SeqAn3 3.4.0
The Modern C++ library for sequence analysis.
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seqan3::rna15 Class Reference
Alphabet » Nucleotide

The 15 letter RNA alphabet, containing all IUPAC smybols minus the gap. More...

#include <seqan3/alphabet/nucleotide/rna15.hpp>

Inheritance diagram for seqan3::rna15:

Public Member Functions

Constructors, destructor and assignment
constexpr rna15 () noexcept=default
 Defaulted.
constexpr rna15 (rna15 const &) noexcept=default
 Defaulted.
constexpr rna15 (rna15 &&) noexcept=default
 Defaulted.
constexpr rna15 & operator= (rna15 const &) noexcept=default
 Defaulted.
constexpr rna15 & operator= (rna15 &&) noexcept=default
 Defaulted.
 ~rna15 () noexcept=default
 Defaulted.
template<std::same_as< dna15 > t>
constexpr rna15 (t const &r) noexcept
 Allow implicit construction from seqan3::dna15 of the same size.
Public Member Functions inherited from seqan3::nucleotide_base< rna15, 15 >
constexpr rank_type to_rank () const noexcept
 Return the letter's numeric value (rank in the alphabet).
constexpr rna15 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.

(Note that these are not member symbols.)

using rna15_vector = std::vector<rna15>
 Alias for a std::vector of seqan3::rna15.
constexpr rna15 operator""_rna15 (char const c) noexcept
 The seqan3::rna15 char literal.
constexpr rna15_vector operator""_rna15 (char const *s, std::size_t n)
 The seqan3::rna15 string literal.

Additional Inherited Members

Static Public Member Functions inherited from seqan3::nucleotide_base< rna15, 15 >
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::nucleotide_base< rna15, 15 >
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.
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()).

Detailed Description

The 15 letter RNA alphabet, containing all IUPAC smybols minus the gap.

This alphabet has the same internal representation as seqan3::dna15, the only difference is that it prints 'U' on character conversion instead of 'T'. You can assign between values of seqan3::dna15 and seqan3::rna15.

Like most alphabets, this alphabet cannot be initialised directly from its character representation. Instead initialise/assign from the character literal 'A'_rna15 or use the function seqan3::rna15::assign_char().

// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
#include <seqan3/alphabet/nucleotide/rna15.hpp>
#include <seqan3/core/debug_stream.hpp>
int main()
{
using namespace seqan3::literals;
seqan3::rna15 letter{'A'_rna15};
letter.assign_char('C');
seqan3::debug_stream << letter << '\n'; // prints "C"
letter.assign_char('F'); // Unknown characters are implicitly converted to N.
seqan3::debug_stream << letter << '\n'; // prints "N"
}
seqan3::alphabet_base::assign_char
constexpr derived_type & assign_char(char_type const chr) noexcept
Assign from a character, implicitly converts invalid characters.
Definition alphabet_base.hpp:160
seqan3::rna15
The 15 letter RNA alphabet, containing all IUPAC smybols minus the gap.
Definition rna15.hpp:48
debug_stream.hpp
Provides seqan3::debug_stream and related types.
seqan3::debug_stream
debug_stream_type debug_stream
A global instance of seqan3::debug_stream_type.
Definition debug_stream.hpp:38
seqan3::literals
The SeqAn namespace for literals.
rna15.hpp
Provides seqan3::rna15, container aliases and string literals.

This entity is stable. Since version 3.1.

Constructor & Destructor Documentation

◆ rna15()

template<std::same_as< dna15 > t>
seqan3::rna15::rna15 ( t const & r)
inlineconstexprnoexcept

Allow implicit construction from seqan3::dna15 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::rna15 and seqan3::dna15 are interchangeable as they behave nearly the same (e.g. same ranks, same char to rank conversion).

#include <seqan3/alphabet/nucleotide/dna15.hpp>
#include <seqan3/alphabet/nucleotide/rna15.hpp>
int main()
{
using namespace seqan3::literals;
seqan3::rna15 letter1 = 'C'_dna15; // implicitly converted
seqan3::rna15 letter2{};
letter2 = 'C'_dna15; // implicitly converted
}


seqan3::sequences (e.g. seqan3::rna15_vector) in general are not implicitly convertible and must be explicitly copied to be converted:

#include <vector>
#include <seqan3/alphabet/nucleotide/dna15.hpp>
#include <seqan3/alphabet/nucleotide/rna15.hpp>
int main()
{
using namespace seqan3::literals;
seqan3::rna15_vector vector{'A'_dna15, 'C'_dna15, 'G'_dna15}; // (element-wise) implicit conversion
// but this won't work:
// seqan3::rna15_vector rna15_vector{"ACGT"_dna15};
// as a workaround you can use:
// side note: this would also work without the implicit conversion.
seqan3::dna15_vector dna15_vector = "ACGT"_dna15;
seqan3::rna15_vector rna15_vector{dna15_vector.begin(), dna15_vector.end()};
}


You can avoid this copy by using std::ranges::views:

#include <vector>
#include <seqan3/alphabet/nucleotide/dna15.hpp>
#include <seqan3/alphabet/nucleotide/rna15.hpp>
#include <seqan3/utility/views/convert.hpp>
int main()
{
using namespace seqan3::literals;
seqan3::rna15_vector vector = "ACG"_rna15;
auto dna15_view = vector | seqan3::views::convert<seqan3::dna15>;
for (auto && chr : dna15_view) // converts lazily on-the-fly
{
static_assert(std::same_as<decltype(chr), seqan3::dna15 &&>);
}
}


This conversion constructor only allows converting seqan3::dna15 to seqan3::rna15. Other alphabets that inherit from seqan3::dna15 will not be implicitly convertible to seqan3::rna15.

#include <seqan3/alphabet/nucleotide/dna15.hpp>
#include <seqan3/alphabet/nucleotide/rna15.hpp>
struct my_rna15 : public seqan3::rna15
{
// using seqan3::rna15::rna15; // uncomment to import implicit conversion shown by letter1
};
struct my_dna15 : public seqan3::dna15
{};
int main()
{
using namespace seqan3::literals;
// my_rna15 letter1 = 'C'_dna15; // NO automatic implicit conversion!
// seqan3::rna15 letter2 = my_dna15{}; // seqan3::rna15 only allows implicit conversion from seqan3::dna15!
}

This entity is stable. Since version 3.1.

◆ operator""_rna15() [1/2]

rna15_vector operator""_rna15 ( char const * s,
std::size_t n )
related

The seqan3::rna15 string literal.

Returns
seqan3::rna15_vector

You can use this string literal to easily assign to rna15_vector:

// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
// generated from test/snippet/alphabet/nucleotide/@target_alphabet@_literal.cpp.in
#include <seqan3/alphabet/nucleotide/rna15.hpp>
int main()
{
using namespace seqan3::literals;
seqan3::rna15_vector sequence1{"ACGTTA"_rna15};
seqan3::rna15_vector sequence2 = "ACGTTA"_rna15;
auto sequence3 = "ACGTTA"_rna15;
}

This entity is stable. Since version 3.1.

◆ operator""_rna15() [2/2]

rna15 operator""_rna15 ( char const c)
related

The seqan3::rna15 char literal.

Returns
seqan3::rna15

You can use this char literal to assign a seqan3::rna15 character:

#include <seqan3/alphabet/nucleotide/rna15.hpp>
int main()
{
using namespace seqan3::literals;
seqan3::rna15 letter1{'A'_rna15};
auto letter2 = 'A'_rna15;
}

This entity is stable. Since version 3.1.

◆ rna15_vector

using rna15_vector = std::vector<rna15>
related

Alias for a std::vector of seqan3::rna15.

This entity is stable. Since version 3.1.

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