SeqAn3  3.2.0-rc.1
The Modern C++ library for sequence analysis.
nucleotide_base.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 #include <seqan3/alphabet/detail/convert.hpp>
19 
20 namespace seqan3
21 {
22 
41 template <typename derived_type, auto size>
42 class nucleotide_base : public alphabet_base<derived_type, size, char>
43 {
44 private:
47 
51  constexpr nucleotide_base() noexcept = default;
52  constexpr nucleotide_base(nucleotide_base const &) noexcept = default;
53  constexpr nucleotide_base(nucleotide_base &&) noexcept = default;
54  constexpr nucleotide_base & operator=(nucleotide_base const &) noexcept = default;
55  constexpr nucleotide_base & operator=(nucleotide_base &&) noexcept = default;
56  ~nucleotide_base() noexcept = default;
57 
59 
61  friend derived_type;
62 
63 protected:
64  // Import from base:
65  using typename base_t::char_type;
66  using typename base_t::rank_type;
67 
68 public:
70  using base_t::to_rank;
71 
75  // This constructor needs to be public, because constructor templates are not inherited otherwise
80  template <typename other_nucl_type>
81  requires (!std::same_as<nucleotide_base, other_nucl_type>)
82  && (!std::same_as<derived_type, other_nucl_type>) && nucleotide_alphabet<other_nucl_type>
83  explicit constexpr nucleotide_base(other_nucl_type const & other) noexcept
84  {
85  static_cast<derived_type &>(*this) =
86  detail::convert_through_char_representation<other_nucl_type, derived_type>[seqan3::to_rank(other)];
87  }
89 
112  constexpr derived_type complement() const noexcept
113  {
114  return derived_type{}.assign_rank(derived_type{}.rank_complement(to_rank()));
115  }
117 
139  static constexpr bool char_is_valid(char_type const c) noexcept
140  {
141  return valid_char_table[static_cast<uint8_t>(c)];
142  }
143 
144 private:
146  static constexpr std::array<bool, 256> valid_char_table{[]() constexpr {// init with false
147  std::array<bool, 256> ret{};
148 
149  // the original valid chars and their lower cases
150  for (size_t rank = 0u; rank < derived_type::alphabet_size; ++rank)
151  {
152  uint8_t c = derived_type::rank_to_char(rank);
153  ret[c] = true;
154  ret[to_lower(c)] = true;
155  }
156 
157  // U and T shall be accepted for all
158  ret['U'] = true;
159  ret['T'] = true;
160  ret['u'] = true;
161  ret['t'] = true;
162 
163  return ret;
164 }()
165 }; // namespace seqan3
166 }
167 ;
168 
169 } // namespace seqan3
Provides seqan3::nucleotide_alphabet.
Provides seqan3::alphabet_base.
A CRTP-base that makes defining a custom alphabet easier.
Definition: alphabet_base.hpp:57
constexpr rank_type to_rank() const noexcept
Return the letter's numeric value (rank in the alphabet).
Definition: alphabet_base.hpp:137
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, void >, char, char > 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 nucleotides.
Definition: nucleotide_base.hpp:43
constexpr auto complement
Return the complement of a nucleotide object.
Definition: alphabet/nucleotide/concept.hpp:105
requires requires
The rank_type of the semi-alphabet; defined as the return type of seqan3::to_rank....
Definition: alphabet/concept.hpp:164
constexpr auto to_rank
Return the rank representation of a (semi-)alphabet object.
Definition: alphabet/concept.hpp:155
A concept that indicates whether an alphabet represents nucleotides.
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 utilities for modifying characters.