SeqAn3  3.0.2
The Modern C++ library for sequence analysis.
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

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 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...
 
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 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...
 
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_rnaoperator= (structured_rna const &) noexcept=default
 Defaulted.
 
constexpr structured_rnaoperator= (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_rnaoperator= (component_type const alph) noexcept
 Assignment via a value of one of the components. More...
 
constexpr structured_rnaoperator= (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_rnaassign_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 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 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.
 

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.
 

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_tType 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_tTypes 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.

int main()
{
using seqan3::operator""_rna4;
using seqan3::operator""_db3;
using seqan3::get;
<< seqan3::to_rank(get<0>(letter)) << ' '
<< seqan3::to_rank(get<1>(letter)) << '\n';
// 6 2 1
<< 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;
// U
}

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

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_typeMust be one uniquely contained in the type list of the composite.
Parameters
alphThe 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).

int main()
{
using seqan3::operator""_dna4;
// creates {'C'_dna4, seqan3::phred42{0}}
// 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_typeType that models seqan3::weakly_assignable_from for one of the component types.
Parameters
alphThe 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).

int main()
{
using seqan3::operator""_dna4;
using seqan3::operator""_rna4;
// The following creates {'C'_dna4, phred42{0}}
// The following also creates {'C'_dna4, seqan3::phred42{0}}, since rna4 assignable to dna4
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
cThe 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 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
cThe 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<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_typeOne of the component types. Must be uniquely contained in the type list of the composite.
Parameters
alphThe 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).

int main()
{
using seqan3::operator""_dna4;
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_typeType that models seqan3::weakly_assignable_from for one of the component types.
Parameters
alphThe 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).

int main()
{
using seqan3::operator""_dna4;
using seqan3::operator""_rna4;
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_char()

constexpr char_type seqan3::alphabet_base< structured_rna< sequence_alphabet_t, structure_alphabet_t > , size, void >::to_char
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< structured_rna< sequence_alphabet_t, structure_alphabet_t > , size, void >::to_rank
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.


The documentation for this class was generated from the following file:
debug_stream.hpp
Provides seqan3::debug_stream and related types.
qualified.hpp
Provides quality alphabet composites.
dna4.hpp
Provides seqan3::dna4, container aliases and string literals.
seqan3::to_char
constexpr auto to_char
Return the char representation of an alphabet object.
Definition: concept.hpp:321
seqan3::to_rank
constexpr auto to_rank
Return the rank representation of a (semi-)alphabet object.
Definition: concept.hpp:143
rna4.hpp
Provides seqan3::rna4, container aliases and string literals.
all.hpp
Meta-header for the nucleotide submodule; includes all headers from alphabet/nucleotide/.
dot_bracket3.hpp
Provides the dot bracket format for RNA structure.
seqan3::phred42
Quality type for traditional Sanger and modern Illumina Phred scores (typical range).
Definition: phred42.hpp:43
seqan3::structured_rna
A seqan3::alphabet_tuple_base that joins a nucleotide alphabet with an RNA structure alphabet.
Definition: structured_rna.hpp:52
seqan3::qualified
Joins an arbitrary alphabet with a quality alphabet.
Definition: qualified.hpp:56
seqan3::debug_stream
debug_stream_type debug_stream
A global instance of seqan3::debug_stream_type.
Definition: debug_stream.hpp:42
structured_rna.hpp
Provides the composite of nucleotide with structure alphabets.
phred42.hpp
Provides seqan3::phred42 quality scores.
seqan3::get
constexpr const auto & get(configuration< configs_t... > const &config) noexcept
This is an overloaded member function, provided for convenience. It differs from the above function o...
Definition: configuration.hpp:627