nucleotide_base.hpp

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// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2022, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2022, 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/seqan/seqan3/blob/master/LICENSE.md
// -----------------------------------------------------------------------------------------------------
 
#pragma once
 
#include <seqan3/alphabet/alphabet_base.hpp>
#include <seqan3/alphabet/detail/convert.hpp>
#include <seqan3/alphabet/nucleotide/concept.hpp>
#include <seqan3/utility/char_operations/transform.hpp>
 
namespace seqan3
{
 
template <typename derived_type, auto size>
class nucleotide_base : public alphabet_base<derived_type, size, char>
{
private:
    using base_t = alphabet_base<derived_type, size, char>;
 
    constexpr nucleotide_base() noexcept = default;                                    
    constexpr nucleotide_base(nucleotide_base const &) noexcept = default;             
    constexpr nucleotide_base(nucleotide_base &&) noexcept = default;                  
    constexpr nucleotide_base & operator=(nucleotide_base const &) noexcept = default; 
    constexpr nucleotide_base & operator=(nucleotide_base &&) noexcept = default;      
    ~nucleotide_base() noexcept = default;                                             
 
 
    friend derived_type;
 
protected:
    // Import from base:
    using typename base_t::char_type;
    using typename base_t::rank_type;
 
public:
    using base_t::alphabet_size;
    using base_t::to_rank;
 
    // This constructor needs to be public, because constructor templates are not inherited otherwise
    template <typename other_nucl_type>
        requires (!std::same_as<nucleotide_base, other_nucl_type>)
              && (!std::same_as<derived_type, other_nucl_type>) && nucleotide_alphabet<other_nucl_type>
    explicit constexpr nucleotide_base(other_nucl_type const & other) noexcept
    {
        static_cast<derived_type &>(*this) =
            detail::convert_through_char_representation<other_nucl_type, derived_type>[seqan3::to_rank(other)];
    }
 
    constexpr derived_type complement() const noexcept
    {
        return derived_type{}.assign_rank(derived_type{}.rank_complement(to_rank()));
    }
 
    static constexpr bool char_is_valid(char_type const c) noexcept
    {
        return valid_char_table[static_cast<uint8_t>(c)];
    }
 
private:
    static constexpr std::array<bool, 256> valid_char_table{[]() constexpr {// init with false
                                                                            std::array<bool, 256> ret{};
 
    // the original valid chars and their lower cases
    for (size_t rank = 0u; rank < derived_type::alphabet_size; ++rank)
    {
        uint8_t c = derived_type::rank_to_char(rank);
        ret[c] = true;
        ret[to_lower(c)] = true;
    }
 
    // U and T shall be accepted for all
    ret['U'] = true;
    ret['T'] = true;
    ret['u'] = true;
    ret['t'] = true;
 
    return ret;
}()
}; // namespace seqan3
}
;
 
} // namespace seqan3