OpenMS  3.0.0
TransitionExperiment.h
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31 // $Maintainer: Hannes Roest $
32 // $Authors: Hannes Roest $
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34 
35 #pragma once
36 
37 #include <string>
38 #include <vector>
39 #include <map>
40 
41 #include <OpenMS/OPENSWATHALGO/OpenSwathAlgoConfig.h>
42 
43 namespace OpenSwath
44 {
46  {
47 public:
48 
50  precursor_im(-1),
52  {
53  }
54 
55  std::string transition_name;
56  std::string peptide_ref;
58  double product_mz;
59  double precursor_mz;
60  double precursor_im;
62  bool decoy;
66 
68  {
69  return fragment_charge;
70  }
71 
73  {
74  return !(fragment_charge == 0);
75  }
76 
77  bool isPrecursorImSet() const
78  {
79  return !(precursor_im == -1);
80  }
81 
82  std::string getNativeID() const
83  {
84  return transition_name;
85  }
86 
87  std::string getPeptideRef() const
88  {
89  return peptide_ref;
90  }
91 
92  std::string getCompoundRef() const
93  {
94  return peptide_ref;
95  }
96 
97  double getLibraryIntensity() const
98  {
99  return library_intensity;
100  }
101 
102  void setLibraryIntensity(double l)
103  {
104  library_intensity = l;
105  }
106 
107  double getProductMZ() const
108  {
109  return product_mz;
110  }
111 
112  double getPrecursorMZ() const
113  {
114  return precursor_mz;
115  }
116 
117  double getPrecursorIM() const
118  {
119  return precursor_im;
120  }
121 
123  {
125  }
126 
128  {
129  return detecting_transition;
130  }
131 
133  {
135  }
136 
138  {
139  return quantifying_transition;
140  }
141 
143  {
145  }
146 
148  {
149  return identifying_transition;
150  }
151  };
152 
154  {
155  int location;
157  };
158 
159  // A compound is either a peptide or a metabolite
161  {
162 
164  drift_time(-1),
165  charge(0)
166  {
167  }
168 
169  double drift_time;
170  double rt;
171  int charge;
172  std::string sequence;
173  std::vector<std::string> protein_refs;
174  // Peptide group label (corresponds to MS:1000893, all peptides that are isotopic forms of the same peptide should be assigned the same peptide group label)
175  std::string peptide_group_label;
176  std::string gene_name;
177  std::string id;
178 
179  // for metabolites
180  std::string sum_formula;
181  std::string compound_name;
182 
183  // By convention, if there is no (metabolic) compound name, it is a peptide
184  bool isPeptide() const
185  {
186  return compound_name.empty();
187  }
188 
189  void setChargeState(int ch)
190  {
191  charge = ch;
192  }
193 
194  int getChargeState() const
195  {
196  return charge;
197  }
198 
199  void setDriftTime(double d)
200  {
201  drift_time = d;
202  }
203 
204  double getDriftTime() const
205  {
206  return drift_time;
207  }
208 
209  std::vector<LightModification> modifications;
210  };
211 
213  {
214  std::string id;
215  std::string sequence;
216  };
217 
219  {
221 
226 
227  std::vector<LightTransition> transitions;
228  std::vector<LightCompound> compounds;
229  std::vector<LightProtein> proteins;
230  std::vector<LightTransition> & getTransitions()
231  {
232  return transitions;
233  }
234 
235  const std::vector<LightTransition> & getTransitions() const
236  {
237  return transitions;
238  }
239 
240  std::vector<LightCompound> & getCompounds()
241  {
242  return compounds;
243  }
244 
245  const std::vector<LightCompound> & getCompounds() const
246  {
247  return compounds;
248  }
249 
250  std::vector<LightProtein> & getProteins()
251  {
252  return proteins;
253  }
254 
255  const std::vector<LightProtein> & getProteins() const
256  {
257  return proteins;
258  }
259 
260  // legacy
261  const LightCompound& getPeptideByRef(const std::string& ref)
262  {
263  return getCompoundByRef(ref);
264  }
265 
266  const LightCompound& getCompoundByRef(const std::string& ref)
267  {
269  {
271  }
272  return *(compound_reference_map_[ref]);
273  }
274 
275  private:
276 
278  {
279  for (size_t i = 0; i < getCompounds().size(); i++)
280  {
282  }
284  }
285 
286  // Map of compounds (peptides or metabolites)
288  std::map<std::string, LightCompound*> compound_reference_map_;
289 
290  };
291 
292 } //end Namespace OpenSwath
293 
OpenSwath::LightCompound::id
std::string id
Definition: TransitionExperiment.h:177
OpenSwath::LightTargetedExperiment::getTransitions
const std::vector< LightTransition > & getTransitions() const
Definition: TransitionExperiment.h:235
OpenSwath::LightTransition::isQuantifyingTransition
bool isQuantifyingTransition() const
Definition: TransitionExperiment.h:137
OpenSwath::LightCompound::protein_refs
std::vector< std::string > protein_refs
Definition: TransitionExperiment.h:173
OpenSwath::LightTransition::product_mz
double product_mz
Definition: TransitionExperiment.h:58
OpenSwath::LightTargetedExperiment::compound_reference_map_dirty_
bool compound_reference_map_dirty_
Definition: TransitionExperiment.h:287
OpenSwath
Definition: Scoring.h:43
OpenSwath::LightTransition::library_intensity
double library_intensity
Definition: TransitionExperiment.h:57
OpenSwath::LightTransition::detecting_transition
bool detecting_transition
Definition: TransitionExperiment.h:63
OpenSwath::LightCompound::setDriftTime
void setDriftTime(double d)
Definition: TransitionExperiment.h:199
OpenSwath::LightTransition::getPeptideRef
std::string getPeptideRef() const
Definition: TransitionExperiment.h:87
OpenSwath::LightTransition::decoy
bool decoy
Definition: TransitionExperiment.h:62
OpenSwath::LightTransition::precursor_mz
double precursor_mz
Definition: TransitionExperiment.h:59
OpenSwath::LightTransition::fragment_charge
int fragment_charge
Definition: TransitionExperiment.h:61
OpenSwath::LightTargetedExperiment::getCompounds
const std::vector< LightCompound > & getCompounds() const
Definition: TransitionExperiment.h:245
OpenSwath::LightTransition::getLibraryIntensity
double getLibraryIntensity() const
Definition: TransitionExperiment.h:97
OpenSwath::LightTargetedExperiment::LightTargetedExperiment
LightTargetedExperiment()
Definition: TransitionExperiment.h:220
OpenSwath::LightTransition::getCompoundRef
std::string getCompoundRef() const
Definition: TransitionExperiment.h:92
OpenSwath::LightModification
Definition: TransitionExperiment.h:153
OpenSwath::LightTransition::transition_name
std::string transition_name
Definition: TransitionExperiment.h:55
OpenSwath::LightCompound::isPeptide
bool isPeptide() const
Definition: TransitionExperiment.h:184
OpenSwath::LightModification::unimod_id
int unimod_id
Definition: TransitionExperiment.h:156
OpenSwath::LightTargetedExperiment
Definition: TransitionExperiment.h:218
OpenSwath::LightTransition::setLibraryIntensity
void setLibraryIntensity(double l)
Definition: TransitionExperiment.h:102
OpenSwath::LightTransition::isPrecursorImSet
bool isPrecursorImSet() const
Definition: TransitionExperiment.h:77
OpenSwath::LightTransition::isIdentifyingTransition
bool isIdentifyingTransition() const
Definition: TransitionExperiment.h:147
OpenSwath::LightTransition::precursor_im
double precursor_im
Definition: TransitionExperiment.h:60
OpenSwath::LightProtein::id
std::string id
Definition: TransitionExperiment.h:214
OpenSwath::LightTargetedExperiment::getProteins
std::vector< LightProtein > & getProteins()
Definition: TransitionExperiment.h:250
OpenSwath::LightCompound::drift_time
double drift_time
Definition: TransitionExperiment.h:169
OpenSwath::LightProtein::sequence
std::string sequence
Definition: TransitionExperiment.h:215
OpenSwath::LightCompound
Definition: TransitionExperiment.h:160
OpenSwath::LightTargetedExperiment::getCompounds
std::vector< LightCompound > & getCompounds()
Definition: TransitionExperiment.h:240
OpenSwath::LightTargetedExperiment::getTransitions
std::vector< LightTransition > & getTransitions()
Definition: TransitionExperiment.h:230
OpenSwath::LightTargetedExperiment::Transition
LightTransition Transition
Definition: TransitionExperiment.h:222
OpenSwath::LightTargetedExperiment::compound_reference_map_
std::map< std::string, LightCompound * > compound_reference_map_
Definition: TransitionExperiment.h:288
OpenSwath::LightTargetedExperiment::compounds
std::vector< LightCompound > compounds
Definition: TransitionExperiment.h:228
OpenSwath::LightCompound::getDriftTime
double getDriftTime() const
Definition: TransitionExperiment.h:204
OpenSwath::LightCompound::LightCompound
LightCompound()
Definition: TransitionExperiment.h:163
OpenSwath::LightCompound::sum_formula
std::string sum_formula
Definition: TransitionExperiment.h:180
OpenSwath::LightCompound::peptide_group_label
std::string peptide_group_label
Definition: TransitionExperiment.h:175
OpenSwath::LightTransition::identifying_transition
bool identifying_transition
Definition: TransitionExperiment.h:65
OpenSwath::LightTransition::LightTransition
LightTransition()
Definition: TransitionExperiment.h:49
OpenSwath::LightTransition::setIdentifyingTransition
void setIdentifyingTransition(bool i)
Definition: TransitionExperiment.h:142
OpenSwath::LightTargetedExperiment::getProteins
const std::vector< LightProtein > & getProteins() const
Definition: TransitionExperiment.h:255
OpenSwath::LightCompound::rt
double rt
Definition: TransitionExperiment.h:170
OpenSwath::LightTargetedExperiment::transitions
std::vector< LightTransition > transitions
Definition: TransitionExperiment.h:227
OpenSwath::LightTargetedExperiment::getCompoundByRef
const LightCompound & getCompoundByRef(const std::string &ref)
Definition: TransitionExperiment.h:266
OpenSwath::LightModification::location
int location
Definition: TransitionExperiment.h:155
OpenSwath::LightTransition::getPrecursorMZ
double getPrecursorMZ() const
Definition: TransitionExperiment.h:112
OpenSwath::LightTransition::peptide_ref
std::string peptide_ref
Definition: TransitionExperiment.h:56
OpenSwath::LightCompound::getChargeState
int getChargeState() const
Definition: TransitionExperiment.h:194
OpenSwath::LightCompound::modifications
std::vector< LightModification > modifications
Definition: TransitionExperiment.h:209
OpenSwath::LightTransition::setQuantifyingTransition
void setQuantifyingTransition(bool q)
Definition: TransitionExperiment.h:132
OpenSwath::LightTransition::getNativeID
std::string getNativeID() const
Definition: TransitionExperiment.h:82
OpenSwath::LightTargetedExperiment::Protein
LightProtein Protein
Definition: TransitionExperiment.h:225
OpenSwath::LightTransition::getProductMZ
double getProductMZ() const
Definition: TransitionExperiment.h:107
OpenSwath::LightProtein
Definition: TransitionExperiment.h:212
OpenSwath::LightTransition::isDetectingTransition
bool isDetectingTransition() const
Definition: TransitionExperiment.h:127
OpenSwath::LightTargetedExperiment::proteins
std::vector< LightProtein > proteins
Definition: TransitionExperiment.h:229
OpenSwath::LightCompound::sequence
std::string sequence
Definition: TransitionExperiment.h:172
OpenSwath::LightCompound::charge
int charge
Definition: TransitionExperiment.h:171
OpenSwath::LightTargetedExperiment::Compound
LightCompound Compound
Definition: TransitionExperiment.h:224
OpenSwath::LightCompound::compound_name
std::string compound_name
Definition: TransitionExperiment.h:181
OpenSwath::LightTransition::getProductChargeState
int getProductChargeState() const
Definition: TransitionExperiment.h:67
OpenSwath::LightTargetedExperiment::getPeptideByRef
const LightCompound & getPeptideByRef(const std::string &ref)
Definition: TransitionExperiment.h:261
OpenSwath::LightTransition
Definition: TransitionExperiment.h:45
OpenSwath::LightCompound::gene_name
std::string gene_name
Definition: TransitionExperiment.h:176
OpenSwath::LightTransition::getPrecursorIM
double getPrecursorIM() const
Definition: TransitionExperiment.h:117
OpenSwath::LightTransition::quantifying_transition
bool quantifying_transition
Definition: TransitionExperiment.h:64
OpenSwath::LightTransition::isProductChargeStateSet
bool isProductChargeStateSet() const
Definition: TransitionExperiment.h:72
OpenSwath::LightTargetedExperiment::Peptide
LightCompound Peptide
Definition: TransitionExperiment.h:223
OpenSwath::LightTargetedExperiment::createPeptideReferenceMap_
void createPeptideReferenceMap_()
Definition: TransitionExperiment.h:277
OpenSwath::LightCompound::setChargeState
void setChargeState(int ch)
Definition: TransitionExperiment.h:189
OpenSwath::LightTransition::setDetectingTransition
void setDetectingTransition(bool d)
Definition: TransitionExperiment.h:122