A seqan3::cartesian_composition that joins a nucleotide alphabet with an RNA structure alphabet. More...
#include <seqan3/alphabet/structure/structured_rna.hpp>
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_rna & | operator= (structured_rna const &)=default |
constexpr structured_rna & | operator= (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_rna & | operator= (component_type const alph) |
Assignment via a value of one of the components. More... | |
constexpr structured_rna & | operator= (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_rna & | assign_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) | |
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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... | |
A seqan3::cartesian_composition that joins a nucleotide alphabet with an RNA structure alphabet.
sequence_alphabet_t | Type of the first letter; must satisfy seqan3::nucleotide_concept. |
structure_alphabet_t | Types 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.
This seqan3::cartesian_composition itself models both seqan3::nucleotide_concept and seqan3::rna_structure_concept.
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inline |
Construction via a value of one of the components.
component_type | Must be one uniquely contained in the type list of the composition. |
alph | The 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).
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inline |
Construction via a value of a subtype that is assignable to one of the components.
indirect_component_type | Type that models the seqan3::is_assignable_concept 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 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).
|
inlinenoexceptinherited |
Assign from a character.
Satisfies the seqan3::alphabet_concept::assign_char() requirement via the seqan3::assign_char() wrapper.
Constant.
Guaranteed not to throw.
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inlinenoexceptinherited |
Assign from a numeric value.
Satisfies the seqan3::semi_alphabet_concept::assign_rank() requirement via the seqan3::assign_rank() wrapper.
Constant.
Guaranteed not to throw.
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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.
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inlinenoexcept |
Check whether the character represents a leftward interaction in an RNA structure.
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inlinenoexcept |
Check whether the character represents a rightward interaction in an RNA structure.
|
inlinenoexcept |
Check whether the character represents an unpaired position in an RNA structure.
|
inline |
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 composition. |
alph | The 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).
|
inline |
Assignment via a value of a subtype that is assignable to one of the components.
indirect_component_type | Type that models the seqan3::is_assignable_concept for one of the component types. |
alph | The 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).
|
inlinenoexcept |
Get an identifier for a pseudoknotted interaction.
|
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.
Constant.
Guaranteed not to throw.
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related |
Implementation of seqan3::rna_structure_concept::is_pair_close() that delegates to a member function.
structure_type | Must provide a .is_pair_close() member function. |
alph | The alphabet letter which is checked for the pairing property. |
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related |
Implementation of seqan3::rna_structure_concept::is_pair_open() that delegates to a member function.
structure_type | Must provide a .is_pair_open() member function. |
alph | The alphabet letter which is checked for the pairing property. |
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related |
Implementation of seqan3::rna_structure_concept::is_unpaired() that delegates to a member function.
structure_type | Must provide a .is_unpaired() member function. |
alph | The alphabet letter which is checked for the pairing property. |
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related |
Get an identifier for a pseudoknotted interaction.
alph | The alphabet letter which is checked for the pseudoknot id. |
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related |
Implementation of seqan3::rna_structure_concept::pseudoknot_id() that delegates to a member function.
alphabet_type_with_pseudoknot_attribute | If it supports pseudoknots, it must provide a .pseudoknot_id() member function, otherwise it can be omitted. |
alph | The alphabet letter which is checked for the pseudoknot id. |
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related |
Type deduction guide enables usage of structured_rna without specifying template args.