SeqAn3 3.4.0-rc.1
The Modern C++ library for sequence analysis.
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Private Types | Static Private Member Functions | Private Attributes | Static Private Attributes | Related Symbols | List of all members
seqan3::aa20 Class Reference
Alphabet » Aminoacid

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

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.
 
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 aa20_vector = std::vector< aa20 >
 Alias for a std::vector of seqan3::aa20.
 
Literals
constexpr aa20 operator""_aa20 (char const c) noexcept
 The seqan3::aa20 char literal.
 
constexpr aa20_vector operator""_aa20 (char const *const s, size_t const n)
 The seqan3::aa20 string literal.
 
- Related Symbols inherited from semialphabet
alphabet_rank_t< alphabet_t > save_minimal (archive_t const &, alphabet_t const &l)
 Save an alphabet letter to stream.
 
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< 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.
 
- 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 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

// 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/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"
}
aa20.hpp
Provides seqan3::aa20, container aliases and string literals.
seqan3::aa20
The canonical amino acid alphabet.
Definition aa20.hpp:61
seqan3::alphabet_base::assign_char
constexpr derived_type & assign_char(char_type const chr) noexcept
Assign from a character, implicitly converts invalid characters.
Definition alphabet_base.hpp:160
debug_stream.hpp
Provides seqan3::debug_stream and related types.
seqan3::debug_stream
debug_stream_type debug_stream
A global instance of seqan3::debug_stream_type.
Definition debug_stream.hpp:37
seqan3::literals
The SeqAn namespace for literals.

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 Symbol Documentation

◆ aa20_vector

using aa20_vector = std::vector<aa20>
related

Alias for a std::vector of seqan3::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 
)
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:

// 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/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)
related

The seqan3::aa20 char literal.

Parameters
[in]cThe character to assign.
Returns
seqan3::aa20

You can use this char literal to assign a seqan3::aa20 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/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;
}()
}
seqan3::aa20::rank_to_char_table
static constexpr char_type rank_to_char_table[alphabet_size]
The lookup table used in rank_to_char.
Definition aa20.hpp:89
seqan3::alphabet_base::alphabet_size
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.
Definition alphabet_base.hpp:196
std::array::fill
T fill(T... args)
seqan3::to_lower
constexpr char_type to_lower(char_type const c) noexcept
Converts 'A'-'Z' to 'a'-'z' respectively; other characters are returned as is.
Definition transform.hpp:80

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];
}
seqan3::aa20::rank_to_char
static constexpr char_type rank_to_char(rank_type const rank)
Returns the character representation of rank.
Definition aa20.hpp:93
seqan3::alphabet_base::rank_type
detail::min_viable_uint_t< size - 1 > rank_type
The type of the alphabet when represented as a number (e.g. via to_rank()).
Definition alphabet_base.hpp:77
seqan3::alphabet_base::char_type
std::conditional_t< std::same_as< char_t, void >, char, char_t > char_type
The char representation; conditional needed to make semi alphabet definitions legal.
Definition alphabet_base.hpp:69
seqan3::alphabet_base::rank
rank_type rank
The value of the alphabet letter is stored as the rank.
Definition alphabet_base.hpp:258
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:
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