SeqAn3  3.0.2
The Modern C++ library for sequence analysis.
seqan3::aa10li Class Reference

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 aa10lioperator= (aa10li const &) noexcept=default
 Defaulted.
 
constexpr aa10lioperator= (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 aa10liassign_char (char_type const c) noexcept
 Assign from a character, implicitly converts invalid characters. More...
 
constexpr aa10liassign_rank (rank_type const c) noexcept
 Assign from a numeric value. More...
 
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 aa10liassign_char (char_type const c) noexcept
 Assign from a character, implicitly converts invalid characters. More...
 
constexpr aa10liassign_rank (rank_type const c) noexcept
 Assign from a numeric value. More...
 
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 aa10liassign_char (char_type const c) noexcept
 Assign from a character, implicitly converts invalid characters. More...
 
constexpr aa10liassign_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
 The size of the alphabet, i.e. the number of different values it can take.
 

Protected Types

Member types
using char_type = std::conditional_t< std::same_as< char, void >, char, char >
 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()).
 
Member types
using char_type = std::conditional_t< std::same_as< char, void >, char, char >
 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()).
 
Member types
using char_type = std::conditional_t< std::same_as< char, void >, char, char >
 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()).
 

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...
 

Related Functions

(Note that these are not member functions.)

using aa10li_vector = std::vector< aa10li >
 Alias for an std::vector of seqan3::aa10li.
 
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...
 

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) F1,2

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

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 'S'_aa10li implicitly
if (my_letter.to_char() == 'S')
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;
}

Member Function Documentation

◆ assign_char()

constexpr aa10li & seqan3::alphabet_base< aa10li , size, char >::assign_char ( char_type const  c)
inlineconstexprnoexceptinherited

Assign from a character, implicitly converts invalid characters.

Parameters
cThe character to be assigned.

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

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ assign_rank()

constexpr aa10li & seqan3::alphabet_base< aa10li , size, char >::assign_rank ( rank_type const  c)
inlineconstexprnoexceptinherited

Assign from a numeric value.

Parameters
cThe rank to be assigned.

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

Complexity

Constant.

Exceptions

Guaranteed not to throw.

◆ 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.

◆ to_char()

constexpr char_type seqan3::alphabet_base< aa10li , size, char >::to_char
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.

◆ to_rank()

constexpr rank_type seqan3::alphabet_base< aa10li , size, char >::to_rank
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.

Friends And Related Function Documentation

◆ operator""_aa10li() [1/2]

aa10li_vector operator""_aa10li ( char const *const  s,
size_t const  n 
)
related

The seqan3::aa10li string literal.

Parameters
[in]sA pointer to the character string to assign.
[in]nThe 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!

◆ operator""_aa10li() [2/2]

constexpr aa10li operator""_aa10li ( char const  c)
related

The seqan3::aa10li char literal.

Parameters
[in]cThe character to assign.
Returns
seqan3::aa10li

Member Data Documentation

◆ 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:
debug_stream.hpp
Provides seqan3::debug_stream and related types.
convert.hpp
Provides seqan3::views::convert.
seqan3::alphabet_base::assign_char
constexpr derived_type & assign_char(char_type const c) noexcept
Assign from a character, implicitly converts invalid characters.
Definition: alphabet_base.hpp:142
aa27.hpp
Provides seqan3::aa27, container aliases and string literals.
seqan3::debug_stream
debug_stream_type debug_stream
A global instance of seqan3::debug_stream_type.
Definition: debug_stream.hpp:42
seqan3::aa10li
The reduced Li amino acid alphabet.
Definition: aa10li.hpp:80
aa10li.hpp
Provides seqan3::aa10li, container aliases and string literals.