type_traits.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 <seqan3/alignment/configuration/all.hpp>
#include <seqan3/alignment/matrix/trace_directions.hpp>
#include <seqan3/alignment/pairwise/detail/concept.hpp>
#include <seqan3/core/algorithm/configuration.hpp>
#include <seqan3/core/bit_manipulation.hpp>
#include <seqan3/core/simd/simd_traits.hpp>
#include <seqan3/core/simd/simd.hpp>
#include <seqan3/core/type_traits/template_inspection.hpp>
#include <seqan3/range/views/chunk.hpp>
#include <seqan3/range/views/zip.hpp>
#include <seqan3/std/ranges>
 
namespace seqan3::detail
{
 
template <typename sequence_pairs_t>
    requires sequence_pair_range<std::remove_reference_t<sequence_pairs_t>>
struct chunked_indexed_sequence_pairs
{
    using type = decltype(views::zip(std::declval<sequence_pairs_t>(), std::views::iota(0)) | views::chunk(1));
};
 
template <typename config_t>
    requires is_type_specialisation_of_v<config_t, configuration>
struct alignment_configuration_traits
{
    static constexpr bool is_vectorised = config_t::template exists<remove_cvref_t<decltype(align_cfg::vectorise)>>();
    static constexpr bool is_parallel = config_t::template exists<align_cfg::parallel>();
    static constexpr bool is_global = config_t::template exists<align_cfg::mode<detail::global_alignment_type>>();
    static constexpr bool is_aligned_ends = config_t::template exists<align_cfg::aligned_ends>();
    static constexpr bool is_local = config_t::template exists<align_cfg::mode<detail::local_alignment_type>>();
    static constexpr bool is_banded = config_t::template exists<align_cfg::band>();
    static constexpr bool is_debug = config_t::template exists<detail::debug_mode>();
 
    using alignment_mode_t = decltype(get<align_cfg::mode>(std::declval<config_t>()).value);
    using scoring_scheme_t = decltype(get<align_cfg::scoring>(std::declval<config_t>()).value);
    using scoring_scheme_alphabet_t = typename scoring_scheme_t::alphabet_type;
    using result_t = std::remove_reference_t<decltype(seqan3::get<align_cfg::result>(std::declval<config_t>()))>;
    using original_score_t = typename result_t::score_type;
    using score_t = std::conditional_t<is_vectorised, simd_type_t<original_score_t>, original_score_t>;
    using trace_t = std::conditional_t<is_vectorised, simd_type_t<original_score_t>, trace_directions>;
 
    static constexpr size_t alignments_per_vector = [] () constexpr
                                                    {
                                                        if constexpr (is_vectorised)
                                                            return simd_traits<score_t>::length;
                                                        else
                                                            return 1;
                                                    }();
    static constexpr int8_t result_type_rank = static_cast<int8_t>(decltype(std::declval<result_t>().value)::rank);
    static constexpr original_score_t padding_symbol =
        static_cast<original_score_t>(1u << (sizeof_bits<original_score_t> - 1));
};
 
}  // namespace seqan3::detail