24 namespace seqan3::detail
50 template <
typename trace_t,
bool coordinate_only = false>
51 class alignment_trace_matrix_full_banded :
52 protected alignment_trace_matrix_base<trace_t>,
53 public alignment_matrix_column_major_range_base<alignment_trace_matrix_full_banded<trace_t, coordinate_only>>
57 "Value type must either be a trace_directions object or a simd vector.");
60 using matrix_base_t = alignment_trace_matrix_base<trace_t>;
62 using range_base_t = alignment_matrix_column_major_range_base<alignment_trace_matrix_full_banded<trace_t,
68 using typename matrix_base_t::element_type;
69 using typename matrix_base_t::coordinate_type;
70 using typename range_base_t::alignment_column_type;
73 decltype(std::views::iota(coordinate_type{}, coordinate_type{})),
76 std::views::iota(coordinate_type{}, coordinate_type{})))>;
82 using value_type = alignment_trace_matrix_proxy<coordinate_type,
85 detail::ignore_t
const,
88 using reference = value_type;
90 using iterator =
typename range_base_t::iterator;
92 using sentinel =
typename range_base_t::sentinel;
93 using typename matrix_base_t::size_type;
99 constexpr alignment_trace_matrix_full_banded() =
default;
102 constexpr alignment_trace_matrix_full_banded(alignment_trace_matrix_full_banded
const &) =
default;
104 constexpr alignment_trace_matrix_full_banded(alignment_trace_matrix_full_banded &&) =
default;
106 constexpr alignment_trace_matrix_full_banded & operator=(alignment_trace_matrix_full_banded
const &) =
default;
108 constexpr alignment_trace_matrix_full_banded & operator=(alignment_trace_matrix_full_banded &&) =
default;
110 ~alignment_trace_matrix_full_banded() =
default;
127 template <std::ranges::forward_range first_sequence_t, std::ranges::forward_range second_sequence_t>
128 constexpr alignment_trace_matrix_full_banded(first_sequence_t && first,
129 second_sequence_t && second,
130 static_band
const & band,
131 [[maybe_unused]] trace_t
const initial_value = trace_t{})
133 matrix_base_t::num_cols = static_cast<size_type>(std::ranges::distance(first) + 1);
134 matrix_base_t::num_rows = static_cast<size_type>(std::ranges::distance(second) + 1);
136 band_col_index = std::min<int32_t>(std::max<int32_t>(band.upper_bound, 0), matrix_base_t::num_cols - 1);
137 band_row_index = std::min<int32_t>(std::abs(std::min<int32_t>(band.lower_bound, 0)), matrix_base_t::num_rows - 1);
138 band_size = band_col_index + band_row_index + 1;
141 if constexpr (!coordinate_only)
143 matrix_base_t::data =
typename matrix_base_t::pool_type{number_rows{static_cast<size_type>(band_size)},
144 number_cols{matrix_base_t::num_cols}};
145 matrix_base_t::cache_left.resize(band_size + 1, initial_value);
151 auto trace_path(matrix_coordinate
const & trace_begin)
153 static_assert(!coordinate_only,
"Requested trace but storing the trace was disabled!");
155 using matrix_iter_t = std::ranges::iterator_t<typename matrix_base_t::pool_type>;
156 using trace_iterator_t = trace_iterator_banded<matrix_iter_t>;
157 using path_t = std::ranges::subrange<trace_iterator_t, std::ranges::default_sentinel_t>;
159 if (trace_begin.row >= static_cast<size_t>(band_size) || trace_begin.col >= matrix_base_t::num_cols)
162 return path_t{trace_iterator_t{matrix_base_t::data.begin() + matrix_offset{trace_begin},
163 column_index_type{band_col_index}},
164 std::ranges::default_sentinel};
168 int32_t band_col_index{};
170 int32_t band_row_index{};
176 constexpr alignment_column_type initialise_column(size_type
const column_index) noexcept
178 int32_t slice_begin = std::max<int32_t>(0, band_col_index - column_index);
179 int32_t row_end_index = column_index - band_col_index + band_size;
180 int32_t slice_end = band_size - std::max<int32_t>(row_end_index - matrix_base_t::num_rows, 0);
182 assert(row_end_index >= 0);
183 assert(slice_begin >= 0);
184 assert(slice_end > 0);
185 assert(slice_begin < slice_end);
187 coordinate_type row_begin{column_index_type{column_index}, row_index_type{static_cast<size_type>(slice_begin)}};
188 coordinate_type row_end{column_index_type{column_index}, row_index_type{static_cast<size_type>(slice_end)}};
189 if constexpr (coordinate_only)
191 return alignment_column_type{*
this,
192 column_data_view_type{std::views::iota(
std::move(row_begin),
197 matrix_coordinate band_begin{row_index_type{static_cast<size_type>(slice_begin)},
198 column_index_type{column_index}};
199 size_type slice_size = slice_end - slice_begin;
201 auto col = views::zip(
205 return alignment_column_type{*
this, column_data_view_type{
std::move(col)}};
210 template <std::random_access_iterator iter_t>
211 constexpr value_type make_proxy(iter_t host_iter) noexcept
213 if constexpr (coordinate_only)
215 return {*host_iter, std::ignore, std::ignore, std::ignore, std::ignore};
219 return {std::get<2>(*host_iter),
220 std::get<0>(*host_iter),
221 std::get<1>(*(host_iter + 1)),
222 std::get<1>(*host_iter),
223 matrix_base_t::cache_up