SeqAn3  3.2.0
The Modern C++ library for sequence analysis.
cigar_operation.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 // ------------------------------------------------------------------
18 // cigar_operation
19 // ------------------------------------------------------------------
20 
22 {
23 
47 class cigar_operation : public alphabet_base<cigar_operation, 9, char>
48 {
49 private:
52 
54  friend base_t;
55 
56 public:
60  constexpr cigar_operation() noexcept = default;
61  constexpr cigar_operation(cigar_operation const &) noexcept = default;
62  constexpr cigar_operation(cigar_operation &&) noexcept = default;
63  constexpr cigar_operation & operator=(cigar_operation const &) noexcept = default;
64  constexpr cigar_operation & operator=(cigar_operation &&) noexcept = default;
65  ~cigar_operation() noexcept = default;
66 
68 
69 private:
71  static constexpr char_type rank_to_char_table[alphabet_size]{'M', 'D', 'I', 'S', 'H', 'N', 'P', 'X', '='};
72 
74  static constexpr std::array<rank_type, 256> char_to_rank_table{[]() constexpr {std::array<rank_type, 256> ret{};
75 
76  // reverse mapping for characters
77  for (size_t rnk = 0u; rnk < alphabet_size; ++rnk)
78  {
79  ret[rank_to_char_table[rnk]] = rnk;
80  }
81 
82  return ret;
83 }()
84 }; // namespace seqan3::exposition_only
85 
87 static constexpr char_type rank_to_char(rank_type const rank)
88 {
89  return rank_to_char_table[rank];
90 }
91 
93 static constexpr rank_type char_to_rank(char_type const chr)
94 {
95  using index_t = std::make_unsigned_t<char_type>;
96  return char_to_rank_table[static_cast<index_t>(chr)];
97 }
98 }
99 ;
100 
101 } // namespace seqan3::exposition_only
Provides seqan3::alphabet_base.
A CRTP-base that makes defining a custom alphabet easier.
Definition: alphabet_base.hpp:57
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
The actual implementation of seqan3::cigar::operation for documentation purposes only.
Definition: cigar_operation.hpp:48
constexpr cigar_operation() noexcept=default
Defaulted.
A namespace for SeqAn entities that are intended for documentation purposes only.
Definition: cigar_operation.hpp:22