The canonical amino acid alphabet.. More...

#include <seqan3/alphabet/aminoacid/aa20.hpp>

Inheritance diagram for seqan3::aa20:

Public Member Functions
Constructors, destructor and assignment
constexpr	aa20 () noexcept=default
	Defaulted.

constexpr	aa20 (aa20 const &) noexcept=default
	Defaulted.

constexpr	aa20 (aa20 &&) noexcept=default
	Defaulted.

constexpr aa20 &	operator= (aa20 const &) noexcept=default
	Defaulted.

constexpr aa20 &	operator= (aa20 &&) noexcept=default
	Defaulted.

	~aa20 () noexcept=default
	Defaulted.

Public Member Functions inherited from seqan3::aminoacid_base< aa20, 20 >
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< aa20, size, char >
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. More...

constexpr rank_type	to_rank () const noexcept
	Return the letter's numeric value (rank in the alphabet). More...

constexpr aa20 &	assign_char (char_type const chr) noexcept
	Assign from a character, implicitly converts invalid characters. More...

constexpr aa20 &	assign_rank (rank_type const c) noexcept
	Assign from a numeric value. More...

Private Types
using	base_t = aminoacid_base< aa20, 20 >
	The base class.

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

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

Private Attributes
friend	base_t
	Befriend seqan3::aminoacid_base.

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

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

Related Functions
(Note that these are not member functions.)
using	aa20_vector = std::vector< aa20 >
	Alias for a std::vector of seqan3::aa20. More...

Literals
constexpr aa20	operator""_aa20 (char const c) noexcept
	The seqan3::aa20 char literal. More...

constexpr aa20_vector	operator""_aa20 (char const *const s, size_t const n)
	The seqan3::aa20 string literal. More...

Related Functions 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. More...

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. More...

Additional Inherited Members
Static Public Member Functions inherited from seqan3::aminoacid_base< aa20, 20 >
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< aa20, size, char >
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. More...

Protected Types inherited from seqan3::alphabet_base< aa20, size, char >
using	char_type = std::conditional_t< std::same_as< char, void >, char, char >
	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 canonical amino acid alphabet.

.

The alphabet consists of letters A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, Y

The alphabet may be brace initialized from the static letter members (see above). Note that you cannot assign regular characters, but additional functions for this are available.

Note: Letters which belong in the extended alphabet will be automatically converted based on the frequency of their options.
Terminator characters are converted to W, because the most commonly occurring stop codon in higher eukaryotes is UGA². Anything unknown is converted to S, because it occurs most frequently across 53 vertebrates¹.

Input Letter	Converts to
B	D¹
J	L¹
O	L¹
U	C¹
Z	E¹
X (Unknown)	S¹
* (Terminator)	W²

¹King, J. L., & Jukes, T. H. (1969). Non-Darwinian Evolution. Science, 164(3881), 788-798. doi:10.1126/science.164.3881.788
²Trotta, E. (2016). Selective forces and mutational biases drive stop codon usage in the human genome: a comparison with sense codon usage. BMC Genomics, 17, 366. https://doi.org/10.1186/s12864-016-2692-4

#include <seqan3/alphabet/aminoacid/aa20.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::aa20 letter{'A'_aa20};
 
    letter.assign_char('C');
    seqan3::debug_stream << letter << '\n'; // prints "C"
 
    letter.assign_char('?');                // Unknown characters are implicitly converted to S.
    seqan3::debug_stream << letter << '\n'; // prints "S"
}

This entity is stable. Since version 3.1.

Member Function Documentation

◆ char_to_rank()

static constexpr rank_type seqan3::aa20::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::aa20::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 Function Documentation

◆ aa20_vector

using aa20_vector = std::vector<aa20>

This entity is stable. Since version 3.1.

◆ operator""_aa20() [1/2]

constexpr aa20_vector operator""_aa20	(	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::aa20_vector

You can use this string literal to easily assign to aa20_vector:

#include <seqan3/alphabet/aminoacid/aa20.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::aa20_vector sequence1{"ACGTTA"_aa20};
    seqan3::aa20_vector sequence2 = "ACGTTA"_aa20;
    auto sequence3 = "ACGTTA"_aa20;
}

This entity is stable. Since version 3.1.

◆ operator""_aa20() [2/2]

constexpr aa20 operator""_aa20 ( char const c )

Parameters

[in] c The character to assign.

Returns: seqan3::aa20

You can use this char literal to assign a seqan3::aa20 character:

#include <seqan3/alphabet/aminoacid/aa20.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::aa20 letter1{'A'_aa20};
    auto letter2 = 'A'_aa20;
}

This entity is stable. Since version 3.1.

Member Data Documentation

◆ char_to_rank_table

constexpr std::array<rank_type, 256> seqan3::aa20::char_to_rank_table

staticconstexprprivate

Initial value:

{
        []() constexpr {
            std::array<rank_type, 256> ret{};
 
            
            ret.fill(15u);
 
            
            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;
            }
 
            ret['B'] = ret['D'];
            ret['b'] = ret['D']; 
            ret['J'] = ret['L'];
            ret['j'] = ret['L']; 
            ret['O'] = ret['L'];
            ret['o'] = ret['L']; 
            ret['U'] = ret['C'];
            ret['u'] = ret['C']; 
            ret['X'] = ret['S'];
            ret['x'] = ret['S']; 
            ret['Z'] = ret['E'];
            ret['z'] = ret['E']; 
            ret['*'] = ret['W']; 
            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::aa20::rank_to_char_table[alphabet_size]

staticconstexprprivate

Initial value:

{'A', 'C', 'D', 'E', 'F', 'G', 'H', 'I', 'K', 'L',

'M', 'N', 'P', 'Q', 'R', 'S', 'T', 'V', 'W', 'Y'}

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:

aa20.hpp

Public Member Functions

Private Types

Static Private Member Functions

Private Attributes

Static Private Attributes

Related Functions

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ char_to_rank()

◆ rank_to_char()

Friends And Related Function Documentation

◆ aa20_vector

◆ operator""_aa20() [1/2]

◆ operator""_aa20() [2/2]

Member Data Documentation

◆ char_to_rank_table

◆ rank_to_char_table