seqan3::aa27 Class Reference

The twenty-seven letter amino acid alphabet. More...

#include <seqan3/alphabet/aminoacid/aa27.hpp>

Inheritance diagram for seqan3::aa27:

Public Member Functions
Constructors, destructor and assignment
constexpr	aa27 () noexcept=default
	Defaulted.
constexpr	aa27 (aa27 const &) noexcept=default
	Defaulted.
constexpr	aa27 (aa27 &&) noexcept=default
	Defaulted.
constexpr aa27 &	operator= (aa27 const &) noexcept=default
	Defaulted.
constexpr aa27 &	operator= (aa27 &&) noexcept=default
	Defaulted.
	~aa27 () 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	aa27_vector = std::vector< aa27 >
	Alias for an std::vector of seqan3::aa27. More...
Literals
constexpr aa27	operator""_aa27 (char const c) noexcept
	The seqan3::aa27 char literal. More...
aa27_vector	operator""_aa27 (char const *const s, size_t const n)
	The seqan3::aa27 string literal. More...

Detailed Description

The twenty-seven letter amino acid alphabet.

The alphabet consists of letters A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, *

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::aa27::assign_char().

#include <seqan3/alphabet/aminoacid/aa27.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using seqan3::operator""_aa27;
 
    seqan3::aa27 my_letter{'A'_aa27};
 
    my_letter.assign_char('C');
    
    my_letter.assign_char('?'); // all unknown characters are converted to 'X'_aa27 implicitly
    if (my_letter.to_char() == 'X')
        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< aa27 , 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

aa27_vector

using aa27_vector = std::vector<aa27>

related

Alias for an std::vector of seqan3::aa27.

This entity is stable. Since version 3.1.

operator""_aa27() [1/2]

aa27_vector operator""_aa27 ( char const *const  s, size_t const  n  )

related

The seqan3::aa27 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::aa27_vector

You can use this string literal to easily assign to aa27_vector:

#include <seqan3/alphabet/aminoacid/aa27.hpp>
 
int main()
{
    using seqan3::operator""_aa27;
    
    seqan3::aa27_vector foo{"ABFUYR"_aa27};
    seqan3::aa27_vector bar = "ABFUYR"_aa27;
    auto bax = "ABFUYR"_aa27;
}

Attention

All seqan3 literals are in the namespace seqan3!

This entity is stable. Since version 3.1.

operator""_aa27() [2/2]

constexpr aa27 operator""_aa27 ( char const  c )

related

The seqan3::aa27 char literal.

Parameters

[in]

c

The character to assign.

Returns

seqan3::aa27

#include <seqan3/alphabet/aminoacid/aa27.hpp>
 
int main()
{
    using seqan3::operator""_aa27;
 
    seqan3::aa27 acid1{'A'_aa27};
    
    auto acid2 = 'Y'_aa27; // type = aa27
}

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::aa27::char_to_rank

staticconstexprprotected

Initial value:

{
        [] () constexpr
        {
            std::array<rank_type, 256> ret{};
 
            
            for (auto & c : ret)
                c = 23; 
 
            
            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;
            }
 
            return ret;
        }()
    }

Char to value conversion table.

rank_to_char

constexpr char_type seqan3::aa27::rank_to_char[alphabet_size]

staticconstexprprotected

Initial value:

{
        'A',
        'B',
        'C',
        'D',
        'E',
        'F',
        'G',
        'H',
        'I',
        'J',
        'K',
        'L',
        'M',
        'N',
        'O',
        'P',
        'Q',
        'R',
        'S',
        'T',
        'U',
        'V',
        'W',
        'X',
        'Y',
        'Z',
        '*'
    }

Value to char conversion table.

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

• seqan3/alphabet/aminoacid/aa27.hpp