masked.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/composite/alphabet_tuple_base.hpp>
#include <seqan3/alphabet/mask/mask.hpp>
#include <seqan3/utility/char_operations/predicate.hpp>
#include <seqan3/utility/char_operations/transform.hpp>
 
namespace seqan3
{
template <writable_alphabet sequence_alphabet_t>
    requires std::regular<sequence_alphabet_t>
class masked : public alphabet_tuple_base<masked<sequence_alphabet_t>, sequence_alphabet_t, mask>
{
private:
    using base_t = alphabet_tuple_base<masked<sequence_alphabet_t>, sequence_alphabet_t, mask>;
 
public:
    using sequence_alphabet_type = sequence_alphabet_t;

    using char_type = alphabet_char_t<sequence_alphabet_type>;
 
    using base_t::alphabet_size;
    using typename base_t::rank_type;

    constexpr masked() = default;                           
    constexpr masked(masked const &) = default;             
    constexpr masked(masked &&) = default;                  
    constexpr masked & operator=(masked const &) = default; 
    constexpr masked & operator=(masked &&) = default;      
    ~masked() = default;                                    
 
    using base_t::base_t; // Inherit non-default constructors
 
    // Inherit operators from base
    using base_t::operator=;

    constexpr masked & assign_char(char_type const c) noexcept
    {
        using index_t = std::make_unsigned_t<char_type>;
        base_t::assign_rank(char_to_rank[static_cast<index_t>(c)]);
        return *this;
    }


    constexpr char_type to_char() const noexcept
    {
        return rank_to_char[base_t::to_rank()];
    }

 
protected:
    static constexpr std::array<char_type, alphabet_size> rank_to_char{
        []() constexpr
        {
            std::array<char_type, alphabet_size> ret{};
 
            for (size_t i = 0; i < alphabet_size; ++i)
            {
                ret[i] = (i < alphabet_size / 2)
                           ? seqan3::to_char(seqan3::assign_rank_to(i, sequence_alphabet_type{}))
                           : to_lower(seqan3::to_char(seqan3::assign_rank_to(i / 2, sequence_alphabet_type{})));
            }
 
            return ret;
        }()};

    static constexpr std::array<rank_type, detail::size_in_values_v<char_type>> char_to_rank{
        []() constexpr
        {
            std::array<rank_type, detail::size_in_values_v<char_type>> ret{};
 
            for (size_t i = 0; i < 256; ++i)
            {
                char_type const c = static_cast<char_type>(i);
 
                ret[i] = is_lower(c) ? seqan3::to_rank(seqan3::assign_char_to(c, sequence_alphabet_type{})) * 2
                                     : seqan3::to_rank(seqan3::assign_char_to(c, sequence_alphabet_type{}));
            }
 
            return ret;
        }()};
};

template <typename sequence_alphabet_type>
masked(sequence_alphabet_type &&, mask const &) -> masked<std::decay_t<sequence_alphabet_type>>;
 
} //namespace seqan3