masked.hpp

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// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2022 deCODE Genetics
// Copyright (c) 2006-2020, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2020, 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/biocpp/biocpp-core/blob/main/LICENSE.md
// -----------------------------------------------------------------------------------------------------
 
#pragma once
 
#include <bio/alphabet/composite/tuple_base.hpp>
#include <bio/alphabet/detail/to_lower.hpp>
#include <bio/alphabet/mask/mask.hpp>
 
namespace bio::alphabet
{
template <writable_alphabet sequence_alphabet_t>
    requires std::regular<sequence_alphabet_t>
class masked : public tuple_base<masked<sequence_alphabet_t>, sequence_alphabet_t, mask>
{
private:
    using base_t = tuple_base<masked<sequence_alphabet_t>, sequence_alphabet_t, mask>;
 
public:
    using sequence_alphabet_type = sequence_alphabet_t;
 
    using char_type = 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 &&) noexcept             = default; 
    constexpr masked & operator=(masked const &)     = default; 
    constexpr masked & operator=(masked &&) noexcept = 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 = []()
    {
        std::array<char_type, alphabet_size> ret{};
 
        for (size_t i = 0; i < alphabet_size / 2; ++i)
        {
            ret[i]                     = alphabet::to_char(assign_rank_to(i, sequence_alphabet_type{}));
            ret[i + alphabet_size / 2] = detail::to_lower(ret[i]);
        }
 
        return ret;
    }();
 
    static constexpr std::array<rank_type, meta::detail::size_in_values_v<char_type>> char_to_rank = []()
    {
        std::array<rank_type, meta::detail::size_in_values_v<char_type>> ret{};
 
        for (size_t i = 0; i < meta::detail::size_in_values_v<char_type>; ++i)
        {
            char_type c = static_cast<char_type>(i);
 
            ret[i] =
              detail::is_lower(c)
                ? alphabet::to_rank(assign_char_to(detail::to_upper(c), sequence_alphabet_type{})) + alphabet_size / 2
                : alphabet::to_rank(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 bio::alphabet