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PILISIdentification.h
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34 
35 
36 #ifndef OPENMS_ANALYSIS_ID_PILISIDENTIFICATION_H
37 #define OPENMS_ANALYSIS_ID_PILISIDENTIFICATION_H
38 
42 
43 #include <vector>
44 #include <map>
45 
46 namespace OpenMS
47 {
48  // forward declarations
49  class PeakSpectrumCompareFunctor;
50 
61  class OPENMS_DLLAPI PILISIdentification :
62  public DefaultParamHandler
63  {
64 
65 public:
66 
72 
75 
77  virtual ~PILISIdentification();
79 
81  PILISIdentification & operator=(const PILISIdentification & source);
82 
86  //void setSequenceDB(const SuffixArrayPeptideFinder& sapf);
88 
90  void setModel(PILISModel * hmm_model);
91 
93  void getIdentifications(const std::vector<std::map<String, UInt> > & candidates, std::vector<PeptideIdentification> & ids, const RichPeakMap & exp);
94 
96  void getIdentification(const std::map<String, UInt> & candidates, PeptideIdentification & id, const RichPeakSpectrum & spectrum);
98 
99 protected:
100 
102  void getSpectrum_(RichPeakSpectrum & spec, const String & sequence, int charge);
103 
105  void getPreIdentification_(PeptideIdentification & id, const RichPeakSpectrum & spec, const std::map<String, UInt> & cand_peptides);
106 
108  void getFinalIdentification_(PeptideIdentification & id, const RichPeakSpectrum & spec, const PeptideIdentification & pre_id);
109 
111  PILISModel * getPILISModel_();
112 
114  //PILISSequenceDB* getSequenceDB_();
115  //SuffixArrayPeptideFinder* getSequenceDB_();
116 
118  //PILISSequenceDB* sequence_db_;
119  //SuffixArrayPeptideFinder sapf_;
120 
123 
126 
129 
132 
135 
137  std::vector<RichPeakSpectrum> sim_specs_;
138 
141 
144 
146  void updateMembers_();
147  };
148 }
149 
150 #endif
RichPeak1D p_
a peaks, just to not instantiate it over and over again
Definition: PILISIdentification.h:134
A more convenient string class.
Definition: String.h:57
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
A 1-dimensional raw data point or peak with meta information.
Definition: RichPeak1D.h:52
PILISModel * hmm_model_
returns the sequence database pointer
Definition: PILISIdentification.h:122
bool own_model_
flag whether the instance has a internal model
Definition: PILISIdentification.h:143
Map< char, double > aa_weight_
amino acids weights for the simple spectra generator
Definition: PILISIdentification.h:125
PeakSpectrumCompareFunctor * scorer_
scorer for spectra comparison
Definition: PILISIdentification.h:131
This class actually implements a complete ProteinIdentification run with PILIS.
Definition: PILISIdentification.h:61
This class implements the simulation of the spectra from PILIS.
Definition: PILISModel.h:67
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:69
std::vector< RichPeakSpectrum > sim_specs_
Definition: PILISIdentification.h:137
Base class for compare functors of spectra, that return a similarity value for two spectra...
Definition: PeakSpectrumCompareFunctor.h:53
PeakSpectrumCompareFunctor * pre_scorer_
scorer for pre comparison
Definition: PILISIdentification.h:128
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
bool own_sequence_db_
flag whether the instance has a internal sequence db
Definition: PILISIdentification.h:140
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63

OpenMS / TOPP release 2.0.0 Documentation generated on Tue Aug 25 2015 05:53:51 using doxygen 1.8.9.1