24 namespace seqan3::detail
49 template <
typename trace_t,
bool coordinate_only = false>
50 class alignment_trace_matrix_full :
51 protected alignment_trace_matrix_base<trace_t>,
52 public alignment_matrix_column_major_range_base<alignment_trace_matrix_full<trace_t, coordinate_only>>
55 static_assert(std::same_as<trace_t, trace_directions> || simd_concept<trace_t>,
56 "Value type must either be a trace_directions object or a simd vector.");
59 using matrix_base_t = alignment_trace_matrix_base<trace_t>;
61 using range_base_t = alignment_matrix_column_major_range_base<alignment_trace_matrix_full<trace_t, coordinate_only>>;
67 using typename matrix_base_t::element_type;
68 using typename matrix_base_t::coordinate_type;
69 using typename range_base_t::alignment_column_type;
72 decltype(std::views::iota(coordinate_type{}, coordinate_type{})),
75 std::views::iota(coordinate_type{}, coordinate_type{})))>;
82 using value_type = alignment_trace_matrix_proxy<coordinate_type,
84 detail::ignore_t
const,
87 using reference = value_type;
89 using iterator =
typename range_base_t::iterator;
91 using sentinel =
typename range_base_t::sentinel;
92 using typename matrix_base_t::size_type;
98 constexpr alignment_trace_matrix_full() =
default;
99 constexpr alignment_trace_matrix_full(alignment_trace_matrix_full
const &) =
default;
100 constexpr alignment_trace_matrix_full(alignment_trace_matrix_full &&) =
default;
101 constexpr alignment_trace_matrix_full & operator=(alignment_trace_matrix_full
const &) =
default;
102 constexpr alignment_trace_matrix_full & operator=(alignment_trace_matrix_full &&) =
default;
103 ~alignment_trace_matrix_full() =
default;
118 template <std::ranges::forward_range first_sequence_t, std::ranges::forward_range second_sequence_t>
119 constexpr alignment_trace_matrix_full(first_sequence_t && first,
120 second_sequence_t && second,
121 [[maybe_unused]] trace_t
const initial_value = trace_t{})
123 matrix_base_t::num_cols =
static_cast<size_type
>(std::ranges::distance(first) + 1);
124 matrix_base_t::num_rows =
static_cast<size_type
>(std::ranges::distance(second) + 1);
126 if constexpr (!coordinate_only)
129 matrix_base_t::data =
typename matrix_base_t::pool_type{number_rows{matrix_base_t::num_rows},
130 number_cols{matrix_base_t::num_cols}};
131 matrix_base_t::cache_left.resize(matrix_base_t::num_rows, initial_value);
142 auto trace_path(matrix_coordinate
const & trace_begin)
144 static_assert(!coordinate_only,
"Requested trace but storing the trace was disabled!");
146 using matrix_iter_t = std::ranges::iterator_t<typename matrix_base_t::pool_type>;
147 using trace_iterator_t = trace_iterator<matrix_iter_t>;
148 using path_t = std::ranges::subrange<trace_iterator_t, std::default_sentinel_t>;
150 if (trace_begin.row >= matrix_base_t::num_rows || trace_begin.col >= matrix_base_t::num_cols)
151 throw std::invalid_argument{
"The given coordinate exceeds the matrix in vertical or horizontal direction."};
153 return path_t{trace_iterator_t{matrix_base_t::data.begin() + matrix_offset{trace_begin}},
154 std::default_sentinel};
159 constexpr alignment_column_type initialise_column(size_type
const column_index) noexcept
161 coordinate_type row_begin{column_index_type{column_index}, row_index_type{0u}};
162 coordinate_type row_end{column_index_type{column_index}, row_index_type{matrix_base_t::num_rows}};
163 if constexpr (coordinate_only)
165 return alignment_column_type{*
this,
166 column_data_view_type{std::views::iota(
std::move(row_begin),
171 matrix_coordinate current_position{row_index_type{0u}, column_index_type{column_index}};
173 matrix_base_t::num_rows},
176 return alignment_column_type{*
this, column_data_view_type{col}};
181 template <std::random_access_iterator iter_t>
182 constexpr value_type make_proxy(iter_t host_iter) noexcept
184 if constexpr (coordinate_only)
186 return {*host_iter, std::ignore, std::ignore, std::ignore, std::ignore};
190 return {std::get<2>(*host_iter),
191 std::get<0>(*host_iter),
192 std::get<1>(*host_iter),
193 std::get<1>(*host_iter),
194 matrix_base_t::cache_up,
Provides seqan3::detail::alignment_matrix_column_major_range_base.
Provides seqan3::detail::alignment_trace_matrix_base.
Provides seqan3::detail::alignment_trace_matrix_proxy.
constexpr auto zip
A zip view.
Definition: zip.hpp:29
auto const move
A view that turns lvalue-references into rvalue-references.
Definition: move.hpp:74
Provides C++20 additions to the <iterator> header.
Adaptations of concepts from the Ranges TS.
Provides seqan3::detail::trace_iterator.
Provides seqan3::views::zip.