Here is a list of all documented class members with links to the class documentation for each member:
- s -
- 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
- scheme
: seqan3::align_cfg::scoring_scheme< scoring_scheme_t >
- score()
: scoring_scheme_for
, seqan3::align_cfg::min_score
, seqan3::alignment_result< alignment_result_value_t >
, seqan3::gap_scheme< score_t >
, seqan3::scoring_scheme_base< derived_t, alphabet_t, score_t >
- score_type()
: scoring_scheme_for
, seqan3::align_cfg::score_type< score_t >
, seqan3::gap_scheme< score_t >
, seqan3::scoring_scheme_base< derived_t, alphabet_t, 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 >
- search_result()
: seqan3::search_result< query_id_type, cursor_type, reference_id_type, reference_begin_position_type >
- second
: seqan3::alignment_coordinate
- 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_ >
- semialphabet_any()
: seqan3::semialphabet_any< size >
- sentinel
: 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_ >
- 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_ >
- 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
, 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_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_quality_type
: seqan3::sequence_file_input< traits_type_, selected_field_ids_, valid_formats_ >
- 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_ >
- set()
: seqan3::dynamic_bitset< bit_capacity >
- set_affine()
: seqan3::gap_scheme< score_t >
- 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_linear()
: seqan3::gap_scheme< score_t >
- set_similarity_matrix()
: seqan3::aminoacid_scoring_scheme< score_type >
- set_simple_scheme()
: seqan3::scoring_scheme_base< derived_t, alphabet_t, score_t >
- set_underlying_stream()
: seqan3::debug_stream_type< char_t >
- setf()
: seqan3::debug_stream_type< char_t >
- shape()
: seqan3::shape
- short_copyright
: seqan3::argument_parser_meta_data
- short_description
: seqan3::argument_parser_meta_data
- shrink_to_fit()
: seqan3::bitpacked_sequence< alphabet_type >
, seqan3::concatenated_sequences< inner_type, data_delimiters_type >
, seqan3::dynamic_bitset< bit_capacity >
, seqan3::small_vector< value_type_, capacity_ >
- size()
: seqan3::bi_fm_index< alphabet_t, text_layout_mode_, sdsl_index_type_ >
, seqan3::bitpacked_sequence< alphabet_type >
, seqan3::concatenated_sequences< inner_type, data_delimiters_type >
, seqan3::configuration< configs_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::binning_bitvector
, seqan3::small_vector< value_type_, capacity_ >
, seqan3::type_list< types >
- size_type()
: bi_fm_index_cursor_specialisation
, fm_index_cursor_specialisation
, fm_index_specialisation
, 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< inner_type, data_delimiters_type >
, 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_ >
- small_string()
: seqan3::small_string< capacity_ >
- small_vector()
: seqan3::small_vector< value_type_, capacity_ >
- sorting
: seqan3::sam_file_header< ref_ids_type >
- static_band()
: seqan3::static_band
- str()
: seqan3::small_string< capacity_ >
- stratum
: seqan3::search_cfg::hit_strata
- 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_ >
- 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_ >
- subsorting
: seqan3::sam_file_header< ref_ids_type >
- suffix_array_interval()
: seqan3::fm_index_cursor< index_t >
- swap()
: seqan3::bitpacked_sequence< alphabet_type >
, seqan3::concatenated_sequences< inner_type, data_delimiters_type >
, seqan3::dynamic_bitset< bit_capacity >
, seqan3::small_vector< value_type_, capacity_ >
- synopsis
: seqan3::argument_parser_meta_data