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< 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 detail::min_viable_uint_t< size > constexpr	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< 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. More...

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...

Requirements for std::StrictTotallyOrdered
You can expect these functions on all types that implement std::StrictTotallyOrdered.
bool	operator< (type const &lhs, type const &rhs)
	Less-than, greater-than and -or-equal comparisons. More...

bool	operator<= (type const &lhs, type const &rhs)
	Less-than, greater-than and -or-equal comparisons. More...

bool	operator> (type const &lhs, type const &rhs)
	Less-than, greater-than and -or-equal comparisons. More...

bool	operator>= (type const &lhs, type const &rhs)
	Less-than, greater-than and -or-equal comparisons. More...

Requirements for std::EqualityComparable
You can expect these functions on all types that implement std::Equality_comparable.
bool	operator== (type const &lhs, type const &rhs)
	(In-)Equality comparison. More...

bool	operator!= (type const &lhs, type const &rhs)
	(In-)Equality comparison. More...

Requirements for std::Swappable
You can expect these functions on all types that implement std::Swappable.
void	swap (t &lhs, t &rhs)
	Swaps the contents of two objects. 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().

dna4 my_letter{'A'_dna4};
// doesn't work:
// dna4 my_letter{'A'};
my_letter.assign_char('C'); // <- this does!
my_letter.assign_char('F'); // unknown characters are implicitly converted to A.
if (my_letter.to_char() == 'A')
    debug_stream << "yeah\n"; // "yeah";

Member Function Documentation

◆ assign_char()

constexpr dna4 & seqan3::alphabet_base< dna4 , size, char >::assign_char ( char_type const c )

inlinenoexceptinherited

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.

◆ assign_rank()

constexpr dna4 & seqan3::alphabet_base< dna4 , size, char >::assign_rank ( rank_type const c )

inlinenoexceptinherited

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.

◆ char_is_valid()

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

inlinestaticnoexceptinherited

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

inlinenoexceptinherited

Return the complement of the letter.

See Nucleotide for the actual values.

Provides an implementation for seqan3::complement, required to model seqan3::NucleotideAlphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ to_char()

constexpr char_type seqan3::alphabet_base< dna4 , size, char >::to_char ( ) const

inlinenoexceptinherited

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< dna4 , size, char >::to_rank ( ) const

inlinenoexceptinherited

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

◆ dna4_vector

using dna4_vector = std::vector<dna4>

◆ operator""_dna4() [1/2]

constexpr dna4 operator""_dna4 ( char const c )

Returns: seqan3::dna4

◆ operator""_dna4() [2/2]

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

Returns: seqan3::dna4_vector

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

// these don't work:
// dna4_vector foo{"ACGTTA"};
// dna4_vector bar = "ACGTTA";
// but these do:
dna4_vector foo{"ACGTTA"_dna4};
dna4_vector bar = "ACGTTA"_dna4;
auto bax = "ACGTTA"_dna4;

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

seqan3/alphabet/nucleotide/dna4.hpp

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Types

Related Functions

Detailed Description

Member Function Documentation

◆ assign_char()

Complexity

Exceptions

◆ assign_rank()

Complexity

Exceptions

◆ char_is_valid()

Complexity

Exceptions

◆ complement()

Complexity

Exceptions

◆ to_char()

Complexity

Exceptions

◆ to_rank()

Complexity

Exceptions

Friends And Related Function Documentation

◆ dna4_vector

◆ operator""_dna4() [1/2]

◆ operator""_dna4() [2/2]