A CRTP-base that refines seqan3::alphabet_base and is used by the nucleotides. More...
#include <seqan3/alphabet/nucleotide/nucleotide_base.hpp>
Public Member Functions | |
Read functions | |
constexpr derived_type | complement () const noexcept |
Return the complement of the letter. More... | |
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 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 | |
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 = 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_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. | |
A CRTP-base that refines seqan3::alphabet_base and is used by the nucleotides.
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.
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inlineconstexprnoexceptinherited |
Assign from a character, implicitly converts invalid characters.
c | The character to be assigned. |
Provides an implementation for seqan3::assign_char_to, required to model seqan3::alphabet.
Constant.
Guaranteed not to throw.
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inlineconstexprnoexceptinherited |
Assign from a numeric value.
c | The rank to be assigned. |
Provides an implementation for seqan3::assign_rank_to, required to model seqan3::semialphabet.
Constant.
Guaranteed not to throw.
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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'.
Constant.
Guaranteed not to throw.
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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.
Constant.
Guaranteed not to throw.
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inlineconstexprnoexceptinherited |
Return the letter as a character of char_type.
Provides an implementation for seqan3::to_char, required to model seqan3::alphabet.
Constant.
Guaranteed not to throw.
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inlineconstexprnoexceptinherited |
Return the letter's numeric value (rank in the alphabet).
Provides an implementation for seqan3::to_rank, required to model seqan3::semialphabet.
Constant.
Guaranteed not to throw.