alignment_configurator.hpp File Reference

Provides seqan3::detail::alignment_selector. More...

#include <functional>
#include <tuple>
#include <utility>
#include <vector>
#include <seqan3/alignment/configuration/align_config_output.hpp>
#include <seqan3/alignment/configuration/align_config_result_type.hpp>
#include <seqan3/alignment/matrix/detail/alignment_score_matrix_one_column.hpp>
#include <seqan3/alignment/matrix/detail/alignment_score_matrix_one_column_banded.hpp>
#include <seqan3/alignment/matrix/detail/alignment_trace_matrix_full.hpp>
#include <seqan3/alignment/matrix/detail/alignment_trace_matrix_full_banded.hpp>
#include <seqan3/alignment/matrix/detail/combined_score_and_trace_matrix.hpp>
#include <seqan3/alignment/matrix/detail/score_matrix_single_column.hpp>
#include <seqan3/alignment/matrix/detail/trace_matrix_full.hpp>
#include <seqan3/alignment/pairwise/align_result_selector.hpp>
#include <seqan3/alignment/pairwise/alignment_algorithm.hpp>
#include <seqan3/alignment/pairwise/alignment_result.hpp>
#include <seqan3/alignment/pairwise/detail/concept.hpp>
#include <seqan3/alignment/pairwise/detail/pairwise_alignment_algorithm.hpp>
#include <seqan3/alignment/pairwise/detail/pairwise_alignment_algorithm_banded.hpp>
#include <seqan3/alignment/pairwise/detail/policy_affine_gap_recursion.hpp>
#include <seqan3/alignment/pairwise/detail/policy_affine_gap_recursion_banded.hpp>
#include <seqan3/alignment/pairwise/detail/policy_affine_gap_with_trace_recursion.hpp>
#include <seqan3/alignment/pairwise/detail/policy_affine_gap_with_trace_recursion_banded.hpp>
#include <seqan3/alignment/pairwise/detail/policy_alignment_matrix.hpp>
#include <seqan3/alignment/pairwise/detail/policy_alignment_result_builder.hpp>
#include <seqan3/alignment/pairwise/detail/policy_optimum_tracker.hpp>
#include <seqan3/alignment/pairwise/detail/policy_optimum_tracker_simd.hpp>
#include <seqan3/alignment/pairwise/detail/policy_scoring_scheme.hpp>
#include <seqan3/alignment/pairwise/detail/type_traits.hpp>
#include <seqan3/alignment/pairwise/edit_distance_algorithm.hpp>
#include <seqan3/alignment/pairwise/policy/affine_gap_init_policy.hpp>
#include <seqan3/alignment/pairwise/policy/affine_gap_policy.hpp>
#include <seqan3/alignment/pairwise/policy/alignment_matrix_policy.hpp>
#include <seqan3/alignment/pairwise/policy/find_optimum_policy.hpp>
#include <seqan3/alignment/pairwise/policy/scoring_scheme_policy.hpp>
#include <seqan3/alignment/pairwise/policy/simd_affine_gap_policy.hpp>
#include <seqan3/alignment/pairwise/policy/simd_find_optimum_policy.hpp>
#include <seqan3/alignment/scoring/aminoacid_scoring_scheme.hpp>
#include <seqan3/alignment/scoring/detail/simd_match_mismatch_scoring_scheme.hpp>
#include <seqan3/alignment/scoring/detail/simd_matrix_scoring_scheme.hpp>
#include <seqan3/alignment/scoring/nucleotide_scoring_scheme.hpp>
#include <seqan3/core/detail/deferred_crtp_base.hpp>
#include <seqan3/core/detail/template_inspection.hpp>
#include <seqan3/utility/simd/simd.hpp>
#include <seqan3/utility/tuple/concept.hpp>
#include <seqan3/utility/type_traits/lazy_conditional.hpp>
#include <seqan3/utility/views/type_reduce.hpp>
#include <seqan3/utility/views/zip.hpp>

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Classes
struct	seqan3::detail::alignment_configurator
	Configures the alignment algorithm given the sequences and the configuration object. More...
struct	seqan3::detail::alignment_contract< range_type, alignment_config_type >
	Provides several contracts to test when configuring the alignment algorithm. More...
struct	seqan3::detail::alignment_configurator::select_find_optimum_policy< traits_t >
	Transformation trait that chooses the correct find optimum policy. More...
struct	seqan3::detail::alignment_configurator::select_gap_policy< traits_t >
	Transformation trait that chooses the correct gap policy. More...
struct	seqan3::detail::alignment_configurator::select_gap_recursion_policy< config_t >
	Selects the gap recursion policy. More...
struct	seqan3::detail::alignment_configurator::select_matrix_policy< traits_t >
	Transformation trait that chooses the correct matrix policy. More...

Namespaces
namespace	seqan3
	The main SeqAn3 namespace.
namespace	seqan3::detail
	The internal SeqAn3 namespace.

Detailed Description

Provides seqan3::detail::alignment_selector.

Author

Rene Rahn <rene.rahn AT fu-berlin.de>