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SvmTheoreticalSpectrumGeneratorTrainer.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Sandro Andreotti $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/KERNEL/StandardDeclarations.h>
38 #include <OpenMS/KERNEL/StandardTypes.h>
39 #include <OpenMS/KERNEL/MSSpectrum.h>
40 #include <OpenMS/KERNEL/MSExperiment.h>
41
42 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
43 #include <OpenMS/CHEMISTRY/SvmTheoreticalSpectrumGenerator.h>
44 #include <OpenMS/FORMAT/TextFile.h>
45
46 namespace OpenMS
47 {
65 class OPENMS_DLLAPI SvmTheoreticalSpectrumGeneratorTrainer :
66 public DefaultParamHandler
67 {
68 typedef SvmTheoreticalSpectrumGenerator::IonType IonType;
69 typedef SvmTheoreticalSpectrumGenerator::DescriptorSet DescriptorSet;
70 typedef std::map<std::pair<IonType, Size>, std::vector<double> > ObservedIntensMap;
71
73 void countIntensities_(const PeakSpectrum & spectrum,
74 const AASequence & annotation,
75 IonType type,
76 std::map<std::pair<IonType, Size>, std::vector<double> > & observed_intensities,
77 double tolerance,
78 Size number_of_regions
79 );
80
82 void trainSecondaryTypes_(TextFile & info_outfile,
83 Size number_of_regions,
84 Size number_of_intensity_levels,
85 ObservedIntensMap & observed_intensities,
86 const std::vector<IonType> & ion_types,
87 const std::vector<bool> & is_primary
88 );
89 public:
90
94 SvmTheoreticalSpectrumGeneratorTrainer();
96
98 SvmTheoreticalSpectrumGeneratorTrainer(const SvmTheoreticalSpectrumGeneratorTrainer & source);
99
101 ~SvmTheoreticalSpectrumGeneratorTrainer() override;
103
105 SvmTheoreticalSpectrumGeneratorTrainer & operator=(const SvmTheoreticalSpectrumGeneratorTrainer & tsg);
106
108 void trainModel(const PeakMap & spectra, const std::vector<AASequence> & annotations, String filename, Int precursor_charge);
109
111 void normalizeIntensity(PeakSpectrum & S) const;
112
113 protected:
114
116 void writeTrainingFile_(std::vector<DescriptorSet> & training_input, std::vector<double> & training_output, String filename);
117
118 };
119 }
120
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::SvmTheoreticalSpectrumGeneratorTrainer::IonType
SvmTheoreticalSpectrumGenerator::IonType IonType
Definition: SvmTheoreticalSpectrumGeneratorTrainer.h:68
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
StandardDeclarations.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::SvmTheoreticalSpectrumGenerator::IonType
nested class
Definition: SvmTheoreticalSpectrumGenerator.h:82
OpenMS::SvmTheoreticalSpectrumGeneratorTrainer::DescriptorSet
SvmTheoreticalSpectrumGenerator::DescriptorSet DescriptorSet
Definition: SvmTheoreticalSpectrumGeneratorTrainer.h:69
StandardTypes.h
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
TextFile.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::SvmTheoreticalSpectrumGenerator::DescriptorSet
A set of descriptors for a single training row.
Definition: SvmTheoreticalSpectrumGenerator.h:140
MSExperiment.h
OpenMS::SvmTheoreticalSpectrumGeneratorTrainer
Train SVM models that are used by SvmTheoreticalSpectrumGenerator.
Definition: SvmTheoreticalSpectrumGeneratorTrainer.h:65
DefaultParamHandler.h
MSSpectrum.h
OpenMS::SvmTheoreticalSpectrumGeneratorTrainer::ObservedIntensMap
std::map< std::pair< IonType, Size >, std::vector< double > > ObservedIntensMap
Definition: SvmTheoreticalSpectrumGeneratorTrainer.h:70
int
SvmTheoreticalSpectrumGenerator.h
OpenMS::TextFile
This class provides some basic file handling methods for text files.
Definition: TextFile.h:46
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127