SeqAn3  3.2.0
The Modern C++ library for sequence analysis.
rna5.hpp
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1 // -----------------------------------------------------------------------------------------------------
2 // Copyright (c) 2006-2022, Knut Reinert & Freie Universität Berlin
3 // Copyright (c) 2016-2022, 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 
19 
20 // ------------------------------------------------------------------
21 // rna5
22 // ------------------------------------------------------------------
23 
24 namespace seqan3
25 {
26 
48 class rna5 : public nucleotide_base<rna5, 5>
49 {
50 private:
53 
55  friend base_t;
57  friend base_t::base_t;
59 
60 public:
64  constexpr rna5() noexcept = default;
65  constexpr rna5(rna5 const &) noexcept = default;
66  constexpr rna5(rna5 &&) noexcept = default;
67  constexpr rna5 & operator=(rna5 const &) noexcept = default;
68  constexpr rna5 & operator=(rna5 &&) noexcept = default;
69  ~rna5() noexcept = default;
70 
71  using base_t::base_t;
72 
80  template <std::same_as<dna5> t>
81  constexpr rna5(t const & r) noexcept
82  {
83  assign_rank(r.to_rank());
84  }
86 
87 private:
89  static constexpr char_type rank_to_char_table[alphabet_size]{'A', 'C', 'G', 'N', 'U'};
90 
92  static constexpr rank_type rank_complement(rank_type const rank)
93  {
94  return dna5::rank_complement(rank);
95  }
96 
98  static constexpr char_type rank_to_char(rank_type const rank)
99  {
100  return rank_to_char_table[rank];
101  }
102 
104  static constexpr rank_type char_to_rank(char_type const chr)
105  {
106  return dna5::char_to_rank(chr);
107  }
108 };
109 
110 // ------------------------------------------------------------------
111 // containers
112 // ------------------------------------------------------------------
113 
120 
121 // ------------------------------------------------------------------
122 // literals
123 // ------------------------------------------------------------------
124 inline namespace literals
125 {
126 
141 constexpr rna5 operator""_rna5(char const c) noexcept
142 {
143  return rna5{}.assign_char(c);
144 }
145 
155 inline rna5_vector operator""_rna5(char const * s, std::size_t n)
156 {
157  rna5_vector r;
158  r.resize(n);
159 
160  for (size_t i = 0; i < n; ++i)
161  r[i].assign_char(s[i]);
162 
163  return r;
164 }
166 
167 } // namespace literals
168 
169 } // namespace seqan3
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 requires(!std
Assign from a character, implicitly converts invalid characters.
Definition: alphabet_base.hpp:163
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:199
constexpr derived_type & assign_rank(rank_type const c) noexcept
Assign from a numeric value.
Definition: alphabet_base.hpp:187
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:72
The five letter DNA alphabet of A,C,G,T and the unknown character N.
Definition: dna5.hpp:51
A CRTP-base that refines seqan3::alphabet_base and is used by the nucleotides.
Definition: nucleotide_base.hpp:43
The five letter RNA alphabet of A,C,G,U and the unknown character N.
Definition: rna5.hpp:49
constexpr rna5() noexcept=default
Defaulted.
Provides seqan3::dna5, container aliases and string literals.
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
SeqAn specific customisations in the standard namespace.
Provides seqan3::nucleotide_base.
T resize(T... args)