The three letter RNA structure alphabet of the characters ".()". More...
#include <seqan3/alphabet/structure/dot_bracket3.hpp>
Public Types | |
Member types | |
using | char_type = char |
The type of the alphabet when converted to char (e.g. via to_char()). | |
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()). | |
Public Member Functions | |
Constructors, destructor and assignment | |
constexpr | dot_bracket3 () |
constexpr | dot_bracket3 (dot_bracket3 const &)=default |
constexpr | dot_bracket3 (dot_bracket3 &&)=default |
constexpr dot_bracket3 & | operator= (dot_bracket3 const &)=default |
constexpr dot_bracket3 & | operator= (dot_bracket3 &&)=default |
~dot_bracket3 ()=default | |
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 dot_bracket3 & | assign_char (std::conditional_t< std::Same< char_type, void >, char, char_type > const c) noexcept |
Assign from a character. More... | |
constexpr dot_bracket3 & | assign_rank (rank_type const c) noexcept |
Assign from a numeric value. More... | |
Static Public Attributes | |
static detail::min_viable_uint_t< size > constexpr | value_size |
The size of the alphabet, i.e. the number of different values it can take. | |
Letter values | |
Static member "letters" that can be assigned to the alphabet or used in aggregate initialization. Similar to an Enum interface. Don't worry about the | |
static const dot_bracket3 | UNPAIRED = dot_bracket3{}.assign_char('.') |
static const dot_bracket3 | PAIR_OPEN = dot_bracket3{}.assign_char('(') |
static const dot_bracket3 | PAIR_CLOSE = dot_bracket3{}.assign_char(')') |
static const dot_bracket3 | UNKNOWN = dot_bracket3::UNPAIRED |
Related Functions | |
(Note that these are not member functions.) | |
std::vector< dot_bracket3 > | operator""_db3 (const char *str, std::size_t len) |
dot_bracket3 literal More... | |
std::optional< uint8_t > | pseudoknot_id (structure_type const alph) |
Get an identifier for a pseudoknotted interaction. 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... | |
RNA structure properties | |
static constexpr uint8_t | max_pseudoknot_depth {1} |
The ability of this alphabet to represent pseudoknots, i.e. crossing interactions, up to a certain depth. More... | |
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... | |
The three letter RNA structure alphabet of the characters ".()".
The brackets denote RNA base pair interactions. Every left bracket must have a corresponding right bracket. Pseudoknots cannot be expressed in this format. A dot (.) represents a character that is not paired.
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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 |
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.
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inlinenoexcept |
Check whether the character represents an unpaired position in an RNA structure.
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inlinenoexceptinherited |
Return the letter as a character of char_type.
Satisfies the seqan3::alphabet_concept::to_char() requirement via the seqan3::to_char() wrapper.
Constant.
Guaranteed not to throw.
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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 |
dot_bracket3 literal
You can use this string literal to easily assign to a vector of dot_bracket3 characters:
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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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static |
The ability of this alphabet to represent pseudoknots, i.e. crossing interactions, up to a certain depth.
It is the number of distinct pairs of interaction symbols the format supports. The value 1 denotes no pseudoknot support.