Class RawDataHandler¶

Defined in File RawDataHandler.h

Class Documentation¶

class RawDataHandler¶

Public Functions

RawDataHandler()¶: constructor required to initialize shared_ptr members

void setFeatureMap(const OpenMS::FeatureMap &feature_map)¶

OpenMS::FeatureMap &getFeatureMap()¶

const OpenMS::FeatureMap &getFeatureMap() const¶

void setFeatureMap(const std::string &name, const OpenMS::FeatureMap &feature_map)¶

OpenMS::FeatureMap &getFeatureMap(const std::string &name)¶

const OpenMS::FeatureMap &getFeatureMap(const std::string &name) const¶

void setMetaData(const MetaDataHandler &meta_data)¶

void setMetaData(std::shared_ptr<MetaDataHandler> &meta_data)¶

MetaDataHandler &getMetaData()¶

const MetaDataHandler &getMetaData() const¶

std::shared_ptr<MetaDataHandler> &getMetaDataShared()¶

void setParameters(const ParameterSet &parameters)¶

void setParameters(std::shared_ptr<ParameterSet> &parameters)¶

ParameterSet &getParameters()¶

const ParameterSet &getParameters() const¶

std::shared_ptr<ParameterSet> &getParametersShared()¶

void setTargetedExperiment(const OpenMS::TargetedExperiment &targeted_exp)¶

void setTargetedExperiment(std::shared_ptr<OpenMS::TargetedExperiment> &targeted_exp)¶

OpenMS::TargetedExperiment &getTargetedExperiment()¶

const OpenMS::TargetedExperiment &getTargetedExperiment() const¶

std::shared_ptr<OpenMS::TargetedExperiment> &getTargetedExperimentShared()¶

void setReferenceData(const std::vector<std::map<std::string, CastValue>> &reference_data)¶

void setReferenceData(std::shared_ptr<std::vector<std::map<std::string, CastValue>>> &reference_data)¶

std::vector<std::map<std::string, CastValue>> &getReferenceData()¶

const std::vector<std::map<std::string, CastValue>> &getReferenceData() const¶

std::shared_ptr<std::vector<std::map<std::string, CastValue>>> &getReferenceDataShared()¶

void setQuantitationMethods(const std::vector<OpenMS::AbsoluteQuantitationMethod> &quantitation_methods)¶

void setQuantitationMethods(std::shared_ptr<std::vector<OpenMS::AbsoluteQuantitationMethod>> &quantitation_methods)¶

std::vector<OpenMS::AbsoluteQuantitationMethod> &getQuantitationMethods()¶

const std::vector<OpenMS::AbsoluteQuantitationMethod> &getQuantitationMethods() const¶

std::shared_ptr<std::vector<OpenMS::AbsoluteQuantitationMethod>> &getQuantitationMethodsShared()¶

void setFeatureFilter(const OpenMS::MRMFeatureQC &feature_filter)¶

void setFeatureFilter(std::shared_ptr<OpenMS::MRMFeatureQC> &feature_filter)¶

OpenMS::MRMFeatureQC &getFeatureFilter()¶

const OpenMS::MRMFeatureQC &getFeatureFilter() const¶

std::shared_ptr<OpenMS::MRMFeatureQC> &getFeatureFilterShared()¶

void setFeatureQC(const OpenMS::MRMFeatureQC &feature_qc)¶

void setFeatureQC(std::shared_ptr<OpenMS::MRMFeatureQC> &feature_qc)¶

OpenMS::MRMFeatureQC &getFeatureQC()¶

const OpenMS::MRMFeatureQC &getFeatureQC() const¶

std::shared_ptr<OpenMS::MRMFeatureQC> &getFeatureQCShared()¶

void setFeatureRSDFilter(const OpenMS::MRMFeatureQC &feature_rsd_filter)¶

void setFeatureRSDFilter(std::shared_ptr<OpenMS::MRMFeatureQC> &feature_rsd_filter)¶

OpenMS::MRMFeatureQC &getFeatureRSDFilter()¶

const OpenMS::MRMFeatureQC &getFeatureRSDFilter() const¶

std::shared_ptr<OpenMS::MRMFeatureQC> &getFeatureRSDFilterShared()¶

void setFeatureRSDQC(const OpenMS::MRMFeatureQC &feature_rsd_qc)¶

void setFeatureRSDQC(std::shared_ptr<OpenMS::MRMFeatureQC> &feature_rsd_qc)¶

OpenMS::MRMFeatureQC &getFeatureRSDQC()¶

const OpenMS::MRMFeatureQC &getFeatureRSDQC() const¶

std::shared_ptr<OpenMS::MRMFeatureQC> &getFeatureRSDQCShared()¶

void setFeatureBackgroundFilter(const OpenMS::MRMFeatureQC &feature_background_filter)¶

void setFeatureBackgroundFilter(std::shared_ptr<OpenMS::MRMFeatureQC> &feature_background_filter)¶

OpenMS::MRMFeatureQC &getFeatureBackgroundFilter()¶

const OpenMS::MRMFeatureQC &getFeatureBackgroundFilter() const¶

std::shared_ptr<OpenMS::MRMFeatureQC> &getFeatureBackgroundFilterShared()¶

void setFeatureBackgroundQC(const OpenMS::MRMFeatureQC &feature_background_qc)¶

void setFeatureBackgroundQC(std::shared_ptr<OpenMS::MRMFeatureQC> &feature_background_qc)¶

OpenMS::MRMFeatureQC &getFeatureBackgroundQC()¶

const OpenMS::MRMFeatureQC &getFeatureBackgroundQC() const¶

std::shared_ptr<OpenMS::MRMFeatureQC> &getFeatureBackgroundQCShared()¶

void setFeatureRSDEstimations(const OpenMS::MRMFeatureQC &feature_rsd_estimations)¶

void setFeatureRSDEstimations(std::shared_ptr<OpenMS::MRMFeatureQC> &feature_rsd_estimations)¶

OpenMS::MRMFeatureQC &getFeatureRSDEstimations()¶

const OpenMS::MRMFeatureQC &getFeatureRSDEstimations() const¶

std::shared_ptr<OpenMS::MRMFeatureQC> &getFeatureRSDEstimationsShared()¶

void setFeatureBackgroundEstimations(const OpenMS::MRMFeatureQC &feature_background_estimations)¶

void setFeatureBackgroundEstimations(std::shared_ptr<OpenMS::MRMFeatureQC> &feature_background_estimations)¶

OpenMS::MRMFeatureQC &getFeatureBackgroundEstimations()¶

const OpenMS::MRMFeatureQC &getFeatureBackgroundEstimations() const¶

std::shared_ptr<OpenMS::MRMFeatureQC> &getFeatureBackgroundEstimationsShared()¶

void setSpectraLibrary(const OpenMS::MSExperiment &library)¶

void setSpectraLibrary(std::shared_ptr<OpenMS::MSExperiment> &library)¶

OpenMS::MSExperiment &getSpectraLibrary()¶

const OpenMS::MSExperiment &getSpectraLibrary() const¶

std::shared_ptr<OpenMS::MSExperiment> &getSpectraLibraryShared()¶

void setFeatureMapHistory(const OpenMS::FeatureMap &feature_map_history)¶

OpenMS::FeatureMap &getFeatureMapHistory()¶

const OpenMS::FeatureMap &getFeatureMapHistory() const¶

void setExperiment(const OpenMS::MSExperiment &experiment)¶

OpenMS::MSExperiment &getExperiment()¶

const OpenMS::MSExperiment &getExperiment() const¶

void setChromatogramMap(const OpenMS::MSExperiment &chromatogram_map)¶

OpenMS::MSExperiment &getChromatogramMap()¶

const OpenMS::MSExperiment &getChromatogramMap() const¶

void setTransformationDescription(const OpenMS::TransformationDescription &trafo)¶

OpenMS::TransformationDescription &getTransformationDescription()¶

const OpenMS::TransformationDescription &getTransformationDescription() const¶

void setSWATH(const OpenMS::MSExperiment &swath)¶

OpenMS::MSExperiment &getSWATH()¶

const OpenMS::MSExperiment &getSWATH() const¶

void setValidationMetrics(const std::map<std::string, float> &validation_metrics)¶

std::map<std::string, float> &getValidationMetrics()¶

const std::map<std::string, float> &getValidationMetrics() const¶

void setMzTab(const OpenMS::MzTab &mz_tab)¶

OpenMS::MzTab &getMzTab()¶

const OpenMS::MzTab &getMzTab() const¶

void clear()¶

void clearNonSharedData()¶

void updateFeatureMapHistory()¶

Update the Feature map history based on the filtered, selected, or new features in the current featureMap.

All new features are initialized as “used_” = True with the “modified_” attribute set to the current time-stamp. All removed features are changed to “used_” = False with the “modified_” attribute set to the current time-stamp.

ASSUMPTIONS: the unique ID attribute is set within OpenMS

void makeFeatureMapFromHistory()¶: Make the feature map from the feature map history by filtering out all features/subordinates where “used_” = False.