SeqAn3 3.4.0-rc.1
The Modern C++ library for sequence analysis.
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structured_aa.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
16
17namespace seqan3
18{
19
46template <writable_alphabet sequence_alphabet_t = aa27, writable_alphabet structure_alphabet_t = dssp9>
47 requires (!std::is_reference_v<sequence_alphabet_t>) && (!std::is_reference_v<structure_alphabet_t>)
49 public alphabet_tuple_base<structured_aa<sequence_alphabet_t, structure_alphabet_t>,
50 sequence_alphabet_t,
51 structure_alphabet_t>
52{
53private:
56 sequence_alphabet_t,
57 structure_alphabet_t>;
58
59public:
64 using sequence_alphabet_type = sequence_alphabet_t;
69 using structure_alphabet_type = structure_alphabet_t;
70
76
80 constexpr structured_aa() noexcept = default;
81 constexpr structured_aa(structured_aa const &) noexcept = default;
82 constexpr structured_aa(structured_aa &&) noexcept = default;
83 constexpr structured_aa & operator=(structured_aa const &) noexcept = default;
84 constexpr structured_aa & operator=(structured_aa &&) noexcept = default;
85 ~structured_aa() noexcept = default;
86
87 using base_type::base_type; // Inherit non-default constructors
88
89#if SEQAN3_DOXYGEN_ONLY(1) 0
96 template <typename component_type>
97 constexpr structured_aa(component_type const alph)
98 {}
99
106 template <typename indirect_component_type>
107 constexpr structured_aa(indirect_component_type const alph)
108 {}
109
116 template <typename component_type>
117 constexpr structured_aa & operator=(component_type const alph)
118 {}
119
126 template <typename indirect_component_type>
127 constexpr structured_aa & operator=(indirect_component_type const alph)
128 {}
129#endif
130
135 using base_type::operator=;
137
145 constexpr structured_aa & assign_char(char_type const c) noexcept
146 {
147 seqan3::assign_char_to(c, get<0>(*this));
148 return *this;
149 }
151
159 constexpr char_type to_char() const noexcept
160 {
161 return seqan3::to_char(get<0>(*this));
162 }
164
169 static constexpr bool char_is_valid(char_type const c) noexcept
170 {
171 return char_is_valid_for<sequence_alphabet_type>(c);
172 }
173};
174
177template <typename sequence_alphabet_type, typename structure_alphabet_type>
180
181} // namespace seqan3
Provides seqan3::aa27, container aliases and string literals.
Core alphabet concept and free function/type trait wrappers.
Provides seqan3::alphabet_tuple_base.
The CRTP base for a combined alphabet that contains multiple values of different alphabets at the sam...
Definition alphabet_tuple_base.hpp:113
A seqan3::alphabet_tuple_base that joins an aminoacid alphabet with a protein structure alphabet.
Definition structured_aa.hpp:52
constexpr structured_aa(component_type const alph)
Construction via a value of one of the components.
Definition structured_aa.hpp:97
sequence_alphabet_t sequence_alphabet_type
First template parameter as member type.
Definition structured_aa.hpp:64
constexpr char_type to_char() const noexcept
Return a character. This reads the internal sequence letter.
Definition structured_aa.hpp:159
constexpr structured_aa & operator=(component_type const alph)
Assignment via a value of one of the components.
Definition structured_aa.hpp:117
static constexpr bool char_is_valid(char_type const c) noexcept
Validate whether a character is valid in the sequence alphabet.
Definition structured_aa.hpp:169
structure_alphabet_t structure_alphabet_type
Second template parameter as member type.
Definition structured_aa.hpp:69
constexpr structured_aa() noexcept=default
Defaulted.
alphabet_char_t< sequence_alphabet_type > char_type
Equals the char_type of sequence_alphabet_type.
Definition structured_aa.hpp:75
constexpr structured_aa & operator=(indirect_component_type const alph)
Assignment via a value of a subtype that is assignable to one of the components.
Definition structured_aa.hpp:127
constexpr structured_aa(indirect_component_type const alph)
Construction via a value of a subtype that is assignable to one of the components.
Definition structured_aa.hpp:107
constexpr structured_aa & assign_char(char_type const c) noexcept
Assign from a nucleotide character. This modifies the internal sequence letter.
Definition structured_aa.hpp:145
structured_aa(sequence_alphabet_type &&, structure_alphabet_type &&) -> structured_aa< std::decay_t< sequence_alphabet_type >, std::decay_t< structure_alphabet_type > >
Type deduction guide enables usage of structured_aa without specifying template args.
Provides the dssp format for protein structure.
constexpr auto assign_char_to
Assign a character to an alphabet object.
Definition alphabet/concept.hpp:521
constexpr auto to_char
Return the char representation of an alphabet object.
Definition alphabet/concept.hpp:383
decltype(seqan3::to_char(std::declval< alphabet_type const >())) alphabet_char_t
The char_type of the alphabet; defined as the return type of seqan3::to_char.
Definition alphabet/concept.hpp:397
The main SeqAn3 namespace.
Definition aligned_sequence_concept.hpp:26
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