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
Assign from a nucleotide character. This modifies the internal sequence letter.
constexpr structured_rna &	assign_char (char_type const c) noexcept

structured_rna &	assign_char_strictly (char_type const c)
	Strict 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.

Comparison operators (against indirect component_list)
`*this` is cast to the component type before comparison. (These overloads enable comparison for all types that a component type is comparable with).
constexpr bool	operator== (indirect_component_type const rhs) const noexcept

constexpr bool	operator!= (indirect_component_type const rhs) const noexcept

constexpr bool	operator< (indirect_component_type const rhs) const noexcept

constexpr bool	operator> (indirect_component_type const rhs) const noexcept

constexpr bool	operator<= (indirect_component_type const rhs) const noexcept

constexpr bool	operator>= (indirect_component_type const rhs) const noexcept

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

Write functions
constexpr derived_type &	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 detail::min_viable_uint_t< size > constexpr	alphabet_size = size
	The size of the alphabet, i.e. the number of different values it can take.

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()).

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. More...

Requirements for std::StrictTotallyOrdered
You can expect these functions on all types that implement std::StrictTotallyOrdered.
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::EqualityComparable
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...

Comparison operators
Free function (in-)equality comparison operators that forward to member operators (for types != self).
constexpr bool	operator== (indirect_component_type const lhs, alphabet_tuple_base< structured_rna< sequence_alphabet_t, structure_alphabet_t >, component_types... > const rhs) noexcept

constexpr bool	operator!= (indirect_component_type const lhs, alphabet_tuple_base< structured_rna< sequence_alphabet_t, structure_alphabet_t >, indirect_component_types... > const rhs) noexcept

constexpr bool	operator< (indirect_component_type const lhs, alphabet_tuple_base< structured_rna< sequence_alphabet_t, structure_alphabet_t >, indirect_component_types... > const rhs) noexcept

constexpr bool	operator> (indirect_component_type const lhs, alphabet_tuple_base< structured_rna< sequence_alphabet_t, structure_alphabet_t >, indirect_component_types... > const rhs) noexcept

constexpr bool	operator<= (indirect_component_type const lhs, alphabet_tuple_base< structured_rna< sequence_alphabet_t, structure_alphabet_t >, indirect_component_types... > const rhs) noexcept

constexpr bool	operator>= (indirect_component_type const lhs, alphabet_tuple_base< structured_rna< sequence_alphabet_t, structure_alphabet_t >, indirect_component_types... > const rhs) noexcept

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<NucleotideAlphabet sequence_alphabet_t, RnaStructureAlphabet 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::WritableAlphabet, seqan3::NucleotideAlphabet and satisfy the requirements on arguments by seqan3::alphabet_tuple_base.
structure_alphabet_t	Types of further letters; must model seqan3::WritableAlphabet, seqan3::RnaStructureAlphabet 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.

structured_rna<rna4, dot_bracket3> letter{'G'_rna4, '('_db3};
debug_stream << int(to_rank(letter)) << ' '
          << int(to_rank(get<0>(letter))) << ' '
          << int(to_rank(get<1>(letter))) << '\n';
// 6 2 1
debug_stream << to_char(letter) << ' '
          << to_char(get<0>(letter)) << ' '
          << to_char(get<1>(letter)) << '\n';
// G G (
// modify via structured bindings and references:
auto & [ seq_l, structure_l ] = letter;
seq_l = 'U'_rna4;
debug_stream << to_char(letter) << '\n';
// U

This seqan3::alphabet_tuple_base itself models both seqan3::NucleotideAlphabet and seqan3::RnaStructureAlphabet.

Constructor & Destructor Documentation

◆ structured_rna() [1/2]

template<NucleotideAlphabet sequence_alphabet_t, RnaStructureAlphabet structure_alphabet_t>

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

inlinenoexcept

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).

qualified<dna4, phred42> letter1{'C'_dna4}; // creates {'C'_dna4, phred42{0}}

qualified<dna4, phred42> letter2{phred42{1}}; // creates {'A'_dna4, phred42{1}}

◆ structured_rna() [2/2]

template<NucleotideAlphabet sequence_alphabet_t, RnaStructureAlphabet structure_alphabet_t>

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

inlinenoexcept

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

Template Parameters

indirect_component_type Type that models seqan3::WeaklyAssignable 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<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).

// The following creates {'C'_dna4, phre42{0}}
qualified<dna4, phred42> letter1{'C'_dna4};
// The following also creates {'C'_dna4, phred42{0}}, since rna4 assignable to dna4
qualified<dna4, phred42> letter2{'C'_rna4};
if (letter1 == letter2)
    debug_stream << "yeah\n"; // yeah

Member Function Documentation

◆ assign_rank()

template<typename derived_type, size_t size, typename char_t = char>

constexpr derived_type& seqan3::alphabet_base< derived_type, size, char_t >::assign_rank ( rank_type const c )

inlinenoexceptinherited

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.

◆ complement()

template<NucleotideAlphabet sequence_alphabet_t, RnaStructureAlphabet structure_alphabet_t>

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

inlinenoexcept

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

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

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ is_pair_close()

template<NucleotideAlphabet sequence_alphabet_t, RnaStructureAlphabet structure_alphabet_t>

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

inlinenoexcept

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<NucleotideAlphabet sequence_alphabet_t, RnaStructureAlphabet structure_alphabet_t>

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

inlinenoexcept

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<NucleotideAlphabet sequence_alphabet_t, RnaStructureAlphabet structure_alphabet_t>

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

inlinenoexcept

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<NucleotideAlphabet sequence_alphabet_t, RnaStructureAlphabet structure_alphabet_t>

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

inlinenoexcept

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).

qualified<dna4, phred42> letter1{'T'_dna4, phred42{1}};
letter1 = 'C'_dna4; // yields {'C'_dna4, phred42{1}}
letter1 = phred42{2}; // yields {'C'_dna4, phred42{2}}

◆ operator=() [2/2]

template<NucleotideAlphabet sequence_alphabet_t, RnaStructureAlphabet structure_alphabet_t>

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

inlinenoexcept

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

Template Parameters

indirect_component_type Type that models seqan3::WeaklyAssignable 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).

qualified<dna4, phred42> letter1{'T'_dna4, phred42{1}};
letter1 = 'C'_rna4; // yields {'C'_dna4, phred42{1}}

◆ pseudoknot_id()

template<NucleotideAlphabet sequence_alphabet_t, RnaStructureAlphabet structure_alphabet_t>

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

inlinenoexcept

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()

template<typename derived_type, size_t size, typename char_t = char>

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

inlinenoexceptinherited

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

◆ structured_rna()

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 >>

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

Related Functions

RNA structure properties

Detailed Description

template<NucleotideAlphabet sequence_alphabet_t, RnaStructureAlphabet structure_alphabet_t> class seqan3::structured_rna< sequence_alphabet_t, structure_alphabet_t >

Constructor & Destructor Documentation

◆ structured_rna() [1/2]

◆ structured_rna() [2/2]

Member Function Documentation

◆ 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

◆ structured_rna()

template<NucleotideAlphabet sequence_alphabet_t, RnaStructureAlphabet structure_alphabet_t>
class seqan3::structured_rna< sequence_alphabet_t, structure_alphabet_t >