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 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 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. More...

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. More...
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()). More...

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().

#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/core/debug_stream.hpp>
 
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";
}

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 Typedef Documentation

char_type

template<typename derived_type , size_t size, typename char_t = char>

using seqan3::alphabet_base< derived_type, size, char_t >::char_type = std::conditional_t<std::same_as<char_t, void>, char, char_t>

protectedinherited

The char representation; conditional needed to make semi alphabet definitions legal.

We need a return type for seqan3::alphabet_base::to_char and seqan3::alphabet_base::assign_char other than void to make these in-class definitions valid when char_t is void.

This entity is stable. Since version 3.1.

rank_type

template<typename derived_type , size_t size, typename char_t = char>

using seqan3::alphabet_base< derived_type, size, char_t >::rank_type = detail::min_viable_uint_t<size - 1>

protectedinherited

The type of the alphabet when represented as a number (e.g. via to_rank()).

This entity is stable. Since version 3.1.

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

c	The character to be assigned.

Provides an implementation for seqan3::assign_char_to, required to model seqan3::alphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

This entity is stable. Since version 3.1.

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

c	The rank to be assigned.

Provides an implementation for seqan3::assign_rank_to, required to model seqan3::semialphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

This entity is stable. Since version 3.1.

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.

This entity is stable. Since version 3.1.

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.

This entity is stable. Since version 3.1.

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:

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

Member Data Documentation

alphabet_size

template<typename derived_type , size_t size, typename char_t = char>

constexpr detail::min_viable_uint_t<size> seqan3::alphabet_base< derived_type, size, char_t >::alphabet_size = size

staticconstexprinherited

The size of the alphabet, i.e. the number of different values it can take.

This entity is stable. Since version 3.1.

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

• seqan3/alphabet/nucleotide/dna4.hpp