dot_bracket3.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/structure/concept.hpp>
#include <seqan3/utility/char_operations/transform.hpp>
 
// ------------------------------------------------------------------
// dot_bracket3
// ------------------------------------------------------------------
 
namespace seqan3
{

class dot_bracket3 : public alphabet_base<dot_bracket3, 3>
{
private:
    using base_t = alphabet_base<dot_bracket3, 3>;

    friend base_t;
 
public:
    constexpr dot_bracket3() noexcept = default;                                 
    constexpr dot_bracket3(dot_bracket3 const &) noexcept = default;             
    constexpr dot_bracket3(dot_bracket3 &&) noexcept = default;                  
    constexpr dot_bracket3 & operator=(dot_bracket3 const &) noexcept = default; 
    constexpr dot_bracket3 & operator=(dot_bracket3 &&) noexcept = default;      
    ~dot_bracket3() noexcept = default;                                          



    constexpr bool is_pair_open() const noexcept
    {
        return to_rank() == 1u;
    }

    constexpr bool is_pair_close() const noexcept
    {
        return to_rank() == 2u;
    }

    constexpr bool is_unpaired() const noexcept
    {
        return to_rank() == 0u;
    }

    static constexpr uint8_t max_pseudoknot_depth{1u};

    constexpr std::optional<uint8_t> pseudoknot_id() const noexcept
    {
        if (is_unpaired())
            return std::nullopt;
        else
            return 0;
    }

 
private:
    static constexpr char_type rank_to_char_table[alphabet_size]{'.', '(', ')'};

    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> rank_table{};
 
                                                                       // Value-initialisation of std::array does usually initialise. `fill` is explicit.
                                                                       rank_table.fill(0u);
 
                                                                       // canonical
                                                                       rank_table['.'] = 0u;
                                                                       rank_table['('] = 1u;
                                                                       rank_table[')'] = 2u;
 
                                                                       return rank_table;
                                                                   }()};
};
 
inline namespace literals
{

constexpr dot_bracket3 operator""_db3(char const ch) noexcept
{
    return dot_bracket3{}.assign_char(ch);
}

SEQAN3_WORKAROUND_LITERAL std::vector<dot_bracket3> operator""_db3(char const * str, std::size_t len)
{
    std::vector<dot_bracket3> vec;
    vec.resize(len);
 
    for (size_t idx = 0ul; idx < len; ++idx)
        vec[idx].assign_char(str[idx]);
 
    return vec;
}

 
} // namespace literals
 
} // namespace seqan3