OpenMS  3.0.0
Ribonucleotide.h
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32 // $Authors: Hendrik Weisser $
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34 
35 #pragma once
36 
39 #include <iosfwd>
40 
41 namespace OpenMS
42 {
51  class OPENMS_DLLAPI Ribonucleotide
52  {
53  friend class RibonucleotideDB;
54  public:
55 
57  {
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:
180 
186  char origin_;
187  double mono_mass_;
188  double avg_mass_;
189  enum TermSpecificityNuc term_spec_;
191  };
192 
194  OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const Ribonucleotide& ribo);
195 
198 
199 }
OpenMS::Ribonucleotide::origin_
char origin_
character of unmodified version of ribonucleotide
Definition: Ribonucleotide.h:186
OpenMS::Ribonucleotide::baseloss_formula_
EmpiricalFormula baseloss_formula_
sum formula after loss of the nucleobase
Definition: Ribonucleotide.h:190
OpenMS::Ribonucleotide::default_baseloss_
static const EmpiricalFormula default_baseloss_
Default value for sum formula after nucleobase loss.
Definition: Ribonucleotide.h:179
OpenMS::Ribonucleotide::name_
String name_
full name
Definition: Ribonucleotide.h:181
OpenMS::Ribonucleotide::THREE_PRIME
Definition: Ribonucleotide.h:60
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::ANYWHERE
Definition: Ribonucleotide.h:58
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::Ribonucleotide::avg_mass_
double avg_mass_
average mass
Definition: Ribonucleotide.h:188
OpenMS::Ribonucleotide::mono_mass_
double mono_mass_
monoisotopic mass
Definition: Ribonucleotide.h:187
OpenMS::Ribonucleotide::html_code_
String html_code_
RNAMods code.
Definition: Ribonucleotide.h:184
OpenMS::Ribonucleotide::code_
String code_
short name
Definition: Ribonucleotide.h:182
OpenMS::Ribonucleotide::TermSpecificityNuc
TermSpecificityNuc
Definition: Ribonucleotide.h:56
OpenMS::RibonucleotideDB
Database of ribonucleotides (modified and unmodified)
Definition: RibonucleotideDB.h:50
OpenMS::operator<<
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
OpenMS::Ribonucleotide::new_code_
String new_code_
Modomics code.
Definition: Ribonucleotide.h:183
EmpiricalFormula.h
OpenMS::Internal::operator==
bool operator==(const IDBoostGraph::ProteinGroup &lhs, const IDBoostGraph::ProteinGroup &rhs)
OpenMS::EmpiricalFormula
Representation of an empirical formula.
Definition: EmpiricalFormula.h:84
String.h
OpenMS::Ribonucleotide::formula_
EmpiricalFormula formula_
sum formula
Definition: Ribonucleotide.h:185
OpenMS::Ribonucleotide::FIVE_PRIME
Definition: Ribonucleotide.h:59