Class SequenceSegmentHandler¶

Defined in File SequenceSegmentHandler.h

Class Documentation¶

class SequenceSegmentHandler¶

Public Functions

SequenceSegmentHandler()¶: constructor to initialize shared resources

void clear()¶

void setSequenceSegmentName(const std::string &sequence_segment_name)¶

std::string &getSequenceSegmentName()¶

const std::string &getSequenceSegmentName() const¶

void setSampleIndices(const std::vector<size_t> &sample_indices)¶

std::vector<size_t> &getSampleIndices()¶

const std::vector<size_t> &getSampleIndices() const¶

void setStandardsConcentrations(const std::vector<OpenMS::AbsoluteQuantitationStandards::runConcentration> &standards_concentrations)¶

std::vector<OpenMS::AbsoluteQuantitationStandards::runConcentration> &getStandardsConcentrations()¶

const std::vector<OpenMS::AbsoluteQuantitationStandards::runConcentration> &getStandardsConcentrations() const¶

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 setComponentsToConcentrations(const std::map<std::string, std::vector<OpenMS::AbsoluteQuantitationStandards::featureConcentration>> components_to_concentrations)¶

std::map<std::string, std::vector<OpenMS::AbsoluteQuantitationStandards::featureConcentration>> &getComponentsToConcentrations()¶

const std::map<std::string, std::vector<OpenMS::AbsoluteQuantitationStandards::featureConcentration>> &getComponentsToConcentrations() const¶

void setExcludedComponentsToConcentrations(const std::map<std::string, std::vector<OpenMS::AbsoluteQuantitationStandards::featureConcentration>> components_to_concentrations)¶

std::map<std::string, std::vector<OpenMS::AbsoluteQuantitationStandards::featureConcentration>> &getExcludedComponentsToConcentrations()¶

const std::map<std::string, std::vector<OpenMS::AbsoluteQuantitationStandards::featureConcentration>> &getExcludedComponentsToConcentrations() const¶

std::vector<OpenMS::AbsoluteQuantitationStandards::featureConcentration> getFeatureConcentrationsPruned(const std::vector<OpenMS::AbsoluteQuantitationStandards::featureConcentration> feature_concentrations) const¶: remove features with an actual concentration of 0.0 or less