dna15.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/nucleotide/nucleotide_base.hpp>
#include <seqan3/utility/char_operations/transform.hpp>
 
// ------------------------------------------------------------------
// dna15
// ------------------------------------------------------------------
 
namespace seqan3
{
 
class rna15;

class dna15 : public nucleotide_base<dna15, 15>
{
private:
    using base_t = nucleotide_base<dna15, 15>;

    friend base_t;
    friend base_t::base_t;
    friend rna15;
 
public:
    constexpr dna15() noexcept = default;                          
    constexpr dna15(dna15 const &) noexcept = default;             
    constexpr dna15(dna15 &&) noexcept = default;                  
    constexpr dna15 & operator=(dna15 const &) noexcept = default; 
    constexpr dna15 & operator=(dna15 &&) noexcept = default;      
    ~dna15() noexcept = default;                                   
 
    using base_t::base_t;

    template <std::same_as<rna15> t> // Accept incomplete type
    constexpr dna15(t const & r) noexcept
    {
        assign_rank(r.to_rank());
    }

 
private:
    static constexpr char_type
        rank_to_char_table[alphabet_size]{'A', 'B', 'C', 'D', 'G', 'H', 'K', 'M', 'N', 'R', 'S', 'T', 'V', 'W', 'Y'};

    static constexpr rank_type rank_complement_table[alphabet_size]{
        11, // T is complement of 'A'_dna15
        12, // V is complement of 'B'_dna15
        4,  // G is complement of 'C'_dna15
        5,  // H is complement of 'D'_dna15
        2,  // C is complement of 'G'_dna15
        3,  // D is complement of 'H'_dna15
        7,  // M is complement of 'K'_dna15
        6,  // K is complement of 'M'_dna15
        8,  // N is complement of 'N'_dna15
        14, // Y is complement of 'R'_dna15
        10, // S is complement of 'S'_dna15
        0,  // A is complement of 'T'_dna15
        1,  // B is complement of 'V'_dna15
        13, // W is complement of 'W'_dna15
        9   // R is complement of 'Y'_dna15
    };

    static constexpr rank_type rank_complement(rank_type const rank)
    {
        return rank_complement_table[rank];
    }

    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); // initialize with UNKNOWN ('N')
 
                                                                       // reverse mapping for characters and their lowercase
                                                                       for (size_t rnk = 0u; rnk < alphabet_size; ++rnk)
                                                                       {
                                                                           ret[rank_to_char_table[rnk]] = rnk;
                                                                           ret[to_lower(rank_to_char_table[rnk])] = rnk;
                                                                       }
 
                                                                       // set U equal to T
                                                                       ret['U'] = ret['T'];
                                                                       ret['u'] = ret['t'];
 
                                                                       return ret;
                                                                   }()};
};
 
// ------------------------------------------------------------------
// containers
// ------------------------------------------------------------------

using dna15_vector = std::vector<dna15>;
 
// ------------------------------------------------------------------
// literals
// ------------------------------------------------------------------
inline namespace literals
{


constexpr dna15 operator""_dna15(char const c) noexcept
{
    return dna15{}.assign_char(c);
}

SEQAN3_WORKAROUND_LITERAL dna15_vector operator""_dna15(char const * s, std::size_t n)
{
    dna15_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