Uses of Class
com.compomics.util.parameters.identification.advanced.PsmScoringParameters

Packages that use PsmScoringParameters

Package	Description
com.compomics.util.gui.parameters.identification.advanced	Dialogs for advanced identification parameters.
com.compomics.util.parameters.identification	Identification parameters.
com.compomics.util.parameters.identification.advanced	Advanced Identification parameters.

Uses of PsmScoringParameters in com.compomics.util.gui.parameters.identification.advanced

Methods in com.compomics.util.gui.parameters.identification.advanced that return PsmScoringParameters

Modifier and Type	Method	Description
PsmScoringParameters	PsmScoringParametersDialog.getPsmScoringPreferences()	Returns the PSM scoring preferences as set by the user.

Constructors in com.compomics.util.gui.parameters.identification.advanced with parameters of type PsmScoringParameters

Modifier	Constructor	Description
	PsmScoringParametersDialog(Dialog owner, Frame parentFrame, PsmScoringParameters psmScoringPreferences, boolean editable)	Creates a new PsmScoringSettingsDialog with a dialog as owner.
	PsmScoringParametersDialog(Frame parentFrame, PsmScoringParameters psmScoringPreferences, boolean editable)	Creates a new PsmScoringSettingsDialog with a frame as owner.

Uses of PsmScoringParameters in com.compomics.util.parameters.identification

Methods in com.compomics.util.parameters.identification that return PsmScoringParameters

Modifier and Type	Method	Description
PsmScoringParameters	IdentificationParameters.getPsmScoringParameters()	Returns the scoring parameters used when scoring PSMs.

Methods in com.compomics.util.parameters.identification with parameters of type PsmScoringParameters

Modifier and Type	Method	Description
void	IdentificationParameters.setPsmScoringParameters(PsmScoringParameters psmScoringParameters)	Sets the scoring preferences used when scoring PSMs.

Constructors in com.compomics.util.parameters.identification with parameters of type PsmScoringParameters

Modifier	Constructor	Description
	IdentificationParameters(String name, String description, SearchParameters searchParameters, AnnotationParameters annotationParameters, SequenceMatchingParameters sequenceMatchingParameters, PeptideVariantsParameters peptideVariantsParameters, GeneParameters geneParameters, PsmScoringParameters psmScoringParameters, PeptideAssumptionFilter peptideAssumptionFilter, ModificationLocalizationParameters ModificationLocalizationParameters, ProteinInferenceParameters proteinInferenceParameters, IdMatchValidationParameters idValidationParameters, FractionParameters fractionParameters, FastaParameters fastaParameters)	Constructor.

Uses of PsmScoringParameters in com.compomics.util.parameters.identification.advanced

Methods in com.compomics.util.parameters.identification.advanced with parameters of type PsmScoringParameters

Modifier and Type	Method	Description
boolean	PsmScoringParameters.equals(PsmScoringParameters otherPsmScoringPreferences)	Returns true if the objects have identical settings.