SeqAn3
3.3.0
The Modern C++ library for sequence analysis.
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Here is a list of all documented functions with links to the class documentation for each member:
- o -
off_type() :
input_stream_over
,
output_stream_over
offset_type() :
structure_file_input_traits
on_result() :
seqan3::align_cfg::on_result< callback_t >
,
seqan3::search_cfg::on_result< callback_t >
operator alphabet_type() :
seqan3::alphabet_proxy< derived_type, alphabet_type >
operator other_alph_t() :
seqan3::semialphabet_any< size >
operator other_t() :
seqan3::alphabet_proxy< derived_type, alphabet_type >
operator std::string() :
seqan3::small_string< capacity_ >
operator std::string_view() :
seqan3::small_string< capacity_ >
operator type() :
seqan3::alphabet_tuple_base< derived_type, component_types >
operator!=() :
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::fm_index< alphabet_t, text_layout_mode_, sdsl_index_type_ >
,
seqan3::fm_index_cursor< index_t >
,
seqan3::pod_tuple< type0 >
,
seqan3::pod_tuple< type0, types... >
,
seqan3::scoring_scheme_base< derived_t, alphabet_t, score_t >
operator""_cigar_operation() :
seqan3::cigar
operator""_phred42() :
seqan3::phred42
operator""_phred63() :
seqan3::phred63
operator""_phred68solexa() :
seqan3::phred68solexa
operator""_phred94() :
seqan3::phred94
operator""_shape() :
seqan3::shape
operator""_tag() :
seqan3::sam_tag_dictionary
operator&() :
enum_bitwise_operators
operator&=() :
enum_bitwise_operators
,
seqan3::dynamic_bitset< bit_capacity >
operator()() :
seqan3::arithmetic_range_validator< option_value_t >
,
seqan3::file_validator_base
,
seqan3::input_directory_validator
,
seqan3::input_file_validator< file_t >
,
seqan3::output_directory_validator
,
seqan3::output_file_validator< file_t >
,
seqan3::regex_validator
,
seqan3::value_list_validator< option_value_t >
,
std::hash< alphabet_t >
,
std::hash< urng_t >
,
validator
operator*() :
seqan3::algorithm_result_generator_range< algorithm_executor_type >::algorithm_range_iterator
operator++() :
seqan3::algorithm_result_generator_range< algorithm_executor_type >::algorithm_range_iterator
operator+=() :
seqan3::counting_vector< value_t >
operator-=() :
seqan3::counting_vector< value_t >
operator->() :
seqan3::algorithm_result_generator_range< algorithm_executor_type >::algorithm_range_iterator
operator<() :
seqan3::bitpacked_sequence< alphabet_type >
,
seqan3::concatenated_sequences< underlying_container_type, data_delimiters_type >
,
seqan3::pod_tuple< type0 >
,
seqan3::pod_tuple< type0, types... >
operator<<() :
output_stream_over
,
seqan3::debug_stream_type< char_t >
,
seqan3::dynamic_bitset< bit_capacity >
operator<<=() :
seqan3::dynamic_bitset< bit_capacity >
operator<=() :
seqan3::bitpacked_sequence< alphabet_type >
,
seqan3::concatenated_sequences< underlying_container_type, data_delimiters_type >
,
seqan3::pod_tuple< type0 >
,
seqan3::pod_tuple< type0, types... >
operator=() :
seqan3::aa10li
,
seqan3::aa10murphy
,
seqan3::aa20
,
seqan3::aa27
,
seqan3::algorithm_result_generator_range< algorithm_executor_type >::algorithm_range_iterator
,
seqan3::algorithm_result_generator_range< algorithm_executor_type >
,
seqan3::align_cfg::band_fixed_size
,
seqan3::align_cfg::gap_cost_affine
,
seqan3::align_cfg::method_global
,
seqan3::align_cfg::method_local
,
seqan3::align_cfg::min_score
,
seqan3::align_cfg::on_result< callback_t >
,
seqan3::align_cfg::output_alignment
,
seqan3::align_cfg::output_begin_position
,
seqan3::align_cfg::output_end_position
,
seqan3::align_cfg::output_score
,
seqan3::align_cfg::output_sequence1_id
,
seqan3::align_cfg::output_sequence2_id
,
seqan3::align_cfg::score_type< score_t >
,
seqan3::align_cfg::scoring_scheme< scoring_scheme_t >
,
seqan3::align_cfg::vectorised
,
seqan3::aligned_allocator< value_t, alignment_v >
,
seqan3::alignment_result< alignment_result_value_t >
,
seqan3::alphabet_base< derived_type, size, char_t >
,
seqan3::alphabet_tuple_base< derived_type, component_types >
,
seqan3::alphabet_variant< alternative_types >
,
seqan3::argument_parser
,
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::cigar
,
seqan3::concatenated_sequences< underlying_container_type, data_delimiters_type >
,
seqan3::configuration< configs_t >
,
seqan3::counting_vector< value_t >
,
seqan3::debug_stream_type< char_t >
,
seqan3::dna15
,
seqan3::dna16sam
,
seqan3::dna3bs
,
seqan3::dna4
,
seqan3::dna5
,
seqan3::dot_bracket3
,
seqan3::dssp9
,
seqan3::dynamic_bitset< bit_capacity >
,
seqan3::exposition_only::cigar_operation
,
seqan3::file_validator_base
,
seqan3::fm_index< alphabet_t, text_layout_mode_, sdsl_index_type_ >
,
seqan3::fm_index_cursor< index_t >
,
seqan3::format_bam
,
seqan3::format_embl
,
seqan3::format_fasta
,
seqan3::format_fastq
,
seqan3::format_genbank
,
seqan3::format_sam
,
seqan3::format_vienna
,
seqan3::gap
,
seqan3::gap_decorator< inner_type >
,
seqan3::input_directory_validator
,
seqan3::input_file_validator< file_t >
,
seqan3::interleaved_bloom_filter< data_layout_mode_ >::counting_agent_type< value_t >
,
seqan3::interleaved_bloom_filter< data_layout_mode_ >::membership_agent_type::binning_bitvector
,
seqan3::interleaved_bloom_filter< data_layout_mode_ >::membership_agent_type
,
seqan3::interleaved_bloom_filter< data_layout_mode_ >
,
seqan3::mask
,
seqan3::masked< sequence_alphabet_t >
,
seqan3::output_directory_validator
,
seqan3::output_file_validator< file_t >
,
seqan3::phred42
,
seqan3::phred63
,
seqan3::phred68solexa
,
seqan3::phred94
,
seqan3::qualified< sequence_alphabet_t, quality_alphabet_t >
,
seqan3::record< field_types, field_ids >
,
seqan3::rna15
,
seqan3::rna4
,
seqan3::rna5
,
seqan3::sam_file_header< ref_ids_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::sam_record< field_types, field_ids >
,
seqan3::scoring_scheme_base< derived_t, alphabet_t, score_t >
,
seqan3::search_cfg::hit
,
seqan3::search_cfg::hit_all
,
seqan3::search_cfg::hit_all_best
,
seqan3::search_cfg::hit_single_best
,
seqan3::search_cfg::hit_strata
,
seqan3::search_cfg::max_error_deletion
,
seqan3::search_cfg::max_error_insertion
,
seqan3::search_cfg::max_error_substitution
,
seqan3::search_cfg::max_error_total
,
seqan3::search_cfg::on_result< callback_t >
,
seqan3::search_cfg::output_index_cursor
,
seqan3::search_cfg::output_query_id
,
seqan3::search_cfg::output_reference_begin_position
,
seqan3::search_cfg::output_reference_id
,
seqan3::search_result< query_id_type, cursor_type, reference_id_type, reference_begin_position_type >
,
seqan3::semialphabet_any< size >
,
seqan3::sequence_file_input< traits_type_, selected_field_ids_, valid_formats_ >
,
seqan3::sequence_file_output< selected_field_ids_, valid_formats_ >
,
seqan3::sequence_record< field_types, field_ids >
,
seqan3::shape
,
seqan3::small_string< capacity_ >
,
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_ >
,
seqan3::structure_record< field_types, field_ids >
,
seqan3::structured_aa< sequence_alphabet_t, structure_alphabet_t >
,
seqan3::structured_rna< sequence_alphabet_t, structure_alphabet_t >
,
seqan3::value_list_validator< option_value_t >
,
seqan3::views::deep< underlying_adaptor_t >
,
seqan3::wuss< SIZE >
operator==() :
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::fm_index< alphabet_t, text_layout_mode_, sdsl_index_type_ >
,
seqan3::fm_index_cursor< index_t >
,
seqan3::pod_tuple< type0 >
,
seqan3::pod_tuple< type0, types... >
,
seqan3::scoring_scheme_base< derived_t, alphabet_t, score_t >
operator>() :
seqan3::bitpacked_sequence< alphabet_type >
,
seqan3::concatenated_sequences< underlying_container_type, data_delimiters_type >
,
seqan3::pod_tuple< type0 >
,
seqan3::pod_tuple< type0, types... >
operator>=() :
seqan3::bitpacked_sequence< alphabet_type >
,
seqan3::concatenated_sequences< underlying_container_type, data_delimiters_type >
,
seqan3::pod_tuple< type0 >
,
seqan3::pod_tuple< type0, types... >
operator>>() :
input_stream_over
,
seqan3::dynamic_bitset< bit_capacity >
operator>>=() :
seqan3::dynamic_bitset< bit_capacity >
operator[]() :
seqan3::bitpacked_sequence< alphabet_type >
,
seqan3::concatenated_sequences< underlying_container_type, data_delimiters_type >
,
seqan3::dynamic_bitset< bit_capacity >
,
seqan3::gap_decorator< inner_type >
,
seqan3::interleaved_bloom_filter< data_layout_mode_ >::membership_agent_type::binning_bitvector
,
seqan3::small_vector< value_type_, capacity_ >
operator^() :
enum_bitwise_operators
operator^=() :
enum_bitwise_operators
,
seqan3::dynamic_bitset< bit_capacity >
operator|() :
enum_bitwise_operators
,
seqan3::configuration< configs_t >
operator|=() :
enum_bitwise_operators
,
seqan3::dynamic_bitset< bit_capacity >
operator~() :
enum_bitwise_operators
,
seqan3::dynamic_bitset< bit_capacity >
option_declared_multiple_times() :
seqan3::option_declared_multiple_times
option_value_type() :
validator
output_alignment() :
seqan3::align_cfg::output_alignment
output_begin_position() :
seqan3::align_cfg::output_begin_position
output_directory_validator() :
seqan3::output_directory_validator
output_end_position() :
seqan3::align_cfg::output_end_position
output_file_validator() :
seqan3::output_file_validator< file_t >
output_index_cursor() :
seqan3::search_cfg::output_index_cursor
output_query_id() :
seqan3::search_cfg::output_query_id
output_reference_begin_position() :
seqan3::search_cfg::output_reference_begin_position
output_reference_id() :
seqan3::search_cfg::output_reference_id
output_score() :
seqan3::align_cfg::output_score
output_sequence1_id() :
seqan3::align_cfg::output_sequence1_id
output_sequence2_id() :
seqan3::align_cfg::output_sequence2_id
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