qualified.hpp

Go to the documentation of this file.

// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2022 deCODE Genetics
// 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/biocpp/biocpp-core/blob/main/LICENSE.md
// -----------------------------------------------------------------------------------------------------
 
#pragma once
 
#include <bio/alphabet/composite/tuple_base.hpp>
#include <bio/alphabet/nucleotide/concept.hpp>
#include <bio/alphabet/quality/concept.hpp>
 
namespace bio::alphabet
{
 
template <writable_alphabet sequence_alphabet_t, writable_quality quality_alphabet_t>
class qualified :
  public tuple_base<qualified<sequence_alphabet_t, quality_alphabet_t>, sequence_alphabet_t, quality_alphabet_t>
{
private:
    using base_type =
      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  = char_t<sequence_alphabet_type>;
    using phred_type = 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::alphabet_size;
    using base_type::base_type; // non-default constructors
    using base_type::to_rank;
    using base_type::operator=;
 
    BIOCPP_DOXYGEN_ONLY((constexpr qualified(component_type const alph) noexcept {}))
    BIOCPP_DOXYGEN_ONLY((constexpr qualified(indirect_component_type const alph) noexcept {}))
    BIOCPP_DOXYGEN_ONLY((constexpr qualified & operator=(component_type const alph) noexcept {}))
    BIOCPP_DOXYGEN_ONLY((constexpr qualified & operator=(indirect_component_type const alph) noexcept {}))
 
    constexpr qualified & assign_char(char_type const c) noexcept
    {
        base_type::assign_rank((bio::alphabet::to_rank(bio::alphabet::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>(
        //     bio::alphabet::to_rank(bio::alphabet::assign_char_to(c, sequence_alphabet_type{})));
        return *this;
    }
 
    constexpr qualified & assign_phred(phred_type const c) noexcept
    {
        bio::alphabet::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<sequence_alphabet_t>
    {
        return qualified{bio::alphabet::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 constexpr std::array<char_type, alphabet_size> 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]) % bio::alphabet::size<quality_alphabet_type>;
 
            ret[i] = bio::alphabet::to_char(bio::alphabet::assign_rank_to(seq_rank, sequence_alphabet_type{}));
        }
 
        return ret;
    }();
 
    static constexpr std::array<char_type, alphabet_size> 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]) % bio::alphabet::size<quality_alphabet_type>;
 
            ret[i] = bio::alphabet::to_phred(bio::alphabet::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 bio::alphabet