57template <writable_alphabet sequence_alphabet_t, writable_quality_alphabet quality_alphabet_t>
60 sequence_alphabet_t, quality_alphabet_t>
65 sequence_alphabet_t, quality_alphabet_t>;
107 SEQAN3_DOXYGEN_ONLY(( constexpr
qualified(component_type const alph) noexcept {} ))
109 SEQAN3_DOXYGEN_ONLY((
constexpr qualified(indirect_component_type
const alph)
noexcept {} ))
111 SEQAN3_DOXYGEN_ONLY(( constexpr
qualified & operator=(component_type const alph) noexcept {} ))
113 SEQAN3_DOXYGEN_ONLY((
constexpr qualified &
operator=(indirect_component_type
const alph)
noexcept {} ))
127 base_type::cummulative_alph_sizes[0]) +
128 (base_type::template to_component_rank<1>() * base_type::cummulative_alph_sizes[1]));
156 return rank_to_phred[
to_rank()];
165 return rank_to_char(
to_rank());
189 return char_is_valid_for<sequence_alphabet_type>(c);
202 size_t seq_rank = (i / base_type::cummulative_alph_sizes[0]) %
203 seqan3::alphabet_size<quality_alphabet_type>;
221 size_t qual_rank = (i / base_type::cummulative_alph_sizes[1]) %
222 seqan3::alphabet_size<quality_alphabet_type>;
234 return rank_to_char_table[rank];
241template <
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:139
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:203
constexpr qualified< sequence_alphabet_t, quality_alphabet_t > & assign_rank(rank_type const c) noexcept
Assign from a numeric value.
Definition: alphabet_base.hpp:191
The CRTP base for a combined alphabet that contains multiple values of different alphabets at the sam...
Definition: alphabet_tuple_base.hpp:124
Joins an arbitrary alphabet with a quality alphabet.
Definition: qualified.hpp:61
static constexpr bool char_is_valid(char_type const c) noexcept
Validate whether a character is valid in the sequence alphabet.
Definition: qualified.hpp:187
constexpr char_type to_char() const noexcept
Return a character. This reads the internal sequence letter.
Definition: qualified.hpp:163
constexpr phred_type to_phred() const noexcept
Return the Phred score value. This reads the internal quality letter.
Definition: qualified.hpp:154
alphabet_char_t< sequence_alphabet_type > char_type
Equals the char_type of sequence_alphabet_type.
Definition: qualified.hpp:83
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:109
constexpr qualified & assign_phred(phred_type const c) noexcept
Assign from a Phred score value. This modifies the internal quality letter.
Definition: qualified.hpp:140
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.
constexpr qualified complement() const noexcept
Return a qualified where the quality is preserved, but the sequence letter is complemented.
Definition: qualified.hpp:174
quality_alphabet_t quality_alphabet_type
Second template parameter as member type.
Definition: qualified.hpp:77
constexpr qualified & assign_char(char_type const c) noexcept
Assign from a character. This modifies the internal sequence letter.
Definition: qualified.hpp:123
alphabet_phred_t< quality_alphabet_type > phred_type
Equals the phred_type of the quality_alphabet_type.
Definition: qualified.hpp:88
sequence_alphabet_t sequence_alphabet_type
First template parameter as member type.
Definition: qualified.hpp:72
constexpr auto complement
Return the complement of a nucleotide object.
Definition: concept.hpp:104
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:112
constexpr auto assign_phred_to
Assign a Phred score to a quality alphabet object.
Definition: concept.hpp:231
constexpr auto assign_char_to
Assign a character to an alphabet object.
Definition: concept.hpp:526
constexpr auto to_char
Return the char representation of an alphabet object.
Definition: concept.hpp:387
constexpr auto assign_rank_to
Assign a rank to an alphabet object.
Definition: concept.hpp:294
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:399
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: cigar_operation_table.hpp:2