qualified.hpp

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// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: BSD-3-Clause
 
#pragma once
 
#include <seqan3/alphabet/composite/alphabet_tuple_base.hpp>
#include <seqan3/alphabet/nucleotide/concept.hpp>
#include <seqan3/alphabet/quality/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::alphabet_size;
    using base_type::base_type; // non-default constructors
    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_char(char_type const c) noexcept {…}
 
    constexpr qualified & assign_phred(phred_type const c) noexcept
    {
        seqan3::assign_phred_to(c, get<1>(*this));
        return *this;
    }
    constexpr qualified & assign_phred(phred_type const c) noexcept {…}
 
    constexpr phred_type to_phred() const noexcept
    {
        return rank_to_phred[to_rank()];
    }
    constexpr phred_type to_phred() const noexcept {…}
 
    constexpr char_type to_char() const noexcept
    {
        return rank_to_char(to_rank());
    }
    constexpr char_type to_char() const noexcept {…}
 
    constexpr qualified complement() const noexcept
        requires nucleotide_alphabet<sequence_alphabet_t>
    {
        return qualified{seqan3::complement(get<0>(*this)), get<1>(*this)};
    }
    constexpr qualified complement() const noexcept {…}
 
    static constexpr bool char_is_valid(char_type const c) noexcept
    {
        return char_is_valid_for<sequence_alphabet_type>(c);
    }
    static constexpr bool char_is_valid(char_type const c) noexcept {…}
 
private:
    static constexpr char_type rank_to_char(typename base_type::rank_type const rank)
    {
        return rank_to_char_table[rank];
    }
 
    static constexpr std::array<char_type, alphabet_size> rank_to_char_table{
        []() constexpr
        {
            std::array<char_type, alphabet_size> ret{};
 
            for (size_t i = 0; i < alphabet_size; ++i)
            {
                size_t const 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 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]) % seqan3::alphabet_size<quality_alphabet_type>;
 
                ret[i] = seqan3::to_phred(seqan3::assign_rank_to(qual_rank, quality_alphabet_type{}));
            }
 
            return ret;
        }()};
};
class qualified : {…};
 
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