SeqAn3  3.0.3
The Modern C++ library for sequence analysis.
seqan3::rna4 Class Reference

The four letter RNA alphabet of A,C,G,U. More...

#include <seqan3/alphabet/nucleotide/rna4.hpp>

+ Inheritance diagram for seqan3::rna4:

Public Member Functions

Constructors, destructor and assignment
constexpr rna4 () noexcept=default
constexpr rna4 (rna4 const &) noexcept=default
constexpr rna4 (rna4 &&) noexcept=default
constexpr rna4operator= (rna4 const &) noexcept=default
constexpr rna4operator= (rna4 &&) noexcept=default
 ~rna4 () noexcept=default
constexpr rna4 (dna4 const &r) noexcept
 Allow implicit construction from dna/rna 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. More...
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
constexpr alphabet_base (alphabet_base const &) noexcept=default
constexpr alphabet_base (alphabet_base &&) noexcept=default
constexpr alphabet_baseoperator= (alphabet_base const &) noexcept=default
constexpr alphabet_baseoperator= (alphabet_base &&) noexcept=default
 ~alphabet_base () noexcept=default
constexpr char_type to_char () const noexcept
 Return the letter as a character of char_type. More...
constexpr rank_type to_rank () const noexcept
 Return the letter's numeric value (rank in the alphabet). More...
constexpr derived_type & assign_char (char_type const c) noexcept
 Assign from a character, implicitly converts invalid characters. More...
constexpr derived_type & assign_rank (rank_type const c) noexcept
 Assign from a numeric value. More...

Private Types

using base_t = nucleotide_base< rna4, 4 >
 The base class.

Private Attributes

friend base_t
 Befriend seqan3::nucleotide_base.

Static Private Attributes

static constexpr std::array< rank_type, 256 > char_to_rank = dna4::char_to_rank
 Char to value conversion table. More...
static const std::array< rna4, alphabet_sizecomplement_table
 The complement table. More...
static constexpr char_type rank_to_char [alphabet_size]
 Value to char conversion table. More...

Related Functions

(Note that these are not member functions.)

using rna4_vector = std::vector< rna4 >
 Alias for an std::vector of seqan3::rna4.
constexpr rna4 operator""_rna4 (char const c) noexcept
 The seqan3::rna4 char literal. More...
rna4_vector operator""_rna4 (char const *s, std::size_t n)
 The seqan3::rna4 string literal. More...

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. More...
- 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. More...
- 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. More...
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()). More...

Detailed Description

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 or use the function seqan3::rna4::assign_char().

int main()
using seqan3::operator""_rna4;
seqan3::rna4 my_letter{'A'_rna4};
my_letter.assign_char('F'); // unknown characters are implicitly converted to A.
if (my_letter.to_char() == 'A')
seqan3::debug_stream << "yeah\n"; // "yeah";
constexpr derived_type & assign_char(char_type const c) noexcept
Assign from a character, implicitly converts invalid characters.
Definition: alphabet_base.hpp:159
The four letter RNA alphabet of A,C,G,U.
Definition: rna4.hpp:47
Provides seqan3::debug_stream and related types.
debug_stream_type debug_stream
A global instance of seqan3::debug_stream_type.
Definition: debug_stream.hpp:42
Provides seqan3::rna4, container aliases and string literals.

Friends And Related Function Documentation

◆ operator""_rna4() [1/2]

rna4_vector operator""_rna4 ( char const *  s,
std::size_t  n 

The seqan3::rna4 string literal.


You can use this string literal to easily assign to rna4_vector:

int main()
using seqan3::operator""_rna4;
seqan3::rna4_vector foo{"ACGTTA"_rna4};
seqan3::rna4_vector bar = "ACGTTA"_rna4;
auto bax = "ACGTTA"_rna4;

◆ operator""_rna4() [2/2]

constexpr rna4 operator""_rna4 ( char const  c)

The seqan3::rna4 char literal.


Member Data Documentation

◆ char_to_rank

constexpr std::array<rank_type, 256> seqan3::rna4::char_to_rank = dna4::char_to_rank

Char to value conversion table.

◆ complement_table

constexpr std::array< rna4, rna4::alphabet_size > seqan3::rna4::complement_table
Initial value:

The complement table.

◆ rank_to_char

constexpr char_type seqan3::rna4::rank_to_char[alphabet_size]
Initial value:

Value to char conversion table.

The documentation for this class was generated from the following file: