|
class | aa20 |
| The canonical amino acid alphabet. More...
|
|
class | aa27 |
| The twenty-seven letter amino acid alphabet. More...
|
|
struct | align_result |
| Stores the alignment results and offers a tuple-like interface. More...
|
|
class | aligned_allocator |
| Allocates uninitialized storage whose memory-alignment is specified by alignment. More...
|
|
interface | aligned_sequence_concept |
| The generic concept for an aligned sequence.This concept describes the requirements a sequence must fulfil in order to be part of the seqan3::alignment object. More...
|
|
class | alignment_file_format_sam |
| The SAM format. More...
|
|
struct | alignment_file_header |
| Stores the header information of alignment files. More...
|
|
struct | alignment_file_in_options |
| The options type defines various option members that influence the behaviour of all or some formats. More...
|
|
class | alignment_file_output |
| A class for writing alignment files, e.g. SAM, BAL, BLAST, ... More...
|
|
interface | alignment_file_output_format_concept |
| The generic concept for alignment file out formats. More...
|
|
struct | alignment_file_output_options |
| The options type defines various option members that influence the behavior of all or some formats. More...
|
|
class | alignment_range |
| The alignment. More...
|
|
class | alphabet_base |
| A CRTP-base that makes defining a custom alphabet easier. More...
|
|
interface | alphabet_concept |
| The generic alphabet concept that covers most data types used in ranges.This is the core alphabet concept that many other alphabet concepts refine. More...
|
|
class | alphabet_proxy |
| A CRTP-base that eases the definition of proxy types returned in place of regular alphabets. More...
|
|
struct | alphabet_size |
| The size of the alphabet. [value metafunction base template]. More...
|
|
struct | alphabet_size< alphabet_type_with_members > |
| Specialisation of seqan3::alphabet_size that delegates to alphabet_type::value_size . More...
|
|
struct | alphabet_size< char_type > |
| Specialisation of seqan3::alphabet_size that delegates for char types. More...
|
|
struct | alphabet_size< uint_type > |
| Specialisation of seqan3::alphabet_size that delegates for uint types. More...
|
|
class | aminoacid_base |
| A CRTP-base that refines seqan3::alphabet_base and is used by the amino acids. More...
|
|
interface | aminoacid_concept |
| A concept that indicates whether an alphabet represents amino acids.In addition to the requirements for seqan3::alphabet_concept, the amino_acid_concept expects conforming alphabets to provide an enum-like interface with all possible 27 amino acids as values (although some may be mapped to others if the alphabet is smaller than 27). More...
|
|
class | aminoacid_scoring_scheme |
| A data structure for managing and computing the score of two amino acids. More...
|
|
class | argument_parser |
| The SeqAn command line parser. More...
|
|
struct | argument_parser_meta_data |
| Stores all parser related meta information of the seqan3::argument_parser. More...
|
|
interface | arithmetic_concept |
| A type that satisfies std::is_arithmetic_v<t>. More...
|
|
struct | band_static |
| Data structure for a static band. More...
|
|
class | bi_fm_index |
| The SeqAn Bidirectional FM Index. More...
|
|
interface | bi_fm_index_concept |
| Concept for bidirectional FM indices. More...
|
|
struct | bi_fm_index_default_traits |
| The default Bidirectional FM Index Configuration. More...
|
|
class | bi_fm_index_iterator |
| The SeqAn Bidirectional FM Index Iterator. More...
|
|
interface | bi_fm_index_iterator_concept |
| Concept for bidirectional FM index iterators. More...
|
|
interface | bi_fm_index_traits_concept |
| Concept for bidirectional FM Index traits. More...
|
|
class | bitcompressed_vector |
| A space-optimised version of std::vector that compresses multiple letters into a single byte. More...
|
|
class | cartesian_composition |
| The CRTP base for a combined alphabet that contains multiple values of different alphabets at the same time. More...
|
|
interface | cereal_archive_concept |
| All archives of the Cereal library satisfy this. More...
|
|
interface | cereal_input_archive_concept |
| All input archives of the Cereal library satisfy this. More...
|
|
interface | cereal_output_archive_concept |
| All output archives of the Cereal library satisfy this. More...
|
|
interface | cereal_text_archive_concept |
| All text archives of the Cereal library satisfy this. More...
|
|
interface | cerealisable_concept |
| Specifies the requirements for types that are serialisable via Cereal. More...
|
|
interface | char_adaptation_concept |
| A concept that covers char type adaptations for seqan3::alphabet_concept. More...
|
|
interface | char_concept |
| This concept encompasses exactly the types char , signed char , unsigned char , wchar_t , char16_t and char32_t . More...
|
|
interface | compatible_concept |
| Two types are "compatible" if their seqan3::dimension_v and their seqan3::innermost_value_type_t are the same. More...
|
|
class | concatenated_sequences |
| Container that stores sequences concatenated internally. More...
|
|
interface | const_iterable_concept |
| Specifies requirements of an input range type for which the const version of that type satisfies the same strength input range concept as the non-const version. More...
|
|
struct | const_reference |
| Type metafunction that returns the const_reference of another type [metafunction declaration]. More...
|
|
struct | const_reference< rng_t > |
| Type metafunction that returns the const_reference of another type [specialisation for input ranges]. More...
|
|
class | constexpr_string |
| Implements a constexpr string that can be used for compile time computations. More...
|
|
interface | container_concept |
| The (most general) container concept as defined by the standard library. More...
|
|
class | debug_stream_type |
| A "pretty printer" for most SeqAn data structures and related types. More...
|
|
struct | difference_type |
| Type metafunction that returns the difference_type of another type [metafunction declaration]. More...
|
|
struct | difference_type< it_t > |
| Type metafunction that returns the difference_type of another type [specialisation for iterators]. More...
|
|
struct | difference_type< rng_t > |
| Type metafunction that returns the difference_type of another type [specialisation for ranges]. More...
|
|
class | dna15 |
| The 15 letter DNA alphabet, containing all IUPAC smybols minus the gap. More...
|
|
class | dna4 |
| The four letter DNA alphabet of A,C,G,T. More...
|
|
class | dna5 |
| The five letter DNA alphabet of A,C,G,T and the unknown character N. More...
|
|
class | dot_bracket3 |
| The three letter RNA structure alphabet of the characters ".()". More...
|
|
class | dssp9 |
| The protein structure alphabet of the characters "HGIEBTSCX". More...
|
|
interface | explicitly_convertible_to_concept |
| Resolves to std::ranges::ExplicitlyConvertibleTo<type1, type2>() . More...
|
|
struct | fields |
| A class template that holds a choice of seqan3::field. More...
|
|
class | file_existance_validator |
| A validator that checks if a file exists. More...
|
|
class | file_ext_validator |
| A validator that checks if a filenames has one of the valid extensions. More...
|
|
struct | file_open_error |
| Thrown if there is an unspecified filesystem or stream error while opening, e.g. permission problem. More...
|
|
interface | floating_point_concept |
| An arithmetic type that also satisfies std::is_floating_point_v<t>. More...
|
|
class | fm_index |
| The SeqAn FM Index. More...
|
|
interface | fm_index_concept |
| Concept for unidirectional FM indices. More...
|
|
struct | fm_index_default_traits |
| The default FM Index Configuration. More...
|
|
class | fm_index_iterator |
| The SeqAn FM Index Iterator. More...
|
|
interface | fm_index_iterator_concept |
| Concept for unidirectional FM index iterators. More...
|
|
interface | fm_index_traits_concept |
| Concept for unidirectional FM Index traits. More...
|
|
struct | format_error |
| Thrown if information given to output format didn't match expectations. More...
|
|
struct | gap |
| The alphabet of a gap character '-'. More...
|
|
class | gap_erase_failure |
| Thrown in function seqan3::erase_gap, if a position does not contain a gap. More...
|
|
struct | gap_open_score |
| A strong type of underlying type score_type that represents an additional score (usually negative) that is incurred once additionaly per stretch of consecutive gaps. More...
|
|
class | gap_scheme |
| A scheme for representing and computing scores against gap characters. More...
|
|
struct | gap_score |
| A strong type of underlying type score_type that represents the score of any character against a gap character. More...
|
|
interface | implicitly_convertible_to_concept |
| Resolves to std::ranges::ImplicitlyConvertibleTo<type1, type2>() . More...
|
|
struct | innermost_value_type |
| Recursively determines the value_type on containers and/or iterators [Type metafunction]. More...
|
|
class | integral_range_validator< option_value_type > |
| A validator that checks whether a number is inside a given range. More...
|
|
interface | istream_concept |
| Concept for input streams. More...
|
|
struct | lower_bound |
| Type for a lower boundary. More...
|
|
class | mask |
| Implementation of a masked alphabet to be used for cartesian compositions. More...
|
|
class | masked |
| Implementation of a masked composition, which extends a given alphabet with a mask. More...
|
|
struct | match_score |
| A strong type of underlying type score_type that represents the score of two matching characters. More...
|
|
struct | max_pseudoknot_depth |
| Metafunction that indicates to what extent an alphabet can handle pseudoknots. [value metafunction base template]. More...
|
|
struct | max_pseudoknot_depth< alphabet_type_with_pseudoknot_attribute > |
| Specialisation of seqan3::max_pseudoknot_depth that delegates to structure_type::max_pseudoknot_depth. More...
|
|
struct | mismatch_score |
| A strong type of underlying type score_type that represents the score two different characters. More...
|
|
class | nucleotide_base |
| A CRTP-base that refines seqan3::alphabet_base and is used by the nucleotides. More...
|
|
interface | nucleotide_concept |
| A concept that indicates whether an alphabet represents nucleotides.In addition to the requirements for seqan3::alphabet_concept, the nucleotide_concept introduces a requirement for a complement function: seqan3::nucleotide_concept::complement. More...
|
|
class | nucleotide_scoring_scheme |
| A data structure for managing and computing the score of two nucleotides. More...
|
|
class | option_declared_multiple_times |
| Argument parser exception thrown when a non-list option is declared multiple times. More...
|
|
interface | ostream_concept |
| Concept for output streams. More...
|
|
class | overflow_error_on_conversion |
| Argument parser exception thrown when an argument could not be casted to the according type. More...
|
|
struct | parse_asserter |
| A condition checker, that wraps a parse condition and throws a specified exception if the condition was not met. More...
|
|
struct | parse_error |
| Thrown if there is a parse error, such as reading an unexpected character from an input stream. More...
|
|
class | parser_design_error |
| Argument parser exception that is thrown whenever there is an design error directed at the developer of the application (e.g. Reuse of option). More...
|
|
class | parser_interruption |
| This exception is not an error but expected behavior that shall terminate the program (e.g. when printing the help page). More...
|
|
class | parser_invalid_argument |
| Argument parser exception that is thrown whenever there is an error while parsing the command line arguments. More...
|
|
class | phred42 |
| Quality type for traditional Sanger and modern Illumina Phred scores (typical range). More...
|
|
class | phred63 |
| Quality type for traditional Sanger and modern Illumina Phred scores (full range). More...
|
|
class | phred68legacy |
| Quality type for Solexa and deprecated Illumina formats. More...
|
|
struct | pod_tuple |
| cond More...
|
|
struct | pod_tuple< type0 > |
| Recursion anchor for pod_tuple. More...
|
|
struct | pod_tuple< type0, types... > |
| endcond More...
|
|
class | qualified |
| Joins an arbitrary alphabet with a quality alphabet. More...
|
|
class | quality_base |
| A CRTP-base that refines seqan3::alphabet_base and is used by the quality alphabets. More...
|
|
interface | quality_concept |
| A concept that indicates whether an alphabet represents quality scores.In addition to the requirements for seqan3::alphabet_concept, the quality_concept introduces a requirement for conversion functions from and to a Phred score. More...
|
|
interface | random_access_container_concept |
| A more refined container concept than seqan3::sequence_container_concept. More...
|
|
struct | record |
| The class template that file records are based on; behaves like an std::tuple. More...
|
|
struct | reference |
| Type metafunction that returns the reference of another type [metafunction declaration]. More...
|
|
struct | reference< it_t > |
| Type metafunction that returns the reference of another type [specialisation for input iterators]. More...
|
|
struct | reference< rng_t > |
| Type metafunction that returns the reference of another type [specialisation for input ranges]. More...
|
|
class | regex_validator< std::string > |
| A validator that checks if a matches a regular expression pattern. More...
|
|
class | regex_validator< std::vector< std::string > > |
| A validator that checks if each value in a container satisfies a regex expression. More...
|
|
class | required_option_missing |
| Argument parser exception thrown when a required option is missing. More...
|
|
interface | reservable_container_concept |
| A more refined container concept than seqan3::random_access_container_concept. More...
|
|
class | rna15 |
| The 15 letter RNA alphabet, containing all IUPAC smybols minus the gap. More...
|
|
class | rna4 |
| The four letter RNA alphabet of A,C,G,U. More...
|
|
class | rna5 |
| The five letter RNA alphabet of A,C,G,U and the unknown character N. More...
|
|
interface | rna_structure_concept |
| A concept that indicates whether an alphabet represents RNA structure. More...
|
|
struct | rvalue_reference |
| Type metafunction that returns the rvalue_reference of another type [metafunction declaration]. More...
|
|
struct | rvalue_reference< it_t > |
| Type metafunction that returns the rvalue_reference of another type [specialisation for input iterators]. More...
|
|
struct | rvalue_reference< rng_t > |
| Type metafunction that returns the rvalue_reference of another type [specialisation for input ranges]. More...
|
|
class | sam_tag_dictionary |
| The SAM tag dictionary class that stores all optional SAM fields. More...
|
|
struct | sam_tag_type |
| The generic base class. More...
|
|
class | scoring_scheme_base |
| A CRTP base class for scoring schemes. More...
|
|
interface | scoring_scheme_concept |
| A concept that requires that type be able to score two letters. More...
|
|
interface | semi_alphabet_concept |
| The basis for seqan3::alphabet_concept, but requires only rank interface (not char). More...
|
|
interface | sequence_container_concept |
| A more refined container concept than seqan3::container_concept. More...
|
|
class | sequence_file_format_fasta |
| The FastA format. More...
|
|
class | sequence_file_format_fastq |
| The FastQ format. More...
|
|
class | sequence_file_input |
| A class for reading sequence files, e.g. FASTA, FASTQ ... More...
|
|
struct | sequence_file_input_default_traits_aa |
| A traits type that specifies input as amino acids. More...
|
|
struct | sequence_file_input_default_traits_dna |
| The default traits for seqan3::sequence_file_input. More...
|
|
interface | sequence_file_input_format_concept |
| The generic concept for sequence file in formats. More...
|
|
struct | sequence_file_input_options |
| The options type defines various option members that influence the behaviour of all or some formats. More...
|
|
interface | sequence_file_input_traits_concept |
| The requirements a traits_type for seqan3::sequence_file_input must meet. More...
|
|
class | sequence_file_output |
| A class for writing sequence files, e.g. FASTA, FASTQ ... More...
|
|
interface | sequence_file_output_format_concept |
| The generic concept for sequence file out formats. More...
|
|
struct | sequence_file_output_options |
| The options type defines various option members that influence the behaviour of all or some formats. More...
|
|
struct | size_type |
| Type metafunction that returns the size_type of another type [metafunction declaration]. More...
|
|
struct | size_type< it_t > |
| Type metafunction that returns the size_type of another type [specialisation for iterators]. More...
|
|
struct | size_type< rng_t > |
| Type metafunction that returns the size_type of another type [specialisation for sized ranges]. More...
|
|
interface | standard_layout_concept |
| Resolves to std::is_standard_layout_v<t>. More...
|
|
interface | stream_concept |
| Concept for i/o streams permitting both directions.An object satisfying the requirements of a stream concept can be used to stream in both (input and output) directions. More...
|
|
class | structure_file_format_vienna |
| The Vienna format (dot bracket notation) for RNA sequences with secondary structure. More...
|
|
class | structure_file_in |
| A class for reading structured sequence files, e.g. Stockholm, Connect, Vienna, ViennaRNA bpp matrix ... More...
|
|
struct | structure_file_input_default_traits_aa |
| A traits type that specifies input as amino acids. More...
|
|
struct | structure_file_input_default_traits_rna |
| The default traits for seqan3::structure_file_in. More...
|
|
interface | structure_file_input_format_concept |
| The generic concept for structure file in formats. More...
|
|
struct | structure_file_input_options |
| The options type defines various option members that influence the behaviour of all or some formats. More...
|
|
interface | structure_file_input_traits_concept |
| The requirements a traits_type for seqan3::structure_file_in must meet. More...
|
|
class | structure_file_out |
| A class for writing structured sequence files, e.g. Stockholm, Connect, Vienna, ViennaRNA bpp matrix ... More...
|
|
interface | structure_file_output_format_concept |
| The generic concept for sequence file out formats. More...
|
|
struct | structure_file_output_options |
| The options type defines various option members that influence the behaviour of all or some formats. More...
|
|
class | structured_aa |
| A seqan3::cartesian_composition that joins an aminoacid alphabet with a protein structure alphabet. More...
|
|
class | structured_rna |
| A seqan3::cartesian_composition that joins a nucleotide alphabet with an RNA structure alphabet. More...
|
|
class | too_few_arguments |
| Argument parser exception thrown when too few arguments are provided. More...
|
|
class | too_many_arguments |
| Argument parser exception thrown when too many arguments are provided. More...
|
|
interface | trivial_concept |
| A type that satisfies seqan3::trivially_copyable_concept and seqan3::trivially_destructible_concept. More...
|
|
interface | trivially_copyable_concept |
| A type that satisfies std::is_trivially_copyable_v<t>. More...
|
|
interface | trivially_destructible_concept |
| A type that satisfies std::is_trivially_destructible_v<t>. More...
|
|
interface | tuple_like_concept |
| Whether a type behaves like a tuple. More...
|
|
class | type_conversion_failed |
| Argument parser exception thrown when an argument could not be casted to the according type. More...
|
|
interface | uint_adaptation_concept |
| A concept that covers uint type adaptations for seqan3::alphabet_concept. More...
|
|
struct | underlying_char |
| The char_type of the alphabet. [type metafunction base template]. More...
|
|
struct | underlying_char< alphabet_type_with_members > |
| Specialisation of seqan3::underlying_char that delegates to typename alphabet_type::char_type . More...
|
|
struct | underlying_char< char_type > |
| Specialisation of seqan3::underlying_char for char types. More...
|
|
struct | underlying_char< uint_type > |
| Specialisation of seqan3::underlying_char for uint types. More...
|
|
struct | underlying_phred |
|
struct | underlying_phred< alphabet_with_member_type > |
| The internal phred type. More...
|
|
struct | underlying_rank |
| The rank_type of the semi_alphabet. [type metafunction base template]. More...
|
|
struct | underlying_rank< alphabet_type_with_members > |
| Specialisation of seqan3::underlying_rank that delegates to typename alphabet_type::rank_type . More...
|
|
struct | underlying_rank< char_type > |
| Specialisation of seqan3::underlying_rank for char types. More...
|
|
struct | underlying_rank< uint_type > |
| Specialisation of seqan3::underlying_rank for uint types. More...
|
|
struct | unexpected_end_of_input |
| Thrown if I/O was expecting more input (e.g. a delimiter or a new line), but the end of input was reached. More...
|
|
struct | unhandled_extension_error |
| Thrown if there is no format that accepts a given file extension. More...
|
|
class | union_composition |
| A combined alphabet that can hold values of either of its alternatives. More...
|
|
class | unknown_option |
| Argument parser exception thrown when encountering unknown option. More...
|
|
struct | upper_bound |
| Type for an upper boundary. More...
|
|
class | validation_failed |
| Argument parser exception thrown when an argument could not be casted to the according type. More...
|
|
interface | validator_concept |
| The concept for option validators passed to add_option/positional_option. More...
|
|
class | value_list_validator |
| A validator that checks whether a value is inside a list of valid values. More...
|
|
class | value_list_validator< option_value_type > |
| A validator that checks if each value in a container appears in a list of valid values. More...
|
|
struct | value_type |
| Type metafunction that returns the value_type of another type [metafunction declaration]. More...
|
|
struct | value_type< it_t > |
| Type metafunction that returns the value_type of another type [specialisation for input iterators]. More...
|
|
struct | value_type< rng_t > |
| Type metafunction that returns the value_type of another type [specialisation for input ranges]. More...
|
|
interface | weakly_assignable_concept |
| Resolves to std::is_assignable_v<t>. More...
|
|
interface | weakly_ordered_with_concept |
| Requires the two operands to be comparable with == and != in both directions. More...
|
|
class | wuss |
| The WUSS structure alphabet of the characters .<>:,-_~;()[]{}AaBbCcDd ... More...
|
|
|
template<typename char_t , char_t ... s> |
constexpr uint16_t | operator""_tag () |
| The SAM tag literal, such that tags can be used in constant expressions. More...
|
|
template<typename simd_t > |
debug_stream_type & | operator<< (debug_stream_type &s, simd_t &&simd) |
| Overload for debug_stream for simd types.
|
|
template<tuple_like_concept tuple_t> |
debug_stream_type & | operator<< (debug_stream_type &stream, tuple_t const &alignment) |
| Streaming operator for alignments, which are represented as tuples of aligned sequences. More...
|
|
template<validator_concept validator1_type, validator_concept validator2_type> |
auto | operator| (validator1_type &&vali1, validator2_type &&vali2) |
| Enables the chaining of validators. ! More...
|
|
template<fm_index_concept index_t, typename queries_t , typename configuration_t > |
auto | search (index_t const &index, queries_t &&queries, configuration_t const &cfg) |
| Search a query or a range of queries in an index. More...
|
|
template<fm_index_concept index_t, typename queries_t > |
auto | search (index_t const &index, queries_t &&queries) |
| Search a query or a range of queries in an index. It will not allow for any errors and will output all matches as positions in the text. More...
|
|
template<genetic_code gc = genetic_code::CANONICAL, nucleotide_concept nucl_type> |
constexpr aa27 | translate_triplet (nucl_type const &n1, nucl_type const &n2, nucl_type const &n3) noexcept |
| Translate one nucleotide triplet into single amino acid (single nucleotide interface). More...
|
|
template<genetic_code gc = genetic_code::CANONICAL, typename tuple_type > |
constexpr aa27 | translate_triplet (tuple_type const &input_tuple) noexcept |
| Translate one nucleotide triplet into single amino acid (tuple interface). More...
|
|
template<genetic_code gc = genetic_code::CANONICAL, std::ranges::InputRange range_type> |
constexpr aa27 | translate_triplet (range_type &&input_range) |
| Translate one nucleotide triplet into single amino acid (range interface). More...
|
|
|
Provides a special overload for the get interface using seqan3::search_cfg::id as identifier.
|
|
These functions and metafunctions expose member variables and types so that they satisfy seqan3::semi_alphabet_concept.
|
template<typename alphabet_type > |
constexpr underlying_rank_t< alphabet_type > | to_rank (alphabet_type const alph) requires requires(alphabet_type alph) |
| Implementation of seqan3::semi_alphabet_concept::to_rank() that delegates to a member function. More...
|
|
template<typename alphabet_type > |
constexpr alphabet_type & | assign_rank (alphabet_type &alph, underlying_rank_t< alphabet_type > const rank) requires requires(alphabet_type alph) |
| Implementation of seqan3::semi_alphabet_concept::assign_rank() that delegates to a member function. More...
|
|
template<typename alphabet_type > |
constexpr alphabet_type && | assign_rank (alphabet_type &&alph, underlying_rank_t< alphabet_type > const rank) requires requires(alphabet_type alph) |
| Implementation of seqan3::semi_alphabet_concept::assign_rank() that delegates to a member function. More...
|
|
|
These functions and metafunctions expose member variables and types so that they satisfy seqan3::alphabet_concept.
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template<typename alphabet_type > |
constexpr underlying_char_t< alphabet_type > | to_char (alphabet_type const alph) requires requires(alphabet_type alph) |
| Implementation of seqan3::alphabet_concept::to_char() that delegates to a member function. More...
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template<typename alphabet_type > |
constexpr alphabet_type & | assign_char (alphabet_type &alph, underlying_char_t< alphabet_type > const chr) requires requires(alphabet_type alph) |
| Implementation of seqan3::alphabet_concept::assign_char() that delegates to a member function. More...
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template<typename alphabet_type > |
constexpr alphabet_type && | assign_char (alphabet_type &&alph, underlying_char_t< alphabet_type > const chr) requires requires(alphabet_type alph) |
| Implementation of seqan3::alphabet_concept::assign_char() that delegates to a member function. More...
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These functions and metafunctions expose member variables and types so that they satisfy seqan3::nucleotide_concept.
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Perform binary operations like on ints or weak enums. These overloads are available if seqan3::add_enum_bitwise_operators is defined for your type.
- See also
- seqan3::add_enum_bitwise_operators
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template<typename t > |
constexpr t | operator & (t lhs, t rhs) noexcept requires std |
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template<typename t > |
constexpr t | operator| (t lhs, t rhs) noexcept requires std |
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template<typename t > |
constexpr t | operator^ (t lhs, t rhs) noexcept requires std |
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template<typename t > |
constexpr t | operator~ (t lhs) noexcept requires std |
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template<typename t > |
constexpr t & | operator &= (t &lhs, t rhs) noexcept requires std |
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template<typename t > |
constexpr t & | operator|= (t &lhs, t rhs) noexcept requires std |
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template<typename t > |
constexpr t & | operator^= (t &lhs, t rhs) noexcept requires std |
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Helper functions for tuple like objects.
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template<size_t pivot_c, template< typename ... > typename tuple_t, typename ... ts> |
constexpr auto | tuple_split (tuple_t< ts... > const &t) |
| Splits a tuple like data structure at the given position. More...
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template<size_t pivot_c, template< typename ... > typename tuple_t, typename ... ts> |
constexpr auto | tuple_split (tuple_t< ts... > &&t) |
| Splits a tuple like data structure at the given position. More...
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template<typename pivot_t , tuple_like_concept tuple_t> |
constexpr auto | tuple_split (tuple_t &&t) |
| Splits a tuple like data structure at the first position of the given type. More...
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template<tuple_like_concept tuple_t> |
constexpr auto | tuple_pop_front (tuple_t &&t) |
| Removes the first element of a tuple. More...
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template<char_concept char_type> |
constexpr char_type | to_lower (char_type const c) noexcept |
| Converts 'A'-'Z' to 'a'-'z' respectively; other characters are returned as is. More...
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template<char_concept char_type> |
constexpr char_type | to_upper (char_type const c) noexcept |
| Converts 'a'-'z' to 'A'-'Z' respectively; other characters are returned as is. More...
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template<typename t > |
constexpr bool | add_enum_bitwise_operators = false |
| Set to true for a scoped enum to have binary operators overloaded. More...
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template<> |
constexpr bool | add_enum_bitwise_operators< fmtflags2 > = true |
| Overload bitwise operators for seqan3::fmtflags2.
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template<> |
constexpr bool | add_enum_bitwise_operators< translation_frames > = true |
| Enable bitwise operators for enum translation_frames.
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debug_stream_type | debug_stream {} |
| A global instance of seqan3::debug_stream_type.
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template<typename t > |
constexpr size_t | dimension_v = 1 |
| Returns the number of times you can call seqan3::value_type_t recursively on t [Value metafunction]. More...
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std::string const | seqan3_version |
| The full version as std::string . More...
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constexpr uint8_t | seqan3_version_major = SEQAN3_VERSION_MAJOR |
| The major version.
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constexpr uint8_t | seqan3_version_minor = SEQAN3_VERSION_MINOR |
| The minor version.
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constexpr uint8_t | seqan3_version_patch = SEQAN3_VERSION_PATCH |
| The patch version.
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Parse conditions are function like objects that can be used to check if a character c fulfills certain constraints. SeqAn3 implements all parse condition also available in the standard library and some more.
Disjunction and Negation
In contrast to the standard library (where the checks are implemented as functions), the functors in SeqAn3 can be joined efficiently, maintaining constant-time evaluation independent of the number of checks. Functors can be combined with the ||-operator or negated via the !-operator :
auto constexpr my_cond = is_char<'%'> || is_digit; bool is_percent = my_cond(*example_it); Defining complex combinations and using them in e.g. input/output can increase speed significantly over checking multiple functions: we measured speed-ups of 10x for a single check and speed-ups of over 20x for complex combinations.
Custom conditions
Standard library conditions
SeqAn offers the 12 conditions exactly as defined in the standard library except that we have introduced an underscore in the name to be consistent with our other naming.
The following table lists the predefined parse conditions and which constraints are associated with them.
ASCII values | characters |
is_cntrl
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is_print
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is_space
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is_blank
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is_graph
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is_punct
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is_alnum
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is_alpha
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is_upper
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is_lower
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is_digit
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is_xdigit
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decimal | hexadecimal | octal |
0–8 | \x0 –\x8 | \0 –\10 | control codes (NUL , etc.) | ≠0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
9 | \x9 | \11 | tab (\t ) | ≠0 | 0 | ≠0 | ≠0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
10–13 | \xA –\xD | \12 –\15 | whitespaces (\n , \v , \f , \r ) | ≠0 | 0 | ≠0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
14–31 | \xE –\x1F | \16 –\37 | control codes | ≠0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
32 | \x20 | \40 | space | 0 | ≠0 | ≠0 | ≠0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
33–47 | \x21 –\x2F | \41 –\57 | !"#$%&'()*+,-./ | 0 | ≠0 | 0 | 0 | ≠0 | ≠0 | 0 | 0 | 0 | 0 | 0 | 0 |
48–57 | \x30 –\x39 | \60 –\71 | 0123456789 | 0 | ≠0 | 0 | 0 | ≠0 | 0 | ≠0 | 0 | 0 | 0 | ≠0 | ≠0 |
58–64 | \x3A –\x40 | \72 –\100 | :;<=>?@ | 0 | ≠0 | 0 | 0 | ≠0 | ≠0 | 0 | 0 | 0 | 0 | 0 | 0 |
65–70 | \x41 –\x46 | \101 –\106 | ABCDEF | 0 | ≠0 | 0 | 0 | ≠0 | 0 | ≠0 | ≠0 | ≠0 | 0 | 0 | ≠0 |
71–90 | \x47 –\x5A | \107 –\132 | GHIJKLMNOP
QRSTUVWXYZ | 0 | ≠0 | 0 | 0 | ≠0 | 0 | ≠0 | ≠0 | ≠0 | 0 | 0 | 0 |
91–96 | \x5B –\x60 | \133 –\140 | []^_` | 0 | ≠0 | 0 | 0 | ≠0 | ≠0 | 0 | 0 | 0 | 0 | 0 | 0 |
97–102 | \x61 –\x66 | \141 –\146 | abcdef | 0 | ≠0 | 0 | 0 | ≠0 | 0 | ≠0 | ≠0 | 0 | ≠0 | 0 | ≠0 |
103–122 | \x67 –\x7A | \147 –\172 | ghijklmnop
qrstuvwxyz | 0 | ≠0 | 0 | 0 | ≠0 | 0 | ≠0 | ≠0 | 0 | ≠0 | 0 | 0 |
123–126 | \x7B –\x7E | \172 –\176 | {|}~ | 0 | ≠0 | 0 | 0 | ≠0 | ≠0 | 0 | 0 | 0 | 0 | 0 | 0 |
127 | \x7F | \177 | backspace character (DEL ) | ≠0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
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template<uint8_t interval_first, uint8_t interval_last> |
detail::is_in_interval_type< interval_first, interval_last > constexpr | is_in_interval {} |
| Checks whether a given letter is in the specified interval. More...
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template<alphabet_concept alphabet_t> |
detail::is_in_alphabet_type< alphabet_t > constexpr | is_in_alphabet {} |
| Checks whether a given letter is valid for the specified seqan3::alphabet_concept. More...
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template<int char_v> |
detail::is_char_type< char_v > constexpr | is_char |
| Checks whether a given letter is the same as the template non-type argument. More...
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auto constexpr | is_eof = is_char<EOF> |
| Checks whether a given letter is equal to the EOF constant defined in <cstdio> . More...
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auto constexpr | is_cntrl |
| Checks whether c is a control character. More...
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auto constexpr | is_print = is_in_interval<' ', '~'> |
| Checks whether c is a printable character. More...
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auto constexpr | is_space = is_in_interval<'\t', '\r'> || is_char<' '> |
| Checks whether c is a space character. More...
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auto constexpr | is_blank = is_char<'\t'> || is_char<' '> |
| Checks whether c is a blank character. More...
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auto constexpr | is_graph = is_in_interval<'!', '~'> |
| Checks whether c is a graphic character. More...
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auto constexpr | is_punct |
| Checks whether c is a punctuation character. More...
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auto constexpr | is_alnum |
| Checks whether c is a alphanumeric character. More...
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auto constexpr | is_alpha = is_in_interval<'A', 'Z'> || is_in_interval<'a', 'z'> |
| Checks whether c is a alphabetical character. More...
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auto constexpr | is_upper = is_in_interval<'A', 'Z'> |
| Checks whether c is a upper case character. More...
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auto constexpr | is_lower = is_in_interval<'a', 'z'> |
| Checks whether c is a lower case character. More...
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auto constexpr | is_digit = is_in_interval<'0', '9'> |
| Checks whether c is a digital character. More...
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auto constexpr | is_xdigit |
| Checks whether c is a hexadecimal character. More...
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