seqan3::aa20 Class Reference

The canonical amino acid alphabet. More...

#include <seqan3/alphabet/aminoacid/aa20.hpp>

Inheritance diagram for seqan3::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. 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...

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

Related Functions
(Note that these are not member functions.)
using	aa20_vector = std::vector< aa20 >
	Alias for an std::vector of seqan3::aa20. More...
Literals
constexpr aa20	operator""_aa20 (char const c) noexcept
	The seqan3::aa20 char literal. More...
aa20_vector	operator""_aa20 (char const *const s, size_t const n)
	The seqan3::aa20 string literal. More...

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 <seqan3/alphabet/aminoacid/aa20.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using seqan3::operator""_aa20;
 
    seqan3::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')
        seqan3::debug_stream << "yeah\n"; // "yeah";
}

This entity is stable. Since version 3.1.

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::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 seqan3::semialphabet::char_is_valid_for() requirement via the seqan3::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.

This entity is experimental and subject to change in the future. Experimental since version 3.1.

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

aa20_vector

using aa20_vector = std::vector<aa20>

related

Alias for an std::vector of seqan3::aa20.

This entity is stable. Since version 3.1.

operator""_aa20() [1/2]

aa20_vector operator""_aa20 ( char const *const  s, size_t const  n  )

related

The seqan3::aa20 string literal.

Parameters

[in]	s	A pointer to the character string to assign.
[in]	n	The size of the character string to assign.

Returns

seqan3::aa20_vector

You can use this string literal to easily assign to aa20_vector:

#include <seqan3/alphabet/aminoacid/aa20.hpp>
 
int main()
{
    using seqan3::operator""_aa20;
    
    seqan3::aa20_vector foo{"ABFUYR"_aa20};
    seqan3::aa20_vector bar = "ABFUYR"_aa20;
    auto bax = "ABFUYR"_aa20;
}

Attention

All seqan3 literals are in the namespace seqan3!

This entity is stable. Since version 3.1.

operator""_aa20() [2/2]

constexpr aa20 operator""_aa20 ( char const  c )

related

The seqan3::aa20 char literal.

Parameters

[in]

c

The character to assign.

Returns

seqan3::aa20

#include <seqan3/alphabet/aminoacid/aa20.hpp>
 
int main()
{
    using seqan3::operator""_aa20;
 
    seqan3::aa20 acid1{'A'_aa20};
    
    auto acid2 = 'Y'_aa20; // type = aa20
}

This entity is stable. Since version 3.1.

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.

char_to_rank

constexpr std::array<rank_type, 256> seqan3::aa20::char_to_rank

staticconstexprprotected

Initial value:

{
        [] () constexpr
        {
            std::array<rank_type, 256> ret{};
 
            
            for (auto & c : ret)
                c = 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>(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 char_type seqan3::aa20::rank_to_char[alphabet_size]

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:

• seqan3/alphabet/aminoacid/aa20.hpp