Struct SequenceSegmentProcessor

Inheritance Relationships

Base Types

Derived Types

Struct Documentation

struct SequenceSegmentProcessor : public SmartPeak::IProcessorDescription, public SmartPeak::IFilenamesHandler

Subclassed by SmartPeak::EstimateFeatureBackgroundInterferences, SmartPeak::EstimateFeatureFilterValues, SmartPeak::EstimateFeatureQCValues, SmartPeak::EstimateFeatureRSDs, SmartPeak::FitCalibration, SmartPeak::LoadFeatureBackgroundEstimations, SmartPeak::LoadFeatureBackgroundFilters, SmartPeak::LoadFeatureBackgroundQCs, SmartPeak::LoadFeatureFilters, SmartPeak::LoadFeatureQCs, SmartPeak::LoadFeatureRSDEstimations, SmartPeak::LoadFeatureRSDFilters, SmartPeak::LoadFeatureRSDQCs, SmartPeak::LoadQuantitationMethods, SmartPeak::LoadStandardsConcentrations, SmartPeak::OptimizeCalibration, SmartPeak::StoreFeatureBackgroundEstimations, SmartPeak::StoreFeatureBackgroundFilters, SmartPeak::StoreFeatureBackgroundQCs, SmartPeak::StoreFeatureFilters, SmartPeak::StoreFeatureQCs, SmartPeak::StoreFeatureRSDEstimations, SmartPeak::StoreFeatureRSDFilters, SmartPeak::StoreFeatureRSDQCs, SmartPeak::StoreQuantitationMethods, SmartPeak::StoreStandardsConcentrations, SmartPeak::TransferLOQToFeatureFilters, SmartPeak::TransferLOQToFeatureQCs

Public Functions

SequenceSegmentProcessor(const SequenceSegmentProcessor &other) = delete
SequenceSegmentProcessor &operator=(const SequenceSegmentProcessor &other) = delete
virtual ~SequenceSegmentProcessor() = default
virtual void process(SequenceSegmentHandler &sequenceSegmentHandler_IO, const SequenceHandler &sequenceHandler_I, const ParameterSet &params_I, Filenames &filenames_I) const

Interface to all sequence segment processing methods.

Parameters

  • sequenceSegmentHandler_IO – [inout] Sequence segment handler

  • sequenceHandler_I – [in] Sequence handler

  • 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

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.

Public Members

SequenceSegmentObservable *sequence_segment_observable_ = nullptr

Public Static Functions

static void getSampleIndicesBySampleType(const SequenceSegmentHandler &sequenceSegmentHandler, const SequenceHandler &sequenceHandler, const SampleType sampleType, std::vector<size_t> &sampleIndices)

Return all injection indices that belong to a given sample type.

Parameters

  • sequenceSegmentHandler – [in] Sequence segment handler

  • sequenceHandler – [in] Sequence handler

  • sampleType – [in] Sample type filter

  • sampleIndices – [out] Output sample indices

Protected Functions

virtual void doProcess(SequenceSegmentHandler &sequenceSegmentHandler_IO, const SequenceHandler &sequenceHandler_I, const ParameterSet &params_I, Filenames &filenames_I) const = 0
SequenceSegmentProcessor() = default
void processForAllSegments(std::vector<SmartPeak::SequenceSegmentHandler> &sequence_segment_handlers, SequenceSegmentObservable *sequence_segment_observable, Filenames &filenames)
std::string constructFilename(const std::string &filename, bool static_filename) const

Utility method: most of the loading / storing processors can load / store per sequence But also from one unique file to or from multiple sequence (static filename) this method aims at returning the appropriate filename based on “static filename” behavior.