Here is a list of all documented functions 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 >
• save_minimal() : semialphabet
• 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::alignment_result< alignment_result_value_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_delta_of_word() : seqan3::detail::edit_distance_score_matrix_full< word_t, score_t, is_semi_global, use_max_errors >
• 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_matrix() : seqan3::alignment_result< alignment_result_value_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_single_column() : seqan3::detail::score_matrix_single_column< score_t >
• score_type() : scoring_scheme_for, seqan3::align_cfg::score_type< score_t >
• scoring_scheme() : seqan3::align_cfg::scoring_scheme< scoring_scheme_t >
• scoring_scheme_base() : seqan3::scoring_scheme_base< derived_t, alphabet_t, score_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 >
• search_algo_bi() : seqan3::detail::search_scheme_algorithm< configuration_t, index_t, policies_t >
• search_result() : seqan3::search_result< query_id_type, cursor_type, reference_id_type, reference_begin_position_type >
• search_scheme_algorithm() : seqan3::detail::search_scheme_algorithm< configuration_t, index_t, policies_t >
• search_trivial() : seqan3::detail::unidirectional_search_algorithm< configuration_t, index_t, policies_t >
• second_sequence() : seqan3::detail::debug_matrix< matrix_t, first_sequence_t, second_sequence_t >
• seek_to() : seqan3::detail::in_file_iterator< file_type >
• select_and_return_algorithm() : seqan3::detail::search_configurator
• 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::combined_score_and_trace_matrix< score_matrix_t, trace_matrix_t >::sentinel
• seq_alphabet() : structure_file_input_traits
• seq_container() : structure_file_input_traits
• seq_legal_alphabet() : structure_file_input_traits
• 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 >
• 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 >
• sequence_alphabet() : sam_file_input_traits, sequence_file_input_traits
• sequence_container() : sam_file_input_traits, sequence_file_input_traits
• sequence_file_input() : 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_legal_alphabet() : sam_file_input_traits, 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 >
• 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_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_too_long_error() : seqan3::detail::kmer_hash_view< urng_t >
• 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_ >
• simd_affine_gap_policy() : seqan3::detail::simd_affine_gap_policy< alignment_algorithm_t, score_t, align_local_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 >
• single_pass_input_view() : seqan3::detail::single_pass_input_view< urng_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 >, 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_type() : sdsl_index, seqan3::detail::matrix< matrix_t >
• skills() : derived_from_strong_type
• 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_clipping_at_front() : seqan3::detail::format_sam_base
• spin_delay() : seqan3::detail::spin_delay
• split_into_sub_matrices() : seqan3::detail::view_to_simd< urng_t, simd_t >::iterator_type
• stop_and_wait() : seqan3::detail::execution_handler_parallel::internal_state
• store_help_page_element() : seqan3::detail::format_help_base< derived_type >
• str() : seqan3::small_string< capacity_ >
• 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 >
• strong_type() : seqan3::detail::strong_type< value_t, derived_t, skills_ >
• structure_alphabet() : structure_file_input_traits
• structure_container() : 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 >
• structured_aa() : seqan3::structured_aa< sequence_alphabet_t, structure_alphabet_t >
• structured_rna() : seqan3::structured_rna< sequence_alphabet_t, structure_alphabet_t >
• sub_matrix() : seqan3::detail::debug_matrix< matrix_t, first_sequence_t, second_sequence_t >
• 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_ >