SeqAn3 3.4.0-rc.3
The Modern C++ library for sequence analysis.
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Class Hierarchy

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This inheritance list is sorted roughly, but not completely, alphabetically:
[detail level 123456]
 Cdetail:: strong_type
 Cseqan3::detail::adaptor_base< deep< underlying_adaptor_t >, underlying_adaptor_t >
 Cseqan3::advanceable_alignment_coordinate_printer< typename >
 Cseqan3::advanceable_alignment_coordinate_printer< detail::advanceable_alignment_coordinate< state_t > >The printer for seqan3::detail::advanceable_alignment_coordinate
 Cseqan3::aligned_allocator< value_t, alignment_v >Allocates uninitialized storage whose memory-alignment is specified by alignment
 Cseqan3::alignment_matrix_printer< typename >
 Cseqan3::alignment_matrix_printer< alignment_matrix_t >The printer for alignment scoring and trace matrices
 Cseqan3::alignment_printer< typename >
 Cseqan3::alignment_printer< alignment_t >The printer for alignment
 Cseqan3::alignment_result< alignment_result_value_t >Stores the alignment results and gives access to score, alignment and the front and end positions
 Cseqan3::alignment_result_printer< typename >
 Cseqan3::alignment_result_printer< alignment_result< result_value_t > >The printer used for formatted output of the alignment result
 CAlignmentFileFormat
 Cseqan3::custom::alphabet< t >A type that can be specialised to provide customisation point implementations so that third party types model alphabet concepts
 Cseqan3::custom::alphabet< char_type >Alphabet specific customisations for builtin char types
 Cseqan3::custom::alphabet< uint_type >Alphabet specific customisations for unsigned integral types
 Cseqan3::alphabet_base< derived_type, size, char_t >A CRTP-base that makes defining a custom alphabet easier
 Cseqan3::alphabet_base< aa10li, size, char >
 Cseqan3::alphabet_base< aa10murphy, size, char >
 Cseqan3::alphabet_base< aa20, size, char >
 Cseqan3::alphabet_base< aa27, size, char >
 Cseqan3::alphabet_base< alphabet_variant< alternative_types... >,(static_cast< size_t >(alphabet_size< alternative_types >)+...), char >
 Cseqan3::alphabet_base< cigar,(1 *... *alphabet_size< component_types >), void >
 Cseqan3::alphabet_base< cigar_operation, 9, char >
 Cseqan3::alphabet_base< derived_type, size, char >
 Cseqan3::alphabet_base< derived_type,(1 *... *alphabet_size< component_types >), void >
 Cseqan3::alphabet_base< dna15, size, char >
 Cseqan3::alphabet_base< dna16sam, size, char >
 Cseqan3::alphabet_base< dna3bs, size, char >
 Cseqan3::alphabet_base< dna4, size, char >
 Cseqan3::alphabet_base< dna5, size, char >
 Cseqan3::alphabet_base< dot_bracket3, 3 >
 Cseqan3::alphabet_base< dssp9, 9 >
 Cseqan3::alphabet_base< gap, 1, char >
 Cseqan3::alphabet_base< mask, 2, void >
 Cseqan3::alphabet_base< masked< sequence_alphabet_t >,(1 *... *alphabet_size< component_types >), void >
 Cseqan3::alphabet_base< phred42, size, char >
 Cseqan3::alphabet_base< phred63, size, char >
 Cseqan3::alphabet_base< phred68solexa, size, char >
 Cseqan3::alphabet_base< phred94, size, char >
 Cseqan3::alphabet_base< qualified< sequence_alphabet_t, quality_alphabet_t >,(1 *... *alphabet_size< component_types >), void >
 Cseqan3::alphabet_base< rna15, size, char >
 Cseqan3::alphabet_base< rna4, size, char >
 Cseqan3::alphabet_base< rna5, size, char >
 Cseqan3::alphabet_base< semialphabet_any< size >, size, void >
 Cseqan3::alphabet_base< structured_aa< aa27, dssp9 >,(1 *... *alphabet_size< component_types >), void >
 Cseqan3::alphabet_base< structured_rna< sequence_alphabet_t, structure_alphabet_t >,(1 *... *alphabet_size< component_types >), void >
 Cseqan3::alphabet_base< wuss< 51 >, 51 >
 Cseqan3::alphabet_printer< typename >
 Cseqan3::alphabet_printer< alphabet_t >The printer used for formatted output of seqan3::alphabet types
 Cseqan3::aminoacid_empty_baseThis is an empty base class that can be inherited by types that shall model seqan3::aminoacid_alphabet
 Cseqan3::argument_parserThe SeqAn command line parser
 Cargument_parser_compatible_optionChecks whether the the type can be used in an add_(positional_)option call on the argument parser
 Cseqan3::argument_parser_meta_dataStores all parser related meta information of the seqan3::argument_parser
 Cseqan3::custom::argument_parsing< t >A type that can be specialised to provide customisation point implementations for the seqan3::argument_parser such that third party types may be adapted
 CarithmeticA type that satisfies std::is_arithmetic_v<t>
 Cseqan3::bin_literalA strong type of underlying type uint64_t that represents the shape in binary representation
 Cseqan3::interleaved_bloom_filter< data_layout_mode_ >::membership_agent_type::binning_bitvectorA bitvector representing the result of a call to bulk_contains of the seqan3::interleaved_bloom_filter
 Ccereal_archiveAll archives of the Cereal library satisfy this
 CcerealisableSpecifies the requirements for types that are serialisable via Cereal
 Cseqan3::char_sequence_printer< typename >
 Cseqan3::char_sequence_printer< char_sequence_t >A printer for character sequences
 Cseqan3::cigar_clipped_basesHelper struct to specialise soft and hard clipping when using seqan3::cigar_from_alignment
 Cseqan3::cigar_printer< typename >
 Cseqan3::cigar_printer< cigar >The printer used for formatted output of the cigar alphabets
 Cstd::ranges::common_range
 Cstd::conditional_t [external]
 Cstd::conditional_t< std::is_class_v< alphabet_type >, alphabet_type, alphabet_base< derived_type, alphabet_size< alphabet_type >, detail::valid_template_spec_or_t< void, alphabet_char_t, alphabet_type > > > [external]
 Cstd::copy_constructible
 Cstd::copyable
 Cseqan3::interleaved_bloom_filter< data_layout_mode_ >::counting_agent_type< value_t >Manages counting ranges of values for the seqan3::interleaved_bloom_filter
 Cseqan3::debug_stream_printer< typename >
 Cseqan3::debug_stream_printer< value_t >A struct that provides a debug stream printer for a specific value type
 Cseqan3::debug_stream_type< char_t >A "pretty printer" for most SeqAn data structures and related types
 Cstd::destructible
 Cseqan3::dynamic_bitset_printer< typename >
 Cseqan3::dynamic_bitset_printer< dynamic_bitset< bit_capacity > >Prints seqan3::dynamic_bitset.
This entity is experimental and subject to change in the future. Experimental since version 3.1.
 Cenum_bitwise_operatorsYou can expect these functions on all types that overload seqan3::add_enum_bitwise_operators
 Cseqan3::enumeration_printer< typename >
 Cseqan3::enumeration_printer< enum_t >A type (e.g. an enum) can be made debug streamable by customizing the seqan3::enumeration_names
 Cexplicitly_convertible_toChecks whether from can be explicitly converted to to
 Cstd::ios_base::failure [external]
 Cstd::false_type [external]
 Cseqan3::fields< fs >A class template that holds a choice of seqan3::field
 Cseqan3::file_validator_baseAn abstract base class for the file and directory validators
 Cseqan3::detail::format_sam_baseThe alignment base format
 Cstd::forward_iterator
 Cstd::ranges::forward_range
 Cseqan3::function_traits< std::function< return_t(args_t...)> >A traits class to provide a uniform interface to the properties of a function type
 Cseqan3::hamming_scoring_schemeA scoring scheme that assigns a score of 0 to matching letters and -1 to mismatching letters
 Cstd::hash< alphabet_t >Struct for hashing a character
 Cstd::hash< seqan3::dynamic_bitset< cap > >Struct for hashing a seqan3::dynamic_bitset
 Cstd::hash< urng_t >Struct for hashing a range of characters
 Cimplicitly_convertible_toChecks whether from can be implicityly converted to to
 Cstd::input_iterator
 Cstd::input_range
 Cstd::ranges::input_range
 Cseqan3::input_range_printer< typename >
 Cseqan3::input_range_printer< integer_sequence_t >
 Cseqan3::input_range_printer< rng_t >A printer for arbitrary input ranges
 Cinput_stream_overConcept for input streams
 Cseqan3::integer_sequence_printer< typename >
 Cstd::integral
 Cstd::integral_constant< size_t, seqan3::list_traits::size< tuple_t::seqan3_required_types > > [external]
 Cstd::integral_constant< std::size_t, sizeof...(types)> [external]
 Cseqan3::integral_printer< typename >
 Cseqan3::integral_printer< integral_t >The printer for integral types
 Cstd::invalid_argument [external]
 Cstd::logic_error [external]
 Cstd::map< uint16_t, detail::sam_tag_variant > [external]
 Cseqan3::mask_printer< typename >
 Cseqan3::mask_printer< mask_t >The printer used for formatted output of seqan3::mask alphabet
 Cseqan3::interleaved_bloom_filter< data_layout_mode_ >::membership_agent_typeManages membership queries for the seqan3::interleaved_bloom_filter
 Cnamed_enumerationChecks whether the free function seqan3::enumeration_names can be called on the type
 Cseqan3::no_printer_foundA tag that indicates that no printer was found for the given type
 Cnonrecursive_rangeA concept that checks whether a range is non-recursive
 Cseqan3::optional_printer< typename >
 Cseqan3::optional_printer< std::nullopt_t >Printer for formatted output of std::nullopt_t
 Cseqan3::optional_printer< std::optional< T > >Printer for formatted output of a std::optional
 Coutput_stream_overConcept for output streams
 Cseqan3::pipeable_config_elementAdds pipe interface to configuration elements
 Cseqan3::pod_tuple< types >
 Cseqan3::pod_tuple< type0 >Recursion anchor for seqan3::pod_tuple
 Cprintable_withThe concept for a printable object
 Cseqan3::printer_order< printer_templates_t >The printer_order is a variadic template that defines the order of the printers
 Cseqan3::printer_order< debug_stream_printer, alignment_result_printer, search_result_printer, alignment_printer, advanceable_alignment_coordinate_printer, alignment_matrix_printer, trace_directions_printer, mask_printer, integral_printer, cigar_printer, alphabet_printer, sam_flag_printer, simd_printer, dynamic_bitset_printer, char_sequence_printer, integer_sequence_printer, sequence_printer, input_range_printer, strong_type_printer, optional_printer, enumeration_printer, tuple_printer, std_byte_printer, std_variant_printer, std_printer >
 Cstd::ranges::random_access_range
 Cseqan3::aligned_allocator< value_t, alignment_v >::rebind< new_value_type >The aligned_allocator member template class aligned_allocator::rebind provides a way to obtain an allocator for a different type
 Crecord_likeThe concept for a type that models a record
 Cseqan3::ref_info_not_givenType tag which indicates that no reference information has been passed to the SAM file on construction
 Cstd::regular
 Cstd::runtime_error [external]
 Cseqan3::sam_file_header< ref_ids_type >Stores the header information of SAM/BAM files
 Cseqan3::sam_file_input< traits_type_, selected_field_ids_, valid_formats_ >A class for reading SAM files, both SAM and its binary representation BAM are supported
 Cseqan3::sam_file_input_format< t >The generic concept for alignment file input formats
 Cseqan3::sam_file_input_options< sequence_legal_alphabet >The options type defines various option members that influence the behaviour of all or some formats
 Cseqan3::sam_file_input_options< typename traits_type::sequence_legal_alphabet >
 Csam_file_input_traitsThe requirements a traits_type for seqan3::sam_file_input must meet
 Cseqan3::sam_file_output< selected_field_ids_, valid_formats_, ref_ids_type >A class for writing SAM files, both SAM and its binary representation BAM are supported
 Cseqan3::sam_file_output_format< t >The generic concept for alignment file out formats
 Cseqan3::sam_file_output_optionsThe options type defines various option members that influence the behavior of all or some formats
 Cseqan3::sam_file_program_info_tStores information of the program/tool that was used to create a SAM/BAM file
 Cseqan3::sam_flag_printer< typename >
 Cseqan3::sam_flag_printer< sam_flag >A sam_flag can be printed as an integer value
 Cseqan3::sam_tag_type< tag_value >The generic base class
 Cseqan3::scoring_scheme
 Cscoring_scheme_forA concept that requires that type be able to score two letters
 Cseqan3::search_result< query_id_type, cursor_type, reference_id_type, reference_begin_position_type >The result class generated by the seqan3::seach algorithm
 Cseqan3::search_result_printer< typename >
 Cseqan3::search_result_printer< search_result< specs_t... > >The printer used for formatted output of the search result
 Cseqan3::sequence_file_input< traits_type_, selected_field_ids_, valid_formats_ >A class for reading sequence files, e.g. FASTA, FASTQ ..
 Cseqan3::sequence_file_input_format< t >The generic concept for sequence file in formats
 Cseqan3::sequence_file_input_options< sequence_legal_alphabet >The options type defines various option members that influence the behaviour of all or some formats
 Cseqan3::sequence_file_input_options< typename traits_type::sequence_legal_alphabet >
 Csequence_file_input_traitsThe requirements a traits_type for seqan3::sequence_file_input must meet
 Cseqan3::sequence_file_output< selected_field_ids_, valid_formats_ >A class for writing sequence files, e.g. FASTA, FASTQ ..
 Cseqan3::sequence_file_output_format< t >The generic concept for sequence file out formats
 Cseqan3::sequence_file_output_optionsThe options type defines various option members that influence the behaviour of all or some formats
 Cseqan3::sequence_printer< typename >
 Cseqan3::sequence_printer< sequence_t >A printer for (biological) sequences
 CSequenceFileFormat
 Cseqan3::simd_printer< typename >
 Cstd::ranges::sized_range
 Cstandard_layoutResolves to std::is_standard_layout_v<t>
 Cseqan3::std_byte_printer< typename >
 Cseqan3::std_byte_printer< std::byte >A std::byte can be printed by printing its value as integer
 Cseqan3::std_printer< typename >
 Cseqan3::std_printer< type_t >The printer for standard output streams
 Cseqan3::std_variant_printer< typename >
 Cseqan3::std_variant_printer< std::variant< variant_ts... > >A std::variant can be printed by visiting the stream operator for the corresponding type
 Cseqan3::detail::strong_type< bool, free_end_gaps_sequence1_leading >
 Cseqan3::detail::strong_type< bool, free_end_gaps_sequence1_trailing >
 Cseqan3::detail::strong_type< bool, free_end_gaps_sequence2_leading >
 Cseqan3::detail::strong_type< bool, free_end_gaps_sequence2_trailing >
 Cseqan3::detail::strong_type< double, error_rate, detail::strong_type_skill::convert|detail::strong_type_skill::comparable >
 Cseqan3::detail::strong_type< int32_t, extension_score, seqan3::detail::strong_type_skill::convert >
 Cseqan3::detail::strong_type< int32_t, lower_diagonal >
 Cseqan3::detail::strong_type< int32_t, open_score, seqan3::detail::strong_type_skill::convert >
 Cseqan3::detail::strong_type< int32_t, upper_diagonal >
 Cseqan3::detail::strong_type< score_type, match_score< score_type >, detail::strong_type_skill::convert >
 Cseqan3::detail::strong_type< score_type, mismatch_score< score_type >, detail::strong_type_skill::convert >
 Cseqan3::detail::strong_type< size_t, bin_count, detail::strong_type_skill::convert >
 Cseqan3::detail::strong_type< size_t, bin_index, detail::strong_type_skill::convert >
 Cseqan3::detail::strong_type< size_t, bin_size, detail::strong_type_skill::convert >
 Cseqan3::detail::strong_type< size_t, hash_function_count, detail::strong_type_skill::convert >
 Cseqan3::detail::strong_type< uint32_t, window_size >
 Cseqan3::detail::strong_type< uint64_t, seed >
 Cseqan3::strong_type_printer< typename >
 Cseqan3::structure_file_input< traits_type_, selected_field_ids_, valid_formats_ >A class for reading structured sequence files, e.g. Stockholm, Connect, Vienna, ViennaRNA bpp matrix ..
 Cseqan3::structure_file_input_format< t >The generic concept for structure file in formats
 Cseqan3::structure_file_input_options< seq_legal_alphabet, structured_seq_combined >The options type defines various option members that influence the behaviour of all or some formats
 Cseqan3::structure_file_input_options< typename traits_type::seq_legal_alphabet, selected_field_ids::contains(field::structured_seq)>
 Cstructure_file_input_traitsThe requirements a traits_type for seqan3::structure_file_input must meet
 Cseqan3::structure_file_output< selected_field_ids_, valid_formats_ >A class for writing structured sequence files, e.g. Stockholm, Connect, Vienna, ViennaRNA bpp matrix ..
 Cseqan3::structure_file_output_format< t >The generic concept for structure file out formats
 Cseqan3::structure_file_output_optionsThe options type defines various option members that influence the behaviour of all or some formats
 Cseqan3::suffix_array_intervalThe underlying suffix array interval
 Cstd::totally_ordered
 Cseqan3::trace_directions_printer< typename >
 Cseqan3::trace_directions_printer< detail::trace_directions >Prints trace_directions as ascii or as utf8 to output stream
 Cdetail::transfer_template_args_onto_t
 Ctransformation_traitConcept for a transformation trait
 Cstd::tuple< configs_t... > [external]
 Ctuple_element
 Cseqan3::tuple_printer< typename >
 Cseqan3::tuple_printer< tuple_t >Printer for formatted output of tuple like objects
 Ctuple_size< seqan3::sam_record< field_types, field_ids >::base_type >
 Ctuple_size< seqan3::sequence_record< field_types, field_ids >::base_type >
 Ctuple_size< seqan3::structure_record< field_types, field_ids >::base_type >
 Cseqan3::type_list< types >Type that contains multiple types
 Cunary_type_traitConcept for a unary traits type
 Cseqan3::ungappedA strong type of underlying type uint8_t that represents the ungapped shape size
 CvalidatorThe concept for option validators passed to add_option/positional_option
 Cstd::vector< value_t > [external]
 Cweakly_assignable_fromResolves to std::is_assignable_v<t>
 Csdsl_index_type_
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