The 15 letter DNA alphabet, containing all IUPAC smybols minus the gap. More...

#include <seqan3/alphabet/nucleotide/dna15.hpp>

Inheritance diagram for seqan3::dna15:

Public Member Functions
Constructors, destructor and assignment
constexpr	dna15 () noexcept=default
	Defaulted.

constexpr	dna15 (dna15 const &) noexcept=default
	Defaulted.

constexpr	dna15 (dna15 &&) noexcept=default
	Defaulted.

constexpr dna15 &	operator= (dna15 const &) noexcept=default
	Defaulted.

constexpr dna15 &	operator= (dna15 &&) noexcept=default
	Defaulted.

	~dna15 () noexcept=default
	Defaulted.

template<std::same_as< rna15 > t>
constexpr	dna15 (t const &r) noexcept
	Allow implicit construction from seqan3::rna15 of the same size. More...

Public Member Functions inherited from seqan3::nucleotide_base< dna15, 15 >
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 dna15	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_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. 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	dna15_vector = std::vector< dna15 >
	Alias for an std::vector of seqan3::dna15. More...

Nucleotide literals
constexpr dna15	operator""_dna15 (char const c) noexcept
	The seqan3::dna15 char literal. More...

dna15_vector	operator""_dna15 (char const *s, std::size_t n)
	The seqan3::dna15 string literal. More...

Additional Inherited Members
Static Public Member Functions inherited from seqan3::nucleotide_base< dna15, 15 >
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 15 letter DNA alphabet, containing all IUPAC smybols minus the gap.

Note that you can assign 'U' as a character to dna15 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'_dna15 or use the function seqan3::dna15::assign_char().

#include <seqan3/alphabet/nucleotide/dna15.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::dna15 letter{'A'_dna15};
 
    letter.assign_char('C');
    seqan3::debug_stream << letter << '\n'; // prints "C"
 
    letter.assign_char('F'); // Unknown characters are implicitly converted to N.
    seqan3::debug_stream << letter << '\n'; // prints "N"
}

This entity is stable. Since version 3.1.

Constructor & Destructor Documentation

◆ dna15()

template<std::same_as< rna15 > t>

constexpr seqan3::dna15::dna15 ( t const & r )

inlineconstexprnoexcept

Allow implicit construction from seqan3::rna15 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::dna15 and seqan3::rna15 are interchangeable as they behave nearly the same (e.g. same ranks, same char to rank conversion).

#include <seqan3/alphabet/nucleotide/dna15.hpp>
#include <seqan3/alphabet/nucleotide/rna15.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::dna15 letter1 = 'C'_rna15; // implicitly converted
    seqan3::dna15 letter2{};
    letter2 = 'C'_rna15; // implicitly converted
}

seqan3::sequences (e.g. seqan3::dna15_vector) in general aren't implicitly convertible and must be explicitly copied to be converted:

#include <vector>
 
#include <seqan3/alphabet/nucleotide/dna15.hpp>
#include <seqan3/alphabet/nucleotide/rna15.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::dna15_vector vector{'A'_rna15, 'C'_rna15, 'G'_rna15}; // (element-wise) implicit conversion
 
    // but this won't work:
    // seqan3::dna15_vector dna15_vector{"ACGT"_rna15};
 
    // as a workaround you can use:
    // side note: this would also work without the implicit conversion.
    seqan3::rna15_vector rna15_vector = "ACGT"_rna15;
    seqan3::dna15_vector dna15_vector{rna15_vector.begin(), rna15_vector.end()};
}

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

#include <vector>
 
#include <seqan3/alphabet/nucleotide/dna15.hpp>
#include <seqan3/alphabet/nucleotide/rna15.hpp>
#include <seqan3/utility/views/convert.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::dna15_vector vector = "ACG"_dna15;
 
    auto rna15_view = vector | seqan3::views::convert<seqan3::rna15>;
 
    for (auto && chr: rna15_view) // converts lazily on-the-fly
    {
        static_assert(std::same_as<decltype(chr), seqan3::rna15 &&>);
    }
}

This conversion constructor only allows converting seqan3::rna15 to seqan3::dna15. Other alphabets that inherit from seqan3::rna15 will not be implicitly convertible to seqan3::dna15.

#include <seqan3/alphabet/nucleotide/dna15.hpp>
#include <seqan3/alphabet/nucleotide/rna15.hpp>
 
struct my_dna15 : public seqan3::dna15
{
    // using seqan3::dna15::dna15; // uncomment to import implicit conversion shown by letter1
};
 
struct my_rna15 : public seqan3::rna15
{};
 
int main()
{
    using namespace seqan3::literals;
 
    // my_dna15 letter1 = 'C'_rna15; // NO automatic implicit conversion!
    // seqan3::dna15 letter2 = my_rna15{}; // seqan3::dna15 only allows implicit conversion from seqan3::rna15!
}

This entity is stable. Since version 3.1.

Friends And Related Function Documentation

◆ dna15_vector

using dna15_vector = std::vector<dna15>

This entity is stable. Since version 3.1.

◆ operator""_dna15() [1/2]

dna15_vector operator""_dna15	(	char const *	s,
		std::size_t	n
	)

Returns: seqan3::dna15_vector

You can use this string literal to easily assign to dna15_vector:

// generated from test/snippet/alphabet/nucleotide/@target_alphabet@_literal.cpp.in
 
#include <seqan3/alphabet/nucleotide/dna15.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::dna15_vector sequence1{"ACGTTA"_dna15};
    seqan3::dna15_vector sequence2 = "ACGTTA"_dna15;
    auto sequence3 = "ACGTTA"_dna15;
}

This entity is stable. Since version 3.1.

◆ operator""_dna15() [2/2]

constexpr dna15 operator""_dna15 ( char const c )

Returns: seqan3::dna15

You can use this char literal to assign a seqan3::dna15 character:

#include <seqan3/alphabet/nucleotide/dna15.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::dna15 letter1{'A'_dna15};
    auto letter2 = 'A'_dna15;
}

This entity is stable. Since version 3.1.

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

seqan3/alphabet/nucleotide/dna15.hpp

Public Member Functions

Related Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ dna15()

Friends And Related Function Documentation

◆ dna15_vector

◆ operator""_dna15() [1/2]

◆ operator""_dna15() [2/2]