|
struct | access_restrictor_fn |
| A functor that always throws when calling operator() (needed for the alignment "dummy" sequence). More...
|
|
class | adaptor_base |
| CRTP-base to simplify the definition of range adaptor closure objects and similar types. More...
|
|
class | adaptor_for_view_without_args |
| Template for range adaptor closure objects that store no arguments and always delegate to the view constructor. More...
|
|
class | adaptor_from_functor |
| Template for range adaptor closure objects that store arguments and wrap a proto-adaptor. More...
|
|
class | advanceable_alignment_coordinate |
| Implements an internal alignment coordinate that can be used as an argument to the std::ranges::iota_view. More...
|
|
class | affine_cell_proxy |
| A proxy for an affine score matrix cell. More...
|
|
class | affine_gap_init_policy |
| The CRTP-policy that implements the initialisation of the dynamic programming matrix with affine gaps. More...
|
|
class | affine_gap_policy |
| The CRTP-policy that computes a single cell in the alignment matrix. More...
|
|
class | algorithm_executor_blocking |
| A blocking algorithm executor for algorithms. More...
|
|
struct | align_result_selector |
| Helper metafunction to select the alignment result type based on the configuration. More...
|
|
class | aligned_sequence_builder |
| Builds the alignment for a given pair of sequences and the respective trace. More...
|
|
class | alignment_algorithm |
| The alignment algorithm type to compute standard pairwise alignment using dynamic programming. More...
|
|
struct | alignment_algorithm_state |
| Local state for the standard alignment algorithm. More...
|
|
struct | alignment_configuration_traits |
| A traits type for the alignment algorithm that exposes static information stored within the alignment configuration object. More...
|
|
struct | alignment_configurator |
| Configures the alignment algorithm given the sequences and the configuration object. More...
|
|
struct | alignment_contract |
| Provides several contracts to test when configuring the alignment algorithm. More...
|
|
struct | alignment_function_traits |
| A traits class to provide a uniform access to the properties of the wrapped alignment algorithm. More...
|
|
class | alignment_matrix_column_major_range_base |
| Provides a range interface for alignment matrices. More...
|
|
class | alignment_matrix_policy |
| Manages the alignment and score matrix. More...
|
|
struct | alignment_optimum |
| Stores the current optimum of the alignment algorithm. More...
|
|
struct | alignment_result_value_type |
| A struct that contains the actual alignment result data. More...
|
|
struct | alignment_result_value_type_accessor< alignment_result< result_value_t > > |
| Transformation trait to access the hidden result value type of the seqan3::alignment_result class. More...
|
|
class | alignment_score_matrix_one_column |
| An alignment score matrix storing only a single column for the computation. More...
|
|
class | alignment_score_matrix_one_column_banded |
| A banded alignment score matrix storing only a single banded column for the computation. More...
|
|
struct | alignment_score_matrix_one_column_base |
| A base class for alignment score matrices using only one column to compute the matrix. More...
|
|
struct | alignment_score_matrix_proxy |
| A proxy type for a unified access to the score matrix during alignment computation. More...
|
|
struct | alignment_trace_matrix_base |
| A crtp-base class for alignment traceback matrices. More...
|
|
class | alignment_trace_matrix_full |
| An alignment traceback matrix storing the entire traceback matrix. More...
|
|
class | alignment_trace_matrix_full_banded |
| An alignment traceback matrix storing the entire banded traceback matrix. More...
|
|
struct | alignment_trace_matrix_proxy |
| A proxy type for a unified access to the traceback matrix during alignment computation. More...
|
|
struct | as_const_fn |
| Function object for seqan3::views::as_const. More...
|
|
struct | assignable_from |
| 'Callable' helper class that is invokable by meta::invoke. Returns an std::true_type if the type is assignable from T . More...
|
|
struct | async_input_buffer_fn |
| Definition of the range adaptor object type for seqan3::views::async_input_buffer. More...
|
|
class | async_input_buffer_view |
| The type returned by seqan3::views::async_input_buffer. More...
|
|
class | basic_iterator |
| Forward declaration. More...
|
|
class | basic_iterator< single_pass_input_view< view_type > > |
| An input_iterator over the associated range. More...
|
|
struct | bgzf_compression |
| A tag signifying a bgzf compressed file. More...
|
|
struct | builtin_simd |
| A class that holds the type of a simd implementation called vector extension (formerly known as "seqan simd" in seqan2). More...
|
|
struct | builtin_simd< scalar_t, length > |
| A class that holds the type of a simd implementation called vector extension (formerly known as "seqan simd" in seqan2). More...
|
|
struct | builtin_simd_traits_helper |
| Helper struct for seqan3::detail::is_builtin_simd. More...
|
|
struct | builtin_simd_traits_helper< builtin_simd_t > |
| Helper struct for seqan3::detail::is_builtin_simd. More...
|
|
struct | bz2_compression |
| A tag signifying a bz2 compressed file. More...
|
|
struct | char_predicate_base |
| An abstract CRTP base class for parse conditions to add logical disjunction and negation operator. More...
|
|
struct | char_predicate_disjunction |
| Logical disjunction operator for parse conditions. More...
|
|
struct | char_predicate_negator |
| Logical not operator for a parse condition. More...
|
|
struct | chunked_indexed_sequence_pairs |
| A transformation trait to retrieve the chunked range over indexed sequence pairs. More...
|
|
struct | column_index_type |
| A strong type for designated initialisation of the column index of a matrix. More...
|
|
class | combined_adaptor |
| Template for range adaptor closure objects that consist of two other range adaptor closure objects. More...
|
|
class | combined_score_and_trace_matrix |
| An alignment matrix that combines a score matrix with a trace matrix into a common interface. More...
|
|
struct | concatenated_sequences_reference_proxy |
| The reference type of seqan3::concatenated_sequences. More...
|
|
struct | const_reference |
| This is helper structure to deprecate seqan3::const_reference and will be removed before SeqAn 3.1. More...
|
|
struct | const_reference< rng_t > |
| Exposes the const_reference of another type. More...
|
|
class | constexpr_pseudo_bitset |
| A data structure that implements a subset of std::bitset as constexpr. More...
|
|
struct | constructible_from |
| 'Callable' helper class that is invokable by meta::invoke. Returns an std::true_type if the type is constructable from T . More...
|
|
class | coordinate_matrix |
| A matrix over coordinates. More...
|
|
class | counted_simd_iterator |
| Implements a special version of a counted iterator over a simd vector. More...
|
|
class | debug_matrix |
| A debug matrix to wrap alignment matrices and sequences and make them printable together. More...
|
|
class | debug_mode |
| A global configuration type used to enabled debugging of algorithms. More...
|
|
struct | default_edit_distance_trait_type |
| The default traits type for the edit distance algorithm. More...
|
|
struct | default_validator |
| Validator that always returns true. More...
|
|
struct | deferred_crtp_base |
| An invocable wrapper that defers the instantiation of a crtp_base class. More...
|
|
struct | deferred_crtp_base_vargs |
| An invocable wrapper that defers the instantiation of a crtp_base class. More...
|
|
struct | deferred_type |
| Return the type identity; further arguments are ignored, but can make this type dependent if they are. More...
|
|
struct | difference_type |
| This is helper structure to deprecate seqan3::difference_type and will be removed before SeqAn 3.1. More...
|
|
struct | difference_type< it_t > |
| Exposes the difference_type of another type. More...
|
|
struct | difference_type< rng_t > |
| Exposes the difference_type of another type. More...
|
|
struct | drop_fn |
| View adaptor definition for views::drop and views::drop_or_throw. More...
|
|
class | edit_distance_algorithm |
| This algorithm unifies different edit distance implementations and uses the appropriate one depending on the given configuration. More...
|
|
class | edit_distance_score_matrix_full |
| The underlying data structure of seqan3::detail::edit_distance_unbanded that represents the score matrix. More...
|
|
class | edit_distance_trace_matrix_full |
| The underlying data structure of seqan3::detail::edit_distance_unbanded that represents the trace matrix. More...
|
|
class | edit_distance_unbanded |
| This calculates an alignment using the edit distance and without a band. More...
|
|
class | edit_distance_unbanded_global_policy |
| Only available when default_edit_distance_trait_type::is_global is true. More...
|
|
class | edit_distance_unbanded_max_errors_policy |
| Only available when default_edit_distance_trait_type::use_max_errors is true. More...
|
|
class | edit_distance_unbanded_score_matrix_policy |
| Only available when default_edit_distance_trait_type::compute_score_matrix is true. More...
|
|
class | edit_distance_unbanded_semi_global_policy |
| Only available when default_edit_distance_trait_type::is_semi_global is true. More...
|
|
class | edit_distance_unbanded_trace_matrix_policy |
| Only available when default_edit_distance_trait_type::compute_trace_matrix is true. More...
|
|
struct | empty_state |
| Store no state for state_t. More...
|
|
struct | empty_type |
| An empty class type used in meta programming. More...
|
|
class | execution_handler_parallel |
| Handles the parallel execution of algorithms. More...
|
|
struct | execution_handler_sequential |
| Handles the sequential execution of algorithms. More...
|
|
class | fast_istreambuf_iterator |
| Functionally the same as std::istreambuf_iterator, but faster. More...
|
|
class | fast_ostreambuf_iterator |
| Functionally the same as std::ostreambuf_iterator, but offers writing a range more efficiently. More...
|
|
class | find_optimum_policy |
| The CRTP-policy to determine the optimum of the dynamic programming matrix. More...
|
|
struct | fm_index_cursor_node |
| Internal representation of the node of an FM index cursor. More...
|
|
struct | fm_index_validator |
| Class used to validate the requirements on the input text of the fm_index. More...
|
|
class | format_base |
| The format that contains all helper functions needed in all formats. More...
|
|
class | format_copyright |
| The format that prints the copyright information to std::cout. More...
|
|
class | format_help |
| The format that prints the help page to std::cout. More...
|
|
class | format_help_base |
| The format that contains all helper functions needed in all formats for printing the interface description of the application (to std::cout). More...
|
|
class | format_html |
| The format that prints the help page as html to std::cout. More...
|
|
class | format_man |
| The format that prints the help page information formatted for a man page to std::cout. More...
|
|
class | format_parse |
| The format that organizes the actual parsing of command line arguments. More...
|
|
class | format_sam_base |
| The alignment base format. More...
|
|
class | format_short_help |
| The format that prints a short help message to std::cout. More...
|
|
class | format_version |
| The format that prints the version to std::cout. More...
|
|
struct | gz_compression |
| A tag signifying a gz compressed file. More...
|
|
class | ignore_output_iterator |
| An output iterator that emulates writing to a null -stream in order to dispose the output. More...
|
|
struct | implicitly_convertible_from |
| 'Callable' helper class that is invokable by meta::invoke. Returns an std::true_type if the T is implicitly convertible to type . More...
|
|
class | in_file_iterator |
| Input iterator necessary for providing a range-like interface in input file. More...
|
|
class | inherited_iterator_base |
| A CRTP base template for creating iterators that inherit from other iterators. More...
|
|
struct | instantiate |
| A transformation trait that instantiates seqan3::lazy types. Base template is the identity transformation. More...
|
|
struct | instantiate< lazy< template_t, spec_t... > > |
| A transformation trait that instantiates seqan3::lazy types. More...
|
|
struct | instantiate_if |
| A transformation trait that instantiates seqan3::lazy types given a boolean condition. Base template is std::false_type. More...
|
|
struct | instantiate_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. More...
|
|
struct | instantiate_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. More...
|
|
struct | interleave_fn |
| views::interleave's range adaptor object type (non-closure). More...
|
|
class | iota_simd_view |
| The simd iota view. More...
|
|
struct | iota_simd_view_fn |
| The view adaptor returning the seqan3::detail::iota_simd_view. More...
|
|
struct | is_basic_string |
| Returns whether basic_string_t is of type std::basic_string<value_t, traits_t, allocator_t> . More...
|
|
struct | is_basic_string< std::basic_string< value_t, traits_t, allocator_t > > |
| Returns whether basic_string_t is of type std::basic_string<value_t, traits_t, allocator_t> . More...
|
|
struct | is_builtin_simd |
| This class inherits from std::true_type, iff seqan3::detail::builtin_simd<scalar_t, length>::type is a builtin simd type. More...
|
|
struct | is_char_type |
| Parse condition that checks if a given value is equal to char_v . More...
|
|
struct | is_class_template_declarable_with |
| An unary type trait that tests whether a template class can be declared with the given template type parameters. More...
|
|
struct | is_configuration_valid |
| Checks if a given type is compatible with a list of other types. More...
|
|
struct | is_derived_from_record |
| Helper struct to implement seqan3::detail::record_like. More...
|
|
struct | is_in_alphabet_type |
| Parse condition that checks if a given value is within the given alphabet alphabet_t . More...
|
|
struct | is_in_interval_type |
| Parse condition that checks if a given value is in the range of rng_beg and interval_last . More...
|
|
struct | is_native_builtin_simd |
| This class inherits from std::true_type, iff the builtin simd type is supported by the current architecture. More...
|
|
struct | is_same_configuration_f |
| Helper meta function to check if a template type is contained in a seqan3::configuration. More...
|
|
struct | is_type_specialisation_of |
| Determines whether a source_type is a specialisation of another template. More...
|
|
struct | is_type_specialisation_of< source_t, target_template > |
| This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts. More...
|
|
struct | is_value_specialisation_of< source_t, target_template > |
| Determines whether a source_type is a specialisation of another template. More...
|
|
struct | istreambuf_fn |
| View adaptor/factory definition for views::istream. More...
|
|
struct | iter_pointer |
| This is like std::iter_value_t, but for the pointer type. More...
|
|
struct | kmer_hash_fn |
| views::kmer_hash's range adaptor object type (non-closure). More...
|
|
class | kmer_hash_view |
| The type returned by seqan3::views::kmer_hash. More...
|
|
class | latch |
| A single-use synchronisation point to coordinate concurrent threads. More...
|
|
struct | lazy |
| An empty type whose only purpose is to hold an uninstantiated template plus its arguments. More...
|
|
struct | lazy_conditional |
| Behaves like std::conditional, but instantiates types wrapped in seqan3::lazy. More...
|
|
struct | make_aligned_sequence_type |
| A transformation trait that returns the correct aligned sequence type for a given sequence type. More...
|
|
struct | make_pairwise_alignment_type |
| A transformation trait that returns the correct pairwise alignment type for two given sequence types. More...
|
|
struct | matrix_index |
| A representation of a location or offset within a two-dimensional matrix. More...
|
|
struct | max_score_banded_updater |
| A function object that compares and possibly updates the alignment optimum with the current cell. More...
|
|
struct | max_score_updater |
| A function object that compares and possibly updates the alignment optimum with the current cell. More...
|
|
struct | max_score_updater_simd_global |
| Function object that compares and updates the alignment optimum for the vectorised global alignment algorithm. More...
|
|
struct | minimiser_fn |
| views::minimiser's range adaptor object type (non-closure). More...
|
|
struct | minimiser_hash_fn |
| seqan3::views::minimiser_hash's range adaptor object type (non-closure). More...
|
|
class | minimiser_view |
| The type returned by seqan3::views::minimiser. More...
|
|
struct | models_strict_totally_ordered |
| Helper type trait function to check for std::totally_ordered on all elements of the given tuple type. More...
|
|
struct | multi_invocable |
| A type that can conveniently inherit multiple invocables and acts as a union over them. More...
|
|
struct | number_cols |
| Strong type for setting the column dimension of a matrix. More...
|
|
struct | number_rows |
| Strong type for setting the row dimension of a matrix. More...
|
|
class | out_file_iterator |
| Output iterator necessary for providing a range-like interface in output file. More...
|
|
class | pairwise_alignment_algorithm |
| The alignment algorithm type to compute standard pairwise alignment using dynamic programming. More...
|
|
class | pairwise_alignment_algorithm_banded |
| The alignment algorithm type to compute the banded standard pairwise alignment using dynamic programming. More...
|
|
class | pairwise_combine_view |
| Generates all pairwise combinations of the elements in the underlying range. More...
|
|
class | parallel_mode |
| A global configuration type used to enable parallel execution of algorithms. More...
|
|
class | persist_fn |
| [adaptor_def] More...
|
|
class | policy_affine_gap_recursion |
| Implements the alignment recursion function for the alignment algorithm using affine gap costs. More...
|
|
class | policy_affine_gap_recursion_banded |
| Implements the alignment recursion function for the banded alignment algorithm using affine gap costs. More...
|
|
class | policy_affine_gap_with_trace_recursion |
| Implements the alignment recursion function for the alignment algorithm using affine gap costs with trace information. More...
|
|
class | policy_affine_gap_with_trace_recursion_banded |
| Implements the alignment recursion function for the banded alignment algorithm using affine gap costs with trace information. More...
|
|
class | policy_alignment_matrix |
| A policy that provides a common interface to acquire the correct alignment matrices. More...
|
|
class | policy_alignment_result_builder |
| Implements the alignment result builder. More...
|
|
struct | policy_max_error |
| Provides the function max_error_counts if inherited by a search algorithm. More...
|
|
class | policy_optimum_tracker |
| Implements the tracker to store the global optimum for a particular alignment computation. More...
|
|
class | policy_optimum_tracker_simd |
| Implements the tracker to store the global optimum for a particular alignment computation. More...
|
|
class | policy_scoring_scheme |
| Stores the configured scoring scheme used for this algorithm. More...
|
|
struct | policy_search_result_builder |
| Provides the function make_results if inherited by a search algorithm. More...
|
|
struct | priority_tag |
| A tag that allows controlled overload resolution via implicit base conversion rules. More...
|
|
struct | priority_tag< 0 > |
| Recursion anchor for seqan3::detail::priority_tag. More...
|
|
class | proxy_reference |
| The same as value_t & but it is default constructible and is re-assignable. More...
|
|
struct | pseudo_random_access_fn |
| View adaptor definition for seqan3::views::enforce_random_access. More...
|
|
class | random_access_iterator |
| A generic random access iterator that delegates most operations to the range. More...
|
|
class | random_access_iterator_base |
| A CRTP base template for creating random access iterators. More...
|
|
struct | reader_count |
| A strong type to set the reader count of a seqan3::detail::reader_writer_manager. More...
|
|
class | reader_writer_manager |
| A single-use synchronisation point for closable concurrent data structures. More...
|
|
struct | recursive_required_types |
| Like seqan3::detail::required_types, but recursive. More...
|
|
struct | recursive_required_types< t > |
| Like seqan3::detail::required_types, but recursive. More...
|
|
struct | reference |
| This is helper structure to deprecate seqan3::reference and will be removed before SeqAn 3.1. More...
|
|
struct | reference< it_t > |
| Exposes the reference type of another type. More...
|
|
struct | reference< rng_t > |
| Exposes the reference of another type. More...
|
|
struct | repeat_fn |
| View factory definition for views::repeat. More...
|
|
struct | repeat_n_fn |
| The underlying type of seqan3::views::repeat_n. More...
|
|
class | repeat_view |
| The type returned by seqan3::views::repeat. More...
|
|
struct | required_types |
| A seqan3::type_list with types that the given type depends on. More...
|
|
struct | required_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]. More...
|
|
class | reverse_fm_index |
| An FM Index specialisation that handles reversing the given text. More...
|
|
struct | row_index_type |
| A strong type for designated initialisation of the row index of a matrix. More...
|
|
struct | rvalue_reference |
| This is helper structure to deprecate seqan3::rvalue_reference and will be removed before SeqAn 3.1. More...
|
|
struct | rvalue_reference< it_t > |
| Exposes the rvalue_reference type of another type. More...
|
|
struct | rvalue_reference< rng_t > |
| Exposes the rvalue_reference of another type. More...
|
|
class | safe_filesystem_entry |
| A safe guard to manage a filesystem entry, e.g. a file or a directory. More...
|
|
struct | sam_file_input_format_exposer |
| Internal class used to expose the actual format interface to read alignment records from the file. More...
|
|
struct | sam_file_output_format_exposer |
| Internal class used to expose the actual format interface to write alignment records into the file. More...
|
|
class | score_matrix_single_column |
| Score matrix for the pairwise alignment using only a single column. More...
|
|
class | scoring_scheme_policy |
| The CRTP-policy that stores the scoring scheme used for this alignment algorithm. More...
|
|
struct | search |
| Object storing information for a search (of a search scheme). More...
|
|
struct | search_configuration_validator |
| Class used to validate the search configuration. More...
|
|
class | search_configurator |
| Class used to update the search configuration, e.g. add defaults. More...
|
|
struct | search_dyn |
| Object storing information for a search (of a search scheme). More...
|
|
struct | search_param |
| Object grouping numbers of errors for different kind of error types. More...
|
|
class | search_scheme_algorithm |
| The algorithm that performs a bidirectional search on a bidirectional FM index using (optimal) search schemes. More...
|
|
struct | search_traits |
| A collection of traits extracted from the search configuration. More...
|
|
struct | select_types_with_ids |
| Exposes a subset of types as a seqan3::type_list selected based on their IDs. More...
|
|
struct | selector |
| The same as std::conditional but for template template parameters. More...
|
|
struct | sequence_file_input_format_exposer |
| Internal class used to expose the actual format interface to read sequence records from the file. More...
|
|
struct | sequence_file_output_format_exposer |
| Internal class used to expose the actual format interface to write sequence records into the file. More...
|
|
class | simd_affine_gap_policy |
| The CRTP-policy that computes a batch of cells in the alignment matrix using simd instructions. More...
|
|
class | simd_find_optimum_policy |
| The CRTP-policy to determine the optimum of the dynamic programming matrix. More...
|
|
struct | simd_global_alignment_state |
| A state that is only used for global alignments. More...
|
|
class | simd_match_mismatch_scoring_scheme |
| A vectorised scoring scheme handling matches and mismatches only. More...
|
|
class | simd_matrix_scoring_scheme |
| A vectorised scoring scheme to handle scoring matrices using gather strategy. More...
|
|
class | single_pass_input_view |
| Adds single_pass_input behavior to the underlying range. More...
|
|
struct | size_type |
| This is helper structure to deprecate seqan3::size_type and will be removed before SeqAn 3.1. More...
|
|
struct | size_type< it_t > |
| Exposes the size_type of another type. More...
|
|
struct | size_type< rng_t > |
| Exposes the size_type of another type. More...
|
|
struct | slice_fn |
| View adaptor definition for views::slice. More...
|
|
class | spin_delay |
| A delay for threads waiting for a shared resource. More...
|
|
struct | stream_buffer_exposer |
| Functionally the same as std::basic_streambuf<char_t, traits_t_>, but exposes protected members as public. More...
|
|
class | strong_type |
| CRTP base class to declare a strong typedef for a regular type to avoid ambiguous parameter settings in function calls. More...
|
|
struct | structure_file_input_format_exposer |
| Internal class used to expose the actual format interface to read structure records from the file. More...
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struct | structure_file_output_format_exposer |
| Internal class used to expose the actual format interface to write structure records into the file. More...
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struct | take_fn |
| View adaptor definition for views::take and views::take_or_throw. More...
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struct | take_until_fn |
| View adaptor definition for views::take_until and views::take_until_or_throw. More...
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struct | to_simd_fn |
| views::to_simd's range adaptor closure object type. More...
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class | trace_iterator |
| A trace iterator an unbanded trace matrix. More...
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class | trace_iterator_banded |
| A trace iterator for banded trace matrices. More...
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class | trace_iterator_base |
| A CRTP-base class for trace iterator implementations for the alignment algorithms. More...
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class | trace_matrix_full |
| Trace matrix for the pairwise alignment using the full trace matrix. More...
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struct | transfer_template_args_onto< source_template< source_arg_types... >, target_template > |
| Extracts a type template's type arguments and specialises another template with them. More...
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struct | transfer_template_vargs_onto< source_template< source_varg_types... >, target_template > |
| Extracts a type template's non-type arguments and specialises another template with them. More...
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struct | transfer_type_modifier_onto |
| Transfers the type modifier & , && and const (and any combination) to the target type. More...
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struct | translate_fn |
| Definition of the range adaptor object type for seqan3::views::translate and seqan3::views::translate_single. More...
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struct | translate_join_fn |
| Definition of the range adaptor object type for seqan3::views::translate_join. More...
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struct | translation_table |
| Generic translation table for canonical genetic code. More...
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struct | translation_table< dna15, seqan3::genetic_code::canonical, void_type > |
| Translation table for canonical genetic code and dna15 alphabet. More...
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struct | trim_fn |
| The underlying type of seqan3::views::trim_quality. More...
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struct | tuple_type_list |
| Transformation trait to expose the tuple element types as seqan3::type_list. More...
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class | two_dimensional_matrix |
| A two dimensional matrix used inside of alignment algorithms. More...
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class | two_dimensional_matrix_iterator_base |
| A crtp-base class for iterators over seqan3::detail::two_dimensional_matrix. More...
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struct | type_list_expander< type_list_t< args_t... > > |
| Helper class to invoke a meta algorithm on the types contained in a seqan3::type_list. More...
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class | type_reduce_fn |
| View adaptor definition for views::type_reduce. More...
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struct | unaligned_seq |
| Default transformation trait that shall expose the unaligned sequence type of t when specialised. More...
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struct | unaligned_seq< t > |
| Exposes the unaligned sequence type given an aligned sequence container type. More...
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class | unidirectional_search_algorithm |
| The algorithm that performs a unidirectional search on an FM index using trivial backtracking. More...
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struct | valid_template_spec_or |
| Exposes templ_t<spec_t...> if that is valid, otherwise fallback_t . More...
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struct | valid_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. More...
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class | validator_chain_adaptor |
| A helper struct to chain validators recursively via the pipe operator. More...
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struct | value_type |
| This is helper structure to deprecate seqan3::value_type and will be removed before SeqAn 3.1. More...
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struct | value_type< it_t > |
| Exposes the value_type of another type. More...
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struct | value_type< rng_t > |
| Exposes the value_type of another type. More...
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struct | variant_from_tags |
| Base class to deduce the std::variant type from format tags. More...
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struct | variant_from_tags< type_list< ts... >, output_t > |
| Transfers a list of format tags (...ts ) onto a std::variant by specialising output_t with each. More...
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class | version_checker |
| A functor whose operator() performs the server http request and version checks. More...
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class | view_enforce_random_access |
| View to force random access range iterator for seqan3::pseudo_random_access_range. More...
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struct | view_equality_fn |
| Comparator that is able two compare two views. More...
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class | view_interleave |
| The type returned by seqan3::views::interleave. More...
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class | view_persist |
| The type returned by seqan3::views::persist. More...
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class | view_take |
| The type returned by seqan3::views::take and seqan3::views::take_or_throw. More...
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class | view_take_until |
| The type returned by seqan3::views::take_until and seqan3::views::take_until_or_throw. More...
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class | view_to_simd |
| Transforms a range of ranges into chunks of seqan3::simd vectors. More...
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class | view_translate |
| The return type of seqan3::views::translate. More...
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class | view_translate_join |
| The return type of seqan3::views::translate_join. More...
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class | view_translate_single |
| The return type of seqan3::views::translate_single. More...
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struct | weakly_equality_comparable_with_ |
| 'Callable' helper class that is invokable by meta::invoke. Returns an std::true_type if the type is weakly equality comparable to T . More...
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struct | weakly_equality_comparable_with_trait |
| Binary type trait that behaves like the seqan3::detail::weakly_equality_comparable_with concept. More...
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struct | weakly_ordered_with_ |
| 'Callable' helper class that is invokable by meta::invoke. Returns an std::true_type if the type is comparable via <,<=,>,>= to T . More...
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struct | weakly_ordered_with_trait |
| Binary type trait that behaves like the seqan3::detail::weakly_ordered_with concept. More...
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struct | writer_count |
| A strong type to set the writer count of a seqan3::detail::reader_writer_manager. More...
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struct | zstd_compression |
| A tag signifying a zstd compressed file. More...
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using | compression_formats = pack_traits::drop_front< void > |
| A seqan3::type_list containing the available compression formats.
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template<typename t > |
using | const_reference_t = typename const_reference< t >::type |
| This is helper structure to deprecate seqan3::const_reference_t and will be removed before SeqAn 3.1.
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template<typename scalar_t , size_t length> |
using | default_simd_backend = builtin_simd< scalar_t, length > |
| seqan3::detail::default_simd_backend is the default used implementation of seqan3::simd::simd_type. More...
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template<typename t , typename ... dependent_ts> |
using | deferred_type_t = typename deferred_type< t, dependent_ts... >::type |
| Return the type identity; further arguments are ignored, but can make this type dependent if they are (transformation_trait shortcut). More...
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template<typename t > |
using | difference_type_t = typename difference_type< t >::type |
| This is helper structure to deprecate seqan3::difference_type_t and will be removed before SeqAn 3.1.
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template<bool enable_policy, template< typename ... > typename policy_t, typename edit_traits , typename derived_t > |
using | edit_distance_base = invoke_deferred_crtp_base< deferred_crtp_base< selector< enable_policy, policy_t, empty_state >::template select, edit_traits >, derived_t > |
| A base class for edit_distance_unbanded.
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template<bool enabled, typename state_t > |
using | enable_state_t = std::conditional_t< enabled, state_t, empty_state< state_t > > |
| If enabled is true state_t will be added to state_type.
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using | ignore_t = std::remove_cvref_t< decltype(std::ignore)> |
| Return the type of std::ignore with const , volatile and references removed (type trait).
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template<typename deferred_crtp_base_t , typename derived_t > |
using | invoke_deferred_crtp_base = typename deferred_crtp_base_t::template invoke< derived_t > |
| Template alias to instantiate the deferred crtp base with the derived class. More...
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template<typename it_t > |
using | iter_pointer_t = typename iter_pointer< it_t >::type |
| Return the pointer type of the input type (transformation_trait shortcut). More...
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template<typename it_t > |
using | iterator_category_tag_t = typename std::iterator_traits< it_t >::iterator_category |
| Exposes the iterator_category from the modelled concept. More...
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template<typename it_t > |
using | iterator_concept_tag_t = std::conditional_t< std::contiguous_iterator< it_t >, std::contiguous_iterator_tag, std::conditional_t< std::random_access_iterator< it_t >, std::random_access_iterator_tag, std::conditional_t< std::bidirectional_iterator< it_t >, std::bidirectional_iterator_tag, std::conditional_t< std::forward_iterator< it_t >, std::forward_iterator_tag, std::conditional_t< std::input_iterator< it_t >, std::input_iterator_tag, std::output_iterator_tag > >> >> |
| Exposes the iterator_concept from the modelled concept. More...
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using | matrix_offset = matrix_index< std::ptrdiff_t > |
| An offset type to move a matrix iterator in two-dimensional space.
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template<bool const_range, typename range_t > |
using | maybe_const_iterator_t = std::ranges::iterator_t< maybe_const_range_t< const_range, range_t > > |
| Returns the const iterator of range_t if const_range is true; otherwise the non-const iterator.
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template<bool const_range, typename range_t > |
using | maybe_const_range_t = std::conditional_t< const_range, range_t const, range_t > |
| Makes range_t const if const_range is true; otherwise keeps range_t as is.
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template<bool const_v, typename range_t > |
using | maybe_const_sentinel_t = std::ranges::sentinel_t< maybe_const_range_t< const_v, range_t > > |
| Returns the const sentinel of range_t if const_range is true; otherwise the non-const sentinel.
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template<uint64_t value> |
using | min_viable_uint_t = std::conditional_t< value<=1ull, bool, std::conditional_t< value<=255ull, uint8_t, std::conditional_t< value<=65535ull, uint16_t, std::conditional_t< value<=4294967295ull, uint32_t, uint64_t > >> > |
| Given a value, return the smallest unsigned integer that can hold it.
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template<typename t > |
using | reference_t = typename reference< t >::type |
| This is helper structure to deprecate seqan3::reference_t and will be removed before SeqAn 3.1.
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template<typename value_t > |
using | row_wise_matrix = two_dimensional_matrix< value_t > |
| A matrix represented in a one-dimensional std::vector accessing the data in row-major-order. More...
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template<typename t > |
using | rvalue_reference_t = typename rvalue_reference< t >::type |
| This is helper structure to deprecate seqan3::rvalue_reference_t and will be removed before SeqAn 3.1.
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using | sam_tag_variant = std::variant< char, int32_t, float, std::string, std::vector< std::byte >, std::vector< int8_t >, std::vector< uint8_t >, std::vector< int16_t >, std::vector< uint16_t >, std::vector< int32_t >, std::vector< uint32_t >, std::vector< float > > |
| std::variant of allowed types for optional tag fields of the SAM format.
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using | search_scheme_dyn_type = std::vector< search_dyn > |
| Type for storing search schemes. Number of blocks do not have to be known at compile time.
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template<uint8_t nbr_searches, uint8_t nbr_blocks> |
using | search_scheme_type = std::array< search< nbr_blocks >, nbr_searches > |
| Type for storing search schemes. Number of blocks have to be known at compile time.
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template<simd_index index_t> |
using | simd_matrix_coordinate = matrix_index< index_t > |
| A coordinate type to access an element inside of a two-dimensional simd vector matrix. More...
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template<typename t > |
using | size_type_t = typename size_type< t >::type |
| This is helper structure to deprecate seqan3::size_type_t and will be removed before SeqAn 3.1.
|
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template<typename type > |
using | strip_cereal_wrapper_t = type |
| Removes type-mangling that Cereal does with certain types on loading. More...
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template<typename t > |
using | strip_type_identity_t = std::conditional_t< is_type_specialisation_of_v< t, std::type_identity >, transformation_trait_or_t< t, void >, t > |
| A transformation trait shortcut that returns the type inside a std::type_identity or the type itself. More...
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|
template<typename source_type , template< typename ... > typename target_template> |
using | transfer_template_args_onto_t = typename transfer_template_args_onto< source_type, target_template >::type |
| Shortcut for seqan3::detail::transfer_template_args_onto (transformation_trait shortcut). More...
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|
template<typename source_type , template< auto ... > typename target_template> |
using | transfer_template_vargs_onto_t = typename transfer_template_vargs_onto< source_type, target_template >::type |
| Shortcut for seqan3::detail::transfer_template_vargs_onto (transformation_trait shortcut). More...
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|
template<typename type_t , typename default_t > |
using | transformation_trait_or = std::conditional_t< transformation_trait< type_t >, type_t, std::type_identity< default_t > > |
| This gives a fallback type if type_t::type is not defined. More...
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|
template<typename type_t , typename default_t > |
using | transformation_trait_or_t = typename transformation_trait_or< type_t, default_t >::type |
| Helper type of seqan3::detail::transformation_trait_or (transformation_trait shortcut). More...
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template<detail::tuple_size tuple_t> |
using | tuple_type_list_t = typename tuple_type_list< tuple_t >::type |
| Helper type for seqan3::detail::tuple_type_list. More...
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|
template<typename t > |
using | unaligned_seq_t = typename unaligned_seq< t >::type |
| Helper type that delegates to seqan3::detail::unaligned_seq::type.
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|
template<typename fallback_t , template< typename ... > typename templ_t, typename ... spec_t> |
using | valid_template_spec_or_t = typename valid_template_spec_or< fallback_t, templ_t, spec_t... >::type |
| Helper for seqan3::detail::valid_template_spec_or (transformation_trait shortcut). More...
|
|
template<typename t > |
using | value_type_t = typename value_type< t >::type |
| This is helper structure to deprecate seqan3::value_type_t and will be removed before SeqAn 3.1.
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template<seqan3::detail::writable_pairwise_alignment alignment_type> |
void | alignment_from_cigar (alignment_type &alignment, std::vector< cigar > const &cigar_vector) |
| Transforms a std::vector of operation-count pairs (representing the cigar string). More...
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|
template<typename type_list_t , typename unary_predicate_t > |
constexpr bool | all_of (unary_predicate_t &&fn) |
| Tests whether a given predicate evaluates to true for each type in a seqan3::type_list. More...
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|
template<typename unary_predicate_t , typename ... pack_t> |
constexpr bool | all_of (unary_predicate_t &&fn, pack_t &&...args) |
| Tests whether a given predicate evaluates to true for each element in the function parameter pack. More...
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|
template<typename structure_alph_type , typename bpp_type , std::ranges::range structure_type> |
void | bpp_from_rna_structure (bpp_type &bpp, structure_type const &structure, double weight=1.) |
| Transforms a structure annotation string into a base pair probability matrix. More...
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|
void | call_server (std::string const &command, std::promise< bool > prom) |
| Writes a timestamp file and performs the server call to get the newest version information. More...
|
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template<std::unsigned_integral unsigned_t> |
constexpr unsigned_t | ceil_log2 (unsigned_t const n) noexcept |
| Computes the ceil of the logarithm to the base of two for unsigned integers. More...
|
|
std::vector< search_dyn > | compute_ss (uint8_t const min_error, uint8_t const max_error) |
| Computes a (non-optimal) search scheme. Currently the generated search scheme represents trivial backtracking. More...
|
|
template<std::ranges::input_range rng_t> |
constexpr void | consume (rng_t &&rng) |
| Iterate over a range (consumes single-pass input ranges). More...
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|
template<uint8_t index, simd::simd_concept simd_t> |
constexpr simd_t | extract_eighth (simd_t const &src) |
| Extracts one eighth of the given simd vector and stores it in the lower eighth of the target vector. More...
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template<uint8_t index, simd::simd_concept simd_t> |
constexpr simd_t | extract_eighth_avx2 (simd_t const &src) |
| Extracts one eighth of the given simd vector and stores it in the lower eighth of the target vector. More...
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|
template<uint8_t index, simd::simd_concept simd_t> |
constexpr simd_t | extract_eighth_avx512 (simd_t const &src) |
| Extracts one eighth of the given simd vector and stores it in the lower eighth of the target vector. More...
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|
template<uint8_t index, simd::simd_concept simd_t> |
constexpr simd_t | extract_eighth_sse4 (simd_t const &src) |
| Extracts one eighth of the given simd vector and stores it in the lower eighth of the target vector. More...
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|
template<uint8_t index, simd::simd_concept simd_t> |
constexpr simd_t | extract_half (simd_t const &src) |
| Extracts one half of the given simd vector and stores the result in the lower half of the target vector. More...
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|
template<uint8_t index, simd::simd_concept simd_t> |
constexpr simd_t | extract_half_avx2 (simd_t const &src) |
| Extracts one half of the given simd vector and stores the result in the lower half of the target vector. More...
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|
template<uint8_t index, simd::simd_concept simd_t> |
constexpr simd_t | extract_half_avx512 (simd_t const &src) |
| Extracts one half of the given simd vector and stores the result in the lower half of the target vector. More...
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|
template<uint8_t index, simd::simd_concept simd_t> |
constexpr simd_t | extract_half_sse4 (simd_t const &src) |
| Extracts one half of the given simd vector and stores the result in the lower half of the target vector. More...
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|
template<size_t divisor, simd_concept simd_t> |
constexpr simd_t | extract_impl (simd_t const &src, uint8_t const mask) |
| Helper function to extract a part of the given simd vector. More...
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|
template<uint8_t index, simd::simd_concept simd_t> |
constexpr simd_t | extract_quarter (simd_t const &src) |
| Extracts one quarter of the given simd vector and stores it in the lower quarter of the target vector. More...
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|
template<uint8_t index, simd::simd_concept simd_t> |
constexpr simd_t | extract_quarter_avx2 (simd_t const &src) |
| Extracts one quarter of the given simd vector and stores it in the lower quarter of the target vector. More...
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|
template<uint8_t index, simd::simd_concept simd_t> |
constexpr simd_t | extract_quarter_avx512 (simd_t const &src) |
| Extracts one quarter of the given simd vector and stores it in the lower quarter of the target vector. More...
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|
template<uint8_t index, simd::simd_concept simd_t> |
constexpr simd_t | extract_quarter_sse4 (simd_t const &src) |
| Extracts one quarter of the given simd vector and stores it in the lower quarter of the target vector. More...
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|
template<simd::simd_concept simd_t, size_t... I> |
constexpr simd_t | fill_impl (typename simd_traits< simd_t >::scalar_type const scalar, std::index_sequence< I... >) noexcept |
| Helper function for seqan3::simd::fill.
|
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template<std::unsigned_integral unsigned_t> |
constexpr unsigned_t | floor_log2 (unsigned_t const n) noexcept |
| Computes the floor of the logarithm to the base of two for unsigned integers. More...
|
|
template<typename type_list_t , typename unary_function_t > |
constexpr void | for_each (unary_function_t &&fn) |
| Applies a function element wise to all types of a type list. More...
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|
template<typename unary_function_t , typename ... pack_t> |
constexpr void | for_each (unary_function_t &&fn, pack_t &&...args) |
| Applies a function to each element of the given function parameter pack. More...
|
|
template<seqan3::detail::pairwise_alignment alignment_type> |
std::string | get_cigar_string (alignment_type &&alignment, uint32_t const query_start_pos=0, uint32_t const query_end_pos=0, bool const extended_cigar=false) |
| Creates a cigar string (SAM format) given a seqan3::detail::pairwise_alignment. More...
|
|
template<seqan3::aligned_sequence ref_seq_type, seqan3::aligned_sequence query_seq_type> |
std::string | get_cigar_string (ref_seq_type &&ref_seq, query_seq_type &&query_seq, uint32_t const query_start_pos=0, uint32_t const query_end_pos=0, bool const extended_cigar=false) |
| Transforms an alignment represented by two seqan3::aligned_sequence's into the corresponding cigar string. More...
|
|
std::string | get_cigar_string (std::vector< cigar > const &cigar_vector) |
| Transforms a vector of cigar elements into a string representation. More...
|
|
template<seqan3::detail::pairwise_alignment alignment_type> |
std::vector< cigar > | get_cigar_vector (alignment_type &&alignment, uint32_t const query_start_pos=0, uint32_t const query_end_pos=0, bool const extended_cigar=false) |
| Creates a cigar string (SAM format) given a seqan3::detail::pairwise_alignment represented by two seqan3::aligned_sequence's. More...
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|
template<field f, typename field_types , typename field_ids , typename or_type > |
decltype(auto) | get_or (record< field_types, field_ids > &r, or_type &&or_value) |
| Access an element in a std::tuple or seqan3::record; return or_value if not contained.
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template<field f, typename field_types , typename field_ids , typename or_type > |
decltype(auto) | get_or (record< field_types, field_ids > const &r, or_type &&or_value) |
| Access an element in a std::tuple or seqan3::record; return or_value if not contained. More...
|
|
template<size_t i, typename or_type , typename ... types> |
decltype(auto) | get_or (std::tuple< types... > &t, or_type &&or_value) |
| Access an element in a std::tuple or seqan3::record; return or_value if not contained. More...
|
|
template<size_t i, typename or_type , typename ... types> |
decltype(auto) | get_or (std::tuple< types... > const &t, or_type &&or_value) |
| Access an element in a std::tuple or seqan3::record; return or_value if not contained. More...
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|
template<field f, typename field_types , typename field_ids > |
auto & | get_or_ignore (record< field_types, field_ids > &r) |
| Access an element in a std::tuple or seqan3::record; return reference to std::ignore if not contained.
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template<field f, typename field_types , typename field_ids > |
auto const & | get_or_ignore (record< field_types, field_ids > const &r) |
| Access an element in a std::tuple or seqan3::record; return reference to std::ignore if not contained. More...
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|
template<size_t i, tuple_like tuple_t> |
auto & | get_or_ignore (tuple_t &t) |
| Access an element in a std::tuple or seqan3::record; return reference to std::ignore if not contained. More...
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|
template<size_t i, tuple_like tuple_t> |
auto const & | get_or_ignore (tuple_t const &t) |
| Access an element in a std::tuple or seqan3::record; return reference to std::ignore if not contained. More...
|
|
unsigned | get_terminal_width () |
| Retrieve size of terminal. More...
|
|
template<simd::simd_concept simd_t, typename scalar_t , scalar_t... I> |
constexpr simd_t | iota_impl (scalar_t const offset, std::integer_sequence< scalar_t, I... >) |
| Helper function for seqan3::simd::iota.
|
|
bool | is_terminal () |
| Check whether we are printing to a terminal. More...
|
|
template<std::ranges::viewable_range rng_t> |
| kmer_hash_view (rng_t &&, shape const &shape_) -> kmer_hash_view< std::views::all_t< rng_t >> |
| A deduction guide for the view class template.
|
|
template<simd::simd_concept simd_t> |
constexpr simd_t | load_avx2 (void const *mem_addr) |
| Load simd_t size bits of integral data from memory. More...
|
|
template<simd::simd_concept simd_t> |
constexpr simd_t | load_avx512 (void const *mem_addr) |
| Load simd_t size bits of integral data from memory. More...
|
|
template<simd::simd_concept simd_t> |
constexpr simd_t | load_sse4 (void const *mem_addr) |
| Load simd_t size bits of integral data from memory. More...
|
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std::string | make_printable (char const c) |
| Returns a printable value for the given character c . More...
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template<builtin_character char_t> |
auto | make_secondary_istream (std::basic_istream< char_t > &primary_stream) |
| This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
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template<builtin_character char_t> |
auto | make_secondary_istream (std::basic_istream< char_t > &primary_stream, std::filesystem::path &filename) -> std::unique_ptr< std::basic_istream< char_t >, std::function< void(std::basic_istream< char_t > *)>> |
| Depending on the magic bytes of the given stream, return a decompression stream or forward the primary stream. More...
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template<builtin_character char_t> |
auto | make_secondary_ostream (std::basic_ostream< char_t > &primary_stream, std::filesystem::path &filename) -> std::unique_ptr< std::basic_ostream< char_t >, std::function< void(std::basic_ostream< char_t > *)>> |
| Depending on the given filename/extension, create a compression stream or just forward the primary stream. More...
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template<typename reference_char_type , typename query_char_type > |
constexpr cigar::operation | map_aligned_values_to_cigar_op (reference_char_type const reference_char, query_char_type const query_char, bool const extended_cigar) |
| Compares two seqan3::aligned_sequence values and returns their cigar operation. More...
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template<std::ranges::viewable_range rng1_t, std::ranges::viewable_range rng2_t> |
| minimiser_view (rng1_t &&, rng2_t &&, size_t const window_size) -> minimiser_view< std::views::all_t< rng1_t >, std::views::all_t< rng2_t >> |
| A deduction guide for the view class template.
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template<std::ranges::viewable_range rng1_t> |
| minimiser_view (rng1_t &&, size_t const window_size) -> minimiser_view< std::views::all_t< rng1_t >> |
| A deduction guide for the view class template.
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template<typename ... invocable_ts> |
| multi_invocable (invocable_ts...) -> multi_invocable< invocable_ts... > |
| Deduction guides for seqan3::detail::multi_invocable.
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template<typename char_t , typename tuple_t , std::size_t ... I> |
void | print_tuple (debug_stream_type< char_t > &s, tuple_t &&t, std::index_sequence< I... > const &) |
| Helper function to print elements of a tuple separately.
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auto | range_wrap_ignore (ignore_t const &) |
| If the argument is std::ignore, return an infinite range of std::ignore values. More...
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template<std::ranges::input_range rng_t> |
auto & | range_wrap_ignore (rng_t &range) |
| Pass through the reference to the argument in case the argument satisfies std::ranges::input_range.
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template<template< typename ... > typename container_type, template< typename ... > typename allocator_type, typename seq_alph_t , typename ... rest_t> |
constexpr auto | remove_gap_from_value_type (container_type< gapped< seq_alph_t >, allocator_type< gapped< seq_alph_t >>, rest_t... >) -> container_type< seq_alph_t, allocator_type< seq_alph_t >, rest_t... > |
| This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.
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template<template< typename ... > typename container_type, typename seq_alph_t , typename ... rest_t> |
constexpr auto | remove_gap_from_value_type (container_type< gapped< seq_alph_t >, rest_t... >) -> container_type< seq_alph_t, rest_t... > |
| Helper function to deduce the unaligned sequence type from an aligned sequence container.
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template<typename search_scheme_t > |
auto | search_scheme_block_info (search_scheme_t const &search_scheme, size_t const query_length) |
| Returns for each search the cumulative length of blocks in the order of blocks in each search and the starting position of the first block in the query sequence. More...
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template<bool abort_on_hit, typename cursor_t , typename query_t , typename search_t , typename blocks_length_t , typename delegate_t > |
bool | search_ss (cursor_t cur, query_t &query, typename cursor_t::size_type const lb, typename cursor_t::size_type const rb, uint8_t const errors_spent, uint8_t const block_id, bool const go_right, search_t const &search, blocks_length_t const &blocks_length, search_param const error_left, delegate_t &&delegate) |
| Searches a query sequence in a bidirectional index using a single search of a search schemes. More...
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template<bool abort_on_hit, typename index_t , typename query_t , typename search_scheme_t , typename delegate_t > |
void | search_ss (index_t const &index, query_t &query, search_param const error_left, search_scheme_t const &search_scheme, delegate_t &&delegate) |
| Searches a query sequence in a bidirectional index using search schemes. More...
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template<bool abort_on_hit, typename cursor_t , typename query_t , typename search_t , typename blocks_length_t , typename delegate_t > |
bool | search_ss_children (cursor_t cur, query_t &query, typename cursor_t::size_type const lb, typename cursor_t::size_type const rb, uint8_t const errors_spent, uint8_t const block_id, bool const go_right, uint8_t const min_error_left_in_block, search_t const &search, blocks_length_t const &blocks_length, search_param const error_left, delegate_t &&delegate) |
| Searches a query sequence in a bidirectional index using a single search of a search schemes. Sub-function for approximate search step (iterating over all children in a conceptual suffix tree). More...
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template<bool abort_on_hit, typename cursor_t , typename query_t , typename search_t , typename blocks_length_t , typename delegate_t > |
bool | search_ss_deletion (cursor_t cur, query_t &query, typename cursor_t::size_type const lb, typename cursor_t::size_type const rb, uint8_t const errors_spent, uint8_t const block_id, bool const go_right, search_t const &search, blocks_length_t const &blocks_length, search_param const error_left, delegate_t &&delegate) |
| Searches a query sequence in a bidirectional index using a single search of a search schemes. Sub-function for deletions at the end of a block. More...
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template<bool abort_on_hit, typename cursor_t , typename query_t , typename search_t , typename blocks_length_t , typename delegate_t > |
bool | search_ss_exact (cursor_t cur, query_t &query, typename cursor_t::size_type const lb, typename cursor_t::size_type const rb, uint8_t const errors_spent, uint8_t const block_id, bool const go_right, search_t const &search, blocks_length_t const &blocks_length, search_param const error_left, delegate_t &&delegate) |
| Searches a query sequence in a bidirectional index using a single search of a search scheme. Sub-function for searching the remaining part of the current block without any errors. More...
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template<typename format_variant_type > |
void | set_format (format_variant_type &format, std::filesystem::path const &file_name) |
| Sets the file format according to the file name extension. More...
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template<std::ranges::forward_range ref_t, std::ranges::forward_range query_t> |
bool | starts_with (ref_t &&reference, query_t &&query) |
| Check whether the query range is a prefix of the reference range. More...
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template<typename char_t , tuple_like alignment_t, size_t ... idx> |
void | stream_alignment (debug_stream_type< char_t > &stream, alignment_t const &align, std::index_sequence< idx... > const &) |
| Create the formatted alignment output and add it to the provided debug_stream. More...
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template<std::integral type> |
constexpr type | to_little_endian (type const in) noexcept |
| Convert the byte encoding of integer values to little-endian byte order. More...
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template<typename ... value_type> |
std::string | to_string (value_type &&...values) |
| Streams all parameters via the seqan3::debug_stream and returns a concatenated string. More...
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template<simd::simd_concept simd_t> |
void | transpose_matrix_avx2 (std::array< simd_t, simd_traits< simd_t >::length > &matrix) |
| Transposes the given simd vector matrix. More...
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template<simd::simd_concept simd_t> |
void | transpose_matrix_avx512 (std::array< simd_t, simd_traits< simd_t >::length > &matrix) |
| Transposes the given simd vector matrix. More...
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template<simd::simd_concept simd_t> |
void | transpose_matrix_sse4 (std::array< simd_t, simd_traits< simd_t >::length > &matrix) |
| Transposes the given simd vector matrix. More...
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template<size_t beg, template< typename ... > typename tuple_t, size_t ... Is, typename ... ts> |
constexpr auto | tuple_split (tuple_t< ts... > &&t, std::index_sequence< Is... > const &idx) |
| Helper function for seqan3::tuple_split. More...
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template<size_t beg, template< typename ... > typename tuple_t, size_t ... Is, typename ... ts> |
constexpr auto | tuple_split (tuple_t< ts... > const &t, std::index_sequence< Is... > const &idx) |
| Helper function for seqan3::tuple_split. More...
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template<simd::simd_concept target_simd_t, simd::simd_concept source_simd_t> |
constexpr target_simd_t | upcast_signed (source_simd_t const &src) |
| Upcasts the given vector into the target vector using signed extension of packed values. More...
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template<simd::simd_concept target_simd_t, simd::simd_concept source_simd_t> |
constexpr target_simd_t | upcast_signed_avx2 (source_simd_t const &src) |
| Upcasts the given vector into the target vector using signed extension of packed values. More...
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template<simd::simd_concept target_simd_t, simd::simd_concept source_simd_t> |
constexpr target_simd_t | upcast_signed_avx512 (source_simd_t const &src) |
| Upcasts the given vector into the target vector using signed extension of packed values. More...
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template<simd::simd_concept target_simd_t, simd::simd_concept source_simd_t> |
constexpr target_simd_t | upcast_signed_sse4 (source_simd_t const &src) |
| Upcasts the given vector into the target vector using signed extension of packed values. More...
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template<simd::simd_concept target_simd_t, simd::simd_concept source_simd_t> |
constexpr target_simd_t | upcast_unsigned (source_simd_t const &src) |
| Upcasts the given vector into the target vector using unsigned extension of packed values. More...
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template<simd::simd_concept target_simd_t, simd::simd_concept source_simd_t> |
constexpr target_simd_t | upcast_unsigned_avx2 (source_simd_t const &src) |
| Upcasts the given vector into the target vector using unsigned extension of packed values. More...
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template<simd::simd_concept target_simd_t, simd::simd_concept source_simd_t> |
constexpr target_simd_t | upcast_unsigned_avx512 (source_simd_t const &src) |
| Upcasts the given vector into the target vector using unsigned extension of packed values. More...
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template<simd::simd_concept target_simd_t, simd::simd_concept source_simd_t> |
constexpr target_simd_t | upcast_unsigned_sse4 (source_simd_t const &src) |
| Upcasts the given vector into the target vector using unsigned extension of packed values. More...
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template<typename formats_t > |
std::vector< std::string > | valid_file_extensions () |
| Returns a list of valid file extensions. More...
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template<typename urng_t > |
| view_translate (urng_t &&, translation_frames const =translation_frames{}) -> view_translate< std::views::all_t< urng_t >> |
| Class template argument deduction for view_translate.
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template<typename urng_t > |
| view_translate_join (urng_t &&, translation_frames const =translation_frames{}) -> view_translate_join< std::views::all_t< urng_t >> |
| Class template argument deduction for view_translate_join.
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template<typename urng_t > |
| view_translate_single (urng_t &&) -> view_translate_single< std::views::all_t< urng_t >> |
| Class template argument deduction for view_translate_single with default translation_frames.
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template<typename urng_t > |
| view_translate_single (urng_t &&, translation_frames const) -> view_translate_single< std::views::all_t< urng_t >> |
| Class template argument deduction for view_translate_single.
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template<std::output_iterator< char > it_t> |
constexpr void | write_eol (it_t &it, bool const add_cr) |
| Write "\n" or "\r\n" to the stream iterator, depending on arguments. More...
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| alignment_result_value_type () -> alignment_result_value_type< std::nullopt_t *, std::nullopt_t *, std::nullopt_t * > |
| Type deduction for an empty object. It will always fail the compilation, if any field is accessed.
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template<typename sequence1_id_t , typename sequence2_id_t , typename score_t > |
| alignment_result_value_type (sequence1_id_t, sequence2_id_t, score_t) -> alignment_result_value_type< sequence1_id_t, sequence2_id_t, score_t > |
| Type deduction for id and score only.
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template<typename sequence1_id_t , typename sequence2_id_t , typename score_t , typename end_positions_t > |
| alignment_result_value_type (sequence1_id_t, sequence2_id_t, score_t, end_positions_t) -> alignment_result_value_type< sequence1_id_t, sequence2_id_t, score_t, end_positions_t > |
| Type deduction for id, score and end positions.
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template<typename sequence1_id_t , typename sequence2_id_t , typename score_t , typename end_positions_t , typename begin_positions_t > |
| alignment_result_value_type (sequence1_id_t, sequence2_id_t, score_t, end_positions_t, begin_positions_t) -> alignment_result_value_type< sequence1_id_t, sequence2_id_t, score_t, end_positions_t, begin_positions_t > |
| Type deduction for id, score, end positions and begin positions.
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template<typename sequence1_id_t , typename sequence2_id_t , typename score_t , typename end_positions_t , typename begin_positions_t , typename alignment_t > |
| alignment_result_value_type (sequence1_id_t, sequence2_id_t, score_t, end_positions_t, begin_positions_t, alignment_t) -> alignment_result_value_type< sequence1_id_t, sequence2_id_t, score_t, end_positions_t, begin_positions_t, alignment_t > |
| Type deduction for id, score, end positions, begin positions and alignment.
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template<std::ranges::viewable_range other_range_t> |
| pairwise_combine_view (other_range_t &&range) -> pairwise_combine_view< std::views::all_t< other_range_t >> |
| Deduces the correct template type from a non-view lvalue range by wrapping the range in std::views::all.
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template<typename ... elems> |
constexpr bool | all_model_aligned_seq = (aligned_sequence<elems> && ...) |
| True, if each type models seqan3::aligned_sequence; false otherwise. More...
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template<typename ... elems> |
constexpr bool | all_model_aligned_seq< type_list< elems... > > = all_model_aligned_seq<elems...> |
| True, if each type in the seqan3::type_list models seqan3::aligned_sequence; false otherwise. More...
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template<typename type_t > |
constexpr auto | bits_of = min_viable_uint_v<CHAR_BIT * sizeof(type_t)> |
| How many bits has a type? More...
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template<typename algorithm_id_type > |
constexpr std::array< std::array< void *, 0 >, 0 > | compatibility_table {} |
| Declaration of algorithm specific compatibility table. More...
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template<> |
constexpr std::array< std::array< bool, static_cast< uint8_t >align_config_id::SIZE)>, static_cast< uint8_t >align_config_id::SIZE)> | compatibility_table< align_config_id > |
| Declaration of algorithm specific compatibility table. More...
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template<> |
constexpr std::array< std::array< bool, static_cast< uint8_t >search_config_id::SIZE)>, static_cast< uint8_t >search_config_id::SIZE)> | compatibility_table< search_config_id > |
| Compatibility matrix to check how search configuration elements can be combined. More...
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template<alphabet out_t, alphabet in_t> |
constexpr std::array< out_t, alphabet_size< in_t > > | convert_through_char_representation |
| A precomputed conversion table for two alphabets based on their char representations. More...
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template<typename rng_t > |
SEQAN3_CONCEPT | debug_stream_range_guard |
| A helper concept definition for ranges that can be streamed to the seqan3::debug_stream. More...
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template<typename t > |
constexpr bool | decays_to_ignore_v = std::is_same_v<std::remove_cvref_t<t>, ignore_t> |
| Return whether the input type with const , volatile and references removed is std::ignore's type. (type trait). More...
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template<typename scalar_t , template< typename, size_t > typename simd_backend_t> |
constexpr auto | default_simd_length |
| seqan3::detail::default_simd_length returns the default length depending on the given scalar_t type, which is used in seqan3::simd::simd_type. More...
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template<template< typename, size_t > typename simd_backend_t> |
constexpr auto | default_simd_max_length = 0u |
| seqan3 auto-detects the maximum number of packable [u]int8_t types. More...
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template<> |
constexpr auto | default_simd_max_length< builtin_simd > |
| This function specializes seqan3::detail::default_simd_max_length for seqan3::detail::builtin_simd. More...
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template<typename list_t > |
constexpr bool | has_member_file_extensions = false |
| Helper function to determine if all types in a format type list have a static member file_extensions . More...
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template<typename query_t > |
constexpr bool | has_type_valid_formats = false |
| Helper function to determine if a type has a static member valid_formats . More...
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template<typename basic_string_t > |
constexpr bool | is_basic_string_v = is_basic_string<basic_string_t>::value |
| Shorthand of seqan3::detail::is_basic_string. More...
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template<typename builtin_simd_t > |
constexpr bool | is_builtin_simd_v = is_builtin_simd<builtin_simd_t>::value |
| Helper variable to test whether a type is a simd builtin type. More...
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template<typename type > |
constexpr bool | is_char_adaptation_v |
| Whether a type is char , char16_t , char32_t or wchar_t (type trait).
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template<typename t > |
constexpr bool | is_gapped_alphabet = false |
| Helper variable to determine if an alphabet is gapped [default: false].
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template<typename t > |
constexpr bool | is_gapped_alphabet< gapped< t > > = true |
| Helper variable to determine if an alphabet is gapped, true for specilisations of seqan3::gapped.
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template<typename builtin_simd_t > |
constexpr bool | is_native_builtin_simd_v = is_native_builtin_simd<builtin_simd_t>::value |
| Helper variable to test whether a type is a native simd builtin type. More...
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template<typename t > |
constexpr bool | is_type_list_of_sam_file_input_formats_v = false |
| Auxiliary value metafuncton that checks whether a type is a seqan3::type_list and all types meet seqan3::sam_file_input_format [default is false]. More...
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template<typename ... ts> |
constexpr bool | is_type_list_of_sam_file_input_formats_v< type_list< ts... > > = (sam_file_input_format<ts> && ...) |
| Auxiliary value metafuncton that checks whether a type is a seqan3::type_list and all types meet seqan3::sam_file_input_format [overload]. More...
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template<typename t > |
constexpr bool | is_type_list_of_sam_file_output_formats_v = false |
| Auxiliary value metafuncton that checks whether a type is a seqan3::type_list and all types meet seqan3::sam_file_output_format [default is false]. More...
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template<typename ... ts> |
constexpr bool | is_type_list_of_sam_file_output_formats_v< type_list< ts... > > = (sam_file_output_format<ts> && ...) |
| Auxiliary value metafuncton that checks whether a type is a seqan3::type_list and all types meet seqan3::sam_file_output_format [overload]. More...
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template<typename t > |
constexpr bool | is_type_list_of_sequence_file_input_formats_v = false |
| Auxiliary value metafuncton that checks whether a type is a seqan3::type_list and all types meet seqan3::sequence_file_input_format [default is false]. More...
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template<typename ... ts> |
constexpr bool | is_type_list_of_sequence_file_input_formats_v< type_list< ts... > > |
| Auxiliary value metafuncton that checks whether a type is a seqan3::type_list and all types meet seqan3::sequence_file_input_format [overload]. More...
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template<typename t > |
constexpr bool | is_type_list_of_sequence_file_output_formats_v = false |
| Auxiliary value metafuncton that checks whether a type is a seqan3::type_list and all types meet seqan3::sequence_file_output_format [default is false]. More...
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template<typename ... ts> |
constexpr bool | is_type_list_of_sequence_file_output_formats_v< type_list< ts... > > |
| Auxiliary value metafuncton that checks whether a type is a seqan3::type_list and all types meet seqan3::sequence_file_output_format [overload]. More...
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template<typename t > |
constexpr bool | is_type_list_of_structure_file_input_formats_v = false |
| Auxiliary value metafuncton that checks whether a type is a seqan3::type_list and all types meet seqan3::structure_file_input_format [default is false]. More...
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template<typename ... ts> |
constexpr bool | is_type_list_of_structure_file_input_formats_v< type_list< ts... > > = (structure_file_input_format<ts> && ...) |
| Auxiliary value metafuncton that checks whether a type is a seqan3::type_list and all types meet seqan3::structure_file_input_format [overload]. More...
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template<typename t > |
constexpr bool | is_type_list_of_structure_file_output_formats_v = false |
| Auxiliary value metafuncton that checks whether a type is a seqan3::type_list and all types meet seqan3::structure_file_output_format [default is false]. More...
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template<typename ... ts> |
constexpr bool | is_type_list_of_structure_file_output_formats_v< type_list< ts... > > = (structure_file_output_format<ts> && ...) |
| Auxiliary value metafuncton that checks whether a type is a seqan3::type_list and all types meet seqan3::structure_file_output_format [overload]. More...
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template<typename type > |
constexpr bool | is_uint_adaptation_v |
| Whether a type is uint8_t , uint16_t or uint32_t .
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template<typename score_type > |
constexpr score_type | matrix_inf = std::numeric_limits<score_type>::max() |
| A special score which represents infinity.
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template<uint64_t value> |
constexpr auto | min_viable_uint_v = static_cast<min_viable_uint_t<value>>(value) |
| Given a value, cast the value as the smallest unsigned integer that can hold it. More...
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template<uint8_t min_error, uint8_t max_error> |
constexpr int | optimum_search_scheme |
| Search scheme that is optimal in the running time for the specified lower and upper error bound. More...
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template<std::ranges::range rng_t, typename char_t > |
constexpr bool | reference_type_is_streamable_v = false |
| Helper template variable that checks if the reference type of a range can be streamed into an instance of seqan3::debug_stream_type . More...
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constexpr char | sam_tag_type_char [12] = {'A', 'i', 'f', 'Z', 'H', 'B', 'B', 'B', 'B', 'B', 'B', 'B'} |
| Each SAM tag type char identifier. Index corresponds to the seqan3::detail::sam_tag_variant types.
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constexpr char | sam_tag_type_char_extra [12] = {'\0', '\0', '\0', '\0', '\0', 'c', 'C', 's', 'S', 'i', 'I', 'f'} |
| Each types SAM tag type extra char id. Index corresponds to the seqan3::detail::sam_tag_variant types.
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template<typename int_t > |
constexpr size_t | size_in_values_v |
| Return the number of values an integral type can have, i.e. the difference between min and max. More...
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template<typename char_type > |
constexpr std::array< char_type, detail::size_in_values_v< char_type > > | to_lower_table |
| Auxiliary table for seqan3::to_lower. More...
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template<typename char_type > |
constexpr std::array< char_type, detail::size_in_values_v< char_type > > | to_upper_table |
| Auxiliary table for seqan3::to_upper. More...
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template<typename lhs_t , typename tuple_derived_t , typename rhs_t , typename ... component_types> |
constexpr bool | tuple_eq_guard |
| Prevents wrong instantiations of seqan3::alphabet_tuple_base's equality comparison operators. More...
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template<typename tuple_derived_t , typename rhs_t , typename ... component_types> |
constexpr bool | tuple_general_guard |
| Prevents wrong instantiations of seqan3::alphabet_tuple_base's equality comparison operators. More...
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template<typename lhs_t , typename tuple_derived_t , typename rhs_t , typename ... component_types> |
constexpr bool | tuple_order_guard |
| Prevents wrong instantiations of seqan3::alphabet_tuple_base's ordered comparison operators. More...
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template<typename t > |
SEQAN3_CONCEPT | type_list_of_sam_file_input_formats = is_type_list_of_sam_file_input_formats_v<t> |
| Auxiliary concept that checks whether a type is a seqan3::type_list and all types meet seqan3::sam_file_input_format. More...
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template<typename t > |
SEQAN3_CONCEPT | type_list_of_sam_file_output_formats = is_type_list_of_sam_file_output_formats_v<t> |
| Auxiliary concept that checks whether a type is a seqan3::type_list and all types meet seqan3::sam_file_output_format. More...
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template<typename t > |
SEQAN3_CONCEPT | type_list_of_sequence_file_input_formats = is_type_list_of_sequence_file_input_formats_v<t> |
| Auxiliary concept that checks whether a type is a seqan3::type_list and all types meet seqan3::sequence_file_input_format. More...
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template<typename t > |
SEQAN3_CONCEPT | type_list_of_sequence_file_output_formats = is_type_list_of_sequence_file_output_formats_v<t> |
| Auxiliary concept that checks whether a type is a seqan3::type_list and all types meet seqan3::sequence_file_output_format. More...
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template<typename t > |
SEQAN3_CONCEPT | type_list_of_structure_file_input_formats = is_type_list_of_structure_file_input_formats_v<t> |
| Auxiliary concept that checks whether a type is a seqan3::type_list and all types meet seqan3::structure_file_input_format. More...
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template<typename t > |
SEQAN3_CONCEPT | type_list_of_structure_file_output_formats = is_type_list_of_structure_file_output_formats_v<t> |
| Auxiliary concept that checks whether a type is a seqan3::type_list and all types meet seqan3::structure_file_output_format. More...
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template<typename type > |
std::string const | type_name_as_string |
| Defines the human-readable name of the given type using the typeid operator. More...
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template<typename lhs_t , typename rhs_t , bool lhs_rhs_switched, typename ... alternative_types> |
constexpr bool | variant_comparison_guard |
| Prevents wrong instantiations of std::alphabet_variant's comparison operators. More...
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template<typename other_t , typename ... alternative_types> |
constexpr bool | variant_general_guard |
| Prevents wrong instantiations of std::alphabet_variant's constructors. More...
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