SeqAn3  3.0.2
The Modern C++ library for sequence analysis.
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 aa27operator= (aa27 const &) noexcept=default
 Defaulted.
 
constexpr aa27operator= (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 aa27assign_char (char_type const c) noexcept
 Assign from a character, implicitly converts invalid characters. More...
 
constexpr aa27assign_rank (rank_type const c) noexcept
 Assign from a numeric value. More...
 
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 aa27assign_char (char_type const c) noexcept
 Assign from a character, implicitly converts invalid characters. More...
 
constexpr aa27assign_rank (rank_type const c) noexcept
 Assign from a numeric value. More...
 
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 aa27assign_char (char_type const c) noexcept
 Assign from a character, implicitly converts invalid characters. More...
 
constexpr aa27assign_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
 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, void >, char, char >
 The char representation; conditional needed to make semi alphabet definitions legal.
 
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()).
 
Member types
using char_type = std::conditional_t< std::same_as< char, void >, char, char >
 The char representation; conditional needed to make semi alphabet definitions legal.
 
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()).
 
Member types
using char_type = std::conditional_t< std::same_as< char, void >, char, char >
 The char representation; conditional needed to make semi alphabet definitions legal.
 
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()).
 

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.
 
Literals
constexpr aa27 operator""_aa27 (char const c) noexcept
 The seqan3::aa27 char literal. More...
 
aa27_vector operator""_aa27 (const char *s, std::size_t 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().

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";
}

Member Function Documentation

◆ assign_char()

constexpr aa27 & seqan3::alphabet_base< aa27 , size, char >::assign_char ( char_type const  c)
inlineconstexprnoexceptinherited

Assign from a character, implicitly converts invalid characters.

Parameters
cThe character to be assigned.

Provides an implementation for seqan3::assign_char_to, required to model seqan3::alphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ assign_rank()

constexpr aa27 & seqan3::alphabet_base< aa27 , size, char >::assign_rank ( rank_type const  c)
inlineconstexprnoexceptinherited

Assign from a numeric value.

Parameters
cThe rank to be assigned.

Provides an implementation for seqan3::assign_rank_to, required to model seqan3::semialphabet.

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ 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.

◆ to_char()

constexpr char_type seqan3::alphabet_base< aa27 , size, char >::to_char
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.

◆ to_rank()

constexpr rank_type seqan3::alphabet_base< aa27 , size, char >::to_rank
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.

Friends And Related Function Documentation

◆ operator""_aa27() [1/2]

constexpr aa27 operator""_aa27 ( char const  c)
related

The seqan3::aa27 char literal.

Parameters
[in]cThe character to assign.
Returns
seqan3::aa27
int main()
{
using seqan3::operator""_aa27;
seqan3::aa27 acid1{'A'_aa27};
auto acid2 = 'Y'_aa27; // type = aa27
}

◆ operator""_aa27() [2/2]

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

The seqan3::aa27 string literal.

Parameters
[in]sA pointer to the character string to assign.
[in]nThe size of the character string to assign.
Returns
seqan3::aa27_vector

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

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!

Member Data Documentation

◆ char_to_rank

constexpr std::array<rank_type, 256> seqan3::aa27::char_to_rank
staticconstexprprotected
Initial value:
{
[] () constexpr
{
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.


The documentation for this class was generated from the following file:
debug_stream.hpp
Provides seqan3::debug_stream and related types.
seqan3::alphabet_base< aa27, size, char >::alphabet_size
static constexpr detail::min_viable_uint_t< size > alphabet_size
The size of the alphabet, i.e. the number of different values it can take.
Definition: alphabet_base.hpp:176
seqan3::alphabet_base::assign_char
constexpr derived_type & assign_char(char_type const c) noexcept
Assign from a character, implicitly converts invalid characters.
Definition: alphabet_base.hpp:142
aa27.hpp
Provides seqan3::aa27, container aliases and string literals.
seqan3::alphabet_base< aa27, size, char >::rank_type
detail::min_viable_uint_t< size - 1 > rank_type
The type of the alphabet when represented as a number (e.g. via to_rank()).
Definition: alphabet_base.hpp:64
std::array< rank_type, 256 >
seqan3::aa27::rank_to_char
static constexpr char_type rank_to_char[alphabet_size]
Value to char conversion table.
Definition: aa27.hpp:72
seqan3::debug_stream
debug_stream_type debug_stream
A global instance of seqan3::debug_stream_type.
Definition: debug_stream.hpp:42
seqan3::to_lower
constexpr char_type to_lower(char_type const c) noexcept
Converts 'A'-'Z' to 'a'-'z' respectively; other characters are returned as is.
Definition: transform.hpp:81
seqan3::aa27
The twenty-seven letter amino acid alphabet.
Definition: aa27.hpp:43