dna16sam.hpp

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// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2021, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2021, 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/nucleotide/nucleotide_base.hpp>
 
namespace seqan3
{
 
class dna16sam : public nucleotide_base<dna16sam, 16>
{
private:
    using base_t = nucleotide_base<dna16sam, 16>;
 
    friend base_t;
    friend base_t::base_t;
 
public:
    constexpr dna16sam()                             noexcept = default; 
    constexpr dna16sam(dna16sam const &)             noexcept = default; 
    constexpr dna16sam(dna16sam &&)                  noexcept = default; 
    constexpr dna16sam & operator=(dna16sam const &) noexcept = default; 
    constexpr dna16sam & operator=(dna16sam &&)      noexcept = default; 
    ~dna16sam()                                      noexcept = default; 
 
    using base_t::base_t;
 
private:
    static constexpr char_type rank_to_char_table[alphabet_size]
    {
        '=',
        'A',
        'C',
        'M',
        'G',
        'R',
        'S',
        'V',
        'T',
        'W',
        'Y',
        'H',
        'K',
        'D',
        'B',
        'N'
    };
 
    static constexpr std::array<rank_type, 256> char_to_rank_table
    {
        [] () constexpr
        {
            std::array<rank_type, 256> ret{};
 
            // initialize with UNKNOWN (std::array::fill unfortunately not constexpr)
            for (auto & c : ret)
                c = 15; // rank of '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;
        }()
    };
 
    static constexpr rank_type rank_complement_table[alphabet_size]
    {
        15, // N is complement of '='_dna16sam  0
        8,  // T is complement of 'A'_dna16sam  1
        4,  // G is complement of 'C'_dna16sam  2
        12, // K is complement of 'M'_dna16sam  3
        2,  // C is complement of 'G'_dna16sam  4
        10, // Y is complement of 'R'_dna16sam  5
        6,  // S is complement of 'S'_dna16sam  6
        14, // B is complement of 'V'_dna16sam  7
        1,  // A is complement of 'T'_dna16sam  8
        9,  // W is complement of 'W'_dna16sam  9
        5,  // R is complement of 'Y'_dna16sam 10
        13, // D is complement of 'H'_dna16sam 11
        3,  // M is complement of 'K'_dna16sam 12
        11, // H is complement of 'D'_dna16sam 13
        7,  // V is complement of 'B'_dna16sam 14
        15  // N is complement of 'N'_dna16sam 15
    };
 
    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)];
    }
};
 
// ------------------------------------------------------------------
// containers
// ------------------------------------------------------------------
 
using dna16sam_vector = std::vector<dna16sam>;
 
#ifdef SEQAN3_DEPRECATED_310
using sam_dna16 SEQAN3_DEPRECATED_310 = seqan3::dna16sam;
 
using sam_dna16_vector SEQAN3_DEPRECATED_310 = dna16sam_vector;
#endif // SEQAN3_DEPRECATED_310
 
// ------------------------------------------------------------------
// literals
// ------------------------------------------------------------------
inline namespace literals
{
 
constexpr dna16sam operator""_dna16sam(char const c) noexcept
{
    return dna16sam{}.assign_char(c);
}
 
inline dna16sam_vector operator""_dna16sam(char const * s, size_t n)
{
    dna16sam_vector r;
    r.resize(n);
 
    for (size_t i = 0; i < n; ++i)
        r[i].assign_char(s[i]);
 
    return r;
}
 
#ifdef SEQAN3_DEPRECATED_310
SEQAN3_DEPRECATED_310 constexpr dna16sam operator""_sam_dna16(char const c) noexcept
{
    return seqan3::operator""_dna16sam(c);
}
 
SEQAN3_DEPRECATED_310 inline dna16sam_vector operator""_sam_dna16(char const * s, size_t n)
{
    return seqan3::operator""_dna16sam(s, n);
}
#endif // SEQAN3_DEPRECATED_310
 
} // inline namespace literals
 
} // namespace seqan3