SeqAn3  3.2.0-rc.1
The Modern C++ library for sequence analysis.
dna15.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 // dna15
22 // ------------------------------------------------------------------
23 
24 namespace seqan3
25 {
26 
27 class rna15;
28 
50 class dna15 : public nucleotide_base<dna15, 15>
51 {
52 private:
55 
57  friend base_t;
59  friend base_t::base_t;
62  friend rna15;
63 
64 public:
68  constexpr dna15() noexcept = default;
69  constexpr dna15(dna15 const &) noexcept = default;
70  constexpr dna15(dna15 &&) noexcept = default;
71  constexpr dna15 & operator=(dna15 const &) noexcept = default;
72  constexpr dna15 & operator=(dna15 &&) noexcept = default;
73  ~dna15() noexcept = default;
74 
75  using base_t::base_t;
76 
84  template <std::same_as<rna15> t> // Accept incomplete type
85  constexpr dna15(t const & r) noexcept
86  {
87  assign_rank(r.to_rank());
88  }
90 
91 private:
93  static constexpr char_type
94  rank_to_char_table[alphabet_size]{'A', 'B', 'C', 'D', 'G', 'H', 'K', 'M', 'N', 'R', 'S', 'T', 'V', 'W', 'Y'};
95 
97  static constexpr std::array<rank_type, 256> char_to_rank_table{[]() constexpr {std::array<rank_type, 256> ret{};
98 
99  // initialize with UNKNOWN (std::array::fill unfortunately not constexpr)
100  for (auto & c : ret)
101  c = 8; // rank of 'N'
102 
103  // reverse mapping for characters and their lowercase
104  for (size_t rnk = 0u; rnk < alphabet_size; ++rnk)
105  {
106  ret[rank_to_char_table[rnk]] = rnk;
107  ret[to_lower(rank_to_char_table[rnk])] = rnk;
108  }
109 
110  // set U equal to T
111  ret['U'] = ret['T'];
112  ret['u'] = ret['t'];
113 
114  return ret;
115 }()
116 }; // namespace seqan3
117 
119 static constexpr rank_type rank_complement_table[alphabet_size]{
120  11, // T is complement of 'A'_dna15
121  12, // V is complement of 'B'_dna15
122  4, // G is complement of 'C'_dna15
123  5, // H is complement of 'D'_dna15
124  2, // C is complement of 'G'_dna15
125  3, // D is complement of 'H'_dna15
126  7, // M is complement of 'K'_dna15
127  6, // K is complement of 'M'_dna15
128  8, // N is complement of 'N'_dna15
129  14, // Y is complement of 'R'_dna15
130  10, // S is complement of 'S'_dna15
131  0, // A is complement of 'T'_dna15
132  1, // B is complement of 'V'_dna15
133  13, // W is complement of 'W'_dna15
134  9 // R is complement of 'Y'_dna15
135 };
136 
138 static constexpr rank_type rank_complement(rank_type const rank)
139 {
140  return rank_complement_table[rank];
141 }
142 
144 static constexpr char_type rank_to_char(rank_type const rank)
145 {
146  return rank_to_char_table[rank];
147 }
148 
150 static constexpr rank_type char_to_rank(char_type const chr)
151 {
152  using index_t = std::make_unsigned_t<char_type>;
153  return char_to_rank_table[static_cast<index_t>(chr)];
154 }
155 }
156 ;
157 
158 // ------------------------------------------------------------------
159 // containers
160 // ------------------------------------------------------------------
161 
168 
169 // ------------------------------------------------------------------
170 // literals
171 // ------------------------------------------------------------------
172 inline namespace literals
173 {
174 
189 constexpr dna15 operator""_dna15(char const c) noexcept
190 {
191  return dna15{}.assign_char(c);
192 }
193 
203 inline dna15_vector operator""_dna15(char const * s, std::size_t n)
204 {
205  dna15_vector r;
206  r.resize(n);
207 
208  for (size_t i = 0; i < n; ++i)
209  r[i].assign_char(s[i]);
210 
211  return r;
212 }
214 
215 } // namespace literals
216 
217 } // 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
constexpr dna15() noexcept=default
Defaulted.
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
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
SeqAn specific customisations in the standard namespace.
Provides seqan3::nucleotide_base.
T resize(T... args)
Provides utilities for modifying characters.