alignment_score_matrix_one_column.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/matrix/detail/alignment_matrix_column_major_range_base.hpp>
#include <seqan3/alignment/matrix/detail/alignment_score_matrix_one_column_base.hpp>
#include <seqan3/alignment/matrix/detail/alignment_score_matrix_proxy.hpp>
#include <seqan3/core/concept/core_language.hpp>
#include <seqan3/core/simd/concept.hpp>
#include <seqan3/std/iterator>
#include <seqan3/std/ranges>
#include <seqan3/std/span>
 
namespace seqan3::detail
{
 
template <typename score_t>
class alignment_score_matrix_one_column :
    protected alignment_score_matrix_one_column_base<score_t>,
    public alignment_matrix_column_major_range_base<alignment_score_matrix_one_column<score_t>>
{
private:
    static_assert(arithmetic<score_t> || simd_concept<score_t>,
                  "The score type must be either an arithmetic type or a simd vector type.");
    using matrix_base_t = alignment_score_matrix_one_column_base<score_t>;
    using range_base_t = alignment_matrix_column_major_range_base<alignment_score_matrix_one_column<score_t>>;
 
    friend range_base_t;
 
protected:
    using typename matrix_base_t::element_type;
    using typename range_base_t::alignment_column_type;
    using column_data_view_type = std::span<element_type>;
 
    using matrix_base_t::num_cols;
 
public:
    using value_type = alignment_score_matrix_proxy<score_t>;
    using reference = value_type;
    using iterator = typename range_base_t::iterator;
    using sentinel = typename range_base_t::sentinel;
    using typename matrix_base_t::size_type;
    using typename matrix_base_t::underlying_type;
 
    constexpr alignment_score_matrix_one_column() = default;
    constexpr alignment_score_matrix_one_column(alignment_score_matrix_one_column const &) = default;
    constexpr alignment_score_matrix_one_column(alignment_score_matrix_one_column &&) = default;
    constexpr alignment_score_matrix_one_column & operator=(alignment_score_matrix_one_column const &) = default;
    constexpr alignment_score_matrix_one_column & operator=(alignment_score_matrix_one_column &&) = default;
    ~alignment_score_matrix_one_column() = default;
 
    template <std::ranges::forward_range first_sequence_t, std::ranges::forward_range second_sequence_t>
    constexpr alignment_score_matrix_one_column(first_sequence_t && first,
                                                second_sequence_t && second,
                                                score_t const initial_value = score_t{})
    {
        matrix_base_t::num_cols = static_cast<size_type>(std::ranges::distance(first) + 1);
        matrix_base_t::num_rows = static_cast<size_type>(std::ranges::distance(second) + 1);
        matrix_base_t::pool.resize(matrix_base_t::num_rows + 1, element_type{initial_value, initial_value});
    }
 
private:
    constexpr alignment_column_type initialise_column(size_type const SEQAN3_DOXYGEN_ONLY(column_index)) noexcept
    {
        return alignment_column_type{*this,
                                     column_data_view_type{std::addressof(matrix_base_t::pool[0]),
                                                           matrix_base_t::num_rows}};
    }
 
    template <std::random_access_iterator iter_t>
    constexpr value_type make_proxy(iter_t host_iter) noexcept
    {
        return {std::get<0>(*host_iter),            // current
                std::get<0>(matrix_base_t::cache),  // last diagonal
                std::get<1>(*host_iter),            // last left (read)
                std::get<1>(*host_iter),            // next left (write)
                std::get<2>(matrix_base_t::cache)}; // last up
    }
 
    template <std::random_access_iterator iter_t>
    constexpr void on_column_iterator_creation(iter_t host_iter) noexcept
    {
        // Cache the next diagonal value.
        std::get<1>(matrix_base_t::cache) = std::get<0>(*host_iter);
    }
 
    template <std::random_access_iterator iter_t>
    constexpr void before_column_iterator_increment(iter_t SEQAN3_DOXYGEN_ONLY(host_iter)) noexcept
    {
        // Update the last diagonal value.
        std::get<0>(matrix_base_t::cache) = std::move(std::get<1>(matrix_base_t::cache));
    }
 
    template <std::random_access_iterator iter_t>
    constexpr void after_column_iterator_increment(iter_t host_iter) noexcept
    {
        // Cache the next diagonal value.
        std::get<1>(matrix_base_t::cache) = std::move(std::get<0>(*host_iter));
    }
};
 
} // namespace seqan3::detail