combined_score_and_trace_matrix.hpp

Go to the documentation of this file.

// -----------------------------------------------------------------------------------------------------
// 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 <ranges>
 
#include <seqan3/alignment/matrix/detail/affine_cell_proxy.hpp>
#include <seqan3/alignment/matrix/detail/matrix_coordinate.hpp>
#include <seqan3/core/range/type_traits.hpp>
#include <seqan3/utility/concept.hpp>
#include <seqan3/utility/views/zip.hpp>
 
namespace seqan3::detail
{
template <std::ranges::input_range score_matrix_t, std::ranges::input_range trace_matrix_t>
    requires (std::ranges::input_range<std::ranges::range_reference_t<score_matrix_t>>
              && std::ranges::input_range<std::ranges::range_reference_t<trace_matrix_t>>)
class combined_score_and_trace_matrix
{
private:
    using score_type = std::remove_cvref_t<std::tuple_element_t<0, range_innermost_value_t<score_matrix_t>>>;
 
    class iterator;
    class sentinel;
 
    score_matrix_t score_matrix{};
    trace_matrix_t trace_matrix{};
 
public:
    combined_score_and_trace_matrix() = default;                                                    
    combined_score_and_trace_matrix(combined_score_and_trace_matrix const &) = default;             
    combined_score_and_trace_matrix(combined_score_and_trace_matrix &&) = default;                  
    combined_score_and_trace_matrix & operator=(combined_score_and_trace_matrix const &) = default; 
    combined_score_and_trace_matrix & operator=(combined_score_and_trace_matrix &&) = default;      
    ~combined_score_and_trace_matrix() = 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,
                score_type const initial_score = score_type{})
    {
        score_matrix_t tmp_score_matrix{};
        tmp_score_matrix.resize(column_count, row_count, initial_score);
 
        trace_matrix_t tmp_trace_matrix{};
        tmp_trace_matrix.resize(column_count, row_count);
 
        score_matrix = std::move(tmp_score_matrix);
        trace_matrix = std::move(tmp_trace_matrix);
    }
 
    iterator begin()
    {
        return iterator{score_matrix.begin(), trace_matrix.begin()};
    }
 
    iterator begin() const = delete;
 
    sentinel end()
    {
        return sentinel{score_matrix.end()};
    }
 
    sentinel end() const = delete;
 
    auto trace_path(matrix_coordinate const & from_coordinate) const
    {
        return trace_matrix.trace_path(from_coordinate);
    }
};
 
template <std::ranges::input_range score_matrix_t, std::ranges::input_range trace_matrix_t>
    requires (std::ranges::input_range<std::ranges::range_reference_t<score_matrix_t>>
              && std::ranges::input_range<std::ranges::range_reference_t<trace_matrix_t>>)
class combined_score_and_trace_matrix<score_matrix_t, trace_matrix_t>::iterator
{
private:
    using score_matrix_reference_type = std::ranges::range_reference_t<score_matrix_t>;
    using trace_matrix_reference_type = std::ranges::range_reference_t<trace_matrix_t>;
 
    static_assert(std::ranges::viewable_range<score_matrix_reference_type>);
    static_assert(std::ranges::viewable_range<trace_matrix_reference_type>);
 
    using combined_column_type =
        decltype(views::zip(std::declval<score_matrix_reference_type>(), std::declval<trace_matrix_reference_type>()));
    using score_matrix_iter_type = std::ranges::iterator_t<score_matrix_t>;
    using trace_matrix_iter_type = std::ranges::iterator_t<trace_matrix_t>;
 
    // Befriend the base class.
    template <std::ranges::input_range other_score_matrix_t, std::ranges::input_range other_trace_matrix_t>
        requires (std::ranges::input_range<std::ranges::range_reference_t<other_score_matrix_t>>
                  && std::ranges::input_range<std::ranges::range_reference_t<other_trace_matrix_t>>)
    friend class combined_score_and_trace_matrix;
 
    static constexpr auto transform_to_combined_matrix_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_iter_type score_matrix_it;
    trace_matrix_iter_type trace_matrix_it;
 
public:
    using value_type = decltype(std::declval<combined_column_type>() | transform_to_combined_matrix_cell);
    using reference = value_type;
    using pointer = void;
    using difference_type = std::ptrdiff_t;
    using iterator_concept = std::input_iterator_tag;
 
    iterator() = default;                             
    iterator(iterator const &) = default;             
    iterator(iterator &&) = default;                  
    iterator & operator=(iterator const &) = default; 
    iterator & operator=(iterator &&) = default;      
    ~iterator() = default;                            
 
    explicit iterator(score_matrix_iter_type score_matrix_it, trace_matrix_iter_type trace_matrix_it) noexcept :
        score_matrix_it{std::move(score_matrix_it)},
        trace_matrix_it{std::move(trace_matrix_it)}
    {}
 
    reference operator*() const
    {
        return views::zip(*score_matrix_it, *trace_matrix_it) | transform_to_combined_matrix_cell;
    }
 
    iterator & operator++()
    {
        ++score_matrix_it;
        ++trace_matrix_it;
        return *this;
    }
 
    void operator++(int)
    {
        ++(*this);
    }
};
 
template <std::ranges::input_range score_matrix_t, std::ranges::input_range trace_matrix_t>
    requires (std::ranges::input_range<std::ranges::range_reference_t<score_matrix_t>>
              && std::ranges::input_range<std::ranges::range_reference_t<trace_matrix_t>>)
class combined_score_and_trace_matrix<score_matrix_t, trace_matrix_t>::sentinel
{
private:
    using score_matrix_sentinel_type = std::ranges::sentinel_t<score_matrix_t>;
 
    score_matrix_sentinel_type score_matrix_sentinel{};
 
public:
    sentinel() = default;                             
    sentinel(sentinel const &) = default;             
    sentinel(sentinel &&) = default;                  
    sentinel & operator=(sentinel const &) = default; 
    sentinel & operator=(sentinel &&) = default;      
    ~sentinel() = default;                            
 
    explicit sentinel(score_matrix_sentinel_type score_matrix_sentinel) noexcept :
        score_matrix_sentinel{std::move(score_matrix_sentinel)}
    {}
 
    friend bool operator==(iterator const & lhs, sentinel const & rhs) noexcept
    {
        return rhs.equal(lhs);
    }
 
    friend bool operator==(sentinel const & lhs, iterator const & rhs) noexcept
    {
        return rhs == lhs;
    }
 
    friend bool operator!=(iterator const & lhs, sentinel const & rhs) noexcept
    {
        return !(lhs == rhs);
    }
 
    friend bool operator!=(sentinel const & lhs, iterator const & rhs) noexcept
    {
        return !(lhs == rhs);
    }
 
private:
    constexpr bool equal(iterator const & iter) const noexcept
    {
        return iter.score_matrix_it == score_matrix_sentinel;
    }
};
 
} // namespace seqan3::detail