trace_matrix_full.hpp

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// -----------------------------------------------------------------------------------------------------
// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin
// Copyright (c) 2016-2023, 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 <ranges>
#include <span>
#include <vector>
 
#include <seqan3/alignment/matrix/detail/matrix_coordinate.hpp>
#include <seqan3/alignment/matrix/detail/trace_directions.hpp>
#include <seqan3/alignment/matrix/detail/trace_iterator.hpp>
#include <seqan3/alignment/matrix/detail/two_dimensional_matrix.hpp>
#include <seqan3/core/detail/template_inspection.hpp>
#include <seqan3/utility/concept.hpp>
#include <seqan3/utility/container/aligned_allocator.hpp>
#include <seqan3/utility/views/repeat_n.hpp>
#include <seqan3/utility/views/zip.hpp>
 
namespace seqan3::detail
{
 
template <typename trace_t>
    requires std::same_as<trace_t, trace_directions>
class trace_matrix_full
{
private:
    using matrix_t =
        two_dimensional_matrix<trace_t, aligned_allocator<trace_t, sizeof(trace_t)>, matrix_major_order::column>;
    using physical_column_t = std::vector<trace_t>;
    using virtual_column_t = decltype(views::repeat_n(trace_t{}, 1));
 
    class iterator;
 
    matrix_t complete_matrix{};
    physical_column_t horizontal_column{};
    virtual_column_t vertical_column{};
    size_t column_count{};
    size_t row_count{};
 
public:
    trace_matrix_full() = default;                                      
    trace_matrix_full(trace_matrix_full const &) = default;             
    trace_matrix_full(trace_matrix_full &&) = default;                  
    trace_matrix_full & operator=(trace_matrix_full const &) = default; 
    trace_matrix_full & operator=(trace_matrix_full &&) = default;      
    ~trace_matrix_full() = default;                                     
 
 
    template <std::integral column_index_t, std::integral row_index_t>
    void resize(column_index_type<column_index_t> const column_count, row_index_type<row_index_t> const row_count)
    {
        this->column_count = column_count.get();
        this->row_count = row_count.get();
        complete_matrix.resize(number_rows{this->row_count}, number_cols{this->column_count});
        horizontal_column.resize(this->row_count);
        vertical_column = views::repeat_n(trace_t{}, this->row_count);
    }
 
    auto trace_path(matrix_coordinate const & trace_begin) const
    {
        using matrix_iter_t = std::ranges::iterator_t<matrix_t const>;
        using trace_iterator_t = trace_iterator<matrix_iter_t>;
        using path_t = std::ranges::subrange<trace_iterator_t, std::default_sentinel_t>;
 
        if (trace_begin.row >= row_count || trace_begin.col >= column_count)
            throw std::invalid_argument{"The given coordinate exceeds the matrix in vertical or horizontal direction."};
 
        return path_t{trace_iterator_t{complete_matrix.begin() + matrix_offset{trace_begin}}, std::default_sentinel};
    }
 
    iterator begin()
    {
        return iterator{*this, 0u};
    }
 
    iterator begin() const = delete;
 
    iterator end()
    {
        return iterator{*this, column_count};
    }
 
    iterator end() const = delete;
};
 
template <typename trace_t>
    requires std::same_as<trace_t, trace_directions>
class trace_matrix_full<trace_t>::iterator
{
private:
    using single_trace_column_type = std::span<trace_t>;
    using matrix_column_type = decltype(views::zip(std::declval<single_trace_column_type>(),
                                                   std::declval<physical_column_t &>(),
                                                   std::declval<virtual_column_t &>()));
    using matrix_column_value_t = std::vector<std::ranges::range_value_t<matrix_column_type>>;
 
    // Defines a proxy that can be converted to the value type.
    class column_proxy;
 
    trace_matrix_full * host_ptr{nullptr};
    size_t current_column_id{};
 
public:
    using value_type = matrix_column_value_t;
    using reference = column_proxy;
    using pointer = void;
    using difference_type = std::ptrdiff_t;
    using iterator_category = std::input_iterator_tag;
 
    iterator() noexcept = default;                             
    iterator(iterator const &) noexcept = default;             
    iterator(iterator &&) noexcept = default;                  
    iterator & operator=(iterator const &) noexcept = default; 
    iterator & operator=(iterator &&) noexcept = default;      
    ~iterator() = default;                                     
 
    explicit iterator(trace_matrix_full & host_matrix, size_t const initial_column_id) noexcept :
        host_ptr{std::addressof(host_matrix)},
        current_column_id{initial_column_id}
    {}
 
    reference operator*() const
    {
        auto column_begin = host_ptr->complete_matrix.data() + current_column_id * host_ptr->row_count;
        single_trace_column_type single_trace_column{column_begin, column_begin + host_ptr->row_count};
 
        return column_proxy{
            views::zip(std::move(single_trace_column), host_ptr->horizontal_column, host_ptr->vertical_column)};
    }
 
    iterator & operator++()
    {
        ++current_column_id;
        return *this;
    }
 
    void operator++(int)
    {
        ++(*this);
    }
 
    friend bool operator==(iterator const & lhs, iterator const & rhs) noexcept
    {
        return lhs.current_column_id == rhs.current_column_id;
    }
 
    friend bool operator!=(iterator const & lhs, iterator const & rhs) noexcept
    {
        return !(lhs == rhs);
    }
};
 
template <typename trace_t>
    requires std::same_as<trace_t, trace_directions>
class trace_matrix_full<trace_t>::iterator::column_proxy : public std::ranges::view_interface<column_proxy>
{
private:
    matrix_column_type column{};
 
public:
    column_proxy() = default;                                 
    column_proxy(column_proxy const &) = default;             
    column_proxy(column_proxy &&) = default;                  
    column_proxy & operator=(column_proxy const &) = default; 
    column_proxy & operator=(column_proxy &&) = default;      
    ~column_proxy() = default;                                
 
    explicit column_proxy(matrix_column_type && column) noexcept : column{std::move(column)}
    {}
 
    std::ranges::iterator_t<matrix_column_type> begin()
    {
        return column.begin();
    }
    std::ranges::iterator_t<matrix_column_type> begin() const = delete;
 
    std::ranges::sentinel_t<matrix_column_type> end()
    {
        return column.end();
    }
 
    std::ranges::sentinel_t<matrix_column_type> end() const = delete;
 
    constexpr operator matrix_column_value_t() const
    {
        matrix_column_value_t target{};
        std::ranges::copy(column, std::back_inserter(target));
        return target;
    }
};
 
} // namespace seqan3::detail