23 namespace seqan3::detail
39 template <
typename score_t>
40 class alignment_score_matrix_one_column_banded :
41 protected alignment_score_matrix_one_column_base<score_t>,
42 public alignment_matrix_column_major_range_base<alignment_score_matrix_one_column_banded<score_t>>
46 using matrix_base_t = alignment_score_matrix_one_column_base<score_t>;
48 using range_base_t = alignment_matrix_column_major_range_base<alignment_score_matrix_one_column_banded<score_t>>;
54 using typename matrix_base_t::element_type;
55 using typename range_base_t::alignment_column_type;
60 using matrix_base_t::num_cols;
61 using matrix_base_t::num_rows;
66 using value_type = alignment_score_matrix_proxy<score_t>;
69 using reference = value_type;
71 using iterator =
typename range_base_t::iterator;
73 using sentinel =
typename range_base_t::sentinel;
74 using typename matrix_base_t::size_type;
75 using typename matrix_base_t::underlying_type;
81 constexpr alignment_score_matrix_one_column_banded() =
default;
84 constexpr alignment_score_matrix_one_column_banded(alignment_score_matrix_one_column_banded
const &) =
default;
86 constexpr alignment_score_matrix_one_column_banded(alignment_score_matrix_one_column_banded &&) =
default;
88 constexpr alignment_score_matrix_one_column_banded &
89 operator=(alignment_score_matrix_one_column_banded
const &) =
default;
91 constexpr alignment_score_matrix_one_column_banded &
92 operator=(alignment_score_matrix_one_column_banded &&) =
default;
94 ~alignment_score_matrix_one_column_banded() =
default;
110 template <std::ranges::forward_range first_sequence_t,
111 std::ranges::forward_range second_sequence_t>
112 constexpr alignment_score_matrix_one_column_banded(first_sequence_t && first,
113 second_sequence_t && second,
114 align_cfg::band_fixed_size
const & band,
115 score_t
const initial_value = score_t{})
117 matrix_base_t::num_cols =
static_cast<size_type
>(std::ranges::distance(first) + 1);
118 matrix_base_t::num_rows =
static_cast<size_type
>(std::ranges::distance(second) + 1);
120 band_col_index = std::min<int32_t>(std::max<int32_t>(band.upper_diagonal, 0), matrix_base_t::num_cols - 1);
121 band_row_index = std::min<int32_t>(std::abs(std::min<int32_t>(band.lower_diagonal, 0)),
122 matrix_base_t::num_rows - 1);
124 band_size = band_col_index + band_row_index + 1;
126 matrix_base_t::pool.resize(band_size + 1, element_type{initial_value, initial_value});
131 int32_t band_col_index{};
133 int32_t band_row_index{};
139 constexpr alignment_column_type initialise_column(size_type
const column_index) noexcept
141 int32_t slice_begin = std::max<int32_t>(0, band_col_index - column_index);
142 int32_t row_end_index = column_index - band_col_index + band_size;
143 int32_t slice_end = band_size - std::max<int32_t>(row_end_index - matrix_base_t::num_rows, 0);
145 assert(row_end_index >= 0);
146 assert(slice_begin >= 0);
147 assert(slice_end > 0);
148 assert(slice_begin < slice_end);
150 return alignment_column_type{*
this,
151 column_data_view_type{
std::addressof(matrix_base_t::pool[slice_begin]),
156 template <std::random_access_iterator iter_t>
157 constexpr value_type make_proxy(iter_t host_iter) noexcept
159 return {std::get<0>(*host_iter),
160 std::get<0>(matrix_base_t::cache),
161 std::get<1>(*(host_iter + 1)),
162 std::get<1>(*(host_iter)),
163 std::get<1>(matrix_base_t::cache)};
167 template <std::random_access_iterator iter_t>
168 constexpr
void on_column_iterator_creation(iter_t host_iter) noexcept
171 std::get<0>(matrix_base_t::cache) = std::get<0>(*host_iter);
175 template <std::random_access_iterator iter_t>
176 constexpr
void before_column_iterator_increment(iter_t SEQAN3_DOXYGEN_ONLY(host_iter)) noexcept
182 template <std::random_access_iterator iter_t>
183 constexpr
void after_column_iterator_increment(iter_t host_iter) noexcept
186 std::get<0>(matrix_base_t::cache) = std::get<0>(*host_iter);