SeqAn3 3.3.0-rc.1
The Modern C++ library for sequence analysis.
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structured_aa.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
19
20namespace seqan3
21{
22
49template <writable_alphabet sequence_alphabet_t = aa27, writable_alphabet structure_alphabet_t = dssp9>
50 requires (!std::is_reference_v<sequence_alphabet_t>) && (!std::is_reference_v<structure_alphabet_t>)
52 public alphabet_tuple_base<structured_aa<sequence_alphabet_t, structure_alphabet_t>,
53 sequence_alphabet_t,
54 structure_alphabet_t>
55{
56private:
59 sequence_alphabet_t,
60 structure_alphabet_t>;
61
62public:
67 using sequence_alphabet_type = sequence_alphabet_t;
72 using structure_alphabet_type = structure_alphabet_t;
73
79
83 constexpr structured_aa() noexcept = default;
84 constexpr structured_aa(structured_aa const &) noexcept = default;
85 constexpr structured_aa(structured_aa &&) noexcept = default;
86 constexpr structured_aa & operator=(structured_aa const &) noexcept = default;
87 constexpr structured_aa & operator=(structured_aa &&) noexcept = default;
88 ~structured_aa() noexcept = default;
89
90 using base_type::base_type; // Inherit non-default constructors
91
92#if SEQAN3_DOXYGEN_ONLY(1) 0
99 template <typename component_type>
100 constexpr structured_aa(component_type const alph)
101 {}
102
109 template <typename indirect_component_type>
110 constexpr structured_aa(indirect_component_type const alph)
111 {}
112
119 template <typename component_type>
120 constexpr structured_aa & operator=(component_type const alph)
121 {}
122
129 template <typename indirect_component_type>
130 constexpr structured_aa & operator=(indirect_component_type const alph)
131 {}
132#endif
133
138 using base_type::operator=;
140
148 constexpr structured_aa & assign_char(char_type const c) noexcept
149 {
150 seqan3::assign_char_to(c, get<0>(*this));
151 return *this;
152 }
154
162 constexpr char_type to_char() const noexcept
163 {
164 return seqan3::to_char(get<0>(*this));
165 }
167
172 static constexpr bool char_is_valid(char_type const c) noexcept
173 {
174 return char_is_valid_for<sequence_alphabet_type>(c);
175 }
176};
177
180template <typename sequence_alphabet_type, typename structure_alphabet_type>
183
184} // 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:116
A seqan3::alphabet_tuple_base that joins an aminoacid alphabet with a protein structure alphabet....
Definition: structured_aa.hpp:55
constexpr structured_aa(component_type const alph)
Construction via a value of one of the components.
Definition: structured_aa.hpp:100
sequence_alphabet_t sequence_alphabet_type
First template parameter as member type.
Definition: structured_aa.hpp:67
constexpr char_type to_char() const noexcept
Return a character. This reads the internal sequence letter.
Definition: structured_aa.hpp:162
constexpr structured_aa & operator=(component_type const alph)
Assignment via a value of one of the components.
Definition: structured_aa.hpp:120
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:172
structure_alphabet_t structure_alphabet_type
Second template parameter as member type.
Definition: structured_aa.hpp:72
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:78
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:130
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:110
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:148
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:524
constexpr auto to_char
Return the char representation of an alphabet object.
Definition: alphabet/concept.hpp:386
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:400
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29