SeqAn3  3.0.2
The Modern C++ library for sequence analysis.
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

Read functions
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...
 
Write functions
constexpr rna5assign_char (char_type const c) noexcept
 Assign from a character, implicitly converts invalid characters. More...
 
constexpr rna5assign_rank (rank_type const c) noexcept
 Assign from a numeric value. More...
 
Read functions
constexpr rna5 complement () const noexcept
 Return the complement of the letter. More...
 
Read functions
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...
 
Write functions
constexpr rna5assign_char (char_type const c) noexcept
 Assign from a character, implicitly converts invalid characters. More...
 
constexpr rna5assign_rank (rank_type const c) noexcept
 Assign from a numeric value. More...
 
Constructors, destructor and assignment
constexpr rna5 () noexcept=default
 Defaulted.
 
constexpr rna5 (rna5 const &) noexcept=default
 Defaulted.
 
constexpr rna5 (rna5 &&) noexcept=default
 Defaulted.
 
constexpr rna5operator= (rna5 const &) noexcept=default
 Defaulted.
 
constexpr rna5operator= (rna5 &&) noexcept=default
 Defaulted.
 
 ~rna5 () noexcept=default
 Defaulted.
 
constexpr rna5 (dna5 const &r) noexcept
 Allow implicit construction from dna/rna of the same size.
 
Read functions
constexpr rna5 complement () const noexcept
 Return the complement of the letter. More...
 
Read functions
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...
 
Write functions
constexpr rna5assign_char (char_type const c) noexcept
 Assign from a character, implicitly converts invalid characters. More...
 
constexpr rna5assign_rank (rank_type const c) noexcept
 Assign from a numeric value. More...
 

Static Public Member Functions

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

static constexpr detail::min_viable_uint_t< size > alphabet_size
 The size of the alphabet, i.e. the number of different values it can take.
 

Protected Types

Member types
using char_type = std::conditional_t< std::same_as< char, void >, char, char >
 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()).
 
Member types
using char_type = std::conditional_t< std::same_as< char, void >, char, char >
 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()).
 
Member types
using char_type = std::conditional_t< std::same_as< char, void >, char, char >
 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()).
 

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...
 

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().

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";
}

Member Function Documentation

◆ assign_char()

constexpr rna5 & seqan3::alphabet_base< rna5 , size, char >::assign_char ( char_type const  c)
inlineconstexprnoexceptinherited

Assign from a character, implicitly converts invalid characters.

Parameters
cThe character to be assigned.

Provides an implementation for seqan3::assign_char_to, required to model seqan3::alphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ assign_rank()

constexpr rna5 & seqan3::alphabet_base< rna5 , size, char >::assign_rank ( rank_type const  c)
inlineconstexprnoexceptinherited

Assign from a numeric value.

Parameters
cThe rank to be assigned.

Provides an implementation for seqan3::assign_rank_to, required to model seqan3::semialphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ char_is_valid()

static constexpr bool seqan3::nucleotide_base< rna5 , size >::char_is_valid ( char_type const  c)
inlinestaticconstexprnoexceptinherited

Validate whether a character value has a one-to-one mapping to an alphabet value.

Satisfies the seqan3::semialphabet::char_is_valid_for() requirement via the seqan3::char_is_valid_for() wrapper.

Behaviour specific to nucleotides: True also for lower case letters that silently convert to their upper case and true also for U/T respectively, e.g. 'U' is a valid character for seqan3::dna4, because its informational content is identical to 'T'.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ complement()

constexpr rna5 seqan3::nucleotide_base< rna5 , size >::complement
inlineconstexprnoexceptinherited

Return the complement of the letter.

See Nucleotide for the actual values.

Provides an implementation for seqan3::complement, required to model seqan3::nucleotide_alphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ to_char()

constexpr char_type seqan3::alphabet_base< rna5 , size, char >::to_char
inlineconstexprnoexceptinherited

Return the letter as a character of char_type.

Provides an implementation for seqan3::to_char, required to model seqan3::alphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ to_rank()

constexpr rank_type seqan3::alphabet_base< rna5 , size, char >::to_rank
inlineconstexprnoexceptinherited

Return the letter's numeric value (rank in the alphabet).

Provides an implementation for seqan3::to_rank, required to model seqan3::semialphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

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:

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

The documentation for this class was generated from the following file:
debug_stream.hpp
Provides seqan3::debug_stream and related types.
seqan3::alphabet_base::assign_char
constexpr derived_type & assign_char(char_type const c) noexcept
Assign from a character, implicitly converts invalid characters.
Definition: alphabet_base.hpp:142
seqan3::rna5
The five letter RNA alphabet of A,C,G,U and the unknown character N.
Definition: rna5.hpp:46
rna5.hpp
Provides seqan3::rna5, container aliases and string literals.
seqan3::debug_stream
debug_stream_type debug_stream
A global instance of seqan3::debug_stream_type.
Definition: debug_stream.hpp:42