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OpenMS
2.6.0
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76 std::map<std::pair<IonType, Size>, std::vector<double> > & observed_intensities,
78 Size number_of_regions
82 void trainSecondaryTypes_(
TextFile & info_outfile,
83 Size number_of_regions,
84 Size number_of_intensity_levels,
86 const std::vector<IonType> & ion_types,
87 const std::vector<bool> & is_primary
108 void trainModel(
const PeakMap & spectra,
const std::vector<AASequence> & annotations,
String filename,
Int precursor_charge);
116 void writeTrainingFile_(std::vector<DescriptorSet> & training_input, std::vector<double> & training_output,
String filename);
Base class for TOPP applications.
Definition: TOPPBase.h:144
SvmTheoreticalSpectrumGenerator::DescriptorSet DescriptorSet
Definition: SvmTheoreticalSpectrumGeneratorTrainer.h:69
Param copy(const String &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
void setValue(const String &key, const DataValue &value, const String &description="", const StringList &tags=StringList())
Sets a value.
Train SVM models that are used by SvmTheoreticalSpectrumGenerator.
Definition: SvmTheoreticalSpectrumGeneratorTrainer.h:65
std::map< std::pair< IonType, Size >, std::vector< double > > ObservedIntensMap
Definition: SvmTheoreticalSpectrumGeneratorTrainer.h:70
File adapter for MzML files.
Definition: MzMLFile.h:55
A more convenient string class.
Definition: String.h:59
Iterator begin()
Definition: MSExperiment.h:157
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
This class provides some basic file handling methods for text files.
Definition: TextFile.h:46
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
SvmTheoreticalSpectrumGenerator::IonType IonType
Definition: SvmTheoreticalSpectrumGeneratorTrainer.h:68
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.
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
void load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
Loads the identifications of an idXML file without identifier.
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
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...
Base::iterator iterator
Definition: MSExperiment.h:124
void setParameters(const Param ¶m)
Sets the parameters.
const Param & getDefaults() const
Non-mutable access to the default parameters.
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
void remove(const String &key)
Remove the entry key or a section key (when suffix is ':')
Iterator end()
Definition: MSExperiment.h:167
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....
Management and storage of parameters / INI files.
Definition: Param.h:73
Representation of a peptide/protein sequence.
Definition: AASequence.h:111
Annotates an MSExperiment, FeatureMap or ConsensusMap with peptide identifications.
Definition: IDMapper.h:66
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
nested class
Definition: SvmTheoreticalSpectrumGenerator.h:82
Used to load and store idXML files.
Definition: IdXMLFile.h:63
A set of descriptors for a single training row.
Definition: SvmTheoreticalSpectrumGenerator.h:140