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
 Defaulted.
 
constexpr dna4 (dna4 const &) noexcept=default
 Defaulted.
 
constexpr dna4 (dna4 &&) noexcept=default
 Defaulted.
 
constexpr dna4operator= (dna4 const &) noexcept=default
 Defaulted.
 
constexpr dna4operator= (dna4 &&) noexcept=default
 Defaulted.
 
 ~dna4 () noexcept=default
 Defaulted.
 
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 nucleotide_base (other_nucl_type const &other) noexcept
 Allow explicit construction from any other nucleotide type and convert via the character representation. More...
 
constexpr dna4 complement () const noexcept
 Return the complement of the letter. More...
 
- 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_baseoperator= (alphabet_base const &) noexcept=default
 Defaulted.
 
constexpr alphabet_baseoperator= (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. 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 chr) 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...
 

Related Functions

(Note that these are not member functions.)

using dna4_vector = std::vector< dna4 >
 Alias for an std::vector of seqan3::dna4. More...
 
Nucleotide literals
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 namespace seqan3::literals;
seqan3::dna4 letter{'C'_dna4};
letter.assign_char('F'); // Characters other than IUPAC characters are implicitly converted to A.
seqan3::debug_stream << letter << '\n'; // prints "A"
// IUPAC characters are implicitly converted to their best fitting representative
seqan3::debug_stream << letter.assign_char('R') << '\n'; // prints "A"
seqan3::debug_stream << letter.assign_char('Y') << '\n'; // prints "C"
seqan3::debug_stream << letter.assign_char('S') << '\n'; // prints "C"
seqan3::debug_stream << letter.assign_char('W') << '\n'; // prints "A"
seqan3::debug_stream << letter.assign_char('K') << '\n'; // prints "G"
seqan3::debug_stream << letter.assign_char('M') << '\n'; // prints "A"
seqan3::debug_stream << letter.assign_char('B') << '\n'; // prints "C"
seqan3::debug_stream << letter.assign_char('D') << '\n'; // prints "A"
seqan3::debug_stream << letter.assign_char('H') << '\n'; // prints "A"
seqan3::debug_stream << letter.assign_char('V') << '\n'; // prints "A"
letter.assign_char('a'); // Lower case letters are the same as their upper case equivalent.
seqan3::debug_stream << letter << '\n'; // prints "A"
}
constexpr derived_type & assign_char(char_type const chr) noexcept
Assign from a character, implicitly converts invalid characters.
Definition: alphabet_base.hpp:211
The four letter DNA alphabet of A,C,G,T.
Definition: dna4.hpp:53
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
The SeqAn namespace for literals.

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

This entity is stable. Since version 3.1.

Friends And Related Function Documentation

◆ dna4_vector

using dna4_vector = std::vector<dna4>
related

Alias for an std::vector of seqan3::dna4.

This entity is stable. Since version 3.1.

◆ operator""_dna4() [1/2]

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

The seqan3::dna4 string literal.

Returns
seqan3::dna4_vector

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

int main()
{
using namespace seqan3::literals;
seqan3::dna4_vector sequence1{"ACGTTA"_dna4};
seqan3::dna4_vector sequence2 = "ACGTTA"_dna4;
auto sequence3 = "ACGTTA"_dna4;
}

This entity is stable. Since version 3.1.

◆ operator""_dna4() [2/2]

constexpr dna4 operator""_dna4 ( char const  c)
related

The seqan3::dna4 char literal.

Returns
seqan3::dna4

You can use this char literal to assign a seqan3::dna4 character:

int main()
{
using namespace seqan3::literals;
seqan3::dna4 letter1{'A'_dna4};
auto letter2 = 'A'_dna4;
}

This entity is stable. Since version 3.1.


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