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SvmTheoreticalSpectrumGeneratorTrainer.h
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31 // $Maintainer: Sandro Andreotti $
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34 
35 #ifndef OPENMS_CHEMISTRY_SVMTHEORETICALSPECTRUMGENERATORTRAINER_H
36 #define OPENMS_CHEMISTRY_SVMTHEORETICALSPECTRUMGENERATORTRAINER_H
37 
41 #include <OpenMS/FORMAT/TextFile.h>
42 
43 namespace OpenMS
44 {
63  public DefaultParamHandler
64  {
67  typedef std::map<std::pair<IonType, Size>, std::vector<double> > ObservedIntensMap;
68 
70  void countIntensities_(const PeakSpectrum & spectrum,
71  const AASequence & annotation,
72  IonType type,
73  std::map<std::pair<IonType, Size>, std::vector<double> > & observed_intensities,
74  double tolerance,
75  Size number_of_regions
76  );
77 
79  void trainSecondaryTypes_(TextFile & info_outfile,
80  Size number_of_regions,
81  Size number_of_intensity_levels,
82  ObservedIntensMap & observed_intensities,
83  const std::vector<IonType> & ion_types,
84  const std::vector<bool> & is_primary
85  );
86 public:
87 
93 
96 
100 
103 
105  void trainModel(const PeakMap & spectra, const std::vector<AASequence> & annotations, String filename, Int precursor_charge);
106 
108  void normalizeIntensity(PeakSpectrum & S) const;
109 
110 protected:
111 
113  void writeTrainingFile_(std::vector<DescriptorSet> & training_input, std::vector<double> & training_output, String filename);
114 
115  };
116 }
117 
118 #endif // SvmTheoreticalSpectrumGeneratorTrainer_H
nested class
Definition: SvmTheoreticalSpectrumGenerator.h:79
A more convenient string class.
Definition: String.h:57
Representation of a peptide/protein sequence.
Definition: AASequence.h:70
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
SvmTheoreticalSpectrumGenerator::IonType IonType
Definition: SvmTheoreticalSpectrumGeneratorTrainer.h:65
Train SVM models that are used by SvmTheoreticalSpectrumGenerator.
Definition: SvmTheoreticalSpectrumGeneratorTrainer.h:62
A set of descriptors for a single training row.
Definition: SvmTheoreticalSpectrumGenerator.h:137
std::map< std::pair< IonType, Size >, std::vector< double > > ObservedIntensMap
Definition: SvmTheoreticalSpectrumGeneratorTrainer.h:67
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
int Int
Signed integer type.
Definition: Types.h:96
SvmTheoreticalSpectrumGenerator::DescriptorSet DescriptorSet
Definition: SvmTheoreticalSpectrumGeneratorTrainer.h:66
This class provides some basic file handling methods for text files.
Definition: TextFile.h:47

OpenMS / TOPP release 2.0.0 Documentation generated on Fri May 29 2015 17:20:31 using doxygen 1.8.9.1