Uses of Class
com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters
Packages that use SpectrumCountingParameters
Package
Description
Classes for the generation of identification features.
Experiment classes related to spectrum counting.
Spectrum counting parameters.
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Uses of SpectrumCountingParameters in com.compomics.util.experiment.identification.features
Methods in com.compomics.util.experiment.identification.features with parameters of type SpectrumCountingParametersModifier and TypeMethodDescriptionstatic doubleIdentificationFeaturesGenerator.estimateSpectrumCounting(Identification identification, SequenceProvider sequenceProvider, long proteinMatchKey, SpectrumCountingParameters spectrumCountingPreferences, int maxPepLength, IdentificationParameters identificationParameters) Returns the spectrum counting index based on the project settings.doubleIdentificationFeaturesGenerator.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.voidIdentificationFeaturesGenerator.setSpectrumCountingPreferences(SpectrumCountingParameters spectrumCountingPreferences) Sets the spectrum counting preferences.Constructors in com.compomics.util.experiment.identification.features with parameters of type SpectrumCountingParametersModifierConstructorDescriptionIdentificationFeaturesGenerator(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 SpectrumCountingParametersModifierConstructorDescriptionScalingFactorsEstimators(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 SpectrumCountingParametersModifier and TypeMethodDescriptionbooleanSpectrumCountingParameters.isSameAs(SpectrumCountingParameters anotherSpectrumCountingPreferences) Compares two spectrum counting preferences.Constructors in com.compomics.util.parameters.quantification.spectrum_counting with parameters of type SpectrumCountingParametersModifierConstructorDescriptionSpectrumCountingParameters(SpectrumCountingParameters otherSpectrumCountingPreferences) Creates new preferences based on other spectrum counting preferences.