quality_base.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 <seqan3/alphabet/alphabet_base.hpp>
#include <seqan3/alphabet/detail/convert.hpp>
#include <seqan3/alphabet/quality/concept.hpp>

namespace seqan3
{

template <typename derived_type, auto size>
class quality_base : public alphabet_base<derived_type, size, char>
{
public:
    using phred_type = int8_t;

private:
    using base_t = alphabet_base<derived_type, size, char>;

    constexpr quality_base()                                  noexcept = default; 
    constexpr quality_base(quality_base const &)              noexcept = default; 
    constexpr quality_base(quality_base &&)                   noexcept = default; 
    constexpr quality_base & operator=(quality_base const &)  noexcept = default; 
    constexpr quality_base & operator=(quality_base &&)       noexcept = default; 
    ~quality_base()                                           noexcept = default; 

    constexpr quality_base(phred_type const p) noexcept
    {
        static_cast<derived_type *>(this)->assign_phred(p);
    }

    friend derived_type;

public:
    // Import from base type:
    using base_t::alphabet_size;
    using base_t::to_rank;
    using base_t::assign_rank;
    using typename base_t::char_type;
    using typename base_t::rank_type;

    // This constructor needs to be public, because constructor templates are not inherited otherwise
    template <typename other_qual_type>
        requires !std::Same<quality_base, other_qual_type> &&
                 !std::Same<derived_type, other_qual_type> &&
                 QualityAlphabet<other_qual_type>
    explicit constexpr quality_base(other_qual_type const & other) noexcept
    {
        assign_phred_to(seqan3::to_phred(other), static_cast<derived_type &>(*this));
    }

    constexpr char_type to_char() const noexcept
    {
        return static_cast<char_type>(to_rank()) + derived_type::offset_char;
    }

    constexpr phred_type to_phred() const noexcept
    {
        return static_cast<phred_type>(to_rank()) + derived_type::offset_phred;
    }

    constexpr derived_type & assign_phred(phred_type const p) noexcept
    {
        return assign_rank(phred_to_rank[static_cast<rank_type>(p)]);
    }

protected:
    static std::array<rank_type, 256> constexpr phred_to_rank
    {
        [] () constexpr
        {
            std::array<rank_type, 256> ret{};

            for (int64_t i = std::numeric_limits<phred_type>::lowest(); i <= std::numeric_limits<phred_type>::max(); ++i)
            {
                if (i < derived_type::offset_phred)                     // map too-small to smallest possible
                    ret[static_cast<rank_type>(i)] = 0;
                else if (i >= derived_type::offset_phred + alphabet_size)  // map too-large to highest possible
                    ret[static_cast<rank_type>(i)] = alphabet_size - 1;
                else                                                    // map valid range to identity
                    ret[static_cast<rank_type>(i)] = i - derived_type::offset_phred;
            }
            return ret;
        }()
    };

    static std::array<rank_type, 256> constexpr char_to_rank
    {
        [] () constexpr
        {
            std::array<rank_type, 256> ret{};

            for (int64_t i = std::numeric_limits<char_type>::lowest(); i <= std::numeric_limits<char_type>::max(); ++i)
            {
                if (i < derived_type::offset_char)                     // map too-small to smallest possible
                    ret[static_cast<rank_type>(i)] = 0;
                else if (i >= derived_type::offset_char + alphabet_size)  // map too-large to highest possible
                    ret[static_cast<rank_type>(i)] = alphabet_size - 1;
                else                                                   // map valid range to identity
                    ret[static_cast<rank_type>(i)] = i - derived_type::offset_char;
            }

            return ret;
        }()
    };
};

} // namespace seqan3