SeqAn3 3.4.0-rc.1
The Modern C++ library for sequence analysis.
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aa27.hpp
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1// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
2// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
3// SPDX-License-Identifier: BSD-3-Clause
4
10#pragma once
11
12#include <vector>
13
17
18namespace seqan3
19{
42class aa27 : public aminoacid_base<aa27, 27>
43{
44private:
47
49 friend base_t;
52 friend base_t::base_t;
54
55public:
59 constexpr aa27() noexcept = default;
60 constexpr aa27(aa27 const &) noexcept = default;
61 constexpr aa27(aa27 &&) noexcept = default;
62 constexpr aa27 & operator=(aa27 const &) noexcept = default;
63 constexpr aa27 & operator=(aa27 &&) noexcept = default;
64 ~aa27() noexcept = default;
65
66 using base_t::base_t;
68
69private:
71 static constexpr char_type rank_to_char_table[alphabet_size]{'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I',
72 'J', 'K', 'L', 'M', 'N', 'O', 'P', 'Q', 'R',
73 'S', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z', '*'};
74
76 static constexpr char_type rank_to_char(rank_type const rank)
77 {
78 return rank_to_char_table[rank];
79 }
80
82 static constexpr rank_type char_to_rank(char_type const chr)
83 {
84 using index_t = std::make_unsigned_t<char_type>;
85 return char_to_rank_table[static_cast<index_t>(chr)];
86 }
87
88 // clang-format off
90 static constexpr std::array<rank_type, 256> char_to_rank_table
91 {
92 []() constexpr {
94
95 // initialize with 'X' (UNKNOWN)
96 ret.fill(23u);
97
98 // reverse mapping for characters and their lowercase
99 for (rank_type rnk = 0u; rnk < alphabet_size; ++rnk)
100 {
101 ret[static_cast<rank_type>(rank_to_char_table[rnk])] = rnk;
102 ret[static_cast<rank_type>(to_lower(rank_to_char_table[rnk]))] = rnk;
103 }
104
105 return ret;
106 }()
107 };
108};
109// clang-format on
110
111// ------------------------------------------------------------------
112// containers
113// ------------------------------------------------------------------
114
121
122// ------------------------------------------------------------------
123// literals
124// ------------------------------------------------------------------
125inline namespace literals
126{
127
142constexpr aa27 operator""_aa27(char const c) noexcept
143{
144 return aa27{}.assign_char(c);
145}
146
158SEQAN3_WORKAROUND_LITERAL aa27_vector operator""_aa27(char const * const s, size_t const n)
159{
160 aa27_vector r;
161 r.resize(n);
162
163 for (size_t i = 0; i < n; ++i)
164 r[i].assign_char(s[i]);
165
166 return r;
167}
169
170} // namespace literals
171
172} // namespace seqan3
Provides seqan3::aminoacid_alphabet.
Provides seqan3::aminoacid_base.
The twenty-seven letter amino acid alphabet.
Definition aa27.hpp:43
constexpr aa27() noexcept=default
Defaulted.
constexpr derived_type & assign_char(char_type const chr) noexcept
Assign from a character, implicitly converts invalid characters.
Definition alphabet_base.hpp:160
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:77
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:196
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:69
A CRTP-base that refines seqan3::alphabet_base and is used by the amino acids.
Definition aminoacid_base.hpp:29
T fill(T... args)
The main SeqAn3 namespace.
Definition aligned_sequence_concept.hpp:26
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:80
#define SEQAN3_WORKAROUND_LITERAL
Our char literals returning std::vector should be constexpr if constexpr std::vector is supported.
Definition platform.hpp:269
T resize(T... args)
Provides utilities for modifying characters.
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