SeqAn3  3.2.0
The Modern C++ library for sequence analysis.
aa27.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 {
45 class aa27 : public aminoacid_base<aa27, 27>
46 {
47 private:
50 
52  friend base_t;
54  friend base_t::base_t;
56 
57 public:
61  constexpr aa27() noexcept = default;
62  constexpr aa27(aa27 const &) noexcept = default;
63  constexpr aa27(aa27 &&) noexcept = default;
64  constexpr aa27 & operator=(aa27 const &) noexcept = default;
65  constexpr aa27 & operator=(aa27 &&) noexcept = default;
66  ~aa27() noexcept = default;
67 
68  using base_t::base_t;
70 
71 private:
73  static constexpr char_type rank_to_char_table[alphabet_size]{'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I',
74  'J', 'K', 'L', 'M', 'N', 'O', 'P', 'Q', 'R',
75  'S', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z', '*'};
76 
78  static constexpr std::array<rank_type, 256> char_to_rank_table{[]() constexpr {std::array<rank_type, 256> ret{};
79 
80  // initialize with UNKNOWN (std::array::fill unfortunately not constexpr)
81  for (auto & c : ret)
82  c = 23; // value of 'X'
83 
84  // reverse mapping for characters and their lowercase
85  for (rank_type rnk = 0u; rnk < alphabet_size; ++rnk)
86  {
87  ret[static_cast<rank_type>(rank_to_char_table[rnk])] = rnk;
88  ret[static_cast<rank_type>(to_lower(rank_to_char_table[rnk]))] = rnk;
89  }
90 
91  return ret;
92 }()
93 }; // namespace seqan3
94 
96 static constexpr char_type rank_to_char(rank_type const rank)
97 {
98  return rank_to_char_table[rank];
99 }
100 
102 static constexpr rank_type char_to_rank(char_type const chr)
103 {
104  using index_t = std::make_unsigned_t<char_type>;
105  return char_to_rank_table[static_cast<index_t>(chr)];
106 }
107 }
108 ;
109 
110 // ------------------------------------------------------------------
111 // containers
112 // ------------------------------------------------------------------
113 
120 
121 // ------------------------------------------------------------------
122 // literals
123 // ------------------------------------------------------------------
124 inline namespace literals
125 {
126 
141 constexpr aa27 operator""_aa27(char const c) noexcept
142 {
143  return aa27{}.assign_char(c);
144 }
145 
157 inline aa27_vector operator""_aa27(char const * const s, size_t const n)
158 {
159  aa27_vector r;
160  r.resize(n);
161 
162  for (size_t i = 0; i < n; ++i)
163  r[i].assign_char(s[i]);
164 
165  return r;
166 }
168 
169 } // namespace literals
170 
171 } // namespace seqan3
Provides seqan3::aminoacid_alphabet.
Provides seqan3::aminoacid_base.
The twenty-seven letter amino acid alphabet.
Definition: aa27.hpp:46
constexpr aa27() 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.