The reduced Li amino acid alphabet. More...

#include <seqan3/alphabet/aminoacid/aa10li.hpp>

Inheritance diagram for seqan3::aa10li:

Public Member Functions
Constructors, destructor and assignment
constexpr	aa10li () noexcept=default
	Defaulted.

constexpr	aa10li (aa10li const &) noexcept=default
	Defaulted.

constexpr	aa10li (aa10li &&) noexcept=default
	Defaulted.

constexpr aa10li &	operator= (aa10li const &) noexcept=default
	Defaulted.

constexpr aa10li &	operator= (aa10li &&) noexcept=default
	Defaulted.

	~aa10li () 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 derived_type &	assign_char (char_type const c) 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...

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 = size
	The size of the alphabet, i.e. the number of different values it can take. More...

Protected Types
Member types
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...

Static Protected Attributes
static constexpr std::array< rank_type, 256 >	char_to_rank
	Char to value conversion table.

static constexpr char_type	rank_to_char [alphabet_size]
	Value to char conversion table. More...

Private Types
using	base_t = aminoacid_base< aa10li, 10 >
	The base class.

Private Attributes
friend	base_t
	Befriend seqan3::aminoacid_base.

friend	derived_type
	Befriend the derived class so it can instantiate.

rank_type	rank {}
	The value of the alphabet letter is stored as the rank.

Static Private Attributes
static constexpr std::array< bool, 256 >	valid_char_table
	Implementation of char_is_valid().

Related Functions
(Note that these are not member functions.)
using	aa10li_vector = std::vector< aa10li >
	Alias for an std::vector of seqan3::aa10li. More...

Literals
constexpr aa10li	operator""_aa10li (char const c) noexcept
	The seqan3::aa10li char literal. More...

aa10li_vector	operator""_aa10li (char const *const s, size_t const n)
	The seqan3::aa10li string literal. More...

Generic serialisation functions for all seqan3::semialphabet
All types that satisfy seqan3::semialphabet can be serialised via Cereal.
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...

Detailed Description

The reduced Li amino acid alphabet.

The alphabet consists of letters A, B, C, F, G, H, I, J, K, P A represents hydrophilic and alocohol residues (A,S,T). B represents charged/polar residues (B,D,E,Q,Z). C represents cystein and the species-specific amino acid Selenocysteine. F represents amino acids with aromatic residues (F,W,Y). H represents a group of hydrophobic residues (H,N). I represents a group of large hydrophobic residues (I,V). J represents a group of large hydrophobic residues (J,L,M). K represents long-chain positively charged residues (K,R) and the species-specific amino acid Pyrrolysine. G and P do not represent any other amino acids other than themselves.

This alphabet allows to reduce the aminoacid alphabet size to 10 but is still able to recognize and represent folding of all proteins. Amino acids are grouped together based on residues.

Note: Letters which belong in the extended alphabet will be automatically converted. Terminator characters are converted to F, because the most commonly occurring stop codon in higher eukaryotes is UGA ². This is most similar to a Tryptophan which in this alphabet gets converted to Phenylalanine. Anything unknown is converted to A.

Input Letter	Converts to
D	B¹
E	B¹
L	J¹
M	J¹
N	H¹
O	K¹
Q	B¹
R	K¹
S	A¹
T	A¹
U	C¹
V	I¹
W	F¹
Y	F¹
Z	B¹
X (Unknown)	A¹
* (Terminator)	F^1,2

¹T. Li, K. Fan, J. Wang, and W. Wang. Reduction of protein sequence complexity by residue grouping. Protein Eng., 16(5):323–330, May 2003.
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/aa10li.hpp>
#include <seqan3/alphabet/aminoacid/aa27.hpp>
#include <seqan3/core/debug_stream.hpp>
#include <seqan3/range/views/convert.hpp>
 
using seqan3::operator""_aa10li;
using seqan3::operator""_aa27;
 
int main()
{
    // Construction of aa10li amino acids from character
    seqan3::aa10li my_letter{'A'_aa10li};
 
    my_letter.assign_char('C');
    my_letter.assign_char('?'); // all unknown characters are converted to 'A'_aa10li implicitly
 
    if (my_letter.to_char() == 'A')
        seqan3::debug_stream << "yeah\n"; // "yeah";
 
    // Convert aa27 alphabet to aa10_murphy
    seqan3::aa27_vector v1{"ALRSTXOUMP"_aa27};
    auto v2 = v1 | seqan3::views::convert<seqan3::aa10li>; // AJKAASKCJP
 
    seqan3::debug_stream << v2 << "\n";
 
    return 0;
}

This entity is stable. Since version 3.1.

Member Typedef Documentation

◆ char_type

template<typename derived_type , size_t size, typename char_t = char>

using seqan3::alphabet_base< derived_type, size, char_t >::char_type = std::conditional_t<std::same_as<char_t, void>, char, char_t>

protectedinherited

The char representation; conditional needed to make semi alphabet definitions legal.

We need a return type for seqan3::alphabet_base::to_char and seqan3::alphabet_base::assign_char other than void to make these in-class definitions valid when char_t is void.

This entity is stable. Since version 3.1.

◆ rank_type

template<typename derived_type , size_t size, typename char_t = char>

using seqan3::alphabet_base< derived_type, size, char_t >::rank_type = detail::min_viable_uint_t<size - 1>

protectedinherited

The type of the alphabet when represented as a number (e.g. via to_rank()).

This entity is stable. Since version 3.1.

Member Function Documentation

◆ assign_char()

template<typename derived_type , size_t size, typename char_t = char>

constexpr derived_type& seqan3::alphabet_base< derived_type, size, char_t >::assign_char ( char_type const c )

inlineconstexprnoexceptinherited

Assign from a character, implicitly converts invalid characters.

Parameters

c	The character to be assigned.

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

Complexity

Constant.

Exceptions

Guaranteed not to throw.

This entity is stable. Since version 3.1.

◆ assign_rank()

template<typename derived_type , size_t size, typename char_t = char>

constexpr derived_type& seqan3::alphabet_base< derived_type, size, char_t >::assign_rank ( rank_type const c )

inlineconstexprnoexceptinherited

Assign from a numeric value.

Parameters

c	The rank to be assigned.

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

Complexity

Constant.

Exceptions

Guaranteed not to throw.

This entity is stable. Since version 3.1.

◆ char_is_valid()

static constexpr bool seqan3::aminoacid_base< aa10li , 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.

This entity is experimental and subject to change in the future. Experimental since version 3.1.

◆ to_char()

template<typename derived_type , size_t size, typename char_t = char>

constexpr char_type seqan3::alphabet_base< derived_type, size, char_t >::to_char ( ) const

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.

This entity is stable. Since version 3.1.

◆ to_rank()

template<typename derived_type , size_t size, typename char_t = char>

constexpr rank_type seqan3::alphabet_base< derived_type, size, char_t >::to_rank ( ) const

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.

This entity is stable. Since version 3.1.

Friends And Related Function Documentation

◆ aa10li_vector

using aa10li_vector = std::vector<aa10li>

This entity is stable. Since version 3.1.

◆ operator""_aa10li() [1/2]

aa10li_vector operator""_aa10li	(	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::aa10li_vector

You can use this string literal to easily assign to aa10li_vector:

Attention: All seqan3 literals are in the namespace seqan3!

This entity is stable. Since version 3.1.

◆ operator""_aa10li() [2/2]

constexpr aa10li operator""_aa10li ( char const c )

Parameters

[in] c The character to assign.

Returns: seqan3::aa10li

This entity is stable. Since version 3.1.

◆ save_minimal()

template<cereal_output_archive archive_t, semialphabet alphabet_t>

alphabet_rank_t< alphabet_t > save_minimal	(	archive_t const &	,
		alphabet_t const &	l
	)

Template Parameters

archive_t	Must satisfy seqan3::cereal_output_archive.
alphabet_t	Type of l; must satisfy seqan3::semialphabet.

Parameters

l	The alphabet letter.

Delegates to seqan3::to_rank.

Attention: These functions are never called directly, see the Alphabet module on how to use serialisation.

This entity is stable. Since version 3.1.

Member Data Documentation

◆ alphabet_size

template<typename derived_type , size_t size, typename char_t = char>

constexpr detail::min_viable_uint_t<size> seqan3::alphabet_base< derived_type, size, char_t >::alphabet_size = size

staticconstexprinherited

The size of the alphabet, i.e. the number of different values it can take.

This entity is stable. Since version 3.1.

◆ rank_to_char

constexpr char_type seqan3::aa10li::rank_to_char[alphabet_size]

staticconstexprprotected

Initial value:

{
        'A',
        'B',
        'C',
        'F',
        'G',
        'H',
        'I',
        'J',
        'K',
        'P',
    }

Value to char conversion table.

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

seqan3/alphabet/aminoacid/aa10li.hpp

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Types

Static Protected Attributes

Private Types

Private Attributes

Static Private Attributes

Related Functions

Detailed Description

Member Typedef Documentation

◆ char_type

◆ rank_type

Member Function Documentation

◆ assign_char()

Complexity

Exceptions

◆ assign_rank()

Complexity

Exceptions

◆ char_is_valid()

Complexity

Exceptions

◆ to_char()

Complexity

Exceptions

◆ to_rank()

Complexity

Exceptions

Friends And Related Function Documentation

◆ aa10li_vector

◆ operator""_aa10li() [1/2]

◆ operator""_aa10li() [2/2]

◆ save_minimal()

Member Data Documentation

◆ alphabet_size

◆ rank_to_char