seqan3::detail::alignment_configuration_traits< configuration_t > Struct Template Reference

A traits type for the alignment algorithm that exposes static information stored within the alignment configuration object. More...

#include <seqan3/alignment/pairwise/detail/type_traits.hpp>

Public Types
using	alignment_result_type = decltype(determine_alignment_result_type())
	The alignment result type if present. Otherwise seqan3::detail::empty_type.
using	matrix_coordinate_type = lazy_conditional_t< is_vectorised, lazy< simd_matrix_coordinate, matrix_index_type >, matrix_coordinate >
	The type of the matrix coordinate.
using	matrix_index_type = std::conditional_t< is_vectorised, simd_type_t< select_scalar_index_t< original_score_type > >, size_t >
	The type of the matrix index.
using	original_score_type = typename std::remove_reference_t< decltype(std::declval< configuration_t >().get_or(align_cfg::score_type< int32_t >{}))>::type
	The original score type selected by the user.
using	score_type = std::conditional_t< is_vectorised, simd_type_t< original_score_type >, original_score_type >
	The score type for the alignment algorithm.
using	scoring_scheme_alphabet_type = typename scoring_scheme_type::alphabet_type
	The alphabet of the selected scoring scheme.
using	scoring_scheme_type = decltype(get< align_cfg::scoring_scheme >(std::declval< configuration_t >()).scheme)
	The selected scoring scheme.
using	trace_type = std::conditional_t< is_vectorised, simd_type_t< original_score_type >, trace_directions >
	The trace directions type for the alignment algorithm.

Static Public Attributes
static constexpr size_t	alignments_per_vector
	The number of alignments that can be computed in one simd vector.
static constexpr bool	compute_begin_positions
	Flag indicating whether the begin positions shall be computed.
static constexpr bool	compute_end_positions = configuration_t::template exists<align_cfg::output_end_position>()
	Flag indicating whether the end positions shall be computed.
static constexpr bool	compute_score = configuration_t::template exists<align_cfg::output_score>()
	Flag indicating whether the score shall be computed.
static constexpr bool	compute_sequence_alignment = configuration_t::template exists<align_cfg::output_alignment>()
	Flag indicating whether the sequence alignment shall be computed.
static constexpr bool	has_output_configuration
	Flag indicating if any output option was set.
static constexpr bool	is_banded = configuration_t::template exists<align_cfg::band_fixed_size>()
	Flag indicating whether banded alignment mode is enabled.
static constexpr bool	is_debug = configuration_t::template exists<detail::debug_mode>()
	Flag indicating whether debug mode is enabled.
static constexpr bool	is_global = configuration_t::template exists<seqan3::align_cfg::method_global>()
	Flag indicating whether global alignment method is enabled.
static constexpr bool	is_local = configuration_t::template exists<seqan3::align_cfg::method_local>()
	Flag indicating whether local alignment mode is enabled.
static constexpr bool	is_one_way_execution = configuration_t::template exists<align_cfg::on_result>()
	Flag indicating whether a user provided callback was given.
static constexpr bool	is_parallel = configuration_t::template exists<align_cfg::parallel>()
	Flag indicating whether parallel alignment mode is enabled.
static constexpr bool	is_vectorised = configuration_t::template exists<align_cfg::vectorised>()
	Flag to indicate vectorised mode.
static constexpr bool	output_sequence1_id = configuration_t::template exists<align_cfg::output_sequence1_id>()
	Flag indicating whether the id of the first sequence shall be returned.
static constexpr bool	output_sequence2_id = configuration_t::template exists<align_cfg::output_sequence2_id>()
	Flag indicating whether the id of the second sequence shall be returned.
static constexpr bool	requires_trace_information = compute_begin_positions || compute_sequence_alignment
	Flag indicating whether the trace matrix needs to be computed.

Private Types
template<arithmetic score_t>
using	select_scalar_index_t = min_viable_uint_t< 1ull<<(bits_of< score_t > - 1)>
	An index type (i.e. unsigned integral) for a score_type which has the same bit size.

Static Private Member Functions
static constexpr auto	determine_alignment_result_type () noexcept
	Helper function to determine the alignment result type.

Detailed Description

template<typename configuration_t>
requires is_type_specialisation_of_v<std::remove_cv_t<configuration_t>, configuration>
struct seqan3::detail::alignment_configuration_traits< configuration_t >

A traits type for the alignment algorithm that exposes static information stored within the alignment configuration object.

Template Parameters

configuration_t

The type of the alignment configuration object; must be a specialisation of seqan3::configuration.

Member Typedef Documentation

select_scalar_index_t

template<typename configuration_t >

template<arithmetic score_t>

using seqan3::detail::alignment_configuration_traits< configuration_t >::select_scalar_index_t = min_viable_uint_t<1ull << (bits_of<score_t> - 1)>

private

An index type (i.e. unsigned integral) for a score_type which has the same bit size.

Template Parameters

score_t

The score type for which the corresponding index type shall be returned; must model seqan3::arithmetic.

If the score type models std::integral it will simply be converted to its unsigned counterpart. For floating point types the bit size is determined and the corresponding minimal viable unsigned integral type (seqan3::detail::min_viable_uint_t) is returned.

Member Data Documentation

alignments_per_vector

template<typename configuration_t >

constexpr size_t seqan3::detail::alignment_configuration_traits< configuration_t >::alignments_per_vector

staticconstexpr

Initial value:

= []() constexpr
    {
        if constexpr (is_vectorised)
            return simd_traits<score_type>::length;
        else
            return 1;
    }()

The number of alignments that can be computed in one simd vector.

compute_begin_positions

template<typename configuration_t >

constexpr bool seqan3::detail::alignment_configuration_traits< configuration_t >::compute_begin_positions

staticconstexpr

Initial value:

=
        configuration_t::template exists<align_cfg::output_begin_position>()

Flag indicating whether the begin positions shall be computed.

has_output_configuration

template<typename configuration_t >

constexpr bool seqan3::detail::alignment_configuration_traits< configuration_t >::has_output_configuration

staticconstexpr

Initial value:

= compute_score || compute_end_positions || compute_begin_positions
                                                  || compute_sequence_alignment || output_sequence1_id
                                                  || output_sequence2_id

Flag indicating if any output option was set.

---

The documentation for this struct was generated from the following file:

• alignment/pairwise/detail/type_traits.hpp