A seqan3::alphabet_tuple_base that joins a nucleotide alphabet with an RNA structure alphabet. More...
#include <seqan3/alphabet/structure/structured_rna.hpp>
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 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... | |
A seqan3::alphabet_tuple_base that joins a nucleotide alphabet with an RNA structure alphabet.
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.
This seqan3::alphabet_tuple_base itself models both seqan3::nucleotide_alphabet and seqan3::rna_structure_alphabet.
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inlineconstexprnoexcept |
Construction via a value of one of the components.
component_type | Must be one uniquely contained in the type list of the composite. |
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).
|
inlineconstexprnoexcept |
Construction via a value of a subtype that is assignable to one of the components.
indirect_component_type | Type that models seqan3::weakly_assignable_from for one of the component types. |
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).
|
inlineconstexprnoexceptinherited |
Assign from a character, implicitly converts invalid characters.
c | The character to be assigned. |
Provides an implementation for seqan3::assign_char_to, required to model seqan3::alphabet.
Constant.
Guaranteed not to throw.
|
inlineconstexprnoexceptinherited |
Assign from a numeric value.
c | The rank to be assigned. |
Provides an implementation for seqan3::assign_rank_to, required to model seqan3::semialphabet.
Constant.
Guaranteed not to throw.
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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.
Constant.
Guaranteed not to throw.
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inlineconstexprnoexcept |
Check whether the character represents a leftward interaction in an RNA structure.
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inlineconstexprnoexcept |
Check whether the character represents a rightward interaction in an RNA structure.
|
inlineconstexprnoexcept |
Check whether the character represents an unpaired position in an RNA structure.
|
inlineconstexprnoexcept |
Assignment via a value of one of the components.
component_type | One of the component types. Must be uniquely contained in the type list of the composite. |
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).
|
inlineconstexprnoexcept |
Assignment via a value of a subtype that is assignable to one of the components.
indirect_component_type | Type that models seqan3::weakly_assignable_from for one of the component types. |
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).
|
inlineconstexprnoexcept |
Get an identifier for a pseudoknotted interaction.
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inlineconstexprnoexceptinherited |
Return the letter as a character of char_type.
Provides an implementation for seqan3::to_char, required to model seqan3::alphabet.
Constant.
Guaranteed not to throw.
|
inlineconstexprnoexceptinherited |
Return the letter's numeric value (rank in the alphabet).
Provides an implementation for seqan3::to_rank, required to model seqan3::semialphabet.
Constant.
Guaranteed not to throw.