SeqAn3  3.0.2
The Modern C++ library for sequence analysis.
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 detail::min_viable_uint_t< size > constexpr alphabet_size
 The size of the alphabet, i.e. the number of different values it can take.
 

Protected Types

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

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.
 

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_typeThe CRTP parameter type.
sizeThe size of the alphabet.

Member Function Documentation

◆ assign_char()

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

Assign from a character, implicitly converts invalid characters.

Parameters
cThe character to be assigned.

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

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ assign_rank()

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

Assign from a numeric value.

Parameters
cThe rank to be assigned.

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

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ 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)
inlinestaticnoexcept

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.

◆ to_char()

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

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.

◆ to_rank()

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

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.


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