SeqAn3  3.0.2
The Modern C++ library for sequence analysis.
seqan3::aa20 Class Reference

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 aa20operator= (aa20 const &) noexcept=default
 Defaulted.
 
constexpr aa20operator= (aa20 &&) noexcept=default
 Defaulted.
 
 ~aa20 () 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 aa20assign_char (char_type const c) noexcept
 Assign from a character, implicitly converts invalid characters. More...
 
constexpr aa20assign_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 detail::min_viable_uint_t< size > constexpr alphabet_size
 The size of the alphabet, i.e. the number of different values it can take.
 

Protected 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.
 
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. More...
 
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 aa20_vector = std::vector< aa20 >
 Alias for an std::vector of seqan3::aa20. More...
 
Literals
constexpr aa20 operator""_aa20 (char const c) noexcept
 The seqan3::aa20 char literal. More...
 
aa20_vector operator""_aa20 (const char *s, std::size_t n)
 The seqan3::aa20 string literal. More...
 
Requirements for std::totally_ordered

You can expect these functions on all types that implement std::totally_ordered.

bool operator< (type const &lhs, type const &rhs)
 Less-than, greater-than and -or-equal comparisons. More...
 
bool operator<= (type const &lhs, type const &rhs)
 Less-than, greater-than and -or-equal comparisons. More...
 
bool operator> (type const &lhs, type const &rhs)
 Less-than, greater-than and -or-equal comparisons. More...
 
bool operator>= (type const &lhs, type const &rhs)
 Less-than, greater-than and -or-equal comparisons. More...
 
Requirements for std::equality_comparable

You can expect these functions on all types that implement std::Equality_comparable.

bool operator== (type const &lhs, type const &rhs)
 (In-)Equality comparison. More...
 
bool operator!= (type const &lhs, type const &rhs)
 (In-)Equality comparison. More...
 
Requirements for std::swappable

You can expect these functions on all types that implement std::swappable.

void swap (t &lhs, t &rhs)
 Swaps the contents of two objects. 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

int main()
{
using seqan3::operator""_aa20;
seqan3::aa20 my_letter{'A'_aa20};
my_letter.assign_char('C');
my_letter.assign_char('?'); // all unknown characters are converted to 'A'_aa20 implicitly
if (my_letter.to_char() == 'A')
seqan3::debug_stream << "yeah\n"; // "yeah";
}

Member Function Documentation

◆ assign_char()

constexpr aa20 & seqan3::alphabet_base< aa20 , size, char >::assign_char ( char_type const  c)
inlinenoexceptinherited

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 aa20 & seqan3::alphabet_base< aa20 , size, char >::assign_rank ( rank_type const  c)
inlinenoexceptinherited

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< aa20 , size >::char_is_valid ( char_type const  c)
inlinestaticnoexceptinherited

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< aa20 , size, char >::to_char ( ) const
inlinenoexceptinherited

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< aa20 , size, char >::to_rank ( ) const
inlinenoexceptinherited

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

◆ aa20_vector

using aa20_vector = std::vector<aa20>
related

Alias for an std::vector of seqan3::aa20.

◆ operator""_aa20() [1/2]

constexpr aa20 operator""_aa20 ( char const  c)
related

The seqan3::aa20 char literal.

Parameters
[in]cThe character to assign.
Returns
seqan3::aa20
int main()
{
using seqan3::operator""_aa20;
seqan3::aa20 acid1{'A'_aa20};
auto acid2 = 'Y'_aa20; // type = aa20
}

◆ operator""_aa20() [2/2]

aa20_vector operator""_aa20 ( const char *  s,
std::size_t  n 
)
related

The seqan3::aa20 string literal.

Parameters
[in]sA pointer to the character string to assign.
[in]nThe size of the character string to assign.
Returns
seqan3::aa20_vector

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

int main()
{
using seqan3::operator""_aa20;
seqan3::aa20_vector foo{"ABFUYR"_aa20};
seqan3::aa20_vector bar = "ABFUYR"_aa20;
auto bax = "ABFUYR"_aa20;
}
Attention
All seqan3 literals are in the namespace seqan3!

Member Data Documentation

◆ char_to_rank

constexpr std::array<rank_type, 256> seqan3::aa20::char_to_rank
staticprotected
Initial value:
{
[] () constexpr
{
for (auto & c : ret)
c = 15;
for (rank_type rnk = 0u; rnk < alphabet_size; ++rnk)
{
ret[static_cast<rank_type>( rank_to_char[rnk]) ] = rnk;
ret[static_cast<rank_type>(to_lower(rank_to_char[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;
}()
}

Char to value conversion table.

◆ rank_to_char

constexpr char_type seqan3::aa20::rank_to_char[alphabet_size]
staticprotected
Initial value:
{
'A',
'C',
'D',
'E',
'F',
'G',
'H',
'I',
'K',
'L',
'M',
'N',
'P',
'Q',
'R',
'S',
'T',
'V',
'W',
'Y',
}

Value to char conversion table.


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