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

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

#include <seqan3/alphabet/nucleotide/nucleotide_base.hpp>

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

Public Member Functions
Read functions
constexpr derived_type	complement () const noexcept
	Return the complement of the letter. More...
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. More...
constexpr rank_type	to_rank () const noexcept
	Return the letter's numeric value (rank in the alphabet). More...
constexpr derived_type &	assign_char (char_type const chr) 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...

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

Additional Inherited Members
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. More...
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. 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...

Detailed Descriptionstable-api

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

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

Template Parameters

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

You can use this class to define your own nucleotide alphabet, but types are not required to be based on it to model seqan3::nucleotide_alphabet, it is purely a way to avoid code duplication.

In addition to the requirements of seqan3::alphabet_base, the derived type needs to define the following static member variable (can be private):

• static std::array<THAT_TYPE, alphabet_size> complement_table that defines for every possible rank value the corresponding complement.

This entity is stable. Since version 3.1.

Constructor & Destructor Documentation

nucleotide_base() [experimental-api]

template<typename derived_type , auto size>

template<typename other_nucl_type >

constexpr seqan3::nucleotide_base< derived_type, size >::nucleotide_base ( other_nucl_type const &  other )

experimental-apiinlineexplicitconstexprnoexcept

Allow explicit construction from any other nucleotide 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() [experimental-api]

template<typename derived_type , auto size>

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

experimental-apiinlinestaticconstexprnoexcept

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

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

Behaviour specific to nucleotides: True also for lower case letters that silently convert to their upper case and true also for U/T respectively, e.g. 'U' is a valid character for seqan3::dna4, because its informational content is identical to 'T'.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

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

complement() [stable-api]

template<typename derived_type , auto size>

constexpr derived_type seqan3::nucleotide_base< derived_type, size >::complement ( ) const

stable-apiinlineconstexprnoexcept

Return the complement of the letter.

See Nucleotide for the actual values.

Provides an implementation for seqan3::complement, required to model seqan3::nucleotide_alphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

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/nucleotide/nucleotide_base.hpp