Uses of Class
com.compomics.util.experiment.identification.peptide_shaker.Metrics

Packages that use Metrics

Package	Description
com.compomics.util.experiment.identification.features	Classes for the generation of identification features.
com.compomics.util.experiment.quantification.spectrumcounting	Experiment classes related to spectrum counting.

Uses of Metrics in com.compomics.util.experiment.identification.features

Methods in com.compomics.util.experiment.identification.features that return Metrics

Modifier and Type	Method	Description
Metrics	IdentificationFeaturesGenerator.getMetrics()	Returns the metrics.

Methods in com.compomics.util.experiment.identification.features with parameters of type Metrics

Modifier and Type	Method	Description
double	IdentificationFeaturesGenerator.getNormalizedSpectrumCounting(long proteinMatchKey, Metrics metrics, UnitOfMeasurement unit, Double referenceMass, SpectrumCountingMethod method)	Returns the spectrum quantification metric of the protein match of interest using the preference settings normalized to the injected protein amount.
double	IdentificationFeaturesGenerator.getNormalizedSpectrumCounting(long proteinMatchKey, SpectrumCountingParameters spectrumCountingPreferences, Metrics metrics)	Returns the spectrum quantification metric of the protein match of interest using the preference settings normalized to the injected protein amount using the given spectrum counting preferences.

Constructors in com.compomics.util.experiment.identification.features with parameters of type Metrics

Modifier	Constructor	Description
	IdentificationFeaturesGenerator(Identification identification, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, SpectrumProvider spectrumProvider, Metrics metrics, SpectrumCountingParameters spectrumCountingPreferences)	Constructor.

Uses of Metrics in com.compomics.util.experiment.quantification.spectrumcounting

Methods in com.compomics.util.experiment.quantification.spectrumcounting with parameters of type Metrics

Modifier and Type	Method	Description
void	ScalingFactorsEstimators.estimateScalingFactors(Identification identification, Metrics metrics, SequenceProvider sequenceProvider, IdentificationFeaturesGenerator identificationFeaturesGenerator, WaitingHandler waitingHandler, ExceptionHandler exceptionHandler, ProcessingParameters processingParameters)	Estimates the scaling factors and stores them in the given metrics.