SeqAn3  3.2.0
The Modern C++ library for sequence analysis.
dna5.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 // 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 
84  template <std::same_as<rna5> t> // Accept incomplete type
85  constexpr dna5(t const & r) noexcept
86  {
87  assign_rank(r.to_rank());
88  }
90 
91 private:
93  static constexpr char_type rank_to_char_table[alphabet_size]{'A', 'C', 'G', 'N', 'T'};
94 
96  static constexpr std::array<rank_type, 256> char_to_rank_table{[]() constexpr {std::array<rank_type, 256> ret{};
97 
98  // initialize with UNKNOWN (std::array::fill unfortunately not constexpr)
99  for (auto & c : ret)
100  c = 3; // == 'N'
101 
102  // reverse mapping for characters and their lowercase
103  for (size_t rnk = 0u; rnk < alphabet_size; ++rnk)
104  {
105  ret[rank_to_char_table[rnk]] = rnk;
106  ret[to_lower(rank_to_char_table[rnk])] = rnk;
107  }
108 
109  // set U equal to T
110  ret['U'] = ret['T'];
111  ret['u'] = ret['t'];
112 
113  // iupac characters are implicitly "UNKNOWN"
114  return ret;
115 }()
116 }; // namespace seqan3
117 
119 static constexpr rank_type rank_complement_table[alphabet_size]{
120  4, // T is complement of 'A'_dna5
121  2, // G is complement of 'C'_dna5
122  1, // C is complement of 'G'_dna5
123  3, // N is complement of 'N'_dna5
124  0 // A is complement of 'T'_dna5
125 };
126 
128 static constexpr rank_type rank_complement(rank_type const rank)
129 {
130  return rank_complement_table[rank];
131 }
132 
134 static constexpr char_type rank_to_char(rank_type const rank)
135 {
136  return rank_to_char_table[rank];
137 }
138 
140 static constexpr rank_type char_to_rank(char_type const chr)
141 {
142  using index_t = std::make_unsigned_t<char_type>;
143  return char_to_rank_table[static_cast<index_t>(chr)];
144 }
145 }
146 ;
147 
148 // ------------------------------------------------------------------
149 // containers
150 // ------------------------------------------------------------------
151 
158 
159 // ------------------------------------------------------------------
160 // literals
161 // ------------------------------------------------------------------
162 inline namespace literals
163 {
164 
179 constexpr dna5 operator""_dna5(char const c) noexcept
180 {
181  return dna5{}.assign_char(c);
182 }
183 
193 inline dna5_vector operator""_dna5(char const * s, std::size_t n)
194 {
195  dna5_vector r;
196  r.resize(n);
197 
198  for (size_t i = 0; i < n; ++i)
199  r[i].assign_char(s[i]);
200 
201  return r;
202 }
204 
205 } // namespace literals
206 
207 } // 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
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:83
SeqAn specific customisations in the standard namespace.
Provides seqan3::nucleotide_base.
T resize(T... args)
Provides utilities for modifying characters.