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TransitionExperiment.h
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34 
35 #ifndef OPENMS_ANALYSIS_OPENSWATH_OPENSWATHALGO_DATAACCESS_TRANSITIONEXPERIMENT_H
36 #define OPENMS_ANALYSIS_OPENSWATH_OPENSWATHALGO_DATAACCESS_TRANSITIONEXPERIMENT_H
37 
38 #include <string>
39 #include <vector>
40 #include <boost/shared_ptr.hpp>
41 
42 #include <OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/OpenSwathAlgoConfig.h>
43 
44 namespace OpenSwath
45 {
46  struct OPENSWATHALGO_DLLAPI LightTransition
47  {
48 public:
49  std::string transition_name;
50  std::string peptide_ref;
52  double product_mz;
53  double precursor_mz;
54  int charge;
55 
57  {
58  return charge;
59  }
60 
61  std::string getNativeID() const
62  {
63  return transition_name;
64  }
65 
66  std::string getPeptideRef() const
67  {
68  return peptide_ref;
69  }
70 
71  double getLibraryIntensity() const
72  {
73  return library_intensity;
74  }
75 
76  void setLibraryIntensity(double l)
77  {
78  library_intensity = l;
79  }
80 
81  double getProductMZ() const
82  {
83  return product_mz;
84  }
85 
86  double getPrecursorMZ() const
87  {
88  return precursor_mz;
89  }
90 
91  };
92 
93  struct OPENSWATHALGO_DLLAPI LightModification
94  {
95  int location;
96  std::string unimod_id;
97  };
98 
99  struct OPENSWATHALGO_DLLAPI LightPeptide
100  {
101  double rt;
102  int charge;
103  std::string sequence;
104  std::string protein_ref;
105  std::string id;
106  int getChargeState() const
107  {
108  return charge;
109  }
110 
111  std::vector<LightModification> modifications;
112  };
113 
114  struct OPENSWATHALGO_DLLAPI LightProtein
115  {
116  std::string id;
117  std::string sequence;
118  };
119 
120  struct OPENSWATHALGO_DLLAPI LightTargetedExperiment
121  {
122  std::vector<LightTransition> transitions;
123  std::vector<LightPeptide> peptides;
124  std::vector<LightProtein> proteins;
125  std::vector<LightTransition> & getTransitions()
126  {
127  return transitions;
128  }
129 
130  std::vector<LightPeptide> & getPeptides()
131  {
132  return peptides;
133  }
134 
135  std::vector<LightProtein> & getProteins()
136  {
137  return proteins;
138  }
139 
140  };
141 
142 
143 } //end Namespace OpenSwath
144 
145 
146 #endif // OPENMS_ANALYSIS_OPENSWATH_OPENSWATHALGO_DATAACCESS_TRANSITIONEXPERIMENT_H
std::string getPeptideRef() const
Definition: TransitionExperiment.h:66
std::vector< LightProtein > & getProteins()
Definition: TransitionExperiment.h:135
double product_mz
Definition: TransitionExperiment.h:52
std::string id
Definition: TransitionExperiment.h:116
double library_intensity
Definition: TransitionExperiment.h:51
std::vector< LightTransition > transitions
Definition: TransitionExperiment.h:122
int getChargeState() const
Definition: TransitionExperiment.h:106
std::vector< LightProtein > proteins
Definition: TransitionExperiment.h:124
int getProductChargeState() const
Definition: TransitionExperiment.h:56
std::string getNativeID() const
Definition: TransitionExperiment.h:61
int charge
Definition: TransitionExperiment.h:102
double precursor_mz
Definition: TransitionExperiment.h:53
std::string protein_ref
Definition: TransitionExperiment.h:104
double getPrecursorMZ() const
Definition: TransitionExperiment.h:86
std::vector< LightPeptide > peptides
Definition: TransitionExperiment.h:123
void setLibraryIntensity(double l)
Definition: TransitionExperiment.h:76
Definition: TransitionExperiment.h:99
std::string sequence
Definition: TransitionExperiment.h:117
double getProductMZ() const
Definition: TransitionExperiment.h:81
int location
Definition: TransitionExperiment.h:95
std::vector< LightTransition > & getTransitions()
Definition: TransitionExperiment.h:125
std::string transition_name
Definition: TransitionExperiment.h:49
std::string id
Definition: TransitionExperiment.h:105
std::string peptide_ref
Definition: TransitionExperiment.h:50
std::string unimod_id
Definition: TransitionExperiment.h:96
Definition: TransitionExperiment.h:46
std::vector< LightPeptide > & getPeptides()
Definition: TransitionExperiment.h:130
int charge
Definition: TransitionExperiment.h:54
double rt
Definition: TransitionExperiment.h:101
Definition: TransitionExperiment.h:114
double getLibraryIntensity() const
Definition: TransitionExperiment.h:71
Definition: TransitionExperiment.h:120
std::string sequence
Definition: TransitionExperiment.h:103
std::vector< LightModification > modifications
Definition: TransitionExperiment.h:111
Definition: TransitionExperiment.h:93

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:22 using doxygen 1.8.5