score_matrix_single_column.hpp

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// 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 <ranges>
#include <vector>
 
#include <seqan3/alignment/matrix/detail/affine_cell_proxy.hpp>
#include <seqan3/alignment/matrix/detail/matrix_coordinate.hpp>
#include <seqan3/utility/concept.hpp>
#include <seqan3/utility/container/aligned_allocator.hpp>
#include <seqan3/utility/simd/concept.hpp>
#include <seqan3/utility/views/repeat_n.hpp>
#include <seqan3/utility/views/zip.hpp>
 
namespace seqan3::detail
{
 
template <typename score_t>
    requires (arithmetic<score_t> || simd_concept<score_t>)
class score_matrix_single_column
{
private:
    using physical_column_t = std::vector<score_t, aligned_allocator<score_t, alignof(score_t)>>;
    using virtual_column_t = decltype(views::repeat_n(score_t{}, 1));
 
    class matrix_iterator;
 
    physical_column_t optimal_column{};
    physical_column_t horizontal_column{};
    virtual_column_t vertical_column{};
    size_t number_of_columns{};
 
public:
    score_matrix_single_column() = default;                                               
    score_matrix_single_column(score_matrix_single_column const &) = default;             
    score_matrix_single_column(score_matrix_single_column &&) = default;                  
    score_matrix_single_column & operator=(score_matrix_single_column const &) = default; 
    score_matrix_single_column & operator=(score_matrix_single_column &&) = default;      
    ~score_matrix_single_column() = default;                                              
 
 
    template <std::integral column_index_t, std::integral row_index_t>
    void resize(column_index_type<column_index_t> const number_of_columns,
                row_index_type<row_index_t> const number_of_rows,
                score_t const initial_value = score_t{})
    {
        this->number_of_columns = number_of_columns.get();
        optimal_column.clear();
        horizontal_column.clear();
        SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY_START(-Wstringop-overflow)
        optimal_column.resize(number_of_rows.get(), initial_value);
        SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY_STOP
        horizontal_column.resize(number_of_rows.get(), initial_value);
        vertical_column = views::repeat_n(initial_value, number_of_rows.get());
    }
 
    matrix_iterator begin()
    {
        return matrix_iterator{*this, 0u};
    }
 
    matrix_iterator begin() const = delete;
 
    matrix_iterator end()
    {
        return matrix_iterator{*this, number_of_columns};
    }
 
    matrix_iterator end() const = delete;
};
 
template <typename score_t>
    requires (arithmetic<score_t> || simd_concept<score_t>)
class score_matrix_single_column<score_t>::matrix_iterator
{
private:
    using matrix_column_t = decltype(views::zip(std::declval<physical_column_t &>(),
                                                std::declval<physical_column_t &>(),
                                                std::declval<virtual_column_t &>()));
 
    static constexpr auto transform_to_affine_cell = std::views::transform(
        [](auto && tpl) -> affine_cell_proxy<std::remove_cvref_t<decltype(tpl)>>
        {
            using fwd_tuple_t = decltype(tpl);
            return affine_cell_proxy<std::remove_cvref_t<fwd_tuple_t>>{std::forward<fwd_tuple_t>(tpl)};
        });
 
    score_matrix_single_column * host_ptr{nullptr};
    size_t current_column_id{};
 
public:
    using value_type = decltype(std::declval<matrix_column_t>() | transform_to_affine_cell);
    using reference = value_type;
    using pointer = void;
    using difference_type = std::ptrdiff_t;
    using iterator_category = std::input_iterator_tag;
 
    matrix_iterator() noexcept = default;                                    
    matrix_iterator(matrix_iterator const &) noexcept = default;             
    matrix_iterator(matrix_iterator &&) noexcept = default;                  
    matrix_iterator & operator=(matrix_iterator const &) noexcept = default; 
    matrix_iterator & operator=(matrix_iterator &&) noexcept = default;      
    ~matrix_iterator() = default;                                            
 
    explicit matrix_iterator(score_matrix_single_column & host_matrix, size_t const initial_column_id) noexcept :
        host_ptr{std::addressof(host_matrix)},
        current_column_id{initial_column_id}
    {}
 
    reference operator*() const
    {
        return views::zip(host_ptr->optimal_column, host_ptr->horizontal_column, host_ptr->vertical_column)
             | transform_to_affine_cell;
    }
 
    matrix_iterator & operator++()
    {
        ++current_column_id;
        return *this;
    }
 
    void operator++(int)
    {
        ++(*this);
    }
 
    friend bool operator==(matrix_iterator const & lhs, matrix_iterator const & rhs) noexcept
    {
        return lhs.current_column_id == rhs.current_column_id;
    }
 
    friend bool operator!=(matrix_iterator const & lhs, matrix_iterator const & rhs) noexcept
    {
        return !(lhs == rhs);
    }
};
 
} // namespace seqan3::detail