Deprecated API

Deprecated Classes

cytoscape.plugin.AbstractPlugin
This class relies on CyWindow, which has been deprecated. Instead, use CytoscapePlugin AbstractPlugin is the class that all Cytoscape plugins must subclass. The plugin should provide a one-argument constructor where the argument is an instance of CyWindow.

It is encouraged, but not mandatory, for plugins to override the describe method to state what the plugin does and how it should be used.

cytoscape.layout.SpringEmbeddedLayouter
Please avoid looking at or using this code -- this code is going away in the next Cytoscape release (the one after 2.1).

Deprecated Methods

cytoscape.view.CytoscapeDesktop.applyLayout(GraphView)

cytoscape.view.CytoscapeDesktop.applySelLayout()

cytoscape.view.CytoscapeDesktop.applyVizmapSettings()

cytoscape.CyNetwork.beginActivity(String)

cytoscape.Cytoscape.clearCytoscape()
WARNING: this should only be used under special circumstances.

cytoscape.CyNetwork.endActivity(String)

cytoscape.CyNetwork.forceClear(String)

cytoscape.CytoscapeObj.getCurrentDirectory()
As of Cytoscape 2.1, replaced by CytoscapeInit.getMRUD();

cytoscape.Cytoscape.getCytoscapeObj()

cytoscape.CyNetwork.getEdgeAttributes()

cytoscape.Cytoscape.getEdgeNetworkData()
This should not be used by any user-code

cytoscape.CyNetwork.getExpressionData()
@see{getNetworkData} Returns the expression data object associated with this network.

cytoscape.CyNetwork.getGraphPerspective()

cytoscape.view.CytoscapeDesktop.getMainFrame()

cytoscape.view.CytoscapeDesktop.getNetwork()

cytoscape.CyNetwork.getNodeAttributes()

cytoscape.Cytoscape.getNodeNetworkData()
This should not be used by any user-code

cytoscape.CyEdge.getSourceNode()

cytoscape.CyEdge.getTargetNode()

cytoscape.view.CytoscapeDesktop.getView()

cytoscape.CytoscapeObj.getViewThreshold()
As of Cytoscape 2.1, replaced by CytoscapeInit.getViewThreshold();

cytoscape.view.CytoscapeDesktop.getWindowTitle()

cytoscape.CyNetwork.isStateClear()

cytoscape.view.CytoscapeDesktop.redrawGraph()

cytoscape.view.CytoscapeDesktop.redrawGraph(boolean)

cytoscape.view.CytoscapeDesktop.redrawGraph(boolean, boolean)

cytoscape.view.CyMenus.refreshOperationsMenu()
This method is no longer needed now that we don't use the NO_OPERATIONS menu placeholder. This method does nothing.

cytoscape.CytoscapeObj.setCurrentDirectory(File)
As of Cytoscape 2.1, replaced by CytoscapeInit.getMRUD();

cytoscape.Cytoscape.setCurrentNetwork(String)

cytoscape.Cytoscape.setCurrentNetworkView(String)

cytoscape.CyNetwork.setExpressionData(ExpressionData)
Sets the expression data object associated with this network.

cytoscape.view.CytoscapeDesktop.setInteractivity(boolean)

cytoscape.CyNetwork.setNewGraphFrom(CyNetwork, boolean)

cytoscape.Cytoscape.setSpecies()
argh!...

cytoscape.CytoscapeObj.setViewThreshold(int)
As of Cytoscape 2.1, replaced by CytoscapeInit.setViewThreshold(int);

cytoscape.view.CytoscapeDesktop.setVisualMapperEnabled(boolean)

cytoscape.view.CytoscapeDesktop.setWindowTitle(String)

cytoscape.view.CytoscapeDesktop.showWindow()

cytoscape.view.CytoscapeDesktop.showWindow(int, int)

cytoscape.view.CytoscapeDesktop.switchToEditMode()

cytoscape.view.CytoscapeDesktop.switchToReadOnlyMode()

cytoscape.view.CytoscapeDesktop.toggleVisualMapperEnabled()