| OpenMS 2.5.0

Ribonucleotide.h
Go to the documentation of this file.
1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
6 //
7 // This software is released under a three-clause BSD license:
8 // * Redistributions of source code must retain the above copyright
9 // notice, this list of conditions and the following disclaimer.
10 // * Redistributions in binary form must reproduce the above copyright
11 // notice, this list of conditions and the following disclaimer in the
12 // documentation and/or other materials provided with the distribution.
13 // * Neither the name of any author or any participating institution
14 // may be used to endorse or promote products derived from this software
15 // without specific prior written permission.
16 // For a full list of authors, refer to the file AUTHORS.
17 // --------------------------------------------------------------------------
18 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21 // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
22 // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
23 // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
24 // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
25 // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
26 // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
27 // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
28 // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Hendrik Weisser $
32 // $Authors: Hendrik Weisser $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/DATASTRUCTURES/String.h>
38 #include <OpenMS/CHEMISTRY/EmpiricalFormula.h>
39 #include <iostream>
40
41 namespace OpenMS
42 {
51 class OPENMS_DLLAPI Ribonucleotide
52 {
53 friend class RibonucleotideDB;
54 public:
55
56 enum TermSpecificityNuc
57 {
58 ANYWHERE,
59 FIVE_PRIME,
60 THREE_PRIME,
61 NUMBER_OF_TERM_SPECIFICITY
62 };
63
67 Ribonucleotide(const String& name = "unknown ribonucleotide",
69 const String& code = ".",
70 const String& new_code = "",
71 const String& html_code = ".",
72 const EmpiricalFormula& formula = EmpiricalFormula(),
73 char origin = '.',
74 double mono_mass = 0.0,
75 double avg_mass = 0.0,
76 enum TermSpecificityNuc term_spec = ANYWHERE,
77 const EmpiricalFormula& baseloss_formula =
78 default_baseloss_);
79
81 Ribonucleotide(const Ribonucleotide& ribo) = default;
82
84 virtual ~Ribonucleotide();
86
90 Ribonucleotide& operator=(const Ribonucleotide& ribo) = default;
93
94
98 bool operator==(const Ribonucleotide& ribonucleotide) const;
101
105
107 const String getCode() const;
108
110 void setCode(const String& code);
111
113 const String getName() const;
114
116 void setName(const String& name);
117
119 const EmpiricalFormula getFormula() const;
120
122 void setFormula(const EmpiricalFormula& formula);
123
125 double getMonoMass() const;
126
128 void setMonoMass(double mono_mass);
129
131 double getAvgMass() const;
132
134 void setAvgMass(double avg_mass);
135
137 const String getNewCode() const;
138
140 void setNewCode(const String &new_code);
141
143 friend OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const Ribonucleotide& ribo);
144
146 char getOrigin() const;
147
149 void setOrigin(char origin);
150
152 String getHTMLCode() const;
153
155 void setHTMLCode(const String& html_code);
156
158 enum TermSpecificityNuc getTermSpecificity() const;
159
161 void setTermSpecificity(enum TermSpecificityNuc term_spec);
162
164 const EmpiricalFormula getBaselossFormula() const;
165
167 void setBaselossFormula(const EmpiricalFormula& formula);
168
170
172 bool isModified() const;
173
175 bool isAmbiguous() const;
176
177 protected:
179 static const EmpiricalFormula default_baseloss_;
180
181 String name_;
182 String code_;
183 String new_code_;
184 String html_code_;
185 EmpiricalFormula formula_;
186 char origin_;
187 double mono_mass_;
188 double avg_mass_;
189 enum TermSpecificityNuc term_spec_;
190 EmpiricalFormula baseloss_formula_;
191 };
192
194 OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const Ribonucleotide& ribo);
195
197 using RibonucleotideChainEnd = Ribonucleotide;
198
199 }
OpenMS::Ribonucleotide::formula_
EmpiricalFormula formula_
sum formula
Definition: Ribonucleotide.h:185
OpenMS::Ribonucleotide::TermSpecificityNuc
TermSpecificityNuc
Definition: Ribonucleotide.h:56
OpenMS::Ribonucleotide
Representation of a ribonucleotide (modified or unmodified)
Definition: Ribonucleotide.h:51
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::Ribonucleotide::avg_mass_
double avg_mass_
average mass
Definition: Ribonucleotide.h:188
OpenMS::Ribonucleotide::html_code_
String html_code_
RNAMods code.
Definition: Ribonucleotide.h:184
OpenMS::Ribonucleotide::name_
String name_
full name
Definition: Ribonucleotide.h:181
OpenMS::RibonucleotideDB
Database of ribonucleotides (modified and unmodified)
Definition: RibonucleotideDB.h:50
OpenMS::Ribonucleotide::FIVE_PRIME
Definition: Ribonucleotide.h:59
String.h
OpenMS::operator<<
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::Ribonucleotide::new_code_
String new_code_
Modomics code.
Definition: Ribonucleotide.h:183
OpenMS::Ribonucleotide::baseloss_formula_
EmpiricalFormula baseloss_formula_
sum formula after loss of the nucleobase
Definition: Ribonucleotide.h:190
OpenMS::Ribonucleotide::mono_mass_
double mono_mass_
monoisotopic mass
Definition: Ribonucleotide.h:187
OpenMS::EmpiricalFormula
Representation of an empirical formula.
Definition: EmpiricalFormula.h:82
OpenMS::Ribonucleotide::default_baseloss_
static const EmpiricalFormula default_baseloss_
Default value for sum formula after nucleobase loss.
Definition: Ribonucleotide.h:179
EmpiricalFormula.h
OpenMS::Ribonucleotide::origin_
char origin_
character of unmodified version of ribonucleotide
Definition: Ribonucleotide.h:186
seqan::isAmbiguous
bool isAmbiguous(AAcid c)
Definition: AhoCorasickAmbiguous.h:578
OpenMS::Ribonucleotide::THREE_PRIME
Definition: Ribonucleotide.h:60
OpenMS::Ribonucleotide::ANYWHERE
Definition: Ribonucleotide.h:58
OpenMS::Ribonucleotide::code_
String code_
short name
Definition: Ribonucleotide.h:182
KDTree::operator==
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806