56template <u
int8_t SIZE = 51>
59 static_assert(SIZE >= 15 && SIZE <= 67 && SIZE % 2 == 1,
60 "The wuss<> alphabet size must be an odd number in range 15..67.");
81 constexpr wuss() noexcept = default;
82 constexpr
wuss(
wuss const &) noexcept = default;
84 constexpr
wuss & operator=(
wuss const &) noexcept = default;
85 constexpr
wuss & operator=(
wuss &&) noexcept = default;
86 ~
wuss() noexcept = default;
167 std::array<char_type, alphabet_size> chars{
'.',
':',
',',
'-',
'_',
'~',
';',
'<',
'(',
'[',
'{',
'>',
')',
174 chars[rnk] =
'A' +
off;
175 chars[rnk + 1u] =
'a' +
off;
209 int8_t cnt_close = 0;
211 for (
rank_type rnk = 0u; rnk <= 6u; ++rnk)
212 interaction_table[rnk] = 0;
214 for (
rank_type rnk = 7u; rnk <= 10u; ++rnk)
215 interaction_table[rnk] = --cnt_open;
217 for (
rank_type rnk = 11u; rnk <= 14u; ++rnk)
218 interaction_table[rnk] = ++cnt_close;
222 interaction_table[rnk] = --cnt_open;
223 interaction_table[rnk + 1u] = ++cnt_close;
226 return interaction_table;
237inline namespace literals
253constexpr wuss51 operator""_wuss51(
char const ch)
noexcept
274 for (
size_t idx = 0ul; idx < len; ++idx)
275 vec[idx].assign_char(str[idx]);
Provides seqan3::rna_structure_alphabet.
Provides seqan3::alphabet_base.
A CRTP-base that makes defining a custom alphabet easier.
Definition alphabet_base.hpp:54
constexpr derived_type & assign_char(char_type const chr) noexcept
Assign from a character, implicitly converts invalid characters.
Definition alphabet_base.hpp:160
constexpr rank_type to_rank() const noexcept
Return the letter's numeric value (rank in the alphabet).
Definition alphabet_base.hpp:134
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:77
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:196
constexpr char_type to_char() const noexcept
Return the letter as a character of char_type.
Definition alphabet_base.hpp:112
std::conditional_t< std::same_as< char_t, void >, char, char_t > char_type
The char representation; conditional needed to make semi alphabet definitions legal.
Definition alphabet_base.hpp:69
rank_type rank
The value of the alphabet letter is stored as the rank.
Definition alphabet_base.hpp:258
The WUSS structure alphabet of the characters .<>:,-_~;()[]{}AaBbCcDd...
Definition wuss.hpp:58
friend base_t
Befriend seqan3::alphabet_base.
Definition wuss.hpp:67
static constexpr uint8_t max_pseudoknot_depth
The ability of this alphabet to represent pseudoknots, i.e. crossing interactions,...
Definition wuss.hpp:129
constexpr bool is_pair_close() const noexcept
Check whether the character represents a leftward interaction in an RNA structure.
Definition wuss.hpp:108
constexpr bool is_pair_open() const noexcept
Check whether the character represents a rightward interaction in an RNA structure.
Definition wuss.hpp:98
static constexpr std::array< char_type, alphabet_size > rank_to_char_table
The lookup table used in rank_to_char.
Definition wuss.hpp:165
constexpr std::optional< uint8_t > pseudoknot_id() const noexcept
Get an identifier for a pseudoknotted interaction, where opening and closing brackets of the same typ...
Definition wuss.hpp:139
static constexpr rank_type char_to_rank(char_type const chr)
Returns the rank representation of character.
Definition wuss.hpp:156
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:196
static constexpr char_type rank_to_char(rank_type const rank)
Returns the character representation of rank.
Definition wuss.hpp:150
static constexpr std::array< int8_t, SIZE > interaction_tab
Lookup table for interactions: unpaired (0), pair-open (< 0), pair-close (> 0). Paired brackets have ...
Definition wuss.hpp:202
constexpr wuss() noexcept=default
Defaulted.
static constexpr std::array< rank_type, 256 > char_to_rank_table
The lookup table used in char_to_rank.
Definition wuss.hpp:184
constexpr bool is_unpaired() const noexcept
Check whether the character represents an unpaired position in an RNA structure.
Definition wuss.hpp:118
constexpr auto to_rank
Return the rank representation of a (semi-)alphabet object.
Definition alphabet/concept.hpp:152
The main SeqAn3 namespace.
Definition aligned_sequence_concept.hpp:26
@ off
Automatic update notifications should be disabled.