align_pairwise.hpp

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// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2021, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2021, 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/std/concepts>
#include <functional>
#include <iostream>
#include <seqan3/std/ranges>
#include <tuple>
#include <type_traits>
 
#include <seqan3/alignment/pairwise/alignment_configurator.hpp>
#include <seqan3/alignment/pairwise/alignment_result.hpp>
#include <seqan3/alignment/pairwise/detail/concept.hpp>
#include <seqan3/alignment/pairwise/detail/type_traits.hpp>
#include <seqan3/core/algorithm/algorithm_result_generator_range.hpp>
#include <seqan3/core/algorithm/detail/algorithm_executor_blocking.hpp>
#include <seqan3/core/detail/persist_view.hpp>
#include <seqan3/utility/simd/simd_traits.hpp>
#include <seqan3/utility/simd/simd.hpp>
#include <seqan3/utility/type_traits/basic.hpp>
 
namespace seqan3
{
 
template <typename sequence_t, typename alignment_config_t>
    requires detail::align_pairwise_single_input<sequence_t> &&
             std::copy_constructible<std::remove_reference_t<sequence_t>> &&
             detail::is_type_specialisation_of_v<alignment_config_t, configuration>
constexpr auto align_pairwise(sequence_t && seq, alignment_config_t const & config)
{
    using std::get;
 
    if constexpr (std::is_lvalue_reference_v<sequence_t>)  // Forward tuple elements as references.
    {
        return align_pairwise(std::tie(get<0>(seq), get<1>(seq)), config);
    }
    else
    {
        static_assert(std::tuple_size_v<std::remove_reference_t<sequence_t>> == 2,
                      "Alignment configuration error: Expects exactly two sequences for pairwise alignments.");
 
        static_assert(std::ranges::viewable_range<std::tuple_element_t<0, std::remove_reference_t<sequence_t>>> &&
                      std::ranges::viewable_range<std::tuple_element_t<1, std::remove_reference_t<sequence_t>>>,
                      "Alignment configuration error: The tuple elements must model std::ranges::viewable_range.");
 
        return align_pairwise(std::views::single(std::forward<sequence_t>(seq)), config);
    }
}
 
template <typename sequence_t, typename alignment_config_t>
    requires detail::align_pairwise_range_input<sequence_t> &&
             detail::is_type_specialisation_of_v<alignment_config_t, configuration>
constexpr auto align_pairwise(sequence_t && sequences,
                              alignment_config_t const & config)
{
    using first_seq_t  = std::tuple_element_t<0, std::ranges::range_value_t<sequence_t>>;
    using second_seq_t = std::tuple_element_t<1, std::ranges::range_value_t<sequence_t>>;
 
    static_assert(std::ranges::random_access_range<first_seq_t> && std::ranges::sized_range<first_seq_t>,
                  "Alignment configuration error: The sequence must model random_access_range and sized_range.");
    static_assert(std::ranges::random_access_range<second_seq_t> && std::ranges::sized_range<second_seq_t>,
                  "Alignment configuration error: The sequence must model random_access_range and sized_range.");
 
    // Pipe with detail::persist to allow rvalue non-view ranges.
    auto seq_view = std::forward<sequence_t>(sequences) | detail::persist;
    // Configure the alignment algorithm.
    auto && [algorithm, complete_config] = detail::alignment_configurator::configure<decltype(seq_view)>(config);
 
    using complete_config_t = std::remove_cvref_t<decltype(complete_config)>;
    using traits_t = detail::alignment_configuration_traits<complete_config_t>;
 
    auto indexed_sequence_chunk_view = views::zip(seq_view, std::views::iota(0))
                                     | views::chunk(traits_t::alignments_per_vector);
 
    using indexed_sequences_t = decltype(indexed_sequence_chunk_view);
    using alignment_result_t = typename traits_t::alignment_result_type;
    using execution_handler_t = std::conditional_t<complete_config_t::template exists<align_cfg::parallel>(),
                                                   detail::execution_handler_parallel,
                                                   detail::execution_handler_sequential>;
    using executor_t = detail::algorithm_executor_blocking<indexed_sequences_t,
                                                           decltype(algorithm),
                                                           alignment_result_t,
                                                           execution_handler_t>;
 
    // Select the execution handler for the alignment configuration.
    auto select_execution_handler = [&] ()
    {
        if constexpr (std::same_as<execution_handler_t, detail::execution_handler_parallel>)
        {
            auto thread_count = get<align_cfg::parallel>(complete_config).thread_count;
            if (!thread_count)
                throw std::runtime_error{"You must configure the number of threads in seqan3::align_cfg::parallel."};
 
            return execution_handler_t{*thread_count};
        }
        else
        {
            return execution_handler_t{};
        }
    };
 
    if constexpr (traits_t::is_one_way_execution) // Just compute alignment and wait until all alignments are computed.
        select_execution_handler().bulk_execute(algorithm,
                                                indexed_sequence_chunk_view,
                                                get<align_cfg::on_result>(complete_config).callback);
    else  // Require two way execution: return the range over the alignments.
        return algorithm_result_generator_range{executor_t{std::move(indexed_sequence_chunk_view),
                                                std::move(algorithm),
                                                alignment_result_t{},
                                                select_execution_handler()}};
}
 
} // namespace seqan3