Deprecated API

Contents

• Deprecated Packages
• Deprecated Interfaces
• Deprecated Classes
• Deprecated Fields
• Deprecated Methods

Deprecated Packages

Package and 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 and 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.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.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.view.vizmap.gui.DefaultViewEditor
org.cytoscape.view.vizmap.gui.DefaultViewPanel
org.cytoscape.session.events.SessionLoadCancelledListener Use SessionLoadedListener instead.
org.cytoscape.work.swing.TaskStatusPanelFactory
org.cytoscape.view.vizmap.gui.VizMapGUI

Deprecated Classes

Class and 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 and Description
org.cytoscape.util.swing.FileUtil.LAST_DIRECTORY
org.cytoscape.application.CyVersion.VERSION_PROPERTY_NAME

Deprecated Methods

Method and Description
org.cytoscape.view.vizmap.gui.util.PropertySheetUtil.addBasicVisualProperty(VisualProperty<?>)
org.cytoscape.command.AvailableCommands.getArgValue(String, String, String)
org.cytoscape.application.swing.CyNetworkViewDesktopMgr.getBounds(CyNetworkView) This method has been deprecated in version 3.4.
org.cytoscape.view.vizmap.gui.DefaultViewEditor.getDefaultView(VisualStyle)
org.cytoscape.view.vizmap.gui.VizMapGUI.getDefaultViewEditor()
org.cytoscape.view.vizmap.gui.VizMapGUI.getDefaultViewPanel()
org.cytoscape.application.swing.CyNetworkViewDesktopMgr.getDesktopViewAreaSize() This method has been deprecated in version 3.4.
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.view.vizmap.gui.DefaultViewPanel.getRenderingEngine()
org.cytoscape.view.vizmap.gui.util.PropertySheetUtil.isAdvancedMode()
org.cytoscape.view.vizmap.gui.util.PropertySheetUtil.isBasic(VisualProperty<?>)
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.removeAnnotation() Use AnnotationManager#removeAnnotation() instead.
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.view.vizmap.gui.util.PropertySheetUtil.setMode(boolean)
org.cytoscape.view.vizmap.gui.DefaultViewEditor.showEditor(Component)