Uses of Class
eu.isas.peptideshaker.preferences.DisplayParameters

Packages that use DisplayParameters

Package	Description
eu.isas.peptideshaker.export	Exporting data from PeptideShaker.
eu.isas.peptideshaker.gui	GUI dialogs and helper classes.
eu.isas.peptideshaker.gui.parameters	Preferences dialogs.
eu.isas.peptideshaker.parameters	Parameter settings.
eu.isas.peptideshaker.utils	Various utilities classes.

Uses of DisplayParameters in eu.isas.peptideshaker.export

Methods in eu.isas.peptideshaker.export with parameters of type DisplayParameters

Modifier and Type

Method and Description

static void

PsdbExporter.saveAs(File destinationFile, com.compomics.util.waiting.WaitingHandler waitingHandler, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingParameters, ProjectDetails projectDetails, com.compomics.util.gui.filtering.FilterParameters filterParameters, com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, com.compomics.util.parameters.peptide_shaker.ProjectType projectType, com.compomics.util.experiment.identification.features.IdentificationFeaturesCache identificationFeaturesCache, boolean emptyCache, DisplayParameters displayParameters, File dbFolder) Saves the given data in a psdb file.

Uses of DisplayParameters in eu.isas.peptideshaker.gui

Methods in eu.isas.peptideshaker.gui that return DisplayParameters

Modifier and Type	Method and Description
DisplayParameters	PeptideShakerGUI.getDisplayParameters() Return the display parameters to use.

Methods in eu.isas.peptideshaker.gui with parameters of type DisplayParameters

Modifier and Type	Method and Description
void	PeptideShakerGUI.setDisplayParameters(DisplayParameters displayParameters) Sets the display parameters to use.

Uses of DisplayParameters in eu.isas.peptideshaker.gui.parameters

Methods in eu.isas.peptideshaker.gui.parameters that return DisplayParameters

Modifier and Type	Method and Description
DisplayParameters	ProjectParametersDialog.getDisplayParameters() Returns the display preferences.
DisplayParameters	DisplayPreferencesDialog.getDisplayPreferences() Returns the new display preferences as set by the user.

Constructors in eu.isas.peptideshaker.gui.parameters with parameters of type DisplayParameters

Constructor and Description
DisplayPreferencesDialog(Frame parentFrame, DisplayParameters displayPreferences) Constructor.
ProjectParametersDialog(Frame parentFrame, Dialog owner, com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingPreferences, DisplayParameters displayPreferences) Creates a new PreferencesDialog with a dialog as owner.
ProjectParametersDialog(Frame parentFrame, com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingPreferences, DisplayParameters displayPreferences) Creates a new PreferencesDialog with a frame as owner.

Uses of DisplayParameters in eu.isas.peptideshaker.parameters

Methods in eu.isas.peptideshaker.parameters that return DisplayParameters

Modifier and Type	Method and Description
DisplayParameters	PeptideShakerParameters.getDisplayParameters() Returns the GUI display parameters.

Constructors in eu.isas.peptideshaker.parameters with parameters of type DisplayParameters

Constructor and Description

PeptideShakerParameters(com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters spectrumCountingPreferences, ProjectDetails projectDetails, com.compomics.util.gui.filtering.FilterParameters filterPreferences, DisplayParameters displayPreferences, com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, com.compomics.util.parameters.peptide_shaker.ProjectType projectType, com.compomics.util.experiment.identification.features.IdentificationFeaturesCache identificationFeaturesCache) Constructor for a PeptideShaker Settings class.

Uses of DisplayParameters in eu.isas.peptideshaker.utils

Fields in eu.isas.peptideshaker.utils declared as DisplayParameters

Modifier and Type	Field and Description
protected DisplayParameters	PsdbParent.displayParameters The display parameters.

Methods in eu.isas.peptideshaker.utils that return DisplayParameters

Modifier and Type	Method and Description
DisplayParameters	PsdbParent.getDisplayParameters() Returns the display preferences.

Methods in eu.isas.peptideshaker.utils with parameters of type DisplayParameters

Modifier and Type	Method and Description
void	PsdbParent.setDisplayParameters(DisplayParameters displayPreferences) Sets the display preferences.

Constructors in eu.isas.peptideshaker.utils with parameters of type DisplayParameters

Constructor and Description
DisplayFeaturesGenerator(com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, DisplayParameters displayParameters, com.compomics.util.experiment.io.biology.protein.SequenceProvider sequenceProvider, com.compomics.util.experiment.io.biology.protein.ProteinDetailsProvider proteinDetailsProvider) Constructor