Deprecated API

Contents

• Packages
• Interfaces
• Classes
• Fields
• Methods
• Constructors

Deprecated Packages

Package	Description
org.cytoscape.app	(As of Cytoscape 3.7) Support for simple apps will be removed in a future version of Cytoscape, please provide an OSGi bundle app instead.
org.cytoscape.app.swing	(As of Cytoscape 3.7) Support for simple apps will be removed in a future version of Cytoscape, please provide an OSGi bundle app instead.

Deprecated Interfaces

Interface	Description
org.cytoscape.app.CyAppAdapter	(As of Cytoscape 3.7) Support for simple apps will be removed in a future version of Cytoscape, please provide an OSGi bundle app instead.
org.cytoscape.app.swing.CySwingAppAdapter	(As of Cytoscape 3.7) Support for simple apps will be removed in a future version of Cytoscape, please provide an OSGi bundle app instead.
org.cytoscape.application.swing.CyHelpBroker	JavaHelp no longer used in Cytoscape as of 3.4. This interface provides access to the Cytoscape Help Broker and Help Set for managing the JavaHelp system.
org.cytoscape.session.events.SessionLoadCancelledListener	Use SessionLoadedListener instead.
org.cytoscape.view.vizmap.gui.DefaultViewEditor
org.cytoscape.view.vizmap.gui.DefaultViewPanel
org.cytoscape.view.vizmap.gui.VizMapGUI
org.cytoscape.work.swing.TaskStatusPanelFactory

Deprecated Classes

Class	Description
org.cytoscape.app.AbstractCyApp	(As of Cytoscape 3.7) Support for simple apps will be removed in a future version of Cytoscape, please provide an OSGi bundle app instead.
org.cytoscape.app.swing.AbstractCySwingApp	(As of Cytoscape 3.7) Support for simple apps will be removed in a future version of Cytoscape, please provide an OSGi bundle app instead.
org.cytoscape.session.events.SessionLoadCancelledEvent	Just listen to SessionLoadedEvent instead now.

Deprecated Fields

Field	Description
org.cytoscape.application.CyVersion.VERSION_PROPERTY_NAME
org.cytoscape.util.swing.FileUtil.LAST_DIRECTORY
org.cytoscape.view.presentation.annotations.Annotation.ZOOM	The zoom should remain at the default of 1.0.

Deprecated Methods

Method	Description
org.cytoscape.application.events.CyShutdownEvent.abortShutdown(String)
org.cytoscape.application.events.CyShutdownEvent.abortShutdownReason()
org.cytoscape.application.events.CyShutdownEvent.actuallyShutdown()
org.cytoscape.application.events.CyShutdownEvent.forceShutdown()
org.cytoscape.application.swing.CyHelpBroker.getHelpBroker()	JavaHelp no longer used in Cytoscape as of 3.4. Returns the HelpBroker.
org.cytoscape.application.swing.CyHelpBroker.getHelpSet()	JavaHelp no longer used in Cytoscape as of 3.4. Returns the HelpSet.
org.cytoscape.application.swing.CyNetworkViewDesktopMgr.getBounds(CyNetworkView)	This method has been deprecated in version 3.4.
org.cytoscape.application.swing.CyNetworkViewDesktopMgr.getDesktopViewAreaSize()	This method has been deprecated in version 3.4.
org.cytoscape.application.swing.CyNetworkViewDesktopMgr.setBounds(CyNetworkView, Rectangle)	This method has been deprecated in version 3.4 and does not do anything anymore.
org.cytoscape.command.AvailableCommands.getArgValue(String, String, String)
org.cytoscape.equations.EquationParser.registerFunction(Function)	Functions registered using this method will work, but will not update properly if the containing bundle is updated. To register a Function, please use CyActivator or CyServiceRegistrar's registerService method to register as a service so updates can be handled properly.
org.cytoscape.view.presentation.annotations.Annotation.getSpecificZoom()
org.cytoscape.view.presentation.annotations.Annotation.getZoom()
org.cytoscape.view.presentation.annotations.Annotation.removeAnnotation()	Use AnnotationManager#removeAnnotation() instead.
org.cytoscape.view.presentation.annotations.Annotation.setSpecificZoom(double)
org.cytoscape.view.presentation.annotations.Annotation.setZoom(double)
org.cytoscape.view.presentation.annotations.ArrowAnnotation.setTarget(CyNode)	Use ArrowAnnotation.setTarget(View) instead.
org.cytoscape.view.presentation.RenderingEngine.getProperties()	Use RenderingEngine.printCanvas(Graphics, Map) instead.
org.cytoscape.view.vizmap.gui.DefaultViewEditor.getDefaultView(VisualStyle)
org.cytoscape.view.vizmap.gui.DefaultViewEditor.showEditor(Component)
org.cytoscape.view.vizmap.gui.DefaultViewPanel.getRenderingEngine()
org.cytoscape.view.vizmap.gui.util.PropertySheetUtil.addBasicVisualProperty(VisualProperty<?>)
org.cytoscape.view.vizmap.gui.util.PropertySheetUtil.isAdvancedMode()
org.cytoscape.view.vizmap.gui.util.PropertySheetUtil.isBasic(VisualProperty<?>)
org.cytoscape.view.vizmap.gui.util.PropertySheetUtil.setMode(boolean)
org.cytoscape.view.vizmap.gui.VizMapGUI.getDefaultViewEditor()
org.cytoscape.view.vizmap.gui.VizMapGUI.getDefaultViewPanel()

Deprecated Constructors

Constructor	Description
org.cytoscape.model.events.ColumnCreatedEvent(CyTable, String)
org.cytoscape.model.events.ColumnDeletedEvent(CyTable, String)