seqan3::dot_bracket3 Class Reference

The three letter RNA structure alphabet of the characters ".()". More...

#include <seqan3/alphabet/structure/dot_bracket3.hpp>

Inheritance diagram for seqan3::dot_bracket3:

Public Member Functions
Constructors, destructor and assignment
constexpr	dot_bracket3 () noexcept=default
	Defaulted.
constexpr	dot_bracket3 (dot_bracket3 const &) noexcept=default
	Defaulted.
constexpr	dot_bracket3 (dot_bracket3 &&) noexcept=default
	Defaulted.
constexpr dot_bracket3 &	operator= (dot_bracket3 const &) noexcept=default
	Defaulted.
constexpr dot_bracket3 &	operator= (dot_bracket3 &&) noexcept=default
	Defaulted.
	~dot_bracket3 () noexcept=default
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 dot_bracket3 &	assign_char (char_type const c) noexcept
	Assign from a character, implicitly converts invalid characters. More...
constexpr dot_bracket3 &	assign_rank (rank_type const c) noexcept
	Assign from a numeric 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()).

Related Functions
(Note that these are not member functions.)
Literals
std::vector< dot_bracket3 >	operator""_db3 (const char *str, std::size_t len)
	The seqan3::db3 string literal. More...
constexpr dot_bracket3	operator""_db3 (char const ch) noexcept
	The seqan3::db3 char literal. More...
Requirements for std::totally_ordered
You can expect these functions on all types that implement std::totally_ordered.
bool	operator< (type const &lhs, type const &rhs)
	Less-than, greater-than and -or-equal comparisons. More...
bool	operator<= (type const &lhs, type const &rhs)
	Less-than, greater-than and -or-equal comparisons. More...
bool	operator> (type const &lhs, type const &rhs)
	Less-than, greater-than and -or-equal comparisons. More...
bool	operator>= (type const &lhs, type const &rhs)
	Less-than, greater-than and -or-equal comparisons. More...
Requirements for std::equality_comparable
You can expect these functions on all types that implement std::Equality_comparable.
bool	operator== (type const &lhs, type const &rhs)
	(In-)Equality comparison. More...
bool	operator!= (type const &lhs, type const &rhs)
	(In-)Equality comparison. More...
Requirements for std::swappable
You can expect these functions on all types that implement std::swappable.
void	swap (t &lhs, t &rhs)
	Swaps the contents of two objects. More...

RNA structure properties
static constexpr uint8_t	max_pseudoknot_depth {1u}
	The ability of this alphabet to represent pseudoknots, i.e. crossing interactions, up to a certain depth. More...
constexpr bool	is_pair_open () const noexcept
	Check whether the character represents a rightward interaction in an RNA structure. More...
constexpr bool	is_pair_close () const noexcept
	Check whether the character represents a leftward interaction in an RNA structure. More...
constexpr bool	is_unpaired () const noexcept
	Check whether the character represents an unpaired position in an RNA structure. More...
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. More...

Detailed Description

The three letter RNA structure alphabet of the characters ".()".

The brackets denote RNA base pair interactions. Every left bracket must have a corresponding right bracket. Pseudoknots cannot be expressed in this format. A dot (.) represents a character that is not paired.

GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUUUGGAGGUCCUGUGUUCGAUCCACAGAAUUCGCA
(((((((..((((........)))).((((.........)))).....(((((.......)))))))))))).

Usage

The following code example creates a dot_bracket3 vector, modifies it, and prints the result to stderr.

#include <vector>
 
#include <seqan3/alphabet/structure/dot_bracket3.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using seqan3::operator""_db3;
 
    // create vector
    std::vector<seqan3::dot_bracket3> vec{'.'_db3, ')'_db3, ')'_db3};
 
    // modify and print
    vec[1] = '('_db3;
 
    for (seqan3::dot_bracket3 chr : vec)
        seqan3::debug_stream << seqan3::to_char(chr);  // .()
 
    seqan3::debug_stream << "\n";
}

Constructor & Destructor Documentation

~dot_bracket3()

seqan3::dot_bracket3::~dot_bracket3 ( )

defaultnoexcept

Defaulted.

Member Function Documentation

assign_char()

constexpr dot_bracket3 & seqan3::alphabet_base< dot_bracket3 , size, char >::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.

assign_rank()

constexpr dot_bracket3 & seqan3::alphabet_base< dot_bracket3 , size, char >::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.

is_pair_close()

constexpr bool seqan3::dot_bracket3::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.

is_pair_open()

constexpr bool seqan3::dot_bracket3::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.

is_unpaired()

constexpr bool seqan3::dot_bracket3::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.

pseudoknot_id()

constexpr std::optional<uint8_t> seqan3::dot_bracket3::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 (always 0) if alph denotes an interaction, and no value otherwise.

to_char()

constexpr char_type seqan3::alphabet_base< dot_bracket3 , size, char >::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.

to_rank()

constexpr rank_type seqan3::alphabet_base< dot_bracket3 , size, char >::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.

Friends And Related Function Documentation

operator""_db3() [1/2]

constexpr dot_bracket3 operator""_db3 ( char const  ch )

related

The seqan3::db3 char literal.

Parameters

[in]

ch

The character to represent as dot bracket.

Returns

seqan3::dot_bracket3

You can use this string literal to assign a seqan3::dot_bracket3 character:

#include <seqan3/alphabet/structure/dot_bracket3.hpp>
 
int main()
{
    using seqan3::operator""_db3;
 
    // Using the char literal to assign a single dot bracket:
    seqan3::dot_bracket3 my_letter{'('_db3};
    
    my_letter.assign_char(')');             // <- assigns the char explicitly
}

operator""_db3() [2/2]

std::vector< dot_bracket3 > operator""_db3 ( const char *  str, std::size_t  len  )

related

The seqan3::db3 string literal.

Parameters

[in]	str	A pointer to the character string to assign.
[in]	len	The size of the character string to assign.

Returns

std::vector<seqan3::dot_bracket3>

You can use this string literal to easily assign to a vector of seqan3::dot_bracket3 characters:

#include <vector>
 
#include <seqan3/alphabet/structure/dot_bracket3.hpp>
 
int main()
{
    using seqan3::operator""_db3;
 
    // Using the string literal to assign a vector of dot brackets:
    std::vector<seqan3::dot_bracket3> foo{".(..)."_db3};
    std::vector<seqan3::dot_bracket3> bar = ".(..)."_db3;
    auto bax = ".(..)."_db3;
}

Member Data Documentation

max_pseudoknot_depth

constexpr uint8_t seqan3::dot_bracket3::max_pseudoknot_depth {1u}

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. The value 1 denotes no pseudoknot support.

---

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

• seqan3/alphabet/structure/dot_bracket3.hpp