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

Packages that use GeneParameters

Package	Description
com.compomics.util.experiment.biology.genes	Classes related to genes.
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 GeneParameters in com.compomics.util.experiment.biology.genes

Methods in com.compomics.util.experiment.biology.genes with parameters of type GeneParameters

Modifier and Type	Method	Description
GeneMaps	ProteinGeneDetailsProvider.getGeneMaps(GeneParameters genePreferences, FastaSummary fastaSummary, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, WaitingHandler waitingHandler)	Returns the gene maps for the given proteins.

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

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

Modifier and Type	Method	Description
GeneParameters	BackgroundSpeciesDialog.getGeneParameters()	Returns the gene preferences.
GeneParameters	GeneParametersDialog.getGeneParameters()	Returns the gene parameters.

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

Modifier	Constructor	Description
	BackgroundSpeciesDialog(JDialog owner, Frame parentFrame, GeneParameters genePreferences, FastaSummary fastaSummary)	Creates a new GenePreferencesDialog with a dialog as owner.
	BackgroundSpeciesDialog(JFrame parentFrame, GeneParameters genePreferences, FastaSummary fastaSummary)	Creates a new GenePreferencesDialog with a frame as owner.
	GeneParametersDialog(JDialog owner, Frame parentFrame, GeneParameters genePreferences, SearchParameters searchParameters, boolean editable)	Creates a new GeneParametersDialog with a dialog as owner.
	GeneParametersDialog(JFrame parentFrame, GeneParameters genePreferences, SearchParameters searchParameters, boolean editable)	Creates a new GeneParametersDialog with a frame as owner.

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

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

Modifier and Type	Method	Description
GeneParameters	IdentificationParameters.getGeneParameters()	Returns the gene parameters.

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

Modifier and Type	Method	Description
void	IdentificationParameters.setGeneParameters(GeneParameters geneParameters)	Sets the gene parameters.

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

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

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

Modifier and Type	Method	Description
boolean	GeneParameters.equals(GeneParameters genePreferences)	Compares these preferences to other preferences.

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

Modifier	Constructor	Description
	GeneParameters(GeneParameters genePreferences)	Creates new gene preferences based on a GenePreferences object.