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 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 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. 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...

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. More...
static constexpr char_type	rank_to_char (rank_type const rank)
	Returns the character representation of rank. More...

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. More...
static const std::array< dna4, alphabet_size >	complement_table
	The complement table. More...
static constexpr char_type	rank_to_char_table [alphabet_size]
	The lookup table used in rank_to_char. 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...
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...
Related Functions 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. 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().

#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.

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_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 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:

#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

Initial value:

{
        [] () constexpr
        {
            std::array<rank_type, 256> ret{};
 
            
            for (size_t rnk = 0u; rnk < alphabet_size; ++rnk)
            {
                ret[rank_to_char_table[rnk]] = rnk;
                ret[to_lower(rank_to_char_table[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;
        }()
    }

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

complement_table

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

staticconstexprprivate

Initial value:

{
    'T'_dna4,    
    'G'_dna4,    
    'C'_dna4,    
    'A'_dna4     
}

The complement table.

rank_to_char_table

constexpr char_type seqan3::dna4::rank_to_char_table[alphabet_size]

staticconstexprprivate

Initial value:

{
        'A',
        'C',
        'G',
        'T'
    }

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

---

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

• seqan3/alphabet/nucleotide/dna4.hpp