alignment_score_matrix_one_column_base.hpp

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// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2022, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2022, 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 <array>
#include <utility>
#include <vector>
 
#include <seqan3/utility/concept.hpp>
#include <seqan3/utility/container/aligned_allocator.hpp>
#include <seqan3/utility/simd/concept.hpp>
 
namespace seqan3::detail
{
 
template <typename score_t>
struct alignment_score_matrix_one_column_base
{
protected:
    static_assert(arithmetic<score_t> || simd_concept<score_t>,
                  "Score type must either be either an arithmetic type or a simd vector type.");
 
    using underlying_type = score_t;
    using element_type = std::tuple<underlying_type, underlying_type>;
    using allocator_type = aligned_allocator<element_type, sizeof(element_type)>;
    using pool_type = std::vector<element_type, allocator_type>;
    using size_type = size_t;
 
public:
    pool_type pool{};
    std::array<underlying_type, 3> cache{}; // Third argument is used to cache next diagonal value in non-banded case.
    size_type num_cols{};
    size_type num_rows{};
};
 
} // namespace seqan3::detail