Uses of Interface
com.compomics.util.experiment.personalization.UrParameter

Packages that use UrParameter

Package	Description
com.compomics.util.experiment.identification.peptide_shaker	Experiment classes used in PeptideShaker calculations.
com.compomics.util.experiment.identification.spectrum_assumptions	Implementations of the SpectrumIdentificationAssumption.
com.compomics.util.experiment.identification.validation.percolator
com.compomics.util.experiment.mass_spectrometry.spectra	Experiment classes related to spectra.
com.compomics.util.experiment.personalization	Experiment customization classes.
com.compomics.util.experiment.refinement_parameters	Experiment classes related to specific parametrization of experiment objects.

Uses of UrParameter in com.compomics.util.experiment.identification.peptide_shaker

Classes in com.compomics.util.experiment.identification.peptide_shaker that implement UrParameter

Modifier and Type	Class	Description
class	PSModificationScores	This class contains the scores for the locations of the possible modifications.
class	PSParameter	PeptideShaker compomics utilities experiment customizable parameter.

Uses of UrParameter in com.compomics.util.experiment.identification.spectrum_assumptions

Classes in com.compomics.util.experiment.identification.spectrum_assumptions that implement UrParameter

Modifier and Type	Class	Description
class	PeptideAssumptionParameter	Parameter for storing additional non-mandatory peptide assumption information.

Uses of UrParameter in com.compomics.util.experiment.identification.validation.percolator

Classes in com.compomics.util.experiment.identification.validation.percolator that implement UrParameter

Modifier and Type	Class	Description
class	PercolatorFeaturesCache	This class serves as a cache for Percolator features.

Uses of UrParameter in com.compomics.util.experiment.mass_spectrometry.spectra

Classes in com.compomics.util.experiment.mass_spectrometry.spectra that implement UrParameter

Modifier and Type	Class	Description
class	PrecursorParameter	Parameter for storing additional non-mandatory precursor information.

Uses of UrParameter in com.compomics.util.experiment.personalization

Methods in com.compomics.util.experiment.personalization that return UrParameter

Modifier and Type	Method	Description
UrParameter	ExperimentObject.getUrParam(UrParameter parameter)	Returns the refinement parameter of the same type as the one provided.

Methods in com.compomics.util.experiment.personalization that return types with arguments of type UrParameter

Modifier and Type	Method	Description
HashMap<Long,UrParameter>	ExperimentObject.getUrParams()	Returns the user parameters map.

Methods in com.compomics.util.experiment.personalization with parameters of type UrParameter

Modifier and Type	Method	Description
void	ExperimentObject.addUrParam(UrParameter parameter)	Adds a user refinement parameter.
UrParameter	ExperimentObject.getUrParam(UrParameter parameter)	Returns the refinement parameter of the same type as the one provided.

Method parameters in com.compomics.util.experiment.personalization with type arguments of type UrParameter

Modifier and Type	Method	Description
void	ExperimentObject.setUrParams(HashMap<Long,UrParameter> urParams)	Sets the user parameters map.

Uses of UrParameter in com.compomics.util.experiment.refinement_parameters

Classes in com.compomics.util.experiment.refinement_parameters that implement UrParameter

Modifier and Type	Class	Description
class	PepnovoAssumptionDetails	This class contains pepnovo assumption details which are not contained in the tag assumption class which will be saved as additional parameter.