SeqAn3
3.4.0-rc.4
The Modern C++ library for sequence analysis.
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Welcome
Setup
Setting up library tests
Quick Setup (using CMake)
Tutorial
First steps with SeqAn
Parsing command line arguments with Sharg
C++ Concepts
Alphabets in SeqAn
Ranges
Minimisers
Sequence File Input and Output
Pairwise Alignment
Indexing and searching with SeqAn
SAM Input and Output in SeqAn
Implementing your own read mapper with SeqAn
How-To
Porting from SeqAn2
How to write an argument parser with subcommands
How to serialise SeqAn data structures
How to write a view
How to write your own alphabet
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Here is a list of all documented class members with links to the class documentation for each member:
- c -
c_str() :
seqan3::small_string< capacity_ >
cache :
seqan3::algorithm_result_generator_range< algorithm_executor_type >
,
seqan3::detail::alignment_score_matrix_one_column_base< score_t >
cache_bytes() :
seqan3::detail::fast_istreambuf_iterator< char_t, traits_t >
cache_left :
seqan3::detail::alignment_trace_matrix_base< trace_t >
cache_record_into() :
seqan3::detail::fast_istreambuf_iterator< char_t, traits_t >
cache_up :
seqan3::detail::alignment_trace_matrix_base< trace_t >
cached() :
seqan3::detail::basic_iterator< single_pass_input_view< view_type > >
cached_iter :
seqan3::detail::view_to_simd< urng_t, simd_t >::iterator_type
cached_sentinel :
seqan3::detail::view_to_simd< urng_t, simd_t >::iterator_type
cached_simd_chunks :
seqan3::detail::view_to_simd< urng_t, simd_t >
cached_urng_iter :
seqan3::detail::single_pass_input_view< urng_t >::state
cached_value :
seqan3::detail::async_input_buffer_view< urng_t >::iterator
callback :
seqan3::align_cfg::on_result< callback_t >
,
seqan3::search_cfg::on_result< callback_t >
callback_type :
seqan3::detail::alignment_function_traits< function_t >
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_ >
carry_d0 :
seqan3::detail::edit_distance_unbanded< database_t, query_t, align_config_t, edit_traits >::compute_state
carry_hn :
seqan3::detail::edit_distance_unbanded< database_t, query_t, align_config_t, edit_traits >::compute_state
carry_hp :
seqan3::detail::edit_distance_unbanded< database_t, query_t, align_config_t, edit_traits >::compute_state
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_ >
centerPadding :
seqan3::detail::format_help::console_layout_struct
cfg_ptr :
seqan3::detail::alignment_algorithm< config_t, algorithm_policies_t >
,
seqan3::detail::edit_distance_algorithm< config_t, traits_t >
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::masked< sequence_alphabet_t >
,
seqan3::phred_base< derived_type, size >
,
seqan3::rna15
,
seqan3::rna4
,
seqan3::rna5
,
seqan3::wuss< SIZE >
char_to_rank_table :
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::wuss< SIZE >
char_to_sam_rank :
seqan3::format_bam
char_type() :
input_stream_over
,
output_stream_over
,
seqan3::alphabet_base< derived_type, size, char_t >
,
seqan3::alphabet_proxy< derived_type, 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 >
,
seqan3::wuss< SIZE >
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 >
chunk_size :
seqan3::detail::view_to_simd< urng_t, simd_t >
chunk_type :
seqan3::detail::view_to_simd< urng_t, simd_t >
chunks_per_load :
seqan3::detail::view_to_simd< urng_t, simd_t >
cigar() :
seqan3::cigar
cigar_operation() :
seqan3::exposition_only::cigar_operation
cigar_sequence() :
seqan3::sam_record< field_types, field_ids >
cigar_type :
seqan3::sam_file_input< traits_type_, selected_field_ids_, valid_formats_ >
citation :
seqan3::argument_parser_meta_data
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 >
cmd_arguments :
seqan3::argument_parser
col :
seqan3::detail::matrix_index< index_t >
col_dim :
seqan3::detail::two_dimensional_matrix< value_t, allocator_t, order >
col_sep :
seqan3::detail::debug_matrix< matrix_t, first_sequence_t, second_sequence_t >::format_type
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 :
seqan3::detail::trace_matrix_full< trace_t >::iterator::column_proxy
column_count :
seqan3::detail::coordinate_matrix< index_t >
,
seqan3::detail::trace_matrix_full< trace_t >
column_data_view_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 >
column_id :
seqan3::detail::coordinate_matrix< index_t >::iterator
column_index :
seqan3::detail::alignment_matrix_column_major_range_base< derived_t >::iterator_type
,
seqan3::detail::alignment_optimum< score_t >
,
seqan3::detail::coordinate_matrix< index_t >::convert_to_matrix_coordinate
column_index_type() :
seqan3::detail::column_index_type< index_type >
column_proxy() :
seqan3::detail::trace_matrix_full< trace_t >::iterator::column_proxy
column_width :
seqan3::detail::debug_matrix< matrix_t, first_sequence_t, second_sequence_t >
columns :
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 >
combine_option_names() :
seqan3::detail::format_parse
combined_adaptor() :
seqan3::detail::combined_adaptor< left_adaptor_t, right_adaptor_t >
combined_column_type :
seqan3::detail::combined_score_and_trace_matrix< score_matrix_t, trace_matrix_t >::iterator
combined_score_and_trace_matrix() :
seqan3::detail::combined_score_and_trace_matrix< score_matrix_t, trace_matrix_t >
command_line_call :
seqan3::sam_file_program_info_t
command_names :
seqan3::detail::format_help_base< derived_type >
comment_alphabet :
seqan3::structure_file_input_default_traits_rna
,
structure_file_input_traits
comment_container :
seqan3::structure_file_input_default_traits_rna
,
structure_file_input_traits
comment_type :
seqan3::structure_file_input< traits_type_, selected_field_ids_, valid_formats_ >
comments :
seqan3::sam_file_header< ref_ids_type >
compare_and_set_optimum :
seqan3::detail::policy_optimum_tracker< alignment_configuration_t, optimum_updater_t >
,
seqan3::detail::policy_optimum_tracker_simd< alignment_configuration_t, optimum_updater_t >
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 >
complete_matrix :
seqan3::detail::trace_matrix_full< trace_t >
completion_fn :
seqan3::detail::reader_writer_manager
component_list :
seqan3::alphabet_tuple_base< derived_type, component_types >
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_begin_positions :
seqan3::detail::alignment_configuration_traits< configuration_t >
,
seqan3::detail::default_edit_distance_trait_type< database_t, query_t, align_config_t, is_semi_global_t, word_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_end_positions :
seqan3::detail::alignment_configuration_traits< configuration_t >
,
seqan3::detail::default_edit_distance_trait_type< database_t, query_t, align_config_t, is_semi_global_t, word_t >
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::default_edit_distance_trait_type< database_t, query_t, align_config_t, is_semi_global_t, word_t >
,
seqan3::detail::pairwise_alignment_algorithm< alignment_configuration_t, policies_t >
,
seqan3::detail::pairwise_alignment_algorithm_banded< alignment_configuration_t, policies_t >
compute_score :
seqan3::detail::alignment_configuration_traits< configuration_t >
,
seqan3::detail::default_edit_distance_trait_type< database_t, query_t, align_config_t, is_semi_global_t, word_t >
compute_score_matrix :
seqan3::detail::default_edit_distance_trait_type< database_t, query_t, align_config_t, is_semi_global_t, word_t >
compute_sequence_alignment :
seqan3::detail::alignment_configuration_traits< configuration_t >
,
seqan3::detail::default_edit_distance_trait_type< database_t, query_t, align_config_t, is_semi_global_t, word_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 >
compute_trace_matrix :
seqan3::detail::default_edit_distance_trait_type< database_t, query_t, align_config_t, is_semi_global_t, word_t >
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 >
condition_message_v :
char_predicate
config :
seqan3::detail::edit_distance_unbanded< database_t, query_t, align_config_t, edit_traits >
configuration() :
seqan3::configuration< configs_t >
configuration_traits_type :
seqan3::detail::edit_distance_algorithm< config_t, traits_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
configured_alignment_type :
seqan3::detail::align_result_selector< first_range_t, second_range_t, configuration_t >
configured_begin_position_type :
seqan3::detail::align_result_selector< first_range_t, second_range_t, configuration_t >
configured_debug_score_matrix_type :
seqan3::detail::align_result_selector< first_range_t, second_range_t, configuration_t >
configured_debug_trace_matrix_type :
seqan3::detail::align_result_selector< first_range_t, second_range_t, configuration_t >
configured_end_position_type :
seqan3::detail::align_result_selector< first_range_t, second_range_t, configuration_t >
configured_score_type :
seqan3::detail::align_result_selector< first_range_t, second_range_t, configuration_t >
configured_sequence1_id_type :
seqan3::detail::align_result_selector< first_range_t, second_range_t, configuration_t >
configured_sequence2_id_type :
seqan3::detail::align_result_selector< first_range_t, second_range_t, configuration_t >
console_layout_struct() :
seqan3::detail::format_help::console_layout_struct
const_iterable :
seqan3::detail::minimiser_view< urng1_t, urng2_t >
,
seqan3::detail::view_take_until< urng_t, fun_t, or_throw, and_consume >
const_iterator :
seqan3::bitpacked_sequence< alphabet_type >
,
seqan3::concatenated_sequences< underlying_container_type, data_delimiters_type >
,
seqan3::detail::pairwise_combine_view< underlying_range_type >
,
seqan3::detail::repeat_view< value_t >
,
seqan3::detail::two_dimensional_matrix< value_t, allocator_t, order >
,
seqan3::detail::view_interleave< urng_t, inserted_rng_t >
,
seqan3::detail::view_take_exactly< urng_t, or_throw >
,
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::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_ >
const_pointer :
seqan3::detail::two_dimensional_matrix< value_t, allocator_t, order >
const_reference :
seqan3::bitpacked_sequence< alphabet_type >
,
seqan3::concatenated_sequences< underlying_container_type, data_delimiters_type >
,
seqan3::detail::debug_matrix< matrix_t, first_sequence_t, second_sequence_t >
,
seqan3::detail::in_file_iterator< file_type >
,
seqan3::detail::out_file_iterator< file_type >
,
seqan3::detail::random_access_iterator_base< range_type, derived_t_template, args_t >
,
seqan3::detail::repeat_view< value_t >
,
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::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_ >
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 >
cookie_path :
seqan3::detail::version_checker
coordinate :
seqan3::detail::alignment_trace_matrix_proxy< coordinate_type, trace_type >
,
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_ :
seqan3::detail::edit_distance_trace_matrix_full< word_t, is_semi_global, use_max_errors >::trace_path_iterator
coordinate_matrix() :
seqan3::detail::coordinate_matrix< index_t >
coordinate_offset :
seqan3::detail::simd_global_alignment_state< simd_t >
coordinate_type :
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 >
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 >
count_simd :
seqan3::detail::counted_simd_iterator< index_simd_t >
counted_simd_iterator() :
seqan3::detail::counted_simd_iterator< index_simd_t >
counter :
seqan3::detail::latch
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
csv :
seqan3::detail::debug_matrix< matrix_t, first_sequence_t, second_sequence_t >
,
seqan3::trace_directions_printer< detail::trace_directions >
cummulative_alph_sizes :
seqan3::alphabet_tuple_base< derived_type, component_types >
current :
seqan3::detail::alignment_score_matrix_proxy< score_type >
,
seqan3::detail::alignment_trace_matrix_proxy< coordinate_type, trace_type >
,
seqan3::detail::spin_delay
current_alignment_column() :
seqan3::detail::alignment_matrix_policy< alignment_algorithm_t, score_matrix_t, trace_matrix_t >
current_chunk_pos :
seqan3::detail::view_to_simd< urng_t, simd_t >::iterator_type
current_column_id :
seqan3::detail::score_matrix_single_column< score_t >::matrix_iterator
,
seqan3::detail::trace_matrix_full< trace_t >::iterator
current_direction :
seqan3::detail::trace_iterator_base< derived_t, matrix_iter_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_ >
cursor_ :
seqan3::search_result< query_id_type, cursor_type, reference_id_type, reference_begin_position_type >
cursor_type :
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 >
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