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PILISNeutralLossModel.h
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34 
35 
36 #ifndef OPENMS_ANALYSIS_ID_PILISNEUTRALLOSSMODEL_H
37 #define OPENMS_ANALYSIS_ID_PILISNEUTRALLOSSMODEL_H
38 
39 #include <vector>
43 #include <OpenMS/CONCEPT/Types.h>
46 
47 namespace OpenMS
48 {
49  class AASequence;
50 
62  class OPENMS_DLLAPI PILISNeutralLossModel :
63  public DefaultParamHandler
64  {
65  friend class PILISNeutralLossModelGenerator;
66 
67 public:
68 
74 
77 
79  virtual ~PILISNeutralLossModel();
81 
83  PILISNeutralLossModel & operator=(const PILISNeutralLossModel & mode);
84 
88  double train(const RichPeakSpectrum & spec, const AASequence & peptide, double ion_weight, UInt charge, double peptide_weight);
90 
92  void getIons(std::vector<RichPeak1D> & peaks, const AASequence & peptide, double initial_prob);
93 
95  void setHMM(const HiddenMarkovModel & model);
96 
98  const HiddenMarkovModel & getHMM() const;
99 
101  void generateModel();
102 
104  void evaluate();
106 
107 protected:
108 
110  double getIntensitiesFromSpectrum_(const RichPeakSpectrum & train_spec, Map<String, double> & pre_ints, double ion_weight, const AASequence & peptide, UInt charge);
111 
113  void trainIons_(double initial_probability, const Map<String, double> & intensities, const AASequence & peptide);
114 
116  void getIons_(Map<String, double> & intensities, double initial_probability, const AASequence & precursor);
117 
119  void enableIonStates_(const AASequence & peptide);
120 
123 
126 
127  void updateMembers_();
128  };
129 }
130 #endif
This class implements the simulation of the spectra from PILIS.
Definition: PILISNeutralLossModel.h:62
Representation of a peptide/protein sequence.
Definition: AASequence.h:70
HiddenMarkovModel hmm_precursor_
precursor model used
Definition: PILISNeutralLossModel.h:122
UInt num_explicit_
Definition: PILISNeutralLossModel.h:125
Hidden Markov Model implementation of PILIS.
Definition: HiddenMarkovModel.h:134
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:51

OpenMS / TOPP release 2.0.0 Documentation generated on Wed Mar 30 2016 16:18:41 using doxygen 1.8.5