seqan3::rna5 Class Reference

The five letter RNA alphabet of A,C,G,U and the unknown character N. More...

#include <seqan3/alphabet/nucleotide/rna5.hpp>

Inheritance diagram for seqan3::rna5:

Public Member Functions
Constructors, destructor and assignment
constexpr	rna5 () noexcept=default
	Defaulted.
constexpr	rna5 (rna5 const &) noexcept=default
	Defaulted.
constexpr	rna5 (rna5 &&) noexcept=default
	Defaulted.
constexpr rna5 &	operator= (rna5 const &) noexcept=default
	Defaulted.
constexpr rna5 &	operator= (rna5 &&) noexcept=default
	Defaulted.
	~rna5 () noexcept=default
	Defaulted.
constexpr	rna5 (dna5 const &r) noexcept
	Allow implicit construction from dna/rna of the same size.
Public Member Functions inherited from seqan3::nucleotide_base< rna5, 5 >
constexpr rna5	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
	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. 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...

Related Functions
(Note that these are not member functions.)
using	rna5_vector = std::vector< rna5 >
	Alias for an std::vector of seqan3::rna5.
Literals
constexpr rna5	operator""_rna5 (char const c) noexcept
	The seqan3::rna5 char literal. More...
rna5_vector	operator""_rna5 (char const *s, std::size_t n)
	The seqan3::rna5 string literal. More...

Additional Inherited Members
Static Public Member Functions inherited from seqan3::nucleotide_base< rna5, 5 >
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 five letter RNA alphabet of A,C,G,U and the unknown character N.

This alphabet has the same internal representation as seqan3::dna5, the only difference is that it prints 'U' on character conversion instead of 'T'. You can assign between values of seqan3::dna5 and seqan3::rna5.

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::rna5::assign_char().

#include <seqan3/alphabet/nucleotide/rna5.hpp>
#include <seqan3/core/debug_stream.hpp>
int main()
{
    using seqan3::operator""_rna5;
 
    seqan3::rna5 my_letter{'A'_rna5};
 
    my_letter.assign_char('C');
    
    my_letter.assign_char('F'); // unknown characters are implicitly converted to N.
    if (my_letter.to_char() == 'N')
        seqan3::debug_stream << "yeah\n"; // "yeah";
}

Friends And Related Function Documentation

operator""_rna5() [1/2]

rna5_vector operator""_rna5 ( char const *  s, std::size_t  n  )

related

The seqan3::rna5 string literal.

Returns

seqan3::rna5_vector

You can use this string literal to easily assign to rna5_vector:

#include <seqan3/alphabet/nucleotide/rna5.hpp>
 
int main()
{
    using seqan3::operator""_rna5;
    
    seqan3::rna5_vector foo{"ACGTTA"_rna5};
    seqan3::rna5_vector bar = "ACGTTA"_rna5;
    auto bax = "ACGTTA"_rna5;
}

operator""_rna5() [2/2]

constexpr rna5 operator""_rna5 ( char const  c )

related

The seqan3::rna5 char literal.

Returns

seqan3::rna5

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

• seqan3/alphabet/nucleotide/rna5.hpp