SeqAn3  3.2.0-rc.1
The Modern C++ library for sequence analysis.
aa10murphy.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 
20 
21 namespace seqan3
22 {
23 
81 class aa10murphy : public aminoacid_base<aa10murphy, 10>
82 {
83 private:
86 
88  friend base_t;
90  friend base_t::base_t;
92 
93 public:
97  constexpr aa10murphy() noexcept = default;
98  constexpr aa10murphy(aa10murphy const &) noexcept = default;
99  constexpr aa10murphy(aa10murphy &&) noexcept = default;
100  constexpr aa10murphy & operator=(aa10murphy const &) noexcept = default;
101  constexpr aa10murphy & operator=(aa10murphy &&) noexcept = default;
102  ~aa10murphy() noexcept = default;
103 
105  using base_t::base_t;
107 
108 private:
110  static constexpr char_type rank_to_char_table[alphabet_size]{'A', 'B', 'C', 'F', 'G', 'H', 'I', 'K', 'P', 'S'};
111 
113  static constexpr std::array<rank_type, 256> char_to_rank_table{[]() constexpr {std::array<rank_type, 256> ret{};
114 
115  // initialize with UNKNOWN (std::array::fill unfortunately not constexpr)
116  for (auto & c : ret)
117  c = 9; // value of 'S', because that appears most frequently
118 
119  // reverse mapping for characters and their lowercase
120  for (rank_type rnk = 0u; rnk < alphabet_size; ++rnk)
121  {
122  ret[static_cast<rank_type>(rank_to_char_table[rnk])] = rnk;
123  ret[static_cast<rank_type>(to_lower(rank_to_char_table[rnk]))] = rnk;
124  }
125 
126  ret['D'] = ret['B'];
127  ret['d'] = ret['B']; // Convert D to B (either D/N).
128  ret['E'] = ret['B'];
129  ret['e'] = ret['B']; // Convert E to B (either D/N).
130  ret['J'] = ret['I'];
131  ret['j'] = ret['I']; // Convert J (either I/L) to I.
132  ret['L'] = ret['I'];
133  ret['l'] = ret['I']; // Convert L to I.
134  ret['M'] = ret['I'];
135  ret['m'] = ret['I']; // Convert M to I.
136  ret['N'] = ret['B'];
137  ret['n'] = ret['B']; // Convert N to B (either D/N).
138  ret['O'] = ret['K'];
139  ret['o'] = ret['K']; // Convert Pyrrolysine to K.
140  ret['Q'] = ret['B'];
141  ret['q'] = ret['B']; // Convert Q to B (either D/N).
142  ret['R'] = ret['K'];
143  ret['r'] = ret['K']; // Convert R to K.
144  ret['T'] = ret['S'];
145  ret['t'] = ret['S']; // Convert T to S.
146  ret['U'] = ret['C'];
147  ret['u'] = ret['C']; // Convert Selenocysteine to C.
148  ret['V'] = ret['I'];
149  ret['v'] = ret['I']; // Convert V to I.
150  ret['W'] = ret['F'];
151  ret['w'] = ret['F']; // Convert W to F.
152  ret['X'] = ret['S'];
153  ret['x'] = ret['S']; // Convert unknown amino acids to Serine.
154  ret['Y'] = ret['F'];
155  ret['y'] = ret['F']; // Convert Y to F.
156  ret['Z'] = ret['B'];
157  ret['z'] = ret['B']; // Convert Z (either E/Q) to B (either D/N).
158  ret['*'] = ret
159  ['F']; // The most common stop codon is UGA. This is most similar to a Tryptophan which in this alphabet gets converted to Phenylalanine.
160  return ret;
161 }()
162 }; // namespace seqan3
163 
165 static constexpr char_type rank_to_char(rank_type const rank)
166 {
167  return rank_to_char_table[rank];
168 }
169 
171 static constexpr rank_type char_to_rank(char_type const chr)
172 {
173  using index_t = std::make_unsigned_t<char_type>;
174  return char_to_rank_table[static_cast<index_t>(chr)];
175 }
176 }
177 ;
178 
179 // ------------------------------------------------------------------
180 // containers
181 // ------------------------------------------------------------------
182 
189 
190 // ------------------------------------------------------------------
191 // literals
192 // ------------------------------------------------------------------
193 inline namespace literals
194 {
195 
209 constexpr aa10murphy operator""_aa10murphy(char const c) noexcept
210 {
211  return aa10murphy{}.assign_char(c);
212 }
213 
225 inline aa10murphy_vector operator""_aa10murphy(char const * const s, size_t const n)
226 {
228  r.resize(n);
229 
230  for (size_t i = 0; i < n; ++i)
231  r[i].assign_char(s[i]);
232 
233  return r;
234 }
236 
237 } // namespace literals
238 
239 } // namespace seqan3
Provides seqan3::aminoacid_alphabet.
Provides seqan3::aminoacid_base.
The reduced Murphy amino acid alphabet.
Definition: aa10murphy.hpp:82
constexpr aa10murphy() noexcept=default
Defaulted.
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 CRTP-base that refines seqan3::alphabet_base and is used by the amino acids.
Definition: aminoacid_base.hpp:32
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
T resize(T... args)
Provides utilities for modifying characters.