57 template <writable_alphabet sequence_alphabet_t, writable_quality_alphabet quality_alphabet_t>
59 public alphabet_tuple_base<qualified<sequence_alphabet_t, quality_alphabet_t>,
65 using base_type = alphabet_tuple_base<qualified<sequence_alphabet_t, quality_alphabet_t>,
85 using char_type = alphabet_char_t<sequence_alphabet_type>;
90 using phred_type = alphabet_phred_t<quality_alphabet_type>;
103 using base_type::alphabet_size;
104 using base_type::base_type;
106 using base_type::operator=;
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);
196 for (
size_t i = 0; i < alphabet_size; ++i)
198 size_t seq_rank = (i / base_type::cummulative_alph_sizes[0]) % seqan3::alphabet_size<quality_alphabet_type>;
211 for (
size_t i = 0; i < alphabet_size; ++i)
213 size_t qual_rank = (i / base_type::cummulative_alph_sizes[1]) % seqan3::alphabet_size<quality_alphabet_type>;
225 static constexpr
char_type rank_to_char(
typename base_type::rank_type
const rank)
227 return rank_to_char_table[rank];
235 template <
typename sequence_alphabet_type,
typename quality_alphabet_type>
Provides seqan3::nucleotide_alphabet.
Quality alphabet concept.
Provides seqan3::alphabet_tuple_base.
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
Definition: qualified.hpp:111
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
alphabet_phred_t< quality_alphabet_type > phred_type
Equals the phred_type of the quality_alphabet_type.
Definition: qualified.hpp:90
constexpr qualified complement() const noexcept requires nucleotide_alphabet< sequence_alphabet_t >
Return a qualified where the quality is preserved, but the sequence letter is complemented.
Definition: qualified.hpp:175
sequence_alphabet_t sequence_alphabet_type
First template parameter as member type.
Definition: qualified.hpp:74
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 & assign_char(char_type const c) noexcept
Assign from a character. This modifies the internal sequence letter.
Definition: qualified.hpp:125
constexpr auto complement
Return the complement of a nucleotide object.
Definition: alphabet/nucleotide/concept.hpp:105
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
constexpr auto assign_char_to
Assign a character to an alphabet object.
Definition: alphabet/concept.hpp:524
constexpr auto to_char
Return the char representation of an alphabet object.
Definition: alphabet/concept.hpp:386
constexpr auto assign_rank_to
Assign a rank to an alphabet object.
Definition: alphabet/concept.hpp:293
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