aa27.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 <vector>
 
#include <seqan3/alphabet/aminoacid/aminoacid_base.hpp>
#include <seqan3/alphabet/aminoacid/concept.hpp>
#include <seqan3/utility/char_operations/transform.hpp>
 
namespace seqan3
{
 
class aa27 : public aminoacid_base<aa27, 27>
{
private:
    using base_t = aminoacid_base<aa27, 27>;

    friend base_t;
    friend base_t::base_t;
 
public:
    constexpr aa27() noexcept = default;                         
    constexpr aa27(aa27 const &) noexcept = default;             
    constexpr aa27(aa27 &&) noexcept = default;                  
    constexpr aa27 & operator=(aa27 const &) noexcept = default; 
    constexpr aa27 & operator=(aa27 &&) noexcept = default;      
    ~aa27() noexcept = default;                                  
 
    using base_t::base_t;
 
private:
    static constexpr char_type rank_to_char_table[alphabet_size]{'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I',
                                                                 'J', 'K', 'L', 'M', 'N', 'O', 'P', 'Q', 'R',
                                                                 'S', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z', '*'};

    static constexpr char_type rank_to_char(rank_type const rank)
    {
        return rank_to_char_table[rank];
    }

    static constexpr rank_type char_to_rank(char_type const chr)
    {
        using index_t = std::make_unsigned_t<char_type>;
        return char_to_rank_table[static_cast<index_t>(chr)];
    }

    static constexpr std::array<rank_type, 256> char_to_rank_table{
        []() constexpr
        {
            std::array<rank_type, 256> ret{};
 
            // initialize with 'X' (UNKNOWN)
            ret.fill(23u);
 
            // reverse mapping for characters and their lowercase
            for (rank_type rnk = 0u; rnk < alphabet_size; ++rnk)
            {
                ret[static_cast<rank_type>(rank_to_char_table[rnk])] = rnk;
                ret[static_cast<rank_type>(to_lower(rank_to_char_table[rnk]))] = rnk;
            }
 
            return ret;
        }()};
};
 
// ------------------------------------------------------------------
// containers
// ------------------------------------------------------------------

using aa27_vector = std::vector<aa27>;
 
// ------------------------------------------------------------------
// literals
// ------------------------------------------------------------------
inline namespace literals
{

constexpr aa27 operator""_aa27(char const c) noexcept
{
    return aa27{}.assign_char(c);
}

SEQAN3_WORKAROUND_LITERAL aa27_vector operator""_aa27(char const * const s, size_t const n)
{
    aa27_vector r;
    r.resize(n);
 
    for (size_t i = 0; i < n; ++i)
        r[i].assign_char(s[i]);
 
    return r;
}

 
} // namespace literals
 
} // namespace seqan3