Uses of Class
com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters

Packages that use SpectrumCountingParameters

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.
com.compomics.util.parameters.quantification.spectrum_counting	Spectrum counting parameters.

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

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

Modifier and Type	Method	Description
static double	IdentificationFeaturesGenerator.estimateSpectrumCounting(Identification identification, SequenceProvider sequenceProvider, long proteinMatchKey, SpectrumCountingParameters spectrumCountingPreferences, int maxPepLength, IdentificationParameters identificationParameters)	Returns the spectrum counting index based on the project settings.
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.
void	IdentificationFeaturesGenerator.setSpectrumCountingPreferences(SpectrumCountingParameters spectrumCountingPreferences)	Sets the spectrum counting preferences.

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

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

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

Constructors in com.compomics.util.experiment.quantification.spectrumcounting with parameters of type SpectrumCountingParameters

Modifier	Constructor	Description
	ScalingFactorsEstimators(SpectrumCountingParameters spectrumCountingParameters)	Constructor.

Uses of SpectrumCountingParameters in com.compomics.util.parameters.quantification.spectrum_counting

Methods in com.compomics.util.parameters.quantification.spectrum_counting with parameters of type SpectrumCountingParameters

Modifier and Type	Method	Description
boolean	SpectrumCountingParameters.isSameAs(SpectrumCountingParameters anotherSpectrumCountingPreferences)	Compares two spectrum counting preferences.

Constructors in com.compomics.util.parameters.quantification.spectrum_counting with parameters of type SpectrumCountingParameters

Modifier	Constructor	Description
	SpectrumCountingParameters(SpectrumCountingParameters otherSpectrumCountingPreferences)	Creates new preferences based on other spectrum counting preferences.