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.

Private Types
using	base_t = nucleotide_base< dna4, 4 >
	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 rank_type	rank_complement (rank_type const rank)
	Returns the complement by rank.
static constexpr char_type	rank_to_char (rank_type const rank)
	Returns the character representation of rank.

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_table
	The lookup table used in char_to_rank.
static constexpr rank_type	rank_complement_table [alphabet_size]
	The rank complement table.
static constexpr char_type	rank_to_char_table [alphabet_size] {'A', 'C', 'G', 'T'}
	The lookup table used in rank_to_char.

Related Symbols
(Note that these are not member symbols.)
using	dna4_vector = std::vector< dna4 >
	Alias for a std::vector of seqan3::dna4.
Nucleotide literals
constexpr dna4	operator""_dna4 (char const c) noexcept
	The seqan3::dna4 char literal.
constexpr dna4_vector	operator""_dna4 (char const *s, std::size_t n)
	The seqan3::dna4 string literal.
Related Symbols inherited from semialphabet
template<cereal_output_archive archive_t, semialphabet alphabet_t>
alphabet_rank_t< alphabet_t >	save_minimal (archive_t const &, alphabet_t const &l)
	Save an alphabet letter to stream.
template<cereal_input_archive archive_t, typename wrapped_alphabet_t >
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::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: 2006-2025 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2025 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.

Member Function Documentation

char_to_rank()

static constexpr rank_type seqan3::dna4::char_to_rank ( char_type const  chr )

inlinestaticconstexprprivate

Returns the rank representation of character.

This function is required by seqan3::alphabet_base.

rank_complement()

static constexpr rank_type seqan3::dna4::rank_complement ( rank_type const  rank )

inlinestaticconstexprprivate

Returns the complement by rank.

This function is required by seqan3::nucleotide_base.

rank_to_char()

static constexpr char_type seqan3::dna4::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

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.

operator""_dna4() [1/2]

constexpr 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:

// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0
 
// generated from test/snippet/alphabet/nucleotide/@target_alphabet@_literal.cpp.in
 
#include <seqan3/alphabet/nucleotide/dna4.hpp>
 
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:

#include <seqan3/alphabet/nucleotide/dna4.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::dna4 letter1{'A'_dna4};
    auto letter2 = 'A'_dna4;
}

This entity is stable. Since version 3.1.

Member Data Documentation

char_to_rank_table

constexpr std::array<rank_type, 256> seqan3::dna4::char_to_rank_table

staticconstexprprivate

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];
}

See also

https://gcc.gnu.org/bugzilla/show_bug.cgi?id=99320 for the progress on gcc

rank_complement_table

constexpr rank_type seqan3::dna4::rank_complement_table[alphabet_size]

staticconstexprprivate

Initial value:

{
        3, 
        2, 
        1, 
        0  
    }

The rank complement table.

rank_to_char_table

constexpr char_type seqan3::dna4::rank_to_char_table[alphabet_size] {'A', 'C', 'G', 'T'}

staticconstexprprivate

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

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

• dna4.hpp