sam_dna16.hpp

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// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2020, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2020, 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 sam_dna16 : public nucleotide_base<sam_dna16, 16>
{
private:
    using base_t = nucleotide_base<sam_dna16, 16>;
 
    friend base_t;
    friend base_t::base_t;
 
public:
    constexpr sam_dna16()                              noexcept = default; 
    constexpr sam_dna16(sam_dna16 const &)             noexcept = default; 
    constexpr sam_dna16(sam_dna16 &&)                  noexcept = default; 
    constexpr sam_dna16 & operator=(sam_dna16 const &) noexcept = default; 
    constexpr sam_dna16 & operator=(sam_dna16 &&)      noexcept = default; 
    ~sam_dna16()                                       noexcept = default; 
 
    using base_t::base_t;
 
protected:
 
    static constexpr char_type rank_to_char[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
    {
        [] () 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[rnk] ] = rnk;
                ret[to_lower(rank_to_char[rnk])] = rnk;
            }
 
            // set U equal to T
            ret['U'] = ret['T']; ret['u'] = ret['t'];
 
            return ret;
        }()
    };
 
    static const std::array<sam_dna16, alphabet_size> complement_table;
};
 
// ------------------------------------------------------------------
// containers
// ------------------------------------------------------------------
 
using sam_dna16_vector = std::vector<sam_dna16>;
 
// ------------------------------------------------------------------
// literals
// ------------------------------------------------------------------
 
constexpr sam_dna16 operator""_sam_dna16(char const c) noexcept
{
    return sam_dna16{}.assign_char(c);
}
 
inline sam_dna16_vector operator""_sam_dna16(char const * s, size_t n)
{
    sam_dna16_vector r;
    r.resize(n);
 
    for (size_t i = 0; i < n; ++i)
        r[i].assign_char(s[i]);
 
    return r;
}
 
// ------------------------------------------------------------------
// complement deferred definition
// ------------------------------------------------------------------
 
constexpr std::array<sam_dna16, sam_dna16::alphabet_size> sam_dna16::complement_table
{
    'N'_sam_dna16,    // complement of '='_sam_dna16
    'T'_sam_dna16,    // complement of 'A'_sam_dna16
    'G'_sam_dna16,    // complement of 'C'_sam_dna16
    'K'_sam_dna16,    // complement of 'M'_sam_dna16
    'C'_sam_dna16,    // complement of 'G'_sam_dna16
    'Y'_sam_dna16,    // complement of 'R'_sam_dna16
    'S'_sam_dna16,    // complement of 'S'_sam_dna16
    'B'_sam_dna16,    // complement of 'V'_sam_dna16
    'A'_sam_dna16,    // complement of 'T'_sam_dna16
    'W'_sam_dna16,    // complement of 'W'_sam_dna16
    'R'_sam_dna16,    // complement of 'Y'_sam_dna16
    'D'_sam_dna16,    // complement of 'H'_sam_dna16
    'M'_sam_dna16,    // complement of 'K'_sam_dna16
    'H'_sam_dna16,    // complement of 'D'_sam_dna16
    'V'_sam_dna16,    // complement of 'B'_sam_dna16
    'N'_sam_dna16     // complement of 'N'_sam_dna16
};
 
} // namespace seqan3