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

Packages that use ProteinInferenceParameters

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 ProteinInferenceParameters in com.compomics.util.gui.parameters.identification.advanced

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

Modifier and Type	Method	Description
ProteinInferenceParameters	ProteinInferenceParametersDialog.getProteinInferencePreferences()	Returns the protein inference preferences.

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

Modifier	Constructor	Description
	ProteinInferenceParametersDialog(Dialog owner, Frame parentFrame, ProteinInferenceParameters proteinInferencePreferences, Image normalIcon, Image waitingIcon, boolean editable)	Creates a new ProteinInferenceSettingsDialog with a dialog as owner.
	ProteinInferenceParametersDialog(Frame parentFrame, ProteinInferenceParameters proteinInferencePreferences, Image normalIcon, Image waitingIcon, boolean editable)	Creates a new ProteinInferenceSettingsDialog with a frame as owner.

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

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

Modifier and Type	Method	Description
ProteinInferenceParameters	IdentificationParameters.getProteinInferenceParameters()	Returns the protein inference parameters.

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

Modifier and Type	Method	Description
void	IdentificationParameters.setProteinInferenceParameters(ProteinInferenceParameters proteinInferenceParameters)	Sets the protein inference parameters.

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

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 ProteinInferenceParameters in com.compomics.util.parameters.identification.advanced

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

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