bio::alphabet::nucleotide_base< derived_type, size > Class Template Reference

A CRTP-base that refines bio::alphabet::base and is used by the nucleotides. More...

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

Inheritance diagram for bio::alphabet::nucleotide_base< derived_type, size >:

Public Member Functions
Read functions
constexpr derived_type	complement () const noexcept
	Return the complement of the letter.
Read functions
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).
Write functions
constexpr derived_type &	assign_char (char_type const c) 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 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.

Static Public Attributes
static constexpr size_t	alphabet_size
	The size of the alphabet, i.e. the number of different values it can take.

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.
using	rank_type = meta::detail::min_viable_uint_t< size - 1 >
	The type of the alphabet when represented as a number (e.g. via to_rank()).

Friends
constexpr derived_type	tag_invoke (custom::complement, derived_type const a) noexcept
	tag_invoke() wrapper around member.

Constructors, destructor and assignment
template<meta::different_from< derived_type > other_nucl_type> requires nucleotide<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.

Detailed Description

template<typename derived_type, auto size>
class bio::alphabet::nucleotide_base< derived_type, size >

A CRTP-base that refines bio::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 bio::alphabet::nucleotide, it is purely a way to avoid code duplication.

In addition to the requirements of bio::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.

Member Function Documentation

assign_char()

constexpr derived_type & bio::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 bio::alphabet::assign_char_to, required to model bio::alphabet::alphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

assign_rank()

constexpr derived_type & bio::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 bio::alphabet::assign_rank_to, required to model bio::alphabet::semialphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

char_is_valid()

template<typename derived_type , auto size>

static constexpr bool bio::alphabet::nucleotide_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.

Satisfies the bio::alphabet::semialphabet::char_is_valid_for() requirement via the bio::alphabet::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 bio::alphabet::dna4, because its informational content is identical to 'T'.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

complement()

template<typename derived_type , auto size>

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

inlineconstexprnoexcept

Return the complement of the letter.

See Nucleotide for the actual values.

Provides an implementation for bio::alphabet::complement, required to model bio::alphabet::nucleotide.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

to_char()

constexpr char_type bio::alphabet::base< derived_type, size, char >::to_char ( ) const

inlineconstexprnoexceptinherited

Return the letter as a character of char_type.

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

Complexity

Constant.

Exceptions

Guaranteed not to throw.

to_rank()

constexpr rank_type bio::alphabet::base< derived_type, size, char >::to_rank ( ) const

inlineconstexprnoexceptinherited

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

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

Complexity

Constant.

Exceptions

Guaranteed not to throw.

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

• bio/alphabet/nucleotide/nucleotide_base.hpp