SeqAn3
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 12345678910]
 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_, stream_char_type_ >A class for reading alignment files, e.g. SAM, BAM, BLAST ..
 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_output< selected_field_ids_, valid_formats_, stream_char_type_, ref_ids_type >A class for writing alignment files, e.g. SAM, BAL, BLAST, ..
 Cseqan3::alignment_file_output_optionsThe options type defines various option members that influence the behavior of all or some formats
 Cseqan3::alignment_range< alignment_executor_type >The alignment
 Cseqan3::alignment_result< alignment_result_traits >Stores the alignment results and gives access to score, alignment and the front and back coordinates
 CAlignmentFileFormat
 Cseqan3::AlignmentFileInputFormatThe generic concept for alignment file input formats
 Cseqan3::AlignmentFileInputTraitsThe requirements a traits_type for seqan3::alignment_file_input must meet
 Cseqan3::AlignmentFileOutputFormatThe generic concept for alignment file out formats
 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< component_proxy< alphabet_type, index >, alphabet_size< alphabet_type >, detail::valid_template_spec_or_t< void, alphabet_char_t, alphabet_type > >
 Cseqan3::alphabet_base< derived_type, 1ul, char_t >Specialisation of seqan3::alphabet_base for alphabets of size 1
 Cseqan3::alphabet_base< derived_type, alphabet_size< alphabet_type >, detail::valid_template_spec_or_t< void, alphabet_char_t, alphabet_type > >
 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< 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< reference_proxy_type, alphabet_size< alphabet_type >, detail::valid_template_spec_or_t< void, alphabet_char_t, alphabet_type > >
 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::argument_parserThe SeqAn command line parser
 Cseqan3::argument_parser_meta_dataStores all parser related meta information of the seqan3::argument_parser
 Cseqan3::ArithmeticA 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::BiFmIndexConcept for bidirectional FM indices
 Cseqan3::BiFmIndexCursorConcept for bidirectional FM index cursors
 Cseqan3::CerealArchiveAll archives of the Cereal library satisfy this
 Cseqan3::CerealisableSpecifies 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::CompatibleTwo types are "compatible" if their seqan3::dimension_v and their seqan3::innermost_value_type_t are the same
 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::end_gaps< ends_t >Wraps the sequence end-gap specifiers and provides ordered access to the respective values
 Cstd::EqualityComparableThe same as std::WeaklyEqualityComparableWith<t,t>
 Cseqan3::ExplicitlyConvertibleToResolves to std::ranges::ExplicitlyConvertibleTo<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::FmIndexConcept for unidirectional FM indices
 Cseqan3::FmIndexCursorConcept for unidirectional FM index cursors
 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::ImplicitlyConvertibleToResolves to std::ranges::ImplicitlyConvertibleTo<type1, type2>()
 Cstd::incrementable_traits< t >A type trait class that provides uniform interface to the properties of types that model the WeaklyIncrementable concept
 CInputRange
 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, tuple_t::seqan3_tuple_components::size()> [external]
 Cstd::invalid_argument [external]
 Cstd::InvocableSpecifies whether the given callable is invocable with the given arguments
 Cseqan3::IStreamConcept for input streams
 Cstd::logic_error [external]
 Cstd::map< uint16_t, detail::sam_tag_variant > [external]
 Cseqan3::OStreamConcept 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< 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< result< with_type >, with_type >
 Cseqan3::pipeable_config_element< scoring< scoring_scheme_t >, scoring_scheme_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< ref_ids_type >::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
 CRange
 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::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::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::ScoringSchemeA concept that requires that type be able to score two letters
 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_, stream_char_type_ >A class for reading sequence files, e.g. FASTA, FASTQ ..
 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_output< selected_field_ids_, valid_formats_, stream_char_type_ >A class for writing sequence files, e.g. FASTA, FASTQ ..
 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
 Cseqan3::SequenceFileInputFormatThe generic concept for sequence file in formats
 Cseqan3::SequenceFileInputTraitsThe requirements a traits_type for seqan3::sequence_file_input must meet
 Cseqan3::SequenceFileOutputFormatThe generic concept for sequence file out formats
 Cseqan3::StandardLayoutResolves 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_, stream_char_type_ >A class for reading structured sequence files, e.g. Stockholm, Connect, Vienna, ViennaRNA bpp matrix ..
 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_output< selected_field_ids_, valid_formats_, stream_char_type_ >A class for writing structured sequence files, e.g. Stockholm, Connect, Vienna, ViennaRNA bpp matrix ..
 Cseqan3::structure_file_output_optionsThe options type defines various option members that influence the behaviour of all or some formats
 Cseqan3::StructureFileInputFormatThe generic concept for structure file in formats
 Cseqan3::StructureFileInputTraitsThe requirements a traits_type for seqan3::structure_file_input must meet
 Cseqan3::StructureFileOutputFormatThe generic concept for structure file out 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
 Cseqan3::TransformationTraitConcept for a transformation trait
 Cstd::true_type [external]
 Cstd::tuple< configs_t... > [external]
 Ctuple_element
 Cstd::type_identity< t >The identity transformation (a TransformationTrait that returns the input)
 Cseqan3::UnaryTypeTraitConcept for a unary traits type
 Cseqan3::unsequenced_policyUnsequenced execution policy
 Cseqan3::ValidatorThe concept for option validators passed to add_option/positional_option
 Cseqan3::WeaklyAssignableResolves to std::is_assignable_v<t>
 Cstd::detail::WeaklyEqualityComparableWithRequires the two operands to be comparable with == and != in both directions
 Cseqan3::WeaklyOrderedWithRequires 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
 CWritableQualityAlphabet