bio::alphabet::aa20 Class Reference

The canonical amino acid alphabet.. More...

#include <bio/alphabet/aminoacid/aa20.hpp>

Inheritance diagram for bio::alphabet::aa20:

Public Member Functions
Constructors, destructor and assignment
constexpr	aa20 () noexcept=default
	Defaulted.
constexpr	aa20 (aa20 const &) noexcept=default
	Defaulted.
constexpr	aa20 (aa20 &&) noexcept=default
	Defaulted.
constexpr aa20 &	operator= (aa20 const &) noexcept=default
	Defaulted.
constexpr aa20 &	operator= (aa20 &&) noexcept=default
	Defaulted.
	~aa20 () noexcept=default
	Defaulted.
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()).

Static Protected Attributes
static constexpr std::array< rank_type, 256 >	char_to_rank
	Char to value conversion table.
static constexpr std::array< char_type, alphabet_size >	rank_to_char
	Value to char conversion table.

Related Functions
(Note that these are not member functions.)
Literals
consteval aa20	operator""_aa20 (char const c)
	The bio::alphabet::aa20 char literal.
template<meta::detail::literal_buffer_string str>
constexpr std::vector< aa20 >	operator""_aa20 ()
	The bio::alphabet::aa20 string literal.

Detailed Description

The canonical amino acid alphabet.

.

The alphabet consists of letters A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y

The alphabet may be brace initialized from the static letter members (see above). Note that you cannot assign regular characters, but additional functions for this are available.

Note: Letters which belong in the extended alphabet will be automatically converted based on the frequency of their options.
Terminator characters are converted to W, because the most commonly occurring stop codon in higher eukaryotes is UGA². Anything unknown is converted to S, because it occurs most frequently across 53 vertebrates¹.

Input Letter	Converts to
B	D1
J	L1
O	L1
U	C1
Z	E1
X (Unknown)	S1
* (Terminator)	W2

¹King, J. L., & Jukes, T. H. (1969). Non-Darwinian Evolution. Science, 164(3881), 788-798. doi:10.1126/science.164.3881.788
²Trotta, E. (2016). Selective forces and mutational biases drive stop codon usage in the human genome: a comparison with sense codon usage. BMC Genomics, 17, 366. https://doi.org/10.1186/s12864-016-2692-4

#include <bio/alphabet/aminoacid/aa20.hpp>
#include <bio/alphabet/fmt.hpp>
 
int main()
{
    using namespace bio::alphabet::literals;
 
    bio::alphabet::aa20 my_letter{'A'_aa20};
 
    my_letter.assign_char('C');
 
    my_letter.assign_char('?'); // all unknown characters are converted to 'A'_aa20 implicitly
 
    if (my_letter.to_char() == 'A')
        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::aminoacid_base< aa20 , size >::char_is_valid ( char_type const  c )

inlinestaticconstexprnoexceptinherited

Validate whether a character value has a one-to-one mapping to an alphabet value.

Models the bio::alphabet::semialphabet::char_is_valid_for() requirement via the bio::alphabet::char_is_valid_for() wrapper.

Behaviour specific to amino acids: True also for lower case letters that silently convert to their upper case.

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""_aa20() [1/2]

template<meta::detail::literal_buffer_string str>

constexpr std::vector< aa20 > operator""_aa20 ( )

related

The bio::alphabet::aa20 string literal.

Returns

std::vector<bio::alphabet::aa20>

You can use this string literal to easily create a std::vector<bio::alphabet::aa20>:

#include <bio/alphabet/aminoacid/aa20.hpp>
 
int main()
{
    using namespace bio::alphabet::literals;
 
    std::vector<bio::alphabet::aa20> bar = "ADFCYR"_aa20;
    auto bax = "ADFCYR"_aa20;
}

operator""_aa20() [2/2]

consteval aa20 operator""_aa20 ( char const  c )

related

The bio::alphabet::aa20 char literal.

Returns

bio::alphabet::aa20

Member Data Documentation

char_to_rank

constexpr std::array<rank_type, 256> bio::alphabet::aa20::char_to_rank

staticconstexprprotected

Initial value:

= []() constexpr
    {
        std::array<rank_type, 256> ret{};
 
        
        ret.fill(15); 
 
        
        for (rank_type rnk = 0u; rnk < alphabet_size; ++rnk)
        {
            ret[static_cast<rank_type>(rank_to_char[rnk])]                   = rnk;
            ret[static_cast<rank_type>(detail::to_lower(rank_to_char[rnk]))] = rnk;
        }
 
        ret['B'] = ret['D'];
        ret['b'] = ret['D']; 
        ret['J'] = ret['L'];
        ret['j'] = ret['L']; 
        ret['O'] = ret['L'];
        ret['o'] = ret['L']; 
        ret['U'] = ret['C'];
        ret['u'] = ret['C']; 
        ret['X'] = ret['S'];
        ret['x'] = ret['S']; 
        ret['Z'] = ret['E'];
        ret['z'] = ret['E']; 
        ret['*'] = ret['W']; 
        return ret;
    }()

Char to value conversion table.

rank_to_char

constexpr std::array<char_type, alphabet_size> bio::alphabet::aa20::rank_to_char

staticconstexprprotected

Initial value:

{
      'A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L', 'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y',
    }

Value to char conversion table.

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

• bio/alphabet/aminoacid/aa20.hpp