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
constexpr dna4	complement () const noexcept
	Returns the complement of the current nucleotide.
Constructors, destructor and assignment
constexpr	dna4 () noexcept=default
	Defaulted.
constexpr	dna4 (dna4 const &) noexcept=default
	Defaulted.
constexpr	dna4 (dna4 &&) noexcept=default
	Defaulted.
constexpr dna4 &	operator= (dna4 const &) noexcept=default
	Defaulted.
constexpr dna4 &	operator= (dna4 &&) noexcept=default
	Defaulted.
	~dna4 () noexcept=default
	Defaulted.
template<std::same_as< rna4 > t>
constexpr	dna4 (t const &r) noexcept
	Allow implicit construction from seqan3::rna4 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.
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
	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.

Related Symbols
(Note that these are not member symbols.)
using	dna4_vector = std::vector< dna4 >
	Alias for a std::vector of seqan3::dna4.

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.
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 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 'A'_dna4 or use the function seqan3::dna4::assign_char().

// 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/nucleotide/dna4.hpp>
#include <seqan3/core/debug_stream.hpp>
 
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"
}

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.

Constructor & Destructor Documentation

dna4()

template<std::same_as< rna4 > t>

constexpr seqan3::dna4::dna4 ( t const &  r )

inlineconstexprnoexcept

Allow implicit construction from seqan3::rna4 of the same size.

Normally, we do not allow implicit conversion of single argument constructors, but in this case we make an exception, because seqan3::dna4 and seqan3::rna4 are interchangeable as they behave nearly the same (e.g. same ranks, same char to rank conversion).

#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/alphabet/nucleotide/rna4.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::dna4 letter1 = 'C'_rna4; // implicitly converted
    seqan3::dna4 letter2{};
    letter2 = 'C'_rna4; // implicitly converted
}

seqan3::sequences (e.g. seqan3::dna4_vector) in general are not implicitly convertible and must be explicitly copied to be converted:

#include <vector>
 
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/alphabet/nucleotide/rna4.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::dna4_vector vector{'A'_rna4, 'C'_rna4, 'G'_rna4}; // (element-wise) implicit conversion
 
    // but this won't work:
    // seqan3::dna4_vector dna4_vector{"ACGT"_rna4};
 
    // as a workaround you can use:
    // side note: this would also work without the implicit conversion.
    seqan3::rna4_vector rna4_vector = "ACGT"_rna4;
    seqan3::dna4_vector dna4_vector{rna4_vector.begin(), rna4_vector.end()};
}

You can avoid this copy by using std::ranges::views:

#include <vector>
 
#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/alphabet/nucleotide/rna4.hpp>
#include <seqan3/utility/views/convert.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::dna4_vector vector = "ACG"_dna4;
 
    auto rna4_view = vector | seqan3::views::convert<seqan3::rna4>;
 
    for (auto && chr : rna4_view) // converts lazily on-the-fly
    {
        static_assert(std::same_as<decltype(chr), seqan3::rna4 &&>);
    }
}

This conversion constructor only allows converting seqan3::rna4 to seqan3::dna4. Other alphabets that inherit from seqan3::rna4 will not be implicitly convertible to seqan3::dna4.

#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/alphabet/nucleotide/rna4.hpp>
 
struct my_dna4 : public seqan3::dna4
{
    // using seqan3::dna4::dna4; // uncomment to import implicit conversion shown by letter1
};
 
struct my_rna4 : public seqan3::rna4
{};
 
int main()
{
    using namespace seqan3::literals;
 
    // my_dna4 letter1 = 'C'_rna4; // NO automatic implicit conversion!
    // seqan3::dna4 letter2 = my_rna4{}; // seqan3::dna4 only allows implicit conversion from seqan3::rna4!
}

This entity is stable. Since version 3.1.

Friends And Related Symbol Documentation

dna4_vector

using dna4_vector = std::vector<dna4>

related

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

This entity is stable. Since version 3.1.

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

• dna4.hpp