SeqAn3 3.4.0-rc.1
The Modern C++ library for sequence analysis.
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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 rna5operator= (rna5 const &) noexcept=default
 Defaulted.
 
constexpr rna5operator= (rna5 &&) noexcept=default
 Defaulted.
 
 ~rna5 () noexcept=default
 Defaulted.
 
template<std::same_as< dna5 > t>
constexpr rna5 (t const &r) noexcept
 Allow implicit construction from seqan3::dna5 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.
 
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_baseoperator= (alphabet_base const &) noexcept=default
 Defaulted.
 
constexpr alphabet_baseoperator= (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.
 

Private Types

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

Static Private Member Functions

static constexpr rank_type char_to_rank (char_type const chr)
 Returns the rank representation of character.
 
static constexpr rank_type rank_complement (rank_type const rank)
 Returns the complement by rank.
 
static constexpr char_type rank_to_char (rank_type const rank)
 Returns the character representation of rank.
 

Private Attributes

friend base_t
 Befriend nucleotide_base.
 

Static Private Attributes

static constexpr char_type rank_to_char_table [alphabet_size] {'A', 'C', 'G', 'N', 'U'}
 The lookup table used in rank_to_char.
 

Related Symbols

(Note that these are not member symbols.)

using rna5_vector = std::vector< rna5 >
 Alias for a std::vector of seqan3::rna5.
 
Nucleotide literals
constexpr rna5 operator""_rna5 (char const c) noexcept
 The seqan3::rna5 char literal.
 
constexpr rna5_vector operator""_rna5 (char const *s, std::size_t n)
 The seqan3::rna5 string literal.
 

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.
 
- 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 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 'A'_rna5 or use the function seqan3::rna5::assign_char().

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
int main()
{
using namespace seqan3::literals;
seqan3::rna5 letter{'A'_rna5};
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"
}
constexpr derived_type & assign_char(char_type const chr) noexcept
Assign from a character, implicitly converts invalid characters.
Definition alphabet_base.hpp:160
The five letter RNA alphabet of A,C,G,U and the unknown character N.
Definition rna5.hpp:46
Provides seqan3::debug_stream and related types.
debug_stream_type debug_stream
A global instance of seqan3::debug_stream_type.
Definition debug_stream.hpp:37
The SeqAn namespace for literals.
Provides seqan3::rna5, container aliases and string literals.

This entity is stable. Since version 3.1.

Constructor & Destructor Documentation

◆ rna5()

template<std::same_as< dna5 > t>
constexpr seqan3::rna5::rna5 ( t const &  r)
inlineconstexprnoexcept

Allow implicit construction from seqan3::dna5 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::rna5 and seqan3::dna5 are interchangeable as they behave nearly the same (e.g. same ranks, same char to rank conversion).

int main()
{
using namespace seqan3::literals;
seqan3::rna5 letter1 = 'C'_dna5; // implicitly converted
seqan3::rna5 letter2{};
letter2 = 'C'_dna5; // implicitly converted
}
Provides seqan3::dna5, container aliases and string literals.

seqan3::sequences (e.g. seqan3::rna5_vector) in general are not implicitly convertible and must be explicitly copied to be converted:

#include <vector>
int main()
{
using namespace seqan3::literals;
seqan3::rna5_vector vector{'A'_dna5, 'C'_dna5, 'G'_dna5}; // (element-wise) implicit conversion
// but this won't work:
// seqan3::rna5_vector rna5_vector{"ACGT"_dna5};
// as a workaround you can use:
// side note: this would also work without the implicit conversion.
seqan3::dna5_vector dna5_vector = "ACGT"_dna5;
seqan3::rna5_vector rna5_vector{dna5_vector.begin(), dna5_vector.end()};
}
std::vector< rna5 > rna5_vector
Alias for a std::vector of seqan3::rna5.
Definition rna5.hpp:117

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

#include <vector>
int main()
{
using namespace seqan3::literals;
seqan3::rna5_vector vector = "ACG"_rna5;
auto dna5_view = vector | seqan3::views::convert<seqan3::dna5>;
for (auto && chr : dna5_view) // converts lazily on-the-fly
{
static_assert(std::same_as<decltype(chr), seqan3::dna5 &&>);
}
}
The five letter DNA alphabet of A,C,G,T and the unknown character N.
Definition dna5.hpp:48
Provides seqan3::views::convert.

This conversion constructor only allows converting seqan3::dna5 to seqan3::rna5. Other alphabets that inherit from seqan3::dna5 will not be implicitly convertible to seqan3::rna5.

struct my_rna5 : public seqan3::rna5
{
// using seqan3::rna5::rna5; // uncomment to import implicit conversion shown by letter1
};
struct my_dna5 : public seqan3::dna5
{};
int main()
{
using namespace seqan3::literals;
// my_rna5 letter1 = 'C'_dna5; // NO automatic implicit conversion!
// seqan3::rna5 letter2 = my_dna5{}; // seqan3::rna5 only allows implicit conversion from seqan3::dna5!
}

This entity is stable. Since version 3.1.

Member Function Documentation

◆ char_to_rank()

static constexpr rank_type seqan3::rna5::char_to_rank ( char_type const  chr)
inlinestaticconstexprprivate

Returns the rank representation of character.

This function is required by seqan3::alphabet_base.

◆ rank_complement()

static constexpr rank_type seqan3::rna5::rank_complement ( rank_type const  rank)
inlinestaticconstexprprivate

Returns the complement by rank.

This function is required by seqan3::nucleotide_base.

◆ rank_to_char()

static constexpr char_type seqan3::rna5::rank_to_char ( rank_type const  rank)
inlinestaticconstexprprivate

Returns the character representation of rank.

This function is required by seqan3::alphabet_base.

Friends And Related Symbol Documentation

◆ operator""_rna5() [1/2]

constexpr 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:

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
// generated from test/snippet/alphabet/nucleotide/@target_alphabet@_literal.cpp.in
int main()
{
using namespace seqan3::literals;
seqan3::rna5_vector sequence1{"ACGTTA"_rna5};
seqan3::rna5_vector sequence2 = "ACGTTA"_rna5;
auto sequence3 = "ACGTTA"_rna5;
}

This entity is stable. Since version 3.1.

◆ operator""_rna5() [2/2]

constexpr rna5 operator""_rna5 ( char const  c)
related

The seqan3::rna5 char literal.

Returns
seqan3::rna5

You can use this char literal to assign a seqan3::rna5 character:

int main()
{
using namespace seqan3::literals;
seqan3::rna5 letter1{'A'_rna5};
auto letter2 = 'A'_rna5;
}

This entity is stable. Since version 3.1.

◆ rna5_vector

using rna5_vector = std::vector<rna5>
related

Alias for a std::vector of seqan3::rna5.

This entity is stable. Since version 3.1.

Member Data Documentation

◆ rank_to_char_table

constexpr char_type seqan3::rna5::rank_to_char_table[alphabet_size] {'A', 'C', 'G', 'N', 'U'}
staticconstexprprivate

The lookup table used in rank_to_char.

We would have defined these lookup tables directly within their respective constexpr functions, but at the time of writing this, gcc did not (clang >= 4 did!) auto-generate lookup tables.

static constexpr char_type rank_to_char(rank_type const rank)
{
// not possible because of static not being allowed within a constexpr function
static constexpr lookup_table = ...;
return lookup_table[rank];
}
static constexpr char_type rank_to_char(rank_type const rank)
{
// up-to the compiler to optimise, no guarantee that a lookup table is used.
constexpr lookup_table = ...;
return lookup_table[rank];
}
detail::min_viable_uint_t< size - 1 > rank_type
The type of the alphabet when represented as a number (e.g. via to_rank()).
Definition alphabet_base.hpp:77
std::conditional_t< std::same_as< char_t, void >, char, char_t > char_type
The char representation; conditional needed to make semi alphabet definitions legal.
Definition alphabet_base.hpp:69
rank_type rank
The value of the alphabet letter is stored as the rank.
Definition alphabet_base.hpp:258
static constexpr char_type rank_to_char(rank_type const rank)
Returns the character representation of rank.
Definition rna5.hpp:96
See also
https://gcc.gnu.org/bugzilla/show_bug.cgi?id=99320 for the progress on gcc

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