61template <
typename sequence_pairs_t>
80template <
typename configuration_t>
81 requires is_type_specialisation_of_v<std::remove_cv_t<configuration_t>,
configuration>
95 template <arithmetic score_t>
101 if constexpr (configuration_t::template exists<align_cfg::detail::result_type>())
104 std::declval<configuration_t>()))>;
105 return typename result_type_cfg_t::type{};
115 static constexpr bool is_vectorised = configuration_t::template exists<align_cfg::vectorised>();
117 static constexpr bool is_parallel = configuration_t::template exists<align_cfg::parallel>();
119 static constexpr bool is_global = configuration_t::template exists<seqan3::align_cfg::method_global>();
121 static constexpr bool is_local = configuration_t::template exists<seqan3::align_cfg::method_local>();
123 static constexpr bool is_banded = configuration_t::template exists<align_cfg::band_fixed_size>();
125 static constexpr bool is_debug = configuration_t::template exists<detail::debug_mode>();
129 using scoring_scheme_type =
decltype(get<align_cfg::scoring_scheme>(std::declval<configuration_t>()).scheme);
146 lazy_conditional_t<is_vectorised, lazy<simd_matrix_coordinate, matrix_index_type>, matrix_coordinate>;
158 static constexpr bool compute_score = configuration_t::template exists<align_cfg::output_score>();
163 configuration_t::template exists<align_cfg::output_begin_position>();
167 static constexpr bool output_sequence1_id = configuration_t::template exists<align_cfg::output_sequence1_id>();
169 static constexpr bool output_sequence2_id = configuration_t::template exists<align_cfg::output_sequence2_id>();
187template <
typename function_t>
193 using callback_type =
typename function_traits<function_t>::template argument_type_at<1>;
Provides seqan3::detail::align_config_band.
Provides seqan3::align_cfg::detail::debug.
Provides global and local alignment configurations.
Provides seqan3::align_cfg::on_result.
Provides configuration for alignment output.
Provides seqan3::align_cfg::parallel configuration.
Provides seqan3::align_cfg::detail::result_type.
Provides alignment configuration seqan3::align_cfg::score_type.
Provides seqan3::align_cfg::scoring_scheme.
Provides seqan3::align_cfg::vectorised configuration.
Provides concepts needed internally for the alignment algorithms.
Provides utility functions for bit twiddling.
Provides seqan3::views::chunk.
A configuration element to set the score type used in the alignment algorithm.
Definition: align_config_score_type.hpp:36
Collection of elements to configure an algorithm.
Definition: configuration.hpp:45
Provides seqan3::configuration and utility functions.
Provides seqan3::detail::empty_type.
Provides various type traits for use on functions.
trace_directions
The possible directions a trace can have. The values can be combined by the logical |-operator.
Definition: trace_directions.hpp:29
constexpr simd_t iota(typename simd_traits< simd_t >::scalar_type const offset)
Fills a seqan3::simd::simd_type vector with the scalar values offset, offset+1, offset+2,...
Definition: algorithm.hpp:319
constexpr auto chunk
Divide a range in chunks.
Definition: chunk.hpp:823
constexpr auto zip
A view adaptor that takes several views and returns tuple-like values from every i-th element of each...
Definition: zip.hpp:573
A helper concept to check if a type is a range over seqan3::detail::sequence_pair.
Provides lazy template instantiation traits.
Provides seqan3::detail::matrix_index, seqan3::detail::matrix_coordinate and associated strong types.
The internal SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
The <ranges> header from C++20's standard library.
Provides seqan3::simd::simd_type.
Provides seqan3::simd::simd_traits.
A traits type for the alignment algorithm that exposes static information stored within the alignment...
Definition: type_traits.hpp:83
static constexpr bool is_banded
Flag indicating whether banded alignment mode is enabled.
Definition: type_traits.hpp:123
static constexpr bool is_vectorised
Flag to indicate vectorised mode.
Definition: type_traits.hpp:115
static constexpr bool is_local
Flag indicating whether local alignment mode is enabled.
Definition: type_traits.hpp:121
static constexpr bool requires_trace_information
Flag indicating whether the trace matrix needs to be computed.
Definition: type_traits.hpp:175
static constexpr bool has_output_configuration
Flag indicating if any output option was set.
Definition: type_traits.hpp:171
static constexpr bool output_sequence2_id
Flag indicating whether the id of the second sequence shall be returned.
Definition: type_traits.hpp:169
static constexpr bool is_parallel
Flag indicating whether parallel alignment mode is enabled.
Definition: type_traits.hpp:117
typename scoring_scheme_type::alphabet_type scoring_scheme_alphabet_type
The alphabet of the selected scoring scheme.
Definition: type_traits.hpp:131
static constexpr bool compute_sequence_alignment
Flag indicating whether the sequence alignment shall be computed.
Definition: type_traits.hpp:165
static constexpr size_t alignments_per_vector
The number of alignments that can be computed in one simd vector.
Definition: type_traits.hpp:149
static constexpr bool compute_begin_positions
Flag indicating whether the begin positions shall be computed.
Definition: type_traits.hpp:162
static constexpr auto determine_alignment_result_type() noexcept
Helper function to determine the alignment result type.
Definition: type_traits.hpp:99
static constexpr bool is_global
Flag indicating whether global alignment method is enabled.
Definition: type_traits.hpp:119
static constexpr bool is_debug
Flag indicating whether debug mode is enabled.
Definition: type_traits.hpp:125
decltype(get< align_cfg::scoring_scheme >(std::declval< configuration_t >()).scheme) scoring_scheme_type
The selected scoring scheme.
Definition: type_traits.hpp:129
static constexpr bool output_sequence1_id
Flag indicating whether the id of the first sequence shall be returned.
Definition: type_traits.hpp:167
lazy_conditional_t< is_vectorised, lazy< simd_matrix_coordinate, matrix_index_type >, matrix_coordinate > matrix_coordinate_type
The type of the matrix coordinate.
Definition: type_traits.hpp:146
decltype(determine_alignment_result_type()) alignment_result_type
The alignment result type if present. Otherwise seqan3::detail::empty_type.
Definition: type_traits.hpp:140
static constexpr bool is_one_way_execution
Flag indicating whether a user provided callback was given.
Definition: type_traits.hpp:127
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: type_traits.hpp:134
static constexpr bool compute_end_positions
Flag indicating whether the end positions shall be computed.
Definition: type_traits.hpp:160
static constexpr bool compute_score
Flag indicating whether the score shall be computed.
Definition: type_traits.hpp:158
A traits class to provide a uniform access to the properties of the wrapped alignment algorithm.
Definition: type_traits.hpp:189
typename function_traits< function_t >::template argument_type_at< 1 > callback_type
The type of the callback function called when a result was computed.
Definition: type_traits.hpp:193
typename function_traits< function_t >::template argument_type_at< 0 > sequence_input_type
The type of the sequence input to the alignment algorithm.
Definition: type_traits.hpp:191
typename function_traits< callback_type >::template argument_type_at< 0 > alignment_result_type
The type of the alignment result to be computed.
Definition: type_traits.hpp:195
A transformation trait to retrieve the chunked range over indexed sequence pairs.
Definition: type_traits.hpp:64
decltype(views::zip(std::declval< sequence_pairs_t >(), std::views::iota(0))|views::chunk(1)) type
The transformed type that models seqan3::detail::indexed_sequence_pair_range.
Definition: type_traits.hpp:66
An empty class type used in meta programming.
Definition: empty_type.hpp:23
seqan3::simd::simd_traits is the trait class that provides uniform interface to the properties of sim...
Definition: simd_traits.hpp:41
Provides type traits for working with templates.
Provides the declaration of seqan3::detail::trace_directions.
Provides seqan3::views::zip.