SeqAn3  3.0.1
The Modern C++ library for sequence analysis.
Class Hierarchy

Go to the graphical class hierarchy

This inheritance list is sorted roughly, but not completely, alphabetically:
[detail level 1234567]
 Cseqan3::detail::adaptor_base< deep< underlying_adaptor_t >, underlying_adaptor_t >
 Cseqan3::aligned_allocator< value_t, alignment_v >Allocates uninitialized storage whose memory-alignment is specified by alignment
 Cseqan3::alignment_coordinateRepresents the begin/end of the pairwise alignment in the respective sequences
 Cseqan3::alignment_file_header< ref_ids_type >Stores the header information of alignment files
 Cseqan3::alignment_file_input< traits_type_, selected_field_ids_, valid_formats_ >A class for reading alignment files, e.g. SAM, BAM, BLAST ..
 Cseqan3::alignment_file_input_formatThe generic concept for alignment file input formats
 Cseqan3::alignment_file_input_options< sequence_legal_alphabet >The options type defines various option members that influence the behaviour of all or some formats
 Cseqan3::alignment_file_input_options< typename traits_type::sequence_legal_alphabet >
 Cseqan3::alignment_file_input_traitsThe requirements a traits_type for seqan3::alignment_file_input must meet
 Cseqan3::alignment_file_output< selected_field_ids_, valid_formats_, ref_ids_type >A class for writing alignment files, e.g. SAM, BAL, BLAST, ..
 Cseqan3::alignment_file_output_formatThe generic concept for alignment file out formats
 Cseqan3::alignment_file_output_optionsThe options type defines various option members that influence the behavior of all or some formats
 Cseqan3::alignment_result< alignment_result_traits >Stores the alignment results and gives access to score, alignment and the front and back coordinates
 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_op, 9, char >
 Cseqan3::alphabet_base< derived_type, 1ul, char_t >Specialisation of seqan3::alphabet_base for alphabets of size 1
 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< 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< phred42, size, char >
 Cseqan3::alphabet_base< phred63, size, char >
 Cseqan3::alphabet_base< phred68legacy, size, char >
 Cseqan3::alphabet_base< rna15, size, char >
 Cseqan3::alphabet_base< rna4, size, char >
 Cseqan3::alphabet_base< rna5, size, char >
 Cseqan3::alphabet_base< sam_dna16, size, char >
 Cseqan3::alphabet_base< semialphabet_any< size >, size, void >
 Cseqan3::alphabet_base< wuss< SIZE >, SIZE >
 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
 Cseqan3::argument_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
 Cseqan3::arithmeticA type that satisfies std::is_arithmetic_v<t>
 Cstd::assignable_fromThe concept std::assignable_from<LHS, RHS> specifies that an expression of the type and value category specified by RHS can be assigned to an lvalue expression whose type is specified by LHS
 Cseqan3::bi_fm_index_cursor_specialisationConcept for bidirectional FM index cursors
 Cseqan3::bi_fm_index_specialisationConcept for bidirectional FM indices
 Cseqan3::bin_literalA strong type of underlying type uint64_t that represents the shape in binary representation
 Cseqan3::cereal_archiveAll archives of the Cereal library satisfy this
 Cseqan3::cerealisableSpecifies the requirements for types that are serialisable via Cereal
 Ccommon_range
 Cstd::common_reference_withThe concept std::common_reference_with<T, U> specifies that two types T and U share a common reference type (as computed by std::common_reference_t) to which both can be converted
 Cstd::common_withThe concept std::common_with<T, U> specifies that two types T and U share a common type (as computed by std::common_type_t) to which both can be converted
 Cseqan3::compatibleTwo types are "compatible" if their seqan3::dimension_v and their seqan3::innermost_value_type_t are the same
 Cstd::conditional_t< std::is_class_v< alphabet_type >, alphabet_type, alphabet_base< component_proxy< alphabet_type, index >, alphabet_size< alphabet_type >, detail::valid_template_spec_or_t< void, alphabet_char_t, alphabet_type > > > [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::conditional_t< std::is_class_v< alphabet_type >, alphabet_type, alphabet_base< reference_proxy_type, alphabet_size< alphabet_type >, detail::valid_template_spec_or_t< void, alphabet_char_t, alphabet_type > > > [external]
 Cstd::convertible_toThe concept std::convertible_to<From, To> specifies that an expression of the type and value category specified by From can be implicitly and explicitly converted to the type To, and the two forms of conversion are equivalent
 Cseqan3::debug_stream_type< char_t >A "pretty printer" for most SeqAn data structures and related types
 Cstd::derived_fromThe concept std::derived_from<Derived, Base> is satisfied if and only if Base is a class type that is either Derived or a public and unambiguous base of Derived, ignoring cv-qualifiers
 Cstd::destructibleThe concept std::destructible specifies the concept of all types whose instances can safely be destroyed at the end of their lifetime (including reference types)
 Cseqan3::end_gaps< ends_t >Wraps the sequence end-gap specifiers and provides ordered access to the respective values
 Cstd::equality_comparableThe same as std::weakly_equality_comparable_with<t,t>
 Cseqan3::explicitly_convertible_toResolves to std::ranges::explicitly_convertible_to<type1, type2>()
 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::fm_index_cursor_specialisationConcept for unidirectional FM index cursors
 Cseqan3::fm_index_specialisationConcept for unidirectional FM indices
 Cseqan3::detail::format_sam_baseThe alignment base format
 Cforward_iterator
 Cforward_range
 Cstd::from_chars_resultResult type of std::from_chars
 Cseqan3::gap_scheme< score_t >A scheme for representing and computing scores against gap characters
 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
 Cseqan3::implicitly_convertible_toResolves to std::ranges::implicitly_convertible_to<type1, type2>()
 Cinput_iterator
 Cinput_range
 Cinput_range
 Cseqan3::input_stream_overConcept for input streams
 Cstd::integralThe concept integral is satisfied if and only if T is an integral type
 Cstd::integral_constant< bool, SEQAN3_IS_CONSTEXPR(t{})> [external]
 Cstd::integral_constant< size_t, seqan3::list_traits::size< tuple_t::seqan3_required_types > > [external]
 Cstd::invalid_argument [external]
 Cstd::invocableSpecifies whether the given callable is invocable with the given arguments
 Cstd::logic_error [external]
 Cstd::map< uint16_t, detail::sam_tag_variant > [external]
 Cseqan3::named_enumerationChecks whether the free function seqan3::enumeration_names can be called on the type
 Cseqan3::output_stream_overConcept for output streams
 Cseqan3::parallel_policyParallel execution policy
 Cseqan3::parallel_unsequenced_policyParallel and unsequenced execution policy
 Cseqan3::pipeable_config_element< derived_t, value_t >Adds pipe interface to configuration elements
 Cseqan3::pipeable_config_element< aligned_ends< end_gaps_t >, end_gaps_t >
 Cseqan3::pipeable_config_element< band< band_t >, band_t >
 Cseqan3::pipeable_config_element< debug_mode< wrapped_config_id_t >, bool >
 Cseqan3::pipeable_config_element< gap< gap_scheme_t >, gap_scheme_t >
 Cseqan3::pipeable_config_element< max_error, uint32_t >
 Cseqan3::pipeable_config_element< max_error< errors_t... >, std::array< uint8_t, 4 > >
 Cseqan3::pipeable_config_element< max_error_rate< errors_t... >, std::array< double, 4 > >
 Cseqan3::pipeable_config_element< mode< mode_t >, mode_t >
 Cseqan3::pipeable_config_element< mode< mode_type >, mode_type >
 Cseqan3::pipeable_config_element< output< output_t >, output_t >
 Cseqan3::pipeable_config_element< parallel_mode< wrapped_config_id_t >, uint32_t >
 Cseqan3::pipeable_config_element< result< alignment_result_tag_t, score_t >, alignment_result_tag_t >
 Cseqan3::pipeable_config_element< scoring< scoring_scheme_t >, scoring_scheme_t >
 Cseqan3::pipeable_config_element< vectorise_tag, empty_type >
 Csdsl::plain_byte_alphabetByte alphabet that does no mapping of char_type to comp_char_type and vice versa
 Cseqan3::pod_tuple< types >Cond
 Cseqan3::pod_tuple< type0 >Recursion anchor for pod_tuple
 Cseqan3::alignment_file_header< ref_ids_type >::program_info_tStores information of the program/tool that was used to create the file
 Crandom_access_range
 Crange
 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
 Cseqan3::ref_info_not_givenType tag which indicates that no reference information has been passed to the alignment file on construction
 Cstd::runtime_error [external]
 Cseqan3::sam_tag_type< tag_value >The generic base class
 Cstd::same_asThe concept std::same_as<T, U> is satisfied if and only if T and U denote the same type
 Cseqan3::scoring_schemeA concept that requires that type be able to score two letters
 Cseqan3::scoring_scheme_base< derived_t, alphabet_t, score_t >A CRTP base class for scoring schemes
 Cseqan3::scoring_scheme_base< aminoacid_scoring_scheme< score_type >, aa27, score_type >
 Cseqan3::scoring_scheme_base< nucleotide_scoring_scheme< score_type >, dna15, score_type >
 Cseqan3::sequence_end_gap_specifier_base< value_t, _is_static, _value >A mixin class which can maintain a static or a dynamic bool state
 Cseqan3::sequence_end_gap_specifier_base< value_t >
 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_formatThe generic concept for sequence file in formats
 Cseqan3::sequence_file_input_options< sequence_legal_alphabet, seq_qual_combined >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, selected_field_ids::contains(field::seq_qual)>
 Cseqan3::sequence_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_formatThe 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::sequenced_policySequenced execution policy
 CSequenceFileFormat
 Csized_range
 Cseqan3::standard_layoutResolves to std::is_standard_layout_v<t>
 Cseqan3::static_bandData structure for a static band
 Cseqan3::detail::strong_type< score_type, gap_open_score< score_type >, detail::strong_type_skill::convert >
 Cseqan3::detail::strong_type< score_type, gap_score< score_type >, detail::strong_type_skill::convert >
 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< uint8_t, strata, detail::strong_type_skill::convert >
 Cseqan3::detail::strong_type< value_t, deletion< value_t >, detail::strong_type_skill::convert >
 Cseqan3::detail::strong_type< value_t, insertion< value_t >, detail::strong_type_skill::convert >
 Cseqan3::detail::strong_type< value_t, lower_bound< value_t > >
 Cseqan3::detail::strong_type< value_t, substitution< value_t >, detail::strong_type_skill::convert >
 Cseqan3::detail::strong_type< value_t, total< value_t >, detail::strong_type_skill::convert >
 Cseqan3::detail::strong_type< value_t, upper_bound< value_t > >
 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_formatThe 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)>
 Cseqan3::structure_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_formatThe 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
 Cstd::swappableThe concept std::swappable specifies that lvalues of type T are swappable
 Cstd::swappable_withThe concept std::swappable_with<T, U> specifies that expressions of the type and value category encoded by T and U are swappable with each other
 Cstd::to_chars_resultResult type of std::to_chars
 Ctransfer_template_args_onto_t
 Cseqan3::transformation_traitConcept for a transformation trait
 Cstd::tuple< configs_t... > [external]
 Ctuple_element
 Cstd::type_identity< t >The identity transformation (a transformation_trait that returns the input)
 Cstd::type_identity< std::conditional_t< decision, on_true_t, on_false_t > >
 Cseqan3::unary_type_traitConcept for a unary traits type
 Cseqan3::ungappedA strong type of underlying type uint8_t that represents the ungapped shape size
 Cseqan3::unsequenced_policyUnsequenced execution policy
 Cseqan3::validatorThe concept for option validators passed to add_option/positional_option
 Cseqan3::weakly_assignable_fromResolves to std::is_assignable_v<t>
 Cseqan3::detail::weakly_equality_comparable_withRequires the two operands to be comparable with == and != in both directions