SeqAn3  3.0.3
The Modern C++ library for sequence analysis.
seqan3::dna4 Class Reference

The four letter DNA alphabet of A,C,G,T. More...

#include <seqan3/alphabet/nucleotide/dna4.hpp>

+ Inheritance diagram for seqan3::dna4:

Public Member Functions

Constructors, destructor and assignment
constexpr dna4 () noexcept=default
constexpr dna4 (dna4 const &) noexcept=default
constexpr dna4 (dna4 &&) noexcept=default
constexpr dna4operator= (dna4 const &) noexcept=default
constexpr dna4operator= (dna4 &&) noexcept=default
 ~dna4 () noexcept=default
template<std::same_as< rna4 > t>
constexpr dna4 (t const &r) noexcept
 Allow implicit construction from dna/rna of the same size.
- Public Member Functions inherited from seqan3::nucleotide_base< dna4, 4 >
constexpr dna4 complement () const noexcept
 Return the complement of the letter. More...
constexpr nucleotide_base (other_nucl_type const &other) noexcept
 Allow explicit construction from any other nucleotide 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
constexpr alphabet_base (alphabet_base const &) noexcept=default
constexpr alphabet_base (alphabet_base &&) noexcept=default
constexpr alphabet_baseoperator= (alphabet_base const &) noexcept=default
constexpr alphabet_baseoperator= (alphabet_base &&) noexcept=default
 ~alphabet_base () noexcept=default
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 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...

Private Types

using base_t = nucleotide_base< dna4, 4 >
 The base class.

Private Attributes

friend base_t
 Befriend seqan3::nucleotide_base.
friend rna4
 Befriend seqan3::rna4 so it can copy char_to_rank.

Static Private Attributes

static constexpr std::array< rank_type, 256 > char_to_rank
 Char to value conversion table. More...
static const std::array< dna4, alphabet_sizecomplement_table
 The complement 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 dna4_vector = std::vector< dna4 >
 Alias for an std::vector of seqan3::dna4.
constexpr dna4 operator""_dna4 (char const c) noexcept
 The seqan3::dna4 char literal. More...
dna4_vector operator""_dna4 (char const *s, std::size_t n)
 The seqan3::dna4 string literal. More...

Additional Inherited Members

- Static Public Member Functions inherited from seqan3::nucleotide_base< dna4, 4 >
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< 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. More...
- 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. 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 four letter DNA alphabet of A,C,G,T.

Note that you can assign 'U' as a character to dna4 and it will silently be converted to 'T'.

Like most alphabets, this alphabet cannot be initialised directly from its character representation. Instead initialise/assign from the character literal or use the function seqan3::dna4::assign_char().

int main()
using seqan3::operator""_dna4;
seqan3::dna4 my_letter{'C'_dna4};
my_letter.assign_char('F'); // characters other than IUPAC characters are implicitly converted to A.
seqan3::debug_stream << my_letter; // prints "F"
// IUPAC characters are implicitly converted to their best fitting representative
seqan3::debug_stream << my_letter.assign_char('R'); // prints "A"
seqan3::debug_stream << my_letter.assign_char('Y'); // prints "C"
seqan3::debug_stream << my_letter.assign_char('S'); // prints "C"
seqan3::debug_stream << my_letter.assign_char('W'); // prints "A"
seqan3::debug_stream << my_letter.assign_char('K'); // prints "G"
seqan3::debug_stream << my_letter.assign_char('M'); // prints "A"
seqan3::debug_stream << my_letter.assign_char('B'); // prints "C"
seqan3::debug_stream << my_letter.assign_char('D'); // prints "A"
seqan3::debug_stream << my_letter.assign_char('H'); // prints "A"
seqan3::debug_stream << my_letter.assign_char('V'); // prints "A"
my_letter.assign_char('a'); // lower case letters are the same as their upper case equivalent
seqan3::debug_stream << my_letter; // prints "A";
constexpr derived_type & assign_char(char_type const c) noexcept
Assign from a character, implicitly converts invalid characters.
Definition: alphabet_base.hpp:159
The four letter DNA alphabet of A,C,G,T.
Definition: dna4.hpp:51
Provides seqan3::debug_stream and related types.
Provides seqan3::dna4, container aliases and string literals.
debug_stream_type debug_stream
A global instance of seqan3::debug_stream_type.
Definition: debug_stream.hpp:42

If the special char conversion of IUPAC characters is not your desired behavior, refer to our cookbook for an example of A custom dna4 alphabet that converts all unknown characters to A to change the conversion behavior.

Friends And Related Function Documentation

◆ operator""_dna4() [1/2]

dna4_vector operator""_dna4 ( char const *  s,
std::size_t  n 

The seqan3::dna4 string literal.


You can use this string literal to easily assign to dna4_vector:

int main()
using seqan3::operator""_dna4;
seqan3::dna4_vector foo{"ACGTTA"_dna4};
seqan3::dna4_vector bar = "ACGTTA"_dna4;
auto bax = "ACGTTA"_dna4;

◆ operator""_dna4() [2/2]

constexpr dna4 operator""_dna4 ( char const  c)

The seqan3::dna4 char literal.


Member Data Documentation

◆ char_to_rank

constexpr std::array<rank_type, 256> seqan3::dna4::char_to_rank
Initial value:
[] () constexpr
for (size_t rnk = 0u; rnk < alphabet_size; ++rnk)
ret[ rank_to_char[rnk] ] = rnk;
ret[to_lower(rank_to_char[rnk])] = rnk;
ret['U'] = ret['T']; ret['u'] = ret['t'];
ret['R'] = ret['A']; ret['r'] = ret['A'];
ret['Y'] = ret['C']; ret['y'] = ret['C'];
ret['S'] = ret['C']; ret['s'] = ret['C'];
ret['W'] = ret['A']; ret['w'] = ret['A'];
ret['K'] = ret['G']; ret['k'] = ret['G'];
ret['M'] = ret['A']; ret['m'] = ret['A'];
ret['B'] = ret['C']; ret['b'] = ret['C'];
ret['D'] = ret['A']; ret['d'] = ret['A'];
ret['H'] = ret['A']; ret['h'] = ret['A'];
ret['V'] = ret['A']; ret['v'] = ret['A'];
return ret;
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:198
static constexpr char_type rank_to_char[alphabet_size]
Value to char conversion table.
Definition: dna4.hpp:90
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:81

Char to value conversion table.

◆ complement_table

constexpr std::array< dna4, dna4::alphabet_size > seqan3::dna4::complement_table
Initial value:

The complement table.

◆ rank_to_char

constexpr char_type seqan3::dna4::rank_to_char[alphabet_size]
Initial value:

Value to char conversion table.

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