| ►Cseqan3::detail::adaptor_base< deep< underlying_adaptor_t >, underlying_adaptor_t > | |
| Cseqan3::views::deep< underlying_adaptor_t > | A wrapper type around an existing view adaptor that enables "deep view" behaviour for that view |
| Cseqan3::aligned_allocator< value_t, alignment_v > | Allocates uninitialized storage whose memory-alignment is specified by alignment |
| Cseqan3::alignment_coordinate | Represents 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_format | The 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_traits | The requirements a traits_type for seqan3::alignment_file_input must meet |
| Cseqan3::alignment_file_input_default_traits< ref_sequences_t, ref_ids_t > | The default traits for seqan3::alignment_file_input |
| 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_format | The generic concept for alignment file out formats |
| Cseqan3::alignment_file_output_options | The 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::format_bam | The BAM format |
| Cseqan3::format_sam | The SAM format (tag) |
| 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_tuple_base< cigar, uint32_t, cigar_op > | |
| Cseqan3::cigar | The cigar semialphabet pairs a counter with a seqan3::cigar_op letter |
| ►Cseqan3::alphabet_tuple_base< masked< sequence_alphabet_t >, sequence_alphabet_t, mask > | |
| Cseqan3::masked< sequence_alphabet_t > | Implementation of a masked composite, which extends a given alphabet with a mask |
| ►Cseqan3::alphabet_tuple_base< qualified< sequence_alphabet_t, quality_alphabet_t >, sequence_alphabet_t, quality_alphabet_t > | |
| Cseqan3::qualified< sequence_alphabet_t, quality_alphabet_t > | Joins an arbitrary alphabet with a quality alphabet |
| ►Cseqan3::alphabet_tuple_base< structured_aa< sequence_alphabet_t, structure_alphabet_t >, sequence_alphabet_t, structure_alphabet_t > | |
| Cseqan3::structured_aa< sequence_alphabet_t, structure_alphabet_t > | A seqan3::alphabet_tuple_base that joins an aminoacid alphabet with a protein structure alphabet |
| ►Cseqan3::alphabet_tuple_base< structured_rna< sequence_alphabet_t, structure_alphabet_t >, sequence_alphabet_t, structure_alphabet_t > | |
| Cseqan3::structured_rna< sequence_alphabet_t, structure_alphabet_t > | A seqan3::alphabet_tuple_base that joins a nucleotide alphabet with an RNA structure alphabet |
| ►Cseqan3::alphabet_base< aa10li, size, char > | |
| ►Cseqan3::aminoacid_base< aa10li, 10 > | |
| Cseqan3::aa10li | The reduced Li amino acid alphabet |
| ►Cseqan3::alphabet_base< aa10murphy, size, char > | |
| ►Cseqan3::aminoacid_base< aa10murphy, 10 > | |
| Cseqan3::aa10murphy | The reduced Murphy amino acid alphabet |
| ►Cseqan3::alphabet_base< aa20, size, char > | |
| ►Cseqan3::aminoacid_base< aa20, 20 > | |
| Cseqan3::aa20 | The canonical amino acid alphabet |
| ►Cseqan3::alphabet_base< aa27, size, char > | |
| ►Cseqan3::aminoacid_base< aa27, 27 > | |
| Cseqan3::aa27 | The twenty-seven letter amino acid alphabet |
| ►Cseqan3::alphabet_base< alphabet_variant< alternative_types... >,(static_cast< size_t >(alphabet_size< alternative_types >)+...), char > | |
| Cseqan3::alphabet_variant< alternative_types > | A combined alphabet that can hold values of either of its alternatives |
| ►Cseqan3::alphabet_base< cigar_op, 9, char > | |
| Cseqan3::cigar_op | The (extended) cigar operation alphabet of M,D,I,H,N,P,S,X,= |
| 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::aminoacid_base< derived_type, size > | A CRTP-base that refines seqan3::alphabet_base and is used by the amino acids |
| Cseqan3::nucleotide_base< derived_type, size > | A CRTP-base that refines seqan3::alphabet_base and is used by the nucleotides |
| Cseqan3::quality_base< derived_type, size > | A CRTP-base that refines seqan3::alphabet_base and is used by the quality alphabets |
| ►Cseqan3::alphabet_base< derived_type,(1 *... *alphabet_size< component_types >), void > | |
| Cseqan3::alphabet_tuple_base< derived_type, component_types > | The CRTP base for a combined alphabet that contains multiple values of different alphabets at the same time |
| ►Cseqan3::alphabet_base< dna15, size, char > | |
| ►Cseqan3::nucleotide_base< dna15, 15 > | |
| Cseqan3::dna15 | The 15 letter DNA alphabet, containing all IUPAC smybols minus the gap |
| ►Cseqan3::alphabet_base< dna3bs, size, char > | |
| ►Cseqan3::nucleotide_base< dna3bs, 3 > | |
| Cseqan3::dna3bs | The three letter reduced DNA alphabet for bisulfite sequencing mode (A,G,T(=C)) |
| ►Cseqan3::alphabet_base< dna4, size, char > | |
| ►Cseqan3::nucleotide_base< dna4, 4 > | |
| Cseqan3::dna4 | The four letter DNA alphabet of A,C,G,T |
| ►Cseqan3::alphabet_base< dna5, size, char > | |
| ►Cseqan3::nucleotide_base< dna5, 5 > | |
| Cseqan3::dna5 | The five letter DNA alphabet of A,C,G,T and the unknown character N |
| ►Cseqan3::alphabet_base< dot_bracket3, 3 > | |
| Cseqan3::dot_bracket3 | The three letter RNA structure alphabet of the characters ".()" |
| ►Cseqan3::alphabet_base< dssp9, 9 > | |
| Cseqan3::dssp9 | The protein structure alphabet of the characters "HGIEBTSCX" |
| ►Cseqan3::alphabet_base< gap, 1, char > | |
| Cseqan3::gap | The alphabet of a gap character '-' |
| ►Cseqan3::alphabet_base< mask, 2, void > | |
| Cseqan3::mask | Implementation of a masked alphabet to be used for tuple composites |
| ►Cseqan3::alphabet_base< phred42, size, char > | |
| ►Cseqan3::quality_base< phred42, 42 > | |
| Cseqan3::phred42 | Quality type for traditional Sanger and modern Illumina Phred scores (typical range) |
| ►Cseqan3::alphabet_base< phred63, size, char > | |
| ►Cseqan3::quality_base< phred63, 63 > | |
| Cseqan3::phred63 | Quality type for traditional Sanger and modern Illumina Phred scores (full range) |
| ►Cseqan3::alphabet_base< phred68legacy, size, char > | |
| ►Cseqan3::quality_base< phred68legacy, 68 > | |
| Cseqan3::phred68legacy | Quality type for Solexa and deprecated Illumina formats |
| ►Cseqan3::alphabet_base< rna15, size, char > | |
| ►Cseqan3::nucleotide_base< rna15, 15 > | |
| Cseqan3::rna15 | The 15 letter RNA alphabet, containing all IUPAC smybols minus the gap |
| ►Cseqan3::alphabet_base< rna4, size, char > | |
| ►Cseqan3::nucleotide_base< rna4, 4 > | |
| Cseqan3::rna4 | The four letter RNA alphabet of A,C,G,U |
| ►Cseqan3::alphabet_base< rna5, size, char > | |
| ►Cseqan3::nucleotide_base< rna5, 5 > | |
| Cseqan3::rna5 | The five letter RNA alphabet of A,C,G,U and the unknown character N |
| ►Cseqan3::alphabet_base< sam_dna16, size, char > | |
| ►Cseqan3::nucleotide_base< sam_dna16, 16 > | |
| Cseqan3::sam_dna16 | A 16 letter DNA alphabet, containing all IUPAC symbols minus the gap and plus an equality sign ('=') |
| ►Cseqan3::alphabet_base< semialphabet_any< size >, size, void > | |
| Cseqan3::semialphabet_any< size > | A semi-alphabet that type erases all other semi-alphabets of the same size |
| ►Cseqan3::alphabet_base< wuss< SIZE >, SIZE > | |
| Cseqan3::wuss< SIZE > | The WUSS structure alphabet of the characters .<>:,-_~;()[]{}AaBbCcDd.. |
| ►Cseqan3::aminoacid_empty_base | This is an empty base class that can be inherited by types that shall model seqan3::aminoacid_alphabet |
| Cseqan3::aminoacid_base< aa10li, 10 > | |
| Cseqan3::aminoacid_base< aa10murphy, 10 > | |
| Cseqan3::aminoacid_base< aa20, 20 > | |
| Cseqan3::aminoacid_base< aa27, 27 > | |
| Cseqan3::aminoacid_base< derived_type, size > | A CRTP-base that refines seqan3::alphabet_base and is used by the amino acids |
| Cseqan3::argument_parser | The SeqAn command line parser |
| Cseqan3::argument_parser_compatible_option | Checks whether the the type can be used in an add_(positional_)option call on the argument parser |
| Cseqan3::argument_parser_meta_data | Stores 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::arithmetic | A type that satisfies std::is_arithmetic_v<t> |
| Cseqan3::floating_point | An arithmetic type that also satisfies std::is_floating_point_v<t> |
| ►Cstd::assignable_from | The 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 |
| ►Cstd::movable | Subsumes std::Object, std::move_constructible, std::swappable bool and requires that the type be std::assignable_from bool from a value of itself |
| Cstd::boolean | Specifies that a type can be used in boolean contexts |
| ►Cstd::copyable | Subsumes std::movable, std::copy_constructible, and requires that the type be std::assignable_from bool from a const & of itself |
| ►Cseqan3::trivially_copyable | A type that satisfies std::is_trivially_copyable_v<t> |
| Cseqan3::aa10li | The reduced Li amino acid alphabet |
| Cseqan3::aa10murphy | The reduced Murphy amino acid alphabet |
| Cseqan3::aa20 | The canonical amino acid alphabet |
| Cseqan3::aa27 | The twenty-seven letter amino acid alphabet |
| Cseqan3::alphabet_variant< alternative_types > | A combined alphabet that can hold values of either of its alternatives |
| Cseqan3::cigar | The cigar semialphabet pairs a counter with a seqan3::cigar_op letter |
| Cseqan3::cigar_op | The (extended) cigar operation alphabet of M,D,I,H,N,P,S,X,= |
| Cseqan3::dna15 | The 15 letter DNA alphabet, containing all IUPAC smybols minus the gap |
| Cseqan3::dna3bs | The three letter reduced DNA alphabet for bisulfite sequencing mode (A,G,T(=C)) |
| Cseqan3::dna4 | The four letter DNA alphabet of A,C,G,T |
| Cseqan3::dna5 | The five letter DNA alphabet of A,C,G,T and the unknown character N |
| Cseqan3::dot_bracket3 | The three letter RNA structure alphabet of the characters ".()" |
| Cseqan3::dssp9 | The protein structure alphabet of the characters "HGIEBTSCX" |
| Cseqan3::gap | The alphabet of a gap character '-' |
| Cseqan3::mask | Implementation of a masked alphabet to be used for tuple composites |
| Cseqan3::masked< sequence_alphabet_t > | Implementation of a masked composite, which extends a given alphabet with a mask |
| Cseqan3::phred42 | Quality type for traditional Sanger and modern Illumina Phred scores (typical range) |
| Cseqan3::phred63 | Quality type for traditional Sanger and modern Illumina Phred scores (full range) |
| Cseqan3::phred68legacy | Quality type for Solexa and deprecated Illumina formats |
| Cseqan3::qualified< sequence_alphabet_t, quality_alphabet_t > | Joins an arbitrary alphabet with a quality alphabet |
| Cseqan3::rna15 | The 15 letter RNA alphabet, containing all IUPAC smybols minus the gap |
| Cseqan3::rna4 | The four letter RNA alphabet of A,C,G,U |
| Cseqan3::rna5 | The five letter RNA alphabet of A,C,G,U and the unknown character N |
| Cseqan3::sam_dna16 | A 16 letter DNA alphabet, containing all IUPAC symbols minus the gap and plus an equality sign ('=') |
| Cseqan3::semialphabet_any< size > | A semi-alphabet that type erases all other semi-alphabets of the same size |
| Cseqan3::structured_aa< sequence_alphabet_t, structure_alphabet_t > | A seqan3::alphabet_tuple_base that joins an aminoacid alphabet with a protein structure alphabet |
| Cseqan3::structured_rna< sequence_alphabet_t, structure_alphabet_t > | A seqan3::alphabet_tuple_base that joins a nucleotide alphabet with an RNA structure alphabet |
| Cseqan3::trivial | A type that satisfies seqan3::trivially_copyable and seqan3::trivially_destructible |
| Cseqan3::wuss< SIZE > | The WUSS structure alphabet of the characters .<>:,-_~;()[]{}AaBbCcDd.. |
| ►Cstd::semiregular | Subsumes std::copyable and std::default_constructible |
| ►Cstd::regular | Subsumes std::semiregular and std::equality_comparable |
| Cseqan3::aa10li | The reduced Li amino acid alphabet |
| Cseqan3::aa10murphy | The reduced Murphy amino acid alphabet |
| Cseqan3::aa20 | The canonical amino acid alphabet |
| Cseqan3::aa27 | The twenty-seven letter amino acid alphabet |
| Cseqan3::cigar | The cigar semialphabet pairs a counter with a seqan3::cigar_op letter |
| Cseqan3::cigar_op | The (extended) cigar operation alphabet of M,D,I,H,N,P,S,X,= |
| Cseqan3::dna15 | The 15 letter DNA alphabet, containing all IUPAC smybols minus the gap |
| Cseqan3::dna3bs | The three letter reduced DNA alphabet for bisulfite sequencing mode (A,G,T(=C)) |
| Cseqan3::dna4 | The four letter DNA alphabet of A,C,G,T |
| Cseqan3::dna5 | The five letter DNA alphabet of A,C,G,T and the unknown character N |
| Cseqan3::dot_bracket3 | The three letter RNA structure alphabet of the characters ".()" |
| Cseqan3::dssp9 | The protein structure alphabet of the characters "HGIEBTSCX" |
| Cseqan3::gap | The alphabet of a gap character '-' |
| Cseqan3::mask | Implementation of a masked alphabet to be used for tuple composites |
| Cseqan3::masked< sequence_alphabet_t > | Implementation of a masked composite, which extends a given alphabet with a mask |
| Cseqan3::phred42 | Quality type for traditional Sanger and modern Illumina Phred scores (typical range) |
| Cseqan3::phred63 | Quality type for traditional Sanger and modern Illumina Phred scores (full range) |
| Cseqan3::phred68legacy | Quality type for Solexa and deprecated Illumina formats |
| Cseqan3::qualified< sequence_alphabet_t, quality_alphabet_t > | Joins an arbitrary alphabet with a quality alphabet |
| Cseqan3::rna15 | The 15 letter RNA alphabet, containing all IUPAC smybols minus the gap |
| Cseqan3::rna4 | The four letter RNA alphabet of A,C,G,U |
| Cseqan3::rna5 | The five letter RNA alphabet of A,C,G,U and the unknown character N |
| Cseqan3::wuss< SIZE > | The WUSS structure alphabet of the characters .<>:,-_~;()[]{}AaBbCcDd.. |
| ►Cseqan3::bi_fm_index_cursor_specialisation | Concept for bidirectional FM index cursors |
| Cseqan3::bi_fm_index_cursor< index_t > | The SeqAn Bidirectional FM Index Cursor |
| ►Cseqan3::bi_fm_index_specialisation | Concept for bidirectional FM indices |
| Cseqan3::bi_fm_index< alphabet_t, text_layout_mode_, sdsl_index_type_ > | The SeqAn Bidirectional FM Index |
| Cseqan3::bin_literal | A strong type of underlying type uint64_t that represents the shape in binary representation |
| ►Cseqan3::cereal_archive | All archives of the Cereal library satisfy this |
| Cseqan3::cereal_input_archive | All input archives of the Cereal library satisfy this |
| Cseqan3::cereal_output_archive | All output archives of the Cereal library satisfy this |
| Cseqan3::cereal_text_archive | All text archives of the Cereal library satisfy this |
| ►Cseqan3::cerealisable | Specifies the requirements for types that are serialisable via Cereal |
| ►Cseqan3::dynamic_bitset< 58 > | |
| Cseqan3::shape | A class that defines what positions of a pattern to hash |
| Cseqan3::bitcompressed_vector< alphabet_type > | A space-optimised version of std::vector that compresses multiple letters into a single byte |
| Cseqan3::dynamic_bitset< bit_capacity > | A constexpr bitset implementation with dynamic size at compile time |
| Cseqan3::small_vector< value_type_, capacity_ > | A constexpr vector implementation with dynamic size at compile time |
| ►Cseqan3::small_vector< char, capacity_+1 > | |
| Cseqan3::small_string< capacity_ > | Implements a small string that can be used for compile time computations |
| ►Ccommon_range | |
| ►Cseqan3::container | The (most general) container concept as defined by the standard library |
| ►Cseqan3::sequence_container | A more refined container concept than seqan3::container |
| ►Cseqan3::random_access_container | A more refined container concept than seqan3::sequence_container |
| ►Cseqan3::reservible_container | A more refined container concept than seqan3::random_access_container |
| Cseqan3::dynamic_bitset< 58 > | |
| Cseqan3::bitcompressed_vector< alphabet_type > | A space-optimised version of std::vector that compresses multiple letters into a single byte |
| Cseqan3::concatenated_sequences< inner_type, data_delimiters_type > | Container that stores sequences concatenated internally |
| Cseqan3::dynamic_bitset< bit_capacity > | A constexpr bitset implementation with dynamic size at compile time |
| Cseqan3::small_string< capacity_ > | Implements a small string that can be used for compile time computations |
| Cseqan3::small_vector< value_type_, capacity_ > | A constexpr vector implementation with dynamic size at compile time |
| Cseqan3::small_vector< char, capacity_+1 > | |
| Cstd::common_reference_with | The 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_with | The 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::compatible | Two 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] | |
| Cseqan3::alphabet_proxy< component_proxy< alphabet_type, index >, alphabet_type > | |
| ►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] | |
| Cseqan3::alphabet_proxy< derived_type, alphabet_type > | A CRTP-base that eases the definition of proxy types returned in place of regular alphabets |
| ►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] | |
| Cseqan3::alphabet_proxy< reference_proxy_type, alphabet_type > | |
| ►Cstd::convertible_to | The 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 |
| ►Cstd::move_constructible | The concept std::move_constructible is satisfied if T is a reference type, or if it is an object type where an object of that type can constructed from an rvalue of that type in both direct- and copy-initialization contexts, with the usual semantics |
| ►Cstd::copy_constructible | The concept std::copy_constructible is satisfied if T is an lvalue reference type, or if it is a move_constructible object type where an object of that type can constructed from a (possibly const) lvalue or const rvalue of that type in both direct- and copy-initialization contexts with the usual semantics (a copy is constructed with the source unchanged) |
| ►Cseqan3::semialphabet | The basis for seqan3::alphabet, but requires only rank interface (not char) |
| ►Cseqan3::alphabet | The generic alphabet concept that covers most data types used in ranges |
| ►Cseqan3::aminoacid_alphabet | A concept that indicates whether an alphabet represents amino acids.Since an amino acid alphabet has no specific characteristics (like the complement function for nucleotide alphabets), we distinguish an amino acid alphabet by the seqan3::is_aminoacid type trait |
| Cseqan3::aa10li | The reduced Li amino acid alphabet |
| Cseqan3::aa10murphy | The reduced Murphy amino acid alphabet |
| Cseqan3::aa20 | The canonical amino acid alphabet |
| Cseqan3::aa27 | The twenty-seven letter amino acid alphabet |
| ►Cseqan3::nucleotide_alphabet | A concept that indicates whether an alphabet represents nucleotides |
| Cseqan3::dna15 | The 15 letter DNA alphabet, containing all IUPAC smybols minus the gap |
| Cseqan3::dna3bs | The three letter reduced DNA alphabet for bisulfite sequencing mode (A,G,T(=C)) |
| Cseqan3::dna4 | The four letter DNA alphabet of A,C,G,T |
| Cseqan3::dna5 | The five letter DNA alphabet of A,C,G,T and the unknown character N |
| Cseqan3::rna15 | The 15 letter RNA alphabet, containing all IUPAC smybols minus the gap |
| Cseqan3::rna4 | The four letter RNA alphabet of A,C,G,U |
| Cseqan3::rna5 | The five letter RNA alphabet of A,C,G,U and the unknown character N |
| Cseqan3::sam_dna16 | A 16 letter DNA alphabet, containing all IUPAC symbols minus the gap and plus an equality sign ('=') |
| Cseqan3::structured_rna< sequence_alphabet_t, structure_alphabet_t > | A seqan3::alphabet_tuple_base that joins a nucleotide alphabet with an RNA structure alphabet |
| Cseqan3::quality_alphabet | A concept that indicates whether an alphabet represents quality scores |
| ►Cseqan3::rna_structure_alphabet | A concept that indicates whether an alphabet represents RNA structure |
| Cseqan3::dot_bracket3 | The three letter RNA structure alphabet of the characters ".()" |
| Cseqan3::structured_rna< sequence_alphabet_t, structure_alphabet_t > | A seqan3::alphabet_tuple_base that joins a nucleotide alphabet with an RNA structure alphabet |
| Cseqan3::wuss< SIZE > | The WUSS structure alphabet of the characters .<>:,-_~;()[]{}AaBbCcDd.. |
| ►Cseqan3::writable_alphabet | Refines seqan3::alphabet and adds assignability |
| Cseqan3::aa10li | The reduced Li amino acid alphabet |
| Cseqan3::aa10murphy | The reduced Murphy amino acid alphabet |
| Cseqan3::aa20 | The canonical amino acid alphabet |
| Cseqan3::aa27 | The twenty-seven letter amino acid alphabet |
| Cseqan3::alphabet_variant< alternative_types > | A combined alphabet that can hold values of either of its alternatives |
| Cseqan3::cigar_op | The (extended) cigar operation alphabet of M,D,I,H,N,P,S,X,= |
| Cseqan3::dna15 | The 15 letter DNA alphabet, containing all IUPAC smybols minus the gap |
| Cseqan3::dna3bs | The three letter reduced DNA alphabet for bisulfite sequencing mode (A,G,T(=C)) |
| Cseqan3::dna4 | The four letter DNA alphabet of A,C,G,T |
| Cseqan3::dna5 | The five letter DNA alphabet of A,C,G,T and the unknown character N |
| Cseqan3::dot_bracket3 | The three letter RNA structure alphabet of the characters ".()" |
| Cseqan3::dssp9 | The protein structure alphabet of the characters "HGIEBTSCX" |
| Cseqan3::dssp9 | The protein structure alphabet of the characters "HGIEBTSCX" |
| Cseqan3::gap | The alphabet of a gap character '-' |
| Cseqan3::masked< sequence_alphabet_t > | Implementation of a masked composite, which extends a given alphabet with a mask |
| Cseqan3::rna15 | The 15 letter RNA alphabet, containing all IUPAC smybols minus the gap |
| Cseqan3::rna4 | The four letter RNA alphabet of A,C,G,U |
| Cseqan3::rna5 | The five letter RNA alphabet of A,C,G,U and the unknown character N |
| Cseqan3::sam_dna16 | A 16 letter DNA alphabet, containing all IUPAC symbols minus the gap and plus an equality sign ('=') |
| Cseqan3::structured_aa< sequence_alphabet_t, structure_alphabet_t > | A seqan3::alphabet_tuple_base that joins an aminoacid alphabet with a protein structure alphabet |
| Cseqan3::structured_rna< sequence_alphabet_t, structure_alphabet_t > | A seqan3::alphabet_tuple_base that joins a nucleotide alphabet with an RNA structure alphabet |
| Cseqan3::wuss< SIZE > | The WUSS structure alphabet of the characters .<>:,-_~;()[]{}AaBbCcDd.. |
| ►Cseqan3::writable_quality_alphabet | A concept that indicates whether a writable alphabet represents quality scores |
| Cseqan3::phred42 | Quality type for traditional Sanger and modern Illumina Phred scores (typical range) |
| Cseqan3::phred63 | Quality type for traditional Sanger and modern Illumina Phred scores (full range) |
| Cseqan3::phred68legacy | Quality type for Solexa and deprecated Illumina formats |
| Cseqan3::qualified< sequence_alphabet_t, quality_alphabet_t > | Joins an arbitrary alphabet with a quality alphabet |
| Cseqan3::semialphabet_any< size > | A semi-alphabet that type erases all other semi-alphabets of the same size |
| ►Cseqan3::writable_semialphabet | A refinement of seqan3::semialphabet that adds assignability |
| Cseqan3::alphabet_tuple_base< cigar, uint32_t, cigar_op > | |
| Cseqan3::alphabet_tuple_base< masked< sequence_alphabet_t >, sequence_alphabet_t, mask > | |
| Cseqan3::alphabet_tuple_base< qualified< sequence_alphabet_t, quality_alphabet_t >, sequence_alphabet_t, quality_alphabet_t > | |
| Cseqan3::alphabet_tuple_base< structured_aa< sequence_alphabet_t, structure_alphabet_t >, sequence_alphabet_t, structure_alphabet_t > | |
| Cseqan3::alphabet_tuple_base< structured_rna< sequence_alphabet_t, structure_alphabet_t >, sequence_alphabet_t, structure_alphabet_t > | |
| Cseqan3::alphabet_tuple_base< derived_type, component_types > | The CRTP base for a combined alphabet that contains multiple values of different alphabets at the same time |
| Cseqan3::cigar | The cigar semialphabet pairs a counter with a seqan3::cigar_op letter |
| Cseqan3::mask | Implementation of a masked alphabet to be used for tuple composites |
| Cseqan3::writable_alphabet | Refines seqan3::alphabet and adds assignability |
| Cstd::copyable | Subsumes std::movable, std::copy_constructible, and requires that the type be std::assignable_from bool from a const & of itself |
| Cstd::movable | Subsumes std::Object, std::move_constructible, std::swappable bool and requires that the type be std::assignable_from bool from a value of itself |
| Cseqan3::debug_stream_type< char_t > | A "pretty printer" for most SeqAn data structures and related types |
| Cstd::derived_from | The 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::destructible | The 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::trivially_destructible | A type that satisfies std::is_trivially_destructible_v<t> |
| Cseqan3::trivial | A type that satisfies seqan3::trivially_copyable and seqan3::trivially_destructible |
| ►Cstd::constructible_from | The std::constructible_from concept specifies that a variable of type T can be initialized with the given set of argument types Args... |
| ►Cstd::default_constructible | The std::default_constructible concept provides a shorthand for the common case when the question is whether a type can be constructed with no arguments |
| Cstd::semiregular | Subsumes std::copyable and std::default_constructible |
| Cstd::move_constructible | The concept std::move_constructible is satisfied if T is a reference type, or if it is an object type where an object of that type can constructed from an rvalue of that type in both direct- and copy-initialization contexts, with the usual semantics |
| Cseqan3::end_gaps< ends_t > | Wraps the sequence end-gap specifiers and provides ordered access to the respective values |
| ►Cstd::equality_comparable | The same as std::weakly_equality_comparable_with<t,t> |
| Cstd::regular | Subsumes std::semiregular and std::equality_comparable |
| ►Cstd::totally_ordered | Requires std::equality_comparable and all remaing comparison operators (<, <=, >, >=) |
| Cseqan3::semialphabet | The basis for seqan3::alphabet, but requires only rank interface (not char) |
| ►Cseqan3::tuple_like | Whether a type behaves like a tuple |
| Cseqan3::pod_tuple< type0, types... > | Behaves like std::tuple but is an aggregate PODType |
| Cseqan3::record< field_types, field_ids > | The class template that file records are based on; behaves like an std::tuple |
| Cseqan3::explicitly_convertible_to | Resolves to std::ranges::explicitly_convertible_to<type1, type2>() |
| ►Cstd::ios_base::failure [external] | |
| Cseqan3::io_error | Thrown if there is an io error in low level io operations such as in std::basic_streambuf operations |
| ►Cstd::false_type [external] | |
| Cseqan3::is_constexpr_default_constructible< t > | Whether a type std::is_default_constructible in constexpr-context |
| Cseqan3::is_execution_policy< t > | Test whether a class represents an execution policy |
| Cseqan3::fields< fs > | A class template that holds a choice of seqan3::field |
| ►Cseqan3::file_validator_base | An abstract base class for the file and directory validators |
| Cseqan3::input_directory_validator | A validator that checks if a given path is a valid input directory |
| Cseqan3::input_file_validator< file_t > | A validator that checks if a given path is a valid input file |
| Cseqan3::output_directory_validator | A validator that checks if a given path is a valid output directory |
| Cseqan3::output_file_validator< file_t > | A validator that checks if a given path is a valid output file |
| ►Cseqan3::fm_index_cursor_specialisation | Concept for unidirectional FM index cursors |
| Cseqan3::fm_index_cursor< index_t > | The SeqAn FM Index Cursor |
| ►Cseqan3::fm_index_specialisation | Concept for unidirectional FM indices |
| Cseqan3::fm_index< alphabet_t, text_layout_mode_, sdsl_index_type > | |
| Cseqan3::fm_index< alphabet_t, text_layout_mode_, sdsl_index_type_ > | The SeqAn FM Index |
| ►Cseqan3::detail::format_sam_base | The alignment base format |
| Cseqan3::format_bam | The BAM format |
| Cseqan3::format_sam | The SAM format (tag) |
| ►Cforward_iterator | |
| ►Cseqan3::pseudo_random_access_iterator | This concept checks if an iterator type models pseudo random access |
| Cseqan3::gap_decorator< inner_type >::gap_decorator_iterator | The iterator type over a seqan3::gap_decorator |
| ►Cforward_range | |
| ►Cseqan3::aligned_sequence | The generic concept for an aligned sequence.This concept describes the requirements a sequence must fulfil in order to be used inside of the alignment algorithm to store the final alignment |
| Cseqan3::gap_decorator< inner_type > | A gap decorator allows the annotation of sequences with gap symbols while leaving the underlying sequence unmodified |
| Cseqan3::container | The (most general) container concept as defined by the standard library |
| Cseqan3::pseudo_random_access_range | This concept checks if a type models a pseudo random access range |
| Cstd::from_chars_result | Result 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_to | Resolves to std::ranges::implicitly_convertible_to<type1, type2>() |
| ►Cinput_iterator | |
| Cseqan3::alignment_range< alignment_executor_type >::alignment_range_iterator | The iterator of seqan3::detail::alignment_range |
| ►Cinput_range | |
| Cseqan3::alignment_range< alignment_executor_type > | An input range over the alignment results generated by the underlying alignment executor |
| ►Cinput_range | |
| ►Cseqan3::const_iterable_range | Specifies requirements of an input range type for which the const version of that type satisfies the same strength input range concept as the non-const version |
| Cseqan3::container | The (most general) container concept as defined by the standard library |
| ►Cseqan3::input_stream_over | Concept for input streams |
| Cseqan3::stream_REMOVEME | Concept for i/o streams permitting both directions.An object satisfying the requirements of a stream concept can be used to stream in both (input and output) directions |
| ►Cstd::integral | The concept integral is satisfied if and only if T is an integral type |
| Cseqan3::builtin_character | This concept encompasses exactly the types char, signed char, unsigned char, wchar_t, char16_t and char32_t |
| Cstd::signed_integral | The concept std::signed_integral is satisfied if and only if T is an integral type and std::is_signed_v<T> is true |
| Cstd::unsigned_integral | The concept std::unsigned_integral is satisfied if and only if T is an integral type and std::is_signed_v<T> is false |
| ►Cstd::integral_constant< bool, SEQAN3_IS_CONSTEXPR(t{})> [external] | |
| Cseqan3::is_constexpr_default_constructible< t > | Whether a type std::is_default_constructible in constexpr-context (unary_type_trait specialisation) |
| ►Cstd::integral_constant< size_t, seqan3::list_traits::size< tuple_t::seqan3_required_types > > [external] | |
| Cstd::tuple_size< tuple_t > | Provides access to the number of elements in a tuple as a compile-time constant expression |
| ►Cstd::invalid_argument [external] | |
| Cseqan3::format_error | Thrown if information given to output format didn't match expectations |
| Cseqan3::invalid_alignment_configuration | Thrown if the configuration of the alignment algorithm is invalid |
| ►Cseqan3::parser_invalid_argument | Argument parser exception that is thrown whenever there is an error while parsing the command line arguments |
| Cseqan3::option_declared_multiple_times | Argument parser exception thrown when a non-list option is declared multiple times |
| Cseqan3::overflow_error_on_conversion | Argument parser exception thrown when an argument could not be casted to the according type |
| Cseqan3::required_option_missing | Argument parser exception thrown when a required option is missing |
| Cseqan3::too_few_arguments | Argument parser exception thrown when too few arguments are provided |
| Cseqan3::too_many_arguments | Argument parser exception thrown when too many arguments are provided |
| Cseqan3::type_conversion_failed | Argument parser exception thrown when an argument could not be casted to the according type |
| Cseqan3::unknown_option | Argument parser exception thrown when encountering unknown option |
| Cseqan3::validation_failed | Argument parser exception thrown when an argument could not be casted to the according type |
| Cseqan3::unhandled_extension_error | Thrown if there is no format that accepts a given file extension |
| ►Cstd::invocable | Specifies whether the given callable is invocable with the given arguments |
| ►Cstd::regular_invocable | Specifies whether the given callable is invocable with the given arguments and equality preserving (invocations change neither the callable, nor the arguments) |
| ►Cstd::predicate | Specifies whether the given callable is std::regular_invocable and returns bool |
| ►Cstd::relation | Specifies that R defines a binary relation over the set of expressions whose type and value category are those encoded by either t or u |
| Cstd::strict_weak_order | The concept strict_weak_order<R, T, U> specifies that the relation R imposes a strict weak ordering on its arguments |
| ►Cstd::logic_error [external] | |
| Cseqan3::gap_erase_failure | Thrown in function seqan3::erase_gap, if a position does not contain a gap |
| Cseqan3::parser_design_error | Argument parser exception that is thrown whenever there is an design error directed at the developer of the application (e.g. Reuse of option) |
| ►Cstd::map< uint16_t, detail::sam_tag_variant > [external] | |
| Cseqan3::sam_tag_dictionary | The SAM tag dictionary class that stores all optional SAM fields |
| Cseqan3::named_enumeration | Checks whether the free function seqan3::enumeration_names can be called on the type |
| ►Cseqan3::output_stream_over | Concept for output streams |
| Cseqan3::stream_REMOVEME | Concept for i/o streams permitting both directions.An object satisfying the requirements of a stream concept can be used to stream in both (input and output) directions |
| Cseqan3::parallel_policy | Parallel execution policy |
| Cseqan3::parallel_unsequenced_policy | Parallel 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::align_cfg::aligned_ends< end_gaps_t > | The configuration for aligned sequence ends |
| ►Cseqan3::pipeable_config_element< band< band_t >, band_t > | |
| Cseqan3::align_cfg::band< band_t > | Configuration element for setting the band |
| Cseqan3::pipeable_config_element< debug_mode< wrapped_config_id_t >, bool > | |
| ►Cseqan3::pipeable_config_element< gap< gap_scheme_t >, gap_scheme_t > | |
| Cseqan3::align_cfg::gap< gap_scheme_t > | A configuration element for the gap scheme |
| ►Cseqan3::pipeable_config_element< max_error, uint32_t > | |
| Cseqan3::align_cfg::max_error | Sets the maximal errors allowed during an edit distance computation |
| ►Cseqan3::pipeable_config_element< max_error< errors_t... >, std::array< uint8_t, 4 > > | |
| Cseqan3::search_cfg::max_error< errors_t > | A configuration element for the maximum number of errors across all error types (mismatches, insertions, deletions). This is an upper bound of errors independent from error numbers of specific error types |
| ►Cseqan3::pipeable_config_element< max_error_rate< errors_t... >, std::array< double, 4 > > | |
| Cseqan3::search_cfg::max_error_rate< errors_t > | A configuration element for the maximum number of errors in percent of the query length across all error types (mismatches, insertions, deletions). This is an upper bound of errors independent from error rates of specific error types |
| ►Cseqan3::pipeable_config_element< mode< mode_t >, mode_t > | |
| Cseqan3::search_cfg::mode< mode_t > | Configuration element to determine the search mode |
| ►Cseqan3::pipeable_config_element< mode< mode_type >, mode_type > | |
| Cseqan3::align_cfg::mode< mode_type > | Sets the alignment mode |
| ►Cseqan3::pipeable_config_element< output< output_t >, output_t > | |
| Cseqan3::search_cfg::output< output_t > | Configuration element to determine the output type of hits |
| 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::align_cfg::result< alignment_result_tag_t, score_t > | Sets the result of the alignment computation |
| ►Cseqan3::pipeable_config_element< scoring< scoring_scheme_t >, scoring_scheme_t > | |
| Cseqan3::align_cfg::scoring< scoring_scheme_t > | Sets the scoring scheme for the alignment algorithm |
| Cseqan3::pipeable_config_element< vectorise_tag, empty_type > | |
| Csdsl::plain_byte_alphabet | Byte 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_t | Stores information of the program/tool that was used to create the file |
| ►Crandom_access_range | |
| Cseqan3::random_access_container | A more refined container concept than seqan3::sequence_container |
| ►Crange | |
| Cseqan3::forwarding_range | Specifies a range whose iterators may outlive the range and remain valid |
| 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_given | Type tag which indicates that no reference information has been passed to the alignment file on construction |
| ►Cstd::runtime_error [external] | |
| Cseqan3::file_open_error | Thrown if there is an unspecified filesystem or stream error while opening, e.g. permission problem |
| Cseqan3::invalid_char_assignment | An exception typically thrown by seqan3::alphabet::assign_char_strict |
| Cseqan3::parse_error | Thrown if there is a parse error, such as reading an unexpected character from an input stream |
| Cseqan3::unexpected_end_of_input | Thrown if I/O was expecting more input (e.g. a delimiter or a new line), but the end of input was reached |
| Cseqan3::sam_tag_type< tag_value > | The generic base class |
| Cstd::same_as | The concept std::same_as<T, U> is satisfied if and only if T and U denote the same type |
| ►Cseqan3::scoring_scheme | A concept that requires that type be able to score two letters |
| Cseqan3::aminoacid_scoring_scheme< score_type > | A data structure for managing and computing the score of two amino acids |
| Cseqan3::nucleotide_scoring_scheme< score_type > | A data structure for managing and computing the score of two nucleotides |
| 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::aminoacid_scoring_scheme< score_type > | A data structure for managing and computing the score of two amino acids |
| ►Cseqan3::scoring_scheme_base< nucleotide_scoring_scheme< score_type >, dna15, score_type > | |
| Cseqan3::nucleotide_scoring_scheme< score_type > | A data structure for managing and computing the score of two nucleotides |
| 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::back_end_first< value_t > | The penalty configuration for aligning the back of the first sequence with a gap |
| Cseqan3::back_end_second< value_t > | The penalty configuration for aligning the back of the second sequence with a gap |
| Cseqan3::front_end_first< value_t > | The penalty configuration for aligning the front of the first sequence with a gap |
| Cseqan3::front_end_second< value_t > | The penalty configuration for aligning the front of the second sequence with a gap |
| 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 | The generic concept for sequence file in formats |
| Cseqan3::format_embl | The EMBL format |
| Cseqan3::format_fasta | The FastA format |
| Cseqan3::format_genbank | The GenBank format |
| 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 | The requirements a traits_type for seqan3::sequence_file_input must meet |
| ►Cseqan3::sequence_file_input_default_traits_dna | The default traits for seqan3::sequence_file_input |
| Cseqan3::sequence_file_input_default_traits_aa | A traits type that specifies input as amino acids |
| Cseqan3::sequence_file_output< selected_field_ids_, valid_formats_ > | A class for writing sequence files, e.g. FASTA, FASTQ .. |
| ►Cseqan3::sequence_file_output_format | The generic concept for sequence file out formats |
| Cseqan3::format_embl | The EMBL format |
| Cseqan3::format_fasta | The FastA format |
| Cseqan3::format_genbank | The GenBank format |
| Cseqan3::sequence_file_output_options | The options type defines various option members that influence the behaviour of all or some formats |
| Cseqan3::sequenced_policy | Sequenced execution policy |
| ►CSequenceFileFormat | |
| Cseqan3::format_fastq | The FastQ format |
| ►Csized_range | |
| Cseqan3::container | The (most general) container concept as defined by the standard library |
| ►Cseqan3::standard_layout | Resolves to std::is_standard_layout_v<t> |
| Cseqan3::aa10li | The reduced Li amino acid alphabet |
| Cseqan3::aa10murphy | The reduced Murphy amino acid alphabet |
| Cseqan3::aa20 | The canonical amino acid alphabet |
| Cseqan3::aa27 | The twenty-seven letter amino acid alphabet |
| Cseqan3::alphabet_variant< alternative_types > | A combined alphabet that can hold values of either of its alternatives |
| Cseqan3::cigar | The cigar semialphabet pairs a counter with a seqan3::cigar_op letter |
| Cseqan3::cigar_op | The (extended) cigar operation alphabet of M,D,I,H,N,P,S,X,= |
| Cseqan3::dna15 | The 15 letter DNA alphabet, containing all IUPAC smybols minus the gap |
| Cseqan3::dna3bs | The three letter reduced DNA alphabet for bisulfite sequencing mode (A,G,T(=C)) |
| Cseqan3::dna4 | The four letter DNA alphabet of A,C,G,T |
| Cseqan3::dna5 | The five letter DNA alphabet of A,C,G,T and the unknown character N |
| Cseqan3::dot_bracket3 | The three letter RNA structure alphabet of the characters ".()" |
| Cseqan3::dssp9 | The protein structure alphabet of the characters "HGIEBTSCX" |
| Cseqan3::gap | The alphabet of a gap character '-' |
| Cseqan3::mask | Implementation of a masked alphabet to be used for tuple composites |
| Cseqan3::masked< sequence_alphabet_t > | Implementation of a masked composite, which extends a given alphabet with a mask |
| Cseqan3::phred42 | Quality type for traditional Sanger and modern Illumina Phred scores (typical range) |
| Cseqan3::phred63 | Quality type for traditional Sanger and modern Illumina Phred scores (full range) |
| Cseqan3::phred68legacy | Quality type for Solexa and deprecated Illumina formats |
| Cseqan3::qualified< sequence_alphabet_t, quality_alphabet_t > | Joins an arbitrary alphabet with a quality alphabet |
| Cseqan3::rna15 | The 15 letter RNA alphabet, containing all IUPAC smybols minus the gap |
| Cseqan3::rna4 | The four letter RNA alphabet of A,C,G,U |
| Cseqan3::rna5 | The five letter RNA alphabet of A,C,G,U and the unknown character N |
| Cseqan3::sam_dna16 | A 16 letter DNA alphabet, containing all IUPAC symbols minus the gap and plus an equality sign ('=') |
| Cseqan3::semialphabet_any< size > | A semi-alphabet that type erases all other semi-alphabets of the same size |
| Cseqan3::structured_aa< sequence_alphabet_t, structure_alphabet_t > | A seqan3::alphabet_tuple_base that joins an aminoacid alphabet with a protein structure alphabet |
| Cseqan3::structured_rna< sequence_alphabet_t, structure_alphabet_t > | A seqan3::alphabet_tuple_base that joins a nucleotide alphabet with an RNA structure alphabet |
| Cseqan3::wuss< SIZE > | The WUSS structure alphabet of the characters .<>:,-_~;()[]{}AaBbCcDd.. |
| Cseqan3::static_band | Data structure for a static band |
| ►Cseqan3::detail::strong_type< score_type, gap_open_score< score_type >, detail::strong_type_skill::convert > | |
| Cseqan3::gap_open_score< score_type > | A strong type of underlying type score_type that represents an additional score (usually negative) that is incurred once additionaly per stretch of consecutive gaps |
| ►Cseqan3::detail::strong_type< score_type, gap_score< score_type >, detail::strong_type_skill::convert > | |
| Cseqan3::gap_score< score_type > | A strong type of underlying type score_type that represents the score of any character against a gap character |
| ►Cseqan3::detail::strong_type< score_type, match_score< score_type >, detail::strong_type_skill::convert > | |
| Cseqan3::match_score< score_type > | A strong type of underlying type score_type that represents the score of two matching characters |
| ►Cseqan3::detail::strong_type< score_type, mismatch_score< score_type >, detail::strong_type_skill::convert > | |
| Cseqan3::mismatch_score< score_type > | A strong type of underlying type score_type that represents the score two different characters |
| ►Cseqan3::detail::strong_type< uint8_t, strata, detail::strong_type_skill::convert > | |
| Cseqan3::search_cfg::strata | Configuration element to receive all hits with the best number of errors plus the strata value. A strong type of underlying type uint8_t that represents the number or errors for strata. All hits are found with the fewest numbererrors plus 'value' |
| ►Cseqan3::detail::strong_type< value_t, deletion< value_t >, detail::strong_type_skill::convert > | |
| Cseqan3::search_cfg::deletion< value_t > | A strong type of underlying type uint8_t or double that represents the number or rate of deletions |
| ►Cseqan3::detail::strong_type< value_t, insertion< value_t >, detail::strong_type_skill::convert > | |
| Cseqan3::search_cfg::insertion< value_t > | A strong type of underlying type uint8_t or double that represents the number or rate of insertions |
| ►Cseqan3::detail::strong_type< value_t, lower_bound< value_t > > | |
| Cseqan3::lower_bound< value_t > | Type for a lower boundary |
| ►Cseqan3::detail::strong_type< value_t, substitution< value_t >, detail::strong_type_skill::convert > | |
| Cseqan3::search_cfg::substitution< value_t > | A strong type of underlying type uint8_t or double that represents the number or rate of substitutions |
| ►Cseqan3::detail::strong_type< value_t, total< value_t >, detail::strong_type_skill::convert > | |
| Cseqan3::search_cfg::total< value_t > | A strong type of underlying type uint8_t or double that represents the number or rate of total errors |
| ►Cseqan3::detail::strong_type< value_t, upper_bound< value_t > > | |
| Cseqan3::upper_bound< value_t > | Type for an upper boundary |
| 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 | The generic concept for structure file in formats |
| Cseqan3::format_vienna | The Vienna format (dot bracket notation) for RNA sequences with secondary structure |
| 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 | The requirements a traits_type for seqan3::structure_file_input must meet |
| ►Cseqan3::structure_file_input_default_traits_rna | The default traits for seqan3::structure_file_input |
| Cseqan3::structure_file_input_default_traits_aa | A traits type that specifies input as amino acids |
| 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 | The generic concept for structure file out formats |
| Cseqan3::format_vienna | The Vienna format (dot bracket notation) for RNA sequences with secondary structure |
| Cseqan3::structure_file_output_options | The options type defines various option members that influence the behaviour of all or some formats |
| ►Cstd::swappable | The concept std::swappable specifies that lvalues of type T are swappable |
| Cstd::movable | Subsumes std::Object, std::move_constructible, std::swappable bool and requires that the type be std::assignable_from bool from a value of itself |
| Cstd::swappable_with | The 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_result | Result type of std::to_chars |
| ►Ctransfer_template_args_onto_t | |
| Cseqan3::record< field_types, field_ids > | The class template that file records are based on; behaves like an std::tuple |
| ►Cseqan3::transformation_trait | Concept for a transformation trait |
| Cseqan3::const_reference< t > | Exposes the const_reference of another type |
| Cseqan3::const_reference< rng_t > | Exposes the const_reference of another type |
| Cseqan3::difference_type< t > | Exposes the difference_type of another type |
| Cseqan3::difference_type< it_t > | Exposes the difference_type of another type |
| Cseqan3::difference_type< rng_t > | Exposes the difference_type of another type |
| Cseqan3::innermost_value_type< t > | Recursively determines the value_type on containers and/or iterators |
| Cseqan3::iterator_tag< it_t > | Exposes the iterator_category from the modelled concept |
| Cseqan3::reference< t > | Exposes the reference of another type |
| Cseqan3::reference< it_t > | Exposes the reference type of another type |
| Cseqan3::reference< rng_t > | Exposes the reference of another type |
| Cseqan3::remove_rvalue_reference< t > | Return the input type with && removed, but lvalue references preserved |
| Cseqan3::rvalue_reference< t > | Exposes the rvalue_reference of another type |
| Cseqan3::rvalue_reference< it_t > | Exposes the rvalue_reference type of another type |
| Cseqan3::rvalue_reference< rng_t > | Exposes the rvalue_reference of another type |
| Cseqan3::size_type< t > | Exposes the size_type of another type |
| Cseqan3::size_type< it_t > | Exposes the size_type of another type |
| Cseqan3::size_type< rng_t > | Exposes the size_type of another type |
| Cseqan3::value_type< t > | Exposes the value_type of another type |
| Cseqan3::value_type< it_t > | Exposes the value_type of another type |
| Cseqan3::value_type< rng_t > | Exposes the value_type of another type |
| Cstd::tuple_element< elem_no, seqan3::alignment_file_input< traits_type, selected_field_ids, valid_formats > > | Obtains the type of the specified element |
| Cstd::tuple_element< elem_no, seqan3::record< field_types, field_ids > > | Obtains the type of the specified element |
| Cstd::tuple_element< i, tuple_t > | Obtains the type of the specified element |
| ►Cstd::tuple< configs_t... > [external] | |
| Cseqan3::configuration< configs_t > | Collection of elements to configure an algorithm |
| ►Ctuple_element | |
| Cstd::tuple_element< elem_no, seqan3::alignment_file_input< traits_type, selected_field_ids, valid_formats > > | Obtains the type of the specified 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_trait | Concept for a unary traits type |
| Cseqan3::is_constexpr_default_constructible< t > | Whether a type std::is_default_constructible in constexpr-context |
| Cstd::tuple_size< seqan3::alignment_file_input< traits_type, selected_field_ids, valid_formats > > | Provides access to the number of elements in a tuple as a compile-time constant expression |
| Cstd::tuple_size< seqan3::record< field_types, field_ids > > | Provides access to the number of elements in a tuple as a compile-time constant expression |
| Cstd::tuple_size< tuple_t > | Provides access to the number of elements in a tuple as a compile-time constant expression |
| Cseqan3::ungapped | A strong type of underlying type uint8_t that represents the ungapped shape size |
| Cseqan3::unsequenced_policy | Unsequenced execution policy |
| ►Cseqan3::validator | The concept for option validators passed to add_option/positional_option |
| Cseqan3::arithmetic_range_validator | A validator that checks whether a number is inside a given range |
| Cseqan3::input_directory_validator | A validator that checks if a given path is a valid input directory |
| Cseqan3::input_file_validator< file_t > | A validator that checks if a given path is a valid input file |
| Cseqan3::output_directory_validator | A validator that checks if a given path is a valid output directory |
| Cseqan3::output_file_validator< file_t > | A validator that checks if a given path is a valid output file |
| Cseqan3::regex_validator | A validator that checks if a matches a regular expression pattern |
| Cseqan3::value_list_validator< option_value_t > | A validator that checks whether a value is inside a list of valid values |
| Cseqan3::weakly_assignable_from | Resolves to std::is_assignable_v<t> |
| ►Cseqan3::detail::weakly_equality_comparable_with | Requires the two operands to be comparable with == and != in both directions |
| ►Cstd::equality_comparable_with | Requires seqan3::detail::weakly_equality_comparable_witht<t1,t2>, but also that t1 and t2, as well as their common_reference_t satisfy std::equality_comparable |
| Cstd::totally_ordered_with | Requires std::equality_comparable and all remaing comparison operators (<, <=, >, >=) |
1.8.13