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SeqAn3
3.0.2
The Modern C++ library for sequence analysis.
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56 template <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.");
79 constexpr
wuss() noexcept = default;
80 constexpr
wuss(
wuss const &) noexcept = default;
82 constexpr
wuss & operator=(
wuss const &) noexcept = default;
83 constexpr
wuss & operator=(
wuss &&) noexcept = default;
84 ~
wuss() noexcept = default;
95 return interaction_tab[
to_rank()] < 0;
103 return interaction_tab[
to_rank()] > 0;
111 return interaction_tab[
to_rank()] == 0;
127 if (interaction_tab[
to_rank()] != 0)
128 return std::abs(interaction_tab[
to_rank()]) - 1;
143 '.',
':',
',',
'-',
'_',
'~',
';',
'<',
'(',
'[',
'{',
'>',
')',
']',
'}'
150 chars[rnk] =
'A' + off;
151 chars[rnk + 1u] =
'a' + off;
171 rank_table[rank_to_char[rnk]] = rnk;
182 template <u
int8_t SIZE>
189 for (rank_type rnk = 0u; rnk <= 6u; ++rnk)
191 interaction_table[rnk] = 0;
194 for (rank_type rnk = 7u; rnk <= 10u; ++rnk)
196 interaction_table[rnk] = --cnt_open;
199 for (rank_type rnk = 11u; rnk <= 14u; ++rnk)
201 interaction_table[rnk] = ++cnt_close;
204 for (rank_type rnk = 15u; rnk + 1u <
alphabet_size; rnk += 2u)
206 interaction_table[rnk] = --cnt_open;
207 interaction_table[rnk + 1u] = ++cnt_close;
210 return interaction_table;
235 for (
size_t idx = 0ul; idx < len; ++idx)
236 vec[idx].assign_char(str[idx]);
250 constexpr
wuss51 operator""_wuss51(
char const ch) noexcept
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:62
Provides seqan3::rna_structure_alphabet.
Provides seqan3::alphabet_base.
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:176
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:64
constexpr char_type to_char() const noexcept
Return the letter as a character of char_type.
Definition: alphabet_base.hpp:96
static constexpr uint8_t max_pseudoknot_depth
The ability of this alphabet to represent pseudoknots, i.e. crossing interactions,...
Definition: wuss.hpp:118
A CRTP-base that makes defining a custom alphabet easier.
Definition: alphabet_base.hpp:54
constexpr derived_type & assign_char(char_type const c) noexcept
Assign from a character, implicitly converts invalid characters.
Definition: alphabet_base.hpp:142
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:125
constexpr bool is_pair_close() const noexcept
Check whether the character represents a leftward interaction in an RNA structure.
Definition: wuss.hpp:101
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:64
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
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:176
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:62
constexpr bool is_pair_open() const noexcept
Check whether the character represents a rightward interaction in an RNA structure.
Definition: wuss.hpp:93
constexpr bool is_unpaired() const noexcept
Check whether the character represents an unpaired position in an RNA structure.
Definition: wuss.hpp:109
constexpr wuss() noexcept=default
Defaulted.
constexpr rank_type to_rank() const noexcept
Return the letter's numeric value (rank in the alphabet).
Definition: alphabet_base.hpp:118
constexpr auto alphabet_size
A type trait that holds the size of a (semi-)alphabet.
Definition: concept.hpp:707
constexpr rank_type to_rank() const noexcept
Return the letter's numeric value (rank in the alphabet).
Definition: alphabet_base.hpp:118
The WUSS structure alphabet of the characters .<>:,-_~;()[]{}AaBbCcDd...
Definition: wuss.hpp:58