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.
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 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...

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 = size
	The size of the alphabet, i.e. the number of different values it can take. More...

Protected Types
Member types
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...

Private Types
using	base_t = nucleotide_base< rna5, 5 >
	The base class.

Private Attributes
friend	base_t
	Befriend nucleotide_base.
friend	derived_type
	Befriend the derived_type so it can instantiate.
rank_type	rank {}
	The value of the alphabet letter is stored as the rank.

Static Private Attributes
static constexpr std::array< rank_type, 256 >	char_to_rank = dna5::char_to_rank
	Char to value conversion table. More...
static const std::array< rna5, alphabet_size >	complement_table
	The complement table. More...
static constexpr char_type	rank_to_char [alphabet_size]
	Value to char conversion table. More...
static constexpr std::array< bool, 256 >	valid_char_table
	Implementation of char_is_valid().

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...
Generic serialisation functions for all seqan3::semialphabet
All types that satisfy seqan3::semialphabet can be serialised via Cereal.
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. 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";
}

Member Typedef Documentation

char_type

template<typename derived_type , size_t size, typename char_t = char>

using seqan3::alphabet_base< derived_type, size, char_t >::char_type = std::conditional_t<std::same_as<char_t, void>, char, char_t>

protectedinherited

The char representation; conditional needed to make semi alphabet definitions legal.

We need a return type for seqan3::alphabet_base::to_char and seqan3::alphabet_base::assign_char other than void to make these in-class definitions valid when char_t is void.

This entity is stable. Since version 3.1.

rank_type

template<typename derived_type , size_t size, typename char_t = char>

using seqan3::alphabet_base< derived_type, size, char_t >::rank_type = detail::min_viable_uint_t<size - 1>

protectedinherited

The type of the alphabet when represented as a number (e.g. via to_rank()).

This entity is stable. Since version 3.1.

Member Function Documentation

assign_char()

template<typename derived_type , size_t size, typename char_t = char>

constexpr derived_type& seqan3::alphabet_base< derived_type, size, char_t >::assign_char ( char_type const  c )

inlineconstexprnoexceptinherited

Assign from a character, implicitly converts invalid characters.

Parameters

c	The character to be assigned.

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

Complexity

Constant.

Exceptions

Guaranteed not to throw.

This entity is stable. Since version 3.1.

assign_rank()

template<typename derived_type , size_t size, typename char_t = char>

constexpr derived_type& seqan3::alphabet_base< derived_type, size, char_t >::assign_rank ( rank_type const  c )

inlineconstexprnoexceptinherited

Assign from a numeric value.

Parameters

c	The rank to be assigned.

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

Complexity

Constant.

Exceptions

Guaranteed not to throw.

This entity is stable. Since version 3.1.

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 ( ) const

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()

template<typename derived_type , size_t size, typename char_t = char>

constexpr char_type seqan3::alphabet_base< derived_type, size, char_t >::to_char ( ) const

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.

This entity is stable. Since version 3.1.

to_rank()

template<typename derived_type , size_t size, typename char_t = char>

constexpr rank_type seqan3::alphabet_base< derived_type, size, char_t >::to_rank ( ) const

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.

This entity is stable. Since version 3.1.

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

save_minimal()

template<cereal_output_archive archive_t, semialphabet alphabet_t>

alphabet_rank_t< alphabet_t > save_minimal ( archive_t const &  , alphabet_t const &  l  )

related

Save an alphabet letter to stream.

Template Parameters

archive_t	Must satisfy seqan3::cereal_output_archive.
alphabet_t	Type of l; must satisfy seqan3::semialphabet.

Parameters

l	The alphabet letter.

Delegates to seqan3::to_rank.

Attention

These functions are never called directly, see the Alphabet module on how to use serialisation.

This entity is stable. Since version 3.1.

Member Data Documentation

alphabet_size

template<typename derived_type , size_t size, typename char_t = char>

constexpr detail::min_viable_uint_t<size> seqan3::alphabet_base< derived_type, size, char_t >::alphabet_size = size

staticconstexprinherited

The size of the alphabet, i.e. the number of different values it can take.

This entity is stable. Since version 3.1.

char_to_rank

constexpr std::array<rank_type, 256> seqan3::rna5::char_to_rank = dna5::char_to_rank

staticconstexprprivate

Char to value conversion table.

complement_table

constexpr std::array< rna5, rna5::alphabet_size > seqan3::rna5::complement_table

staticconstexprprivate

Initial value:

{
    'U'_rna5,    
    'G'_rna5,    
    'C'_rna5,    
    'N'_rna5,    
    'A'_rna5     
}

The complement table.

rank_to_char

constexpr char_type seqan3::rna5::rank_to_char[alphabet_size]

staticconstexprprivate

Initial value:

{
        'A',
        'C',
        'G',
        'N',
        'U'
    }

Value to char conversion table.

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

• seqan3/alphabet/nucleotide/rna5.hpp