A seqan3::alphabet_tuple_base that joins an aminoacid alphabet with a protein structure alphabet. More...
#include <seqan3/alphabet/structure/structured_aa.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_aa () noexcept=default |
Defaulted. | |
constexpr | structured_aa (structured_aa const &) noexcept=default |
Defaulted. | |
constexpr | structured_aa (structured_aa &&) noexcept=default |
Defaulted. | |
constexpr structured_aa & | operator= (structured_aa const &) noexcept=default |
Defaulted. | |
constexpr structured_aa & | operator= (structured_aa &&) noexcept=default |
Defaulted. | |
~structured_aa () noexcept=default | |
Defaulted. | |
constexpr | structured_aa (component_type const alph) |
Construction via a value of one of the components. More... | |
constexpr | structured_aa (indirect_component_type const alph) |
Construction via a value of a subtype that is assignable to one of the components. More... | |
constexpr structured_aa & | operator= (component_type const alph) |
Assignment via a value of one of the components. More... | |
constexpr structured_aa & | operator= (indirect_component_type const alph) |
Assignment via a value of a subtype that is assignable to one of the components. More... | |
Write functions | |
constexpr structured_aa & | 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. | |
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 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... | |
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 = 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_aa (sequence_alphabet_type &&, structure_alphabet_type &&) -> structured_aa< std::decay_t< sequence_alphabet_type >, std::decay_t< structure_alphabet_type >> | |
Type deduction guide enables usage of structured_aa without specifying template args. | |
Requirements for std::totally_ordered | |
You can expect these functions on all types that implement std::totally_ordered. | |
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... | |
Requirements for std::equality_comparable | |
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::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... | |
A seqan3::alphabet_tuple_base that joins an aminoacid alphabet with a protein structure alphabet.
sequence_alphabet_t | Type of the first aminoacid letter; must model seqan3::writable_alphabet, seqan3::aminoacid_alphabet and satisfy the requirements on arguments by seqan3::alphabet_tuple_base. |
structure_alphabet_t | Types of further structure letters; must model seqan3::writable_alphabet and satisfy the requirements on arguments by seqan3::alphabet_tuple_base. |
This composite pairs an aminoacid 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 fulfills seqan3::alphabet.
|
inlineconstexpr |
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).
|
inlineconstexpr |
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 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.
|
inlineconstexpr |
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).
|
inlineconstexpr |
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).
|
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.