alignment_trace_matrix_base.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 <vector>
 
#include <seqan3/alignment/matrix/detail/advanceable_alignment_coordinate.hpp>
#include <seqan3/alignment/matrix/detail/trace_directions.hpp>
#include <seqan3/alignment/matrix/detail/two_dimensional_matrix.hpp>
#include <seqan3/utility/container/aligned_allocator.hpp>
#include <seqan3/utility/simd/concept.hpp>
 
namespace seqan3::detail
{
 
template <typename trace_t>
struct alignment_trace_matrix_base
{
protected:
    static_assert(std::same_as<trace_t, trace_directions> || simd_concept<trace_t>,
                  "Value type must either be a trace_directions object or a simd vector.");
 
    using coordinate_type = advanceable_alignment_coordinate<advanceable_alignment_coordinate_state::row>;
    using element_type = trace_t;
    using allocator_type = std::conditional_t<detail::simd_concept<trace_t>,
                                              aligned_allocator<element_type, sizeof(element_type)>,
                                              std::allocator<element_type>>;
    using pool_type = two_dimensional_matrix<element_type, allocator_type, matrix_major_order::column>;
    using size_type = size_t;
 
public:
    pool_type data{};
    std::vector<element_type, allocator_type> cache_left{};
    element_type cache_up{};
    size_type num_cols{};
    size_type num_rows{};
};
 
} // namespace seqan3::detail