aa20.hpp

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// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2019, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2019, 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 <vector>

#include <seqan3/alphabet/aminoacid/aminoacid_base.hpp>
#include <seqan3/alphabet/aminoacid/concept.hpp>
#include <seqan3/core/char_operations/transform.hpp>

namespace seqan3
{

class aa20 : public aminoacid_base<aa20, 20>
{
private:
    using base_t = aminoacid_base<aa20, 20>;

    friend base_t;
    friend base_t::base_t;

public:
    constexpr aa20()                         noexcept = default; 
    constexpr aa20(aa20 const &)             noexcept = default; 
    constexpr aa20(aa20 &&)                  noexcept = default; 
    constexpr aa20 & operator=(aa20 const &) noexcept = default; 
    constexpr aa20 & operator=(aa20 &&)      noexcept = default; 
    ~aa20()                                  noexcept = default; 

    using base_t::base_t;

protected:
    static constexpr char_type rank_to_char[alphabet_size]
    {
        'A',
        'C',
        'D',
        'E',
        'F',
        'G',
        'H',
        'I',
        'K',
        'L',
        'M',
        'N',
        'P',
        'Q',
        'R',
        'S',
        'T',
        'V',
        'W',
        'Y',
    };

    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; // value of 'S', because that appears most frequently

            // reverse mapping for characters and their lowercase
            for (rank_type rnk = 0u; rnk < alphabet_size; ++rnk)
            {
                ret[static_cast<rank_type>(         rank_to_char[rnk]) ] = rnk;
                ret[static_cast<rank_type>(to_lower(rank_to_char[rnk]))] = rnk;
            }

            ret['B'] = ret['D']; ret['b'] = ret['D']; // Convert b (either D/N) to D, since D occurs more frequently.
            ret['J'] = ret['L']; ret['j'] = ret['L']; // Convert j (either I/L) to L, since L occurs more frequently.
            ret['O'] = ret['L']; ret['o'] = ret['L']; // Convert Pyrrolysine to lysine.
            ret['U'] = ret['C']; ret['u'] = ret['C']; // Convert Selenocysteine to cysteine.
            ret['X'] = ret['S']; ret['x'] = ret['S']; // Convert unknown amino acids to serine.
            ret['Z'] = ret['E']; ret['z'] = ret['E']; // Convert z (either E/Q) to E, since E occurs more frequently.
            ret['*'] = ret['W']; // The most common stop codon is UGA. This is most similar to a Tryptophan.
            return ret;
        }()
    };
};

} // namespace seqan3

// ------------------------------------------------------------------
// type traits
// ------------------------------------------------------------------

namespace seqan3
{

template <>
struct is_aminoacid<aa20> : std::true_type {};

} // namespace seqan3

// ------------------------------------------------------------------
// containers
// ------------------------------------------------------------------

namespace seqan3
{
using aa20_vector = std::vector<aa20>;

} // namespace seqan3

// ------------------------------------------------------------------
// literals
// ------------------------------------------------------------------

namespace seqan3
{

constexpr aa20 operator""_aa20(char const c) noexcept
{
    return aa20{}.assign_char(c);
}

inline aa20_vector operator""_aa20(const char * s, std::size_t n)
{
    aa20_vector r;
    r.resize(n);

    for (size_t i = 0; i < n; ++i)
        r[i].assign_char(s[i]);

    return r;
}

} // namespace seqan3