OpenMS  3.0.0
SvmTheoreticalSpectrumGeneratorTrainer.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Sandro Andreotti $
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34 
35 #pragma once
36 
41 
44 #include <OpenMS/FORMAT/TextFile.h>
45 
46 namespace OpenMS
47 {
66  public DefaultParamHandler
67  {
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 
96 
99 
103 
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 
DefaultParamHandler.h
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:147
OpenMS::SvmTheoreticalSpectrumGeneratorTrainer::DescriptorSet
SvmTheoreticalSpectrumGenerator::DescriptorSet DescriptorSet
Definition: SvmTheoreticalSpectrumGeneratorTrainer.h:69
TextFile.h
OpenMS::Param::setValue
void setValue(const std::string &key, const ParamValue &value, const std::string &description="", const std::vector< std::string > &tags=std::vector< std::string >())
Sets a value.
SvmTheoreticalSpectrumGeneratorTrainer.h
OpenMS::SvmTheoreticalSpectrumGeneratorTrainer
Train SVM models that are used by SvmTheoreticalSpectrumGenerator.
Definition: SvmTheoreticalSpectrumGeneratorTrainer.h:65
OpenMS::SvmTheoreticalSpectrumGeneratorTrainer::ObservedIntensMap
std::map< std::pair< IonType, Size >, std::vector< double > > ObservedIntensMap
Definition: SvmTheoreticalSpectrumGeneratorTrainer.h:70
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:57
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::MSExperiment::begin
Iterator begin()
Definition: MSExperiment.h:150
MzMLFile.h
Int
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
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
IdXMLFile.h
OpenMS::SvmTheoreticalSpectrumGeneratorTrainer::IonType
SvmTheoreticalSpectrumGenerator::IonType IonType
Definition: SvmTheoreticalSpectrumGeneratorTrainer.h:68
OpenMS::IDMapper::annotate
void annotate(PeakMap &map, const std::vector< PeptideIdentification > &peptide_ids, const std::vector< ProteinIdentification > &protein_ids, const bool clear_ids=false, const bool map_ms1=false)
Mapping method for peak maps.
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OpenMS::IdXMLFile::load
void load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
Loads the identifications of an idXML file without identifier.
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::MzMLFile::load
void load(const String &filename, PeakMap &map)
Loads a map from a MzML file. Spectra and chromatograms are sorted by default (this can be disabled u...
OpenMS::MSExperiment::iterator
Base::iterator iterator
Definition: MSExperiment.h:117
OpenMS::DefaultParamHandler::setParameters
void setParameters(const Param &param)
Sets the parameters.
OpenMS::DefaultParamHandler::getDefaults
const Param & getDefaults() const
Non-mutable access to the default parameters.
IDMapper.h
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:71
MSExperiment.h
SvmTheoreticalSpectrumGenerator.h
OpenMS::Param::copy
Param copy(const std::string &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
OpenMS::MSExperiment::end
Iterator end()
Definition: MSExperiment.h:160
OpenMS::SvmTheoreticalSpectrumGeneratorTrainer::trainModel
void trainModel(const PeakMap &spectra, const std::vector< AASequence > &annotations, String filename, Int precursor_charge)
trains an SVM for each ion_type and stores them in files <filename>_residue_loss_charge....
StandardDeclarations.h
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:69
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:111
OpenMS::IDMapper
Annotates an MSExperiment, FeatureMap or ConsensusMap with peptide identifications.
Definition: IDMapper.h:64
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
OpenMS::SvmTheoreticalSpectrumGenerator::IonType
nested class
Definition: SvmTheoreticalSpectrumGenerator.h:82
OpenMS::Param::remove
void remove(const std::string &key)
Remove the entry key or a section key (when suffix is ':')
StandardTypes.h
TOPPBase.h
MSSpectrum.h
OpenMS::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:68
OpenMS::SvmTheoreticalSpectrumGenerator::DescriptorSet
A set of descriptors for a single training row.
Definition: SvmTheoreticalSpectrumGenerator.h:219