SeqAn3  3.0.3
The Modern C++ library for sequence analysis.
dna5.hpp
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1 // -----------------------------------------------------------------------------------------------------
2 // Copyright (c) 2006-2020, Knut Reinert & Freie Universität Berlin
3 // Copyright (c) 2016-2020, 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 // dna5
22 // ------------------------------------------------------------------
23 
24 namespace seqan3
25 {
26 
27 class rna5;
28 
50 class dna5 : public nucleotide_base<dna5, 5>
51 {
52 private:
55 
57  friend base_t;
59  friend base_t::base_t;
62  friend rna5;
63 
64 public:
68  constexpr dna5() noexcept = default;
69  constexpr dna5(dna5 const &) noexcept = default;
70  constexpr dna5(dna5 &&) noexcept = default;
71  constexpr dna5 & operator=(dna5 const &) noexcept = default;
72  constexpr dna5 & operator=(dna5 &&) noexcept = default;
73  ~dna5() noexcept = default;
74 
75  using base_t::base_t;
76 
81  template <std::same_as<rna5> t> // Accept incomplete type
82  constexpr dna5(t const & r) noexcept
83  {
84  assign_rank(r.to_rank());
85  }
87 
88 private:
90  static constexpr char_type rank_to_char_table[alphabet_size]
91  {
92  'A',
93  'C',
94  'G',
95  'N',
96  'T'
97  };
98 
100  static constexpr std::array<rank_type, 256> char_to_rank_table
101  {
102  [] () constexpr
103  {
105 
106  // initialize with UNKNOWN (std::array::fill unfortunately not constexpr)
107  for (auto & c : ret)
108  c = 3; // == 'N'
109 
110  // reverse mapping for characters and their lowercase
111  for (size_t rnk = 0u; rnk < alphabet_size; ++rnk)
112  {
113  ret[rank_to_char_table[rnk]] = rnk;
114  ret[to_lower(rank_to_char_table[rnk])] = rnk;
115  }
116 
117  // set U equal to T
118  ret['U'] = ret['T']; ret['u'] = ret['t'];
119 
120  // iupac characters are implicitly "UNKNOWN"
121  return ret;
122  }()
123  };
124 
126  static const std::array<dna5, alphabet_size> complement_table;
127 
129  static constexpr char_type rank_to_char(rank_type const rank)
130  {
131  return rank_to_char_table[rank];
132  }
133 
135  static constexpr rank_type char_to_rank(char_type const chr)
136  {
137  using index_t = std::make_unsigned_t<char_type>;
138  return char_to_rank_table[static_cast<index_t>(chr)];
139  }
140 };
141 
142 // ------------------------------------------------------------------
143 // containers
144 // ------------------------------------------------------------------
145 
152 
153 // ------------------------------------------------------------------
154 // literals
155 // ------------------------------------------------------------------
156 inline namespace literals
157 {
158 
172 constexpr dna5 operator""_dna5(char const c) noexcept
173 {
174  return dna5{}.assign_char(c);
175 }
176 
186 inline dna5_vector operator""_dna5(char const * s, std::size_t n)
187 {
188  dna5_vector r;
189  r.resize(n);
190 
191  for (size_t i = 0; i < n; ++i)
192  r[i].assign_char(s[i]);
193 
194  return r;
195 }
197 
198 } // inline namespace literals
199 
200 // ------------------------------------------------------------------
201 // dna5 (deferred definition)
202 // ------------------------------------------------------------------
203 
204 constexpr std::array<dna5, dna5::alphabet_size> dna5::complement_table
205 {
206  'T'_dna5, // complement of 'A'_dna5
207  'G'_dna5, // complement of 'C'_dna5
208  'C'_dna5, // complement of 'G'_dna5
209  'N'_dna5, // complement of 'N'_dna5
210  'A'_dna5 // complement of 'T'_dna5
211 };
212 
213 } // namespace seqan3
A CRTP-base that makes defining a custom alphabet easier.
Definition: alphabet_base.hpp:81
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:104
constexpr derived_type & assign_char(char_type const chr) noexcept
Assign from a character, implicitly converts invalid characters.
Definition: alphabet_base.hpp:211
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:276
constexpr derived_type & assign_rank(rank_type const c) noexcept
Assign from a numeric value.
Definition: alphabet_base.hpp:264
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:96
The five letter DNA alphabet of A,C,G,T and the unknown character N.
Definition: dna5.hpp:51
constexpr dna5() noexcept=default
Defaulted.
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
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:81
SeqAn specific customisations in the standard namespace.
Provides seqan3::nucleotide_base.
T resize(T... args)
Provides utilities for modifying characters.