OpenMS  2.4.0
ResidueModification.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Andreas Bertsch $
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34 //
35 
36 #pragma once
37 
40 
41 #include <set>
42 
43 namespace OpenMS
44 {
45  // forward declaration
46  class Residue;
47 
76  class OPENMS_DLLAPI ResidueModification
77  {
78 public:
79 
96  {
97  ANYWHERE = 0,
98  C_TERM = 1,
99  N_TERM = 2,
100  PROTEIN_C_TERM = 3,
101  PROTEIN_N_TERM = 4,
102  NUMBER_OF_TERM_SPECIFICITY
103  };
104 
108  {
109  ARTIFACT = 0,
125  NUMBER_OF_SOURCE_CLASSIFICATIONS
126  };
128 
134 
136  ResidueModification(const ResidueModification& modification);
137 
139  virtual ~ResidueModification();
141 
145  ResidueModification& operator=(const ResidueModification& modification);
148 
152  void setId(const String& id);
154 
156  const String& getId() const;
157 
165  void setFullId(const String& full_id = "");
166 
168 
177  const String& getFullId() const;
178 
180  void setUniModRecordId(const Int& id);
181 
183  const Int& getUniModRecordId() const;
184 
186  const String getUniModAccession() const;
187 
189  void setPSIMODAccession(const String& id);
190 
192  const String& getPSIMODAccession() const;
193 
195  void setFullName(const String& full_name);
196 
198  const String& getFullName() const;
199 
201  void setName(const String& name);
202 
204  const String& getName() const;
205 
211  void setTermSpecificity(TermSpecificity term_spec);
212 
220  void setTermSpecificity(const String& name);
221 
223  TermSpecificity getTermSpecificity() const;
224 
231  String getTermSpecificityName(TermSpecificity term_spec = NUMBER_OF_TERM_SPECIFICITY) const;
232 
241  void setOrigin(char origin);
242 
244  char getOrigin() const;
245 
247  void setSourceClassification(const String& classification);
248 
250  void setSourceClassification(SourceClassification classification);
251 
253  SourceClassification getSourceClassification() const;
254 
256  String getSourceClassificationName(SourceClassification classification = NUMBER_OF_SOURCE_CLASSIFICATIONS) const;
257 
259  void setAverageMass(double mass);
260 
262  double getAverageMass() const;
263 
265  void setMonoMass(double mass);
266 
268  double getMonoMass() const;
269 
271  void setDiffAverageMass(double mass);
272 
274  double getDiffAverageMass() const;
275 
277  void setDiffMonoMass(double mass);
278 
280  double getDiffMonoMass() const;
281 
283  void setFormula(const String& composition);
284 
286  const String& getFormula() const;
287 
289  void setDiffFormula(const EmpiricalFormula& diff_formula);
290 
292  const EmpiricalFormula& getDiffFormula() const;
293 
295  void setSynonyms(const std::set<String>& synonyms);
296 
298  void addSynonym(const String& synonym);
299 
301  const std::set<String>& getSynonyms() const;
302 
304  void setNeutralLossDiffFormula(const EmpiricalFormula& loss);
305 
307  const EmpiricalFormula& getNeutralLossDiffFormula() const;
308 
310  void setNeutralLossMonoMass(double mono_mass);
311 
313  double getNeutralLossMonoMass() const;
314 
316  void setNeutralLossAverageMass(double average_mass);
317 
319  double getNeutralLossAverageMass() const;
321 
325  bool hasNeutralLoss() const;
327 
329  bool isUserDefined() const;
330 
332  bool operator==(const ResidueModification& modification) const;
333 
335  bool operator!=(const ResidueModification& modification) const;
336 
338  bool operator<(const ResidueModification& modification) const;
340 
341 protected:
342 
344 
346 
348 
349  // The UniMod record id (an integer)
351 
353 
355 
357 
358  char origin_;
359 
361 
363 
364  double mono_mass_;
365 
367 
369 
371 
373 
374  std::set<String> synonyms_;
375 
377 
379 
381  };
382 }
383 
OpenMS::ResidueModification::classification_
SourceClassification classification_
Definition: ResidueModification.h:360
OpenMS::ResidueModification::full_id_
String full_id_
Definition: ResidueModification.h:345
OpenMS::ResidueModification::OTHER_GLYCOSYLATION
@ OTHER_GLYCOSYLATION
Definition: ResidueModification.h:117
OpenMS::ResidueModification
Representation of a modification.
Definition: ResidueModification.h:76
OpenMS::ResidueModification::HYPOTHETICAL
@ HYPOTHETICAL
Definition: ResidueModification.h:110
OpenMS::ResidueModification::ISOTOPIC_LABEL
@ ISOTOPIC_LABEL
Definition: ResidueModification.h:115
OpenMS::ResidueModification::neutral_loss_diff_formula_
EmpiricalFormula neutral_loss_diff_formula_
Definition: ResidueModification.h:376
OpenMS::String
A more convenient string class.
Definition: String.h:57
OpenMS::ResidueModification::full_name_
String full_name_
Definition: ResidueModification.h:352
KDTree::operator!=
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
OpenMS::ResidueModification::MULTIPLE
@ MULTIPLE
Definition: ResidueModification.h:113
OpenMS::ResidueModification::NATURAL
@ NATURAL
Definition: ResidueModification.h:111
OpenMS::ResidueModification::NONSTANDARD_RESIDUE
@ NONSTANDARD_RESIDUE
Definition: ResidueModification.h:121
OpenMS::ResidueModification::name_
String name_
Definition: ResidueModification.h:354
OpenMS::ResidueModification::UNKNOWN
@ UNKNOWN
Definition: ResidueModification.h:124
OpenMS::operator<
bool operator<(const MultiplexDeltaMasses &dm1, const MultiplexDeltaMasses &dm2)
OpenMS::ResidueModification::COTRANSLATIONAL
@ COTRANSLATIONAL
Definition: ResidueModification.h:122
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS::ResidueModification::PRETRANSLATIONAL
@ PRETRANSLATIONAL
Definition: ResidueModification.h:116
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::ResidueModification::origin_
char origin_
Definition: ResidueModification.h:358
OpenMS::ResidueModification::CHEMICAL_DERIVATIVE
@ CHEMICAL_DERIVATIVE
Definition: ResidueModification.h:114
OpenMS::ResidueModification::TermSpecificity
TermSpecificity
Position where the modification is allowed to occur.
Definition: ResidueModification.h:95
OpenMS::ResidueModification::OTHER
@ OTHER
Definition: ResidueModification.h:120
OpenMS::ResidueModification::AA_SUBSTITUTION
@ AA_SUBSTITUTION
Definition: ResidueModification.h:119
OpenMS::ResidueModification::SourceClassification
SourceClassification
Classification of the modification.
Definition: ResidueModification.h:107
OpenMS::ResidueModification::synonyms_
std::set< String > synonyms_
Definition: ResidueModification.h:374
OpenMS::ResidueModification::average_mass_
double average_mass_
Definition: ResidueModification.h:362
OpenMS::ResidueModification::psi_mod_accession_
String psi_mod_accession_
Definition: ResidueModification.h:347
KDTree::operator==
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806
EmpiricalFormula.h
OpenMS::ResidueModification::id_
String id_
Definition: ResidueModification.h:343
OpenMS::ResidueModification::NLINKED_GLYCOSYLATION
@ NLINKED_GLYCOSYLATION
Definition: ResidueModification.h:118
OpenMS::EmpiricalFormula
Representation of an empirical formula.
Definition: EmpiricalFormula.h:81
OpenMS::ResidueModification::formula_
String formula_
Definition: ResidueModification.h:370
OpenMS::ResidueModification::diff_mono_mass_
double diff_mono_mass_
Definition: ResidueModification.h:368
OpenMS::ResidueModification::mono_mass_
double mono_mass_
Definition: ResidueModification.h:364
String.h
OpenMS::ResidueModification::neutral_loss_average_mass_
double neutral_loss_average_mass_
Definition: ResidueModification.h:380
OpenMS::ResidueModification::diff_average_mass_
double diff_average_mass_
Definition: ResidueModification.h:366
OpenMS::ResidueModification::OLINKED_GLYCOSYLATION
@ OLINKED_GLYCOSYLATION
Definition: ResidueModification.h:123
OpenMS::ResidueModification::unimod_record_id_
Int unimod_record_id_
Definition: ResidueModification.h:350
OpenMS::ResidueModification::diff_formula_
EmpiricalFormula diff_formula_
Definition: ResidueModification.h:372
OpenMS::ResidueModification::POSTTRANSLATIONAL
@ POSTTRANSLATIONAL
Definition: ResidueModification.h:112
OpenMS::ResidueModification::neutral_loss_mono_mass_
double neutral_loss_mono_mass_
Definition: ResidueModification.h:378
OpenMS::ResidueModification::term_spec_
TermSpecificity term_spec_
Definition: ResidueModification.h:356