};
 
} // namespace seqan3::detail::adl_only
 
namespace seqan3
{
 
inline constexpr auto to_char = detail::adl_only::to_char_cpo{};
 
template <typename alphabet_type>
    requires requires (alphabet_type const a) {
        { seqan3::to_char(a) };
    }
using alphabet_char_t = decltype(seqan3::to_char(std::declval<alphabet_type const>()));
 
} // namespace seqan3
 
// ============================================================================
// assign_char_to()
// ============================================================================
 
namespace seqan3::detail::adl_only
{
 
template <typename... args_t>
void assign_char_to(args_t...) = delete;
 
struct assign_char_to_cpo : public detail::customisation_point_object<assign_char_to_cpo, 2>
{
    using base_t = detail::customisation_point_object<assign_char_to_cpo, 2>;
    using base_t::base_t;
 
    template <typename alphabet_t>
    static constexpr auto
    SEQAN3_CPO_OVERLOAD(priority_tag<2>, seqan3::alphabet_char_t<alphabet_t> const chr, alphabet_t && alphabet)(
        /*return*/ static_cast<alphabet_t>(seqan3::custom::alphabet<alphabet_t>::assign_char_to(chr, alphabet)) /*;*/
    );
 
    template <typename alphabet_t>
    static constexpr auto
    SEQAN3_CPO_OVERLOAD(priority_tag<1>, seqan3::alphabet_char_t<alphabet_t> const chr, alphabet_t && alphabet)(
        /*return*/ static_cast<alphabet_t>(assign_char_to(chr, alphabet)) /*;*/
    );
 
    template <typename alphabet_t> // least priority
    static constexpr auto
    SEQAN3_CPO_OVERLOAD(priority_tag<0>, seqan3::alphabet_char_t<alphabet_t> const chr, alphabet_t && alphabet)(
        /*return*/ static_cast<alphabet_t>(alphabet.assign_char(chr)) /*;*/
    );
};
 
} // namespace seqan3::detail::adl_only
 
namespace seqan3
{
 
inline constexpr auto assign_char_to = detail::adl_only::assign_char_to_cpo{};
} // namespace seqan3
 
// ============================================================================
// char_is_valid_for()
// ============================================================================
 
namespace seqan3::detail::adl_only
{
 
template <typename... args_t>
void char_is_valid_for(args_t...) = delete;
 
template <typename alphabet_t>
struct char_is_valid_for_cpo : public detail::customisation_point_object<char_is_valid_for_cpo<alphabet_t>, 3>
{
    using base_t = detail::customisation_point_object<char_is_valid_for_cpo<alphabet_t>, 3>;
    using base_t::base_t;
 
    template <typename alphabet_type>
    using alphabet_or_type_identity =
        std::conditional_t<std::is_nothrow_default_constructible_v<std::remove_cvref_t<alphabet_type>>,
                           std::remove_cvref_t<alphabet_type>,
                           std::type_identity<alphabet_type>>;
 
    template <typename alphabet_type = alphabet_t>
    static constexpr auto SEQAN3_CPO_OVERLOAD(priority_tag<3>, alphabet_char_t<alphabet_type> const chr)(
        /*return*/ seqan3::custom::alphabet<alphabet_type>::char_is_valid(chr) == true /*;*/
    );
 
    template <typename alphabet_type = alphabet_t>
    static constexpr auto SEQAN3_CPO_OVERLOAD(priority_tag<2>, alphabet_char_t<alphabet_type> const chr)(
        /*return*/ char_is_valid_for(chr, alphabet_or_type_identity<alphabet_type>{}) == true /*;*/
    );
 
    template <typename alphabet_type = alphabet_t>
    static constexpr auto SEQAN3_CPO_OVERLOAD(priority_tag<1>, alphabet_char_t<alphabet_type> const chr)(
        /*return*/ std::remove_cvref_t<alphabet_type>::char_is_valid(chr) == true /*;*/
    );
 
    template <typename alphabet_type = alphabet_t>
    static constexpr auto SEQAN3_CPO_OVERLOAD(priority_tag<0>, alphabet_char_t<alphabet_type> const chr)(
        /*return*/ seqan3::to_char(seqan3::assign_char_to(chr, alphabet_or_type_identity<alphabet_type>{})) == chr /*;*/
    );
};
 
} // namespace seqan3::detail::adl_only
 
namespace seqan3
{
 
template <typename alph_t>
    requires requires {
        { to_char(std::declval<alph_t>()) };
    } // to_char() is required by some defs
inline constexpr auto char_is_valid_for = detail::adl_only::char_is_valid_for_cpo<alph_t>{};
} // namespace seqan3
 
// ============================================================================
// assign_char_strictly_to()
// ============================================================================
 
namespace seqan3::detail::adl_only
{
 
struct assign_char_strictly_to_fn
{
    template <typename alphabet_t>
    constexpr decltype(auto) operator()(seqan3::alphabet_char_t<alphabet_t> const chr, alphabet_t && alphabet) const
        requires requires () {
            { seqan3::assign_char_to(chr, std::forward<alphabet_t>(alphabet)) } -> std::convertible_to<alphabet_t>;
            { seqan3::char_is_valid_for<alphabet_t>(chr) } -> std::same_as<bool>;
        }
    {
        if (!seqan3::char_is_valid_for<alphabet_t>(chr))
            throw seqan3::invalid_char_assignment{detail::type_name_as_string<alphabet_t>, chr};
 
        return seqan3::assign_char_to(chr, std::forward<alphabet_t>(alphabet));
    }
};
 
} // namespace seqan3::detail::adl_only
 
namespace seqan3
{
 
inline constexpr auto assign_char_strictly_to = detail::adl_only::assign_char_strictly_to_fn{};
} // namespace seqan3
 
// ============================================================================
// alphabet_size
// ============================================================================
 
namespace seqan3::detail::adl_only
{
 
template <typename... args_t>
void alphabet_size(args_t...) = delete;
 
template <typename alphabet_t>
struct alphabet_size_cpo : public detail::customisation_point_object<alphabet_size_cpo<alphabet_t>, 2>
{
    using base_t = detail::customisation_point_object<alphabet_size_cpo<alphabet_t>, 2>;
    using base_t::base_t;
 
    template <typename alphabet_type>
    using alphabet_or_type_identity =
        std::conditional_t<std::is_nothrow_default_constructible_v<std::remove_cvref_t<alphabet_type>>
                               && seqan3::is_constexpr_default_constructible_v<std::remove_cvref_t<alphabet_type>>,
                           std::remove_cvref_t<alphabet_type>,
                           std::type_identity<alphabet_type>>;
 
    template <typename alphabet_type = alphabet_t>
    static constexpr auto SEQAN3_CPO_OVERLOAD(priority_tag<2>)(
        /*return*/ seqan3::custom::alphabet<alphabet_type>::alphabet_size /*;*/
    );
 
    template <typename alphabet_type = alphabet_t>
    static constexpr auto SEQAN3_CPO_OVERLOAD(priority_tag<1>)(
        /*return*/ alphabet_size(alphabet_or_type_identity<alphabet_type>{}) /*;*/
    );
 
    template <typename alphabet_type = alphabet_t>
    static constexpr auto SEQAN3_CPO_OVERLOAD(priority_tag<0>)(
        /*return*/ std::remove_cvref_t<alphabet_type>::alphabet_size /*;*/
    );
};
 
} // namespace seqan3::detail::adl_only
 
namespace seqan3
{
 
template <typename alph_t>
    requires requires {
        { detail::adl_only::alphabet_size_cpo<alph_t>{}() };
    }
inline constexpr auto alphabet_size = detail::adl_only::alphabet_size_cpo<alph_t>{}();
 
// ============================================================================
// semialphabet
// ============================================================================
 
template <typename t>
concept semialphabet =
    std::totally_ordered<t> && std::copy_constructible<t> && std::is_nothrow_copy_constructible_v<t> && requires (t v) {
        { seqan3::alphabet_size<t> };
        { seqan3::to_rank(v) };
    };
 
// ============================================================================
// writable_semialphabet
// ============================================================================
 
template <typename t>
concept writable_semialphabet = semialphabet<t> && requires (t v, alphabet_rank_t<t> r) {
    { seqan3::assign_rank_to(r, v) };
};
 
// ============================================================================
// alphabet
// ============================================================================
 
template <typename t>
concept alphabet = semialphabet<t> && requires (t v) {
    { seqan3::to_char(v) };
};
 
// ============================================================================
// writable_alphabet
// ============================================================================
 
template <typename t>
concept writable_alphabet = alphabet<t> && writable_semialphabet<t> && requires (t v, alphabet_char_t<t> c) {
    { seqan3::assign_char_to(c, v) };
};
 
// ============================================================================
//  serialisation
// ============================================================================
 
template <cereal_output_archive archive_t, semialphabet alphabet_t>
alphabet_rank_t<alphabet_t> CEREAL_SAVE_MINIMAL_FUNCTION_NAME(archive_t const &, alphabet_t const & l)
{
    return to_rank(l);
}
 
template <cereal_input_archive archive_t, typename wrapped_alphabet_t>
void CEREAL_LOAD_MINIMAL_FUNCTION_NAME(archive_t const &,
                                       wrapped_alphabet_t && l,
                                       alphabet_rank_t<detail::strip_cereal_wrapper_t<wrapped_alphabet_t>> const & r)
    requires semialphabet<detail::strip_cereal_wrapper_t<wrapped_alphabet_t>>
{
    assign_rank_to(r, static_cast<detail::strip_cereal_wrapper_t<wrapped_alphabet_t> &>(l));
}
} // namespace seqan3
 
namespace seqan3::detail
{
// ============================================================================
// constexpr_semialphabet
// ============================================================================
 
template <typename t>
concept constexpr_semialphabet = semialphabet<t> && requires {
    // currently only tests rvalue interfaces, because we have no constexpr values in this scope to get references to
    requires SEQAN3_IS_CONSTEXPR(to_rank(std::remove_reference_t<t>{}));
};
 
// ============================================================================
// writable_constexpr_semialphabet
// ============================================================================
 
template <typename t>
concept writable_constexpr_semialphabet = constexpr_semialphabet<t> && writable_semialphabet<t> && requires {
    // currently only tests rvalue interfaces, because we have no constexpr values in this scope to get references to
    requires SEQAN3_IS_CONSTEXPR(seqan3::assign_rank_to(alphabet_rank_t<t>{}, std::remove_reference_t<t>{}));
};
 
// ============================================================================
// constexpr_alphabet
// ============================================================================
 
template <typename t>
concept constexpr_alphabet = constexpr_semialphabet<t> && alphabet<t> && requires {
    // currently only tests rvalue interfaces, because we have no constexpr values in this scope to get references to
    requires SEQAN3_IS_CONSTEXPR(to_char(std::remove_reference_t<t>{}));
};
 
// ============================================================================
// writable_constexpr_alphabet
// ============================================================================
 
template <typename t>
concept writable_constexpr_alphabet =
    constexpr_alphabet<t> && writable_constexpr_semialphabet<t> && writable_alphabet<t> && requires {
        // currently only tests rvalue interfaces, because we have no constexpr values in this scope to get references to
        requires SEQAN3_IS_CONSTEXPR(seqan3::assign_char_to(alphabet_char_t<t>{}, std::remove_reference_t<t>{}));
    };
 
} // namespace seqan3::detail