SeqAn3
Class Hierarchy

Go to the graphical class hierarchy

This inheritance list is sorted roughly, but not completely, alphabetically:
[detail level 123456789]
 Cseqan3::aligned_allocator< value_t, alignment_v >Allocates uninitialized storage whose memory-alignment is specified by alignment
 Calignment_file_format_concept
 Cseqan3::alignment_file_headerStores the header information of alignment files
 Cseqan3::alignment_file_in_optionsThe options type defines various option members that influence the behaviour of all or some formats
 Cseqan3::alignment_file_output< selected_field_ids_, valid_formats_, stream_type_ >A class for writing alignment files, e.g. SAM, BAL, BLAST, ..
 Cseqan3::alignment_file_output_format_conceptThe 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_range< range_buffer_t >The alignment
 Cseqan3::alphabet_base< derived_type, size, char_t >A CRTP-base that makes defining a custom alphabet easier
 Cseqan3::alphabet_base< aa20, size, char >
 Cseqan3::alphabet_base< aa27, size, char >
 Cseqan3::alphabet_base< component_proxy< alphabet_type, index >, alphabet_size_v< alphabet_type >, detail::transformation_trait_or_t< underlying_char< alphabet_type >, void > >
 Cseqan3::alphabet_base< derived_type, alphabet_size_v< alphabet_type >, detail::transformation_trait_or_t< underlying_char< alphabet_type >, void > >
 Cseqan3::alphabet_base< derived_type, size, char >
 Cseqan3::alphabet_base< derived_type,(1 *... *alphabet_size_v< component_types >), void >
 Cseqan3::alphabet_base< dna15, 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< mask, 2, void >
 Cseqan3::alphabet_base< phred42, size, char >
 Cseqan3::alphabet_base< phred63, size, char >
 Cseqan3::alphabet_base< phred68legacy, size, char >
 Cseqan3::alphabet_base< reference_proxy_type, alphabet_size_v< alphabet_type >, detail::transformation_trait_or_t< underlying_char< alphabet_type >, void > >
 Cseqan3::alphabet_base< rna15, size, char >
 Cseqan3::alphabet_base< rna4, size, char >
 Cseqan3::alphabet_base< rna5, size, char >
 Cseqan3::alphabet_base< union_composition< alternative_types... >,(static_cast< size_t >(alphabet_size_v< alternative_types >)+...), char >
 Cseqan3::alphabet_base< wuss< SIZE >, SIZE >
 Cseqan3::alphabet_size< alphabet_type >The size of the alphabet. [value metafunction base template]
 Cseqan3::alphabet_size< alphabet_type_with_members >Specialisation of seqan3::alphabet_size that delegates to alphabet_type::value_size
 Cseqan3::alphabet_size< char_type >Specialisation of seqan3::alphabet_size that delegates for char types
 Cseqan3::alphabet_size< uint_type >Specialisation of seqan3::alphabet_size that delegates for uint types
 Cseqan3::argument_parserThe SeqAn command line parser
 Cseqan3::argument_parser_meta_dataStores all parser related meta information of the seqan3::argument_parser
 Cseqan3::arithmetic_conceptA type that satisfies std::is_arithmetic_v<t>
 Cstd::AssignableThe concept std::Assignable<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::band_static< value_t >Data structure for a static band
 Cbasic_ios
 Cbasic_istream
 Cbasic_ostream
 Cbasic_streambuf
 Cseqan3::bi_fm_index_conceptConcept for bidirectional FM indices
 Cseqan3::bi_fm_index_default_traitsThe default Bidirectional FM Index Configuration
 Cseqan3::bi_fm_index_iterator_conceptConcept for bidirectional FM index iterators
 Cseqan3::bi_fm_index_traits_conceptConcept for bidirectional FM Index traits
 Cseqan3::cereal_archive_conceptAll archives of the Cereal library satisfy this
 Cseqan3::cerealisable_conceptSpecifies the requirements for types that are serialisable via Cereal
 Cstd::CommonThe concept std::Common<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
 Cstd::CommonReferenceThe concept std::CommonReference<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
 Cseqan3::compatible_conceptTwo types are "compatible" if their seqan3::dimension_v and their seqan3::innermost_value_type_t are the same
 Cseqan3::const_reference< t >Type metafunction that returns the const_reference of another type [metafunction declaration]
 Cseqan3::const_reference< rng_t >Type metafunction that returns the const_reference of another type [specialisation for input ranges]
 Cstd::ConvertibleToThe concept std::ConvertibleTo<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_typeA "pretty printer" for most SeqAn data structures and related types
 Cstd::DerivedFromThe concept std::DerivedFrom<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::difference_type< t >Type metafunction that returns the difference_type of another type [metafunction declaration]
 Cseqan3::difference_type< it_t >Type metafunction that returns the difference_type of another type [specialisation for iterators]
 Cseqan3::difference_type< rng_t >Type metafunction that returns the difference_type of another type [specialisation for ranges]
 Cstd::EqualityComparableThe same as std::WeaklyEqualityComparableWith<t,t>
 Cexception
 Cseqan3::explicitly_convertible_to_conceptResolves to std::ranges::ExplicitlyConvertibleTo<type1, type2>()
 Cseqan3::fields< fs >A class template that holds a choice of seqan3::field
 Cseqan3::file_existance_validatorA validator that checks if a file exists
 Cseqan3::fm_index_conceptConcept for unidirectional FM indices
 Cseqan3::fm_index_default_traitsThe default FM Index Configuration
 Cseqan3::fm_index_iterator_conceptConcept for unidirectional FM index iterators
 Cseqan3::fm_index_traits_conceptConcept for unidirectional FM Index traits
 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< urng_t >Struct for hashing a range of characters
 Cseqan3::implicitly_convertible_to_conceptResolves to std::ranges::ImplicitlyConvertibleTo<type1, type2>()
 Cseqan3::innermost_value_type< t >Recursively determines the value_type on containers and/or iterators [Type metafunction]
 CInputRange
 Cstd::IntegralThe concept Integral is satisfied if and only if T is an integral type
 Cintegral_constant
 Cinvalid_argument
 Cstd::InvocableSpecifies whether the given callable is invocable with the given arguments
 Cseqan3::istream_conceptConcept for input streams
 Clogic_error
 Cmap
 Cseqan3::max_pseudoknot_depth< alphabet_type >Metafunction that indicates to what extent an alphabet can handle pseudoknots. [value metafunction base template]
 Cseqan3::max_pseudoknot_depth< alphabet_type_with_pseudoknot_attribute >Specialisation of seqan3::max_pseudoknot_depth that delegates to structure_type::max_pseudoknot_depth
 Cmax_pseudoknot_depth< structure_type >The ability of this alphabet to represent pseudoknots, i.e. crossing interactions, up to a certain depth
 Cseqan3::ostream_conceptConcept for output streams
 Cseqan3::parse_asserter< condition_type >A condition checker, that wraps a parse condition and throws a specified exception if the condition was not met
 Cseqan3::detail::pipable_adaptor_base< deep< underlying_adaptor_t > >
 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::program_info_tStores information of the program/tool that was used to create the file
 Cstd::ranges::RangeDefines the requirements of a type that allows iteration over its elements by providing a begin iterator and an end sentinel
 Cstd::ReadableThe concept Readable is satisfied by types that are readable by applying operator*, such as pointers, smart pointers, and iterators
 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::reference< t >Type metafunction that returns the reference of another type [metafunction declaration]
 Cseqan3::reference< it_t >Type metafunction that returns the reference of another type [specialisation for input iterators]
 Cseqan3::reference< rng_t >Type metafunction that returns the reference of another type [specialisation for input ranges]
 Cregex_validator
 Cruntime_error
 Cseqan3::rvalue_reference< t >Type metafunction that returns the rvalue_reference of another type [metafunction declaration]
 Cseqan3::rvalue_reference< it_t >Type metafunction that returns the rvalue_reference of another type [specialisation for input iterators]
 Cseqan3::rvalue_reference< rng_t >Type metafunction that returns the rvalue_reference of another type [specialisation for input ranges]
 Cseqan3::sam_tag_type< tag_value >The generic base class
 Cstd::SameThe concept std::Same<T, U> is satisfied if and only if T and U denote the same type
 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::scoring_scheme_conceptA concept that requires that type be able to score two letters
 Csemi_constexpr_alphabet_concept
 Csequence_file_format_concept
 Cseqan3::sequence_file_input< traits_type_, selected_field_ids_, valid_formats_, stream_type_ >A class for reading sequence files, e.g. FASTA, FASTQ ..
 Cseqan3::sequence_file_input_format_conceptThe 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_traits_conceptThe requirements a traits_type for seqan3::sequence_file_input must meet
 Cseqan3::sequence_file_output< selected_field_ids_, valid_formats_, stream_type_ >A class for writing sequence files, e.g. FASTA, FASTQ ..
 Cseqan3::sequence_file_output_format_conceptThe 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
 Csimd_backend
 Cseqan3::simd::simd_conceptThe generic simd concept
 Cseqan3::simd::simd_traits< simd_t >Seqan3::simd::simd_traits is the trait class that provides uniform interface to the properties of simd_t types
 Cseqan3::simd::simd_traits< builtin_simd_t >This class specializes seqan3::simd::simd_traits for seqan3::detail::builtin_simd types
 Cseqan3::size_type< t >Type metafunction that returns the size_type of another type [metafunction declaration]
 Cseqan3::size_type< it_t >Type metafunction that returns the size_type of another type [specialisation for iterators]
 Cseqan3::size_type< rng_t >Type metafunction that returns the size_type of another type [specialisation for sized ranges]
 Cseqan3::standard_layout_conceptResolves to std::is_standard_layout_v<t>
 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_in< traits_type_, selected_field_ids_, valid_formats_, stream_type_ >A class for reading structured sequence files, e.g. Stockholm, Connect, Vienna, ViennaRNA bpp matrix ..
 Cseqan3::structure_file_input_format_conceptThe 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_traits_conceptThe requirements a traits_type for seqan3::structure_file_in must meet
 Cseqan3::structure_file_out< selected_field_ids_, valid_formats_, stream_type_ >A class for writing structured sequence files, e.g. Stockholm, Connect, Vienna, ViennaRNA bpp matrix ..
 Cseqan3::structure_file_output_format_conceptThe generic concept for sequence 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::SwappableWithThe concept std::SwappableWith<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
 Ctuple
 Ctuple_element
 Cstd::tuple_element< elem_no, seqan3::record< field_types, field_ids > >Value metafunction specialisation for seqan3::record; returns the type of an element in the record
 Cstd::tuple_element< i, tuple_t >Obtains the type of the specified element
 Cstd::tuple_element< idx, seqan3::align_result< output_type_list_t > >Overloads the tuple element type trait function for seqan3::align_result
 Cstd::tuple_size< seqan3::align_result< output_type_list_t > >Overloads the tuple size type trait function for seqan3::align_result
 Cstd::tuple_size< seqan3::record< field_types, field_ids > >Value metafunction specialisation for seqan3::record; returns number of elements in record
 Cstd::tuple_size< seqan3::sequence_file_input< traits_type, selected_field_ids, valid_formats, stream_type > >Std::tuple_size overload for column-like access. [metafunction specialisation for seqan3::sequence_file_input]
 Cstd::tuple_size< seqan3::structure_file_in< traits_type, selected_field_ids, valid_formats, stream_type > >Std::tuple_size overload for column-like access. [metafunction specialisation for seqan3::structure_file_in]
 Cstd::type_identity< t >The identity transformation (a TransformationTrait that returns the input)
 Cseqan3::underlying_char< alphabet_type >The char_type of the alphabet. [type metafunction base template]
 Cseqan3::underlying_char< alphabet_type_with_members >Specialisation of seqan3::underlying_char that delegates to typename alphabet_type::char_type
 Cseqan3::underlying_char< char_type >Specialisation of seqan3::underlying_char for char types
 Cseqan3::underlying_char< uint_type >Specialisation of seqan3::underlying_char for uint types
 Cseqan3::underlying_phred< alphabet_type >
 Cseqan3::underlying_phred< alphabet_with_member_type >The internal phred type
 Cseqan3::underlying_rank< semi_alphabet_type >The rank_type of the semi_alphabet. [type metafunction base template]
 Cseqan3::underlying_rank< alphabet_type_with_members >Specialisation of seqan3::underlying_rank that delegates to typename alphabet_type::rank_type
 Cseqan3::underlying_rank< char_type >Specialisation of seqan3::underlying_rank for char types
 Cseqan3::underlying_rank< uint_type >Specialisation of seqan3::underlying_rank for uint types
 Cseqan3::validator_conceptThe concept for option validators passed to add_option/positional_option
 Cseqan3::value_type< t >Type metafunction that returns the value_type of another type [metafunction declaration]
 Cseqan3::value_type< it_t >Type metafunction that returns the value_type of another type [specialisation for input iterators]
 Cseqan3::value_type< rng_t >Type metafunction that returns the value_type of another type [specialisation for input ranges]
 Cseqan3::weakly_assignable_conceptResolves to std::is_assignable_v<t>
 Cseqan3::weakly_ordered_with_conceptRequires the two operands to be comparable with == and != in both directions
 Cstd::detail::WeaklyEqualityComparableWithRequires the two operands to be comparable with == and != in both directions
 Cstd::WritableThe concept Writable<Out, T> specifies the requirements for writing a value whose type and value category are encoded by T into an iterator Out's referenced object