Here is a list of all documented class members with links to the class documentation for each member:

- s -

• safe_filesystem_entry() : seqan3::detail::safe_filesystem_entry
• sam_file_header() : seqan3::sam_file_header< ref_ids_type >
• sam_file_input() : seqan3::sam_file_input< traits_type_, selected_field_ids_, valid_formats_ >
• sam_file_output() : seqan3::sam_file_output< selected_field_ids_, valid_formats_, ref_ids_type >
• sam_record() : seqan3::sam_record< field_types, field_ids >
• sam_require_header : seqan3::sam_file_output_options
• sam_tag_type_t : seqan3::sam_tag_type< tag_value >
• save_minimal() : semialphabet
• scalar_type : seqan3::detail::builtin_simd_traits_helper< builtin_simd_t >, seqan3::detail::policy_optimum_tracker_simd< alignment_configuration_t, optimum_updater_t >, seqan3::detail::simd_match_mismatch_scoring_scheme< simd_score_t, alphabet_t, alignment_t >, seqan3::detail::simd_matrix_scoring_scheme< simd_score_t, alphabet_t, alignment_t >, seqan3::detail::view_to_simd< urng_t, simd_t >, seqan3::simd::simd_traits< simd_t >, seqan3::simd::simd_traits< builtin_simd_t >
• scheme : seqan3::align_cfg::scoring_scheme< scoring_scheme_t >
• scoped_reader_type() : seqan3::detail::reader_writer_manager::scoped_reader_type
• scoped_writer_type() : seqan3::detail::reader_writer_manager::scoped_writer_type
• score() : scoring_scheme_for, seqan3::align_cfg::min_score, seqan3::alignment_result< alignment_result_value_t >, seqan3::detail::alignment_optimum< score_t >, seqan3::detail::alignment_result_value_type< sequence1_id_t, sequence2_id_t, score_t, end_positions_t, begin_positions_t, alignment_t, score_debug_matrix_t, trace_debug_matrix_t >, seqan3::detail::edit_distance_unbanded_global_policy< derived_t, edit_traits >, seqan3::detail::simd_match_mismatch_scoring_scheme< simd_score_t, alphabet_t, alignment_t >, seqan3::detail::simd_matrix_scoring_scheme< simd_score_t, alphabet_t, alignment_t >, seqan3::hamming_scoring_scheme, seqan3::scoring_scheme_base< derived_t, alphabet_t, score_t >
• score_cell_type : seqan3::detail::affine_cell_proxy< tuple_t >
• score_debug_matrix : seqan3::detail::alignment_algorithm< config_t, algorithm_policies_t >, seqan3::detail::alignment_result_value_type< sequence1_id_t, sequence2_id_t, score_t, end_positions_t, begin_positions_t, alignment_t, score_debug_matrix_t, trace_debug_matrix_t >
• score_debug_matrix_t : seqan3::detail::alignment_algorithm< config_t, algorithm_policies_t >
• score_delta_of_word() : seqan3::detail::edit_distance_score_matrix_full< word_t, score_t, is_semi_global, use_max_errors >
• score_for_padding_symbol : seqan3::detail::simd_matrix_scoring_scheme< simd_score_t, alphabet_t, alignment_t >
• score_init() : seqan3::detail::edit_distance_unbanded_global_policy< derived_t, edit_traits >, seqan3::detail::edit_distance_unbanded_semi_global_policy< derived_t, edit_traits >
• score_mask : seqan3::detail::edit_distance_unbanded< database_t, query_t, align_config_t, edit_traits >
• score_matrix() : seqan3::alignment_result< alignment_result_value_t >, seqan3::detail::alignment_matrix_policy< alignment_algorithm_t, score_matrix_t, trace_matrix_t >, seqan3::detail::combined_score_and_trace_matrix< score_matrix_t, trace_matrix_t >, seqan3::detail::edit_distance_unbanded_score_matrix_policy< derived_t, edit_traits >
• score_matrix_init() : seqan3::detail::edit_distance_unbanded_score_matrix_policy< derived_t, edit_traits >
• score_matrix_it : seqan3::detail::combined_score_and_trace_matrix< score_matrix_t, trace_matrix_t >::iterator
• score_matrix_iter : seqan3::detail::alignment_matrix_policy< alignment_algorithm_t, score_matrix_t, trace_matrix_t >
• score_matrix_iter_type : seqan3::detail::combined_score_and_trace_matrix< score_matrix_t, trace_matrix_t >::iterator
• score_matrix_reference_type : seqan3::detail::combined_score_and_trace_matrix< score_matrix_t, trace_matrix_t >::iterator
• score_matrix_sentinel : seqan3::detail::combined_score_and_trace_matrix< score_matrix_t, trace_matrix_t >::sentinel
• score_matrix_sentinel_type : seqan3::detail::combined_score_and_trace_matrix< score_matrix_t, trace_matrix_t >::sentinel
• score_matrix_single_column() : seqan3::detail::score_matrix_single_column< score_t >
• score_matrix_t : seqan3::detail::alignment_configurator::select_matrix_policy< traits_t >
• score_matrix_type : seqan3::detail::default_edit_distance_trait_type< database_t, query_t, align_config_t, is_semi_global_t, word_t >
• score_offset : seqan3::detail::simd_global_alignment_state< simd_t >
• score_t : seqan3::alignment_result< alignment_result_value_t >, seqan3::detail::alignment_configurator::select_find_optimum_policy< traits_t >, seqan3::detail::alignment_configurator::select_gap_policy< traits_t >
• score_type() : scoring_scheme_for, seqan3::align_cfg::score_type< score_t >, seqan3::detail::align_result_selector< first_range_t, second_range_t, configuration_t >, seqan3::detail::alignment_configuration_traits< configuration_t >, seqan3::detail::combined_score_and_trace_matrix< score_matrix_t, trace_matrix_t >, seqan3::detail::default_edit_distance_trait_type< database_t, query_t, align_config_t, is_semi_global_t, word_t >, seqan3::detail::edit_distance_score_matrix_full< word_t, score_t, is_semi_global, use_max_errors >, seqan3::detail::pairwise_alignment_algorithm< alignment_configuration_t, policies_t >, seqan3::detail::policy_affine_gap_recursion< alignment_configuration_t >, seqan3::detail::policy_affine_gap_recursion_banded< alignment_configuration_t >, seqan3::detail::policy_affine_gap_with_trace_recursion< alignment_configuration_t >, seqan3::detail::policy_affine_gap_with_trace_recursion_banded< alignment_configuration_t >, seqan3::detail::policy_alignment_matrix< traits_t, alignment_matrix_t >, seqan3::detail::policy_optimum_tracker< alignment_configuration_t, optimum_updater_t >, seqan3::detail::policy_optimum_tracker_simd< alignment_configuration_t, optimum_updater_t >, seqan3::hamming_scoring_scheme, seqan3::scoring_scheme_base< derived_t, alphabet_t, score_t >
• scoring_scheme() : seqan3::align_cfg::scoring_scheme< scoring_scheme_t >, seqan3::detail::policy_scoring_scheme< alignment_configuration_t, scoring_scheme_t >, seqan3::detail::scoring_scheme_policy< alignment_algorithm_t, scoring_scheme_t >
• scoring_scheme_alphabet_type : seqan3::detail::alignment_configuration_traits< configuration_t >
• scoring_scheme_base() : seqan3::scoring_scheme_base< derived_t, alphabet_t, score_t >
• scoring_scheme_data : seqan3::detail::simd_matrix_scoring_scheme< simd_score_t, alphabet_t, alignment_t >
• scoring_scheme_policy() : seqan3::detail::scoring_scheme_policy< alignment_algorithm_t, scoring_scheme_t >
• scoring_scheme_profile_column() : seqan3::detail::policy_scoring_scheme< alignment_configuration_t, scoring_scheme_t >, seqan3::detail::scoring_scheme_policy< alignment_algorithm_t, scoring_scheme_t >
• scoring_scheme_type : seqan3::detail::alignment_configuration_traits< configuration_t >
• screenWidth : seqan3::detail::format_help::console_layout_struct
• sdsl_char_type : seqan3::bi_fm_index< alphabet_t, text_layout_mode_, sdsl_index_type_ >, seqan3::bi_fm_index_cursor< index_t >, seqan3::detail::fm_index_cursor_node< index_t >, seqan3::fm_index< alphabet_t, text_layout_mode_, sdsl_index_type_ >, seqan3::fm_index_cursor< index_t >
• sdsl_index_type : seqan3::bi_fm_index< alphabet_t, text_layout_mode_, sdsl_index_type_ >, seqan3::bi_fm_index_cursor< index_t >, seqan3::fm_index< alphabet_t, text_layout_mode_, sdsl_index_type_ >, seqan3::fm_index_cursor< index_t >
• sdsl_sigma_type : seqan3::bi_fm_index< alphabet_t, text_layout_mode_, sdsl_index_type_ >, seqan3::bi_fm_index_cursor< index_t >, seqan3::fm_index< alphabet_t, text_layout_mode_, sdsl_index_type_ >, seqan3::fm_index_cursor< index_t >
• search_algo_bi() : seqan3::detail::search_scheme_algorithm< configuration_t, index_t, policies_t >
• search_all_best_hits : seqan3::detail::search_traits< search_configuration_t >
• search_all_hits : seqan3::detail::search_traits< search_configuration_t >
• search_result() : seqan3::search_result< query_id_type, cursor_type, reference_id_type, reference_begin_position_type >
• search_result_type : seqan3::detail::policy_search_result_builder< search_configuration_t >, seqan3::detail::search_scheme_algorithm< configuration_t, index_t, policies_t >, seqan3::detail::search_traits< search_configuration_t >, seqan3::detail::unidirectional_search_algorithm< configuration_t, index_t, policies_t >
• search_scheme_algorithm() : seqan3::detail::search_scheme_algorithm< configuration_t, index_t, policies_t >
• search_single_best_hit : seqan3::detail::search_traits< search_configuration_t >
• search_strata_hits : seqan3::detail::search_traits< search_configuration_t >
• search_traits_type : seqan3::detail::policy_search_result_builder< search_configuration_t >
• search_trivial() : seqan3::detail::unidirectional_search_algorithm< configuration_t, index_t, policies_t >
• sec_rng : seqan3::detail::aligned_sequence_builder< fst_sequence_t, sec_sequence_t >
• second : seqan3::detail::advanceable_alignment_coordinate< state >
• second_aligned_t : seqan3::detail::make_pairwise_alignment_type< first_sequence_t, second_sequence_t >
• second_it : seqan3::detail::pairwise_combine_view< underlying_range_type >::basic_iterator< range_type >
• second_range_is_given : seqan3::detail::minimiser_view< urng1_t, urng2_t >
• second_seq_t : seqan3::detail::alignment_contract< range_type, alignment_config_type >
• second_sequence() : seqan3::detail::debug_matrix< matrix_t, first_sequence_t, second_sequence_t >
• second_sequence_slice_positions : seqan3::detail::aligned_sequence_builder< fst_sequence_t, sec_sequence_t >::result_type
• secondary_stream : seqan3::sam_file_input< traits_type_, selected_field_ids_, valid_formats_ >, seqan3::sam_file_output< selected_field_ids_, valid_formats_, ref_ids_type >, seqan3::sequence_file_input< traits_type_, selected_field_ids_, valid_formats_ >, seqan3::sequence_file_output< selected_field_ids_, valid_formats_ >, seqan3::structure_file_input< traits_type_, selected_field_ids_, valid_formats_ >, seqan3::structure_file_output< selected_field_ids_, valid_formats_ >
• seek_to() : seqan3::detail::in_file_iterator< file_type >
• select_alignment_algorithm_t : seqan3::detail::alignment_configurator
• select_and_return_algorithm() : seqan3::detail::search_configurator
• select_scalar_index_t : seqan3::detail::alignment_configuration_traits< configuration_t >
• select_types_with_ids_t : seqan3::detail::select_types_with_ids< field_types, field_types_as_ids, selected_field_ids, field_no, return_types >
• selected_field_ids : seqan3::sam_file_input< traits_type_, selected_field_ids_, valid_formats_ >, seqan3::sam_file_output< selected_field_ids_, valid_formats_, ref_ids_type >, seqan3::sequence_file_input< traits_type_, selected_field_ids_, valid_formats_ >, seqan3::sequence_file_output< selected_field_ids_, valid_formats_ >, seqan3::structure_file_input< traits_type_, selected_field_ids_, valid_formats_ >, seqan3::structure_file_output< selected_field_ids_, valid_formats_ >
• selected_frames : seqan3::detail::view_translate< urng_t >, seqan3::detail::view_translate_join< urng_t >
• selected_sequence_format() : seqan3::sequence_file_input< traits_type_, selected_field_ids_, valid_formats_ >::selected_sequence_format< format_t >
• semialphabet_any() : seqan3::semialphabet_any< size >
• sentinel : seqan3::detail::alignment_matrix_column_major_range_base< derived_t >::alignment_column_type, seqan3::detail::alignment_matrix_column_major_range_base< derived_t >, seqan3::detail::alignment_score_matrix_one_column< score_t >, seqan3::detail::alignment_score_matrix_one_column_banded< score_t >, seqan3::detail::alignment_trace_matrix_full< trace_t, coordinate_only >, seqan3::detail::alignment_trace_matrix_full_banded< trace_t, coordinate_only >, seqan3::detail::combined_score_and_trace_matrix< score_matrix_t, trace_matrix_t >::sentinel, seqan3::detail::minimiser_view< urng1_t, urng2_t >, seqan3::detail::single_pass_input_view< urng_t >, seqan3::sam_file_input< traits_type_, selected_field_ids_, valid_formats_ >, seqan3::sam_file_output< selected_field_ids_, valid_formats_, ref_ids_type >, seqan3::sequence_file_input< traits_type_, selected_field_ids_, valid_formats_ >, seqan3::sequence_file_output< selected_field_ids_, valid_formats_ >, seqan3::structure_file_input< traits_type_, selected_field_ids_, valid_formats_ >, seqan3::structure_file_output< selected_field_ids_, valid_formats_ >
• sentinel_t : seqan3::detail::kmer_hash_view< urng_t >::basic_iterator< const_range >
• sentinel_type : seqan3::detail::async_input_buffer_view< urng_t >::iterator, seqan3::detail::basic_iterator< single_pass_input_view< view_type > >, seqan3::detail::repeat_view< value_t >, seqan3::detail::view_take_exactly< urng_t, or_throw >::basic_iterator< const_range >
• seq1_slice_offset : seqan3::detail::alignment_matrix_policy< alignment_algorithm_t, score_matrix_t, trace_matrix_t >
• seq2_slice_offset : seqan3::detail::alignment_matrix_policy< alignment_algorithm_t, score_matrix_t, trace_matrix_t >
• seq_alphabet : seqan3::structure_file_input_default_traits_aa, seqan3::structure_file_input_default_traits_rna, structure_file_input_traits
• seq_container : seqan3::structure_file_input_default_traits_rna, structure_file_input_traits
• seq_legal_alphabet : seqan3::structure_file_input_default_traits_aa, seqan3::structure_file_input_default_traits_rna, structure_file_input_traits
• seq_type : seqan3::structure_file_input< traits_type_, selected_field_ids_, valid_formats_ >
• seqan3_alphabet_tuple_like : seqan3::alphabet_tuple_base< derived_type, component_types >
• seqan3_recursive_required_types : seqan3::alphabet_tuple_base< derived_type, component_types >, seqan3::alphabet_variant< alternative_types >
• seqan3_required_types : seqan3::alphabet_tuple_base< derived_type, component_types >, seqan3::alphabet_variant< alternative_types >
• sequence() : seqan3::sam_record< field_types, field_ids >, seqan3::sequence_record< field_types, field_ids >, seqan3::structure_record< field_types, field_ids >
• sequence1_begin_position() : seqan3::alignment_result< alignment_result_value_t >
• sequence1_end_position() : seqan3::alignment_result< alignment_result_value_t >
• sequence1_id() : seqan3::alignment_result< alignment_result_value_t >, seqan3::detail::alignment_result_value_type< sequence1_id_t, sequence2_id_t, score_t, end_positions_t, begin_positions_t, alignment_t, score_debug_matrix_t, trace_debug_matrix_t >
• sequence1_id_t : seqan3::alignment_result< alignment_result_value_t >
• sequence2_begin_position() : seqan3::alignment_result< alignment_result_value_t >
• sequence2_end_position() : seqan3::alignment_result< alignment_result_value_t >
• sequence2_id() : seqan3::alignment_result< alignment_result_value_t >, seqan3::detail::alignment_result_value_type< sequence1_id_t, sequence2_id_t, score_t, end_positions_t, begin_positions_t, alignment_t, score_debug_matrix_t, trace_debug_matrix_t >
• sequence2_id_t : seqan3::alignment_result< alignment_result_value_t >
• sequence_alphabet() : sam_file_input_traits, seqan3::sam_file_input_default_traits< ref_sequences_t, ref_ids_t >, seqan3::sequence_file_input_default_traits_aa, seqan3::sequence_file_input_default_traits_dna, sequence_file_input_traits
• sequence_alphabet_type : seqan3::masked< sequence_alphabet_t >, seqan3::qualified< sequence_alphabet_t, quality_alphabet_t >, seqan3::structured_aa< sequence_alphabet_t, structure_alphabet_t >, seqan3::structured_rna< sequence_alphabet_t, structure_alphabet_t >
• sequence_container() : sam_file_input_traits, seqan3::sam_file_input_default_traits< ref_sequences_t, ref_ids_t >, seqan3::sequence_file_input_default_traits_dna, sequence_file_input_traits
• sequence_file_input() : seqan3::sequence_file_input< traits_type_, selected_field_ids_, valid_formats_ >
• sequence_file_input_options_type : seqan3::sequence_file_input< traits_type_, selected_field_ids_, valid_formats_ >
• sequence_file_output() : seqan3::sequence_file_output< selected_field_ids_, valid_formats_ >
• sequence_format_base() : seqan3::sequence_file_input< traits_type_, selected_field_ids_, valid_formats_ >::sequence_format_base
• sequence_input_type : seqan3::detail::alignment_function_traits< function_t >
• sequence_legal_alphabet() : sam_file_input_traits, seqan3::sam_file_input_default_traits< ref_sequences_t, ref_ids_t >, seqan3::sequence_file_input_default_traits_aa, seqan3::sequence_file_input_default_traits_dna, sequence_file_input_traits
• sequence_position() : seqan3::sam_record< field_types, field_ids >
• sequence_record() : seqan3::sequence_record< field_types, field_ids >
• sequence_structure() : seqan3::structure_record< field_types, field_ids >
• sequence_type : seqan3::sam_file_input< traits_type_, selected_field_ids_, valid_formats_ >, seqan3::sequence_file_input< traits_type_, selected_field_ids_, valid_formats_ >
• serialize() : seqan3::bi_fm_index< alphabet_t, text_layout_mode_, sdsl_index_type_ >, seqan3::bi_fm_index_cursor< index_t >, seqan3::bitpacked_sequence< alphabet_type >, seqan3::bloom_filter< data_layout_mode_ >, seqan3::concatenated_sequences< underlying_container_type, data_delimiters_type >, seqan3::detail::fm_index_cursor_node< index_t >, seqan3::dynamic_bitset< bit_capacity >, seqan3::fm_index< alphabet_t, text_layout_mode_, sdsl_index_type_ >, seqan3::fm_index_cursor< index_t >, seqan3::interleaved_bloom_filter< data_layout_mode_ >, seqan3::scoring_scheme_base< derived_t, alphabet_t, score_t >, seqan3::small_vector< value_type_, capacity_ >
• set() : seqan3::dynamic_bitset< bit_capacity >::reference_proxy_type, seqan3::dynamic_bitset< bit_capacity >
• set_custom_matrix() : seqan3::scoring_scheme_base< derived_t, alphabet_t, score_t >
• set_hamming_distance() : seqan3::scoring_scheme_base< derived_t, alphabet_t, score_t >
• set_iterator_type : seqan3::gap_decorator< inner_type >
• set_references() : seqan3::sam_file_input< traits_type_, selected_field_ids_, valid_formats_ >
• set_similarity_matrix() : seqan3::aminoacid_scoring_scheme< score_type >
• set_simple_scheme() : seqan3::scoring_scheme_base< derived_t, alphabet_t, score_t >
• set_target_indices() : seqan3::detail::max_score_banded_updater
• set_trace_direction() : seqan3::detail::trace_iterator_base< derived_t, matrix_iter_t >
• set_underlying_stream() : seqan3::debug_stream_type< char_t >
• setf() : seqan3::debug_stream_type< char_t >
• shape() : seqan3::shape
• shape_ : seqan3::detail::kmer_hash_view< urng_t >::basic_iterator< const_range >, seqan3::detail::kmer_hash_view< urng_t >
• shape_too_long_error() : seqan3::detail::kmer_hash_view< urng_t >
• short_copyright : seqan3::argument_parser_meta_data
• short_description : seqan3::argument_parser_meta_data
• show_advanced_options : seqan3::detail::format_help_base< derived_type >
• shrink_to_fit() : seqan3::bitpacked_sequence< alphabet_type >, seqan3::concatenated_sequences< underlying_container_type, data_delimiters_type >, seqan3::dynamic_bitset< bit_capacity >, seqan3::small_vector< value_type_, capacity_ >
• sigma : seqan3::bi_fm_index_cursor< index_t >, seqan3::detail::kmer_hash_view< urng_t >::basic_iterator< const_range >, seqan3::fm_index_cursor< index_t >
• simd_affine_gap_policy() : seqan3::detail::simd_affine_gap_policy< alignment_algorithm_t, score_t, align_local_t >, seqan3::detail::simd_find_optimum_policy< alignment_algorithm_t, simd_t >
• simd_alphabet_ranks_type : seqan3::detail::simd_matrix_scoring_scheme< simd_score_t, alphabet_t, alignment_t >
• simd_find_optimum_policy() : seqan3::detail::simd_find_optimum_policy< alignment_algorithm_t, simd_t >
• simd_match_mismatch_scoring_scheme() : seqan3::detail::simd_match_mismatch_scoring_scheme< simd_score_t, alphabet_t, alignment_t >
• simd_matrix_scoring_scheme() : seqan3::detail::simd_matrix_scoring_scheme< simd_score_t, alphabet_t, alignment_t >
• simd_score_profile_type : seqan3::detail::simd_matrix_scoring_scheme< simd_score_t, alphabet_t, alignment_t >
• single_pass_input_view() : seqan3::detail::single_pass_input_view< urng_t >
• single_trace_column_type : seqan3::detail::trace_matrix_full< trace_t >::iterator
• single_value : seqan3::detail::repeat_view< value_t >
• single_value_t : seqan3::detail::repeat_view< value_t >
• size() : seqan3::bi_fm_index< alphabet_t, text_layout_mode_, sdsl_index_type_ >, seqan3::bitpacked_sequence< alphabet_type >, seqan3::concatenated_sequences< underlying_container_type, data_delimiters_type >, seqan3::configuration< configs_t >, seqan3::detail::alignment_matrix_column_major_range_base< derived_t >::alignment_column_type, seqan3::detail::kmer_hash_view< urng_t >, seqan3::detail::pairwise_combine_view< underlying_range_type >, seqan3::detail::view_interleave< urng_t, inserted_rng_t >, seqan3::detail::view_take_exactly< urng_t, or_throw >, seqan3::detail::view_to_simd< urng_t, simd_t >, seqan3::detail::view_translate< urng_t >, seqan3::detail::view_translate_join< urng_t >, seqan3::detail::view_translate_single< urng_t >, seqan3::dynamic_bitset< bit_capacity >::bitfield, seqan3::dynamic_bitset< bit_capacity >, seqan3::fields< fs >, seqan3::fm_index< alphabet_t, text_layout_mode_, sdsl_index_type_ >, seqan3::gap_decorator< inner_type >, seqan3::interleaved_bloom_filter< data_layout_mode_ >::membership_agent_type::binning_bitvector, seqan3::small_vector< value_type_, capacity_ >, seqan3::type_list< types >
• size_in_bits : seqan3::bloom_filter< data_layout_mode_ >
• size_type() : sdsl_index, seqan3::aligned_allocator< value_t, alignment_v >, seqan3::bi_fm_index< alphabet_t, text_layout_mode_, sdsl_index_type_ >, seqan3::bi_fm_index_cursor< index_t >, seqan3::bitpacked_sequence< alphabet_type >, seqan3::concatenated_sequences< underlying_container_type, data_delimiters_type >, seqan3::detail::alignment_score_matrix_one_column< score_t >, seqan3::detail::alignment_score_matrix_one_column_banded< score_t >, seqan3::detail::alignment_score_matrix_one_column_base< score_t >, seqan3::detail::alignment_trace_matrix_base< trace_t >, seqan3::detail::alignment_trace_matrix_full< trace_t, coordinate_only >, seqan3::detail::alignment_trace_matrix_full_banded< trace_t, coordinate_only >, seqan3::detail::coordinate_matrix< index_t >, seqan3::detail::debug_matrix< matrix_t, first_sequence_t, second_sequence_t >, seqan3::detail::edit_distance_score_matrix_full< word_t, score_t, is_semi_global, use_max_errors >, seqan3::detail::edit_distance_trace_matrix_full< word_t, is_semi_global, use_max_errors >, seqan3::detail::fm_index_cursor_node< index_t >, seqan3::detail::in_file_iterator< file_type >, seqan3::detail::matrix< matrix_t >, seqan3::detail::out_file_iterator< file_type >, seqan3::detail::two_dimensional_matrix< value_t, allocator_t, order >, seqan3::detail::view_interleave< urng_t, inserted_rng_t >, seqan3::detail::view_translate< urng_t >, seqan3::detail::view_translate_join< urng_t >, seqan3::detail::view_translate_single< urng_t >, seqan3::dynamic_bitset< bit_capacity >, seqan3::fm_index< alphabet_t, text_layout_mode_, sdsl_index_type_ >, seqan3::fm_index_cursor< index_t >, seqan3::gap_decorator< inner_type >, seqan3::sam_file_input< traits_type_, selected_field_ids_, valid_formats_ >, seqan3::sam_file_output< selected_field_ids_, valid_formats_, ref_ids_type >, seqan3::sequence_file_input< traits_type_, selected_field_ids_, valid_formats_ >, seqan3::sequence_file_output< selected_field_ids_, valid_formats_ >, seqan3::small_vector< value_type_, capacity_ >, seqan3::structure_file_input< traits_type_, selected_field_ids_, valid_formats_ >, seqan3::structure_file_output< selected_field_ids_, valid_formats_ >
• skills() : derived_from_strong_type, seqan3::detail::strong_type< value_t, derived_t, skills_ >
• slice_sequences() : seqan3::detail::alignment_matrix_policy< alignment_algorithm_t, score_matrix_t, trace_matrix_t >
• small_patterns() : seqan3::detail::edit_distance_unbanded< database_t, query_t, align_config_t, edit_traits >
• small_string() : seqan3::small_string< capacity_ >
• small_vector() : seqan3::small_vector< value_type_, capacity_ >
• soft_back : seqan3::cigar_clipped_bases
• soft_clipping_at_front() : seqan3::detail::format_sam_base
• soft_front : seqan3::cigar_clipped_bases
• sorting : seqan3::sam_file_header< ref_ids_type >
• spin_delay() : seqan3::detail::spin_delay
• split_into_sub_matrices() : seqan3::detail::view_to_simd< urng_t, simd_t >::iterator_type
• state : seqan3::detail::execution_handler_parallel
• state_ptr : seqan3::detail::async_input_buffer_view< urng_t >, seqan3::detail::single_pass_input_view< urng_t >
• step_size : seqan3::detail::view_interleave< urng_t, inserted_rng_t >
• stop_and_wait() : seqan3::detail::execution_handler_parallel::internal_state
• storage : seqan3::detail::two_dimensional_matrix< value_t, allocator_t, order >
• storage_iterator : seqan3::detail::two_dimensional_matrix< value_t, allocator_t, order >::basic_iterator< const_range >
• storage_type : seqan3::detail::two_dimensional_matrix< value_t, allocator_t, order >
• store_help_page_element() : seqan3::detail::format_help_base< derived_type >
• str() : seqan3::small_string< capacity_ >
• stratum : seqan3::detail::search_scheme_algorithm< configuration_t, index_t, policies_t >, seqan3::detail::unidirectional_search_algorithm< configuration_t, index_t, policies_t >, seqan3::search_cfg::hit_strata
• stream : seqan3::debug_stream_type< char_t >
• stream_buf : seqan3::detail::fast_istreambuf_iterator< char_t, traits_t >, seqan3::detail::fast_ostreambuf_iterator< char_t, traits_t >
• stream_buffer : seqan3::sam_file_input< traits_type_, selected_field_ids_, valid_formats_ >, seqan3::sam_file_output< selected_field_ids_, valid_formats_, ref_ids_type >, seqan3::sequence_file_input< traits_type_, selected_field_ids_, valid_formats_ >, seqan3::sequence_file_output< selected_field_ids_, valid_formats_ >, seqan3::structure_file_input< traits_type_, selected_field_ids_, valid_formats_ >, seqan3::structure_file_output< selected_field_ids_, valid_formats_ >
• stream_char_type : seqan3::sam_file_input< traits_type_, selected_field_ids_, valid_formats_ >, seqan3::sam_file_output< selected_field_ids_, valid_formats_, ref_ids_type >, seqan3::sequence_file_input< traits_type_, selected_field_ids_, valid_formats_ >, seqan3::sequence_file_output< selected_field_ids_, valid_formats_ >, seqan3::structure_file_input< traits_type_, selected_field_ids_, valid_formats_ >, seqan3::structure_file_output< selected_field_ids_, valid_formats_ >
• stream_deleter_default() : seqan3::sam_file_input< traits_type_, selected_field_ids_, valid_formats_ >, seqan3::sam_file_output< selected_field_ids_, valid_formats_, ref_ids_type >, seqan3::sequence_file_input< traits_type_, selected_field_ids_, valid_formats_ >, seqan3::sequence_file_output< selected_field_ids_, valid_formats_ >, seqan3::structure_file_input< traits_type_, selected_field_ids_, valid_formats_ >, seqan3::structure_file_output< selected_field_ids_, valid_formats_ >
• stream_deleter_noop() : seqan3::sam_file_input< traits_type_, selected_field_ids_, valid_formats_ >, seqan3::sam_file_output< selected_field_ids_, valid_formats_, ref_ids_type >, seqan3::sequence_file_input< traits_type_, selected_field_ids_, valid_formats_ >, seqan3::sequence_file_output< selected_field_ids_, valid_formats_ >, seqan3::structure_file_input< traits_type_, selected_field_ids_, valid_formats_ >, seqan3::structure_file_output< selected_field_ids_, valid_formats_ >
• stream_matrix() : seqan3::detail::debug_matrix< matrix_t, first_sequence_t, second_sequence_t >
• stream_ptr_t : seqan3::sam_file_input< traits_type_, selected_field_ids_, valid_formats_ >, seqan3::sam_file_output< selected_field_ids_, valid_formats_, ref_ids_type >, seqan3::sequence_file_input< traits_type_, selected_field_ids_, valid_formats_ >, seqan3::sequence_file_output< selected_field_ids_, valid_formats_ >, seqan3::structure_file_input< traits_type_, selected_field_ids_, valid_formats_ >, seqan3::structure_file_output< selected_field_ids_, valid_formats_ >
• string_buffer : seqan3::format_bam
• strong_type() : seqan3::detail::strong_type< value_t, derived_t, skills_ >
• structure_alphabet : seqan3::structure_file_input_default_traits_aa, seqan3::structure_file_input_default_traits_rna, structure_file_input_traits
• structure_alphabet_type : seqan3::structured_aa< sequence_alphabet_t, structure_alphabet_t >, seqan3::structured_rna< sequence_alphabet_t, structure_alphabet_t >
• structure_container : seqan3::structure_file_input_default_traits_rna, structure_file_input_traits
• structure_file_input() : seqan3::structure_file_input< traits_type_, selected_field_ids_, valid_formats_ >
• structure_file_output() : seqan3::structure_file_output< selected_field_ids_, valid_formats_ >
• structure_record() : seqan3::structure_record< field_types, field_ids >
• structure_type : seqan3::structure_file_input< traits_type_, selected_field_ids_, valid_formats_ >
• structured_aa() : seqan3::structured_aa< sequence_alphabet_t, structure_alphabet_t >
• structured_rna() : seqan3::structured_rna< sequence_alphabet_t, structure_alphabet_t >
• structured_seq_alphabet : seqan3::structure_file_input_default_traits_aa, seqan3::structure_file_input_default_traits_rna
• structured_seq_container : seqan3::structure_file_input_default_traits_rna
• structured_seq_type : seqan3::structure_file_input< traits_type_, selected_field_ids_, valid_formats_ >
• sub_matrix() : seqan3::detail::debug_matrix< matrix_t, first_sequence_t, second_sequence_t >
• sub_parser : seqan3::argument_parser
• subcommands : seqan3::argument_parser
• subsorting : seqan3::sam_file_header< ref_ids_type >
• substitution : seqan3::detail::policy_max_error, seqan3::detail::search_param
• suffix_array_interval() : seqan3::fm_index_cursor< index_t >
• swap() : seqan3::bitpacked_sequence< alphabet_type >, seqan3::concatenated_sequences< underlying_container_type, data_delimiters_type >, seqan3::dynamic_bitset< bit_capacity >, seqan3::small_vector< value_type_, capacity_ >
• swizzle_type : seqan3::simd::simd_traits< simd_t >, seqan3::simd::simd_traits< builtin_simd_t >
• synopsis : seqan3::argument_parser_meta_data
• sz : seqan3::small_vector< value_type_, capacity_ >