16 #include <seqan3/alphabet/detail/convert.hpp>
29 template <
typename derived_type,
size_t size>
79 template <typename other_qual_type>
82 explicit constexpr
phred_base(other_qual_type const & other) noexcept
122 constexpr derived_type & assign_phred(
phred_type const p) noexcept
134 if (i < derived_type::offset_phred)
139 ret[
static_cast<rank_type>(i)] = i - derived_type::offset_phred;
150 ret[i] = i + derived_type::offset_phred;
161 int64_t difference =
static_cast<int64_t
>(chr) -
static_cast<int64_t
>(derived_type::offset_char);
162 return std::clamp<int64_t>(difference, 0,
alphabet_size - 1);
168 return rank + derived_type::offset_char;
Quality alphabet concept.
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
constexpr derived_type & assign_rank(rank_type const c) noexcept
Assign from a numeric value.
Definition: alphabet_base.hpp:187
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 quality alphabets.
Definition: phred_base.hpp:31
static constexpr std::array< phred_type, alphabet_size > rank_to_phred
Assign from the numeric Phred score value.
Definition: phred_base.hpp:145
static constexpr char_type rank_to_char(rank_type const rank)
Definition: phred_base.hpp:165
static constexpr rank_type char_to_rank(char_type const chr)
Definition: phred_base.hpp:158
int8_t phred_type
The integer representation of the quality score.
Definition: phred_base.hpp:40
constexpr auto to_phred
The public getter function for the Phred representation of a quality score.
Definition: alphabet/quality/concept.hpp:100
constexpr auto assign_phred_to
Assign a Phred score to a quality alphabet object.
Definition: alphabet/quality/concept.hpp:230
requires requires
The rank_type of the semi-alphabet; defined as the return type of seqan3::to_rank....
Definition: alphabet/concept.hpp:164
A concept that indicates whether an alphabet represents quality scores.
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
SeqAn specific customisations in the standard namespace.