seqan3::aminoacid_base< derived_type, size > Class Template Reference

A CRTP-base that refines seqan3::alphabet_base and is used by the amino acids. More...

#include <seqan3/alphabet/aminoacid/aminoacid_base.hpp>

Inheritance diagram for seqan3::aminoacid_base< derived_type, size >:

Public Member Functions
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 derived_type &	assign_char (char_type const c) noexcept
	Assign from a character, implicitly converts invalid characters. More...
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 value has a one-to-one mapping to an alphabet value. More...

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. More...

Protected Types
Member types
using	char_type = std::conditional_t< std::same_as< char, void >, char, char >
	The char representation; conditional needed to make semi alphabet definitions legal. More...
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()). More...

Constructors, destructor and assignment
template<typename other_aa_type >
constexpr	aminoacid_base (other_aa_type const other) noexcept
	Allow explicit construction from any other aminoacid type and convert via the character representation. More...

Detailed Description

template<typename derived_type, auto size>
class seqan3::aminoacid_base< derived_type, size >

A CRTP-base that refines seqan3::alphabet_base and is used by the amino acids.

Template Parameters

derived_type	The CRTP parameter type.
size	The size of the alphabet.

This entity is stable. Since version 3.1.

Member Typedef Documentation

char_type

using seqan3::alphabet_base< derived_type, size, char >::char_type = std::conditional_t<std::same_as<char , void>, char, char >

protectedinherited

The char representation; conditional needed to make semi alphabet definitions legal.

We need a return type for seqan3::alphabet_base::to_char and seqan3::alphabet_base::assign_char other than void to make these in-class definitions valid when char_t is void.

This entity is stable. Since version 3.1.

rank_type

using seqan3::alphabet_base< derived_type, size, char >::rank_type = detail::min_viable_uint_t<size - 1>

protectedinherited

The type of the alphabet when represented as a number (e.g. via to_rank()).

This entity is stable. Since version 3.1.

Constructor & Destructor Documentation

aminoacid_base()

template<typename derived_type , auto size>

template<typename other_aa_type >

constexpr seqan3::aminoacid_base< derived_type, size >::aminoacid_base ( other_aa_type const  other )

inlineexplicitconstexprnoexcept

Allow explicit construction from any other aminoacid type and convert via the character representation.

This entity is experimental and subject to change in the future. Experimental since version 3.1.

Member Function Documentation

assign_char()

constexpr derived_type& seqan3::alphabet_base< derived_type, size, char >::assign_char ( char_type const  c )

inlineconstexprnoexceptinherited

Assign from a character, implicitly converts invalid characters.

Parameters

c	The character to be assigned.

Provides an implementation for seqan3::assign_char_to, required to model seqan3::alphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

This entity is stable. Since version 3.1.

assign_rank()

constexpr derived_type& seqan3::alphabet_base< derived_type, size, char >::assign_rank ( rank_type const  c )

inlineconstexprnoexceptinherited

Assign from a numeric value.

Parameters

c	The rank to be assigned.

Provides an implementation for seqan3::assign_rank_to, required to model seqan3::semialphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

This entity is stable. Since version 3.1.

char_is_valid()

template<typename derived_type , auto size>

static constexpr bool seqan3::aminoacid_base< derived_type, size >::char_is_valid ( char_type const  c )

inlinestaticconstexprnoexcept

Validate whether a character value has a one-to-one mapping to an alphabet value.

Models the seqan3::semialphabet::char_is_valid_for() requirement via the seqan3::char_is_valid_for() wrapper.

Behaviour specific to amino acids: True also for lower case letters that silently convert to their upper case.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

This entity is experimental and subject to change in the future. Experimental since version 3.1.

to_char()

constexpr char_type seqan3::alphabet_base< derived_type, size, char >::to_char ( ) const

inlineconstexprnoexceptinherited

Return the letter as a character of char_type.

Provides an implementation for seqan3::to_char, required to model seqan3::alphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

This entity is stable. Since version 3.1.

to_rank()

constexpr rank_type seqan3::alphabet_base< derived_type, size, char >::to_rank ( ) const

inlineconstexprnoexceptinherited

Return the letter's numeric value (rank in the alphabet).

Provides an implementation for seqan3::to_rank, required to model seqan3::semialphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

This entity is stable. Since version 3.1.

Member Data Documentation

alphabet_size

constexpr detail::min_viable_uint_t<size> seqan3::alphabet_base< derived_type, size, char >::alphabet_size

staticconstexprinherited

The size of the alphabet, i.e. the number of different values it can take.

This entity is stable. Since version 3.1.

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

• seqan3/alphabet/aminoacid/aminoacid_base.hpp