SeqAn3
The Modern C++ library for sequence analysis.
Here is a list of all documented class members with links to the class documentation for each member:
- o -
off_type() :
input_stream_over
,
output_stream_over
offset_char :
seqan3::phred42
,
seqan3::phred63
,
seqan3::phred68legacy
offset_phred :
seqan3::phred42
,
seqan3::phred63
,
seqan3::phred68legacy
offset_type :
seqan3::alignment_file_input< traits_type_, selected_field_ids_, valid_formats_ >
,
seqan3::structure_file_input< traits_type_, selected_field_ids_, valid_formats_ >
,
seqan3::structure_file_input_default_traits_rna
,
structure_file_input_traits
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 type() :
seqan3::alphabet_tuple_base< derived_type, component_types >
operator!=() :
equality_comparable
,
seqan3::aligned_allocator< value_t, alignment_v >
,
seqan3::alignment_range< alignment_executor_type >::alignment_range_iterator
,
seqan3::alphabet_base< derived_type, size, char_t >
,
seqan3::alphabet_base< derived_type, 1ul, char_t >
,
seqan3::alphabet_proxy< derived_type, alphabet_type >
,
seqan3::alphabet_tuple_base< derived_type, component_types >
,
seqan3::alphabet_variant< alternative_types >
,
seqan3::bi_fm_index< alphabet_t, text_layout_mode_, sdsl_index_type_ >
,
seqan3::bi_fm_index_cursor< index_t >
,
seqan3::bitcompressed_vector< 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 >::gap_decorator_iterator
,
seqan3::gap_decorator< inner_type >
,
seqan3::gap_scheme< score_t >
,
seqan3::pod_tuple< type0 >
,
seqan3::pod_tuple< type0, types... >
,
seqan3::scoring_scheme_base< derived_t, alphabet_t, score_t >
,
seqan3::small_vector< value_type_, capacity_ >
operator""_aa10li() :
seqan3::aa10li
operator""_aa10murphy() :
seqan3::aa10murphy
operator""_aa20() :
seqan3::aa20
operator""_aa27() :
seqan3::aa27
operator""_cigar_op() :
seqan3::cigar_op
operator""_db3() :
seqan3::dot_bracket3
operator""_dna15() :
seqan3::dna15
operator""_dna3bs() :
seqan3::dna3bs
operator""_dna4() :
seqan3::dna4
operator""_dna5() :
seqan3::dna5
operator""_dssp9() :
seqan3::dssp9
operator""_phred42() :
seqan3::phred42
operator""_phred63() :
seqan3::phred63
operator""_phred68legacy() :
seqan3::phred68legacy
operator""_rna15() :
seqan3::rna15
operator""_rna4() :
seqan3::rna4
operator""_rna5() :
seqan3::rna5
operator""_sam_dna16() :
seqan3::sam_dna16
operator""_shape() :
seqan3::shape
operator""_wuss51() :
seqan3::wuss< SIZE >
operator& :
seqan3::dynamic_bitset< bit_capacity >
operator&=() :
seqan3::dynamic_bitset< bit_capacity >
operator()() :
seqan3::arithmetic_range_validator
,
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::sequence_end_gap_specifier_base< value_t, _is_static, _value >
,
seqan3::value_list_validator< option_value_t >
,
std::hash< alphabet_t >
,
std::hash< seqan3::dynamic_bitset< cap > >
,
std::hash< urng_t >
,
validator
operator*() :
seqan3::alignment_range< alignment_executor_type >::alignment_range_iterator
,
seqan3::gap_decorator< inner_type >::gap_decorator_iterator
operator+() :
seqan3::gap_decorator< inner_type >::gap_decorator_iterator
,
seqan3::small_string< capacity_ >
operator++() :
seqan3::alignment_range< alignment_executor_type >::alignment_range_iterator
,
seqan3::gap_decorator< inner_type >::gap_decorator_iterator
operator+=() :
seqan3::gap_decorator< inner_type >::gap_decorator_iterator
operator-() :
seqan3::gap_decorator< inner_type >::gap_decorator_iterator
operator--() :
seqan3::gap_decorator< inner_type >::gap_decorator_iterator
operator-=() :
seqan3::gap_decorator< inner_type >::gap_decorator_iterator
operator->() :
seqan3::alignment_range< alignment_executor_type >::alignment_range_iterator
operator< :
seqan3::alphabet_base< derived_type, size, char_t >
,
seqan3::alphabet_base< derived_type, 1ul, char_t >
,
seqan3::alphabet_tuple_base< derived_type, component_types >
,
seqan3::bitcompressed_vector< alphabet_type >
,
seqan3::concatenated_sequences< inner_type, data_delimiters_type >
,
seqan3::dynamic_bitset< bit_capacity >
,
seqan3::gap_decorator< inner_type >::gap_decorator_iterator
,
seqan3::gap_decorator< inner_type >
,
seqan3::pod_tuple< type0 >
,
seqan3::pod_tuple< type0, types... >
,
seqan3::small_vector< value_type_, capacity_ >
,
totally_ordered
operator<<() :
output_stream_over
,
seqan3::debug_stream_type< char_t >
,
seqan3::dynamic_bitset< bit_capacity >
,
seqan3::small_string< capacity_ >
operator<<=() :
seqan3::dynamic_bitset< bit_capacity >
operator<= :
seqan3::alphabet_base< derived_type, size, char_t >
,
seqan3::alphabet_base< derived_type, 1ul, char_t >
,
seqan3::alphabet_tuple_base< derived_type, component_types >
,
seqan3::bitcompressed_vector< alphabet_type >
,
seqan3::concatenated_sequences< inner_type, data_delimiters_type >
,
seqan3::dynamic_bitset< bit_capacity >
,
seqan3::gap_decorator< inner_type >::gap_decorator_iterator
,
seqan3::gap_decorator< inner_type >
,
seqan3::pod_tuple< type0 >
,
seqan3::pod_tuple< type0, types... >
,
seqan3::small_vector< value_type_, capacity_ >
,
totally_ordered
operator=() :
assignable_from
,
seqan3::aa10li
,
seqan3::aa10murphy
,
seqan3::aa20
,
seqan3::aa27
,
seqan3::align_cfg::result< alignment_result_tag_t, score_t >
,
seqan3::aligned_allocator< value_t, alignment_v >
,
seqan3::alignment_coordinate
,
seqan3::alignment_file_header< ref_ids_type >
,
seqan3::alignment_file_input< traits_type_, selected_field_ids_, valid_formats_ >
,
seqan3::alignment_file_output< selected_field_ids_, valid_formats_, ref_ids_type >
,
seqan3::alignment_range< alignment_executor_type >::alignment_range_iterator
,
seqan3::alignment_range< alignment_executor_type >
,
seqan3::alignment_result< alignment_result_traits >
,
seqan3::alphabet_base< derived_type, size, char_t >
,
seqan3::alphabet_base< derived_type, 1ul, 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::bitcompressed_vector< alphabet_type >
,
seqan3::cigar
,
seqan3::cigar_op
,
seqan3::concatenated_sequences< inner_type, data_delimiters_type >
,
seqan3::configuration< configs_t >
,
seqan3::debug_stream_type< char_t >
,
seqan3::dna15
,
seqan3::dna3bs
,
seqan3::dna4
,
seqan3::dna5
,
seqan3::dot_bracket3
,
seqan3::dssp9
,
seqan3::dynamic_bitset< bit_capacity >
,
seqan3::end_gaps< ends_t >
,
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 >::gap_decorator_iterator
,
seqan3::gap_decorator< inner_type >
,
seqan3::gap_scheme< score_t >
,
seqan3::input_directory_validator
,
seqan3::input_file_validator< file_t >
,
seqan3::mask
,
seqan3::masked< sequence_alphabet_t >
,
seqan3::output_directory_validator
,
seqan3::output_file_validator< file_t >
,
seqan3::phred42
,
seqan3::phred63
,
seqan3::phred68legacy
,
seqan3::qualified< sequence_alphabet_t, quality_alphabet_t >
,
seqan3::record< field_types, field_ids >
,
seqan3::rna15
,
seqan3::rna4
,
seqan3::rna5
,
seqan3::sam_dna16
,
seqan3::scoring_scheme_base< derived_t, alphabet_t, score_t >
,
seqan3::search_cfg::max_error< errors_t >
,
seqan3::search_cfg::max_error_rate< errors_t >
,
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::shape
,
seqan3::small_string< capacity_ >
,
seqan3::small_vector< value_type_, capacity_ >
,
seqan3::static_band
,
seqan3::structure_file_input< traits_type_, selected_field_ids_, valid_formats_ >
,
seqan3::structure_file_output< selected_field_ids_, valid_formats_ >
,
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==() :
equality_comparable
,
seqan3::aligned_allocator< value_t, alignment_v >
,
seqan3::alignment_range< alignment_executor_type >::alignment_range_iterator
,
seqan3::alphabet_base< derived_type, size, char_t >
,
seqan3::alphabet_base< derived_type, 1ul, char_t >
,
seqan3::alphabet_proxy< derived_type, alphabet_type >
,
seqan3::alphabet_tuple_base< derived_type, component_types >
,
seqan3::alphabet_variant< alternative_types >
,
seqan3::bi_fm_index< alphabet_t, text_layout_mode_, sdsl_index_type_ >
,
seqan3::bi_fm_index_cursor< index_t >
,
seqan3::bitcompressed_vector< 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 >::gap_decorator_iterator
,
seqan3::gap_decorator< inner_type >
,
seqan3::gap_scheme< score_t >
,
seqan3::pod_tuple< type0 >
,
seqan3::pod_tuple< type0, types... >
,
seqan3::scoring_scheme_base< derived_t, alphabet_t, score_t >
,
seqan3::small_vector< value_type_, capacity_ >
operator> :
seqan3::alphabet_base< derived_type, size, char_t >
,
seqan3::alphabet_base< derived_type, 1ul, char_t >
,
seqan3::alphabet_tuple_base< derived_type, component_types >
,
seqan3::bitcompressed_vector< alphabet_type >
,
seqan3::concatenated_sequences< inner_type, data_delimiters_type >
,
seqan3::dynamic_bitset< bit_capacity >
,
seqan3::gap_decorator< inner_type >::gap_decorator_iterator
,
seqan3::gap_decorator< inner_type >
,
seqan3::pod_tuple< type0 >
,
seqan3::pod_tuple< type0, types... >
,
seqan3::small_vector< value_type_, capacity_ >
,
totally_ordered
operator>= :
seqan3::alphabet_base< derived_type, size, char_t >
,
seqan3::alphabet_base< derived_type, 1ul, char_t >
,
seqan3::alphabet_tuple_base< derived_type, component_types >
,
seqan3::bitcompressed_vector< alphabet_type >
,
seqan3::concatenated_sequences< inner_type, data_delimiters_type >
,
seqan3::dynamic_bitset< bit_capacity >
,
seqan3::gap_decorator< inner_type >::gap_decorator_iterator
,
seqan3::gap_decorator< inner_type >
,
seqan3::pod_tuple< type0 >
,
seqan3::pod_tuple< type0, types... >
,
seqan3::small_vector< value_type_, capacity_ >
,
totally_ordered
operator>>() :
input_stream_over
,
seqan3::dynamic_bitset< bit_capacity >
,
seqan3::small_string< capacity_ >
operator>>=() :
seqan3::dynamic_bitset< bit_capacity >
operator[]() :
seqan3::bitcompressed_vector< alphabet_type >
,
seqan3::concatenated_sequences< inner_type, data_delimiters_type >
,
seqan3::dynamic_bitset< bit_capacity >
,
seqan3::end_gaps< ends_t >
,
seqan3::gap_decorator< inner_type >::gap_decorator_iterator
,
seqan3::gap_decorator< inner_type >
,
seqan3::small_vector< value_type_, capacity_ >
operator^ :
seqan3::dynamic_bitset< bit_capacity >
operator^=() :
seqan3::dynamic_bitset< bit_capacity >
operator| :
seqan3::alignment_file_output< selected_field_ids_, valid_formats_, ref_ids_type >
,
seqan3::configuration< configs_t >
,
seqan3::dynamic_bitset< bit_capacity >
,
seqan3::sequence_file_output< selected_field_ids_, valid_formats_ >
,
seqan3::structure_file_output< selected_field_ids_, valid_formats_ >
operator|=() :
seqan3::dynamic_bitset< bit_capacity >
operator~() :
seqan3::dynamic_bitset< bit_capacity >
option_declared_multiple_times() :
seqan3::option_declared_multiple_times
option_value_type :
seqan3::arithmetic_range_validator
,
seqan3::file_validator_base
,
seqan3::regex_validator
,
seqan3::value_list_validator< option_value_t >
,
validator
options :
seqan3::alignment_file_input< traits_type_, selected_field_ids_, valid_formats_ >
,
seqan3::alignment_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_ >
other :
seqan3::aligned_allocator< value_t, alignment_v >::rebind< new_value_type >
other_alignment :
seqan3::aligned_allocator< value_t, alignment_v >::rebind< new_value_type >
output() :
seqan3::search_cfg::output< output_t >
output_directory_validator() :
seqan3::output_directory_validator
output_file_validator() :
seqan3::output_file_validator< file_t >
overflow_error_on_conversion() :
seqan3::overflow_error_on_conversion
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