The WUSS structure alphabet of the characters .<>:,-_~;()[]{}AaBbCcDd... More...

#include <seqan3/alphabet/structure/wuss.hpp>

Inheritance diagram for seqan3::wuss< SIZE >:

Public Member Functions
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).

Constructors, destructor and assignment
constexpr	wuss () noexcept=default
	Defaulted.

constexpr	wuss (wuss const &) noexcept=default
	Defaulted.

constexpr	wuss (wuss &&) noexcept=default
	Defaulted.

constexpr wuss &	operator= (wuss const &) noexcept=default
	Defaulted.

constexpr wuss &	operator= (wuss &&) noexcept=default
	Defaulted.

	~wuss () noexcept=default
	Defaulted.

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.

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.

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
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()).

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()).

Related Symbols
(Note that these are not member symbols.)
using	wuss51 = wuss< 51 >
	Alias for the default type wuss51.

RNA structure properties
static constexpr uint8_t	max_pseudoknot_depth {static_cast<uint8_t>((alphabet_size - 7) / 2)}
	The ability of this alphabet to represent pseudoknots, i.e. crossing interactions, up to a certain depth. It is the number of distinct pairs of interaction symbols the format supports: 4..30 (depends on size)

constexpr bool	is_pair_open () const noexcept
	Check whether the character represents a rightward interaction in an RNA structure.

constexpr bool	is_pair_close () const noexcept
	Check whether the character represents a leftward interaction in an RNA structure.

constexpr bool	is_unpaired () const noexcept
	Check whether the character represents an unpaired position in an RNA structure.

constexpr std::optional< uint8_t >	pseudoknot_id () const noexcept
	Get an identifier for a pseudoknotted interaction, where opening and closing brackets of the same type have the same id.

Detailed Description

template<uint8_t SIZE = 51>
class seqan3::wuss< SIZE >

The WUSS structure alphabet of the characters .<>:,-_~;()[]{}AaBbCcDd...

Template Parameters

SIZE	The alphabet size defaults to 51 and must be an odd number in range 15..67. It determines the allowed pseudoknot depth by adding characters AaBb..Zz to the alphabet.

The symbols .:,-_~; denote unpaired characters, brackets <>()[]{} represent base pair interactions and AaBbCcDd... form pseudoknots in the structure. The default alphabet has size 51 (letters until Rr). The size can be varied with the optional template parameter between 15 (no letters for pseudoknots) and 67 (all Aa-Zz for pseudoknots).

<<<___>>>,,<<<__>>>

<<<<_AAAA____>>>>aaaa

Example

// 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
 
#include <seqan3/alphabet/structure/wuss.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::wuss51 letter{':'_wuss51};
 
    letter.assign_char('~');
    seqan3::debug_stream << letter << '\n'; // prints "~"
 
    letter.assign_char('#');                // Unknown characters are implicitly converted to ';'.
    seqan3::debug_stream << letter << '\n'; // prints ";"
}

This entity is experimental and subject to change in the future. Experimental since version 3.1.

Member Typedef Documentation

◆ char_type

template<uint8_t SIZE = 51>

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

protected

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.

Attention: Please use seqan3::alphabet_char_t to access this type.

This entity is stable. Since version 3.1.

◆ rank_type

template<uint8_t SIZE = 51>

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

protected

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

Attention: Please use seqan3::alphabet_rank_t to access this type.

This entity is stable. Since version 3.1.

Member Function Documentation

◆ is_pair_close()

template<uint8_t SIZE = 51>

constexpr bool seqan3::wuss< SIZE >::is_pair_close ( ) const

inlineconstexprnoexcept

Check whether the character represents a leftward interaction in an RNA structure.

Returns: True if the letter represents a leftward interaction, False otherwise.

This entity is experimental and subject to change in the future. Experimental since version 3.1.

◆ is_pair_open()

template<uint8_t SIZE = 51>

constexpr bool seqan3::wuss< SIZE >::is_pair_open ( ) const

inlineconstexprnoexcept

Check whether the character represents a rightward interaction in an RNA structure.

Returns: True if the letter represents a rightward interaction, False otherwise.

This entity is experimental and subject to change in the future. Experimental since version 3.1.

◆ is_unpaired()

template<uint8_t SIZE = 51>

constexpr bool seqan3::wuss< SIZE >::is_unpaired ( ) const

inlineconstexprnoexcept

Check whether the character represents an unpaired position in an RNA structure.

Returns: True if the letter represents an unpaired site, False otherwise.

This entity is experimental and subject to change in the future. Experimental since version 3.1.

◆ pseudoknot_id()

template<uint8_t SIZE = 51>

constexpr std::optional< uint8_t > seqan3::wuss< SIZE >::pseudoknot_id ( ) const

inlineconstexprnoexcept

Get an identifier for a pseudoknotted interaction, where opening and closing brackets of the same type have the same id.

Returns: The pseudoknot id, if alph denotes an interaction, and no value otherwise.

It is guaranteed to be smaller than seqan3::max_pseudoknot_depth.

This entity is experimental and subject to change in the future. Experimental since version 3.1.

◆ to_char()

template<uint8_t SIZE = 51>

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

inlineconstexprnoexcept

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<uint8_t SIZE = 51>

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

inlineconstexprnoexcept

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.

Member Data Documentation

◆ alphabet_size

template<uint8_t SIZE = 51>

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

staticconstexpr

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

This entity is stable. Since version 3.1.

◆ max_pseudoknot_depth

template<uint8_t SIZE = 51>

constexpr uint8_t seqan3::wuss< SIZE >::max_pseudoknot_depth {static_cast<uint8_t>((alphabet_size - 7) / 2)}

staticconstexpr

The ability of this alphabet to represent pseudoknots, i.e. crossing interactions, up to a certain depth. It is the number of distinct pairs of interaction symbols the format supports: 4..30 (depends on size)

This entity is experimental and subject to change in the future. Experimental since version 3.1.

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

wuss.hpp

Public Member Functions

Static Public Attributes

Protected Types

Related Symbols

RNA structure properties

Detailed Description

Example

Member Typedef Documentation

◆ char_type

◆ rank_type

Member Function Documentation

◆ is_pair_close()

◆ is_pair_open()

◆ is_unpaired()

◆ pseudoknot_id()

◆ to_char()

Complexity

Exceptions

◆ to_rank()

Complexity

Exceptions

Member Data Documentation

◆ alphabet_size

◆ max_pseudoknot_depth