qualified.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 <iostream>
#include <string>
#include <utility>

#include <seqan3/alphabet/composite/alphabet_tuple_base.hpp>
#include <seqan3/alphabet/nucleotide/concept.hpp>

namespace seqan3
{

template <WritableAlphabet sequence_alphabet_t, WritableQualityAlphabet 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; 

    using base_type::base_type; // Inherit non-default constructors

    // Inherit operators from base
    using base_type::operator=;
    using base_type::operator==;
    using base_type::operator!=;
    using base_type::operator>=;
    using base_type::operator<=;
    using base_type::operator<;
    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
    {
        seqan3::assign_char_to(c, get<0>(*this));
        return *this;
    }

    qualified & assign_char_strictly(char_type const c)
    {
        seqan3::assign_char_strictly_to(c, get<0>(*this));
        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 seqan3::to_phred(get<1>(*this));
    }

    constexpr char_type to_char() const noexcept
    {
        return seqan3::to_char(get<0>(*this));
    }

    constexpr qualified complement() const noexcept
        requires NucleotideAlphabet<sequence_alphabet_t>
    {
        using seqan3::complement;
        return qualified{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);
    }
};

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