20 namespace seqan3::detail
45 template <
typename alignment_algorithm_t,
typename score_t,
typename align_local_t = std::false_type>
46 class affine_gap_policy
50 friend alignment_algorithm_t;
53 using alignment_state_t = alignment_algorithm_state<score_t>;
59 constexpr affine_gap_policy() noexcept = default;
60 constexpr affine_gap_policy(affine_gap_policy const &) noexcept = default;
61 constexpr affine_gap_policy(affine_gap_policy &&) noexcept = default;
62 constexpr affine_gap_policy & operator=(affine_gap_policy const &) noexcept = default;
63 constexpr affine_gap_policy & operator=(affine_gap_policy &&) noexcept = default;
64 ~affine_gap_policy() noexcept = default;
67 template <typename configuration_t>
68 affine_gap_policy(configuration_t const & )
85 template <
typename cell_t>
86 constexpr
void compute_cell(cell_t && current_cell,
87 alignment_algorithm_state<score_t> & cache,
88 score_t
const score)
const noexcept
92 auto & [score_cell, trace_cell] = current_cell;
95 score_t tmp = score_cell.diagonal + score;
97 if constexpr (with_trace)
99 tmp = (tmp < score_cell.up) ? (trace_cell.current = trace_cell.up, score_cell.up)
100 : (trace_cell.current = trace_directions::diagonal | trace_cell.up, tmp);
101 tmp = (tmp < score_cell.r_left) ? (trace_cell.current = trace_cell.r_left, score_cell.r_left)
102 : (trace_cell.current |= trace_cell.r_left, tmp);
106 tmp = (tmp < score_cell.up) ? score_cell.up : tmp;
107 tmp = (tmp < score_cell.r_left) ? score_cell.r_left : tmp;
110 if constexpr (align_local_t::value)
111 tmp = (tmp < 0) ? (trace_cell.current = trace_directions::none, 0) : tmp;
114 score_cell.current = tmp;
116 static_cast<alignment_algorithm_t
const &
>(*this).check_score_of_cell(current_cell, cache);
119 tmp += cache.gap_open_score;
120 score_cell.up += cache.gap_extension_score;
121 score_cell.w_left = score_cell.r_left + cache.gap_extension_score;
123 score_cell.up = (score_cell.up < tmp) ? (trace_cell.up = trace_directions::up_open, tmp)
124 : (trace_cell.up = trace_directions::up, score_cell.up);
125 score_cell.w_left = (score_cell.w_left < tmp) ? (trace_cell.w_left = trace_directions::left_open, tmp)
126 : (trace_cell.w_left = trace_directions::left, score_cell.w_left);
142 template <
typename cell_t>
143 constexpr
void compute_first_band_cell(cell_t && current_cell,
144 alignment_algorithm_state<score_t> & cache,
145 score_t
const score)
const noexcept
150 auto & [score_cell, trace_cell] = current_cell;
151 score_cell.current = score_cell.diagonal + score;
153 score_cell.current = (score_cell.current < score_cell.r_left)
154 ? (trace_cell.current = trace_cell.r_left, score_cell.r_left)
155 : (trace_cell.current = trace_directions::diagonal, score_cell.current);
157 if constexpr (align_local_t::value)
159 score_cell.current = (score_cell.current < 0) ? (trace_cell.current = trace_directions::none, 0)
160 : score_cell.current;
163 static_cast<alignment_algorithm_t
const &
>(*this).check_score_of_cell(current_cell, cache);
167 score_cell.up = score_cell.current + cache.gap_open_score;
168 trace_cell.up = trace_directions::up_open;
184 template <
typename alignment_configuration_t>
185 constexpr
void initialise_alignment_state(alignment_configuration_t
const & config) noexcept
187 auto scheme = config.get_or(align_cfg::gap_cost_affine{align_cfg::open_score{-10},
188 align_cfg::extension_score{-1}});
190 alignment_state.gap_extension_score =
static_cast<score_t
>(scheme.extension_score);
191 alignment_state.gap_open_score =
static_cast<score_t
>(scheme.extension_score + scheme.open_score);
194 alignment_state_t alignment_state{};