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>
68 static_assert(std::is_unsigned_v<word_type>,
"the word type of edit_distance_unbanded must be unsigned.");
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");
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>();
121template <
bool enable_policy,
template <
typename...>
typename policy_t,
typename edit_traits,
typename derived_t>
127template <std::ranges::viewable_range database_t,
128 std::ranges::viewable_range query_t,
129 typename align_config_t,
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.
The underlying data structure of seqan3::detail::edit_distance_unbanded that represents the score mat...
Definition edit_distance_score_matrix_full.hpp:30
The underlying data structure of seqan3::detail::edit_distance_unbanded that represents the trace mat...
Definition edit_distance_trace_matrix_full.hpp:30
This calculates an alignment using the edit distance and without a band.
Definition edit_distance_unbanded.hpp:711
Provides seqan3::detail::deferred_crtp_base.
typename deferred_crtp_base_t::template invoke< derived_t > invoke_deferred_crtp_base
Template alias to instantiate the deferred crtp base with the derived class.
Definition deferred_crtp_base.hpp:94
The internal SeqAn3 namespace.
Definition aligned_sequence_concept.hpp:26
invoke_deferred_crtp_base< deferred_crtp_base< selector< enable_policy, policy_t, empty_state >::template select, edit_traits >, derived_t > edit_distance_base
A base class for edit_distance_unbanded.
Definition edit_distance_fwd.hpp:124
A traits type for the alignment algorithm that exposes static information stored within the alignment...
Definition alignment/pairwise/detail/type_traits.hpp:80
static constexpr bool has_output_configuration
Flag indicating if any output option was set.
Definition alignment/pairwise/detail/type_traits.hpp:167
static constexpr bool compute_sequence_alignment
Flag indicating whether the sequence alignment shall be computed.
Definition alignment/pairwise/detail/type_traits.hpp:161
static constexpr bool compute_begin_positions
Flag indicating whether the begin positions shall be computed.
Definition alignment/pairwise/detail/type_traits.hpp:158
decltype(determine_alignment_result_type()) alignment_result_type
The alignment result type if present. Otherwise seqan3::detail::empty_type.
Definition alignment/pairwise/detail/type_traits.hpp:137
typename std::remove_reference_t< decltype(std::declval< configuration_t >().get_or(align_cfg::score_type< int32_t >{}))>::type original_score_type
The original score type selected by the user.
Definition alignment/pairwise/detail/type_traits.hpp:131
static constexpr bool compute_end_positions
Flag indicating whether the end positions shall be computed.
Definition alignment/pairwise/detail/type_traits.hpp:156
The default traits type for the edit distance algorithm.
Definition edit_distance_fwd.hpp:61
typename alignment_traits_type::original_score_type score_type
The type of the score.
Definition edit_distance_fwd.hpp:71
word_t word_type
The type of one machine word.
Definition edit_distance_fwd.hpp:67
static constexpr bool is_global
Whether the alignment is a global alignment or not.
Definition edit_distance_fwd.hpp:96
std::ranges::iterator_t< database_type > database_iterator
The type of an iterator of the database sequence.
Definition edit_distance_fwd.hpp:82
static constexpr uint8_t word_size
The size of one machine word.
Definition edit_distance_fwd.hpp:78
static constexpr bool compute_trace_matrix
Whether the alignment configuration indicates to compute and/or store the trace matrix.
Definition edit_distance_fwd.hpp:110
static constexpr bool use_max_errors
When true the computation will use the ukkonen trick with the last active cell and bounds the error t...
Definition edit_distance_fwd.hpp:92
static constexpr bool compute_score_matrix
Whether the alignment configuration indicates to compute and/or store the score matrix.
Definition edit_distance_fwd.hpp:108
static constexpr bool compute_matrix
Whether the alignment configuration indicates to compute and/or store the score or trace matrix.
Definition edit_distance_fwd.hpp:112
static constexpr bool compute_score
Whether the alignment configuration indicates to compute and/or store the score.
Definition edit_distance_fwd.hpp:98
typename alignment_traits_type::alignment_result_type alignment_result_type
The alignment result type generated by the algorithm.
Definition edit_distance_fwd.hpp:86
static constexpr bool is_semi_global
Whether the alignment is a semi-global alignment or not.
Definition edit_distance_fwd.hpp:94
static constexpr bool compute_end_positions
Whether the alignment configuration indicates to compute and/or store the end positions.
Definition edit_distance_fwd.hpp:105
typename alignment_result_value_type_accessor< alignment_result_type >::type result_value_type
The alignment result value type.
Definition edit_distance_fwd.hpp:88
static constexpr bool compute_sequence_alignment
Whether the alignment configuration indicates to compute and/or store the alignment of the sequences.
Definition edit_distance_fwd.hpp:100
static constexpr bool compute_begin_positions
Whether the alignment configuration indicates to compute and/or store the begin positions.
Definition edit_distance_fwd.hpp:102
An invocable wrapper that defers the instantiation of a crtp_base class.
Definition deferred_crtp_base.hpp:40
Store no state for state_t.
Definition edit_distance_fwd.hpp:33
Depending on B, select is the template template parameter T or F.
Definition edit_distance_fwd.hpp:49
The same as std::conditional but for template template parameters.
Definition edit_distance_fwd.hpp:45