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.

Private Types
using	base_t = aminoacid_base< aa27, 27 >
	The base class.

Static Private Member Functions
static constexpr rank_type	char_to_rank (char_type const chr)
	Returns the rank representation of character.

static constexpr char_type	rank_to_char (rank_type const rank)
	Returns the character representation of rank.

Private Attributes
friend	base_t
	Befriend seqan3::nucleotide_base.

Static Private Attributes
static constexpr std::array< rank_type, 256 >	char_to_rank_table
	The lookup table used in char_to_rank.

static constexpr char_type	rank_to_char_table [alphabet_size]
	The lookup table used in rank_to_char.

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

Literals
constexpr aa27	operator""_aa27 (char const c) noexcept
	The seqan3::aa27 char literal.

constexpr aa27_vector	operator""_aa27 (char const *const s, size_t const n)
	The seqan3::aa27 string literal.

Related Symbols inherited from semialphabet
template<cereal_output_archive archive_t, semialphabet alphabet_t>
alphabet_rank_t< alphabet_t >	save_minimal (archive_t const &, alphabet_t const &l)
	Save an alphabet letter to stream.

template<cereal_input_archive archive_t, typename wrapped_alphabet_t >
void	load_minimal (archive_t const &, wrapped_alphabet_t &&l, alphabet_rank_t< detail::strip_cereal_wrapper_t< wrapped_alphabet_t > > const &r)
	Restore an alphabet letter from a saved rank.

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.

Member Function Documentation

◆ char_to_rank()

static constexpr rank_type seqan3::aa27::char_to_rank ( char_type const chr )

inlinestaticconstexprprivate

Returns the rank representation of character.

This function is required by seqan3::alphabet_base.

◆ rank_to_char()

static constexpr char_type seqan3::aa27::rank_to_char ( rank_type const rank )

inlinestaticconstexprprivate

Returns the character representation of rank.

This function is required by seqan3::alphabet_base.

Friends And Related Symbol Documentation

◆ aa27_vector

using aa27_vector = std::vector<aa27>

This entity is stable. Since version 3.1.

◆ operator""_aa27() [1/2]

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

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:

// 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>
 
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 )

Parameters

[in] c The character to assign.

Returns: seqan3::aa27 You can use this char literal to assign a seqan3::aa27 character:
// 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>

int main()

{

using namespace seqan3::literals;

seqan3::aa27 letter1{'A'_aa27};

auto letter2 = 'A'_aa27;

}

This entity is stable. Since version 3.1.

Member Data Documentation

◆ char_to_rank_table

constexpr std::array<rank_type, 256> seqan3::aa27::char_to_rank_table

staticconstexprprivate

Initial value:

{
        []() constexpr {
            std::array<rank_type, 256> ret{};
 
            
            ret.fill(23u);
 
            
            for (rank_type rnk = 0u; rnk < alphabet_size; ++rnk)
            {
                ret[static_cast<rank_type>(rank_to_char_table[rnk])] = rnk;
                ret[static_cast<rank_type>(to_lower(rank_to_char_table[rnk]))] = rnk;
            }
 
            return ret;
        }()
    }

The lookup table used in char_to_rank.

We would have defined these lookup tables directly within their respective constexpr functions, but at the time of writing this, gcc did not (clang >= 4 did!) auto-generate lookup tables.

static constexpr char_type rank_to_char(rank_type const rank)
{
    // not possible because of static not being allowed within a constexpr function
    static constexpr lookup_table = ...;
    return lookup_table[rank];
}
 
static constexpr char_type rank_to_char(rank_type const rank)
{
    // up-to the compiler to optimise, no guarantee that a lookup table is used.
    constexpr lookup_table = ...;
    return lookup_table[rank];
}

See also: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=99320 for the progress on gcc

◆ rank_to_char_table

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

staticconstexprprivate

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', '*'}

The lookup table used in rank_to_char.

We would have defined these lookup tables directly within their respective constexpr functions, but at the time of writing this, gcc did not (clang >= 4 did!) auto-generate lookup tables.

static constexpr char_type rank_to_char(rank_type const rank)
{
    // not possible because of static not being allowed within a constexpr function
    static constexpr lookup_table = ...;
    return lookup_table[rank];
}
 
static constexpr char_type rank_to_char(rank_type const rank)
{
    // up-to the compiler to optimise, no guarantee that a lookup table is used.
    constexpr lookup_table = ...;
    return lookup_table[rank];
}

See also: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=99320 for the progress on gcc

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

aa27.hpp

Public Member Functions

Private Types

Static Private Member Functions

Private Attributes

Static Private Attributes

Related Symbols

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ char_to_rank()

◆ rank_to_char()

Friends And Related Symbol Documentation

◆ aa27_vector

◆ operator""_aa27() [1/2]

◆ operator""_aa27() [2/2]

Member Data Documentation

◆ char_to_rank_table

◆ rank_to_char_table