Struct RawDataProcessor

Inheritance Relationships

Base Types

Derived Types

Struct Documentation

struct RawDataProcessor : public SmartPeak::IProcessorDescription, public SmartPeak::IFilenamesHandler

Subclassed by SmartPeak::CalculateIsotopicPurities, SmartPeak::CalculateMDVAccuracies, SmartPeak::CalculateMDVs, SmartPeak::CheckFeatures, SmartPeak::CheckFeaturesBackgroundInterferences, SmartPeak::CheckFeaturesRSDs, SmartPeak::ClearData, SmartPeak::ConstructTransitionsList, SmartPeak::ExtractChromatogramWindows, SmartPeak::ExtractSpectraNonTargeted, SmartPeak::ExtractSpectraWindows, SmartPeak::FilterFeatures, SmartPeak::FilterFeaturesBackgroundInterferences, SmartPeak::FilterFeaturesRSDs, SmartPeak::FitFeaturesEMG, SmartPeak::IsotopicCorrections, SmartPeak::LoadAnnotations, SmartPeak::LoadFeatureFiltersRDP, SmartPeak::LoadFeatureQCsRDP, SmartPeak::LoadFeatures, SmartPeak::LoadMSP, SmartPeak::LoadParameters, SmartPeak::LoadRawData, SmartPeak::LoadTransitions, SmartPeak::LoadValidationData, SmartPeak::MapChromatograms, SmartPeak::MatchSpectra, SmartPeak::MergeFeaturesMS1, SmartPeak::MergeFeaturesMS2, SmartPeak::MergeSpectra, SmartPeak::Pick2DFeatures, SmartPeak::Pick3DFeatures, SmartPeak::PickMRMFeatures, SmartPeak::PlotFeatures, SmartPeak::QuantifyFeatures, SmartPeak::SearchAccurateMass, SmartPeak::SearchSpectrumMS1, SmartPeak::SearchSpectrumMS2, SmartPeak::SelectFeatures, SmartPeak::StoreAnnotations, SmartPeak::StoreFeatureFiltersRDP, SmartPeak::StoreFeatureQCsRDP, SmartPeak::StoreFeatures, SmartPeak::StoreMSP, SmartPeak::StoreParameters, SmartPeak::StoreRawData, SmartPeak::StoreValidationData, SmartPeak::ValidateFeatures, SmartPeak::ZeroChromatogramBaseline

Public Functions

RawDataProcessor(const RawDataProcessor &other) = delete
RawDataProcessor &operator=(const RawDataProcessor &other) = delete
virtual ~RawDataProcessor() = default
inline virtual ParameterSet getParameterSchema() const override

Get the Schema (possible, default parameters) of the processor.

inline virtual std::vector<std::string> getFilenameRequirements() const override

Returns the list of file ids that has to be defined prior to be process.

inline virtual std::set<std::string> getInputs() const override

Returns the list of data type accepted as input.

inline virtual std::set<std::string> getOutputs() const override

Returns the list of data type produced as output.

virtual void process(RawDataHandler &rawDataHandler_IO, const ParameterSet &params_I, Filenames &filenames_I) const

Interface to all raw data processing methods.

Parameters

  • rawDataHandler_IO – [inout] Raw data file struct

  • params_I – [in] Dictionary of parameter names, values, descriptions, and tags

  • filenames – [in] Info about where data should be read from or written to

inline virtual void getFilenames(Filenames &filenames) const override

add files handled by the processor to the Filnames instance

Protected Functions

RawDataProcessor() = default
virtual void doProcess(RawDataHandler &rawDataHandler_IO, const ParameterSet &params_I, Filenames &filenames_I) const = 0