SeqAn3
seqan3::structured_rna< sequence_alphabet_t, structure_alphabet_t > Class Template Reference

A seqan3::cartesian_composition 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 >:
[legend]

Public Types

using char_type = underlying_char_t< sequence_alphabet_type >
 Equals the char_type of sequence_alphabet_type.
 
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()).
 
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 ()
 
constexpr structured_rna (structured_rna const &)=default
 
constexpr structured_rna (structured_rna &&)=default
 
constexpr structured_rnaoperator= (structured_rna const &)=default
 
constexpr structured_rnaoperator= (structured_rna &&)=default
 
 ~structured_rna ()=default
 
constexpr structured_rna (component_type const alph)
 Construction via a value of one of the components. More...
 
constexpr structured_rna (indirect_component_type const alph)
 Construction via a value of a subtype that is assignable to one of the components. More...
 
constexpr structured_rnaoperator= (component_type const alph)
 Assignment via a value of one of the components. More...
 
constexpr structured_rnaoperator= (indirect_component_type const alph)
 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_rnaassign_char (char_type const c)
 
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
 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...
 
constexpr derived_type & assign_char (std::conditional_t< std::Same< char_type, void >, char, char_type > const c) noexcept
 Assign from a character. More...
 

Static Public Attributes

static detail::min_viable_uint_t< size > constexpr value_size = size
 The size of the alphabet, i.e. the number of different values it can take.
 

Related Functions

(Note that these are not member functions.)

std::optional< uint8_t > pseudoknot_id (structure_type const alph)
 Get an identifier for a pseudoknotted interaction. More...
 
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 seqan3::rna_structure_concept

You can expect these functions on all types that implement seqan3::rna_structure_concept.

template<typename alphabet_type >
constexpr uint8_t max_pseudoknot_depth_v = max_pseudoknot_depth<alphabet_type>::value
 The pseudoknot ability of the alphabet. [value metafunction shortcut]. More...
 
Helpers for seqan3::rna_structure_concept

These functions and metafunctions expose member variables and types so that they satisfy seqan3::rna_structure_concept.

template<typename structure_type >
constexpr bool is_pair_open (structure_type const alph) requires requires(structure_type alph)
 Implementation of seqan3::rna_structure_concept::is_pair_open() that delegates to a member function. More...
 
template<typename structure_type >
constexpr bool is_pair_close (structure_type const alph) requires requires(structure_type alph)
 Implementation of seqan3::rna_structure_concept::is_pair_close() that delegates to a member function. More...
 
template<typename structure_type >
constexpr bool is_unpaired (structure_type const alph) requires requires(structure_type alph)
 Implementation of seqan3::rna_structure_concept::is_unpaired() that delegates to a member function. More...
 
template<typename alphabet_type_with_pseudoknot_attribute >
constexpr std::optional< uint8_t > pseudoknot_id (alphabet_type_with_pseudoknot_attribute const alph)
 Implementation of seqan3::rna_structure_concept::pseudoknot_id() that delegates to a member function. More...
 
Requirements for seqan3::alphabet_concept

You can expect these functions on all types that implement seqan3::alphabet_concept.

template<typename alphabet_type >
using underlying_char_t = typename underlying_char< alphabet_type >::type
 The char_type of the alphabet. [type metafunction shortcut]. More...
 
char_type to_char (alphabet_concept const alph)
 Returns the alphabet letter's value in character representation. More...
 
alphabet_concept && assign_char (alphabet_concept &&alph, char_type const chr)
 Returns the alphabet letter's value in character representation. More...
 
Requirements for seqan3::semi_alphabet_concept

You can expect these functions on all types that implement seqan3::semi_alphabet_concept.

template<typename semi_alphabet_type >
using underlying_rank_t = typename underlying_rank< semi_alphabet_type >::type
 The rank_type of the semi_alphabet. [type metafunction shortcut]. More...
 
template<typename alphabet_type >
constexpr auto alphabet_size_v = alphabet_size<alphabet_type>::value
 The size of the alphabet. [value metafunction shortcut]. More...
 
rank_type to_rank (semi_alphabet_concept const alph)
 Returns the alphabet letter's value in rank representation. More...
 
semi_alphabet_concept && assign_rank (semi_alphabet_concept &&alph, rank_type const rank)
 Returns the alphabet letter's value in rank representation. 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...
 
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::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...
 
Comparison operators

Free function (in-)equality comparison operators that forward to member operators (for types != self).

constexpr bool operator== (indirect_component_type const &lhs, cartesian_composition< structured_rna< sequence_alphabet_t, structure_alphabet_t >, component_types... > const &rhs)
 
constexpr bool operator!= (indirect_component_type const &lhs, cartesian_composition< structured_rna< sequence_alphabet_t, structure_alphabet_t >, indirect_component_types... > const &rhs)
 
constexpr bool operator< (indirect_component_type const &lhs, cartesian_composition< structured_rna< sequence_alphabet_t, structure_alphabet_t >, indirect_component_types... > const &rhs)
 
constexpr bool operator> (indirect_component_type const &lhs, cartesian_composition< structured_rna< sequence_alphabet_t, structure_alphabet_t >, indirect_component_types... > const &rhs)
 
constexpr bool operator<= (indirect_component_type const &lhs, cartesian_composition< structured_rna< sequence_alphabet_t, structure_alphabet_t >, indirect_component_types... > const &rhs)
 
constexpr bool operator>= (indirect_component_type const &lhs, cartesian_composition< structured_rna< sequence_alphabet_t, structure_alphabet_t >, indirect_component_types... > const &rhs)
 

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<typename sequence_alphabet_t, typename structure_alphabet_t>
class seqan3::structured_rna< sequence_alphabet_t, structure_alphabet_t >

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

Template Parameters
sequence_alphabet_tType of the first letter; must satisfy seqan3::nucleotide_concept.
structure_alphabet_tTypes of further letters; must satisfy seqan3::rna_structure_concept.

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

As with all seqan3::cartesian_composition 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, dot_bracket3::PAIR_OPEN};
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::cartesian_composition itself models both seqan3::nucleotide_concept and seqan3::rna_structure_concept.

Constructor & Destructor Documentation

◆ structured_rna() [1/2]

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

Construction via a value of one of the components.

Template Parameters
component_typeMust be one uniquely contained in the type list of the composition.
Parameters
alphThe value of a component that should be assigned.

Note: Since the cartesian_composition 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<typename sequence_alphabet_t, typename structure_alphabet_t>
constexpr seqan3::structured_rna< sequence_alphabet_t, structure_alphabet_t >::structured_rna ( indirect_component_type const  alph)
inline

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

Template Parameters
indirect_component_typeType that models the seqan3::is_assignable_concept 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 the assignable_concept<T, indirect_component_type>, regardless if other types are also fit for assignment.

Note: Since the cartesian_composition 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_char()

template<typename derived_type, size_t size, typename char_t = char>
constexpr derived_type& seqan3::alphabet_base< derived_type, size, char_t >::assign_char ( std::conditional_t< std::Same< char_type, void >, char, char_type > const  c)
inlinenoexceptinherited

Assign from a character.

Satisfies the seqan3::alphabet_concept::assign_char() requirement via the seqan3::assign_char() wrapper.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ 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.

Satisfies the seqan3::semi_alphabet_concept::assign_rank() requirement via the seqan3::assign_rank() wrapper.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ complement()

template<typename sequence_alphabet_t, typename 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::nucleotide_concept::complement() requirement via the seqan3::complement() wrapper. The structure letter is not modified.

Complexity
Constant.
Exceptions
Guaranteed not to throw.

◆ is_pair_close()

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

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 composition.
Parameters
alphThe value of a component that should be assigned.

Note: Since the cartesian_composition 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<typename sequence_alphabet_t, typename structure_alphabet_t>
constexpr structured_rna& seqan3::structured_rna< sequence_alphabet_t, structure_alphabet_t >::operator= ( indirect_component_type const  alph)
inline

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

Template Parameters
indirect_component_typeType that models the seqan3::is_assignable_concept for one of the component types.
Parameters
alphThe value of a component that should be assigned.

Note: Since the cartesian_composition 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<typename sequence_alphabet_t, typename 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).

Satisfies the seqan3::semi_alphabet_concept::to_rank() requirement via the to_rank() wrapper.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

Friends And Related Function Documentation

◆ is_pair_close()

template<typename structure_type >
constexpr bool is_pair_close ( structure_type const  alph)
related

Implementation of seqan3::rna_structure_concept::is_pair_close() that delegates to a member function.

Template Parameters
structure_typeMust provide a .is_pair_close() member function.
Parameters
alphThe alphabet letter which is checked for the pairing property.
Returns
True if the letter represents a leftward interaction, False otherwise.

◆ is_pair_open()

template<typename structure_type >
constexpr bool is_pair_open ( structure_type const  alph)
related

Implementation of seqan3::rna_structure_concept::is_pair_open() that delegates to a member function.

Template Parameters
structure_typeMust provide a .is_pair_open() member function.
Parameters
alphThe alphabet letter which is checked for the pairing property.
Returns
True if the letter represents a rightward interaction, False otherwise.

◆ is_unpaired()

template<typename structure_type >
constexpr bool is_unpaired ( structure_type const  alph)
related

Implementation of seqan3::rna_structure_concept::is_unpaired() that delegates to a member function.

Template Parameters
structure_typeMust provide a .is_unpaired() member function.
Parameters
alphThe alphabet letter which is checked for the pairing property.
Returns
True if the letter represents an unpaired site, False otherwise.

◆ pseudoknot_id() [1/2]

std::optional< uint8_t > pseudoknot_id ( structure_type const  alph)
related

Get an identifier for a pseudoknotted interaction.

Parameters
alphThe alphabet letter which is checked for the pseudoknot id.
Returns
The pseudoknot id, if alph represents an interaction, and no value otherwise. It is guaranteed to be smaller than seqan3::max_pseudoknot_depth.

◆ pseudoknot_id() [2/2]

template<typename alphabet_type_with_pseudoknot_attribute >
constexpr std::optional< uint8_t > pseudoknot_id ( alphabet_type_with_pseudoknot_attribute const  alph)
related

Implementation of seqan3::rna_structure_concept::pseudoknot_id() that delegates to a member function.

Template Parameters
alphabet_type_with_pseudoknot_attributeIf it supports pseudoknots, it must provide a .pseudoknot_id() member function, otherwise it can be omitted.
Parameters
alphThe alphabet letter which is checked for the pseudoknot id.
Returns
The pseudoknot id, if alph represents an interaction, and no value otherwise. It is guaranteed to be smaller than seqan3::max_pseudoknot_depth.

◆ 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 >>
related

Type deduction guide enables usage of structured_rna without specifying template args.


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