seqan3::structured_rna< sequence_alphabet_t, structure_alphabet_t > Class Template Reference

A seqan3::alphabet_tuple_base that joins a nucleotide alphabet with an RNA structure alphabet. More...

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

Inheritance diagram for seqan3::structured_rna< sequence_alphabet_t, structure_alphabet_t >:

Public Types
using	char_type = alphabet_char_t< sequence_alphabet_type >
	Equals the char_type of sequence_alphabet_type.
using	sequence_alphabet_type = sequence_alphabet_t
	First template parameter as member type.
using	structure_alphabet_type = structure_alphabet_t
	Second template parameter as member type.

Public Member Functions
Constructors, destructor and assignment
constexpr	structured_rna () noexcept=default
	Defaulted.
constexpr	structured_rna (structured_rna const &) noexcept=default
	Defaulted.
constexpr	structured_rna (structured_rna &&) noexcept=default
	Defaulted.
constexpr structured_rna &	operator= (structured_rna const &) noexcept=default
	Defaulted.
constexpr structured_rna &	operator= (structured_rna &&) noexcept=default
	Defaulted.
	~structured_rna () noexcept=default
	Defaulted.
constexpr	structured_rna (component_type const alph) noexcept
	Construction via a value of one of the components.
constexpr	structured_rna (indirect_component_type const alph) noexcept
	Construction via a value of a subtype that is assignable to one of the components.
constexpr structured_rna &	operator= (component_type const alph) noexcept
	Assignment via a value of one of the components.
constexpr structured_rna &	operator= (indirect_component_type const alph) noexcept
	Assignment via a value of a subtype that is assignable to one of the components.
Write functions
constexpr structured_rna &	assign_char (char_type const c) noexcept
	Assign from a nucleotide character. This modifies the internal sequence letter.
Read functions
constexpr char_type	to_char () const noexcept
	Return a character. This reads the internal sequence letter.
constexpr structured_rna	complement () const noexcept
	Return a structured_rna where the sequence letter is converted to its complement.
Public Member Functions inherited from seqan3::alphabet_tuple_base< structured_rna< sequence_alphabet_t, structure_alphabet_t >, sequence_alphabet_t, structure_alphabet_t >
constexpr	alphabet_tuple_base (component_types... components) noexcept
	Construction from initialiser-list.
constexpr	alphabet_tuple_base (component_type const alph) noexcept
	Construction via a value of one of the components.
constexpr	alphabet_tuple_base (indirect_component_type const alph) noexcept
	Construction via a value of a subtype that is assignable to one of the components.
constexpr structured_rna< sequence_alphabet_t, structure_alphabet_t > &	operator= (component_type const alph) noexcept
	Assignment via a value of one of the components.
constexpr structured_rna< sequence_alphabet_t, structure_alphabet_t > &	operator= (indirect_component_type const alph) noexcept
	Assignment via a value of a subtype that is assignable to one of the components.
constexpr	operator type () const noexcept
	Implicit cast to a single letter. Works only if the type is unique in the type list.
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 Member Functions
static constexpr bool	char_is_valid (char_type const c) noexcept
	Validate whether a character is valid in the sequence alphabet.

Related Symbols
(Note that these are not member symbols.)
template<typename sequence_alphabet_type , typename structure_alphabet_type >
	structured_rna (sequence_alphabet_type &&, structure_alphabet_type &&) -> structured_rna< std::decay_t< sequence_alphabet_type >, std::decay_t< structure_alphabet_type > >
	Type deduction guide enables usage of structured_rna without specifying template args.

RNA structure properties
static constexpr uint8_t	max_pseudoknot_depth {structure_alphabet_t::max_pseudoknot_depth}
	The ability of this alphabet to represent pseudoknots, i.e. crossing interactions.
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.

Additional Inherited Members
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

template<nucleotide_alphabet sequence_alphabet_t, rna_structure_alphabet structure_alphabet_t>
requires writable_alphabet<sequence_alphabet_t> && writable_alphabet<structure_alphabet_t>
class seqan3::structured_rna< sequence_alphabet_t, structure_alphabet_t >

A seqan3::alphabet_tuple_base that joins a nucleotide alphabet with an RNA structure alphabet.

Template Parameters

sequence_alphabet_t	Type of the first letter; must model seqan3::writable_alphabet, seqan3::nucleotide_alphabet and satisfy the requirements on arguments by seqan3::alphabet_tuple_base.
structure_alphabet_t	Types of further letters; must model seqan3::writable_alphabet, seqan3::rna_structure_alphabet and satisfy the requirements on arguments by seqan3::alphabet_tuple_base.

This composite pairs a nucleotide alphabet with a structure alphabet. The rank values correspond to numeric values in the size of the composite, while the character values are taken from the sequence alphabet and the structure annotation is taken from the structure alphabet.

As with all seqan3::alphabet_tuple_base s you may access the individual alphabet letters in regular c++ tuple notation, i.e. get<0>(t) and objects can be brace-initialized with the individual members.

// 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/nucleotide/rna4.hpp>
#include <seqan3/alphabet/structure/dot_bracket3.hpp>
#include <seqan3/alphabet/structure/structured_rna.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using namespace seqan3::literals;
    using seqan3::get;
 
    seqan3::structured_rna<seqan3::rna4, seqan3::dot_bracket3> letter{'G'_rna4, '('_db3};
 
    seqan3::debug_stream << seqan3::to_rank(letter) << ' '           // 7
                         << seqan3::to_rank(get<0>(letter)) << ' '   // 2
                         << seqan3::to_rank(get<1>(letter)) << '\n'; // 1
 
    seqan3::debug_stream << seqan3::to_char(letter) << ' '           // G
                         << seqan3::to_char(get<0>(letter)) << ' '   // G
                         << seqan3::to_char(get<1>(letter)) << '\n'; // (
 
    // Modify:
    get<0>(letter) = 'U'_rna4;
    seqan3::debug_stream << seqan3::to_char(letter) << '\n'; // U
}

This seqan3::alphabet_tuple_base itself models both seqan3::nucleotide_alphabet and seqan3::rna_structure_alphabet.

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

Member Typedef Documentation

char_type

template<nucleotide_alphabet sequence_alphabet_t, rna_structure_alphabet structure_alphabet_t>

using seqan3::structured_rna< sequence_alphabet_t, structure_alphabet_t >::char_type = alphabet_char_t<sequence_alphabet_type>

Equals the char_type of sequence_alphabet_type.

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

sequence_alphabet_type

template<nucleotide_alphabet sequence_alphabet_t, rna_structure_alphabet structure_alphabet_t>

using seqan3::structured_rna< sequence_alphabet_t, structure_alphabet_t >::sequence_alphabet_type = sequence_alphabet_t

First template parameter as member type.

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

structure_alphabet_type

template<nucleotide_alphabet sequence_alphabet_t, rna_structure_alphabet structure_alphabet_t>

using seqan3::structured_rna< sequence_alphabet_t, structure_alphabet_t >::structure_alphabet_type = structure_alphabet_t

Second template parameter as member type.

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

Constructor & Destructor Documentation

structured_rna() [1/2]

template<nucleotide_alphabet sequence_alphabet_t, rna_structure_alphabet structure_alphabet_t>

constexpr seqan3::structured_rna< sequence_alphabet_t, structure_alphabet_t >::structured_rna ( component_type const  alph )

inlineconstexprnoexcept

Construction via a value of one of the components.

See also

seqan3::alphabet_tuple_base::alphabet_tuple_base(component_type const alph)

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

structured_rna() [2/2]

template<nucleotide_alphabet sequence_alphabet_t, rna_structure_alphabet structure_alphabet_t>

constexpr seqan3::structured_rna< sequence_alphabet_t, structure_alphabet_t >::structured_rna ( indirect_component_type const  alph )

inlineconstexprnoexcept

Construction via a value of a subtype that is assignable to one of the components.

See also

seqan3::alphabet_tuple_base::alphabet_tuple_base(indirect_component_type const alph)

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

Member Function Documentation

assign_char()

template<nucleotide_alphabet sequence_alphabet_t, rna_structure_alphabet structure_alphabet_t>

constexpr structured_rna & seqan3::structured_rna< sequence_alphabet_t, structure_alphabet_t >::assign_char ( char_type const  c )

inlineconstexprnoexcept

Assign from a nucleotide character. This modifies the internal sequence letter.

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

char_is_valid()

template<nucleotide_alphabet sequence_alphabet_t, rna_structure_alphabet structure_alphabet_t>

static constexpr bool seqan3::structured_rna< sequence_alphabet_t, structure_alphabet_t >::char_is_valid ( char_type const  c )

inlinestaticconstexprnoexcept

Validate whether a character is valid in the sequence alphabet.

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

complement()

template<nucleotide_alphabet sequence_alphabet_t, rna_structure_alphabet structure_alphabet_t>

constexpr structured_rna seqan3::structured_rna< sequence_alphabet_t, structure_alphabet_t >::complement ( ) const

inlineconstexprnoexcept

Return a structured_rna where the sequence letter is converted to its complement.

See Nucleotide for the actual values. Satisfies the seqan3::nucleotide_alphabet::complement() requirement via the seqan3::complement() wrapper. The structure letter is not modified.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

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

is_pair_close()

template<nucleotide_alphabet sequence_alphabet_t, rna_structure_alphabet structure_alphabet_t>

constexpr bool seqan3::structured_rna< sequence_alphabet_t, structure_alphabet_t >::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<nucleotide_alphabet sequence_alphabet_t, rna_structure_alphabet structure_alphabet_t>

constexpr bool seqan3::structured_rna< sequence_alphabet_t, structure_alphabet_t >::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<nucleotide_alphabet sequence_alphabet_t, rna_structure_alphabet structure_alphabet_t>

constexpr bool seqan3::structured_rna< sequence_alphabet_t, structure_alphabet_t >::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.

operator=() [1/2]

template<nucleotide_alphabet sequence_alphabet_t, rna_structure_alphabet structure_alphabet_t>

constexpr structured_rna & seqan3::structured_rna< sequence_alphabet_t, structure_alphabet_t >::operator= ( component_type const  alph )

inlineconstexprnoexcept

Assignment via a value of one of the components.

See also

seqan3::alphabet_tuple_base::operator=(component_type const alph)

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

operator=() [2/2]

template<nucleotide_alphabet sequence_alphabet_t, rna_structure_alphabet structure_alphabet_t>

constexpr structured_rna & seqan3::structured_rna< sequence_alphabet_t, structure_alphabet_t >::operator= ( indirect_component_type const  alph )

inlineconstexprnoexcept

Assignment via a value of a subtype that is assignable to one of the components.

See also

seqan3::alphabet_tuple_base::operator=(indirect_component_type const alph)

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

pseudoknot_id()

template<nucleotide_alphabet sequence_alphabet_t, rna_structure_alphabet structure_alphabet_t>

constexpr std::optional< uint8_t > seqan3::structured_rna< sequence_alphabet_t, structure_alphabet_t >::pseudoknot_id ( ) const

inlineconstexprnoexcept

Get an identifier for a pseudoknotted interaction.

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<nucleotide_alphabet sequence_alphabet_t, rna_structure_alphabet structure_alphabet_t>

constexpr char_type seqan3::structured_rna< sequence_alphabet_t, structure_alphabet_t >::to_char ( ) const

inlineconstexprnoexcept

Return a character. This reads the internal sequence letter.

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

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

• structured_rna.hpp