bio::alphabet::dna5 Class Reference

The five letter DNA alphabet of A,C,G,T and the unknown character N.. More...

#include <bio/alphabet/nucleotide/dna5.hpp>

Inheritance diagram for bio::alphabet::dna5:

Public Member Functions
Constructors, destructor and assignment
constexpr	dna5 () noexcept=default
	Defaulted.
constexpr	dna5 (dna5 const &) noexcept=default
	Defaulted.
constexpr	dna5 (dna5 &&) noexcept=default
	Defaulted.
constexpr dna5 &	operator= (dna5 const &) noexcept=default
	Defaulted.
constexpr dna5 &	operator= (dna5 &&) noexcept=default
	Defaulted.
	~dna5 () noexcept=default
	Defaulted.
template<std::same_as< rna5 > t>
constexpr	dna5 (t const &r) noexcept
	Allow implicit construction from dna/rna of the same size.
Read functions
constexpr dna5	complement () const noexcept
	Return the complement of the letter.
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 dna5	operator""_dna5 (char const c)
	The bio::alphabet::dna5 char literal.
template<meta::detail::literal_buffer_string str>
constexpr std::vector< dna5 >	operator""_dna5 ()
	The bio::alphabet::dna5 string literal.

Detailed Description

The five letter DNA alphabet of A,C,G,T and the unknown character N.

.

Note that you can assign 'U' as a character to dna5 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::dna5::assign_char().

#include <bio/alphabet/nucleotide/dna5.hpp>
#include <bio/alphabet/fmt.hpp>
 
int main()
{
    using namespace bio::alphabet::literals;
 
    bio::alphabet::dna5 my_letter{'A'_dna5};
 
    my_letter.assign_char('C');
 
    my_letter.assign_char('F'); // unknown characters are implicitly converted to N.
    if (my_letter.to_char() == 'N')
        fmt::print("{}", "yeah\n"); // "yeah";
}

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< dna5 , 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.

complement()

constexpr dna5 bio::alphabet::nucleotide_base< dna5 , size >::complement ( ) const

inlineconstexprnoexceptinherited

Return the complement of the letter.

See Nucleotide for the actual values.

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

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""_dna5() [1/2]

template<meta::detail::literal_buffer_string str>

constexpr std::vector< dna5 > operator""_dna5 ( )

related

The bio::alphabet::dna5 string literal.

Returns

std::vector<bio::alphabet::dna5>

You can use this string literal to easily create a std::vector<bio::alphabet::dna5>:

#include <bio/alphabet/nucleotide/dna5.hpp>
 
int main()
{
    using namespace bio::alphabet::literals;
 
    std::vector<bio::alphabet::dna5> foo{"ACGTTA"_dna5};
    std::vector<bio::alphabet::dna5> bar = "ACGTTA"_dna5;
    auto bax = "ACGTTA"_dna5;
}

operator""_dna5() [2/2]

consteval dna5 operator""_dna5 ( char const  c )

related

The bio::alphabet::dna5 char literal.

Returns

bio::alphabet::dna5

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

• bio/alphabet/nucleotide/dna5.hpp