qualified.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/composite/alphabet_tuple_base.hpp>
#include <seqan3/alphabet/nucleotide/concept.hpp>
 
namespace seqan3
{
 
template <writable_alphabet sequence_alphabet_t, writable_quality_alphabet quality_alphabet_t>
class qualified :
    public alphabet_tuple_base<qualified<sequence_alphabet_t, quality_alphabet_t>,
                                 sequence_alphabet_t, quality_alphabet_t>
{
private:
    using base_type = alphabet_tuple_base<qualified<sequence_alphabet_t, quality_alphabet_t>,
                                            sequence_alphabet_t, quality_alphabet_t>;
 
public:
    using sequence_alphabet_type = sequence_alphabet_t;
    using quality_alphabet_type = quality_alphabet_t;
 
    using char_type = alphabet_char_t<sequence_alphabet_type>;
    using phred_type = alphabet_phred_t<quality_alphabet_type>;
 
    constexpr qualified()                               noexcept = default; 
    constexpr qualified(qualified const &)              noexcept = default; 
    constexpr qualified(qualified &&)                   noexcept = default; 
    constexpr qualified & operator =(qualified const &) noexcept = default; 
    constexpr qualified & operator =(qualified &&)      noexcept = default; 
    ~qualified()                                        noexcept = default; 
 
    // Inherit from base:
    using base_type::base_type;         // non-default constructors
    using base_type::alphabet_size;
    using base_type::to_rank;
    using base_type::operator=;
 
    SEQAN3_DOXYGEN_ONLY(( constexpr qualified(component_type const alph) noexcept {} ))
    SEQAN3_DOXYGEN_ONLY(( constexpr qualified(indirect_component_type const alph) noexcept {} ))
    SEQAN3_DOXYGEN_ONLY(( constexpr qualified & operator=(component_type const alph) noexcept {} ))
    SEQAN3_DOXYGEN_ONLY(( constexpr qualified & operator=(indirect_component_type const alph) noexcept {} ))
 
    constexpr qualified & assign_char(char_type const c) noexcept
    {
        base_type::assign_rank(
            (seqan3::to_rank(seqan3::assign_char_to(c, sequence_alphabet_type{})) *
             base_type::cummulative_alph_sizes[0]) +
            (base_type::template to_component_rank<1>() * base_type::cummulative_alph_sizes[1]));
 
        // The above is noticeably faster than (no subtraction and no division):
        // base_type::template assign_component_rank<0>(
        //     seqan3::to_rank(seqan3::assign_char_to(c, sequence_alphabet_type{})));
        return *this;
    }
 
    constexpr qualified & assign_phred(phred_type const c) noexcept
    {
        seqan3::assign_phred_to(c, get<1>(*this));
        return *this;
    }
 
    constexpr phred_type to_phred() const noexcept
    {
        return rank_to_phred[to_rank()];
    }
 
    constexpr char_type to_char() const noexcept
    {
        return rank_to_char[to_rank()];
    }
 
    constexpr qualified complement() const noexcept
        requires nucleotide_alphabet<sequence_alphabet_t>
    {
        return qualified{seqan3::complement(get<0>(*this)), get<1>(*this)};
    }
 
    static constexpr bool char_is_valid(char_type const c) noexcept
    {
        return char_is_valid_for<sequence_alphabet_type>(c);
    }
 
protected:
 
    static std::array<char_type, alphabet_size> constexpr rank_to_char
    {
        [] () constexpr
        {
            std::array<char_type, alphabet_size> ret{};
 
            for (size_t i = 0; i < alphabet_size; ++i)
            {
                size_t seq_rank = (i / base_type::cummulative_alph_sizes[0]) %
                                  seqan3::alphabet_size<quality_alphabet_type>;
 
                ret[i] = seqan3::to_char(seqan3::assign_rank_to(seq_rank, sequence_alphabet_type{}));
            }
 
            return ret;
        }()
    };
 
    static std::array<char_type, alphabet_size> constexpr rank_to_phred
    {
        [] () constexpr
        {
            std::array<char_type, alphabet_size> ret{};
 
            for (size_t i = 0; i < alphabet_size; ++i)
            {
                size_t qual_rank = (i / base_type::cummulative_alph_sizes[1]) %
                                    seqan3::alphabet_size<quality_alphabet_type>;
 
                ret[i] = seqan3::to_phred(seqan3::assign_rank_to(qual_rank, quality_alphabet_type{}));
            }
 
            return ret;
        }()
    };
};
 
template <typename sequence_alphabet_type, typename quality_alphabet_type>
qualified(sequence_alphabet_type &&, quality_alphabet_type &&)
    -> qualified<std::decay_t<sequence_alphabet_type>, std::decay_t<quality_alphabet_type>>;
 
} // namespace seqan3