SeqAn3  3.0.2
The Modern C++ library for sequence analysis.
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...
 

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.
 

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.
 

Detailed Description

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_typeThe CRTP parameter type.
sizeThe 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.

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
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)
inlineconstexprnoexceptinherited

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::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 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.

◆ complement()

template<typename derived_type , auto size>
constexpr derived_type seqan3::nucleotide_base< derived_type, size >::complement ( ) const
inlineconstexprnoexcept

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.

◆ 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.

◆ 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.


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