dssp9.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/alphabet_base.hpp>
#include <seqan3/alphabet/concept.hpp>
#include <seqan3/utility/char_operations/transform.hpp>
 
// ------------------------------------------------------------------
// dssp9
// ------------------------------------------------------------------
 
namespace seqan3
{

class dssp9 : public alphabet_base<dssp9, 9>
{
private:
    using base_t = alphabet_base<dssp9, 9>;

    friend base_t;
 
public:
    constexpr dssp9() noexcept = default;                          
    constexpr dssp9(dssp9 const &) noexcept = default;             
    constexpr dssp9(dssp9 &&) noexcept = default;                  
    constexpr dssp9 & operator=(dssp9 const &) noexcept = default; 
    constexpr dssp9 & operator=(dssp9 &&) noexcept = default;      
    ~dssp9() noexcept = default;                                   

 
private:
    static constexpr char_type rank_to_char_table[alphabet_size]{'H', 'B', 'E', 'G', 'I', 'T', 'S', 'C', 'X'};

    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{};
 
            ret.fill(8u);
 
            // reverse mapping for characters
            for (rank_type rnk = 0u; rnk < alphabet_size; ++rnk)
                ret[static_cast<rank_type>(rank_to_char_table[rnk])] = rnk;
 
            return ret;
        }()};
};
 
inline namespace literals
{

constexpr dssp9 operator""_dssp9(char const ch) noexcept
{
    return dssp9{}.assign_char(ch);
}

SEQAN3_WORKAROUND_LITERAL std::vector<dssp9> operator""_dssp9(char const * str, std::size_t len)
{
    std::vector<dssp9> vec;
    vec.resize(len);
 
    for (size_t idx = 0u; idx < len; ++idx)
        vec[idx].assign_char(str[idx]);
 
    return vec;
}

 
} // namespace literals
 
} // namespace seqan3