The main SeqAn3 namespace. More...

Namespaces
namespace	align_cfg
	A special sub namespace for the alignment configurations.
namespace	custom
	A namespace for third party and standard library specialisations of SeqAn customisation points.
namespace	exposition_only
	A namespace for SeqAn entities that are intended for documentation purposes only.
namespace	list_traits
	Namespace containing traits for working on seqan3::type_list.
namespace	literals
	The SeqAn namespace for literals.
namespace	pack_traits
	Namespace containing traits for working on type packs.
namespace	search_cfg
	A special sub namespace for the search configurations.
namespace	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...
struct	advanceable_alignment_coordinate_printer
struct	advanceable_alignment_coordinate_printer< detail::advanceable_alignment_coordinate< state_t > >
	The printer for seqan3::detail::advanceable_alignment_coordinate. 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...
struct	alignment_matrix_printer
struct	alignment_matrix_printer< alignment_matrix_t >
	The printer for alignment scoring and trace matrices. More...
struct	alignment_printer
struct	alignment_printer< alignment_t >
	The printer for alignment. More...
class	alignment_result
	Stores the alignment results and gives access to score, alignment and the front and end positions. More...
struct	alignment_result_printer
struct	alignment_result_printer< alignment_result< result_value_t > >
	The printer used for formatted output of the alignment result. More...
class	alphabet_base
	A CRTP-base that makes defining a custom alphabet easier. More...
struct	alphabet_printer
struct	alphabet_printer< alphabet_t >
	The printer used for formatted output of seqan3::alphabet types. 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	bitpacked_sequence
	A space-optimised version of std::vector that compresses multiple letters into a single byte. More...
class	bloom_filter
	The Bloom Filter. A data structure that efficiently answers set-membership queries. More...
struct	char_sequence_printer
struct	char_sequence_printer< char_sequence_t >
	A printer for character sequences. More...
class	cigar
	The seqan3::cigar semialphabet pairs a counter with a seqan3::cigar::operation letter. More...
struct	cigar_clipped_bases
	Helper struct to specialise soft and hard clipping when using seqan3::cigar_from_alignment. More...
struct	cigar_printer
struct	cigar_printer< cigar >
	The printer used for formatted output of the cigar alphabets. More...
class	concatenated_sequences
	Container that stores sequences concatenated internally. More...
class	configuration
	Collection of elements to configure an algorithm. 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_type::bulk_contains. More...
struct	debug_stream_printer
struct	debug_stream_printer< value_t >
	A struct that provides a debug stream printer for a specific value type. More...
class	debug_stream_type
	A "pretty printer" for most SeqAn data structures and related types. More...
struct	default_printer
	The default printer that is used by seqan3::debug_stream. 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...
class	dna15
	The 15 letter DNA alphabet, containing all IUPAC smybols minus the gap. More...
class	dna16sam
	A 16 letter DNA alphabet, containing all IUPAC symbols minus the gap and plus an equality sign ('='). 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	dynamic_bitset_printer
struct	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. . More...
struct	enumeration_printer
struct	enumeration_printer< enum_t >
	A type (e.g. an enum) can be made debug streamable by customizing the seqan3::enumeration_names. 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...
class	hamming_scoring_scheme
	A scoring scheme that assigns a score of 0 to matching letters and -1 to mismatching letters. 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...
struct	input_range_printer
struct	input_range_printer< rng_t >
	A printer for arbitrary input ranges. More...
struct	integer_sequence_printer
struct	integer_sequence_printer< integer_sequence_t >
	A printer for integer sequences. More...
struct	integral_printer
struct	integral_printer< integral_t >
	The printer for integral types. 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 (unary_type_trait specialisation). More...
class	mask
	Implementation of a masked alphabet to be used for tuple composites. More...
struct	mask_printer
struct	mask_printer< mask_t >
	The printer used for formatted output of seqan3::mask alphabet. 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...
struct	no_printer_found
	A tag that indicates that no printer was found for the given type. 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...
struct	optional_printer
struct	optional_printer< std::nullopt_t >
	Printer for formatted output of std::nullopt_t. More...
struct	optional_printer< std::optional< T > >
	Printer for formatted output of a std::optional. 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...
struct	parse_error
	Thrown if there is a parse error, such as reading an unexpected character from an input stream. More...
class	phred42
	Quality type for traditional Sanger and modern Illumina Phred scores. More...
class	phred63
	Quality type for traditional Sanger and modern Illumina Phred scores. More...
class	phred68solexa
	Quality type for Solexa and deprecated Illumina formats. More...
class	phred94
	Quality type for PacBio Phred scores of HiFi reads. More...
class	phred_base
	A CRTP-base that refines seqan3::alphabet_base and is used by the quality alphabets. More...
struct	pipeable_config_element
	Adds pipe interface to configuration elements. More...
struct	pod_tuple
struct	pod_tuple< type0 >
	Recursion anchor for seqan3::pod_tuple. More...
struct	pod_tuple< type0, types... >
	Behaves like std::tuple but is an aggregate PODType. More...
struct	printer_order
	The printer_order is a variadic template that defines the order of the printers. More...
class	qualified
	Joins an arbitrary alphabet with a quality alphabet. 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 a std::tuple. More...
struct	ref_info_not_given
	Type tag which indicates that no reference information has been passed to the SAM file on construction. 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...
class	sam_file_header
	Stores the header information of SAM/BAM files. More...
class	sam_file_input
	A class for reading SAM files, both SAM and its binary representation BAM are supported. More...
struct	sam_file_input_default_traits
	The default traits for seqan3::sam_file_input. More...
interface	sam_file_input_format
	The generic concept for alignment file input formats. More...
struct	sam_file_input_options
	The options type defines various option members that influence the behaviour of all or some formats. More...
class	sam_file_output
	A class for writing SAM files, both SAM and its binary representation BAM are supported. More...
interface	sam_file_output_format
	The generic concept for alignment file out formats. More...
struct	sam_file_output_options
	The options type defines various option members that influence the behavior of all or some formats. More...
struct	sam_file_program_info_t
	Stores information of the program/tool that was used to create a SAM/BAM file. More...
struct	sam_flag_printer
struct	sam_flag_printer< sam_flag >
	A sam_flag can be printed as an integer value. More...
class	sam_record
	The record type of seqan3::sam_file_input. 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	search_result_printer
struct	search_result_printer< search_result< specs_t... > >
	The printer used for formatted output of the search result. 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...
interface	sequence_file_input_format
	The generic concept for sequence file in formats. 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...
interface	sequence_file_output_format
	The generic concept for sequence file out formats. More...
struct	sequence_file_output_options
	The options type defines various option members that influence the behaviour of all or some formats. More...
struct	sequence_printer
struct	sequence_printer< sequence_t >
	A printer for (biological) sequences. More...
class	sequence_record
	The record type of seqan3::sequence_file_input. More...
class	shape
	A class that defines which positions of a pattern to hash. More...
struct	simd_printer
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...
struct	std_byte_printer
struct	std_byte_printer< std::byte >
	A std::byte can be printed by printing its value as integer. More...
struct	std_printer
struct	std_printer< type_t >
	The printer for standard output streams. More...
struct	std_variant_printer
struct	std_variant_printer< std::variant< variant_ts... > >
	A std::variant can be printed by visiting the stream operator for the corresponding type. More...
struct	strong_type_printer
struct	strong_type_printer< strong_type_t >
	A strong type can be printed by printing its underlying value. 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...
interface	structure_file_input_format
	The generic concept for structure file in formats. 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...
interface	structure_file_output_format
	The generic concept for structure file out formats. More...
struct	structure_file_output_options
	The options type defines various option members that influence the behaviour of all or some formats. More...
class	structure_record
	The record type of seqan3::structure_file_input. 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...
struct	suffix_array_interval
	The underlying suffix array interval. 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...
struct	trace_directions_printer
struct	trace_directions_printer< detail::trace_directions >
	Prints trace_directions as ascii or as utf8 to output stream. More...
struct	tuple_printer
struct	tuple_printer< tuple_t >
	Printer for formatted output of tuple like objects. More...
struct	type_list
	Type that contains multiple types. 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	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	value_list_validator
	A validator that checks whether a value is inside a list of valid values. More...
struct	window_size
	strong_type for the window_size. More...
class	wuss
	The WUSS structure alphabet of the characters .<>:,-_~;()[]{}AaBbCcDd... More...

Concepts
concept	nonrecursive_range
concept	printable_with

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. !
template<typename t1, typename t2>
using	common_pair = seqan::stl::pair<t1, t2>
	A std::pair implementation that incorporates most changes from C++23's standard library.
template<typename... t>
using	common_tuple = seqan::stl::tuple<t...>
	A std::tuple implementation that incorporates most changes from C++23's standard library.
using	default_sdsl_index_type = sdsl_wt_index_type
	The default FM Index Configuration.
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.
template<typename t>
using	range_innermost_value_t = typename range_innermost_value<t>::type
	Shortcut for seqan3::range_innermost_value (transformation_trait shortcut).
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.
using	sdsl_wt_index_type
	The FM Index Configuration using a Wavelet Tree.
template<typename t>
using	type_reduce_t = decltype(views::type_reduce(std::declval<t>()))
	Deduces the return value of seqan3::views::type_reduce.

Enumerations
enum class	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 class	field { field::seq , field::id , field::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 }
	An enumerator for the fields used in file formats. More...
enum class	fmtflags2 : int8_t { fmtflags2::none = 0 , fmtflags2::utf8 = 1 , fmtflags2::small_int_as_number = 1 << 1 , default_ = small_int_as_number }
	Flags that change the behaviour of the seqan3::debug_stream. More...
enum struct	genetic_code : uint8_t { canonical = 1 }
	Genetic codes used for translation of nucleotides into amino acids. More...
enum	option_spec { standard = 0 , required = 1 , advanced = 2 , hidden = 4 }
	Used to further specify argument_parser options/flags. More...
enum class	output_file_open_options { open_or_create , create_new }
	Mode of an output file: Determines whether an existing file can be (silently) overwritten. More...
enum class	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 class	translation_frames : uint8_t { forward_frame0 = 1 , forward_frame1 = 1 << 1 , forward_frame2 = 1 << 2 , reverse_frame0 = 1 << 3 , reverse_frame1 = 1 << 4 , reverse_frame2 = 1 << 5 , forward_reverse0 = forward_frame0 \| reverse_frame0 , forward_reverse1 = forward_frame1 \| reverse_frame1 , forward_reverse2 = forward_frame2 \| reverse_frame2 , forward_frames = forward_frame0 \| forward_frame1 \| forward_frame2 , reverse_frames = reverse_frame0 \| reverse_frame1 \| reverse_frame2 , six_frames = forward_frames \| reverse_frames }
	Specialisation values for single and multiple translation frames. More...
enum class	update_notifications { on , off }
	Indicates whether application allows automatic update notifications by the seqan3::argument_parser. More...

Functions
template<typename sequence_t, typename alignment_config_t> requires detail::align_pairwise_single_input<sequence_t> && std::copy_constructible<std::remove_reference_t<sequence_t>> && detail::is_type_specialisation_of_v<alignment_config_t, configuration>
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.
template<typename reference_type, typename sequence_type>
auto	alignment_from_cigar (std::string const &cigar_string, reference_type const &reference, uint32_t const zero_based_reference_start_position, sequence_type const &query)
template<typename reference_type, typename sequence_type>
auto	alignment_from_cigar (std::vector< cigar > const &cigar_vector, reference_type const &reference, uint32_t const zero_based_reference_start_position, sequence_type const &query)
	Construct an alignment from a CIGAR string and the corresponding sequences.
template<typename alignment_type>
auto	cigar_from_alignment (alignment_type const &alignment, cigar_clipped_bases const &clipped_bases={}, bool const extended_cigar=false)
	Creates a CIGAR string (SAM format) given a seqan3::detail::pairwise_alignment represented by two seqan3::aligned_sequences.
template<typename sequence_alphabet_type>
	masked (sequence_alphabet_type &&, mask const &) -> masked< std::decay_t< sequence_alphabet_type > >
	Type deduction guide enables usage of masked without specifying template args.
template<typename lhs_config_t, typename rhs_config_t>
constexpr auto	operator\| (lhs_config_t &&lhs, rhs_config_t &&rhs)
	Combines two configurations and/or configuration elements forming a new seqan3::configuration.
template<validator validator1_type, validator validator2_type> requires std::common_with<typename std::remove_reference_t<validator1_type>::option_value_type, typename std::remove_reference_t<validator2_type>::option_value_type>
auto	operator\| (validator1_type &&vali1, validator2_type &&vali2)
	Enables the chaining of validators.
template<typename... types>
	pod_tuple (types &&...) -> pod_tuple< types... >
	User defined deduction guide enables easy use.
template<typename base_t, std::unsigned_integral exp_t> requires (std::same_as<base_t, uint64_t> \|\| std::same_as<base_t, int64_t>)
base_t	pow (base_t base, exp_t exp)
	Computes the value of base raised to the power exp.
template<typename sequence_alphabet_type, typename quality_alphabet_type>
	qualified (sequence_alphabet_type &&, quality_alphabet_type &&) -> qualified< std::decay_t< sequence_alphabet_type >, std::decay_t< quality_alphabet_type > >
	Type deduction guide enables usage of qualified without specifying template args.
template<typename index_t, std::ranges::forward_range queries_t, typename configuration_t = decltype(search_cfg::default_configuration)> requires std::ranges::forward_range<std::ranges::range_reference_t<queries_t>> && std::same_as<range_innermost_value_t<queries_t>, typename index_t::alphabet_type>
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.
template<typename sequence_alphabet_type, typename structure_alphabet_type>
	structured_aa (sequence_alphabet_type &&, structure_alphabet_type &&) -> structured_aa< std::decay_t< sequence_alphabet_type >, std::decay_t< structure_alphabet_type > >
	Type deduction guide enables usage of structured_aa without specifying template args.
template<typename sequence_alphabet_type, typename structure_alphabet_type>
	structured_rna (sequence_alphabet_type &&, structure_alphabet_type &&) -> structured_rna< std::decay_t< sequence_alphabet_type >, std::decay_t< structure_alphabet_type > >
	Type deduction guide enables usage of structured_rna without specifying template args.
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).
template<tuple_like tuple_t>
constexpr auto	tuple_pop_front (tuple_t &&t)
	Removes the first element of a tuple.
template<typename pivot_t, tuple_like tuple_t>
constexpr auto	tuple_split (tuple_t &&t)
	Splits a tuple like data structure at the first position of the given type.
template<size_t pivot_c, template< typename... > typename tuple_t, typename... ts> requires tuple_like<tuple_t<ts...>>
constexpr auto	tuple_split (tuple_t< ts... > &&t)
	Splits a tuple like data structure at the given position.
template<size_t pivot_c, template< typename... > typename tuple_t, typename... ts> requires tuple_like<tuple_t<ts...>>
constexpr auto	tuple_split (tuple_t< ts... > const &t)
	Splits a tuple like data structure at the given position.
Aligned sequence interface for ranges that have the corresponding member functions.
Enables ranges to model seqan3::aligned_sequence if they have the member functions insert_gap() and erase_gap().
template<typename range_type> requires requires (range_type v) { v.insert_gap(std::ranges::iterator_t<range_type>{}); v.insert_gap(std::ranges::iterator_t<range_type>{}, typename range_type::size_type{}); }
std::ranges::iterator_t< range_type >	insert_gap (range_type &rng, std::ranges::iterator_t< range_type > const pos_it, typename range_type::size_type const size=1)
	An implementation of seqan3::writable_aligned_sequence::insert_gap for ranges with the corresponding member function insert_gap(it, size).
template<typename range_type> requires requires (range_type v) { v.erase_gap(std::ranges::iterator_t<range_type>{}); }
std::ranges::iterator_t< range_type >	erase_gap (range_type &rng, std::ranges::iterator_t< range_type > const pos_it)
	An implementation of seqan3::writable_aligned_sequence::erase_gap for ranges with the corresponding member function erase_gap(it).
template<typename range_type> requires requires (range_type v) { v.erase_gap(std::ranges::iterator_t<range_type>{}, std::ranges::iterator_t<range_type>{}); }
std::ranges::iterator_t< range_type >	erase_gap (range_type &rng, std::ranges::iterator_t< range_type > const first, std::ranges::iterator_t< range_type > const last)
	An implementation of seqan3::writable_aligned_sequence::erase_gap for ranges with the corresponding member function erase_gap(first, last).
Operations on characters
template<builtin_character char_type>
constexpr char_type	to_lower (char_type const c) noexcept
	Converts 'A'-'Z' to 'a'-'z' respectively; other characters are returned as is.
template<builtin_character char_type>
constexpr char_type	to_upper (char_type const c) noexcept
	Converts 'a'-'z' to 'A'-'Z' respectively; other characters are returned as is.

Variables
template<typename alph_t>
constexpr auto	alphabet_size = detail::adl_only::alphabet_size_cpo<alph_t>{}()
	A type trait that holds the size of a (semi-)alphabet.
debug_stream_type	debug_stream {std::cerr}
	A global instance of seqan3::debug_stream_type.
template<typename t>
constexpr bool	enable_aminoacid
	A trait that indicates whether a type shall model seqan3::aminoacid_alphabet.
template<typename config1_t, typename config2_t>
constexpr bool	is_config_element_combineable_v = detail::config_element_pipeable_with<config1_t, config2_t>
	Helper variable template to test if a configuration element is combineable with another configuration element or configuration.
constexpr auto	is_pair_close = detail::adl_only::is_pair_close_cpo{}
	Check whether the given character represents a leftward interaction in an RNA structure.
constexpr auto	is_pair_open = detail::adl_only::is_pair_open_cpo{}
	Check whether the given character represents a rightward interaction in an RNA structure.
constexpr auto	is_unpaired = detail::adl_only::is_unpaired_cpo{}
	Check whether the given character represents an unpaired nucleotide in an RNA structure.
template<typename alph_t>
constexpr auto	max_pseudoknot_depth = detail::adl_only::max_pseudoknot_depth_cpo<alph_t>{}()
	A type trait that holds the ability of the structure alphabet to represent pseudoknots, i.e. crossing interactions, up to a certain depth.
constexpr auto	pseudoknot_id = detail::adl_only::pseudoknot_id_cpo{}
	Retrieve an id for the level of a pseudoknotted interaction (also known as 'page number').
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).
constexpr std::size_t	seqan3_version = SEQAN3_VERSION
	The full version as std::size_t.
constexpr char const *	seqan3_version_cstring = SEQAN3_VERSION_CSTRING
	The full version as null terminated string.
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.
Function objects
constexpr auto	to_rank = detail::adl_only::to_rank_cpo{}
	Return the rank representation of a (semi-)alphabet object.
constexpr auto	assign_rank_to = detail::adl_only::assign_rank_to_cpo{}
	Assign a rank to an alphabet object.
constexpr auto	to_char = detail::adl_only::to_char_cpo{}
	Return the char representation of an alphabet object.
constexpr auto	assign_char_to = detail::adl_only::assign_char_to_cpo{}
	Assign a character to an alphabet object.
template<typename alph_t>
constexpr auto	char_is_valid_for = detail::adl_only::char_is_valid_for_cpo<alph_t>{}
	Returns whether a character is in the valid set of a seqan3::alphabet (usually implies a bijective mapping to an alphabet value).
constexpr auto	assign_char_strictly_to = detail::adl_only::assign_char_strictly_to_fn{}
	Assign a character to an alphabet object, throw if the character is not valid.
Function objects (Nucleotide)
constexpr auto	complement = detail::adl_only::complement_cpo{}
	Return the complement of a nucleotide object.
Function objects (Quality)
constexpr auto	to_phred = detail::adl_only::to_phred_cpo{}
	The public getter function for the Phred representation of a quality score.
constexpr auto	assign_phred_to = detail::adl_only::assign_phred_to_cpo{}
	Assign a Phred score to a quality alphabet object.
Customisation Points
template<typename option_type>
auto const	enumeration_names = detail::adl_only::enumeration_names_cpo<option_type>{}()
	Return a conversion map from std::string_view to option_type.
Char predicates
A set of function objects to check if a character from an input source fulfills certain characteristics.
template<uint8_t interval_first, uint8_t interval_last>
constexpr auto	is_in_interval
	Checks whether a given letter is in the specified interval.
template<int char_v>
constexpr auto	is_char
	Checks whether a given letter is the same as the template non-type argument.
constexpr auto	is_eof = is_char<EOF>
	Checks whether a given letter is equal to the EOF constant defined in <cstdio>.
constexpr auto	is_cntrl = is_in_interval<'\0', static_cast<char>(31)> \|\| is_char<static_cast<char>(127)>
	Checks whether c is a control character.
constexpr auto	is_print = is_in_interval<' ', '~'>
	Checks whether c is a printable character.
constexpr auto	is_space = is_in_interval<'\t', '\r'> \|\| is_char<' '>
	Checks whether c is a space character.
constexpr auto	is_blank = is_char<'\t'> \|\| is_char<' '>
	Checks whether c is a blank character.
constexpr auto	is_alpha = is_in_interval<'A', 'Z'> \|\| is_in_interval<'a', 'z'>
	Checks whether c is a graphic character.
constexpr auto	is_upper = is_in_interval<'A', 'Z'>
	Checks whether c is a upper case character.
constexpr auto	is_lower = is_in_interval<'a', 'z'>
	Checks whether c is a lower case character.
constexpr auto	is_digit = is_in_interval<'0', '9'>
	Checks whether c is a digital character.
constexpr auto	is_xdigit = is_in_interval<'0', '9'> \|\| is_in_interval<'A', 'F'> \|\| is_in_interval<'a', 'f'>
	Checks whether c is a hexadecimal character.

Type deduction guides
template<std::ranges::viewable_range urng_t> requires (!std::ranges::view<std::remove_reference_t<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<size_t capacity2, typename value_type>
	small_vector (value_type const (&array)[capacity2]) -> small_vector< value_type, capacity2 >
	Deducts the size and value type from an built-in array on construction.
	aminoacid_scoring_scheme () -> aminoacid_scoring_scheme< int8_t >
	Default constructed objects deduce to int8_t.
template<arithmetic score_arg_type>
	aminoacid_scoring_scheme (match_score< score_arg_type >, mismatch_score< score_arg_type >) -> aminoacid_scoring_scheme< int8_t >
	Attention: This guide does not actually deduce from the underlying type, but always defaults to int8_t. To use a larger type, specify the template argument manually.
template<arithmetic score_arg_type>
	aminoacid_scoring_scheme (std::array< std::array< score_arg_type, 27 >, 27 >) -> aminoacid_scoring_scheme< score_arg_type >
	Deduce the score type from the provided matrix.
	aminoacid_scoring_scheme (aminoacid_similarity_matrix) -> aminoacid_scoring_scheme< int8_t >
	Attention: This guide does not actually deduce from the underlying type, but always defaults to int8_t. To use a larger type, specify the template argument manually.
	nucleotide_scoring_scheme () -> nucleotide_scoring_scheme< int8_t >
	Default constructed objects deduce to int8_t.
template<arithmetic score_arg_type>
	nucleotide_scoring_scheme (match_score< score_arg_type >, mismatch_score< score_arg_type >) -> nucleotide_scoring_scheme< int8_t >
	Attention: This guide does not actually deduce from the underlying type, but always defaults to int8_t. To use a larger type, specify the template argument manually.
template<arithmetic score_arg_type>
	nucleotide_scoring_scheme (std::array< std::array< score_arg_type, 15 >, 15 >) -> nucleotide_scoring_scheme< score_arg_type >
	Deduce the score type from the provided matrix.
template<detail::config_element config_t>
	configuration (config_t) -> configuration< config_t >
	Deduces the correct configuration element type from the passed seqan3::pipeable_config_element.
template<input_stream stream_type, sam_file_input_format file_format, detail::fields_specialisation selected_field_ids>
	sam_file_input (stream_type &&stream, file_format const &, selected_field_ids const &) -> sam_file_input< typename sam_file_input<>::traits_type, selected_field_ids, type_list< file_format > >
	Deduce selected fields, file_format, and default the rest.
template<input_stream stream_type, sam_file_input_format file_format, detail::fields_specialisation selected_field_ids>
	sam_file_input (stream_type &stream, file_format const &, selected_field_ids const &) -> sam_file_input< typename sam_file_input<>::traits_type, selected_field_ids, type_list< file_format > >
	Deduce selected fields, file_format, and default the rest.
template<input_stream stream_type, sam_file_input_format file_format>
	sam_file_input (stream_type &&stream, file_format const &) -> sam_file_input< typename sam_file_input<>::traits_type, typename sam_file_input<>::selected_field_ids, type_list< file_format > >
	Deduce file_format, and default the rest.
template<input_stream stream_type, sam_file_input_format file_format>
	sam_file_input (stream_type &stream, file_format const &) -> sam_file_input< typename sam_file_input<>::traits_type, typename sam_file_input<>::selected_field_ids, type_list< file_format > >
	Deduce file_format, and default the rest.
template<std::ranges::forward_range ref_ids_t, std::ranges::forward_range ref_sequences_t, detail::fields_specialisation selected_field_ids>
	sam_file_input (std::filesystem::path path, ref_ids_t &, ref_sequences_t &, selected_field_ids const &) -> sam_file_input< sam_file_input_default_traits< std::remove_reference_t< ref_sequences_t >, std::remove_reference_t< ref_ids_t > >, selected_field_ids, typename sam_file_input<>::valid_formats >
	Deduce selected fields, ref_sequences_t and ref_ids_t, default the rest.
template<std::ranges::forward_range ref_ids_t, std::ranges::forward_range ref_sequences_t>
	sam_file_input (std::filesystem::path path, ref_ids_t &, ref_sequences_t &) -> sam_file_input< sam_file_input_default_traits< std::remove_reference_t< ref_sequences_t >, std::remove_reference_t< ref_ids_t > >, typename sam_file_input<>::selected_field_ids, typename sam_file_input<>::valid_formats >
	Deduce ref_sequences_t and ref_ids_t, default the rest.
template<input_stream stream_type, std::ranges::forward_range ref_ids_t, std::ranges::forward_range ref_sequences_t, sam_file_input_format file_format, detail::fields_specialisation selected_field_ids>
	sam_file_input (stream_type &&stream, ref_ids_t &, ref_sequences_t &, file_format const &, selected_field_ids const &) -> sam_file_input< sam_file_input_default_traits< std::remove_reference_t< ref_sequences_t >, std::remove_reference_t< ref_ids_t > >, selected_field_ids, type_list< file_format > >
	Deduce selected fields, ref_sequences_t and ref_ids_t, and file format.
template<input_stream stream_type, std::ranges::forward_range ref_ids_t, std::ranges::forward_range ref_sequences_t, sam_file_input_format file_format, detail::fields_specialisation selected_field_ids>
	sam_file_input (stream_type &stream, ref_ids_t &, ref_sequences_t &, file_format const &, selected_field_ids const &) -> sam_file_input< sam_file_input_default_traits< std::remove_reference_t< ref_sequences_t >, std::remove_reference_t< ref_ids_t > >, selected_field_ids, type_list< file_format > >
	Deduce selected fields, ref_sequences_t and ref_ids_t, and file format.
template<input_stream stream_type, std::ranges::forward_range ref_ids_t, std::ranges::forward_range ref_sequences_t, sam_file_input_format file_format>
	sam_file_input (stream_type &&stream, ref_ids_t &, ref_sequences_t &, file_format const &) -> sam_file_input< sam_file_input_default_traits< std::remove_reference_t< ref_sequences_t >, std::remove_reference_t< ref_ids_t > >, typename sam_file_input<>::selected_field_ids, type_list< file_format > >
	Deduce ref_sequences_t and ref_ids_t, and file format.
template<input_stream stream_type, std::ranges::forward_range ref_ids_t, std::ranges::forward_range ref_sequences_t, sam_file_input_format file_format>
	sam_file_input (stream_type &stream, ref_ids_t &, ref_sequences_t &, file_format const &) -> sam_file_input< sam_file_input_default_traits< std::remove_reference_t< ref_sequences_t >, std::remove_reference_t< ref_ids_t > >, typename sam_file_input<>::selected_field_ids, type_list< file_format > >
	Deduce selected fields, ref_sequences_t and ref_ids_t, and file format.
template<detail::fields_specialisation selected_field_ids>
	sam_file_output (std::filesystem::path, selected_field_ids const &) -> sam_file_output< selected_field_ids, typename sam_file_output<>::valid_formats, ref_info_not_given >
	Deduces selected_field_ids from input and sets sam_file_output::ref_ids_type to seqan3::detail::ref_info_not_given. valid_formats is set to the default.
template<output_stream stream_type, sam_file_output_format file_format, detail::fields_specialisation selected_field_ids>
	sam_file_output (stream_type &&, file_format const &, selected_field_ids const &) -> sam_file_output< selected_field_ids, type_list< file_format >, ref_info_not_given >
	Deduces selected_field_ids, and the valid format from input and sets sam_file_output::ref_ids_type to seqan3::detail::ref_info_not_given.
template<output_stream stream_type, sam_file_output_format file_format, detail::fields_specialisation selected_field_ids>
	sam_file_output (stream_type &, file_format const &, selected_field_ids const &) -> sam_file_output< selected_field_ids, type_list< file_format >, ref_info_not_given >
	Deduces selected_field_ids, and the valid format from input and sets sam_file_output::ref_ids_type to seqan3::detail::ref_info_not_given.
template<output_stream stream_type, sam_file_output_format file_format>
	sam_file_output (stream_type &&, file_format const &) -> sam_file_output< typename sam_file_output<>::selected_field_ids, type_list< file_format >, ref_info_not_given >
	Deduces the valid format from input and sets sam_file_output::ref_ids_type to seqan3::detail::ref_info_not_given. selected_field_ids is set to the default.
template<output_stream stream_type, sam_file_output_format file_format>
	sam_file_output (stream_type &, file_format const &) -> sam_file_output< typename sam_file_output<>::selected_field_ids, type_list< file_format >, ref_info_not_given >
	Deduces the valid format from input and sets sam_file_output::ref_ids_type to seqan3::detail::ref_info_not_given. selected_field_ids is set to the default.
template<detail::fields_specialisation selected_field_ids, std::ranges::forward_range ref_ids_type, std::ranges::forward_range ref_lengths_type>
	sam_file_output (std::filesystem::path const &, ref_ids_type &&, ref_lengths_type &&, selected_field_ids const &) -> sam_file_output< selected_field_ids, typename sam_file_output<>::valid_formats, std::remove_reference_t< ref_ids_type > >
	Deduces selected_field_ids and ref_ids_type from input. valid_formats is set to the default.
template<std::ranges::forward_range ref_ids_type, std::ranges::forward_range ref_lengths_type>
	sam_file_output (std::filesystem::path const &, ref_ids_type &&, ref_lengths_type &&) -> sam_file_output< typename sam_file_output<>::selected_field_ids, typename sam_file_output<>::valid_formats, std::remove_reference_t< ref_ids_type > >
	Deduces ref_ids_type from input. Valid formats, and selected_field_ids are set to the default.
template<output_stream stream_type, std::ranges::forward_range ref_ids_type, std::ranges::forward_range ref_lengths_type, sam_file_output_format file_format, detail::fields_specialisation selected_field_ids>
	sam_file_output (stream_type &&, ref_ids_type &&, ref_lengths_type &&, file_format const &, selected_field_ids const &) -> sam_file_output< selected_field_ids, type_list< file_format >, std::remove_reference_t< ref_ids_type > >
	Deduces selected_field_ids, the valid format, and the ref_ids_type from input.
template<output_stream stream_type, std::ranges::forward_range ref_ids_type, std::ranges::forward_range ref_lengths_type, sam_file_output_format file_format, detail::fields_specialisation selected_field_ids>
	sam_file_output (stream_type &, ref_ids_type &&, ref_lengths_type &&, file_format const &, selected_field_ids const &) -> sam_file_output< selected_field_ids, type_list< file_format >, std::remove_reference_t< ref_ids_type > >
	Deduces selected_field_ids, the valid format, and the ref_ids_type from input.
template<output_stream stream_type, std::ranges::forward_range ref_ids_type, std::ranges::forward_range ref_lengths_type, sam_file_output_format file_format>
	sam_file_output (stream_type &&, ref_ids_type &&, ref_lengths_type &&, file_format const &) -> sam_file_output< typename sam_file_output<>::selected_field_ids, type_list< file_format >, std::remove_reference_t< ref_ids_type > >
	Deduces the valid format, and the ref_ids_type from input. selected_field_ids set to the default.
template<output_stream stream_type, std::ranges::forward_range ref_ids_type, std::ranges::forward_range ref_lengths_type, sam_file_output_format file_format>
	sam_file_output (stream_type &, ref_ids_type &&, ref_lengths_type &&, file_format const &) -> sam_file_output< typename sam_file_output<>::selected_field_ids, type_list< file_format >, std::remove_reference_t< ref_ids_type > >
	Deduces the valid format, and the ref_ids_type from input. selected_field_ids set to the default.
template<input_stream stream_type, sequence_file_input_format file_format>
	sequence_file_input (stream_type &stream, file_format const &) -> sequence_file_input< typename sequence_file_input<>::traits_type, typename sequence_file_input<>::selected_field_ids, type_list< file_format > >
	Deduces the sequence input file type from the stream and the format.
template<input_stream stream_type, sequence_file_input_format file_format>
	sequence_file_input (stream_type &&stream, file_format const &) -> sequence_file_input< typename sequence_file_input<>::traits_type, typename sequence_file_input<>::selected_field_ids, type_list< file_format > >
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template<input_stream stream_type, sequence_file_input_format file_format, detail::fields_specialisation selected_field_ids>
	sequence_file_input (stream_type &&stream, file_format const &, selected_field_ids const &) -> sequence_file_input< typename sequence_file_input<>::traits_type, selected_field_ids, type_list< file_format > >
	Deduces the sequence input file type from the stream, the format and the field ids.
template<input_stream stream_type, sequence_file_input_format file_format, detail::fields_specialisation selected_field_ids>
	sequence_file_input (stream_type &stream, file_format const &, selected_field_ids const &) -> sequence_file_input< typename sequence_file_input<>::traits_type, selected_field_ids, type_list< file_format > >
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template<output_stream stream_t, sequence_file_output_format file_format>
	sequence_file_output (stream_t &, file_format const &) -> sequence_file_output< typename sequence_file_output<>::selected_field_ids, type_list< file_format > >
	Deduction guide for given stream and file format.
template<output_stream stream_t, sequence_file_output_format file_format>
	sequence_file_output (stream_t &&, file_format const &) -> sequence_file_output< typename sequence_file_output<>::selected_field_ids, type_list< file_format > >
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template<output_stream stream_t, sequence_file_output_format file_format, detail::fields_specialisation selected_field_ids>
	sequence_file_output (stream_t &&, file_format const &, selected_field_ids const &) -> sequence_file_output< selected_field_ids, type_list< file_format > >
	Deduction guide for given stream, file format and field ids.
template<output_stream stream_t, sequence_file_output_format file_format, detail::fields_specialisation selected_field_ids>
	sequence_file_output (stream_t &, file_format const &, selected_field_ids const &) -> sequence_file_output< selected_field_ids, type_list< file_format > >
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template<input_stream stream_type, structure_file_input_format file_format, detail::fields_specialisation selected_field_ids>
	structure_file_input (stream_type &&stream, file_format const &, selected_field_ids const &) -> structure_file_input< typename structure_file_input<>::traits_type, selected_field_ids, type_list< file_format > >
	Deduction of the selected fields, the file format and the stream type.
template<input_stream stream_type, structure_file_input_format file_format, detail::fields_specialisation selected_field_ids>
	structure_file_input (stream_type &stream, file_format const &, selected_field_ids const &) -> structure_file_input< typename structure_file_input<>::traits_type, selected_field_ids, type_list< file_format > >
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template<output_stream stream_t, structure_file_output_format file_format, detail::fields_specialisation selected_field_ids>
	structure_file_output (stream_t &&, file_format const &, selected_field_ids const &) -> structure_file_output< selected_field_ids, type_list< file_format > >
	Deduction of the selected fields, the file format and the stream type.
template<output_stream stream_t, structure_file_output_format file_format, detail::fields_specialisation selected_field_ids>
	structure_file_output (stream_t &, file_format const &, selected_field_ids const &) -> structure_file_output< selected_field_ids, type_list< file_format > >
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

Tuple interface
template<template< typename... > class query_t, typename... configs_t>
constexpr auto const &	get (configuration< configs_t... > const &config) noexcept
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template<template< typename... > class query_t, typename... configs_t>
constexpr auto &&	get (configuration< configs_t... > &&config) noexcept
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template<template< typename... > class query_t, typename... configs_t>
constexpr auto const &&	get (configuration< configs_t... > const &&config) noexcept
	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
template<template< typename... > class query_t, typename... configs_t>
constexpr auto &	get (configuration< configs_t... > &config) noexcept
	Returns the stored element.

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.
template<arithmetic score_type>
	match_score (score_type) -> match_score< score_type >
	Deduce the score type from the provided argument.
template<arithmetic score_type>
	mismatch_score (score_type) -> mismatch_score< score_type >
	Deduce the score type from the provided argument.

Detailed Description

The main SeqAn3 namespace.

Typedef Documentation