The five letter DNA alphabet of A,C,G,T and the unknown character N.. More...
#include <seqan3/alphabet/nucleotide/dna5.hpp>
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 seqan3::rna5 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< dna5, size, char > | |
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 dna5 & | assign_char (char_type const chr) noexcept |
Assign from a character, implicitly converts invalid characters. More... | |
constexpr dna5 & | 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 rank_type | rank_complement (rank_type const rank) |
Returns the complement by rank. 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 constexpr rank_type | rank_complement_table [alphabet_size] |
The rank complement table. More... | |
static constexpr char_type | rank_to_char_table [alphabet_size] {'A', 'C', 'G', 'N', 'T'} |
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 a std::vector of seqan3::dna5. More... | |
Nucleotide literals | |
constexpr dna5 | operator""_dna5 (char const c) noexcept |
The seqan3::dna5 char literal. More... | |
constexpr 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... | |
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. 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< dna5, size, char > | |
static constexpr detail::min_viable_uint_t< size > | alphabet_size |
The size of the alphabet, i.e. the number of different values it can take. More... | |
Protected Types inherited from seqan3::alphabet_base< dna5, size, char > | |
using | char_type = std::conditional_t< std::same_as< char, void >, char, char > |
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... | |
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 'A'_dna5 or use the function seqan3::dna5::assign_char().
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inlineconstexprnoexcept |
Allow implicit construction from seqan3::rna5 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::dna5 and seqan3::rna5 are interchangeable as they behave nearly the same (e.g. same ranks, same char to rank conversion).
seqan3::sequence
s (e.g. seqan3::dna5_vector) in general are not implicitly convertible and must be explicitly copied to be converted: std::ranges::view
s:
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inlinestaticconstexprprivate |
Returns the rank representation of character.
This function is required by seqan3::alphabet_base.
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inlinestaticconstexprprivate |
Returns the complement by rank.
This function is required by seqan3::nucleotide_base.
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inlinestaticconstexprprivate |
Returns the character representation of rank.
This function is required by seqan3::alphabet_base.
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related |
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related |
The seqan3::dna5 string literal.
You can use this string literal to easily assign to dna5_vector:
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related |
The seqan3::dna5 char literal.
You can use this char literal to assign a seqan3::dna4 character:
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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.
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staticconstexprprivate |
The rank complement table.
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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.