The five letter DNA alphabet of A,C,G,T and the unknown character N. More...

#include <seqan3/alphabet/nucleotide/dna5.hpp>

Inheritance diagram for seqan3::dna5:

Public Member Functions
Constructors, destructor and assignment
constexpr	dna5 () noexcept=default
	Defaulted.

constexpr	dna5 (dna5 const &) noexcept=default
	Defaulted.

constexpr	dna5 (dna5 &&) noexcept=default
	Defaulted.

constexpr dna5 &	operator= (dna5 const &) noexcept=default
	Defaulted.

constexpr dna5 &	operator= (dna5 &&) noexcept=default
	Defaulted.

	~dna5 () noexcept=default
	Defaulted.

template<std::same_as< rna5 > t>
constexpr	dna5 (t const &r) noexcept
	Allow implicit construction from dna/rna of the same size. More...

Public Member Functions inherited from seqan3::nucleotide_base< dna5, 5 >
constexpr dna5	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< dna5, 5 >
	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	rna5
	Befriend seqan3::rna5 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< dna5, 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	dna5_vector = std::vector< dna5 >
	Alias for an std::vector of seqan3::dna5. More...

Literals
constexpr dna5	operator""_dna5 (char const c) noexcept
	The seqan3::dna5 char literal. More...

dna5_vector	operator""_dna5 (char const *s, std::size_t n)
	The seqan3::dna5 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< dna5, 5 >
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 five letter DNA alphabet of A,C,G,T and the unknown character N.

Note that you can assign 'U' as a character to dna5 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::dna5::assign_char().

#include <seqan3/alphabet/nucleotide/dna5.hpp>
#include <seqan3/core/debug_stream.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::dna5 letter{'A'_dna5};
 
    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

◆ dna5()

template<std::same_as< rna5 > t>

constexpr seqan3::dna5::dna5 ( t const & r )

inlineconstexprnoexcept

Allow implicit construction from dna/rna of the same size.

This entity is stable. Since version 3.1.

Member Function Documentation

◆ char_to_rank()

static constexpr rank_type seqan3::dna5::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::dna5::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

◆ dna5_vector

using dna5_vector = std::vector<dna5>

This entity is stable. Since version 3.1.

◆ operator""_dna5() [1/2]

dna5_vector operator""_dna5	(	char const *	s,
		std::size_t	n
	)

Returns: seqan3::dna5_vector

You can use this string literal to easily assign to dna5_vector:

#include <seqan3/alphabet/nucleotide/dna5.hpp>
 
int main()
{
    using namespace seqan3::literals;
 
    seqan3::dna5_vector sequence1{"ACGTTA"_dna5};
    seqan3::dna5_vector sequence2 = "ACGTTA"_dna5;
    auto sequence3 = "ACGTTA"_dna5;
}

This entity is stable. Since version 3.1.

◆ operator""_dna5() [2/2]

constexpr dna5 operator""_dna5 ( char const c )

Returns: seqan3::dna5

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::dna5::char_to_rank_table

staticconstexprprivate

Initial value:

{
        [] () constexpr
        {
            std::array<rank_type, 256> ret{};
 
            
            for (auto & c : ret)
                c = 3; 
 
            
            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'];
 
            
            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< dna5, dna5::alphabet_size > seqan3::dna5::complement_table

staticconstexprprivate

Initial value:

{
    'T'_dna5,    
    'G'_dna5,    
    'C'_dna5,    
    'N'_dna5,    
    'A'_dna5     
}

The complement table.

◆ rank_to_char_table

constexpr char_type seqan3::dna5::rank_to_char_table[alphabet_size]

staticconstexprprivate

Initial value:

{
        'A',
        'C',
        'G',
        'N',
        '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/dna5.hpp

Public Member Functions

Private Types

Static Private Member Functions

Private Attributes

Static Private Attributes

Related Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ dna5()

Member Function Documentation

◆ char_to_rank()

◆ rank_to_char()

Friends And Related Function Documentation

◆ dna5_vector

◆ operator""_dna5() [1/2]

◆ operator""_dna5() [2/2]

Member Data Documentation

◆ char_to_rank_table

◆ complement_table

◆ rank_to_char_table