bio::alphabet::dna4 Class Reference

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

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

Inheritance diagram for bio::alphabet::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 char_type	to_char () const noexcept
	Return the letter as a character of char_type.
constexpr rank_type	to_rank () const noexcept
	Return the letter's numeric value (rank in the alphabet).
Write functions
constexpr derived_type &	assign_char (char_type const c) noexcept
	Assign from a character, implicitly converts invalid characters.
constexpr derived_type &	assign_rank (rank_type const c) noexcept
	Assign from a numeric value.

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.

Static Public Attributes
static constexpr size_t	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 = meta::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.)
Literals
consteval dna4	operator""_dna4 (char const c)
	The bio::alphabet::dna4 char literal.
template<meta::detail::literal_buffer_string str>
constexpr std::vector< dna4 >	operator""_dna4 ()
	The bio::alphabet::dna4 string literal.

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 bio::alphabet::dna4::assign_char().

#include <bio/alphabet/nucleotide/dna4.hpp>
#include <bio/alphabet/fmt.hpp>
 
int main()
{
    using namespace bio::alphabet::literals;
 
    bio::alphabet::dna4 my_letter{'C'_dna4};
 
    my_letter.assign_char('F'); // characters other than IUPAC characters are implicitly converted to A.
    fmt::print("{}", my_letter); // prints "F"
 
    // IUPAC characters are implicitly converted to their best fitting representative
    fmt::print("{}", my_letter.assign_char('R')); // prints "A"
    fmt::print("{}", my_letter.assign_char('Y')); // prints "C"
    fmt::print("{}", my_letter.assign_char('S')); // prints "C"
    fmt::print("{}", my_letter.assign_char('W')); // prints "A"
    fmt::print("{}", my_letter.assign_char('K')); // prints "G"
    fmt::print("{}", my_letter.assign_char('M')); // prints "A"
    fmt::print("{}", my_letter.assign_char('B')); // prints "C"
    fmt::print("{}", my_letter.assign_char('D')); // prints "A"
    fmt::print("{}", my_letter.assign_char('H')); // prints "A"
    fmt::print("{}", my_letter.assign_char('V')); // prints "A"
 
    my_letter.assign_char('a'); // lower case letters are the same as their upper case equivalent
    fmt::print("{}", my_letter); // prints "A";
}

Member Function Documentation

assign_char()

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

constexpr derived_type & bio::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 bio::alphabet::assign_char_to, required to model bio::alphabet::alphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

assign_rank()

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

constexpr derived_type & bio::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 bio::alphabet::assign_rank_to, required to model bio::alphabet::semialphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

char_is_valid()

static constexpr bool bio::alphabet::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 bio::alphabet::semialphabet::char_is_valid_for() requirement via the bio::alphabet::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 bio::alphabet::dna4, because its informational content is identical to 'T'.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

to_char()

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

constexpr char_type bio::alphabet::base< derived_type, size, char_t >::to_char ( ) const

inlineconstexprnoexceptinherited

Return the letter as a character of char_type.

Provides an implementation for bio::alphabet::to_char, required to model bio::alphabet::alphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

to_rank()

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

constexpr rank_type bio::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 bio::alphabet::to_rank, required to model bio::alphabet::semialphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

Friends And Related Function Documentation

operator""_dna4() [1/2]

template<meta::detail::literal_buffer_string str>

constexpr std::vector< dna4 > operator""_dna4 ( )

related

The bio::alphabet::dna4 string literal.

Returns

std::vector<bio::alphabet::dna4>

You can use this string literal to easily create a std::vector<bio::alphabet::dna4>:

#include <bio/alphabet/nucleotide/dna4.hpp>
 
int main()
{
    using namespace bio::alphabet::literals;
 
    std::vector<bio::alphabet::dna4> foo{"ACGTTA"_dna4};
    std::vector<bio::alphabet::dna4> bar = "ACGTTA"_dna4;
    auto bax = "ACGTTA"_dna4;
}

operator""_dna4() [2/2]

consteval dna4 operator""_dna4 ( char const  c )

related

The bio::alphabet::dna4 char literal.

Returns

bio::alphabet::dna4

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

• bio/alphabet/nucleotide/dna4.hpp