SeqAn3  3.2.0-rc.1
The Modern C++ library for sequence analysis.
dna3bs.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 // dna3bs
22 // ------------------------------------------------------------------
23 
24 namespace seqan3
25 {
60 class dna3bs : public nucleotide_base<dna3bs, 3>
61 {
62 private:
65 
67  friend base_t;
69  friend base_t::base_t;
71 
72 public:
76  constexpr dna3bs() noexcept = default;
77  constexpr dna3bs(dna3bs const &) noexcept = default;
78  constexpr dna3bs(dna3bs &&) noexcept = default;
79  constexpr dna3bs & operator=(dna3bs const &) noexcept = default;
80  constexpr dna3bs & operator=(dna3bs &&) noexcept = default;
81  ~dna3bs() noexcept = default;
82 
83  using base_t::base_t;
85 
86 private:
88  static constexpr char_type rank_to_char_table[alphabet_size]{'A', 'G', 'T'};
89 
91  static constexpr std::array<rank_type, 256> char_to_rank_table{[]() constexpr {std::array<rank_type, 256> ret{};
92 
93  // reverse mapping for characters and their lowercase
94  for (size_t rnk = 0u; rnk < alphabet_size; ++rnk)
95  {
96  ret[rank_to_char_table[rnk]] = rnk;
97  ret[to_lower(rank_to_char_table[rnk])] = rnk;
98  }
99 
100  // set C and U equal to T
101  ret['C'] = ret['T'];
102  ret['c'] = ret['t'];
103  ret['U'] = ret['T'];
104  ret['u'] = ret['t'];
105 
106  // iupac characters get special treatment, because there is no N
107  ret['R'] = ret['A'];
108  ret['r'] = ret['A']; // A or G becomes A
109  ret['Y'] = ret['T'];
110  ret['y'] = ret['T']; // C or T becomes T
111  ret['S'] = ret['T'];
112  ret['s'] = ret['T']; // C or G becomes T
113  ret['W'] = ret['A'];
114  ret['w'] = ret['A']; // A or T becomes A
115  ret['K'] = ret['G'];
116  ret['k'] = ret['G']; // G or T becomes G
117  ret['M'] = ret['A'];
118  ret['m'] = ret['A']; // A or C becomes A
119  ret['B'] = ret['T'];
120  ret['b'] = ret['T']; // C or G or T becomes T
121  ret['D'] = ret['A'];
122  ret['d'] = ret['A']; // A or G or T becomes A
123  ret['H'] = ret['A'];
124  ret['h'] = ret['A']; // A or C or T becomes A
125  ret['V'] = ret['A'];
126  ret['v'] = ret['A']; // A or C or G becomes A
127 
128  return ret;
129 }()
130 }; // namespace seqan3
131 
133 static constexpr rank_type rank_complement_table[alphabet_size]{
134  2, // T is complement of 'A'_dna3bs
135  2, // T is complement of 'G'_dna3bs
136  0 // A is complement of 'T'_dna3bs
137 };
138 
140 static constexpr rank_type rank_complement(rank_type const rank)
141 {
142  return rank_complement_table[rank];
143 }
144 
146 static constexpr char_type rank_to_char(rank_type const rank)
147 {
148  return rank_to_char_table[rank];
149 }
150 
152 static constexpr rank_type char_to_rank(char_type const chr)
153 {
154  using index_t = std::make_unsigned_t<char_type>;
155  return char_to_rank_table[static_cast<index_t>(chr)];
156 }
157 }
158 ;
159 
160 // ------------------------------------------------------------------
161 // containers
162 // ------------------------------------------------------------------
163 
170 
171 // ------------------------------------------------------------------
172 // literals
173 // ------------------------------------------------------------------
174 inline namespace literals
175 {
176 
191 constexpr dna3bs operator""_dna3bs(char const c) noexcept
192 {
193  return dna3bs{}.assign_char(c);
194 }
195 
205 inline dna3bs_vector operator""_dna3bs(char const * s, std::size_t n)
206 {
207  dna3bs_vector r;
208  r.resize(n);
209 
210  for (size_t i = 0; i < n; ++i)
211  r[i].assign_char(s[i]);
212 
213  return r;
214 }
216 
217 } // namespace literals
218 
219 } // 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
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 three letter reduced DNA alphabet for bisulfite sequencing mode (A,G,T(=C)).
Definition: dna3bs.hpp:61
constexpr dna3bs() noexcept=default
Defaulted.
A CRTP-base that refines seqan3::alphabet_base and is used by the nucleotides.
Definition: nucleotide_base.hpp:43
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
constexpr char_type to_lower(char_type const c) noexcept
Converts 'A'-'Z' to 'a'-'z' respectively; other characters are returned as is.
Definition: transform.hpp:83
Provides seqan3::nucleotide_base.
T resize(T... args)
Provides utilities for modifying characters.