Namespace List

Here is a list of all documented namespaces with brief descriptions:

[detail level 12345]

►Nseqan3	The main SeqAn3 namespace
►Nalign_cfg	A special sub namespace for the alignment configurations
►Ndetail
Cresult_type	Configuration element capturing the configured seqan3::alignment_result for the alignment algorithm
Cband_fixed_size	Configuration element for setting a fixed size band
Cextension_score	A strong type of underlying type int32_t that represents the score (usually negative) of any character against a gap character
Cfree_end_gaps_sequence1_leading	A strong type representing free_end_gaps_sequence1_leading of the seqan3::align_cfg::method_global
Cfree_end_gaps_sequence1_trailing	A strong type representing free_end_gaps_sequence1_trailing of the seqan3::align_cfg::method_global
Cfree_end_gaps_sequence2_leading	A strong type representing free_end_gaps_sequence2_leading of the seqan3::align_cfg::method_global
Cfree_end_gaps_sequence2_trailing	A strong type representing free_end_gaps_sequence2_trailing of the seqan3::align_cfg::method_global
Cgap_cost_affine	A configuration element for the affine gap cost scheme
Clower_diagonal	A strong type representing the lower diagonal of the seqan3::align_cfg::band_fixed_size
Cmethod_global	Sets the global alignment method
Cmethod_local	Sets the local alignment method
Cmin_score	Sets the minimal score (maximal errors) allowed during an distance computation e.g. edit distance
Con_result	Configuration element to provide a user defined callback function for the alignment
Copen_score	A strong type of underlying type int32_t that represents a score (usually negative) that is incurred once per stretch of consecutive gaps
Coutput_alignment	Configures the alignment result to output the alignment
Coutput_begin_position	Configures the alignment result to output the begin positions
Coutput_end_position	Configures the alignment result to output the end position
Coutput_score	Configures the alignment result to output the score
Coutput_sequence1_id	Configures the alignment result to output the id of the first sequence
Coutput_sequence2_id	Configures the alignment result to output the id of the second sequence
Cscore_type	A configuration element to set the score type used in the alignment algorithm
Cscoring_scheme	Sets the scoring scheme for the alignment algorithm
Cupper_diagonal	A strong type representing the upper diagonal of the seqan3::align_cfg::band_fixed_size
Cvectorised	Enables the vectorised alignment computation if possible for the current configuration
►Ncustom	A namespace for third party and standard library specialisations of SeqAn customisation points
Calphabet	A type that can be specialised to provide customisation point implementations so that third party types model alphabet concepts
Calphabet< char_type >	Alphabet specific customisations for builtin char types
Calphabet< uint_type >	Alphabet specific customisations for unsigned integral types
Cargument_parsing	A type that can be specialised to provide customisation point implementations for the seqan3::argument_parser such that third party types may be adapted
►Ndetail	The internal SeqAn3 namespace
Caccess_restrictor_fn	A functor that always throws when calling operator() (needed for the alignment "dummy" sequence)
Cadaptor_base	CRTP-base to simplify the definition of range adaptor closure objects and similar types
Cadaptor_for_view_without_args	Template for range adaptor closure objects that store no arguments and always delegate to the view constructor
Cadaptor_from_functor	Template for range adaptor closure objects that store arguments and wrap a proto-adaptor
Cadvanceable_alignment_coordinate	Implements an internal alignment coordinate that can be used as an argument to the std::ranges::iota_view
Caffine_cell_proxy	A proxy for an affine score matrix cell
Caffine_gap_init_policy	The CRTP-policy that implements the initialisation of the dynamic programming matrix with affine gaps
Caffine_gap_policy	The CRTP-policy that computes a single cell in the alignment matrix
Calgorithm_executor_blocking	A blocking algorithm executor for algorithms
Calign_result_selector	Helper metafunction to select the alignment result type based on the configuration
►Caligned_sequence_builder	Builds the alignment for a given pair of sequences and the respective trace
Cresult_type	The result type when building the aligned sequences
Calignment_algorithm	The alignment algorithm type to compute standard pairwise alignment using dynamic programming
Calignment_algorithm_state	Local state for the standard alignment algorithm
Calignment_configuration_traits	A traits type for the alignment algorithm that exposes static information stored within the alignment configuration object
►Calignment_configurator	Configures the alignment algorithm given the sequences and the configuration object
Cselect_find_optimum_policy	Transformation trait that chooses the correct find optimum policy
Cselect_gap_policy	Transformation trait that chooses the correct gap policy
Cselect_gap_recursion_policy	Selects the gap recursion policy
Cselect_matrix_policy	Transformation trait that chooses the correct matrix policy
Calignment_contract	Provides several contracts to test when configuring the alignment algorithm
Calignment_function_traits	A traits class to provide a uniform access to the properties of the wrapped alignment algorithm
►Calignment_matrix_column_major_range_base	Provides a range interface for alignment matrices
►Calignment_column_type	Represents a column within an alignment matrix
Citerator_type	The iterator over an alignment-column
Citerator_type	A column iterator over the alignment matrix
Calignment_matrix_policy	Manages the alignment and score matrix
Calignment_optimum	Stores the current optimum of the alignment algorithm
Calignment_result_value_type	A struct that contains the actual alignment result data
Calignment_result_value_type_accessor< alignment_result< result_value_t > >	Transformation trait to access the hidden result value type of the seqan3::alignment_result class
Calignment_score_matrix_one_column	An alignment score matrix storing only a single column for the computation
Calignment_score_matrix_one_column_banded	A banded alignment score matrix storing only a single banded column for the computation
Calignment_score_matrix_one_column_base	A base class for alignment score matrices using only one column to compute the matrix
Calignment_score_matrix_proxy	A proxy type for a unified access to the score matrix during alignment computation
Calignment_trace_matrix_base	A crtp-base class for alignment traceback matrices
Calignment_trace_matrix_full	An alignment traceback matrix storing the entire traceback matrix
Calignment_trace_matrix_full_banded	An alignment traceback matrix storing the entire banded traceback matrix
Calignment_trace_matrix_proxy	A proxy type for a unified access to the traceback matrix during alignment computation
Cassignable_from	'Callable' helper class that is invokable by meta::invoke.Returns a std::true_type if the type is assignable from T
Casync_input_buffer_fn	Definition of the range adaptor object type for seqan3::views::async_input_buffer
►Casync_input_buffer_view	The type returned by seqan3::views::async_input_buffer
Citerator	The iterator of the seqan3::detail::async_input_buffer_view
Cstate	Buffer and thread and shared between copies of this type
Cbasic_iterator	Forward declaration
Cbasic_iterator< single_pass_input_view< view_type > >	An input_iterator over the associated range
Cbgzf_compression	A tag signifying a bgzf compressed file
Cbuiltin_simd	A class that holds the type of a simd implementation called [vector extension] (https://gcc.gnu.org/onlinedocs/gcc/Vector-Extensions.html) (formerly known as "seqan simd" in seqan2)
Cbuiltin_simd< scalar_t, length >	A class that holds the type of a simd implementation called [vector extension] (https://gcc.gnu.org/onlinedocs/gcc/Vector-Extensions.html) (formerly known as "seqan simd" in seqan2).
Cbuiltin_simd_traits_helper	Helper struct for seqan3::detail::is_builtin_simd
Cbuiltin_simd_traits_helper< builtin_simd_t >	Helper struct for seqan3::detail::is_builtin_simd
Cbz2_compression	A tag signifying a bz2 compressed file
Cchar_predicate_base	An abstract CRTP base class for parse conditions to add logical disjunction and negation operator
Cchar_predicate_disjunction	Logical disjunction operator for parse conditions
Cchar_predicate_negator	Logical not operator for a parse condition
Cchunked_indexed_sequence_pairs	A transformation trait to retrieve the chunked range over indexed sequence pairs
Ccolumn_index_type	A strong type for designated initialisation of the column index of a matrix
Ccombined_adaptor	Template for range adaptor closure objects that consist of two other range adaptor closure objects
►Ccombined_score_and_trace_matrix	An alignment matrix that combines a score matrix with a trace matrix into a common interface
Citerator	Combined score and trace matrix iterator for the pairwise sequence alignment
Csentinel	The sentinel type for the seqan3::detail::combined_score_and_trace_matrix
Cconstexpr_pseudo_bitset	A data structure that implements a subset of std::bitset as constexpr
Cconstructible_from	'Callable' helper class that is invokable by meta::invoke.Returns a std::true_type if the type is constructable from T
►Ccoordinate_matrix	A matrix over coordinates
Cconvert_to_matrix_coordinate	A function object that converts a column index and a row index to a seqan3::detail::matrix_coordinate
Citerator	The iterator for the seqan3::detail::coordinate_matrix
Ccounted_simd_iterator	Implements a special version of a counted iterator over a simd vector
Ccustomisation_point_object	A CRTP base-class that defines a customisation_point_object (CPO)
►Cdebug_matrix	A debug matrix to wrap alignment matrices and sequences and make them printable together
Cformat_type	Format used by seqan3::detail::debug_matrix
Cdebug_mode	A global configuration type used to enabled debugging of algorithms
Cdefault_edit_distance_trait_type	The default traits type for the edit distance algorithm
Cdefault_validator	Validator that always returns true
Cdeferred_crtp_base	An invocable wrapper that defers the instantiation of a crtp_base class
Cdeferred_crtp_base_vargs	An invocable wrapper that defers the instantiation of a crtp_base class
Cdeferred_type	Return the type identity; further arguments are ignored, but can make this type dependent if they are
Cedit_distance_algorithm	This algorithm unifies different edit distance implementations and uses the appropriate one depending on the given configuration
►Cedit_distance_score_matrix_full	The underlying data structure of seqan3::detail::edit_distance_unbanded that represents the score matrix
Ccolumn_type	The state of one computation step
Cmax_errors_state	If use_max_errors is true store these additional state information in state_type
Cscore_matrix_state	This information is needed to infer the score matrix
►Cedit_distance_trace_matrix_full	The underlying data structure of seqan3::detail::edit_distance_unbanded that represents the trace matrix
Ccolumn_type	The state of one computation step
Cmax_errors_state	If use_max_errors is true store these additional state information in state_type
Ctrace_matrix_state	This information is needed to infer the trace matrix
Ctrace_path_iterator	The iterator needed to implement seqan3::detail::edit_distance_trace_matrix_full::trace_path
►Cedit_distance_unbanded	This calculates an alignment using the edit distance and without a band
Ccompute_state	The internal state needed to compute the alignment
Ccompute_state_trace_matrix	The internal state needed to compute the trace matrix
Cedit_distance_unbanded_global_policy	Only available when default_edit_distance_trait_type::is_global is true
Cedit_distance_unbanded_max_errors_policy	Only available when default_edit_distance_trait_type::use_max_errors is true
Cedit_distance_unbanded_score_matrix_policy	Only available when default_edit_distance_trait_type::compute_score_matrix is true
Cedit_distance_unbanded_semi_global_policy	Only available when default_edit_distance_trait_type::is_semi_global is true
Cedit_distance_unbanded_trace_matrix_policy	Only available when default_edit_distance_trait_type::compute_trace_matrix is true
Cempty_state	Store no state for state_t
Cempty_type	An empty class type used in meta programming
►Cexecution_handler_parallel	Handles the parallel execution of algorithms
Cinternal_state	An internal state stored on the heap to allow safe move construction/assignment of the class
Cexecution_handler_sequential	Handles the sequential execution of algorithms
Cfast_istreambuf_iterator	Functionally the same as std::istreambuf_iterator, but faster
Cfast_ostreambuf_iterator	Functionally the same as std::ostreambuf_iterator, but offers writing a range more efficiently
Cfind_optimum_policy	The CRTP-policy to determine the optimum of the dynamic programming matrix
Cfm_index_cursor_node	Internal representation of the node of an FM index cursor
Cfm_index_validator	Class used to validate the requirements on the input text of the fm_index
Cformat_base	The format that contains all helper functions needed in all formats
Cformat_copyright	The format that prints the copyright information to std::cout
►Cformat_help	The format that prints the help page to std::cout
Cconsole_layout_struct	Stores the relevant parameters of the documentation on the screen
Cformat_help_base	The format that contains all helper functions needed in all formats for printing the interface description of the application (to std::cout)
Cformat_html	The format that prints the help page as html to std::cout
Cformat_man	The format that prints the help page information formatted for a man page to std::cout
Cformat_parse	The format that organizes the actual parsing of command line arguments
Cformat_sam_base	The alignment base format
Cformat_short_help	The format that prints a short help message to std::cout
Cformat_version	The format that prints the version to std::cout
Cgz_compression	A tag signifying a gz compressed file
Cignore_output_iterator	An output iterator that emulates writing to a null-stream in order to dispose the output
Cimplicitly_convertible_from	'Callable' helper class that is invokable by meta::invoke.Returns a std::true_type if the T is implicitly convertible to type
Cin_file_iterator	Input iterator necessary for providing a range-like interface in input file
Cinherited_iterator_base	A CRTP base template for creating iterators that inherit from other iterators
Cinstantiate	A transformation trait that instantiates seqan3::lazy types. Base template is the identity transformation
Cinstantiate< lazy< template_t, spec_t... > >	A transformation trait that instantiates seqan3::lazy types
Cinstantiate_if	A transformation trait that instantiates seqan3::lazy types given a boolean condition. Base template is std::false_type
Cinstantiate_if< lazy< template_t, spec_t... >, true >	A transformation trait that instantiates seqan3::lazy types given a boolean condition. If condition is true and parameter is lazy, the instantiated type
Cinstantiate_if< t, true >	A transformation trait that instantiates seqan3::lazy types given a boolean condition. If condition is true and parameter is not lazy, the type identity
Cinterleave_fn	Views::interleave's range adaptor object type (non-closure)
Ciota_simd_view	The simd iota view
Ciota_simd_view_fn	The view adaptor returning the seqan3::detail::iota_simd_view
Cis_builtin_simd	This class inherits from std::true_type, iff seqan3::detail::builtin_simd<scalar_t, length>::type is a builtin simd type
Cis_char_type	Parse condition that checks if a given value is equal to char_v
Cis_class_template_declarable_with	An unary type trait that tests whether a template class can be declared with the given template type parameters
Cis_derived_from_record	Helper struct to implement seqan3::detail::record_like
Cis_in_interval_type	Parse condition that checks if a given value is in the range of rng_beg and interval_last
Cis_native_builtin_simd	This class inherits from std::true_type, iff the builtin simd type is supported by the current architecture
Cis_same_configuration_f	Helper meta function to check if a template type is contained in a seqan3::configuration
Cis_span	Helper to determine whether a type is a std::span
Cis_type_specialisation_of	Determines whether a source_type is a specialisation of another template
Cis_type_specialisation_of< source_t< source_args... >, source_t >	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts
Cis_value_specialisation_of< source_t< source_args... >, source_t >	Determines whether a source_type is a specialisation of another template
Cistreambuf_fn	View adaptor/factory definition for views::istream
Citer_pointer	This is like std::iter_value_t, but for the pointer type
Ckmer_hash_fn	Views::kmer_hash's range adaptor object type (non-closure)
►Ckmer_hash_view	The type returned by seqan3::views::kmer_hash
Cbasic_iterator	Iterator for calculating hash values via a given seqan3::shape
Clatch	A single-use synchronisation point to coordinate concurrent threads
Clazy	An empty type whose only purpose is to hold an uninstantiated template plus its arguments
Clazy_conditional	Behaves like std::conditional, but instantiates types wrapped in seqan3::lazy
Cmake_aligned_sequence_type	A transformation trait that returns the correct aligned sequence type for a given sequence type
Cmake_pairwise_alignment_type	A transformation trait that returns the correct pairwise alignment type for two given sequence types
Cmatrix	Defines the requirements of a matrix (e.g. score matrices, trace matrices)
Cmatrix_index	A representation of a location or offset within a two-dimensional matrix
Cmax_score_banded_updater	A function object that compares and possibly updates the alignment optimum with the current cell
Cmax_score_updater	A function object that compares and possibly updates the alignment optimum with the current cell
Cmax_score_updater_simd_global	Function object that compares and updates the alignment optimum for the vectorised global alignment algorithm
Cmaybe_inherited_iterator_category	This handles more cases than maybe_iterator_category if you inherit the underling_iterator_t
Cmaybe_iterator_category	Defines iterator_category member if underlying_iterator_t has a valid std::iterator_traits::iterator_category overload
Cminimiser_fn	Seqan3::views::minimiser's range adaptor object type (non-closure)
Cminimiser_hash_fn	Seqan3::views::minimiser_hash's range adaptor object type (non-closure)
►Cminimiser_view	The type returned by seqan3::views::minimiser
Cbasic_iterator	Iterator for calculating minimisers
Cmulti_invocable	A type that can conveniently inherit multiple invocables and acts as a union over them
Cnon_propagating_cache	A helper that enables an input view to temporarily cache values as it is iterated over
Cnumber_cols	Strong type for setting the column dimension of a matrix
Cnumber_rows	Strong type for setting the row dimension of a matrix
Cout_file_iterator	Output iterator necessary for providing a range-like interface in output file
Cpairwise_alignment_algorithm	The alignment algorithm type to compute standard pairwise alignment using dynamic programming
Cpairwise_alignment_algorithm_banded	The alignment algorithm type to compute the banded standard pairwise alignment using dynamic programming
►Cpairwise_combine_view	Generates all pairwise combinations of the elements in the underlying range
Cbasic_iterator	The forward declared iterator type for pairwise_combine_view
Cparallel_mode	A global configuration type used to enable parallel execution of algorithms
Cpolicy_affine_gap_recursion	Implements the alignment recursion function for the alignment algorithm using affine gap costs
Cpolicy_affine_gap_recursion_banded	Implements the alignment recursion function for the banded alignment algorithm using affine gap costs
Cpolicy_affine_gap_with_trace_recursion	Implements the alignment recursion function for the alignment algorithm using affine gap costs with trace information
Cpolicy_affine_gap_with_trace_recursion_banded	Implements the alignment recursion function for the banded alignment algorithm using affine gap costs with trace information
Cpolicy_alignment_matrix	A policy that provides a common interface to acquire the correct alignment matrices
Cpolicy_alignment_result_builder	Implements the alignment result builder
Cpolicy_max_error	Provides the function max_error_counts if inherited by a search algorithm
Cpolicy_optimum_tracker	Implements the tracker to store the global optimum for a particular alignment computation
Cpolicy_optimum_tracker_simd	Implements the tracker to store the global optimum for a particular alignment computation
Cpolicy_scoring_scheme	Stores the configured scoring scheme used for this algorithm
Cpolicy_search_result_builder	Provides the function make_results if inherited by a search algorithm
Cpriority_tag	A tag that allows controlled overload resolution via implicit base conversion rules
Cpriority_tag< 0 >	Recursion anchor for seqan3::detail::priority_tag
Cproxy_reference	The same as value_t & but it is default constructible and is re-assignable
Cpseudo_random_access_fn	View adaptor definition for seqan3::views::enforce_random_access
Crandom_access_iterator	A generic random access iterator that delegates most operations to the range
Crandom_access_iterator_base	A CRTP base template for creating random access iterators
Creader_count	A strong type to set the reader count of a seqan3::detail::reader_writer_manager
►Creader_writer_manager	A single-use synchronisation point for closable concurrent data structures
Cscoped_reader_type	A strictly scope-based seqan3::detail::reader_writer_manager wrapper for consumer threads
Cscoped_writer_type	A strictly scope-based seqan3::detail::reader_writer_manager wrapper for producer threads
Crecursive_required_types	Like seqan3::detail::required_types, but recursive
Crecursive_required_types< t >	Like seqan3::detail::required_types, but recursive
Crepeat_fn	View factory definition for views::repeat
Crepeat_n_fn	The underlying type of seqan3::views::repeat_n
►Crepeat_view	The type returned by seqan3::views::repeat
Cbasic_iterator	The forward declared iterator type for views::repeat (a random access iterator)
Crequired_types	A seqan3::type_list with types that the given type depends on
Crequired_types< t >	A seqan3::type_list with types that the given type depends on. [specialisation for seqan3::alphabet_variant and derivates of seqan3::alphabet_tuple_base]
Creverse_fm_index	An FM Index specialisation that handles reversing the given text
Crow_index_type	A strong type for designated initialisation of the row index of a matrix
Csafe_filesystem_entry	A safe guard to manage a filesystem entry, e.g. a file or a directory
Csam_file_input_format_exposer	Internal class used to expose the actual format interface to read SAM records from the file
Csam_file_output_format_exposer	Internal class used to expose the actual format interface to write SAM/BAM records into the file
►Cscore_matrix_single_column	Score matrix for the pairwise alignment using only a single column
Cmatrix_iterator	Score matrix iterator for the pairwise alignment using only a single column
Cscoring_scheme_policy	The CRTP-policy that stores the scoring scheme used for this alignment algorithm
Csearch	Object storing information for a search (of a search scheme)
Csearch_configuration_validator	Class used to validate the search configuration
►Csearch_configurator	Class used to update the search configuration, e.g. add defaults
Cselect_search_algorithm	Selects the search algorithm based on the index type
Cselect_search_result	Select the search result based on the configuration and the index type
Csearch_dyn	Object storing information for a search (of a search scheme)
Csearch_param	Object grouping numbers of errors for different kind of error types
Csearch_scheme_algorithm	The algorithm that performs a bidirectional search on a bidirectional FM index using (optimal) search schemes
Csearch_traits	A collection of traits extracted from the search configuration
Cselect_types_with_ids	Exposes a subset of types as a seqan3::type_list selected based on their IDs
►Cselector	The same as std::conditional but for template template parameters
Cselect	Depending on B, select is the template template parameter T or F
Csequence_file_input_format_exposer	Internal class used to expose the actual format interface to read sequence records from the file
Csequence_file_output_format_exposer	Internal class used to expose the actual format interface to write sequence records into the file
Csimd_affine_gap_policy	The CRTP-policy that computes a batch of cells in the alignment matrix using simd instructions
Csimd_find_optimum_policy	The CRTP-policy to determine the optimum of the dynamic programming matrix
Csimd_global_alignment_state	A state that is only used for global alignments
Csimd_match_mismatch_scoring_scheme	A vectorised scoring scheme handling matches and mismatches only
Csimd_matrix_scoring_scheme	A vectorised scoring scheme to handle scoring matrices using gather strategy
►Csingle_pass_input_view	Adds single_pass_input behavior to the underlying range
Cstate	An internal state to capture the underlying range and a cached iterator
Cslice_fn	View adaptor definition for views::slice
Cspin_delay	A delay for threads waiting for a shared resource
Cstream_buffer_exposer	Functionally the same as std::basic_streambuf<char_t, traits_t_>, but exposes protected members as public
Cstrong_type	CRTP base class to declare a strong typedef for a regular type to avoid ambiguous parameter settings in function calls
Cstructure_file_input_format_exposer	Internal class used to expose the actual format interface to read structure records from the file
Cstructure_file_output_format_exposer	Internal class used to expose the actual format interface to write structure records into the file
Ctake_exactly_fn	View adaptor definition for views::take and views::take_or_throw
Ctake_until_fn	View adaptor definition for detail::take_until and detail::take_until_or_throw
Cto_simd_fn	Views::to_simd's range adaptor closure object type
Ctrace_iterator	A trace iterator an unbanded trace matrix
Ctrace_iterator_banded	A trace iterator for banded trace matrices
Ctrace_iterator_base	A CRTP-base class for trace iterator implementations for the alignment algorithms
►Ctrace_matrix_full	Trace matrix for the pairwise alignment using the full trace matrix
►Citerator	Trace matrix iterator for the pairwise alignment using the full trace matrix
Ccolumn_proxy	The proxy returned as reference type
Ctransfer_template_args_onto< source_template< source_arg_types... >, target_template >	Extracts a type template's type arguments and specialises another template with them
Ctransfer_template_vargs_onto< source_template< source_varg_types... >, target_template >	Extracts a type template's non-type arguments and specialises another template with them
Ctransfer_type_modifier_onto	Transfers the type modifier &, && and const (and any combination) to the target type
Ctranslate_fn	Definition of the range adaptor object type for seqan3::views::translate and seqan3::views::translate_single
Ctranslate_join_fn	Definition of the range adaptor object type for seqan3::views::translate_join
Ctranslation_table	Generic translation table for canonical genetic code
Ctranslation_table< dna15, seqan3::genetic_code::canonical, void_type >	Translation table for canonical genetic code and dna15 alphabet
Ctrim_fn	The underlying type of seqan3::views::trim_quality
Ctuple_type_list	Transformation trait to expose the tuple element types as seqan3::type_list
►Ctwo_dimensional_matrix	A two dimensional matrix used inside of alignment algorithms
Cbasic_iterator	A two-dimensional matrix iterator
Ctwo_dimensional_matrix_iterator	A concept for iterators over a two dimensional matrix, e.g. seqan3::detail::two_dimensional_matrix
Ctwo_dimensional_matrix_iterator_base	A crtp-base class for iterators over seqan3::detail::two_dimensional_matrix
Ctype_list_expander< type_list_t< args_t... > >	Helper class to invoke a meta algorithm on the types contained in a seqan3::type_list
Ctype_reduce_fn	View adaptor definition for views::type_reduce
Cunaligned_seq	Default transformation trait that shall expose the unaligned sequence type of t when specialised
Cunaligned_seq< t >	Exposes the unaligned sequence type given an aligned sequence container type
Cunidirectional_search_algorithm	The algorithm that performs a unidirectional search on an FM index using trivial backtracking
Cvalid_template_spec_or	Exposes templ_t<spec_t...> if that is valid, otherwise fallback_t
Cvalid_template_spec_or< fallback_t, templ_t, spec_t... >	This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts
Cvalidator_chain_adaptor	A helper struct to chain validators recursively via the pipe operator
Cvariant_from_tags	Base class to deduce the std::variant type from format tags
Cvariant_from_tags< type_list< ts... >, output_t >	Transfers a list of format tags (...ts) onto a std::variant by specialising output_t with each
Cversion_checker	A functor whose operator() performs the server http request and version checks
►Cview_enforce_random_access	View to force random access range iterator for seqan3::pseudo_random_access_range
Cbasic_iterator	Iterator wrapper for the underlying range iterator enforcing std::random_access_iterator_tag
Cview_equality_fn	Comparator that is able two compare two views
Cview_interleave	The type returned by seqan3::views::interleave
►Cview_take_exactly	The type returned by seqan3::views::take, seqan3::detail::take_exactly and seqan3::detail::take_exactly_or_throw
Cbasic_iterator	The forward declared iterator type
►Cview_take_until	The type returned by seqan3::detail::take_until and seqan3::detail::take_until_or_throw
Cbasic_consume_iterator	Special iterator type used when consuming behaviour is selected
Cbasic_sentinel	The sentinel type of take_until, provides the comparison operators
►Cview_to_simd	Transforms a range of ranges into chunks of seqan3::simd vectors
Citerator_type	Iterator that transposes the underlying range of ranges and transforms that to SIMD types
Cview_translate	The return type of seqan3::views::translate
Cview_translate_join	The return type of seqan3::views::translate_join
Cview_translate_single	The return type of seqan3::views::translate_single
Cweakly_equality_comparable_with_	'Callable' helper class that is invokable by meta::invoke.Returns a std::true_type if the type is weakly equality comparable to T
Cweakly_equality_comparable_with_trait	Binary type trait that behaves like the seqan3::detail::weakly_equality_comparable_with concept
Cweakly_ordered_with_	'Callable' helper class that is invokable by meta::invoke.Returns a std::true_type if the type is comparable via <,<=,>,>= to T
Cweakly_ordered_with_trait	Binary type trait that behaves like the seqan3::detail::weakly_ordered_with concept
Cwriter_count	A strong type to set the writer count of a seqan3::detail::reader_writer_manager
Czstd_compression	A tag signifying a zstd compressed file
Rfields_specialisation	Auxiliary concept that checks whether a type is a specialisation of seqan3::fields
Rtype_list_of_sam_file_input_formats	Auxiliary concept that checks whether a type is a seqan3::type_list and all types meet seqan3::sam_file_input_format
Rtype_list_of_sam_file_output_formats	Auxiliary concept that checks whether a type is a seqan3::type_list and all types meet seqan3::sam_file_output_format
Rtype_list_of_sequence_file_input_formats	Auxiliary concept that checks whether a type is a seqan3::type_list and all types meet seqan3::sequence_file_input_format
Rtype_list_of_sequence_file_output_formats	Auxiliary concept that checks whether a type is a seqan3::type_list and all types meet seqan3::sequence_file_output_format
Rtype_list_of_structure_file_input_formats	Auxiliary concept that checks whether a type is a seqan3::type_list and all types meet seqan3::structure_file_input_format
Rtype_list_of_structure_file_output_formats	Auxiliary concept that checks whether a type is a seqan3::type_list and all types meet seqan3::structure_file_output_format
►Nexposition_only	A namespace for SeqAn entities that are intended for documentation purposes only
Ccigar_operation	The actual implementation of seqan3::cigar::operation for documentation purposes only
Nlist_traits	Namespace containing traits for working on seqan3::type_list
Nliterals	The SeqAn namespace for literals
Npack_traits	Namespace containing traits for working on type packs
►Nsearch_cfg	A special sub namespace for the search configurations
Cerror_count	A strong type of underlying type uint8_t that represents the number of errors
Cerror_rate	A strong type of underlying type double that represents the rate of errors
Chit	A dynamic configuration element to configure the hit strategy at runtime
Chit_all	Configuration element to receive all hits within the error bounds
Chit_all_best	Configuration element to receive all hits with the lowest number of errors within the error bounds
Chit_single_best	Configuration element to receive a single best hit with the lowest number of errors within the error bounds
Chit_strata	Configuration element to receive all hits with the best number of errors plus the given stratum. All hits are found with the fewest number of errors plus 'stratum'
Cmax_error_deletion	Configuration element that represents the number or rate of deletion errors
Cmax_error_insertion	Configuration element that represents the number or rate of insertion errors
Cmax_error_substitution	Configuration element that represents the number or rate of substitution errors
Cmax_error_total	Configuration element that represents the number or rate of total errors
Con_result	Configuration element to provide a user defined callback function for the search
Coutput_index_cursor	Include the index_cursor in the seqan3::search_result returned by a call to seqan3::search
Coutput_query_id	Include the query_id in the seqan3::search_result returned by a call to seqan3::search
Coutput_reference_begin_position	Include the reference_begin_position in the seqan3::search_result returned by a call to seqan3::search
Coutput_reference_id	Include the reference_id in the seqan3::search_result returned by a call to seqan3::search
►Nsimd	The SeqAn namespace for simd data types, algorithms and meta functions
Csimd_traits	Seqan3::simd::simd_traits is the trait class that provides uniform interface to the properties of simd_t types
Csimd_traits< builtin_simd_t >	This class specializes seqan3::simd::simd_traits for seqan3::detail::builtin_simd types
Csimd_type	Seqan3::simd::simd_type encapsulates simd vector types, which can be manipulated by simd operations
►Nviews	The SeqAn namespace for views
Cdeep	A wrapper type around an existing view adaptor that enables "deep view" behaviour for that view
Caa10li	The reduced Li amino acid alphabet
Caa10murphy	The reduced Murphy amino acid alphabet
Caa20	The canonical amino acid alphabet
Caa27	The twenty-seven letter amino acid alphabet
Cadvanceable_alignment_coordinate_printer
Cadvanceable_alignment_coordinate_printer< detail::advanceable_alignment_coordinate< state_t > >	The printer for seqan3::detail::advanceable_alignment_coordinate
►Calgorithm_result_generator_range	An input range over the algorithm results generated by the underlying algorithm executor
Calgorithm_range_iterator	The iterator of seqan3::detail::algorithm_result_generator_range
►Caligned_allocator	Allocates uninitialized storage whose memory-alignment is specified by alignment
Crebind	The aligned_allocator member template class aligned_allocator::rebind provides a way to obtain an allocator for a different type
Calignment_matrix_printer
Calignment_matrix_printer< alignment_matrix_t >	The printer for alignment scoring and trace matrices
Calignment_printer
Calignment_printer< alignment_t >	The printer for alignment
Calignment_result	Stores the alignment results and gives access to score, alignment and the front and end positions
Calignment_result_printer
Calignment_result_printer< alignment_result< result_value_t > >	The printer used for formatted output of the alignment result
Calphabet_base	A CRTP-base that makes defining a custom alphabet easier
Calphabet_printer
Calphabet_printer< alphabet_t >	The printer used for formatted output of seqan3::alphabet types
Calphabet_proxy	A CRTP-base that eases the definition of proxy types returned in place of regular alphabets
►Calphabet_tuple_base	The CRTP base for a combined alphabet that contains multiple values of different alphabets at the same time.
Ccomponent_proxy	Specialisation of seqan3::alphabet_proxy that updates the rank of the alphabet_tuple_base
Calphabet_variant	A combined alphabet that can hold values of either of its alternatives.
Caminoacid_base	A CRTP-base that refines seqan3::alphabet_base and is used by the amino acids
Caminoacid_empty_base	This is an empty base class that can be inherited by types that shall model seqan3::aminoacid_alphabet
Caminoacid_scoring_scheme	A data structure for managing and computing the score of two amino acids
Cargument_parser	The SeqAn command line parser
Cargument_parser_error	Argument parser exception that is thrown whenever there is an error while parsing the command line arguments
Cargument_parser_meta_data	Stores all parser related meta information of the seqan3::argument_parser
Carithmetic_range_validator	A validator that checks whether a number is inside a given range
Cbi_fm_index	The SeqAn Bidirectional FM Index
Cbi_fm_index_cursor	The SeqAn Bidirectional FM Index Cursor
Cbin_count	A strong type that represents the number of bins for the seqan3::interleaved_bloom_filter
Cbin_index	A strong type that represents the bin index for the seqan3::interleaved_bloom_filter
Cbin_literal	A strong type of underlying type uint64_t that represents the shape in binary representation
Cbin_size	A strong type that represents the number of bits for each bin in the seqan3::interleaved_bloom_filter
►Cbitpacked_sequence	A space-optimised version of std::vector that compresses multiple letters into a single byte
Creference_proxy_type	Proxy data type returned by seqan3::bitpacked_sequence as reference to element
Cbloom_filter	The Bloom Filter. A data structure that efficiently answers set-membership queries
Cchar_sequence_printer
Cchar_sequence_printer< char_sequence_t >	A printer for character sequences
Ccigar	The seqan3::cigar semialphabet pairs a counter with a seqan3::cigar::operation letter
Ccigar_clipped_bases	Helper struct to specialise soft and hard clipping when using seqan3::cigar_from_alignment
Ccigar_printer
Ccigar_printer< cigar >	The printer used for formatted output of the cigar alphabets
Cconcatenated_sequences	Container that stores sequences concatenated internally
Cconfiguration	Collection of elements to configure an algorithm
Ccounting_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
Cdebug_stream_printer
Cdebug_stream_printer< value_t >	A struct that provides a debug stream printer for a specific value type
Cdebug_stream_type	A "pretty printer" for most SeqAn data structures and related types
Cdefault_printer	The default printer that is used by seqan3::debug_stream
Cdesign_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)
Cdna15	The 15 letter DNA alphabet, containing all IUPAC smybols minus the gap
Cdna16sam	A 16 letter DNA alphabet, containing all IUPAC symbols minus the gap and plus an equality sign ('=')
Cdna3bs	The three letter reduced DNA alphabet for bisulfite sequencing mode (A,G,T(=C))
Cdna4	The four letter DNA alphabet of A,C,G,T
Cdna5	The five letter DNA alphabet of A,C,G,T and the unknown character N
Cdot_bracket3	The three letter RNA structure alphabet of the characters ".()"
Cdssp9	The protein structure alphabet of the characters "HGIEBTSCX"
►Cdynamic_bitset	A constexpr bitset implementation with dynamic size at compile time
Cbitfield	A bit field representing size and bit information stored in one uint64_t
Creference_proxy_type	Proxy data type returned by seqan3::dynamic_bitset as reference to the bit
Cdynamic_bitset_printer
Cdynamic_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.
Cenumeration_printer
Cenumeration_printer< enum_t >	A type (e.g. an enum) can be made debug streamable by customizing the seqan3::enumeration_names
Cfields	A class template that holds a choice of seqan3::field
Cfile_open_error	Thrown if there is an unspecified filesystem or stream error while opening, e.g. permission problem
Cfile_validator_base	An abstract base class for the file and directory validators
Cfm_index	The SeqAn FM Index
Cfm_index_cursor	The SeqAn FM Index Cursor
►Cformat_bam	The BAM format
Calignment_record_core	Stores all fixed length variables which can be read/written directly by reinterpreting the binary stream
Cformat_embl	The EMBL format
Cformat_error	Thrown if information given to output format didn't match expectations
Cformat_fasta	The FASTA format
Cformat_fastq	The FASTQ format
Cformat_genbank	The GenBank format
Cformat_sam	The SAM format (tag)
Cformat_vienna	The Vienna format (dot bracket notation) for RNA sequences with secondary structure
Cfunction_traits< std::function< return_t(args_t...)> >	A traits class to provide a uniform interface to the properties of a function type
Cgap	The alphabet of a gap character '-'
►Cgap_decorator	A gap decorator allows the annotation of sequences with gap symbols while leaving the underlying sequence unmodified
Cbasic_iterator	The iterator type over a seqan3::gap_decorator
Cgap_erase_failure	Thrown in function seqan3::erase_gap, if a position does not contain a gap
Chamming_scoring_scheme	A scoring scheme that assigns a score of 0 to matching letters and -1 to mismatching letters
Chash_function_count	A strong type that represents the number of hash functions for the seqan3::interleaved_bloom_filter
Cinput_directory_validator	A validator that checks if a given path is a valid input directory
Cinput_file_validator	A validator that checks if a given path is a valid input file
Cinput_range_printer
Cinput_range_printer< rng_t >	A printer for arbitrary input ranges
Cinteger_sequence_printer
Cinteger_sequence_printer< integer_sequence_t >	A printer for integer sequences
Cintegral_printer
Cintegral_printer< integral_t >	The printer for integral types
►Cinterleaved_bloom_filter	The IBF binning directory. A data structure that efficiently answers set-membership queries for multiple bins
Ccounting_agent_type	Manages counting ranges of values for the seqan3::interleaved_bloom_filter
►Cmembership_agent_type	Manages membership queries for the seqan3::interleaved_bloom_filter
Cbinning_bitvector	A bitvector representing the result of a call to bulk_contains of the seqan3::interleaved_bloom_filter
Cinvalid_alignment_configuration	Thrown if the configuration of the alignment algorithm is invalid
Cinvalid_char_assignment	An exception typically thrown by seqan3::alphabet::assign_char_strict
Cio_error	Thrown if there is an io error in low level io operations such as in std::basic_streambuf operations
Cis_constexpr_default_constructible	Whether a type std::is_default_constructible in constexpr-context (unary_type_trait specialisation)
Cmask	Implementation of a masked alphabet to be used for tuple composites
Cmask_printer
Cmask_printer< mask_t >	The printer used for formatted output of seqan3::mask alphabet
Cmasked	Implementation of a masked composite, which extends a given alphabet with a mask
Cmatch_score	A strong type of underlying type score_type that represents the score of two matching characters
Cmismatch_score	A strong type of underlying type score_type that represents the score two different characters
Cno_printer_found	A tag that indicates that no printer was found for the given type
Cnucleotide_base	A CRTP-base that refines seqan3::alphabet_base and is used by the nucleotides
Cnucleotide_scoring_scheme	A data structure for managing and computing the score of two nucleotides
Coption_declared_multiple_times	Argument parser exception thrown when a non-list option is declared multiple times
Coptional_printer
Coptional_printer< std::nullopt_t >	Printer for formatted output of std::nullopt_t
Coptional_printer< std::optional< T > >	Printer for formatted output of a std::optional
Coutput_directory_validator	A validator that checks if a given path is a valid output directory
Coutput_file_validator	A validator that checks if a given path is a valid output file
Cparse_error	Thrown if there is a parse error, such as reading an unexpected character from an input stream
Cphred42	Quality type for traditional Sanger and modern Illumina Phred scores
Cphred63	Quality type for traditional Sanger and modern Illumina Phred scores
Cphred68solexa	Quality type for Solexa and deprecated Illumina formats
Cphred94	Quality type for PacBio Phred scores of HiFi reads
Cphred_base	A CRTP-base that refines seqan3::alphabet_base and is used by the quality alphabets
Cpipeable_config_element	Adds pipe interface to configuration elements
Cpod_tuple
Cpod_tuple< type0 >	Recursion anchor for seqan3::pod_tuple
Cpod_tuple< type0, types... >	Behaves like std::tuple but is an aggregate PODType
Cprinter_order	The printer_order is a variadic template that defines the order of the printers
Cqualified	Joins an arbitrary alphabet with a quality alphabet
Crange_innermost_value	Recursively determines the value_type on containers and/or iterators
Crecord	The class template that file records are based on; behaves like a std::tuple
Cref_info_not_given	Type tag which indicates that no reference information has been passed to the SAM file on construction
Cregex_validator	A validator that checks if a matches a regular expression pattern
Cremove_rvalue_reference	Return the input type with && removed, but lvalue references preserved
Crequired_option_missing	Argument parser exception thrown when a required option is missing
Crna15	The 15 letter RNA alphabet, containing all IUPAC smybols minus the gap
Crna4	The four letter RNA alphabet of A,C,G,U
Crna5	The five letter RNA alphabet of A,C,G,U and the unknown character N
►Csam_file_header	Stores the header information of SAM/BAM files
Ckey_hasher	Custom hash function since std::hash is not defined for all range types (e.g. std::span<char>)
Csam_file_input	A class for reading SAM files, both SAM and its binary representation BAM are supported
Csam_file_input_default_traits	The default traits for seqan3::sam_file_input
Csam_file_input_format	The generic concept for alignment file input formats
Csam_file_input_options	The options type defines various option members that influence the behaviour of all or some formats
Csam_file_output	A class for writing SAM files, both SAM and its binary representation BAM are supported
Csam_file_output_format	The generic concept for alignment file out formats
Csam_file_output_options	The options type defines various option members that influence the behavior of all or some formats
Csam_file_program_info_t	Stores information of the program/tool that was used to create a SAM/BAM file
Csam_flag_printer
Csam_flag_printer< sam_flag >	A sam_flag can be printed as an integer value
Csam_record	The record type of seqan3::sam_file_input
Csam_tag_dictionary	The SAM tag dictionary class that stores all optional SAM fields
Csam_tag_type	The generic base class
Cscoring_scheme_base	A CRTP base class for scoring schemes
Csearch_result	The result class generated by the seqan3::seach algorithm
Csearch_result_printer
Csearch_result_printer< search_result< specs_t... > >	The printer used for formatted output of the search result
Cseed	Strong_type for seed
Csemialphabet_any	A semi-alphabet that type erases all other semi-alphabets of the same size
►Csequence_file_input	A class for reading sequence files, e.g. FASTA, FASTQ ..
Cselected_sequence_format	The specific selected format to read the records from
Csequence_format_base	An abstract base class to store the selected input format
Csequence_file_input_default_traits_aa	A traits type that specifies input as amino acids
Csequence_file_input_default_traits_dna	The default traits for seqan3::sequence_file_input
Csequence_file_input_format	The generic concept for sequence file in formats
Csequence_file_input_options	The options type defines various option members that influence the behaviour of all or some formats
Csequence_file_output	A class for writing sequence files, e.g. FASTA, FASTQ ..
Csequence_file_output_format	The generic concept for sequence file out formats
Csequence_file_output_options	The options type defines various option members that influence the behaviour of all or some formats
Csequence_printer
Csequence_printer< sequence_t >	A printer for (biological) sequences
Csequence_record	The record type of seqan3::sequence_file_input
Cshape	A class that defines which positions of a pattern to hash
Csimd_printer
Csimd_printer< simd_t >	Prints simd types
Csimd_traits	Seqan3::simd::simd_traits is the trait class that provides uniform interface to the properties of simd_t types
Csimd_traits< builtin_simd_t >	This class specializes seqan3::simd::simd_traits for seqan3::detail::builtin_simd types
Csimd_type	Seqan3::simd::simd_type encapsulates simd vector types, which can be manipulated by simd operations
Csmall_string	Implements a small string that can be used for compile time computations
Csmall_vector	A constexpr vector implementation with dynamic size at compile time
Cstd_byte_printer
Cstd_byte_printer< std::byte >	A std::byte can be printed by printing its value as integer
Cstd_printer
Cstd_printer< type_t >	The printer for standard output streams
Cstd_variant_printer
Cstd_variant_printer< std::variant< variant_ts... > >	A std::variant can be printed by visiting the stream operator for the corresponding type
Cstrong_type_printer
Cstrong_type_printer< strong_type_t >	A strong type can be printed by printing its underlying value
Cstructure_file_input	A class for reading structured sequence files, e.g. Stockholm, Connect, Vienna, ViennaRNA bpp matrix ..
Cstructure_file_input_default_traits_aa	A traits type that specifies input as amino acids
Cstructure_file_input_default_traits_rna	The default traits for seqan3::structure_file_input
Cstructure_file_input_format	The generic concept for structure file in formats
Cstructure_file_input_options	The options type defines various option members that influence the behaviour of all or some formats
Cstructure_file_output	A class for writing structured sequence files, e.g. Stockholm, Connect, Vienna, ViennaRNA bpp matrix ..
Cstructure_file_output_format	The generic concept for structure file out formats
Cstructure_file_output_options	The options type defines various option members that influence the behaviour of all or some formats
Cstructure_record	The record type of seqan3::structure_file_input
Cstructured_aa	A seqan3::alphabet_tuple_base that joins an aminoacid alphabet with a protein structure alphabet
Cstructured_rna	A seqan3::alphabet_tuple_base that joins a nucleotide alphabet with an RNA structure alphabet
Csuffix_array_interval	The underlying suffix array interval
Ctoo_few_arguments	Argument parser exception thrown when too few arguments are provided
Ctoo_many_arguments	Argument parser exception thrown when too many arguments are provided
Ctrace_directions_printer
Ctrace_directions_printer< detail::trace_directions >	Prints trace_directions as ascii or as utf8 to output stream
Ctuple_printer
Ctuple_printer< tuple_t >	Printer for formatted output of tuple like objects
Ctype_list	Type that contains multiple types
Cunexpected_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
Cungapped	A strong type of underlying type uint8_t that represents the ungapped shape size
Cunhandled_extension_error	Thrown if there is no format that accepts a given file extension
Cunknown_option	Argument parser exception thrown when encountering unknown option
Cuser_input_error	Argument parser exception thrown when an incorrect argument is given as (positional) option value
Cvalidation_error	Argument parser exception thrown when an argument could not be casted to the according type
Cvalue_list_validator	A validator that checks whether a value is inside a list of valid values
Cwindow_size	Strong_type for the window_size
Cwuss	The WUSS structure alphabet of the characters .<>:,-_~;()[]{}AaBbCcDd..
Rprintable_with
Rnonrecursive_range
►Nstd	SeqAn specific customisations in the standard namespace
Chash< alphabet_t >	Struct for hashing a character
Chash< seqan3::dynamic_bitset< cap > >	Struct for hashing a seqan3::dynamic_bitset
Chash< urng_t >	Struct for hashing a range of characters
Ctuple_element< elem_no, seqan3::record< field_types, field_ids > >	Obtains the type of the specified element
Ctuple_element< elem_no, seqan3::sam_record< field_types, field_ids > >	Obtains the type of the specified element
Ctuple_element< elem_no, seqan3::sequence_record< field_types, field_ids > >	Obtains the type of the specified element
Ctuple_element< elem_no, seqan3::structure_record< field_types, field_ids > >	Obtains the type of the specified element
Ctuple_element< i, t< types... > >	Obtains the type of the specified element
Ctuple_element< i, tuple_t >	Obtains the type of the specified element
Ctuple_element< pos, seqan3::configuration< configs_t... > >	Returns the type of the element at the specified position within seqan3::configuration
Ctuple_size< seqan3::configuration< configs_t... > >	Returns the number of elements stored in seqan3::configuration
Ctuple_size< seqan3::record< field_types, field_ids > >	Provides access to the number of elements in a tuple as a compile-time constant expression
Ctuple_size< seqan3::sam_record< field_types, field_ids > >	Provides access to the number of elements in a tuple as a compile-time constant expression
Ctuple_size< seqan3::sequence_record< field_types, field_ids > >	Provides access to the number of elements in a tuple as a compile-time constant expression
Ctuple_size< seqan3::structure_record< field_types, field_ids > >	Provides access to the number of elements in a tuple as a compile-time constant expression
Ctuple_size< t< types... > >	Provides access to the number of elements in a tuple as a compile-time constant expression
Ctuple_size< tuple_t >	Provides access to the number of elements in a tuple as a compile-time constant expression