17namespace seqan3::detail
25template <
typename alignment_configuration_t>
26class policy_affine_gap_with_trace_recursion :
protected policy_affine_gap_recursion<alignment_configuration_t>
30 using base_t = policy_affine_gap_recursion<alignment_configuration_t>;
33 using typename base_t::affine_score_tuple_t;
34 using typename base_t::score_type;
35 using typename base_t::traits_type;
38 using trace_type =
typename traits_type::trace_type;
42 using affine_cell_type = affine_cell_proxy<std::pair<affine_score_tuple_t, affine_trace_tuple_t>>;
45 using base_t::first_column_is_free;
46 using base_t::first_row_is_free;
47 using base_t::gap_extension_score;
48 using base_t::gap_open_score;
53 policy_affine_gap_with_trace_recursion() =
default;
54 policy_affine_gap_with_trace_recursion(policy_affine_gap_with_trace_recursion
const &) =
default;
55 policy_affine_gap_with_trace_recursion(policy_affine_gap_with_trace_recursion &&) =
default;
56 policy_affine_gap_with_trace_recursion &
57 operator=(policy_affine_gap_with_trace_recursion
const &) =
default;
58 policy_affine_gap_with_trace_recursion &
59 operator=(policy_affine_gap_with_trace_recursion &&) =
default;
60 ~policy_affine_gap_with_trace_recursion() =
default;
63 explicit policy_affine_gap_with_trace_recursion(alignment_configuration_t
const & config) : base_t{config}
68 template <
typename affine_cell_t>
69 affine_cell_type compute_inner_cell(score_type diagonal_score,
70 affine_cell_t previous_cell,
71 score_type
const sequence_score)
const noexcept
73 diagonal_score += sequence_score;
74 score_type horizontal_score = previous_cell.horizontal_score();
75 score_type vertical_score = previous_cell.vertical_score();
76 trace_directions best_trace = trace_directions::diagonal;
78 diagonal_score = (diagonal_score < vertical_score)
79 ? (best_trace = previous_cell.vertical_trace(), vertical_score)
80 : (best_trace |= previous_cell.vertical_trace(), diagonal_score);
81 diagonal_score = (diagonal_score < horizontal_score)
82 ? (best_trace = previous_cell.horizontal_trace(), horizontal_score)
83 : (best_trace |= previous_cell.horizontal_trace(), diagonal_score);
85 score_type tmp = diagonal_score + gap_open_score;
86 vertical_score += gap_extension_score;
87 horizontal_score += gap_extension_score;
90 trace_directions next_vertical_trace = trace_directions::up;
91 trace_directions next_horizontal_trace = trace_directions::left;
94 (vertical_score < tmp) ? (next_vertical_trace = trace_directions::up_open, tmp) : vertical_score;
96 (horizontal_score < tmp) ? (next_horizontal_trace = trace_directions::left_open, tmp) : horizontal_score;
98 return {{diagonal_score, horizontal_score, vertical_score},
99 {best_trace, next_horizontal_trace, next_vertical_trace}};
103 affine_cell_type initialise_origin_cell() const noexcept
105 return {base_t::initialise_origin_cell(),
106 {trace_directions::none,
107 first_row_is_free ? trace_directions::none : trace_directions::left_open,
108 first_column_is_free ? trace_directions::none : trace_directions::up_open}};
112 template <
typename affine_cell_t>
113 affine_cell_type initialise_first_column_cell(affine_cell_t previous_cell)
const noexcept
115 return {base_t::initialise_first_column_cell(previous_cell),
116 {previous_cell.vertical_trace(),
117 trace_directions::left_open,
118 first_column_is_free ? trace_directions::none : trace_directions::up}};
122 template <
typename affine_cell_t>
123 affine_cell_type initialise_first_row_cell(affine_cell_t previous_cell)
const noexcept
125 return {base_t::initialise_first_row_cell(previous_cell),
126 {previous_cell.horizontal_trace(),
127 first_row_is_free ? trace_directions::none : trace_directions::left,
128 trace_directions::up_open}};
Provides seqan3::detail::policy_affine_gap_recursion.