The four letter DNA alphabet of A,C,G,T. More...
#include <seqan3/alphabet/nucleotide/dna4.hpp>
Public Member Functions | |
Constructors, destructor and assignment | |
constexpr | dna4 () noexcept=default |
Defaulted. | |
constexpr | dna4 (dna4 const &) noexcept=default |
Defaulted. | |
constexpr | dna4 (dna4 &&) noexcept=default |
Defaulted. | |
constexpr dna4 & | operator= (dna4 const &) noexcept=default |
Defaulted. | |
constexpr dna4 & | operator= (dna4 &&) noexcept=default |
Defaulted. | |
~dna4 () noexcept=default | |
Defaulted. | |
template<std::same_as< rna4 > t> | |
constexpr | dna4 (t const &r) noexcept |
Allow implicit construction from dna/rna of the same size. | |
Read functions | |
constexpr dna4 | 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 dna4 & | assign_char (char_type const c) noexcept |
Assign from a character, implicitly converts invalid characters. More... | |
constexpr dna4 & | 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()). | |
Related Functions | |
(Note that these are not member functions.) | |
using | dna4_vector = std::vector< dna4 > |
Alias for an std::vector of seqan3::dna4. | |
Literals | |
constexpr dna4 | operator""_dna4 (char const c) noexcept |
The seqan3::dna4 char literal. More... | |
dna4_vector | operator""_dna4 (char const *s, std::size_t n) |
The seqan3::dna4 string literal. More... | |
The four letter DNA alphabet of A,C,G,T.
Note that you can assign 'U' as a character to dna4 and it will silently be converted to 'T'.
Like most alphabets, this alphabet cannot be initialised directly from its character representation. Instead initialise/assign from the character literal or use the function seqan3::dna4::assign_char().
If the special char conversion of IUPAC characters is not your desired behavior, refer to our cookbook for an example of A custom dna4 alphabet that converts all unknown characters to A
to change the conversion behavior.
|
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.
|
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.
|
inlinestaticconstexprnoexceptinherited |
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.
|
inlineconstexprnoexceptinherited |
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.
|
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.
|
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.
|
related |
The seqan3::dna4 string literal.
You can use this string literal to easily assign to dna4_vector:
|
related |
The seqan3::dna4 char literal.