add_reverse_complement.hpp

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// -----------------------------------------------------------------------------------------------------
// 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 <ranges>
 
#include <bio/alphabet/nucleotide/concept.hpp>
#include <bio/ranges/views/deep.hpp>
#include <bio/ranges/views/transform_by_pos.hpp>
 
// ============================================================================
//  reverse_complement_or_not_fn (adaptor definition)
// ============================================================================
 
namespace bio::ranges::detail
{
 
struct reverse_complement_or_not_fn
{
private:
    static auto func_nop(auto && urange, size_t pos) { return urange[pos]; }
 
    static auto func_revcomp(auto && urange, size_t pos)
    {
        return bio::alphabet::complement(urange[std::ranges::size(urange) - pos - 1]);
    }
 
public:
    constexpr auto operator()(bool const transform) const { return detail::adaptor_from_functor{*this, transform}; }
 
    template <std::ranges::range urng_t>
    constexpr auto operator()(urng_t && urange, bool const transform) const
    {
        static_assert(std::ranges::viewable_range<urng_t>,
                      "The range parameter to views::reverse_complement_or_not cannot be a temporary of a non-view "
                      "range.");
        static_assert(std::ranges::sized_range<urng_t>,
                      "The range parameter to views::reverse_complement_or_not must model std::ranges::sized_range.");
        static_assert(std::ranges::random_access_range<urng_t>,
                      "The range parameter to views::reverse_complement_or_not must model "
                      "std::ranges::random_access_range.");
        static_assert(alphabet::nucleotide<std::ranges::range_reference_t<urng_t>>,
                      "The range parameter to views::reverse_complement_or_not must be over elements of "
                      "bio::alphabet::nucleotide.");
 
        auto l = &func_nop<std::views::all_t<urng_t> const &>;
        if (transform)
            l = &func_revcomp<std::views::all_t<urng_t> const &>;
        return std::forward<urng_t>(urange) | views::transform_by_pos(l);
    }
};
 
// ============================================================================
//  reverse_complement_or_not (adaptor object)
// ============================================================================
 
inline constexpr auto reverse_complement_or_not = views::deep{reverse_complement_or_not_fn{}};
 
// ============================================================================
//  add_reverse_complement_fn (adaptor definition)
// ============================================================================
 
class add_reverse_complement_fn : public detail::adaptor_base<add_reverse_complement_fn>
{
private:
    using base_type = detail::adaptor_base<add_reverse_complement_fn>;
 
    friend base_type;
 
    template <std::ranges::range urng_t>
    static auto impl(urng_t && urange)
    {
        static_assert(range_dimension_v<urng_t> == 2,
                      "This adaptor only handles range-of-range (two dimensions) as input.");
        static_assert(std::ranges::viewable_range<urng_t>,
                      "The range parameter to views::add_reverse_complement cannot be a temporary of a non-view "
                      "range.");
        static_assert(std::ranges::viewable_range<std::ranges::range_reference_t<urng_t>>,
                      "The inner range of the range parameter to views::add_reverse_complement cannot be a temporary "
                      "of "
                      "a non-view range.");
        static_assert(std::ranges::sized_range<urng_t>,
                      "The range parameter to views::add_reverse_complement must model std::ranges::sized_range.");
        static_assert(std::ranges::sized_range<std::ranges::range_reference_t<urng_t>>,
                      "The inner range of the range parameter to views::add_reverse_complement must model "
                      "std::ranges::sized_range.");
        static_assert(std::ranges::random_access_range<urng_t>,
                      "The range parameter to views::add_reverse_complement must model "
                      "std::ranges::random_access_range.");
        static_assert(std::ranges::random_access_range<std::ranges::range_reference_t<urng_t>>,
                      "The inner range of the range parameter to views::add_reverse_complement must model "
                      "std::ranges::random_access_range.");
        static_assert(alphabet::nucleotide<std::ranges::range_reference_t<std::ranges::range_reference_t<urng_t>>>,
                      "The range parameter to views::add_reverse_complement must be over elements of "
                      "bio::alphabet::nucleotide.");
 
        return std::forward<urng_t>(urange) |
               views::transform_by_pos([](auto && urange, size_t pos)
                                       { return urange[pos / 2] | reverse_complement_or_not(pos % 2 == 1); },
                                       [](auto && urange) { return std::ranges::size(urange) * 2; });
    }
 
public:
    constexpr add_reverse_complement_fn()                                                       = default;
    constexpr add_reverse_complement_fn(add_reverse_complement_fn const &) noexcept             = default;
    constexpr add_reverse_complement_fn(add_reverse_complement_fn &&) noexcept                  = default;
    constexpr add_reverse_complement_fn & operator=(add_reverse_complement_fn const &) noexcept = default;
    constexpr add_reverse_complement_fn & operator=(add_reverse_complement_fn &&) noexcept      = default;
    ~add_reverse_complement_fn() noexcept                                                       = default;
 
    using base_type::base_type;
};
 
} // namespace bio::ranges::detail
 
// ============================================================================
//  add_reverse_complement (adaptor object)
// ============================================================================
 
namespace bio::ranges::views
{
 
inline constexpr auto add_reverse_complement = detail::add_reverse_complement_fn{};
 
} // namespace bio::ranges::views