SeqAn3  3.2.0
The Modern C++ library for sequence analysis.
rna15.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 // rna15
22 // ------------------------------------------------------------------
23 
24 namespace seqan3
25 {
26 
50 class rna15 : public nucleotide_base<rna15, 15>
51 {
52 private:
55 
57  friend base_t;
59  friend base_t::base_t;
61 
62 public:
66  constexpr rna15() noexcept = default;
67  constexpr rna15(rna15 const &) noexcept = default;
68  constexpr rna15(rna15 &&) noexcept = default;
69  constexpr rna15 & operator=(rna15 const &) noexcept = default;
70  constexpr rna15 & operator=(rna15 &&) noexcept = default;
71  ~rna15() noexcept = default;
72 
73  using base_t::base_t;
74 
82  template <std::same_as<dna15> t>
83  constexpr rna15(t const & r) noexcept
84  {
85  assign_rank(r.to_rank());
86  }
88 
89 private:
91  static constexpr char_type
92  rank_to_char_table[alphabet_size]{'A', 'B', 'C', 'D', 'G', 'H', 'K', 'M', 'N', 'R', 'S', 'U', 'V', 'W', 'Y'};
93 
95  static constexpr rank_type rank_complement(rank_type const rank)
96  {
97  return dna15::rank_complement(rank);
98  }
99 
101  static constexpr char_type rank_to_char(rank_type const rank)
102  {
103  return rank_to_char_table[rank];
104  }
105 
107  static constexpr rank_type char_to_rank(char_type const chr)
108  {
109  return dna15::char_to_rank(chr);
110  }
111 };
112 
113 // ------------------------------------------------------------------
114 // containers
115 // ------------------------------------------------------------------
116 
123 
124 // ------------------------------------------------------------------
125 // literals
126 // ------------------------------------------------------------------
127 inline namespace literals
128 {
129 
144 constexpr rna15 operator""_rna15(char const c) noexcept
145 {
146  return rna15{}.assign_char(c);
147 }
148 
158 inline rna15_vector operator""_rna15(char const * s, std::size_t n)
159 {
160  rna15_vector r;
161  r.resize(n);
162 
163  for (size_t i = 0; i < n; ++i)
164  r[i].assign_char(s[i]);
165 
166  return r;
167 }
169 
170 } // namespace literals
171 
172 } // 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 15 letter DNA alphabet, containing all IUPAC smybols minus the gap.
Definition: dna15.hpp:51
A CRTP-base that refines seqan3::alphabet_base and is used by the nucleotides.
Definition: nucleotide_base.hpp:43
The 15 letter RNA alphabet, containing all IUPAC smybols minus the gap.
Definition: rna15.hpp:51
constexpr rna15() noexcept=default
Defaulted.
Provides seqan3::dna15, 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)