OpenMS  2.4.0
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 #include <boost/shared_ptr.hpp>
41 
42 #include <OpenMS/OPENSWATHALGO/OpenSwathAlgoConfig.h>
43 
44 namespace OpenSwath
45 {
47  {
48 public:
49 
52  {
53  }
54 
55  std::string transition_name;
56  std::string peptide_ref;
58  double product_mz;
59  double precursor_mz;
61  bool decoy;
65 
67  {
68  return fragment_charge;
69  }
70 
72  {
73  return !(fragment_charge == 0);
74  }
75 
76  std::string getNativeID() const
77  {
78  return transition_name;
79  }
80 
81  std::string getPeptideRef() const
82  {
83  return peptide_ref;
84  }
85 
86  std::string getCompoundRef() const
87  {
88  return peptide_ref;
89  }
90 
91  double getLibraryIntensity() const
92  {
93  return library_intensity;
94  }
95 
96  void setLibraryIntensity(double l)
97  {
99  }
100 
101  double getProductMZ() const
102  {
103  return product_mz;
104  }
105 
106  double getPrecursorMZ() const
107  {
108  return precursor_mz;
109  }
110 
112  {
114  }
115 
117  {
118  return detecting_transition;
119  }
120 
122  {
124  }
125 
127  {
128  return quantifying_transition;
129  }
130 
132  {
134  }
135 
137  {
138  return identifying_transition;
139  }
140  };
141 
143  {
144  int location;
146  };
147 
148  // A compound is either a peptide or a metabolite
150  {
151 
153  drift_time(-1),
154  charge(0)
155  {
156  }
157 
158  double drift_time;
159  double rt;
160  int charge;
161  std::string sequence;
162  std::vector<std::string> protein_refs;
163  // 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)
164  std::string peptide_group_label;
165  std::string id;
166 
167  // for metabolites
168  std::string sum_formula;
169  std::string compound_name;
170 
171  // By convention, if there is no (metabolic) compound name, it is a peptide
172  bool isPeptide() const
173  {
174  return compound_name.empty();
175  }
176 
177  void setChargeState(int ch)
178  {
179  charge = ch;
180  }
181 
182  int getChargeState() const
183  {
184  return charge;
185  }
186 
187  void setDriftTime(double d)
188  {
189  drift_time = d;
190  }
191 
192  double getDriftTime() const
193  {
194  return drift_time;
195  }
196 
197  std::vector<LightModification> modifications;
198  };
199 
201  {
202  std::string id;
203  std::string sequence;
204  };
205 
207  {
209 
214 
215  std::vector<LightTransition> transitions;
216  std::vector<LightCompound> compounds;
217  std::vector<LightProtein> proteins;
218  std::vector<LightTransition> & getTransitions()
219  {
220  return transitions;
221  }
222 
223  const std::vector<LightTransition> & getTransitions() const
224  {
225  return transitions;
226  }
227 
228  std::vector<LightCompound> & getCompounds()
229  {
230  return compounds;
231  }
232 
233  const std::vector<LightCompound> & getCompounds() const
234  {
235  return compounds;
236  }
237 
238  std::vector<LightProtein> & getProteins()
239  {
240  return proteins;
241  }
242 
243  const std::vector<LightProtein> & getProteins() const
244  {
245  return proteins;
246  }
247 
248  // legacy
249  const LightCompound& getPeptideByRef(const std::string& ref)
250  {
251  return getCompoundByRef(ref);
252  }
253 
254  const LightCompound& getCompoundByRef(const std::string& ref)
255  {
257  {
259  }
260  return *(compound_reference_map_[ref]);
261  }
262 
263  private:
264 
266  {
267  for (size_t i = 0; i < getCompounds().size(); i++)
268  {
270  }
272  }
273 
274  // Map of compounds (peptides or metabolites)
276  std::map<std::string, LightCompound*> compound_reference_map_;
277 
278  };
279 
280 } //end Namespace OpenSwath
281 
282 
std::vector< LightProtein > & getProteins()
Definition: TransitionExperiment.h:238
double product_mz
Definition: TransitionExperiment.h:58
const std::vector< LightCompound > & getCompounds() const
Definition: TransitionExperiment.h:233
std::string id
Definition: TransitionExperiment.h:202
double library_intensity
Definition: TransitionExperiment.h:57
LightCompound()
Definition: TransitionExperiment.h:152
const std::vector< LightProtein > & getProteins() const
Definition: TransitionExperiment.h:243
std::vector< LightTransition > transitions
Definition: TransitionExperiment.h:215
bool isQuantifyingTransition() const
Definition: TransitionExperiment.h:126
const std::vector< LightTransition > & getTransitions() const
Definition: TransitionExperiment.h:223
std::vector< LightModification > modifications
Definition: TransitionExperiment.h:197
bool detecting_transition
Definition: TransitionExperiment.h:62
std::vector< LightProtein > proteins
Definition: TransitionExperiment.h:217
double rt
Definition: TransitionExperiment.h:159
int fragment_charge
Definition: TransitionExperiment.h:60
double getLibraryIntensity() const
Definition: TransitionExperiment.h:91
std::vector< LightCompound > compounds
Definition: TransitionExperiment.h:216
std::string getPeptideRef() const
Definition: TransitionExperiment.h:81
double precursor_mz
Definition: TransitionExperiment.h:59
bool compound_reference_map_dirty_
Definition: TransitionExperiment.h:275
const LightCompound & getCompoundByRef(const std::string &ref)
Definition: TransitionExperiment.h:254
const LightCompound & getPeptideByRef(const std::string &ref)
Definition: TransitionExperiment.h:249
double drift_time
Definition: TransitionExperiment.h:158
bool decoy
Definition: TransitionExperiment.h:61
int getChargeState() const
Definition: TransitionExperiment.h:182
std::string getCompoundRef() const
Definition: TransitionExperiment.h:86
void setLibraryIntensity(double l)
Definition: TransitionExperiment.h:96
void createPeptideReferenceMap_()
Definition: TransitionExperiment.h:265
bool isIdentifyingTransition() const
Definition: TransitionExperiment.h:136
std::string peptide_group_label
Definition: TransitionExperiment.h:164
std::string sequence
Definition: TransitionExperiment.h:203
int location
Definition: TransitionExperiment.h:144
std::vector< LightTransition > & getTransitions()
Definition: TransitionExperiment.h:218
LightTransition Transition
Definition: TransitionExperiment.h:210
std::string transition_name
Definition: TransitionExperiment.h:55
Definition: MRMScoring.h:50
LightCompound Peptide
Definition: TransitionExperiment.h:211
int unimod_id
Definition: TransitionExperiment.h:145
std::string getNativeID() const
Definition: TransitionExperiment.h:76
std::string sum_formula
Definition: TransitionExperiment.h:168
double getPrecursorMZ() const
Definition: TransitionExperiment.h:106
void setQuantifyingTransition(bool q)
Definition: TransitionExperiment.h:121
double getDriftTime() const
Definition: TransitionExperiment.h:192
void setIdentifyingTransition(bool i)
Definition: TransitionExperiment.h:131
std::string peptide_ref
Definition: TransitionExperiment.h:56
LightCompound Compound
Definition: TransitionExperiment.h:212
Definition: TransitionExperiment.h:149
std::string sequence
Definition: TransitionExperiment.h:161
LightTargetedExperiment()
Definition: TransitionExperiment.h:208
std::vector< std::string > protein_refs
Definition: TransitionExperiment.h:162
Definition: TransitionExperiment.h:46
bool identifying_transition
Definition: TransitionExperiment.h:64
void setChargeState(int ch)
Definition: TransitionExperiment.h:177
bool isDetectingTransition() const
Definition: TransitionExperiment.h:116
double getProductMZ() const
Definition: TransitionExperiment.h:101
int getProductChargeState() const
Definition: TransitionExperiment.h:66
LightTransition()
Definition: TransitionExperiment.h:50
std::vector< LightCompound > & getCompounds()
Definition: TransitionExperiment.h:228
void setDetectingTransition(bool d)
Definition: TransitionExperiment.h:111
bool isPeptide() const
Definition: TransitionExperiment.h:172
std::string compound_name
Definition: TransitionExperiment.h:169
std::string id
Definition: TransitionExperiment.h:165
std::map< std::string, LightCompound * > compound_reference_map_
Definition: TransitionExperiment.h:276
bool quantifying_transition
Definition: TransitionExperiment.h:63
void setDriftTime(double d)
Definition: TransitionExperiment.h:187
int charge
Definition: TransitionExperiment.h:160
Definition: TransitionExperiment.h:200
Definition: TransitionExperiment.h:206
bool isProductChargeStateSet() const
Definition: TransitionExperiment.h:71
LightProtein Protein
Definition: TransitionExperiment.h:213
Definition: TransitionExperiment.h:142