|
class | aa10li |
| The reduced Li amino acid alphabet. More...
|
|
class | aa10murphy |
| The reduced Murphy amino acid alphabet. More...
|
|
class | aa20 |
| The canonical amino acid alphabet. More...
|
|
class | aa27 |
| The twenty-seven letter amino acid alphabet. More...
|
|
class | aligned_allocator |
| Allocates uninitialized storage whose memory-alignment is specified by alignment. More...
|
|
class | alignment_coordinate |
| Represents the begin/end of the pairwise alignment in the respective sequences. More...
|
|
class | alignment_file_header |
| Stores the header information of alignment files. More...
|
|
class | alignment_file_input |
| A class for reading alignment files, e.g. SAM, BAM, BLAST ... More...
|
|
struct | alignment_file_input_default_traits |
| The default traits for seqan3::alignment_file_input. More...
|
|
struct | alignment_file_input_options |
| The options type defines various option members that influence the behaviour of all or some formats. More...
|
|
class | alignment_file_output |
| A class for writing alignment files, e.g. SAM, BAL, BLAST, ... More...
|
|
struct | alignment_file_output_options |
| The options type defines various option members that influence the behavior of all or some formats. More...
|
|
class | alignment_range |
| An input range over the alignment results generated by the underlying alignment executor. More...
|
|
class | alignment_result |
| Stores the alignment results and gives access to score, alignment and the front and back coordinates. More...
|
|
class | alphabet_base |
| A CRTP-base that makes defining a custom alphabet easier. More...
|
|
class | alphabet_base< derived_type, 1ul, char_t > |
| Specialisation of seqan3::alphabet_base for alphabets of size 1. More...
|
|
class | alphabet_proxy |
| A CRTP-base that eases the definition of proxy types returned in place of regular alphabets. More...
|
|
class | alphabet_tuple_base |
| The CRTP base for a combined alphabet that contains multiple values of different alphabets at the same time. More...
|
|
class | alphabet_variant |
| A combined alphabet that can hold values of either of its alternatives. More...
|
|
class | aminoacid_base |
| A CRTP-base that refines seqan3::alphabet_base and is used by the amino acids. More...
|
|
struct | aminoacid_empty_base |
| This is an empty base class that can be inherited by types that shall model seqan3::aminoacid_alphabet. More...
|
|
class | aminoacid_scoring_scheme |
| A data structure for managing and computing the score of two amino acids. More...
|
|
class | argument_parser |
| The SeqAn command line parser. More...
|
|
struct | argument_parser_meta_data |
| Stores all parser related meta information of the seqan3::argument_parser. More...
|
|
class | arithmetic_range_validator |
| A validator that checks whether a number is inside a given range. More...
|
|
struct | back_end_first |
| The penalty configuration for aligning the back of the first sequence with a gap. More...
|
|
struct | back_end_second |
| The penalty configuration for aligning the back of the second sequence with a gap. More...
|
|
class | bi_fm_index |
| The SeqAn Bidirectional FM Index. More...
|
|
class | bi_fm_index_cursor |
| The SeqAn Bidirectional FM Index Cursor. More...
|
|
struct | bin_literal |
| A strong type of underlying type uint64_t that represents the shape in binary representation. More...
|
|
class | bitcompressed_vector |
| A space-optimised version of std::vector that compresses multiple letters into a single byte. More...
|
|
class | cigar |
| The cigar semialphabet pairs a counter with a seqan3::cigar_op letter. More...
|
|
class | cigar_op |
| The (extended) cigar operation alphabet of M,D,I,H,N,P,S,X,=. More...
|
|
class | concatenated_sequences |
| Container that stores sequences concatenated internally. More...
|
|
class | configuration |
| Collection of elements to configure an algorithm. More...
|
|
struct | const_reference |
| Exposes the const_reference of another type. More...
|
|
struct | const_reference< rng_t > |
| Exposes the const_reference of another type. More...
|
|
class | debug_stream_type |
| A "pretty printer" for most SeqAn data structures and related types. More...
|
|
struct | difference_type |
| Exposes the difference_type of another type. More...
|
|
struct | difference_type< it_t > |
| Exposes the difference_type of another type. More...
|
|
struct | difference_type< rng_t > |
| Exposes the difference_type of another type. More...
|
|
class | dna15 |
| The 15 letter DNA alphabet, containing all IUPAC smybols minus the gap. More...
|
|
class | dna3bs |
| The three letter reduced DNA alphabet for bisulfite sequencing mode (A,G,T(=C)). More...
|
|
class | dna4 |
| The four letter DNA alphabet of A,C,G,T. More...
|
|
class | dna5 |
| The five letter DNA alphabet of A,C,G,T and the unknown character N. More...
|
|
class | dot_bracket3 |
| The three letter RNA structure alphabet of the characters ".()". More...
|
|
class | dssp9 |
| The protein structure alphabet of the characters "HGIEBTSCX". More...
|
|
class | dynamic_bitset |
| A constexpr bitset implementation with dynamic size at compile time. More...
|
|
class | end_gaps |
| Wraps the sequence end-gap specifiers and provides ordered access to the respective values. More...
|
|
struct | fields |
| A class template that holds a choice of seqan3::field. More...
|
|
struct | file_open_error |
| Thrown if there is an unspecified filesystem or stream error while opening, e.g. permission problem. More...
|
|
class | file_validator_base |
| An abstract base class for the file and directory validators. More...
|
|
class | fm_index |
| The SeqAn FM Index. More...
|
|
class | fm_index_cursor |
| The SeqAn FM Index Cursor. More...
|
|
class | format_bam |
| The BAM format. More...
|
|
class | format_embl |
| The EMBL format. More...
|
|
struct | format_error |
| Thrown if information given to output format didn't match expectations. More...
|
|
class | format_fasta |
| The FastA format. More...
|
|
class | format_fastq |
| The FastQ format. More...
|
|
class | format_genbank |
| The GenBank format. More...
|
|
class | format_sam |
| The SAM format (tag). More...
|
|
class | format_vienna |
| The Vienna format (dot bracket notation) for RNA sequences with secondary structure. More...
|
|
struct | front_end_first |
| The penalty configuration for aligning the front of the first sequence with a gap. More...
|
|
struct | front_end_second |
| The penalty configuration for aligning the front of the second sequence with a gap. More...
|
|
class | gap |
| The alphabet of a gap character '-'. More...
|
|
class | gap_decorator |
| A gap decorator allows the annotation of sequences with gap symbols while leaving the underlying sequence unmodified. More...
|
|
class | gap_erase_failure |
| Thrown in function seqan3::erase_gap, if a position does not contain a gap. More...
|
|
struct | gap_open_score |
| 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. More...
|
|
class | gap_scheme |
| A scheme for representing and computing scores against gap characters. More...
|
|
struct | gap_score |
| A strong type of underlying type score_type that represents the score of any character against a gap character. More...
|
|
struct | innermost_value_type |
| Recursively determines the value_type on containers and/or iterators. More...
|
|
class | input_directory_validator |
| A validator that checks if a given path is a valid input directory. More...
|
|
class | input_file_validator |
| A validator that checks if a given path is a valid input file. More...
|
|
class | invalid_alignment_configuration |
| Thrown if the configuration of the alignment algorithm is invalid. More...
|
|
struct | invalid_char_assignment |
| An exception typically thrown by seqan3::alphabet::assign_char_strict. More...
|
|
struct | io_error |
| Thrown if there is an io error in low level io operations such as in std::basic_streambuf operations. More...
|
|
struct | is_constexpr_default_constructible |
| Whether a type std::is_default_constructible in constexpr -context. More...
|
|
struct | is_constexpr_default_constructible< t > |
| Whether a type std::is_default_constructible in constexpr -context (unary_type_trait specialisation). More...
|
|
struct | is_execution_policy |
| Test whether a class represents an execution policy. More...
|
|
struct | iterator_tag |
| Exposes the iterator_category from the modelled concept. More...
|
|
struct | lower_bound |
| Type for a lower boundary. More...
|
|
class | mask |
| Implementation of a masked alphabet to be used for tuple composites. More...
|
|
class | masked |
| Implementation of a masked composite, which extends a given alphabet with a mask. More...
|
|
struct | match_score |
| A strong type of underlying type score_type that represents the score of two matching characters. More...
|
|
struct | mismatch_score |
| A strong type of underlying type score_type that represents the score two different characters. More...
|
|
class | nucleotide_base |
| A CRTP-base that refines seqan3::alphabet_base and is used by the nucleotides. More...
|
|
class | nucleotide_scoring_scheme |
| A data structure for managing and computing the score of two nucleotides. More...
|
|
class | option_declared_multiple_times |
| Argument parser exception thrown when a non-list option is declared multiple times. More...
|
|
class | output_directory_validator |
| A validator that checks if a given path is a valid output directory. More...
|
|
class | output_file_validator |
| A validator that checks if a given path is a valid output file. More...
|
|
class | overflow_error_on_conversion |
| Argument parser exception thrown when an argument could not be casted to the according type. More...
|
|
class | parallel_policy |
| Parallel execution policy. More...
|
|
class | parallel_unsequenced_policy |
| Parallel and unsequenced execution policy. More...
|
|
struct | parse_error |
| Thrown if there is a parse error, such as reading an unexpected character from an input stream. More...
|
|
class | 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). More...
|
|
class | parser_invalid_argument |
| Argument parser exception that is thrown whenever there is an error while parsing the command line arguments. More...
|
|
class | phred42 |
| Quality type for traditional Sanger and modern Illumina Phred scores (typical range). More...
|
|
class | phred63 |
| Quality type for traditional Sanger and modern Illumina Phred scores (full range). More...
|
|
class | phred68legacy |
| Quality type for Solexa and deprecated Illumina formats. More...
|
|
struct | pipeable_config_element |
| Adds pipe interface to configuration elements. More...
|
|
struct | pod_tuple |
| cond More...
|
|
struct | pod_tuple< type0 > |
| Recursion anchor for pod_tuple. More...
|
|
struct | pod_tuple< type0, types... > |
| Behaves like std::tuple but is an aggregate PODType. More...
|
|
class | qualified |
| Joins an arbitrary alphabet with a quality alphabet. More...
|
|
class | quality_base |
| A CRTP-base that refines seqan3::alphabet_base and is used by the quality alphabets. More...
|
|
struct | record |
| The class template that file records are based on; behaves like an std::tuple. More...
|
|
struct | ref_info_not_given |
| Type tag which indicates that no reference information has been passed to the alignment file on construction. More...
|
|
struct | reference |
| Exposes the reference of another type. More...
|
|
struct | reference< it_t > |
| Exposes the reference type of another type. More...
|
|
struct | reference< rng_t > |
| Exposes the reference of another type. More...
|
|
class | regex_validator |
| A validator that checks if a matches a regular expression pattern. More...
|
|
struct | remove_rvalue_reference |
| Return the input type with && removed, but lvalue references preserved. More...
|
|
class | required_option_missing |
| Argument parser exception thrown when a required option is missing. More...
|
|
class | rna15 |
| The 15 letter RNA alphabet, containing all IUPAC smybols minus the gap. More...
|
|
class | rna4 |
| The four letter RNA alphabet of A,C,G,U. More...
|
|
class | rna5 |
| The five letter RNA alphabet of A,C,G,U and the unknown character N. More...
|
|
struct | rvalue_reference |
| Exposes the rvalue_reference of another type. More...
|
|
struct | rvalue_reference< it_t > |
| Exposes the rvalue_reference type of another type. More...
|
|
struct | rvalue_reference< rng_t > |
| Exposes the rvalue_reference of another type. More...
|
|
class | sam_dna16 |
| A 16 letter DNA alphabet, containing all IUPAC symbols minus the gap and plus an equality sign ('='). More...
|
|
class | sam_tag_dictionary |
| The SAM tag dictionary class that stores all optional SAM fields. More...
|
|
struct | sam_tag_type |
| The generic base class. More...
|
|
class | scoring_scheme_base |
| A CRTP base class for scoring schemes. More...
|
|
class | semialphabet_any |
| A semi-alphabet that type erases all other semi-alphabets of the same size. More...
|
|
struct | sequence_end_gap_specifier_base |
| A mixin class which can maintain a static or a dynamic bool state. More...
|
|
class | sequence_file_input |
| A class for reading sequence files, e.g. FASTA, FASTQ ... More...
|
|
struct | sequence_file_input_default_traits_aa |
| A traits type that specifies input as amino acids. More...
|
|
struct | sequence_file_input_default_traits_dna |
| The default traits for seqan3::sequence_file_input. More...
|
|
struct | sequence_file_input_options |
| The options type defines various option members that influence the behaviour of all or some formats. More...
|
|
class | sequence_file_output |
| A class for writing sequence files, e.g. FASTA, FASTQ ... More...
|
|
struct | sequence_file_output_options |
| The options type defines various option members that influence the behaviour of all or some formats. More...
|
|
class | sequenced_policy |
| Sequenced execution policy. More...
|
|
class | shape |
| A class that defines what positions of a pattern to hash. More...
|
|
struct | simd_traits |
| seqan3::simd::simd_traits is the trait class that provides uniform interface to the properties of simd_t types.
|
|
struct | simd_traits< builtin_simd_t > |
| This class specializes seqan3::simd::simd_traits for seqan3::detail::builtin_simd types.
|
|
struct | simd_type |
| seqan3::simd::simd_type encapsulates simd vector types, which can be manipulated by simd operations.
|
|
struct | size_type |
| Exposes the size_type of another type. More...
|
|
struct | size_type< it_t > |
| Exposes the size_type of another type. More...
|
|
struct | size_type< rng_t > |
| Exposes the size_type of another type. More...
|
|
class | small_string |
| Implements a small string that can be used for compile time computations. More...
|
|
class | small_vector |
| A constexpr vector implementation with dynamic size at compile time. More...
|
|
class | static_band |
| Data structure for a static band. More...
|
|
class | structure_file_input |
| A class for reading structured sequence files, e.g. Stockholm, Connect, Vienna, ViennaRNA bpp matrix ... More...
|
|
struct | structure_file_input_default_traits_aa |
| A traits type that specifies input as amino acids. More...
|
|
struct | structure_file_input_default_traits_rna |
| The default traits for seqan3::structure_file_input. More...
|
|
struct | structure_file_input_options |
| The options type defines various option members that influence the behaviour of all or some formats. More...
|
|
class | structure_file_output |
| A class for writing structured sequence files, e.g. Stockholm, Connect, Vienna, ViennaRNA bpp matrix ... More...
|
|
struct | structure_file_output_options |
| The options type defines various option members that influence the behaviour of all or some formats. More...
|
|
class | structured_aa |
| A seqan3::alphabet_tuple_base that joins an aminoacid alphabet with a protein structure alphabet. More...
|
|
class | structured_rna |
| A seqan3::alphabet_tuple_base that joins a nucleotide alphabet with an RNA structure alphabet. More...
|
|
class | too_few_arguments |
| Argument parser exception thrown when too few arguments are provided. More...
|
|
class | too_many_arguments |
| Argument parser exception thrown when too many arguments are provided. More...
|
|
class | type_conversion_failed |
| Argument parser exception thrown when an argument could not be casted to the according type. More...
|
|
struct | 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. More...
|
|
struct | ungapped |
| A strong type of underlying type uint8_t that represents the ungapped shape size. More...
|
|
struct | unhandled_extension_error |
| Thrown if there is no format that accepts a given file extension. More...
|
|
class | unknown_option |
| Argument parser exception thrown when encountering unknown option. More...
|
|
class | unsequenced_policy |
| Unsequenced execution policy. More...
|
|
struct | upper_bound |
| Type for an upper boundary. More...
|
|
class | validation_failed |
| Argument parser exception thrown when an argument could not be casted to the according type. More...
|
|
class | value_list_validator |
| A validator that checks whether a value is inside a list of valid values. More...
|
|
struct | value_type |
| Exposes the value_type of another type. More...
|
|
struct | value_type< it_t > |
| Exposes the value_type of another type. More...
|
|
struct | value_type< rng_t > |
| Exposes the value_type of another type. More...
|
|
class | wuss |
| The WUSS structure alphabet of the characters .<>:,-_~;()[]{}AaBbCcDd ... More...
|
|
|
template<typename alphabet_type > |
using | alphabet_char_t = decltype(seqan3::to_char(std::declval< alphabet_type const >())) |
| The char_type of the alphabet; defined as the return type of seqan3::to_char.
|
|
template<typename alphabet_type > |
using | alphabet_phred_t = decltype(seqan3::to_phred(std::declval< alphabet_type >())) |
| The phred_type of the alphabet; defined as the return type of seqan3::to_phred.
|
|
template<typename semi_alphabet_type > |
using | alphabet_rank_t = decltype(seqan3::to_rank(std::declval< semi_alphabet_type >())) |
| The rank_type of the semi-alphabet; defined as the return type of seqan3::to_rank.
|
|
using | common_pair = ::ranges::common_pair |
| A common pair type that behaves like a regular std::pair, but can be used as a reference type proxy for output iterators. More...
|
|
using | common_tuple = ::ranges::common_tuple |
| A common tuple type that behaves like a regular std::tuple, but can be used as a reference type proxy for output iterators. More...
|
|
template<typename t > |
using | const_reference_t = typename const_reference< t >::type |
| Shortcut for seqan3::const_reference (transformation_trait shortcut). More...
|
|
using | default_sdsl_index_type = sdsl_wt_index_type |
| The default FM Index Configuration. More...
|
|
template<typename t > |
using | difference_type_t = typename difference_type< t >::type |
| Shortcut for seqan3::difference_type (transformation_trait shortcut). More...
|
|
using | dna15q = qualified< dna15, phred42 > |
| An alphabet that stores a seqan3::dna15 letter and an seqan3::qualified letter at each position.
|
|
using | dna4q = qualified< dna4, phred42 > |
| An alphabet that stores a seqan3::dna4 letter and an seqan3::phred42 letter at each position.
|
|
using | dna5q = qualified< dna5, phred42 > |
| An alphabet that stores a seqan3::dna5 letter and an seqan3::phred42 letter at each position.
|
|
template<typename alphabet_t > |
using | gapped = alphabet_variant< alphabet_t, gap > |
| Extends a given alphabet with a gap character. More...
|
|
template<typename t > |
using | innermost_value_type_t = typename innermost_value_type< t >::type |
| Shortcut for seqan3::innermost_value_type (transformation_trait shortcut). More...
|
|
template<typename it_t > |
using | iterator_tag_t = typename iterator_tag< it_t >::type |
| Return the iterator_category type of the input type (transformation_trait shortcut). More...
|
|
using | ostream_iterator = ::ranges::ostream_iterator |
| Alias for ranges::ostream_iterator. Writes successive elements onto the output stream from which it was constructed.
|
|
using | ostreambuf_iterator = ::ranges::ostreambuf_iterator |
| Alias for ranges::ostreambuf_iterator. Writes successive characters onto the output stream from which it was constructed.
|
|
template<typename t > |
using | reference_t = typename reference< t >::type |
| Shortcut for seqan3::reference (transformation_trait shortcut). More...
|
|
template<typename t > |
using | remove_cvref_t = std::remove_cv_t< std::remove_reference_t< t > > |
| Return the input type with const , volatile and references removed (type trait). More...
|
|
template<typename t > |
using | remove_rvalue_reference_t = typename remove_rvalue_reference< t >::type |
| Return the input type with && removed, but lvalue references preserved (transformation_trait shortcut). More...
|
|
using | rna15q = qualified< rna15, phred42 > |
| An alphabet that stores a seqan3::rna15 letter and an seqan3::qualified letter at each position.
|
|
using | rna4q = qualified< rna4, phred42 > |
| An alphabet that stores a seqan3::rna4 letter and an seqan3::phred42 letter at each position.
|
|
using | rna5q = qualified< rna5, phred42 > |
| An alphabet that stores a seqan3::rna5 letter and an seqan3::phred42 letter at each position.
|
|
template<typename t > |
using | rvalue_reference_t = typename rvalue_reference< t >::type |
| Shortcut for seqan3::rvalue_reference (transformation_trait shortcut). More...
|
|
template<uint16_t tag_value> |
using | sam_tag_type_t = typename sam_tag_type< tag_value >::type |
| Short cut helper for seqan3::sam_tag_type::type.
|
|
using | sdsl_wt_index_type = sdsl::csa_wt< sdsl::wt_blcd< sdsl::bit_vector, sdsl::rank_support_v<>, sdsl::select_support_scan<>, sdsl::select_support_scan< 0 > >, 16, 10000000, sdsl::sa_order_sa_sampling<>, sdsl::isa_sampling<>, sdsl::plain_byte_alphabet > |
| The FM Index Configuration using a Wavelet Tree. More...
|
|
template<typename t > |
using | size_type_t = typename size_type< t >::type |
| Shortcut for seqan3::size_type (transformation_trait shortcut). More...
|
|
template<typename ... types> |
using | type_list = meta::list< types... > |
| Type that contains multiple types, an alias for meta::list.
|
|
template<typename t > |
using | type_reduce_view = decltype(views::type_reduce(std::declval< t >())) |
| Deduces the return value of seqan3::views::type_reduce.
|
|
template<typename t > |
using | value_type_t = typename value_type< t >::type |
| Shortcut for seqan3::value_type (transformation_trait shortcut). More...
|
|
|
template<typename sequence_t , typename alignment_config_t > |
constexpr auto | align_pairwise (sequence_t &&seq, alignment_config_t const &config) |
| Computes the pairwise alignment for a pair of sequences or a range over sequence pairs. More...
|
|
template<typename char_t , char_t ... s> |
constexpr uint16_t | operator""_tag () |
| The SAM tag literal, such that tags can be used in constant expressions. More...
|
|
template<std::ranges::input_range alignment_matrix_t, typename char_t > |
debug_stream_type< char_t > & | operator<< (debug_stream_type< char_t > &s, alignment_matrix_t &&matrix) |
| This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
|
|
template<typename char_t > |
debug_stream_type< char_t > & | operator<< (debug_stream_type< char_t > &s, cigar const c) |
| Overload for the seqan3::debug_stream's operator.
|
|
template<tuple_like tuple_t, typename char_t > |
debug_stream_type< char_t > & | operator<< (debug_stream_type< char_t > &stream, tuple_t const &alignment) |
| Stream operator for alignments, which are represented as tuples of aligned sequences. More...
|
|
template<validator validator1_type, validator validator2_type> |
auto | operator| (validator1_type &&vali1, validator2_type &&vali2) |
| Enables the chaining of validators. More...
|
|
template<fm_index_specialisation index_t, typename queries_t , typename configuration_t = decltype(search_cfg::default_configuration)> |
auto | search (queries_t &&queries, index_t const &index, configuration_t const &cfg=search_cfg::default_configuration) |
| Search a query or a range of queries in an index. More...
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template<genetic_code gc = genetic_code::CANONICAL, nucleotide_alphabet nucl_type> |
constexpr aa27 | translate_triplet (nucl_type const &n1, nucl_type const &n2, nucl_type const &n3) noexcept |
| Translate one nucleotide triplet into single amino acid (single nucleotide interface). More...
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template<genetic_code gc = genetic_code::CANONICAL, std::ranges::input_range range_type> |
constexpr aa27 | translate_triplet (range_type &&input_range) |
| Translate one nucleotide triplet into single amino acid (range interface). More...
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template<genetic_code gc = genetic_code::CANONICAL, std::ranges::random_access_range rng_t> |
constexpr aa27 | translate_triplet (rng_t &&input_range) |
| Translate one nucleotide triplet into single amino acid (range interface, input range allows random access). More...
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template<genetic_code gc = genetic_code::CANONICAL, typename tuple_type > |
constexpr aa27 | translate_triplet (tuple_type const &input_tuple) noexcept |
| Translate one nucleotide triplet into single amino acid (tuple interface). More...
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