align_pairwise.hpp

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// -----------------------------------------------------------------------------------------------------
// 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/seqan/seqan3/blob/master/LICENSE.md
// -----------------------------------------------------------------------------------------------------
 
#pragma once
 
#include <functional>
#include <iostream>
#include <tuple>
#include <type_traits>
 
#include <meta/meta.hpp>
 
#include <seqan3/alignment/configuration/all.hpp>
#include <seqan3/alignment/pairwise/alignment_result.hpp>
#include <seqan3/alignment/pairwise/alignment_configurator.hpp>
#include <seqan3/alignment/pairwise/detail/concept.hpp>
#include <seqan3/alignment/pairwise/detail/type_traits.hpp>
#include <seqan3/alignment/pairwise/execution/all.hpp>
#include <seqan3/core/algorithm/all.hpp>
#include <seqan3/core/parallel/execution.hpp>
#include <seqan3/core/simd/simd_traits.hpp>
#include <seqan3/core/simd/simd.hpp>
#include <seqan3/core/type_traits/basic.hpp>
#include <seqan3/range/views/persist.hpp>
#include <seqan3/std/concepts>
#include <seqan3/std/ranges>
 
namespace seqan3
{
 
template <typename sequence_t, typename alignment_config_t>
    requires detail::align_pairwise_single_input<std::remove_reference_t<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)
{
    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 views::persist to allow rvalue non-view ranges.
    auto seq_view = std::forward<sequence_t>(sequences) | views::persist;
    // Configure the alignment algorithm.
    auto && [algorithm, adapted_config] = detail::alignment_configurator::configure<decltype(seq_view)>(config);
 
    using traits_t = detail::alignment_configuration_traits<remove_cvref_t<decltype(adapted_config)>>;
    constexpr auto get_execution_rule = [] ()
    {
        if constexpr (traits_t::is_parallel)
            return seqan3::par;
        else
            return seqan3::seq;
    };
 
    // Create a two-way executor for the alignment.
    detail::alignment_executor_two_way executor{std::move(seq_view),
                                                std::move(algorithm),
                                                traits_t::alignments_per_vector,
                                                get_execution_rule()};
    // Return the range over the alignments.
    return alignment_range{std::move(executor)};
}
 
} // namespace seqan3