SeqAn3 3.4.0-rc.1
The Modern C++ library for sequence analysis.
|
The four letter RNA alphabet of A,C,G,U. More...
#include <seqan3/alphabet/nucleotide/rna4.hpp>
Public Member Functions | |
Constructors, destructor and assignment | |
constexpr | rna4 () noexcept=default |
Defaulted. | |
constexpr | rna4 (rna4 const &) noexcept=default |
Defaulted. | |
constexpr | rna4 (rna4 &&) noexcept=default |
Defaulted. | |
constexpr rna4 & | operator= (rna4 const &) noexcept=default |
Defaulted. | |
constexpr rna4 & | operator= (rna4 &&) noexcept=default |
Defaulted. | |
~rna4 () noexcept=default | |
Defaulted. | |
template<std::same_as< dna4 > t> | |
constexpr | rna4 (t const &r) noexcept |
Allow implicit construction from seqan3::dna4 of the same size. | |
Public Member Functions inherited from seqan3::nucleotide_base< rna4, 4 > | |
constexpr rna4 | complement () const noexcept |
Return the complement of the letter. | |
constexpr | nucleotide_base (other_nucl_type const &other) noexcept |
Allow explicit construction from any other nucleotide type and convert via the character representation. | |
Public Member Functions inherited from seqan3::alphabet_base< derived_type, size, char_t > | |
constexpr | alphabet_base () noexcept=default |
Defaulted. | |
constexpr | alphabet_base (alphabet_base const &) noexcept=default |
Defaulted. | |
constexpr | alphabet_base (alphabet_base &&) noexcept=default |
Defaulted. | |
constexpr alphabet_base & | operator= (alphabet_base const &) noexcept=default |
Defaulted. | |
constexpr alphabet_base & | operator= (alphabet_base &&) noexcept=default |
Defaulted. | |
~alphabet_base () noexcept=default | |
Defaulted. | |
constexpr char_type | to_char () const noexcept |
Return the letter as a character of char_type. | |
constexpr rank_type | to_rank () const noexcept |
Return the letter's numeric value (rank in the alphabet). | |
constexpr derived_type & | assign_char (char_type const chr) noexcept |
Assign from a character, implicitly converts invalid characters. | |
constexpr derived_type & | assign_rank (rank_type const c) noexcept |
Assign from a numeric value. | |
Private Types | |
using | base_t = nucleotide_base< rna4, 4 > |
The base class. | |
Static Private Member Functions | |
static constexpr rank_type | char_to_rank (char_type const chr) |
Returns the rank representation of character. | |
static constexpr rank_type | rank_complement (rank_type const rank) |
Returns the complement by rank. | |
static constexpr char_type | rank_to_char (rank_type const rank) |
Returns the character representation of rank. | |
Private Attributes | |
friend | base_t |
Befriend seqan3::nucleotide_base. | |
Static Private Attributes | |
static constexpr char_type | rank_to_char_table [alphabet_size] {'A', 'C', 'G', 'U'} |
The lookup table used in rank_to_char. | |
Related Symbols | |
(Note that these are not member symbols.) | |
using | rna4_vector = std::vector< rna4 > |
Alias for a std::vector of seqan3::rna4. | |
Nucleotide literals | |
constexpr rna4 | operator""_rna4 (char const c) noexcept |
The seqan3::rna4 char literal. | |
constexpr rna4_vector | operator""_rna4 (char const *s, std::size_t n) |
The seqan3::rna4 string literal. | |
Related Symbols inherited from semialphabet | |
template<cereal_output_archive archive_t, semialphabet alphabet_t> | |
alphabet_rank_t< alphabet_t > | save_minimal (archive_t const &, alphabet_t const &l) |
Save an alphabet letter to stream. | |
template<cereal_input_archive archive_t, typename wrapped_alphabet_t > | |
void | load_minimal (archive_t const &, wrapped_alphabet_t &&l, alphabet_rank_t< detail::strip_cereal_wrapper_t< wrapped_alphabet_t > > const &r) |
Restore an alphabet letter from a saved rank. | |
Additional Inherited Members | |
Static Public Member Functions inherited from seqan3::nucleotide_base< rna4, 4 > | |
static constexpr bool | char_is_valid (char_type const c) noexcept |
Validate whether a character value has a one-to-one mapping to an alphabet value. | |
Static Public Attributes inherited from seqan3::alphabet_base< derived_type, size, char_t > | |
static constexpr detail::min_viable_uint_t< size > | alphabet_size = size |
The size of the alphabet, i.e. the number of different values it can take. | |
Protected Types inherited from seqan3::alphabet_base< derived_type, size, char_t > | |
using | char_type = std::conditional_t< std::same_as< char_t, void >, char, char_t > |
The char representation; conditional needed to make semi alphabet definitions legal. | |
using | rank_type = detail::min_viable_uint_t< size - 1 > |
The type of the alphabet when represented as a number (e.g. via to_rank()). | |
The four letter RNA alphabet of A,C,G,U.
This alphabet has the same internal representation as seqan3::dna4, the only difference is that it prints 'U' on character conversion instead of 'T'. You can assign between values of seqan3::dna4 and seqan3::rna4.
Like most alphabets, this alphabet cannot be initialised directly from its character representation. Instead initialise/assign from the character literal 'A'_rna4 or use the function seqan3::rna4::assign_char().
|
inlineconstexprnoexcept |
Allow implicit construction from seqan3::dna4 of the same size.
Normally, we do not allow implicit conversion of single argument constructors, but in this case we make an exception, because seqan3::rna4 and seqan3::dna4 are interchangeable as they behave nearly the same (e.g. same ranks, same char to rank conversion).
seqan3::sequence
s (e.g. seqan3::rna4_vector) in general are not implicitly convertible and must be explicitly copied to be converted: std::ranges::view
s:
|
inlinestaticconstexprprivate |
Returns the rank representation of character.
This function is required by seqan3::alphabet_base.
|
inlinestaticconstexprprivate |
Returns the complement by rank.
This function is required by seqan3::nucleotide_base.
|
inlinestaticconstexprprivate |
Returns the character representation of rank.
This function is required by seqan3::alphabet_base.
|
related |
The seqan3::rna4 string literal.
You can use this string literal to easily assign to rna4_vector:
|
related |
The seqan3::rna4 char literal.
You can use this char literal to assign a seqan3::rna4 character:
|
related |
|
staticconstexprprivate |
The lookup table used in rank_to_char.
We would have defined these lookup tables directly within their respective constexpr functions, but at the time of writing this, gcc did not (clang >= 4 did!) auto-generate lookup tables.