22namespace seqan3::detail
24template <
typename word_t,
typename score_t,
bool is_semi_global,
bool use_max_errors>
25class edit_distance_score_matrix_full;
27template <
typename word_t,
bool is_semi_global,
bool use_max_errors>
28class edit_distance_trace_matrix_full;
31template <
typename state_t,
typename...>
36template <
bool enabled,
typename state_t>
43template <
bool B,
template <
typename...>
typename T,
template <
typename...>
typename F>
47 template <
typename... args_t>
55template <std::ranges::viewable_range database_t,
56 std::ranges::viewable_range query_t,
57 typename align_config_t,
58 typename is_semi_global_t,
59 typename word_t = uint_fast64_t>
60struct default_edit_distance_trait_type
65 using alignment_traits_type = alignment_configuration_traits<align_config_type>;
67 using word_type = word_t;
68 static_assert(std::is_unsigned_v<word_type>,
"the word type of edit_distance_unbanded must be unsigned.");
69 static_assert(alignment_traits_type::has_output_configuration,
"We assume the result type was configured.");
71 using score_type =
typename alignment_traits_type::original_score_type;
78 static constexpr uint8_t word_size = bits_of<word_type>;
79 static_assert(bits_of<word_type> <= 64u,
"we assume at most uint64_t as word_type");
82 using database_iterator = std::ranges::iterator_t<database_type>;
86 using alignment_result_type =
typename alignment_traits_type::alignment_result_type;
88 using result_value_type =
typename alignment_result_value_type_accessor<alignment_result_type>::type;
92 static constexpr bool use_max_errors = align_config_type::template exists<align_cfg::min_score>();
94 static constexpr bool is_semi_global = is_semi_global_t::value;
96 static constexpr bool is_global = !is_semi_global;
98 static constexpr bool compute_score =
true;
100 static constexpr bool compute_sequence_alignment = alignment_traits_type::compute_sequence_alignment;
102 static constexpr bool compute_begin_positions =
103 alignment_traits_type::compute_begin_positions || compute_sequence_alignment;
105 static constexpr bool compute_end_positions =
106 alignment_traits_type::compute_end_positions || compute_begin_positions;
108 static constexpr bool compute_score_matrix =
false;
110 static constexpr bool compute_trace_matrix = compute_begin_positions || compute_sequence_alignment;
112 static constexpr bool compute_matrix = compute_score_matrix || compute_trace_matrix;
115 using trace_matrix_type = edit_distance_trace_matrix_full<word_type, is_semi_global, use_max_errors>;
117 using score_matrix_type = edit_distance_score_matrix_full<word_type, score_type, is_semi_global, use_max_errors>;
121template <
bool enable_policy,
template <
typename...>
typename policy_t,
typename edit_traits,
typename derived_t>
122using edit_distance_base = invoke_deferred_crtp_base<
123 deferred_crtp_base<selector<enable_policy, policy_t, empty_state>::template select, edit_traits>,
127template <std::ranges::viewable_range database_t,
128 std::ranges::viewable_range query_t,
129 typename align_config_t,
131class edit_distance_unbanded;
Provides seqan3::align_cfg::min_score configuration.
Provides seqan3::detail::align_result_selector.
Provides helper type traits for the configuration and execution of the alignment algorithm.
Provides utility functions for bit twiddling.
Provides seqan3::detail::deferred_crtp_base.