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. More...

constexpr	structured_rna (indirect_component_type const alph) noexcept
	Construction via a value of a subtype that is assignable to one of the components. More...

constexpr structured_rna &	operator= (component_type const alph) noexcept
	Assignment via a value of one of the components. More...

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. More...

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. More...

Read functions
All read operations are constant complexity.
constexpr	operator type () const noexcept
	Implicit cast to a single letter. Works only if the type is unique in the type list.

Read functions
constexpr rank_type	to_rank () const noexcept
	Return the letter's numeric value (rank in the alphabet). More...

Write functions
constexpr structured_rna< sequence_alphabet_t, structure_alphabet_t > &	assign_char (char_type const c) noexcept
	Assign from a character, implicitly converts invalid characters. More...

constexpr structured_rna< sequence_alphabet_t, structure_alphabet_t > &	assign_rank (rank_type const c) noexcept
	Assign from a numeric value. More...

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.

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. More...

Protected Types
Member types
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()). More...

Private Types
using	base_t = alphabet_base< structured_rna< sequence_alphabet_t, structure_alphabet_t >,(1 ... alphabet_size< component_types >), void >
	The base type of this class.

using	base_type = alphabet_tuple_base< structured_rna< sequence_alphabet_t, structure_alphabet_t >, sequence_alphabet_t, structure_alphabet_t >
	The base type.

using	component_list = meta::list< component_types... >
	A meta::list The types of each component in the composite.

using	seqan3_recursive_required_types = meta::concat< component_list, detail::transformation_trait_or_t< detail::recursive_required_types< component_types >, meta::list<> >... >
	Export this type's components and possibly the components' components in a visible manner.

using	seqan3_required_types = component_list
	Export this type's components in a visible manner.

Private Member Functions
constexpr void	assign_component_rank (ptrdiff_t const r) noexcept
	Assign via the rank of i-th component (does not update other components' state).

constexpr rank_type	to_component_rank () const noexcept
	Return the rank of the i-th component.

Static Private Member Functions
static constexpr rank_type	rank_sum_helper (component_types ... components, std::index_sequence< idx... > const &) noexcept
	For the given components, compute the combined rank.

Private Attributes
friend	derived_type
	Befriend the derived type so that it can instantiate. More...

rank_type	rank
	The value of the alphabet letter is stored as the rank.

Static Private Attributes
static constexpr std::array< rank_type, component_list::size()>	cummulative_alph_sizes
	The cumulative alphabet size products are cached.

static constexpr bool	is_component
	Is set to `true` if the type is contained in the type list.

static constexpr bool	is_unique_component
	Is set to `true` if the type is uniquely contained in the type list.

static constexpr bool	seqan3_alphabet_tuple_like
	Make specialisations of this template identifiable in metapgrogramming contexts.

Related Functions
(Note that these are not member functions.)
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.

Generic serialisation functions for all seqan3::semialphabet
All types that satisfy seqan3::semialphabet can be serialised via Cereal.
template<cereal_output_archive archive_t, semialphabet alphabet_t>
alphabet_rank_t< alphabet_t >	save_minimal (archive_t const &, alphabet_t const &l)
	Save an alphabet letter to stream. More...

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. 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. More...

Detailed Description

template<nucleotide_alphabet sequence_alphabet_t, rna_structure_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 correpsond 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.

#include <seqan3/alphabet/structure/structured_rna.hpp>
#include <seqan3/alphabet/nucleotide/rna4.hpp>
#include <seqan3/alphabet/structure/dot_bracket3.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using seqan3::operator""_rna4;
    using seqan3::operator""_db3;
    using seqan3::get;
 
    seqan3::structured_rna<seqan3::rna4, seqan3::dot_bracket3> letter{'G'_rna4, '('_db3};
    seqan3::debug_stream << seqan3::to_rank(letter) << ' '
                         << seqan3::to_rank(get<0>(letter)) << ' '
                         << seqan3::to_rank(get<1>(letter)) << '\n';
    // 6 2 1
 
    seqan3::debug_stream << seqan3::to_char(letter) << ' '
                         << seqan3::to_char(get<0>(letter)) << ' '
                         << seqan3::to_char(get<1>(letter)) << '\n';
    // G G (
 
    // modify via structured bindings and references:
    auto & [ seq_l, structure_l ] = letter;
    seq_l = '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.

Member Typedef Documentation

◆ rank_type

using seqan3::alphabet_base< structured_rna< sequence_alphabet_t, structure_alphabet_t > , size, void >::rank_type = detail::min_viable_uint_t<size - 1>

protectedinherited

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

This entity is stable. 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.

Template Parameters

component_type Must be one uniquely contained in the type list of the composite.

Parameters

alph	The value of a component that should be assigned.

Note: Since the alphabet_tuple_base is a CRTP base class, we show the working examples with one of its derived classes (seqan3::qualified).

#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/alphabet/quality/phred42.hpp>
#include <seqan3/alphabet/quality/qualified.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using seqan3::operator""_dna4;
 
    seqan3::qualified<seqan3::dna4, seqan3::phred42> letter1{'C'_dna4};
    // creates {'C'_dna4, seqan3::phred42{0}}
    seqan3::qualified<seqan3::dna4, seqan3::phred42> letter2{seqan3::phred42{1}};
    // creates {'A'_dna4, seqan3::phred42{1}}
 
    if (letter1 == letter2)
        seqan3::debug_stream << "yeah\n"; // yeah
}

◆ 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.

Template Parameters

indirect_component_type Type that models seqan3::weakly_assignable_from for one of the component types.

Parameters

alph	The value that should be assigned.

Note that the value will be assigned to the FIRST type T that fulfils assignable_from<T, indirect_component_type>, regardless if other types are also fit for assignment.

Note: Since the alphabet_tuple_base is a CRTP base class, we show the working examples with one of its derived classes (seqan3::qualified).

#include <seqan3/alphabet/nucleotide/all.hpp>
#include <seqan3/alphabet/quality/phred42.hpp>
#include <seqan3/alphabet/quality/qualified.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using seqan3::operator""_dna4;
    using seqan3::operator""_rna4;
 
    // The following creates {'C'_dna4, phred42{0}}
    seqan3::qualified<seqan3::dna4, seqan3::phred42> letter1{'C'_dna4};
    // The following also creates {'C'_dna4, seqan3::phred42{0}}, since rna4 assignable to dna4
    seqan3::qualified<seqan3::dna4, seqan3::phred42> letter2{'C'_rna4};
 
    if (letter1 == letter2)
        seqan3::debug_stream << "yeah\n"; // yeah
}

Member Function Documentation

◆ assign_char()

constexpr structured_rna< sequence_alphabet_t, structure_alphabet_t > & seqan3::alphabet_base< structured_rna< sequence_alphabet_t, structure_alphabet_t > , size, void >::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.

This entity is stable. Since version 3.1.

◆ assign_rank()

constexpr structured_rna< sequence_alphabet_t, structure_alphabet_t > & seqan3::alphabet_base< structured_rna< sequence_alphabet_t, structure_alphabet_t > , size, void >::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.

This entity is stable. 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.

◆ 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.

◆ 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.

◆ 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.

◆ 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.

Template Parameters

component_type One of the component types. Must be uniquely contained in the type list of the composite.

Parameters

alph	The value of a component that should be assigned.

Note: Since the alphabet_tuple_base is a CRTP base class, we show the working examples with one of its derived classes (seqan3::qualified).

#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/alphabet/quality/phred42.hpp>
#include <seqan3/alphabet/quality/qualified.hpp>
 
int main()
{
    using seqan3::operator""_dna4;
 
    seqan3::qualified<seqan3::dna4, seqan3::phred42> letter1{'T'_dna4, seqan3::phred42{1}};
 
    letter1 = 'C'_dna4;           // yields {'C'_dna4, seqan3::phred42{1}}
    letter1 = seqan3::phred42{2}; // yields {'C'_dna4, seqan3::phred42{2}}
}

◆ 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.

Template Parameters

indirect_component_type Type that models seqan3::weakly_assignable_from for one of the component types.

Parameters

alph	The value of a component that should be assigned.

Note: Since the alphabet_tuple_base is a CRTP base class, we show the working examples with one of its derived classes (seqan3::qualified).

#include <seqan3/alphabet/nucleotide/all.hpp>
#include <seqan3/alphabet/quality/phred42.hpp>
#include <seqan3/alphabet/quality/qualified.hpp>
 
int main()
{
    using seqan3::operator""_dna4;
    using seqan3::operator""_rna4;
 
    seqan3::qualified<seqan3::dna4, seqan3::phred42> letter1{'T'_dna4, seqan3::phred42{1}};
 
    letter1 = 'C'_rna4; // yields {'C'_dna4, seqan3::phred42{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.

◆ to_rank()

constexpr rank_type seqan3::alphabet_base< structured_rna< sequence_alphabet_t, structure_alphabet_t > , size, void >::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.

This entity is stable. Since version 3.1.

Friends And Related Function Documentation

◆ save_minimal()

template<cereal_output_archive archive_t, semialphabet alphabet_t>

alphabet_rank_t< alphabet_t > save_minimal	(	archive_t const &	,
		alphabet_t const &	l
	)

Template Parameters

archive_t	Must satisfy seqan3::cereal_output_archive.
alphabet_t	Type of l; must satisfy seqan3::semialphabet.

Parameters

l	The alphabet letter.

Delegates to seqan3::to_rank.

Attention: These functions are never called directly, see the Alphabet module on how to use serialisation.

This entity is stable. Since version 3.1.

Member Data Documentation

◆ alphabet_size

constexpr detail::min_viable_uint_t<size> seqan3::alphabet_base< structured_rna< sequence_alphabet_t, structure_alphabet_t > , size, void >::alphabet_size

staticconstexprinherited

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

This entity is stable. Since version 3.1.

◆ derived_type

friend seqan3::alphabet_tuple_base< structured_rna< sequence_alphabet_t, structure_alphabet_t > , component_types >::structured_rna< sequence_alphabet_t, structure_alphabet_t >

privateinherited

Befriend the derived type so that it can instantiate.

See also: https://isocpp.org/blog/2017/04/quick-q-prevent-user-from-derive-from-incorrect-crtp-base

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

seqan3/alphabet/structure/structured_rna.hpp

Public Types

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Types

Private Types

Private Member Functions

Static Private Member Functions

Private Attributes

Static Private Attributes

Related Functions

RNA structure properties

Detailed Description

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

Member Typedef Documentation

◆ rank_type

Constructor & Destructor Documentation

◆ structured_rna() [1/2]

◆ structured_rna() [2/2]

Member Function Documentation

◆ assign_char()

Complexity

Exceptions

◆ assign_rank()

Complexity

Exceptions

◆ complement()

Complexity

Exceptions

◆ is_pair_close()

◆ is_pair_open()

◆ is_unpaired()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ pseudoknot_id()

◆ to_rank()

Complexity

Exceptions

Friends And Related Function Documentation

◆ save_minimal()

Member Data Documentation

◆ alphabet_size

◆ derived_type

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