| ►Cdetail:: strong_type | |
| Cseqan3::search_cfg::error_count | A strong type of underlying type uint8_t that represents the number of errors |
| ►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::advanceable_alignment_coordinate_printer< typename > | |
| Cseqan3::advanceable_alignment_coordinate_printer< detail::advanceable_alignment_coordinate< state_t > > | The printer for seqan3::detail::advanceable_alignment_coordinate |
| Cseqan3::aligned_allocator< value_t, alignment_v > | Allocates uninitialized storage whose memory-alignment is specified by alignment |
| Cseqan3::alignment_matrix_printer< typename > | |
| Cseqan3::alignment_matrix_printer< alignment_matrix_t > | The printer for alignment scoring and trace matrices |
| Cseqan3::alignment_printer< typename > | |
| Cseqan3::alignment_printer< alignment_t > | The printer for alignment |
| Cseqan3::alignment_result< alignment_result_value_t > | Stores the alignment results and gives access to score, alignment and the front and end positions |
| Cseqan3::alignment_result_printer< typename > | |
| Cseqan3::alignment_result_printer< alignment_result< result_value_t > > | The printer used for formatted output of the alignment result |
| ►CAlignmentFileFormat | |
| Cseqan3::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, exposition_only::cigar_operation > | |
| Cseqan3::cigar | The seqan3::cigar semialphabet pairs a counter with a seqan3::cigar::operation 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< aa27, dssp9 >, aa27, dssp9 > | |
| ►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::aminoacid_base< aa10li, 10 > | |
| Cseqan3::aa10li | The reduced Li amino acid alphabet |
| ►Cseqan3::aminoacid_base< aa10murphy, 10 > | |
| Cseqan3::aa10murphy | The reduced Murphy amino acid alphabet |
| ►Cseqan3::aminoacid_base< aa20, 20 > | |
| Cseqan3::aa20 | The canonical amino acid alphabet |
| ►Cseqan3::aminoacid_base< aa27, 27 > | |
| Cseqan3::aa27 | The twenty-seven letter amino acid alphabet |
| ►Cseqan3::nucleotide_base< dna15, 15 > | |
| Cseqan3::dna15 | The 15 letter DNA alphabet, containing all IUPAC smybols minus the gap |
| ►Cseqan3::nucleotide_base< dna16sam, 16 > | |
| Cseqan3::dna16sam | A 16 letter DNA alphabet, containing all IUPAC symbols minus the gap and plus an equality sign ('=') |
| ►Cseqan3::nucleotide_base< dna3bs, 3 > | |
| Cseqan3::dna3bs | The three letter reduced DNA alphabet for bisulfite sequencing mode (A,G,T(=C)) |
| ►Cseqan3::nucleotide_base< dna4, 4 > | |
| Cseqan3::dna4 | The four letter DNA alphabet of A,C,G,T |
| ►Cseqan3::nucleotide_base< dna5, 5 > | |
| Cseqan3::dna5 | The five letter DNA alphabet of A,C,G,T and the unknown character N |
| ►Cseqan3::nucleotide_base< rna15, 15 > | |
| Cseqan3::rna15 | The 15 letter RNA alphabet, containing all IUPAC smybols minus the gap |
| ►Cseqan3::nucleotide_base< rna4, 4 > | |
| Cseqan3::rna4 | The four letter RNA alphabet of A,C,G,U |
| ►Cseqan3::nucleotide_base< rna5, 5 > | |
| Cseqan3::rna5 | The five letter RNA alphabet of A,C,G,U and the unknown character N |
| ►Cseqan3::phred_base< phred42, 42 > | |
| Cseqan3::phred42 | Quality type for traditional Sanger and modern Illumina Phred scores |
| ►Cseqan3::phred_base< phred63, 63 > | |
| Cseqan3::phred63 | Quality type for traditional Sanger and modern Illumina Phred scores |
| ►Cseqan3::phred_base< phred68solexa, 68 > | |
| Cseqan3::phred68solexa | Quality type for Solexa and deprecated Illumina formats |
| ►Cseqan3::phred_base< phred94, 94 > | |
| Cseqan3::phred94 | Quality type for PacBio Phred scores of HiFi reads |
| Cseqan3::wuss< SIZE > | The WUSS structure alphabet of the characters .<>:,-_~;()[]{}AaBbCcDd.. |
| 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_variant< alternative_types > | A combined alphabet that can hold values of either of its alternatives. |
| Cseqan3::alphabet_base< cigar,(1 *... *alphabet_size< component_types >), void > | |
| ►Cseqan3::alphabet_base< cigar_operation, 9, char > | |
| Cseqan3::exposition_only::cigar_operation | The actual implementation of seqan3::cigar::operation for documentation purposes only |
| ►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::phred_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::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_base< dna15, size, char > | |
| Cseqan3::alphabet_base< dna16sam, size, char > | |
| Cseqan3::alphabet_base< dna3bs, size, char > | |
| Cseqan3::alphabet_base< dna4, size, char > | |
| Cseqan3::alphabet_base< dna5, size, char > | |
| ►Cseqan3::alphabet_base< dot_bracket3, 3 > | |
| Cseqan3::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< masked< sequence_alphabet_t >,(1 *... *alphabet_size< component_types >), void > | |
| Cseqan3::alphabet_base< phred42, size, char > | |
| Cseqan3::alphabet_base< phred63, size, char > | |
| Cseqan3::alphabet_base< phred68solexa, size, char > | |
| Cseqan3::alphabet_base< phred94, size, char > | |
| Cseqan3::alphabet_base< qualified< sequence_alphabet_t, quality_alphabet_t >,(1 *... *alphabet_size< component_types >), void > | |
| Cseqan3::alphabet_base< rna15, size, char > | |
| Cseqan3::alphabet_base< rna4, size, char > | |
| Cseqan3::alphabet_base< rna5, size, char > | |
| ►Cseqan3::alphabet_base< semialphabet_any< size >, size, void > | |
| Cseqan3::semialphabet_any< size > | A semi-alphabet that type erases all other semi-alphabets of the same size |
| Cseqan3::alphabet_base< structured_aa< aa27, dssp9 >,(1 *... *alphabet_size< component_types >), void > | |
| Cseqan3::alphabet_base< structured_rna< sequence_alphabet_t, structure_alphabet_t >,(1 *... *alphabet_size< component_types >), void > | |
| Cseqan3::alphabet_base< wuss< 51 >, 51 > | |
| Cseqan3::alphabet_printer< typename > | |
| Cseqan3::alphabet_printer< alphabet_t > | The printer used for formatted output of seqan3::alphabet types |
| ►Cseqan3::aminoacid_empty_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 |
| Cargument_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 |
| Carithmetic | A type that satisfies std::is_arithmetic_v<t> |
| Cseqan3::bin_literal | A strong type of underlying type uint64_t that represents the shape in binary representation |
| Cseqan3::interleaved_bloom_filter< data_layout_mode_ >::membership_agent_type::binning_bitvector | A bitvector representing the result of a call to bulk_contains of the seqan3::interleaved_bloom_filter |
| ►Ccereal_archive | All archives of the Cereal library satisfy this |
| Ccereal_input_archive | All input archives of the Cereal library satisfy this |
| Ccereal_output_archive | All output archives of the Cereal library satisfy this |
| Ccereal_text_archive | All text archives of the Cereal library satisfy this |
| ►Ccerealisable | Specifies the requirements for types that are serialisable via Cereal |
| ►Cseqan3::dynamic_bitset< 58 > | |
| Cseqan3::shape | A class that defines which positions of a pattern to hash |
| Cseqan3::fm_index< alphabet_t, text_layout_mode, default_sdsl_index_type > | |
| Cseqan3::fm_index< alphabet_t, text_layout_mode_, sdsl_index_type > | |
| Cseqan3::fm_index< alphabet_t, text_layout_mode, sdsl_index_type > | |
| Cseqan3::scoring_scheme_base< aminoacid_scoring_scheme< int8_t >, aa27, int8_t > | |
| Cseqan3::scoring_scheme_base< nucleotide_scoring_scheme< int8_t >, dna15, int8_t > | |
| ►Cseqan3::small_vector< char, capacity_+1 > | |
| Cseqan3::small_string< capacity_ > | Implements a small string that can be used for compile time computations |
| Cseqan3::bi_fm_index< alphabet_t, text_layout_mode_, sdsl_index_type_ > | The SeqAn Bidirectional FM Index |
| Cseqan3::bi_fm_index_cursor< index_t > | The SeqAn Bidirectional FM Index Cursor |
| Cseqan3::bitpacked_sequence< alphabet_type > | A space-optimised version of std::vector that compresses multiple letters into a single byte |
| Cseqan3::bloom_filter< data_layout_mode_ > | The Bloom Filter. A data structure that efficiently answers set-membership queries |
| Cseqan3::concatenated_sequences< underlying_container_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::fm_index< alphabet_t, text_layout_mode_, sdsl_index_type_ > | The SeqAn FM Index |
| Cseqan3::fm_index_cursor< index_t > | The SeqAn FM Index Cursor |
| Cseqan3::interleaved_bloom_filter< data_layout_mode_ > | The IBF binning directory. A data structure that efficiently answers set-membership queries for multiple bins |
| ►Cseqan3::scoring_scheme_base< derived_t, alphabet_t, score_t > | A CRTP base class for scoring schemes |
| 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::small_vector< value_type_, capacity_ > | A constexpr vector implementation with dynamic size at compile time |
| Cseqan3::char_sequence_printer< typename > | |
| Cseqan3::char_sequence_printer< char_sequence_t > | A printer for character sequences |
| Cseqan3::cigar_clipped_bases | Helper struct to specialise soft and hard clipping when using seqan3::cigar_from_alignment |
| Cseqan3::cigar_printer< typename > | |
| Cseqan3::cigar_printer< cigar > | The printer used for formatted output of the cigar alphabets |
| ►Cstd::ranges::common_range | |
| ►Ccontainer | The (most general) container concept as defined by the standard library |
| ►Csequence_container | A more refined container concept than seqan3::container |
| ►Crandom_access_container | A more refined container concept than seqan3::sequence_container |
| ►Creservible_container | A more refined container concept than seqan3::random_access_container |
| Cseqan3::dynamic_bitset< 58 > | |
| Cseqan3::small_vector< char, capacity_+1 > | |
| Cseqan3::bitpacked_sequence< alphabet_type > | A space-optimised version of std::vector that compresses multiple letters into a single byte |
| Cseqan3::concatenated_sequences< underlying_container_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 |
| ►Cstd::conditional_t [external] | |
| Cseqan3::alphabet_proxy< component_proxy< alphabet_type, index >, alphabet_type > | |
| Cseqan3::alphabet_proxy< reference_proxy_type, 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::copy_constructible | |
| ►Csemialphabet | The basis for seqan3::alphabet, but requires only rank interface (not char) |
| ►Calphabet | The generic alphabet concept that covers most data types used in ranges |
| ►Caminoacid_alphabet | A concept that indicates whether an alphabet represents amino acids |
| 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 |
| ►Cconstexpr_alphabet | A seqan3::alphabet that has constexpr accessors |
| ►Cwritable_constexpr_alphabet | A seqan3::writable_alphabet that has constexpr accessors |
| 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::dna15 | The 15 letter DNA alphabet, containing all IUPAC smybols minus the gap |
| Cseqan3::dna16sam | A 16 letter DNA alphabet, containing all IUPAC symbols minus the gap and plus an equality sign ('=') |
| 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::exposition_only::cigar_operation | The actual implementation of seqan3::cigar::operation for documentation purposes only |
| 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 |
| Cseqan3::phred63 | Quality type for traditional Sanger and modern Illumina Phred scores |
| Cseqan3::phred68solexa | Quality type for Solexa and deprecated Illumina formats |
| Cseqan3::phred94 | Quality type for PacBio Phred scores of HiFi reads |
| 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::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.. |
| ►Cnucleotide_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::dna16sam | A 16 letter DNA alphabet, containing all IUPAC symbols minus the gap and plus an equality sign ('=') |
| 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::structured_rna< sequence_alphabet_t, structure_alphabet_t > | A seqan3::alphabet_tuple_base that joins a nucleotide alphabet with an RNA structure alphabet |
| Cquality_alphabet | A concept that indicates whether an alphabet represents quality scores |
| ►Crna_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.. |
| ►Cwritable_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. |
| Cwritable_constexpr_alphabet | A seqan3::writable_alphabet that has constexpr accessors |
| Cseqan3::dna15 | The 15 letter DNA alphabet, containing all IUPAC smybols minus the gap |
| Cseqan3::dna16sam | A 16 letter DNA alphabet, containing all IUPAC symbols minus the gap and plus an equality sign ('=') |
| 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::exposition_only::cigar_operation | The actual implementation of seqan3::cigar::operation for documentation purposes only |
| 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::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.. |
| ►Cwritable_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 |
| Cseqan3::phred63 | Quality type for traditional Sanger and modern Illumina Phred scores |
| Cseqan3::phred68solexa | Quality type for Solexa and deprecated Illumina formats |
| Cseqan3::phred94 | Quality type for PacBio Phred scores of HiFi reads |
| Cseqan3::qualified< sequence_alphabet_t, quality_alphabet_t > | Joins an arbitrary alphabet with a quality alphabet |
| ►Cconstexpr_semialphabet | A seqan3::semialphabet that has constexpr accessors |
| Cconstexpr_alphabet | A seqan3::alphabet that has constexpr accessors |
| ►Cwritable_constexpr_semialphabet | A seqan3::writable_semialphabet that has a constexpr assignment |
| Cwritable_constexpr_alphabet | A seqan3::writable_alphabet that has constexpr accessors |
| Cseqan3::semialphabet_any< size > | A semi-alphabet that type erases all other semi-alphabets of the same size |
| ►Cwritable_semialphabet | A refinement of seqan3::semialphabet that adds assignability |
| Cseqan3::alphabet_tuple_base< cigar, uint32_t, exposition_only::cigar_operation > | |
| 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< aa27, dssp9 >, aa27, dssp9 > | |
| 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 seqan3::cigar semialphabet pairs a counter with a seqan3::cigar::operation letter |
| Cwritable_constexpr_semialphabet | A seqan3::writable_semialphabet that has a constexpr assignment |
| Cseqan3::mask | Implementation of a masked alphabet to be used for tuple composites |
| Cwritable_alphabet | Refines seqan3::alphabet and adds assignability |
| ►Cstd::copyable | |
| ►Ctrivially_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 seqan3::cigar semialphabet pairs a counter with a seqan3::cigar::operation letter |
| Cseqan3::dna15 | The 15 letter DNA alphabet, containing all IUPAC smybols minus the gap |
| Cseqan3::dna16sam | A 16 letter DNA alphabet, containing all IUPAC symbols minus the gap and plus an equality sign ('=') |
| 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::exposition_only::cigar_operation | The actual implementation of seqan3::cigar::operation for documentation purposes only |
| Cseqan3::gap | The alphabet of a gap character '-' |
| Cseqan3::phred42 | Quality type for traditional Sanger and modern Illumina Phred scores |
| Cseqan3::phred63 | Quality type for traditional Sanger and modern Illumina Phred scores |
| Cseqan3::phred68solexa | Quality type for Solexa and deprecated Illumina formats |
| Cseqan3::phred94 | Quality type for PacBio Phred scores of HiFi reads |
| 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::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 |
| Ctrivial | A type that satisfies seqan3::trivially_copyable and seqan3::trivially_destructible |
| Cseqan3::wuss< SIZE > | The WUSS structure alphabet of the characters .<>:,-_~;()[]{}AaBbCcDd.. |
| Cseqan3::interleaved_bloom_filter< data_layout_mode_ >::counting_agent_type< value_t > | Manages counting ranges of values for the seqan3::interleaved_bloom_filter |
| Cseqan3::debug_stream_printer< typename > | |
| Cseqan3::debug_stream_printer< value_t > | A struct that provides a debug stream printer for a specific value type |
| Cseqan3::debug_stream_type< char_t > | A "pretty printer" for most SeqAn data structures and related types |
| ►Cstd::destructible | |
| ►Ctrivially_destructible | A type that satisfies std::is_trivially_destructible_v<t> |
| Ctrivial | A type that satisfies seqan3::trivially_copyable and seqan3::trivially_destructible |
| Cseqan3::dynamic_bitset_printer< typename > | |
| Cseqan3::dynamic_bitset_printer< dynamic_bitset< bit_capacity > > | Prints seqan3::dynamic_bitset. This entity is experimental and subject to change in the future. Experimental since version 3.1. |
| Cenum_bitwise_operators | You can expect these functions on all types that overload seqan3::add_enum_bitwise_operators |
| Cseqan3::enumeration_printer< typename > | |
| Cseqan3::enumeration_printer< enum_t > | A type (e.g. an enum) can be made debug streamable by customizing the seqan3::enumeration_names |
| Cexplicitly_convertible_to | Checks whether from can be explicitly converted to to |
| ►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 (unary_type_trait specialisation) |
| 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::detail::format_sam_base | The alignment base format |
| Cseqan3::format_bam | The BAM format |
| Cseqan3::format_sam | The SAM format (tag) |
| ►Cstd::forward_iterator | |
| Cpseudo_random_access_iterator | This concept checks if an iterator type models pseudo random access |
| ►Cstd::ranges::forward_range | |
| Ccontainer | The (most general) container concept as defined by the standard library |
| Cpseudo_random_access_range | This concept checks if a type models a pseudo random access range |
| ►Cwritable_aligned_sequence | The generic concept for an aligned sequence that is writable |
| Cseqan3::gap_decorator< inner_type > | A gap decorator allows the annotation of sequences with gap symbols while leaving the underlying sequence unmodified |
| Cseqan3::function_traits< std::function< return_t(args_t...)> > | A traits class to provide a uniform interface to the properties of a function type |
| Cseqan3::hamming_scoring_scheme | A scoring scheme that assigns a score of 0 to matching letters and -1 to mismatching letters |
| Cstd::hash< alphabet_t > | Struct for hashing a character |
| Cstd::hash< seqan3::dynamic_bitset< cap > > | Struct for hashing a seqan3::dynamic_bitset |
| Cstd::hash< urng_t > | Struct for hashing a range of characters |
| Cimplicitly_convertible_to | Checks whether from can be implicityly converted to to |
| ►Cstd::input_iterator | |
| Cseqan3::algorithm_result_generator_range< algorithm_executor_type >::algorithm_range_iterator | The iterator of seqan3::detail::algorithm_result_generator_range |
| ►Cstd::input_range | |
| ►Cconst_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 |
| Ccontainer | The (most general) container concept as defined by the standard library |
| ►Cstd::ranges::input_range | |
| Cseqan3::algorithm_result_generator_range< algorithm_executor_type > | An input range over the algorithm results generated by the underlying algorithm executor |
| ►Csequence | The generic concept for a (biological) sequence |
| ►Caligned_sequence | The generic concept for an aligned sequence |
| Cwritable_aligned_sequence | The generic concept for an aligned sequence that is writable |
| Cseqan3::input_range_printer< typename > | |
| ►Cseqan3::input_range_printer< integer_sequence_t > | |
| Cseqan3::integer_sequence_printer< integer_sequence_t > | A printer for integer sequences |
| Cseqan3::input_range_printer< rng_t > | A printer for arbitrary input ranges |
| Cinput_stream_over | Concept for input streams |
| Cseqan3::integer_sequence_printer< typename > | |
| ►Cstd::integral | |
| Cbuiltin_character | This concept encompasses exactly the types char, signed char, unsigned char, wchar_t, char16_t and char32_t |
| ►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::integral_constant< std::size_t, sizeof...(types)> [external] | |
| Cstd::tuple_size< t< types... > > | Provides access to the number of elements in a tuple as a compile-time constant expression |
| Cseqan3::integral_printer< typename > | |
| Cseqan3::integral_printer< integral_t > | The printer for integral types |
| ►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::unhandled_extension_error | Thrown if there is no format that accepts a given file extension |
| ►Cstd::logic_error [external] | |
| Cseqan3::gap_erase_failure | Thrown in function seqan3::erase_gap, if a position does not contain a gap |
| ►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::mask_printer< typename > | |
| Cseqan3::mask_printer< mask_t > | The printer used for formatted output of seqan3::mask alphabet |
| Cseqan3::interleaved_bloom_filter< data_layout_mode_ >::membership_agent_type | Manages membership queries for the seqan3::interleaved_bloom_filter |
| Cnamed_enumeration | Checks whether the free function seqan3::enumeration_names can be called on the type |
| Cseqan3::no_printer_found | A tag that indicates that no printer was found for the given type |
| Cnonrecursive_range | A concept that checks whether a range is non-recursive |
| Cseqan3::optional_printer< typename > | |
| Cseqan3::optional_printer< std::nullopt_t > | Printer for formatted output of std::nullopt_t |
| Cseqan3::optional_printer< std::optional< T > > | Printer for formatted output of a std::optional |
| Coutput_stream_over | Concept for output streams |
| ►Cseqan3::pipeable_config_element | Adds pipe interface to configuration elements |
| Cseqan3::align_cfg::band_fixed_size | Configuration element for setting a fixed size band |
| Cseqan3::align_cfg::detail::result_type< alignment_result_t > | Configuration element capturing the configured seqan3::alignment_result for the alignment algorithm |
| Cseqan3::align_cfg::gap_cost_affine | A configuration element for the affine gap cost scheme |
| Cseqan3::align_cfg::method_global | Sets the global alignment method |
| Cseqan3::align_cfg::method_local | Sets the local alignment method |
| Cseqan3::align_cfg::min_score | Sets the minimal score (maximal errors) allowed during an distance computation e.g. edit distance |
| Cseqan3::align_cfg::on_result< callback_t > | Configuration element to provide a user defined callback function for the alignment |
| Cseqan3::align_cfg::output_alignment | Configures the alignment result to output the alignment |
| Cseqan3::align_cfg::output_begin_position | Configures the alignment result to output the begin positions |
| Cseqan3::align_cfg::output_end_position | Configures the alignment result to output the end position |
| Cseqan3::align_cfg::output_score | Configures the alignment result to output the score |
| Cseqan3::align_cfg::output_sequence1_id | Configures the alignment result to output the id of the first sequence |
| Cseqan3::align_cfg::output_sequence2_id | Configures the alignment result to output the id of the second sequence |
| Cseqan3::align_cfg::score_type< score_t > | A configuration element to set the score type used in the alignment algorithm |
| Cseqan3::align_cfg::scoring_scheme< scoring_scheme_t > | Sets the scoring scheme for the alignment algorithm |
| Cseqan3::align_cfg::vectorised | Enables the vectorised alignment computation if possible for the current configuration |
| Cseqan3::search_cfg::detail::result_type< search_result_t > | Configuration element storing the configured seqan3::search_result for the search algorithm |
| Cseqan3::search_cfg::hit | A dynamic configuration element to configure the hit strategy at runtime |
| Cseqan3::search_cfg::hit_all | Configuration element to receive all hits within the error bounds |
| Cseqan3::search_cfg::hit_all_best | Configuration element to receive all hits with the lowest number of errors within the error bounds |
| Cseqan3::search_cfg::hit_single_best | Configuration element to receive a single best hit with the lowest number of errors within the error bounds |
| Cseqan3::search_cfg::hit_strata | Configuration element to receive all hits with the best number of errors plus the given stratum. All hits are found with the fewest number of errors plus 'stratum' |
| Cseqan3::search_cfg::max_error_deletion | Configuration element that represents the number or rate of deletion errors |
| Cseqan3::search_cfg::max_error_insertion | Configuration element that represents the number or rate of insertion errors |
| Cseqan3::search_cfg::max_error_substitution | Configuration element that represents the number or rate of substitution errors |
| Cseqan3::search_cfg::max_error_total | Configuration element that represents the number or rate of total errors |
| Cseqan3::search_cfg::on_result< callback_t > | Configuration element to provide a user defined callback function for the search |
| Cseqan3::search_cfg::output_index_cursor | Include the index_cursor in the seqan3::search_result returned by a call to seqan3::search |
| Cseqan3::search_cfg::output_query_id | Include the query_id in the seqan3::search_result returned by a call to seqan3::search |
| Cseqan3::search_cfg::output_reference_begin_position | Include the reference_begin_position in the seqan3::search_result returned by a call to seqan3::search |
| Cseqan3::search_cfg::output_reference_id | Include the reference_id in the seqan3::search_result returned by a call to seqan3::search |
| Cseqan3::pod_tuple< types > | |
| Cseqan3::pod_tuple< type0 > | Recursion anchor for seqan3::pod_tuple |
| Cprintable_with | The concept for a printable object |
| Cseqan3::printer_order< printer_templates_t > | The printer_order is a variadic template that defines the order of the printers |
| ►Cseqan3::printer_order< debug_stream_printer, alignment_result_printer, search_result_printer, alignment_printer, advanceable_alignment_coordinate_printer, alignment_matrix_printer, trace_directions_printer, mask_printer, integral_printer, cigar_printer, alphabet_printer, sam_flag_printer, simd_printer, dynamic_bitset_printer, char_sequence_printer, integer_sequence_printer, sequence_printer, input_range_printer, strong_type_printer, optional_printer, enumeration_printer, tuple_printer, std_byte_printer, std_variant_printer, std_printer > | |
| Cseqan3::default_printer | The default printer that is used by seqan3::debug_stream |
| ►Cstd::ranges::random_access_range | |
| Crandom_access_container | A more refined container concept than seqan3::sequence_container |
| Cseqan3::aligned_allocator< value_t, alignment_v >::rebind< new_value_type > | The aligned_allocator member template class aligned_allocator::rebind provides a way to obtain an allocator for a different type |
| ►Crecord_like | The concept for a type that models a record |
| Cseqan3::sam_record< detail::select_types_with_ids_t< field_types, field_ids, selected_field_ids >, selected_field_ids > | |
| Cseqan3::sequence_record< detail::select_types_with_ids_t< field_types, field_ids, selected_field_ids >, selected_field_ids > | |
| Cseqan3::structure_record< detail::select_types_with_ids_t< field_types, field_ids, selected_field_ids >, selected_field_ids > | |
| Cseqan3::sam_record< field_types, field_ids > | The record type of seqan3::sam_file_input |
| Cseqan3::sequence_record< field_types, field_ids > | The record type of seqan3::sequence_file_input |
| Cseqan3::structure_record< field_types, field_ids > | The record type of seqan3::structure_file_input |
| Cseqan3::ref_info_not_given | Type tag which indicates that no reference information has been passed to the SAM file on construction |
| ►Cstd::regular | |
| 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 seqan3::cigar semialphabet pairs a counter with a seqan3::cigar::operation letter |
| 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::exposition_only::cigar_operation | The actual implementation of seqan3::cigar::operation for documentation purposes only |
| Cseqan3::gap | The alphabet of a gap character '-' |
| Cseqan3::phred42 | Quality type for traditional Sanger and modern Illumina Phred scores |
| Cseqan3::phred63 | Quality type for traditional Sanger and modern Illumina Phred scores |
| Cseqan3::phred68solexa | Quality type for Solexa and deprecated Illumina formats |
| Cseqan3::phred94 | Quality type for PacBio Phred scores of HiFi reads |
| 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.. |
| ►Cstd::runtime_error [external] | |
| ►Cseqan3::argument_parser_error | Argument parser exception that is thrown whenever there is an error while parsing the command line arguments |
| Cseqan3::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) |
| Cseqan3::option_declared_multiple_times | Argument parser exception thrown when a non-list option is declared multiple times |
| 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::unknown_option | Argument parser exception thrown when encountering unknown option |
| Cseqan3::user_input_error | Argument parser exception thrown when an incorrect argument is given as (positional) option value |
| Cseqan3::validation_error | Argument parser exception thrown when an argument could not be casted to the according type |
| 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_file_header< ref_ids_type > | Stores the header information of SAM/BAM files |
| Cseqan3::sam_file_input< traits_type_, selected_field_ids_, valid_formats_ > | A class for reading SAM files, both SAM and its binary representation BAM are supported |
| Cseqan3::sam_file_input_format< t > | The generic concept for alignment file input formats |
| Cseqan3::sam_file_input_options< sequence_legal_alphabet > | The options type defines various option members that influence the behaviour of all or some formats |
| Cseqan3::sam_file_input_options< typename traits_type::sequence_legal_alphabet > | |
| ►Csam_file_input_traits | The requirements a traits_type for seqan3::sam_file_input must meet |
| Cseqan3::sam_file_input_default_traits< ref_sequences_t, ref_ids_t > | The default traits for seqan3::sam_file_input |
| Cseqan3::sam_file_output< selected_field_ids_, valid_formats_, ref_ids_type > | A class for writing SAM files, both SAM and its binary representation BAM are supported |
| Cseqan3::sam_file_output_format< t > | The generic concept for alignment file out formats |
| Cseqan3::sam_file_output_options | The options type defines various option members that influence the behavior of all or some formats |
| Cseqan3::sam_file_program_info_t | Stores information of the program/tool that was used to create a SAM/BAM file |
| Cseqan3::sam_flag_printer< typename > | |
| Cseqan3::sam_flag_printer< sam_flag > | A sam_flag can be printed as an integer value |
| Cseqan3::sam_tag_type< tag_value > | The generic base class |
| ►Cseqan3::scoring_scheme | |
| 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 |
| Cscoring_scheme_for | A concept that requires that type be able to score two letters |
| Cseqan3::search_result< query_id_type, cursor_type, reference_id_type, reference_begin_position_type > | The result class generated by the seqan3::seach algorithm |
| Cseqan3::search_result_printer< typename > | |
| Cseqan3::search_result_printer< search_result< specs_t... > > | The printer used for formatted output of the search result |
| Cseqan3::sequence_file_input< traits_type_, selected_field_ids_, valid_formats_ > | A class for reading sequence files, e.g. FASTA, FASTQ .. |
| ►Cseqan3::sequence_file_input_format< t > | The generic concept for sequence file in formats |
| Cseqan3::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 > | The options type defines various option members that influence the behaviour of all or some formats |
| Cseqan3::sequence_file_input_options< typename traits_type::sequence_legal_alphabet > | |
| ►Csequence_file_input_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< t > | 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::sequence_printer< typename > | |
| Cseqan3::sequence_printer< sequence_t > | A printer for (biological) sequences |
| ►CSequenceFileFormat | |
| Cseqan3::format_fastq | The FASTQ format |
| Cseqan3::simd_printer< typename > | |
| ►Cstd::ranges::sized_range | |
| Ccontainer | The (most general) container concept as defined by the standard library |
| ►Cstandard_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 seqan3::cigar semialphabet pairs a counter with a seqan3::cigar::operation letter |
| Cseqan3::dna15 | The 15 letter DNA alphabet, containing all IUPAC smybols minus the gap |
| Cseqan3::dna16sam | A 16 letter DNA alphabet, containing all IUPAC symbols minus the gap and plus an equality sign ('=') |
| 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::exposition_only::cigar_operation | The actual implementation of seqan3::cigar::operation for documentation purposes only |
| Cseqan3::gap | The alphabet of a gap character '-' |
| Cseqan3::phred42 | Quality type for traditional Sanger and modern Illumina Phred scores |
| Cseqan3::phred63 | Quality type for traditional Sanger and modern Illumina Phred scores |
| Cseqan3::phred68solexa | Quality type for Solexa and deprecated Illumina formats |
| Cseqan3::phred94 | Quality type for PacBio Phred scores of HiFi reads |
| 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::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::std_byte_printer< typename > | |
| Cseqan3::std_byte_printer< std::byte > | A std::byte can be printed by printing its value as integer |
| Cseqan3::std_printer< typename > | |
| Cseqan3::std_printer< type_t > | The printer for standard output streams |
| Cseqan3::std_variant_printer< typename > | |
| Cseqan3::std_variant_printer< std::variant< variant_ts... > > | A std::variant can be printed by visiting the stream operator for the corresponding type |
| ►Cseqan3::detail::strong_type< bool, free_end_gaps_sequence1_leading > | |
| Cseqan3::align_cfg::free_end_gaps_sequence1_leading | A strong type representing free_end_gaps_sequence1_leading of the seqan3::align_cfg::method_global |
| ►Cseqan3::detail::strong_type< bool, free_end_gaps_sequence1_trailing > | |
| Cseqan3::align_cfg::free_end_gaps_sequence1_trailing | A strong type representing free_end_gaps_sequence1_trailing of the seqan3::align_cfg::method_global |
| ►Cseqan3::detail::strong_type< bool, free_end_gaps_sequence2_leading > | |
| Cseqan3::align_cfg::free_end_gaps_sequence2_leading | A strong type representing free_end_gaps_sequence2_leading of the seqan3::align_cfg::method_global |
| ►Cseqan3::detail::strong_type< bool, free_end_gaps_sequence2_trailing > | |
| Cseqan3::align_cfg::free_end_gaps_sequence2_trailing | A strong type representing free_end_gaps_sequence2_trailing of the seqan3::align_cfg::method_global |
| ►Cseqan3::detail::strong_type< double, error_rate, detail::strong_type_skill::convert|detail::strong_type_skill::comparable > | |
| Cseqan3::search_cfg::error_rate | A strong type of underlying type double that represents the rate of errors |
| ►Cseqan3::detail::strong_type< int32_t, extension_score, seqan3::detail::strong_type_skill::convert > | |
| Cseqan3::align_cfg::extension_score | A strong type of underlying type int32_t that represents the score (usually negative) of any character against a gap character |
| ►Cseqan3::detail::strong_type< int32_t, lower_diagonal > | |
| Cseqan3::align_cfg::lower_diagonal | A strong type representing the lower diagonal of the seqan3::align_cfg::band_fixed_size |
| ►Cseqan3::detail::strong_type< int32_t, open_score, seqan3::detail::strong_type_skill::convert > | |
| Cseqan3::align_cfg::open_score | A strong type of underlying type int32_t that represents a score (usually negative) that is incurred once per stretch of consecutive gaps |
| ►Cseqan3::detail::strong_type< int32_t, upper_diagonal > | |
| Cseqan3::align_cfg::upper_diagonal | A strong type representing the upper diagonal of the seqan3::align_cfg::band_fixed_size |
| ►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< size_t, bin_count, detail::strong_type_skill::convert > | |
| Cseqan3::bin_count | A strong type that represents the number of bins for the seqan3::interleaved_bloom_filter |
| ►Cseqan3::detail::strong_type< size_t, bin_index, detail::strong_type_skill::convert > | |
| Cseqan3::bin_index | A strong type that represents the bin index for the seqan3::interleaved_bloom_filter |
| ►Cseqan3::detail::strong_type< size_t, bin_size, detail::strong_type_skill::convert > | |
| Cseqan3::bin_size | A strong type that represents the number of bits for each bin in the seqan3::interleaved_bloom_filter |
| ►Cseqan3::detail::strong_type< size_t, hash_function_count, detail::strong_type_skill::convert > | |
| Cseqan3::hash_function_count | A strong type that represents the number of hash functions for the seqan3::interleaved_bloom_filter |
| ►Cseqan3::detail::strong_type< uint32_t, window_size > | |
| Cseqan3::window_size | Strong_type for the window_size |
| ►Cseqan3::detail::strong_type< uint64_t, seed > | |
| Cseqan3::seed | Strong_type for seed |
| Cseqan3::strong_type_printer< typename > | |
| Cseqan3::structure_file_input< traits_type_, selected_field_ids_, valid_formats_ > | A class for reading structured sequence files, e.g. Stockholm, Connect, Vienna, ViennaRNA bpp matrix .. |
| ►Cseqan3::structure_file_input_format< t > | The generic concept for structure file in formats |
| Cseqan3::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)> | |
| ►Cstructure_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< t > | 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 |
| Cseqan3::suffix_array_interval | The underlying suffix array interval |
| ►Cstd::totally_ordered | |
| Csemialphabet | The basis for seqan3::alphabet, but requires only rank interface (not char) |
| ►Ctuple_like | Whether a type behaves like a tuple |
| Cseqan3::record< detail::select_types_with_ids_t< field_types, field_ids, selected_field_ids >, selected_field_ids > | |
| Cpair_like | Whether a type behaves like a tuple with exactly two elements |
| 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 a std::tuple |
| Cseqan3::sam_record< detail::select_types_with_ids_t< field_types, field_ids, selected_field_ids >, selected_field_ids > | |
| Cseqan3::sequence_record< detail::select_types_with_ids_t< field_types, field_ids, selected_field_ids >, selected_field_ids > | |
| Cseqan3::structure_record< detail::select_types_with_ids_t< field_types, field_ids, selected_field_ids >, selected_field_ids > | |
| Cseqan3::sam_record< field_types, field_ids > | The record type of seqan3::sam_file_input |
| Cseqan3::sequence_record< field_types, field_ids > | The record type of seqan3::sequence_file_input |
| Cseqan3::structure_record< field_types, field_ids > | The record type of seqan3::structure_file_input |
| Cseqan3::trace_directions_printer< typename > | |
| Cseqan3::trace_directions_printer< detail::trace_directions > | Prints trace_directions as ascii or as utf8 to output stream |
| ►Cdetail::transfer_template_args_onto_t | |
| Cseqan3::record< detail::select_types_with_ids_t< field_types, field_ids, selected_field_ids >, selected_field_ids > | |
| Cseqan3::record< field_types, field_ids > | The class template that file records are based on; behaves like a std::tuple |
| ►Ctransformation_trait | Concept for a transformation trait |
| Cseqan3::range_innermost_value< t > | Recursively determines the value_type on containers and/or iterators |
| Cseqan3::remove_rvalue_reference< t > | Return the input type with && removed, but lvalue references preserved |
| Cstd::tuple_element< elem_no, seqan3::sam_record< field_types, field_ids > > | Obtains the type of the specified element |
| Cstd::tuple_element< elem_no, seqan3::sequence_record< field_types, field_ids > > | Obtains the type of the specified element |
| Cstd::tuple_element< elem_no, seqan3::structure_record< field_types, field_ids > > | Obtains the type of the specified element |
| Cstd::tuple_element< i, t< types... > > | 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::sam_record< field_types, field_ids > > | Obtains the type of the specified element |
| Cstd::tuple_element< elem_no, seqan3::sequence_record< field_types, field_ids > > | Obtains the type of the specified element |
| Cstd::tuple_element< elem_no, seqan3::structure_record< field_types, field_ids > > | Obtains the type of the specified element |
| Cseqan3::tuple_printer< typename > | |
| Cseqan3::tuple_printer< tuple_t > | Printer for formatted output of tuple like objects |
| ►Ctuple_size< seqan3::sam_record< field_types, field_ids >::base_type > | |
| Cstd::tuple_size< seqan3::sam_record< field_types, field_ids > > | Provides access to the number of elements in a tuple as a compile-time constant expression |
| ►Ctuple_size< seqan3::sequence_record< field_types, field_ids >::base_type > | |
| Cstd::tuple_size< seqan3::sequence_record< field_types, field_ids > > | Provides access to the number of elements in a tuple as a compile-time constant expression |
| ►Ctuple_size< seqan3::structure_record< field_types, field_ids >::base_type > | |
| Cstd::tuple_size< seqan3::structure_record< field_types, field_ids > > | Provides access to the number of elements in a tuple as a compile-time constant expression |
| Cseqan3::type_list< types > | Type that contains multiple types |
| ►Cunary_type_trait | Concept for a unary traits type |
| Cseqan3::is_constexpr_default_constructible< t > | Whether a type std::is_default_constructible in constexpr-context (unary_type_trait specialisation) |
| Cstd::tuple_size< seqan3::sam_record< field_types, field_ids > > | Provides access to the number of elements in a tuple as a compile-time constant expression |
| Cstd::tuple_size< seqan3::sequence_record< field_types, field_ids > > | Provides access to the number of elements in a tuple as a compile-time constant expression |
| Cstd::tuple_size< seqan3::structure_record< field_types, field_ids > > | Provides access to the number of elements in a tuple as a compile-time constant expression |
| Cstd::tuple_size< t< types... > > | 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 |
| ►Cvalidator | The concept for option validators passed to add_option/positional_option |
| Cseqan3::arithmetic_range_validator< option_value_t > | 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 |
| ►Cstd::vector< value_t > [external] | |
| Cseqan3::counting_vector< value_t > | A data structure that behaves like a std::vector and can be used to consolidate the results of multiple calls to seqan3::interleaved_bloom_filter::membership_agent_type::bulk_contains |
| Cweakly_assignable_from | Resolves to std::is_assignable_v<t> |
| Csdsl_index_type_ | |
1.9.8 