Loading...
Searching...
No Matches
alignment_trace_matrix_base.hpp
Go to the documentation of this file.
// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: BSD-3-Clause
#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
advanceable_alignment_coordinate.hpp
Provides seqan3::detail::advanceable_alignment_coordinate.
aligned_allocator.hpp
Provides seqan3::aligned_allocator.
trace_directions.hpp
Provides the declaration of seqan3::detail::trace_directions.
two_dimensional_matrix.hpp
Provides seqan3::detail::two_dimensional_matrix.
vector
Hide me