SeqAn3 3.1.0
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.
 
- Public Member Functions inherited from seqan3::aminoacid_base< aa27, 27 >
constexpr aminoacid_base (other_aa_type const other) noexcept
 Allow explicit construction from any other aminoacid type and convert via the character representation. More...
 
- Public Member Functions inherited from seqan3::alphabet_base< derived_type, size, char_t >
constexpr alphabet_base () noexcept=default
 Defaulted.
 
constexpr alphabet_base (alphabet_base const &) noexcept=default
 Defaulted.
 
constexpr alphabet_base (alphabet_base &&) noexcept=default
 Defaulted.
 
constexpr alphabet_baseoperator= (alphabet_base const &) noexcept=default
 Defaulted.
 
constexpr alphabet_baseoperator= (alphabet_base &&) noexcept=default
 Defaulted.
 
 ~alphabet_base () noexcept=default
 Defaulted.
 
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...
 
constexpr derived_type & assign_char (char_type const chr) 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...
 

Related Functions

(Note that these are not member functions.)

using aa27_vector = std::vector< aa27 >
 Alias for a 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...
 

Additional Inherited Members

- Static Public Member Functions inherited from seqan3::aminoacid_base< aa27, 27 >
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 inherited from seqan3::alphabet_base< derived_type, size, char_t >
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 inherited from seqan3::alphabet_base< derived_type, size, char_t >
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...
 

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 'X'_aa27 or use the function seqan3::aa27::assign_char().

int main()
{
using namespace seqan3::literals;
seqan3::aa27 letter{'A'_aa27};
letter.assign_char('C');
seqan3::debug_stream << letter << '\n'; // prints "C"
letter.assign_char('?'); // Unknown characters are implicitly converted to X.
seqan3::debug_stream << letter << '\n'; // prints "X"
}
Provides seqan3::aa27, container aliases and string literals.
The twenty-seven letter amino acid alphabet..
Definition: aa27.hpp:46
constexpr derived_type & assign_char(char_type const chr) noexcept
Assign from a character, implicitly converts invalid characters.
Definition: alphabet_base.hpp:165
Provides seqan3::debug_stream and related types.
debug_stream_type debug_stream
A global instance of seqan3::debug_stream_type.
Definition: debug_stream.hpp:37
The SeqAn namespace for literals.

This entity is stable. Since version 3.1.

Friends And Related Function Documentation

◆ aa27_vector

using aa27_vector = std::vector<aa27>
related

Alias for a 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]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 namespace seqan3::literals;
seqan3::aa27_vector sequence1{"ACGTTA"_aa27};
seqan3::aa27_vector sequence2 = "ACGTTA"_aa27;
auto sequence3 = "ACGTTA"_aa27;
}

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]cThe character to assign.
Returns
seqan3::aa27 You can use this char literal to assign a seqan3::aa27 character:
int main()
{
using namespace seqan3::literals;
seqan3::aa27 letter1{'A'_aa27};
auto letter2 = 'A'_aa27;
}

This entity is stable. Since version 3.1.


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