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 >:

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.

Private Types
using	base_t = alphabet_base< derived_type, size, char >
	Type of the base class.

Private Attributes
friend	base_t
	Befriend the base class.
friend	derived_type
	Befriend the derived class so it can instantiate.

Static Private Attributes
static constexpr std::array< bool, 256 >	valid_char_table
	Implementation of seqan3::aminoacid_base::char_is_valid().

Constructors, destructor and assignment
constexpr	aminoacid_base () noexcept=default
	Defaulted.
constexpr	aminoacid_base (aminoacid_base const &) noexcept=default
	Defaulted.
constexpr	aminoacid_base (aminoacid_base &&) noexcept=default
	Defaulted.
constexpr aminoacid_base &	operator= (aminoacid_base const &) noexcept=default
	Defaulted.
constexpr aminoacid_base &	operator= (aminoacid_base &&) noexcept=default
	Defaulted.
	~aminoacid_base () noexcept=default
	Defaulted.
template<typename other_aa_type > requires (!std::same_as<aminoacid_base, other_aa_type>) && (!std::same_as<derived_type, other_aa_type>) && aminoacid_alphabet<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.

Additional Inherited Members
Public Member Functions inherited from seqan3::alphabet_base< derived_type, size, char >
constexpr	alphabet_base () noexcept=default
	Defaulted.
constexpr	alphabet_base (alphabet_base const &) noexcept=default
	Defaulted.
constexpr	alphabet_base (alphabet_base &&) noexcept=default
	Defaulted.
constexpr alphabet_base &	operator= (alphabet_base const &) noexcept=default
	Defaulted.
constexpr alphabet_base &	operator= (alphabet_base &&) noexcept=default
	Defaulted.
	~alphabet_base () noexcept=default
	Defaulted.
constexpr char_type	to_char () const noexcept
	Return the letter as a character of char_type.
constexpr rank_type	to_rank () const noexcept
	Return the letter's numeric value (rank in the alphabet).
constexpr derived_type &	assign_char (char_type const chr) noexcept
	Assign from a character, implicitly converts invalid characters.
constexpr derived_type &	assign_rank (rank_type const c) noexcept
	Assign from a numeric value.
Static Public Attributes inherited from seqan3::alphabet_base< derived_type, size, char >
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.
Protected Types inherited from seqan3::alphabet_base< derived_type, size, char >
using	char_type = std::conditional_t< std::same_as< char, void >, char, char >
	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()).

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.

Constructor & Destructor Documentation

aminoacid_base()

template<typename derived_type , auto size>

template<typename other_aa_type >
requires (!std::same_as<aminoacid_base, other_aa_type>) && (!std::same_as<derived_type, other_aa_type>) && aminoacid_alphabet<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

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.

Member Data Documentation

valid_char_table

template<typename derived_type , auto size>

constexpr std::array<bool, 256> seqan3::aminoacid_base< derived_type, size >::valid_char_table

staticconstexprprivate

Initial value:

{
        []() constexpr {
            std::array<bool, 256> ret{};
 
            ret.fill(false); 
 
            
            for (size_t rank = 0u; rank < derived_type::alphabet_size; ++rank)
            {
                uint8_t c = derived_type::rank_to_char(rank);
                ret[c] = true;
                ret[to_lower(c)] = true;
            }
 
            return ret;
        }()
    }

Implementation of seqan3::aminoacid_base::char_is_valid().

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

• aminoacid_base.hpp