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.
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.
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_base &	operator= (alphabet_base const &) noexcept=default
	Defaulted.
constexpr alphabet_base &	operator= (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.
constexpr rank_type	to_rank () const noexcept
	Return the letter's numeric value (rank in the alphabet).
constexpr derived_type &	assign_char (char_type const chr) noexcept
	Assign from a character, implicitly converts invalid characters.
constexpr derived_type &	assign_rank (rank_type const c) noexcept
	Assign from a numeric value.

Related Symbols
(Note that these are not member symbols.)
using	aa27_vector = std::vector< aa27 >
	Alias for a std::vector of seqan3::aa27.

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.
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.
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.
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()).

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().

// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
#include <seqan3/alphabet/aminoacid/aa27.hpp>
#include <seqan3/core/debug_stream.hpp>
 
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"
}

This entity is stable. Since version 3.1.

Friends And Related Symbol 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.

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

• aa27.hpp