alignment_score_matrix_one_column_banded.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 <cassert>
#include <iterator>
#include <ranges>
#include <span>
 
#include <seqan3/alignment/configuration/align_config_band.hpp>
#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>
 
namespace seqan3::detail
{
 
template <typename score_t>
class alignment_score_matrix_one_column_banded :
    protected alignment_score_matrix_one_column_base<score_t>,
    public alignment_matrix_column_major_range_base<alignment_score_matrix_one_column_banded<score_t>>
{
private:
    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_banded<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>;
 
public:
    using matrix_base_t::num_cols;
    using matrix_base_t::num_rows;
 
    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_banded() = default;
    constexpr alignment_score_matrix_one_column_banded(alignment_score_matrix_one_column_banded const &) = default;
    constexpr alignment_score_matrix_one_column_banded(alignment_score_matrix_one_column_banded &&) = default;
    constexpr alignment_score_matrix_one_column_banded &
    operator=(alignment_score_matrix_one_column_banded const &) = default;
    constexpr alignment_score_matrix_one_column_banded &
    operator=(alignment_score_matrix_one_column_banded &&) = default;
    ~alignment_score_matrix_one_column_banded() = default;
 
    template <std::ranges::forward_range first_sequence_t, std::ranges::forward_range second_sequence_t>
    constexpr alignment_score_matrix_one_column_banded(first_sequence_t && first,
                                                       second_sequence_t && second,
                                                       align_cfg::band_fixed_size const & band,
                                                       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);
 
        band_col_index = std::min<int32_t>(std::max<int32_t>(band.upper_diagonal, 0), matrix_base_t::num_cols - 1);
        band_row_index =
            std::min<int32_t>(std::abs(std::min<int32_t>(band.lower_diagonal, 0)), matrix_base_t::num_rows - 1);
 
        band_size = band_col_index + band_row_index + 1;
        // Reserve one more cell to deal with last cell in the banded column which needs only the diagonal and up cell.
        matrix_base_t::pool.resize(band_size + 1, element_type{initial_value, initial_value});
    }
 
    int32_t band_col_index{};
    int32_t band_row_index{};
    int32_t band_size{};
 
private:
    constexpr alignment_column_type initialise_column(size_type const column_index) noexcept
    {
        int32_t slice_begin = std::max<int32_t>(0, band_col_index - column_index);
        int32_t row_end_index = column_index - band_col_index + band_size;
        int32_t slice_end = band_size - std::max<int32_t>(row_end_index - matrix_base_t::num_rows, 0);
 
        assert(row_end_index >= 0);
        assert(slice_begin >= 0);
        assert(slice_end > 0);
        assert(slice_begin < slice_end);
 
        return alignment_column_type{*this,
                                     column_data_view_type{std::addressof(matrix_base_t::pool[slice_begin]),
                                                           std::addressof(matrix_base_t::pool[slice_end])}};
    }
 
    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 + 1)),      // last left (read)
                std::get<1>(*(host_iter)),          // next left (write)
                std::get<1>(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 last diagonal value.
        std::get<0>(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
    {
        // noop.
    }
 
    template <std::random_access_iterator iter_t>
    constexpr void after_column_iterator_increment(iter_t host_iter) noexcept
    {
        // Cache the last diagonal value.
        std::get<0>(matrix_base_t::cache) = std::get<0>(*host_iter);
    }
};
 
} // namespace seqan3::detail