Uses of Class
eu.isas.peptideshaker.gui.PeptideShakerGUI

Packages that use PeptideShakerGUI

Package	Description
eu.isas.peptideshaker.gui	GUI dialogs and helper classes.
eu.isas.peptideshaker.gui.export	GUI export dialogs.
eu.isas.peptideshaker.gui.filtering	GUI filtering dialogs.
eu.isas.peptideshaker.gui.parameters	Preferences dialogs.
eu.isas.peptideshaker.gui.pride	GUI classes for exporting to PRIDE.
eu.isas.peptideshaker.gui.protein_inference	Protein inference dialogs.
eu.isas.peptideshaker.gui.start	Getting started dialog.
eu.isas.peptideshaker.gui.tablemodels	Table models.
eu.isas.peptideshaker.gui.tabpanels	Main GUI panels.

Uses of PeptideShakerGUI in eu.isas.peptideshaker.gui

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

Modifier	Constructor	Description
	FractionDetailsDialog(PeptideShakerGUI peptideShakerGUI, boolean modal)	Creates a new FractionDetailsDialog.
	JumpToPanel(PeptideShakerGUI peptideShakerGUI)	Creates a new JumpToPanel.
	ModificationSiteInferenceDialog(PeptideShakerGUI peptideShakerGUI, long peptideKey, com.compomics.util.experiment.biology.modifications.Modification modification)	Constructor.
	NewDialog(PeptideShakerGUI peptideShakerGui, boolean modal)	Creates a new open dialog.
	NewDialog(WelcomeDialog welcomeDialog, PeptideShakerGUI peptideShakerGui, boolean modal)	Creates a new open dialog.
	SaveDialog(PeptideShakerGUI peptideShakerGUI, boolean modal)	Create a new SaveDialog.
	WelcomeDialog(PeptideShakerGUI peptideShakerGUI, boolean showLowMemoryWarning, boolean showJavaVersionWarning, boolean modal)	Create a new WelcomeDialog.

Uses of PeptideShakerGUI in eu.isas.peptideshaker.gui.export

Methods in eu.isas.peptideshaker.gui.export that return PeptideShakerGUI

Modifier and Type	Method	Description
PeptideShakerGUI	FollowUpExportDialog.getPeptideShakerGUI()	Returns the references to the PeptideShakerGUI.

Constructors in eu.isas.peptideshaker.gui.export with parameters of type PeptideShakerGUI

Modifier	Constructor	Description
	FeaturesExportDialog(PeptideShakerGUI peptideShakerGUI)	Creates a new ExportPreferencesDialog.
	FollowUpExportDialog(PeptideShakerGUI peptideShakerGUI)	Creates a new FollowupPreferencesDialog.
	MethodsSectionDialog(PeptideShakerGUI peptideShakerGUI, boolean modal)	Creates a new MethodsSectionDialog.
	MzIdentMLExportDialog(PeptideShakerGUI peptideShakerGUI, boolean modal)	Create a new MzIdentMLExportDialog.

Uses of PeptideShakerGUI in eu.isas.peptideshaker.gui.filtering

Constructors in eu.isas.peptideshaker.gui.filtering with parameters of type PeptideShakerGUI

Modifier	Constructor	Description
	FiltersDialog(PeptideShakerGUI peptideShakerGUI)	Creates a new FiltersDialog.

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

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

Modifier	Constructor	Description
	ProjectDetailsDialog(PeptideShakerGUI peptideShakerGUI)	Creates a dialog to display the project properties.
	SpectrumColorsDialog(PeptideShakerGUI peptideShakerGUI)	Creates a new SpectrumColorsDialog.

Uses of PeptideShakerGUI in eu.isas.peptideshaker.gui.pride

Methods in eu.isas.peptideshaker.gui.pride that return PeptideShakerGUI

Modifier and Type	Method	Description
PeptideShakerGUI	PrideReshakeGUI.getPeptideShakerGUI()	Returns a reference to the main GUI.

Constructors in eu.isas.peptideshaker.gui.pride with parameters of type PeptideShakerGUI

Modifier	Constructor	Description
	DatabaseHelpDialog(PeptideShakerGUI peptideShakerGUI, com.compomics.util.experiment.io.biology.protein.FastaParameters fastaParameters, com.compomics.util.io.file.LastSelectedFolder lastSelectedFolder, boolean modal, String species)	Creates a new DatabaseHelpDialog.
	PrideReshakeGUI(PeptideShakerGUI peptideShakerGUI)	Creates a new PrideReShakeGUI frame.
	PrideReshakeGUI(PeptideShakerGUI peptideShakerGUI, String pxAccession, boolean privateData)	Creates a new PrideReShakeGUI frame.

Uses of PeptideShakerGUI in eu.isas.peptideshaker.gui.protein_inference

Constructors in eu.isas.peptideshaker.gui.protein_inference with parameters of type PeptideShakerGUI

Modifier	Constructor	Description
	ProteinInferenceDialog(PeptideShakerGUI peptideShakerGUI, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps, long matchKey, com.compomics.util.experiment.identification.Identification identification)	Creates new form ProteinInferenceDialog.
	ProteinInferencePeptideLevelDialog(PeptideShakerGUI peptideShakerGUI, boolean modal, long peptideMatchKey, Long proteinMatchKey, com.compomics.util.experiment.biology.genes.GeneMaps geneMaps)	Create a new ProteinInferencePeptideLevelDialog.

Uses of PeptideShakerGUI in eu.isas.peptideshaker.gui.start

Constructors in eu.isas.peptideshaker.gui.start with parameters of type PeptideShakerGUI

Modifier	Constructor	Description
	GettingStartedDialog(PeptideShakerGUI peptideShakerGUI, WelcomeDialog welcomeDialog, boolean modal)	Creates a new GettingStartedDialog.

Uses of PeptideShakerGUI in eu.isas.peptideshaker.gui.tablemodels

Methods in eu.isas.peptideshaker.gui.tablemodels with parameters of type PeptideShakerGUI

Modifier and Type	Method	Description
void	ProteinFractionTableModel.updateDataModel(PeptideShakerGUI peptideShakerGUI)	Update the data in the table model without having to reset the whole table model.

Constructors in eu.isas.peptideshaker.gui.tablemodels with parameters of type PeptideShakerGUI

Modifier	Constructor	Description
	ProteinFractionTableModel(PeptideShakerGUI peptideShakerGUI)	Constructor which sets a new table.

Uses of PeptideShakerGUI in eu.isas.peptideshaker.gui.tabpanels

Constructors in eu.isas.peptideshaker.gui.tabpanels with parameters of type PeptideShakerGUI

Modifier	Constructor	Description
	AnnotationPanel(PeptideShakerGUI peptideShakerGUI)	Creates a new AnnotationPanel.
	GOEAPanel(PeptideShakerGUI peptideShakerGUI)	Creates a new GOEAPanel.
	ModificationsPanel(PeptideShakerGUI peptideShakerGUI)	Creates a new Modifications tab.
	OverviewPanel(PeptideShakerGUI parent)	Creates a new OverviewPanel.
	ProteinFractionsPanel(PeptideShakerGUI peptideShakerGUI)	Creates a new ProteinFractionsPanel.
	ProteinStructurePanel(PeptideShakerGUI peptideShakerGUI)	Creates a new ProteinPanel.
	QCPanel(PeptideShakerGUI parent)	Creates a new QCPanel.
	SpectrumIdentificationPanel(PeptideShakerGUI peptideShakerGUI)	Create a new SpectrumIdentificationPanel.
	ValidationPanel(PeptideShakerGUI parent)	Create a new StatsPanel.