57template <writable_alphabet sequence_alphabet_t, writable_quality_alphabet quality_alphabet_t>
109 SEQAN3_DOXYGEN_ONLY((constexpr
qualified(component_type const alph) noexcept {}))
111 SEQAN3_DOXYGEN_ONLY((
constexpr qualified(indirect_component_type
const alph)
noexcept {}))
113 SEQAN3_DOXYGEN_ONLY((constexpr
qualified & operator=(component_type const alph) noexcept {}))
115 SEQAN3_DOXYGEN_ONLY((
constexpr qualified &
operator=(indirect_component_type
const alph)
noexcept {}))
128 * base_type::cummulative_alph_sizes[0])
129 + (base_type::template to_component_rank<1>() * base_type::cummulative_alph_sizes[1]));
157 return rank_to_phred[
to_rank()];
166 return rank_to_char(
to_rank());
188 return char_is_valid_for<sequence_alphabet_type>(c);
198 size_t seq_rank = (i / base_type::cummulative_alph_sizes[0]) % seqan3::alphabet_size<quality_alphabet_type>;
213 size_t qual_rank = (i / base_type::cummulative_alph_sizes[1]) % seqan3::alphabet_size<quality_alphabet_type>;
227 return rank_to_char_table[rank];
235template <
typename sequence_alphabet_type,
typename quality_alphabet_type>
Provides seqan3::nucleotide_alphabet.
Quality alphabet concept.
Provides seqan3::alphabet_tuple_base.
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 qualified< sequence_alphabet_t, quality_alphabet_t > & assign_rank(rank_type const c) noexcept
Assign from a numeric value.
Definition: alphabet_base.hpp:187
The CRTP base for a combined alphabet that contains multiple values of different alphabets at the sam...
Definition: alphabet_tuple_base.hpp:116
Joins an arbitrary alphabet with a quality alphabet.
Definition: qualified.hpp:62
static constexpr bool char_is_valid(char_type const c) noexcept
Validate whether a character is valid in the sequence alphabet.
Definition: qualified.hpp:186
constexpr char_type to_char() const noexcept
Return a character. This reads the internal sequence letter.
Definition: qualified.hpp:164
constexpr phred_type to_phred() const noexcept
Return the Phred score value. This reads the internal quality letter.
Definition: qualified.hpp:155
alphabet_char_t< sequence_alphabet_type > char_type
Equals the char_type of sequence_alphabet_type.
Definition: qualified.hpp:85
constexpr qualified(indirect_component_type const alph) noexcept
Construction via a value of a subtype that is assignable to one of the components.
Definition: qualified.hpp:111
constexpr qualified complement() const noexcept
Return a qualified where the quality is preserved, but the sequence letter is complemented.
Definition: qualified.hpp:175
constexpr qualified & assign_phred(phred_type const c) noexcept
Assign from a Phred score value. This modifies the internal quality letter.
Definition: qualified.hpp:141
constexpr qualified() noexcept=default
Defaulted.
qualified(sequence_alphabet_type &&, quality_alphabet_type &&) -> qualified< std::decay_t< sequence_alphabet_type >, std::decay_t< quality_alphabet_type > >
Type deduction guide enables usage of qualified without specifying template args.
quality_alphabet_t quality_alphabet_type
Second template parameter as member type.
Definition: qualified.hpp:79
constexpr qualified & assign_char(char_type const c) noexcept
Assign from a character. This modifies the internal sequence letter.
Definition: qualified.hpp:125
alphabet_phred_t< quality_alphabet_type > phred_type
Equals the phred_type of the quality_alphabet_type.
Definition: qualified.hpp:90
sequence_alphabet_t sequence_alphabet_type
First template parameter as member type.
Definition: qualified.hpp:74
constexpr auto complement
Return the complement of a nucleotide object.
Definition: concept.hpp:105
constexpr auto to_phred
The public getter function for the Phred representation of a quality score.
Definition: concept.hpp:100
decltype(seqan3::to_phred(std::declval< alphabet_type >())) alphabet_phred_t
The phred_type of the alphabet; defined as the return type of seqan3::to_phred.
Definition: concept.hpp:114
constexpr auto assign_phred_to
Assign a Phred score to a quality alphabet object.
Definition: concept.hpp:230
constexpr auto assign_char_to
Assign a character to an alphabet object.
Definition: concept.hpp:524
constexpr auto to_char
Return the char representation of an alphabet object.
Definition: concept.hpp:386
constexpr auto assign_rank_to
Assign a rank to an alphabet object.
Definition: concept.hpp:293
decltype(seqan3::to_char(std::declval< alphabet_type const >())) alphabet_char_t
The char_type of the alphabet; defined as the return type of seqan3::to_char.
Definition: concept.hpp:400
constexpr auto to_rank
Return the rank representation of a (semi-)alphabet object.
Definition: concept.hpp:155
A concept that indicates whether an alphabet represents nucleotides.
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29