Class RawDataHandler

• Defined in File RawDataHandler.h

Class Documentation

class SmartPeak::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 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 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.