SeqAn3  3.0.3
The Modern C++ library for sequence analysis.
seqan3::dna4 Class Reference

The four letter DNA alphabet of A,C,G,T. More...

#include <seqan3/alphabet/nucleotide/dna4.hpp>

+ Inheritance diagram for seqan3::dna4:

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 dna4operator= (dna4 const &) noexcept=default
 Defaulted.
 
constexpr dna4operator= (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 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 = 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_t, void >, char, char_t >
 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...
 

Detailed Description

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().

int main()
{
using seqan3::operator""_dna4;
seqan3::dna4 my_letter{'C'_dna4};
my_letter.assign_char('F'); // characters other than IUPAC characters are implicitly converted to A.
seqan3::debug_stream << my_letter; // prints "F"
// IUPAC characters are implicitly converted to their best fitting representative
seqan3::debug_stream << my_letter.assign_char('R'); // prints "A"
seqan3::debug_stream << my_letter.assign_char('Y'); // prints "C"
seqan3::debug_stream << my_letter.assign_char('S'); // prints "C"
seqan3::debug_stream << my_letter.assign_char('W'); // prints "A"
seqan3::debug_stream << my_letter.assign_char('K'); // prints "G"
seqan3::debug_stream << my_letter.assign_char('M'); // prints "A"
seqan3::debug_stream << my_letter.assign_char('B'); // prints "C"
seqan3::debug_stream << my_letter.assign_char('D'); // prints "A"
seqan3::debug_stream << my_letter.assign_char('H'); // prints "A"
seqan3::debug_stream << my_letter.assign_char('V'); // prints "A"
my_letter.assign_char('a'); // lower case letters are the same as their upper case equivalent
seqan3::debug_stream << my_letter; // prints "A";
}
constexpr derived_type & assign_char(char_type const c) noexcept
Assign from a character, implicitly converts invalid characters.
Definition: alphabet_base.hpp:142
The four letter DNA alphabet of A,C,G,T.
Definition: dna4.hpp:51
Provides seqan3::debug_stream and related types.
Provides seqan3::dna4, container aliases and string literals.
debug_stream_type debug_stream
A global instance of seqan3::debug_stream_type.
Definition: debug_stream.hpp:41

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.

Member Function Documentation

◆ assign_char()

template<typename derived_type , size_t size, typename char_t = char>
constexpr derived_type& seqan3::alphabet_base< derived_type, size, char_t >::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()

template<typename derived_type , size_t size, typename char_t = char>
constexpr derived_type& seqan3::alphabet_base< derived_type, size, char_t >::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()

static constexpr bool seqan3::nucleotide_base< dna4 , size >::char_is_valid ( char_type const  c)
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'.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ complement()

constexpr dna4 seqan3::nucleotide_base< dna4 , size >::complement ( ) const
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.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ to_char()

template<typename derived_type , size_t size, typename char_t = char>
constexpr char_type seqan3::alphabet_base< derived_type, size, char_t >::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()

template<typename derived_type , size_t size, typename char_t = char>
constexpr rank_type seqan3::alphabet_base< derived_type, size, char_t >::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.

Friends And Related Function Documentation

◆ operator""_dna4() [1/2]

dna4_vector operator""_dna4 ( char const *  s,
std::size_t  n 
)
related

The seqan3::dna4 string literal.

Returns
seqan3::dna4_vector

You can use this string literal to easily assign to dna4_vector:

int main()
{
using seqan3::operator""_dna4;
seqan3::dna4_vector foo{"ACGTTA"_dna4};
seqan3::dna4_vector bar = "ACGTTA"_dna4;
auto bax = "ACGTTA"_dna4;
}

◆ operator""_dna4() [2/2]

constexpr dna4 operator""_dna4 ( char const  c)
related

The seqan3::dna4 char literal.

Returns
seqan3::dna4

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