The main SeqAn3 namespace. More...

Namespaces
	align_cfg
	A special sub namespace for the alignment configurations.

	custom
	A namespace for third party and standard library specialisations of SeqAn customisation points.

	list_traits
	Namespace containing traits for working on seqan3::type_list.

	pack_traits
	Namespace containing traits for working on type packs.

	search_cfg
	A special sub namespace for the search configurations.

	views
	The SeqAn namespace for views.

Classes
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	algorithm_result_generator_range
	An input range over the algorithm results generated by the underlying algorithm executor. 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_result
	Stores the alignment results and gives access to score, alignment and the front and end positionss. 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...

class	argument_parser_error
	Argument parser exception that is thrown whenever there is an error while parsing the command line arguments. 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...

class	bi_fm_index
	The SeqAn Bidirectional FM Index. More...

class	bi_fm_index_cursor
	The SeqAn Bidirectional FM Index Cursor. More...

struct	bin_count
	A strong type that represents the number of bins for the seqan3::interleaved_bloom_filter. More...

struct	bin_index
	A strong type that represents the bin index for the seqan3::interleaved_bloom_filter. More...

struct	bin_literal
	A strong type of underlying type `uint64_t` that represents the shape in binary representation. More...

struct	bin_size
	A strong type that represents the number of bits for each bin in the seqan3::interleaved_bloom_filter. 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...

class	counting_vector
	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::bulk_contains. More...

class	debug_stream_type
	A "pretty printer" for most SeqAn data structures and related types. More...

class	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...

struct	difference_type
	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...

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	function_traits< std::function< return_t(args_t...)> >
	A traits class to provide a uniform interface to the properties of a function type. 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	hash_function_count
	A strong type that represents the number of hash functions for the seqan3::interleaved_bloom_filter. 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	interleaved_bloom_filter
	The IBF binning directory. A data structure that efficiently answers set-membership queries for multiple bins. 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	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
	This class is deprecated. 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
	This class is deprecated. More...

class	parser_invalid_argument
	This class is deprecated. 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...

class	pipeable_config_element< derived_t >
	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	range_innermost_value
	Recursively determines the `value_type` on containers and/or iterators. 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...

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...

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	search_result
	The result class generated by the seqan3::seach algorithm. More...

struct	seed
	strong_type for seed. More...

class	semialphabet_any
	A semi-alphabet that type erases all other semi-alphabets of the same size. 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 which 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...

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
	This class is deprecated. 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	user_input_error
	Argument parser exception thrown when an incorrect argument is given as (positional) option value. More...

class	validation_error
	Argument parser exception thrown when an argument could not be casted to the according type. More...

class	validation_failed
	This class is deprecated. 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	window_size
	strong_type for the window_size. More...

class	wuss
	The WUSS structure alphabet of the characters `.<>:,-_~;()[]{}AaBbCcDd`... More...

Typedefs
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 detail::const_reference_t< t >
	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 detail::difference_type_t< t >
	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	range_innermost_value_t = typename range_innermost_value< t >::type
	Shortcut for seqan3::range_innermost_value (transformation_trait shortcut). More...

template<typename t >
using	reference_t = typename detail::reference_t< t >
	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 detail::rvalue_reference_t< t >
	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, 10 '000 '000, sdsl::sa_order_sa_sampling<>, sdsl::isa_sampling<>, sdsl::plain_byte_alphabet >
	The FM Index Configuration using a Wavelet Tree. More...

using	semiregular_box = ::ranges::semiregular_box
	Utility wrapper that behaves like std::optional but makes the type conform with the std::semiregular concept. Imported from ranges::semiregular_box. More...

using	semiregular_box_t = ::ranges::semiregular_box_t
	Utility transformation trait to get a wrapper type that models std::semiregular. Imported from ranges::semiregular_box_t. More...

template<typename t >
using	size_type_t = typename detail::size_type_t< t >
	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 detail::value_type_t< t >
	Shortcut for seqan3::value_type (transformation_trait shortcut). More...

Enumerations
enum	aminoacid_similarity_matrix { aminoacid_similarity_matrix::BLOSUM30, aminoacid_similarity_matrix::BLOSUM45, aminoacid_similarity_matrix::BLOSUM62, aminoacid_similarity_matrix::BLOSUM80 }
	Identifiers for amino acid similarity matrixes. More...

enum	data_layout : bool { uncompressed, compressed }
	Determines if the Interleaved Bloom Filter is compressed. More...

enum	field { field::seq, field::id, field::qual, field::seq_qual, field::offset, field::bpp, field::structure, field::structured_seq, field::energy, field::react, field::react_err, field::comment, field::alignment, field::ref_id, field::ref_seq, field::ref_offset, field::header_ptr, field::flag, field::mate, field::mapq, field::cigar, field::tags, field::bit_score, field::evalue, field::user_defined_0, field::user_defined_1, field::user_defined_2, field::user_defined_3, field::user_defined_4, field::user_defined_5, field::user_defined_6, field::user_defined_7, field::user_defined_8, field::user_defined_9, field::SEQ = seq, field::ID = id, field::QUAL = qual, field::SEQ_QUAL = seq_qual, field::OFFSET = offset, field::BPP = bpp, field::STRUCTURE = structure, field::STRUCTURED_SEQ = structured_seq, field::ENERGY = energy, field::REACT = react, field::REACT_ERR = react_err, field::COMMENT = comment, field::ALIGNMENT = alignment, field::REF_ID = ref_id, field::REF_SEQ = ref_seq, field::REF_OFFSET = ref_offset, field::HEADER_PTR = header_ptr, field::FLAG = flag, field::MATE = mate, field::MAPQ = mapq, field::CIGAR = cigar, field::TAGS = tags, field::BIT_SCORE = bit_score, field::EVALUE = evalue, field::USER_DEFINED_0 = user_defined_0, field::USER_DEFINED_1 = user_defined_1, field::USER_DEFINED_2 = user_defined_2, field::USER_DEFINED_3 = user_defined_3, field::USER_DEFINED_4 = user_defined_4, field::USER_DEFINED_5 = user_defined_5, field::USER_DEFINED_6 = user_defined_6, field::USER_DEFINED_7 = user_defined_7, field::USER_DEFINED_8 = user_defined_8, field::USER_DEFINED_9 = user_defined_9 }
	An enumerator for the fields used in file formats. More...

enum	fmtflags2 { none = 0, utf8 = 1, small_int_as_number = 1 << 1, default_ = small_int_as_number }
	Flags that change the behaviour of the seqan3::debug_stream. More...

enum	genetic_code : uint8_t { CANONICAL =1 }
	Genetic codes used for translation of nucleotides into amino acids. More...

enum	option_spec { DEFAULT = 0, REQUIRED = 1, ADVANCED = 2, HIDDEN = 4 }
	Used to further specify argument_parser options/flags. More...

enum	sam_flag : uint16_t { sam_flag::none = 0, sam_flag::paired = 0x1, sam_flag::proper_pair = 0x2, sam_flag::unmapped = 0x4, sam_flag::mate_unmapped = 0x8, sam_flag::on_reverse_strand = 0x10, sam_flag::mate_on_reverse_strand = 0x20, sam_flag::first_in_pair = 0x40, sam_flag::second_in_pair = 0x80, sam_flag::secondary_alignment = 0x100, sam_flag::failed_filter = 0x200, sam_flag::duplicate = 0x400, sam_flag::supplementary_alignment = 0x800 }
	An enum flag that describes the properties of an aligned read (given as a SAM record). More...

enum	text_layout : bool { single, collection }
	The possible text layouts (single, collection) the seqan3::fm_index and seqan3::bi_fm_index can support. More...

enum	translation_frames : uint8_t { translation_frames::FWD_FRAME_0 = 1, translation_frames::FWD_FRAME_1 = 1 << 1, translation_frames::FWD_FRAME_2 = 1 << 2, translation_frames::REV_FRAME_0 = 1 << 3, translation_frames::REV_FRAME_1 = 1 << 4, translation_frames::REV_FRAME_2 = 1 << 5, translation_frames::FWD_REV_0 = FWD_FRAME_0 \| REV_FRAME_0, translation_frames::FWD_REV_1 = FWD_FRAME_1 \| REV_FRAME_1, translation_frames::FWD_REV_2 = FWD_FRAME_2 \| REV_FRAME_2, translation_frames::FWD = FWD_FRAME_0 \| FWD_FRAME_1 \| FWD_FRAME_2, translation_frames::REV = REV_FRAME_0 \| REV_FRAME_1 \| REV_FRAME_2, translation_frames::SIX_FRAME = FWD \| REV }
	Specialisation values for single and multiple translation frames. More...

Functions
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<typename char_t , std::ranges::input_range alignment_matrix_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<typename char_t , typename t >
debug_stream_type< char_t > &	operator<< (debug_stream_type< char_t > &s, t &&v)
	Forwards to the underlying stream object.

template<typename char_t , typename alignment_t >
debug_stream_type< char_t > &	operator<< (debug_stream_type< char_t > &stream, alignment_t &&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<typename base_t , std::unsigned_integral exp_t>
base_t	pow (base_t base, exp_t exp)
	Computes the value of `base` raised to the power `exp`. More...

template<fm_index_specialisation index_t, std::ranges::forward_range 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...

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...

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...

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...

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...

Variables
template<typename t >
constexpr bool	add_enum_bitwise_operators = false
	Set to true for a scoped enum to have binary operators overloaded. More...

template<>
constexpr bool	add_enum_bitwise_operators< fmtflags2 > = true
	Overload bitwise operators for seqan3::fmtflags2.

template<>
constexpr bool	add_enum_bitwise_operators< sam_flag > = true
	Enables bitwise operations for seqan3::sam_flags.

template<>
constexpr bool	add_enum_bitwise_operators< translation_frames > = true
	Enable bitwise operators for enum translation_frames.

template<typename alph_t >
constexpr auto	alphabet_size = detail::adl_only::alphabet_size_obj<alph_t>()
	A type trait that holds the size of a (semi-)alphabet. More...

debug_stream_type	debug_stream {std::cerr}
	A global instance of seqan3::debug_stream_type.

template<typename t >
constexpr bool	enable_aminoacid = detail::adl_only::enable_aminoacid_dispatcher::dispatch<std::remove_cvref_t<t>>()
	A trait that indicates whether a type shall model seqan3::aminoacid_alphabet. More...

constexpr parallel_policy	par {}
	Global execution policy object for parallel execution policy. More...

constexpr parallel_unsequenced_policy	par_unseq {}
	Global execution policy object for parallel and unsequenced execution policy. More...

template<typename t >
constexpr size_t	range_dimension_v = 1
	Returns the number of times you can call `seqan3::value_type_t` recursively on t (type trait). More...

constexpr sequenced_policy	seq {}
	Global execution policy object for sequenced execution policy. More...

std::string const	seqan3_version
	The full version as `std::string`. More...

constexpr uint8_t	seqan3_version_major = SEQAN3_VERSION_MAJOR
	The major version.

constexpr uint8_t	seqan3_version_minor = SEQAN3_VERSION_MINOR
	The minor version.

constexpr uint8_t	seqan3_version_patch = SEQAN3_VERSION_PATCH
	The patch version.

constexpr unsequenced_policy	unseq {}
	Global execution policy object for unsequenced execution policy. More...

Type deduction guides
template<size_t capacity2, typename value_type >
	small_vector (const value_type(&array)[capacity2]) -> small_vector< value_type, capacity2 >
	Deducts the size and value type from an built-in array on construction.

template<std::ranges::viewable_range urng_t>
	gap_decorator (urng_t &&range) -> gap_decorator< std::remove_reference_t< urng_t > const & >
	Ranges (not views!) always deduce to `const & range_type` since they are access-only anyway.

template<std::ranges::view urng_t>
	gap_decorator (urng_t range) -> gap_decorator< urng_t >
	Views always deduce to their respective type because they are copied.

Template argument type deduction guides
template<std::ranges::range text_t>
	bi_fm_index (text_t &&) -> bi_fm_index< range_innermost_value_t< text_t >, text_layout
	Deduces the dimensions of the text.

template<std::ranges::range text_t>
	fm_index (text_t &&) -> fm_index< range_innermost_value_t< text_t >, text_layout
	Deduces the alphabet and dimensions of the text.

Detailed Description

The main SeqAn3 namespace.

Typedef Documentation

◆ common_pair

using seqan3::common_pair = typedef ::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.

Alias definition of the ranges::common_pair.

◆ common_tuple

using seqan3::common_tuple = typedef ::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.

Alias definition of the ranges::common_tuple.

Enumeration Type Documentation

◆ genetic_code

enum seqan3::genetic_code : uint8_t

strong

Genetic codes used for translation of nucleotides into amino acids.

The numeric values of the enums correspond to the genbank transl_table values (see https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi).

◆ translation_frames

enum seqan3::translation_frames : uint8_t

strong

Specialisation values for single and multiple translation frames.

Enumerator
FWD_FRAME_0	The first forward frame starting at position 0.
FWD_FRAME_1	The second forward frame starting at position 1.
FWD_FRAME_2	The third forward frame starting at position 2.
REV_FRAME_0	The first reverse frame starting at position 0.
REV_FRAME_1	The second reverse frame starting at position 1.
REV_FRAME_2	The third reverse frame starting at position 2.
FWD_REV_0	The first forward and first reverse frame.
FWD_REV_1	The second forward and second reverse frame.
FWD_REV_2	The first third and third reverse frame.
FWD	All forward frames.
REV	All reverse frames.
SIX_FRAME	All frames.

Function Documentation

◆ operator""_tag()

template<typename char_t , char_t ... s>

constexpr uint16_t seqan3::operator""_tag ( )

constexpr

The SAM tag literal, such that tags can be used in constant expressions.

Template Parameters

char_t The char type. Usually char. Parameter pack ...s must be of length 2, since SAM tags consist of two letters (char0 and char1).

Returns: The unique identifier of the SAM tag computed by char0 * 128 + char1.

A SAM tag consists of two letters, initialized via the string literal ""_tag, which delegate to its unique id. e.g.

#include <seqan3/io/alignment_file/sam_tag_dictionary.hpp>
 
using seqan3::operator""_tag;
 
// ...
 
uint16_t tag_id = "NM"_tag; // tag_id = 10061

The purpose of those tags is to fill or query the seqan3::sam_tag_dictionary for a specific key (tag_id) and retrieve the corresponding value.

See also: seqan3::sam_tag_dictionary

◆ to_lower()

template<builtin_character char_type>

constexpr char_type seqan3::to_lower ( char_type const c )

constexprnoexcept

Converts 'A'-'Z' to 'a'-'z' respectively; other characters are returned as is.

Template Parameters

char_type Type of the parameter; must model seqan3::builtin_character.

Parameters

c	The parameter.

Returns: The character converted to lower case.

In contrast to std::tolower this function is independent of locale and can be evaluated in a constexpr context.

◆ to_upper()

template<builtin_character char_type>

constexpr char_type seqan3::to_upper ( char_type const c )

constexprnoexcept

Converts 'a'-'z' to 'A'-'Z' respectively; other characters are returned as is.

Template Parameters

char_type Type of the parameter; must model seqan3::builtin_character.

Parameters

c	The parameter.

Returns: The character converted to upper case.

In contrast to std::to_upper this function is independent of locale and can be evaluated in a constexpr context.

Variable Documentation

◆ seqan3_version

std::string const seqan3::seqan3_version

Initial value:

= std::to_string(seqan3_version_major) + "." +
                                   std::to_string(seqan3_version_minor) + "." +
                                   std::to_string(seqan3_version_patch)

The full version as std::string.

Namespaces

Classes

Typedefs

Enumerations

Functions

Variables

Type deduction guides

Template argument type deduction guides

Detailed Description

Typedef Documentation

◆ common_pair

◆ common_tuple

Enumeration Type Documentation

◆ genetic_code

◆ translation_frames

Function Documentation

◆ operator""_tag()

◆ to_lower()

◆ to_upper()

Variable Documentation

◆ seqan3_version