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 {}))
188 return char_is_valid_for<sequence_alphabet_type>(c);
208 seqan3::alphabet_size<quality_alphabet_type>;
226 seqan3::alphabet_size<quality_alphabet_type>;
240template <
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
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
rank_type rank
The value of the alphabet letter is stored as the rank.
Definition: alphabet_base.hpp:261
The CRTP base for a combined alphabet that contains multiple values of different alphabets at the sam...
Definition: alphabet_tuple_base.hpp:116
static constexpr std::array< rank_type, component_list::size()> cummulative_alph_sizes
The cumulative alphabet size products are cached.
Definition: alphabet_tuple_base.hpp:610
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
static constexpr char_type rank_to_char(typename base_type::rank_type const rank)
Returns the character representation of rank.
Definition: qualified.hpp:193
alphabet_phred_t< quality_alphabet_type > phred_type
Equals the phred_type of the quality_alphabet_type.
Definition: qualified.hpp:90
static constexpr std::array< char_type, alphabet_size > rank_to_char_table
The lookup table used in rank_to_char.
Definition: qualified.hpp:201
sequence_alphabet_t sequence_alphabet_type
First template parameter as member type.
Definition: qualified.hpp:74
static constexpr std::array< char_type, alphabet_size > rank_to_phred
Rank to Phred conversion table.
Definition: qualified.hpp:219
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