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

- c -

• c_str() : seqan3::small_string< capacity_ >
• cache_bytes() : seqan3::detail::fast_istreambuf_iterator< char_t, traits_t >
• cache_record_into() : seqan3::detail::fast_istreambuf_iterator< char_t, traits_t >
• cached() : seqan3::detail::basic_iterator< single_pass_input_view< view_type > >
• capacity() : seqan3::bitpacked_sequence< alphabet_type >, seqan3::concatenated_sequences< underlying_container_type, data_delimiters_type >, seqan3::dynamic_bitset< bit_capacity >, seqan3::small_string< capacity_ >, seqan3::small_vector< value_type_, capacity_ >
• case_insensitive_string_ends_with() : seqan3::file_validator_base
• cbegin() : seqan3::bitpacked_sequence< alphabet_type >, seqan3::concatenated_sequences< underlying_container_type, data_delimiters_type >, seqan3::detail::two_dimensional_matrix< value_t, allocator_t, order >, seqan3::dynamic_bitset< bit_capacity >, seqan3::gap_decorator< inner_type >, seqan3::small_vector< value_type_, capacity_ >
• cend() : seqan3::bitpacked_sequence< alphabet_type >, seqan3::concatenated_sequences< underlying_container_type, data_delimiters_type >, seqan3::detail::two_dimensional_matrix< value_t, allocator_t, order >, seqan3::dynamic_bitset< bit_capacity >, seqan3::gap_decorator< inner_type >, seqan3::small_vector< value_type_, capacity_ >
• char_is_valid() : seqan3::alphabet_proxy< derived_type, alphabet_type >, seqan3::alphabet_variant< alternative_types >, seqan3::aminoacid_base< derived_type, size >, seqan3::nucleotide_base< derived_type, size >, 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 >
• char_to_rank() : seqan3::aa10li, seqan3::aa10murphy, seqan3::aa20, seqan3::aa27, seqan3::alphabet_variant< alternative_types >, seqan3::dna15, seqan3::dna16sam, seqan3::dna3bs, seqan3::dna4, seqan3::dna5, seqan3::dot_bracket3, seqan3::dssp9, seqan3::exposition_only::cigar_operation, seqan3::gap, seqan3::phred_base< derived_type, size >, seqan3::rna15, seqan3::rna4, seqan3::rna5, seqan3::wuss< SIZE >
• char_type() : input_stream_over, output_stream_over
• check_and_assign_ref_id() : seqan3::detail::format_sam_base
• check_and_update() : seqan3::detail::find_optimum_policy< alignment_algorithm_t >, seqan3::detail::simd_find_optimum_policy< alignment_algorithm_t, simd_t >
• check_for_left_over_args() : seqan3::detail::format_parse
• check_for_unknown_ids() : seqan3::detail::format_parse
• check_score_of_cell() : seqan3::detail::find_optimum_policy< alignment_algorithm_t >, seqan3::detail::simd_find_optimum_policy< alignment_algorithm_t, simd_t >
• check_score_of_cells_in_last_column() : seqan3::detail::find_optimum_policy< alignment_algorithm_t >, seqan3::detail::simd_find_optimum_policy< alignment_algorithm_t, simd_t >
• check_score_of_last_cell() : seqan3::detail::find_optimum_policy< alignment_algorithm_t >, seqan3::detail::simd_find_optimum_policy< alignment_algorithm_t, simd_t >
• check_score_of_last_row_cell() : seqan3::detail::find_optimum_policy< alignment_algorithm_t >, seqan3::detail::simd_find_optimum_policy< alignment_algorithm_t, simd_t >
• check_valid_band_configuration() : seqan3::detail::policy_alignment_matrix< traits_t, alignment_matrix_t >
• check_valid_band_parameter() : seqan3::detail::alignment_algorithm< config_t, algorithm_policies_t >
• cigar() : seqan3::cigar
• cigar_operation() : seqan3::exposition_only::cigar_operation
• cigar_sequence() : seqan3::sam_record< field_types, field_ids >
• clear() : seqan3::bitpacked_sequence< alphabet_type >, seqan3::concatenated_sequences< underlying_container_type, data_delimiters_type >, seqan3::dynamic_bitset< bit_capacity >, seqan3::interleaved_bloom_filter< data_layout_mode_ >, seqan3::record< field_types, field_ids >, seqan3::small_string< capacity_ >, seqan3::small_vector< value_type_, capacity_ >
• clear_element() : seqan3::record< field_types, field_ids >
• cols() : 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::matrix< matrix_t >, seqan3::detail::two_dimensional_matrix< value_t, allocator_t, order >
• column_index_type() : seqan3::detail::column_index_type< index_type >
• column_proxy() : seqan3::detail::trace_matrix_full< trace_t >::iterator::column_proxy
• combine_option_names() : seqan3::detail::format_parse
• combined_adaptor() : seqan3::detail::combined_adaptor< left_adaptor_t, right_adaptor_t >
• combined_score_and_trace_matrix() : seqan3::detail::combined_score_and_trace_matrix< score_matrix_t, trace_matrix_t >
• comment_alphabet() : structure_file_input_traits
• comment_container() : structure_file_input_traits
• complement() : seqan3::alphabet_proxy< derived_type, alphabet_type >, seqan3::dna4, seqan3::nucleotide_base< derived_type, size >, seqan3::qualified< sequence_alphabet_t, quality_alphabet_t >, seqan3::structured_rna< sequence_alphabet_t, structure_alphabet_t >
• component_proxy() : seqan3::alphabet_tuple_base< derived_type, component_types >::component_proxy< alphabet_type, index >
• compute() : seqan3::detail::edit_distance_unbanded< database_t, query_t, align_config_t, edit_traits >
• compute_alignment_column() : seqan3::detail::alignment_algorithm< config_t, algorithm_policies_t >
• compute_band_column() : seqan3::detail::pairwise_alignment_algorithm_banded< alignment_configuration_t, policies_t >
• compute_cell() : seqan3::detail::affine_gap_policy< alignment_algorithm_t, score_t, align_local_t >, seqan3::detail::simd_affine_gap_policy< alignment_algorithm_t, score_t, align_local_t >
• compute_column() : seqan3::detail::pairwise_alignment_algorithm< alignment_configuration_t, policies_t >
• compute_empty_query_sequence() : seqan3::detail::edit_distance_unbanded< database_t, query_t, align_config_t, edit_traits >
• compute_first_band_cell() : seqan3::detail::affine_gap_policy< alignment_algorithm_t, score_t, align_local_t >
• compute_inner_cell() : seqan3::detail::policy_affine_gap_recursion< alignment_configuration_t >, seqan3::detail::policy_affine_gap_with_trace_recursion< alignment_configuration_t >
• compute_kernel() : seqan3::detail::edit_distance_unbanded< database_t, query_t, align_config_t, edit_traits >
• compute_matrix() : seqan3::detail::alignment_algorithm< config_t, algorithm_policies_t >, seqan3::detail::pairwise_alignment_algorithm< alignment_configuration_t, policies_t >, seqan3::detail::pairwise_alignment_algorithm_banded< alignment_configuration_t, policies_t >
• compute_single_pair() : seqan3::detail::alignment_algorithm< config_t, algorithm_policies_t >, seqan3::detail::edit_distance_algorithm< config_t, traits_t >
• compute_step() : seqan3::detail::edit_distance_unbanded< database_t, query_t, align_config_t, edit_traits >
• concat() : seqan3::concatenated_sequences< underlying_container_type, data_delimiters_type >
• concat_capacity() : seqan3::concatenated_sequences< underlying_container_type, data_delimiters_type >
• concat_reserve() : seqan3::concatenated_sequences< underlying_container_type, data_delimiters_type >
• concat_size() : seqan3::concatenated_sequences< underlying_container_type, data_delimiters_type >
• concatenated_sequences() : seqan3::concatenated_sequences< underlying_container_type, data_delimiters_type >
• configuration() : seqan3::configuration< configs_t >
• configure() : seqan3::detail::alignment_configurator
• configure_algorithm() : seqan3::detail::search_configurator
• configure_edit_distance() : seqan3::detail::alignment_configurator
• configure_hit_strategy() : seqan3::detail::search_configurator
• configure_scoring_scheme() : seqan3::detail::alignment_configurator
• console_layout_struct() : seqan3::detail::format_help::console_layout_struct
• construct() : seqan3::bi_fm_index< alphabet_t, text_layout_mode_, sdsl_index_type_ >, seqan3::fm_index< alphabet_t, text_layout_mode_, sdsl_index_type_ >
• construct_() : seqan3::detail::reverse_fm_index< alphabet_t, text_layout_mode, sdsl_index_type >
• contains() : seqan3::bloom_filter< data_layout_mode_ >, seqan3::fields< fs >
• convert_batch_of_sequences_to_simd_vector() : seqan3::detail::alignment_algorithm< config_t, algorithm_policies_t >, seqan3::detail::pairwise_alignment_algorithm< alignment_configuration_t, policies_t >
• convert_impl() : seqan3::alphabet_variant< alternative_types >
• convert_single_column() : seqan3::detail::view_to_simd< urng_t, simd_t >::iterator_type
• convert_to() : seqan3::alphabet_variant< alternative_types >
• convert_to_simd() : seqan3::detail::simd_affine_gap_policy< alignment_algorithm_t, score_t, align_local_t >
• convert_to_simd_maybe() : seqan3::detail::affine_gap_init_policy< alignment_algorithm_t >
• convert_unsafely_to() : seqan3::alphabet_variant< alternative_types >
• coordinate() : seqan3::detail::edit_distance_trace_matrix_full< word_t, is_semi_global, use_max_errors >::trace_path_iterator, seqan3::detail::trace_iterator_banded< matrix_iter_t >, seqan3::detail::trace_iterator_base< derived_t, matrix_iter_t >, seqan3::detail::two_dimensional_matrix< value_t, allocator_t, order >::basic_iterator< const_range >, seqan3::detail::two_dimensional_matrix_iterator< iter_t >, seqan3::detail::two_dimensional_matrix_iterator_base< derived_t, order >
• coordinate_matrix() : seqan3::detail::coordinate_matrix< index_t >
• copy_sequence_ranks_shifted_by_one() : seqan3::fm_index< alphabet_t, text_layout_mode_, sdsl_index_type_ >
• count() : seqan3::bi_fm_index_cursor< index_t >, seqan3::bloom_filter< data_layout_mode_ >, seqan3::dynamic_bitset< bit_capacity >, seqan3::fm_index_cursor< index_t >
• counted_simd_iterator() : seqan3::detail::counted_simd_iterator< index_simd_t >
• counting_agent() : seqan3::interleaved_bloom_filter< data_layout_mode_ >
• counting_agent_type() : seqan3::interleaved_bloom_filter< data_layout_mode_ >::counting_agent_type< value_t >
• counting_vector() : seqan3::counting_vector< value_t >
• cpo_overload() : seqan3::detail::adl_only::alphabet_size_cpo< alphabet_t >, seqan3::detail::adl_only::assign_char_to_cpo, seqan3::detail::adl_only::assign_phred_to_cpo, seqan3::detail::adl_only::assign_rank_to_cpo, seqan3::detail::adl_only::char_is_valid_for_cpo< alphabet_t >, seqan3::detail::adl_only::complement_cpo, seqan3::detail::adl_only::enable_aminoacid_cpo< alphabet_t >, seqan3::detail::adl_only::enumeration_names_cpo< option_t >, seqan3::detail::adl_only::is_pair_close_cpo, seqan3::detail::adl_only::is_pair_open_cpo, seqan3::detail::adl_only::is_unpaired_cpo, seqan3::detail::adl_only::max_pseudoknot_depth_cpo< alphabet_t >, seqan3::detail::adl_only::pseudoknot_id_cpo, seqan3::detail::adl_only::to_char_cpo, seqan3::detail::adl_only::to_phred_cpo, seqan3::detail::adl_only::to_rank_cpo
• current_alignment_column() : seqan3::detail::alignment_matrix_policy< alignment_algorithm_t, score_matrix_t, trace_matrix_t >
• cursor() : seqan3::bi_fm_index< alphabet_t, text_layout_mode_, sdsl_index_type_ >, seqan3::fm_index< alphabet_t, text_layout_mode_, sdsl_index_type_ >
• customisation_point_object() : seqan3::detail::customisation_point_object< derived_t, max_priority >
• cycle_back() : seqan3::bi_fm_index_cursor< index_t >, seqan3::fm_index_cursor< index_t >
• cycle_front() : seqan3::bi_fm_index_cursor< index_t >