seqan3::dna5 Class Reference

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.
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.
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 c) 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.

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
	Char to value conversion table. More...
static const std::array< dna5, alphabet_size >	complement_table
	The complement table. More...
static constexpr char_type	rank_to_char [alphabet_size]
	Value to char conversion table. More...

Related Functions
(Note that these are not member functions.)
using	dna5_vector = std::vector< dna5 >
	Alias for an std::vector of seqan3::dna5.
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 seqan3::operator""_dna5;
 
    seqan3::dna5 my_letter{'A'_dna5};
 
    my_letter.assign_char('C');
 
    my_letter.assign_char('F'); // unknown characters are implicitly converted to N.
    if (my_letter.to_char() == 'N')
        seqan3::debug_stream << "yeah\n"; // "yeah";
}

Friends And Related Function Documentation

operator""_dna5() [1/2]

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

related

The seqan3::dna5 string literal.

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 seqan3::operator""_dna5;
    
    seqan3::dna5_vector foo{"ACGTTA"_dna5};
    seqan3::dna5_vector bar = "ACGTTA"_dna5;
    auto bax = "ACGTTA"_dna5;
}

operator""_dna5() [2/2]

constexpr dna5 operator""_dna5 ( char const  c )

related

The seqan3::dna5 char literal.

Returns

seqan3::dna5

Member Data Documentation

char_to_rank

constexpr std::array<rank_type, 256> seqan3::dna5::char_to_rank

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[rnk] ] = rnk;
                ret[to_lower(rank_to_char[rnk])] = rnk;
            }
 
            
            ret['U'] = ret['T']; ret['u'] = ret['t'];
 
            
            return ret;
        }()
    }

Char to value conversion table.

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

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

staticconstexprprivate

Initial value:

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

Value to char conversion table.

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

• seqan3/alphabet/nucleotide/dna5.hpp