SeqAn3 3.1.0
The Modern C++ library for sequence analysis.
dot_bracket3.hpp
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1// -----------------------------------------------------------------------------------------------------
2// Copyright (c) 2006-2021, Knut Reinert & Freie Universität Berlin
3// Copyright (c) 2016-2021, Knut Reinert & MPI für molekulare Genetik
4// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
5// shipped with this file and also available at: https://github.com/seqan/seqan3/blob/master/LICENSE.md
6// -----------------------------------------------------------------------------------------------------
7
13#pragma once
14
15#include <vector>
16
20
21// ------------------------------------------------------------------
22// dot_bracket3
23// ------------------------------------------------------------------
24
25namespace seqan3
26{
27
53class dot_bracket3 : public alphabet_base<dot_bracket3, 3>
54{
55private:
58
60 friend base_t;
61
62public:
66 constexpr dot_bracket3() noexcept = default;
67 constexpr dot_bracket3(dot_bracket3 const &) noexcept = default;
68 constexpr dot_bracket3(dot_bracket3 &&) noexcept = default;
69 constexpr dot_bracket3 & operator=(dot_bracket3 const &) noexcept = default;
70 constexpr dot_bracket3 & operator=(dot_bracket3 &&) noexcept = default;
71 ~dot_bracket3() noexcept = default;
72
74
77
83 constexpr bool is_pair_open() const noexcept
84 {
85 return to_rank() == 1u;
86 }
87
93 constexpr bool is_pair_close() const noexcept
94 {
95 return to_rank() == 2u;
96 }
97
103 constexpr bool is_unpaired() const noexcept
104 {
105 return to_rank() == 0u;
106 }
107
114 static constexpr uint8_t max_pseudoknot_depth{1u};
115
122 constexpr std::optional<uint8_t> pseudoknot_id() const noexcept
123 {
124 if (is_unpaired())
125 return std::nullopt;
126 else
127 return 0;
128 }
130
131private:
133 static constexpr char_type rank_to_char_table[alphabet_size]
134 {
135 '.',
136 '(',
137 ')'
138 };
139
141 static constexpr std::array<rank_type, 256> char_to_rank_table
142 {
143 [] () constexpr
144 {
145 std::array<rank_type, 256> rank_table{};
146
147 // initialize with unpaired (std::array::fill unfortunately not constexpr)
148 for (rank_type & rnk : rank_table)
149 rnk = 0u;
150
151 // canonical
152 rank_table['.'] = 0u;
153 rank_table['('] = 1u;
154 rank_table[')'] = 2u;
155
156 return rank_table;
157 } ()
158 };
159
161 static constexpr char_type rank_to_char(rank_type const rank)
162 {
163 return rank_to_char_table[rank];
164 }
165
167 static constexpr rank_type char_to_rank(char_type const chr)
168 {
169 using index_t = std::make_unsigned_t<char_type>;
170 return char_to_rank_table[static_cast<index_t>(chr)];
171 }
172};
173
174inline namespace literals
175{
176
190constexpr dot_bracket3 operator""_db3(char const ch) noexcept
191{
192 return dot_bracket3{}.assign_char(ch);
193}
194
206inline std::vector<dot_bracket3> operator""_db3(const char * str, std::size_t len)
207{
209 vec.resize(len);
210
211 for (size_t idx = 0ul; idx < len; ++idx)
212 vec[idx].assign_char(str[idx]);
213
214 return vec;
215}
217
218} // inline namespace literals
219
220} // namespace seqan3
Provides seqan3::rna_structure_alphabet.
Provides seqan3::alphabet_base.
A CRTP-base that makes defining a custom alphabet easier.
Definition: alphabet_base.hpp:57
constexpr derived_type & assign_char(char_type const chr) noexcept
Assign from a character, implicitly converts invalid characters.
Definition: alphabet_base.hpp:165
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
std::conditional_t< std::same_as< char, void >, char, char > char_type
The char representation; conditional needed to make semi alphabet definitions legal.
Definition: alphabet_base.hpp:72
The three letter RNA structure alphabet of the characters ".()"..
Definition: dot_bracket3.hpp:54
constexpr bool is_pair_close() const noexcept
Check whether the character represents a leftward interaction in an RNA structure.
Definition: dot_bracket3.hpp:93
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: dot_bracket3.hpp:122
static constexpr uint8_t max_pseudoknot_depth
The ability of this alphabet to represent pseudoknots, i.e. crossing interactions,...
Definition: dot_bracket3.hpp:114
constexpr bool is_unpaired() const noexcept
Check whether the character represents an unpaired position in an RNA structure.
Definition: dot_bracket3.hpp:103
constexpr dot_bracket3() noexcept=default
Defaulted.
constexpr bool is_pair_open() const noexcept
Check whether the character represents a rightward interaction in an RNA structure.
Definition: dot_bracket3.hpp:83
The main SeqAn3 namespace.
Definition: cigar_operation_table.hpp:2
T resize(T... args)
Provides utilities for modifying characters.