SeqAn3  3.2.0
The Modern C++ library for sequence analysis.
dna16sam.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 
16 
17 namespace seqan3
18 {
19 
47 class dna16sam : public nucleotide_base<dna16sam, 16>
48 {
49 private:
52 
54  friend base_t;
56  friend base_t::base_t;
58 
59 public:
63  constexpr dna16sam() noexcept = default;
64  constexpr dna16sam(dna16sam const &) noexcept = default;
65  constexpr dna16sam(dna16sam &&) noexcept = default;
66  constexpr dna16sam & operator=(dna16sam const &) noexcept = default;
67  constexpr dna16sam & operator=(dna16sam &&) noexcept = default;
68  ~dna16sam() noexcept = default;
69 
70  using base_t::base_t;
72 
73 private:
75  static constexpr char_type rank_to_char_table
76  [alphabet_size]{'=', 'A', 'C', 'M', 'G', 'R', 'S', 'V', 'T', 'W', 'Y', 'H', 'K', 'D', 'B', 'N'};
77 
79  static constexpr std::array<rank_type, 256> char_to_rank_table{[]() constexpr {std::array<rank_type, 256> ret{};
80 
81  // initialize with UNKNOWN (std::array::fill unfortunately not constexpr)
82  for (auto & c : ret)
83  c = 15; // rank of 'N'
84 
85  // reverse mapping for characters and their lowercase
86  for (size_t rnk = 0u; rnk < alphabet_size; ++rnk)
87  {
88  ret[rank_to_char_table[rnk]] = rnk;
89  ret[to_lower(rank_to_char_table[rnk])] = rnk;
90  }
91 
92  // set U equal to T
93  ret['U'] = ret['T'];
94  ret['u'] = ret['t'];
95 
96  return ret;
97 }()
98 }; // namespace seqan3
99 
101 static constexpr rank_type rank_complement_table[alphabet_size]{
102  15, // N is complement of '='_dna16sam 0
103  8, // T is complement of 'A'_dna16sam 1
104  4, // G is complement of 'C'_dna16sam 2
105  12, // K is complement of 'M'_dna16sam 3
106  2, // C is complement of 'G'_dna16sam 4
107  10, // Y is complement of 'R'_dna16sam 5
108  6, // S is complement of 'S'_dna16sam 6
109  14, // B is complement of 'V'_dna16sam 7
110  1, // A is complement of 'T'_dna16sam 8
111  9, // W is complement of 'W'_dna16sam 9
112  5, // R is complement of 'Y'_dna16sam 10
113  13, // D is complement of 'H'_dna16sam 11
114  3, // M is complement of 'K'_dna16sam 12
115  11, // H is complement of 'D'_dna16sam 13
116  7, // V is complement of 'B'_dna16sam 14
117  15 // N is complement of 'N'_dna16sam 15
118 };
119 
121 static constexpr rank_type rank_complement(rank_type const rank)
122 {
123  return rank_complement_table[rank];
124 }
125 
130 static constexpr char_type rank_to_char(rank_type const rank)
131 {
132  return rank_to_char_table[rank];
133 }
134 
136 static constexpr rank_type char_to_rank(char_type const chr)
137 {
138  using index_t = std::make_unsigned_t<char_type>;
139  return char_to_rank_table[static_cast<index_t>(chr)];
140 }
141 }
142 ;
143 
144 // ------------------------------------------------------------------
145 // containers
146 // ------------------------------------------------------------------
147 
154 
155 // ------------------------------------------------------------------
156 // literals
157 // ------------------------------------------------------------------
158 inline namespace literals
159 {
160 
175 constexpr dna16sam operator""_dna16sam(char const c) noexcept
176 {
177  return dna16sam{}.assign_char(c);
178 }
179 
191 inline dna16sam_vector operator""_dna16sam(char const * s, size_t n)
192 {
193  dna16sam_vector r;
194  r.resize(n);
195 
196  for (size_t i = 0; i < n; ++i)
197  r[i].assign_char(s[i]);
198 
199  return r;
200 }
202 
203 } // namespace literals
204 
205 } // 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
A 16 letter DNA alphabet, containing all IUPAC symbols minus the gap and plus an equality sign ('=').
Definition: dna16sam.hpp:48
constexpr dna16sam() 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)