16 #include <seqan3/alphabet/detail/convert.hpp>
41 template <
typename derived_type, auto size>
80 template <
typename other_nucl_type>
81 requires (!std::same_as<nucleotide_base, other_nucl_type>)
83 explicit constexpr
nucleotide_base(other_nucl_type
const & other) noexcept
85 static_cast<derived_type &
>(*this) =
86 detail::convert_through_char_representation<other_nucl_type, derived_type>[
seqan3::to_rank(other)];
112 constexpr derived_type
complement()
const noexcept
114 return derived_type{}.assign_rank(derived_type{}.rank_complement(
to_rank()));
139 static constexpr
bool char_is_valid(
char_type const c) noexcept
141 return valid_char_table[
static_cast<uint8_t
>(c)];
150 for (
size_t rank = 0u; rank < derived_type::alphabet_size; ++rank)
152 uint8_t c = derived_type::rank_to_char(rank);
Provides seqan3::nucleotide_alphabet.
Provides seqan3::alphabet_base.
A CRTP-base that makes defining a custom alphabet easier.
Definition: alphabet_base.hpp:57
constexpr rank_type to_rank() const noexcept
Return the letter's numeric value (rank in the alphabet).
Definition: alphabet_base.hpp:137
detail::min_viable_uint_t< size - 1 > rank_type
The type of the alphabet when represented as a number (e.g. via to_rank()).
Definition: alphabet_base.hpp:80
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.
Definition: alphabet_base.hpp:199
std::conditional_t< std::same_as< char, void >, char, char > char_type
The char representation; conditional needed to make semi alphabet definitions legal.
Definition: alphabet_base.hpp:72
A CRTP-base that refines seqan3::alphabet_base and is used by the nucleotides.
Definition: nucleotide_base.hpp:43
constexpr auto complement
Return the complement of a nucleotide object.
Definition: alphabet/nucleotide/concept.hpp:105
requires requires
The rank_type of the semi-alphabet; defined as the return type of seqan3::to_rank....
Definition: alphabet/concept.hpp:164
constexpr auto to_rank
Return the rank representation of a (semi-)alphabet object.
Definition: alphabet/concept.hpp:155
A concept that indicates whether an alphabet represents nucleotides.
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
constexpr char_type to_lower(char_type const c) noexcept
Converts 'A'-'Z' to 'a'-'z' respectively; other characters are returned as is.
Definition: transform.hpp:83