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.data.attr.util.ExtensibleMultiHashMapModel
Use MultiHashMapFactory instead.

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.deleteEdgeAttribute(String)
Use CyAttributes directly. This method will be removed in September, 2006.

cytoscape.CyNetwork.deleteNodeAttribute(String)
Use CyAttributes directly. This method will be removed in September, 2006.

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()
Use Cytoscape.getEdgeAttributes() instead. This method will be removed in September, 2006.

cytoscape.CyNetwork.getEdgeAttributesList()
Use CyAttributes directly. This method will be removed in September, 2006.

cytoscape.Cytoscape.getEdgeAttributesList()
Use CyAttributes directly. This method will be removed in September, 2006.

cytoscape.CyNetwork.getEdgeAttributeValue(Edge, String)
Use CyAttributes directly. This method will be removed in September, 2006.

cytoscape.Cytoscape.getEdgeAttributeValue(Edge, String)
Use CyAttributes directly. This method will be removed in September, 2006.

cytoscape.CyNetwork.getEdgeAttributeValue(int, String)
Use CyAttributes directly. This method will be removed in September, 2006.

cytoscape.Cytoscape.getEdgeNetworkData()
Use Cytoscape.getEdgeAttributes() instead. This method will be removed in September, 2006.

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()
Use Cytoscape.getNodeAttributes() instead. This method will be removed in September, 2006.

cytoscape.CyNetwork.getNodeAttributesList()
Use CyAttributes directly. This method will be removed in September, 2006.

cytoscape.Cytoscape.getNodeAttributesList()
Use CyAttributes directly. This method will be removed in September, 2006.

cytoscape.CyNetwork.getNodeAttributesList(Edge[])
Use CyAttributes directly. This method will be removed in September, 2006.

cytoscape.Cytoscape.getNodeAttributesList(Edge[])
Use CyAttributes directly. This method will be removed in September, 2006.

cytoscape.CyNetwork.getNodeAttributesList(Node[])
Use CyAttributes directly. This method will be removed in September, 2006.

cytoscape.Cytoscape.getNodeAttributesList(Node[])
Use CyAttributes directly. This method will be removed in September, 2006.

cytoscape.CyNetwork.getNodeAttributeValue(int, String)
Use CyAttributes directly. This method will be removed in September, 2006.

cytoscape.CyNetwork.getNodeAttributeValue(Node, String)
Use CyAttributes directly. This method will be removed in September, 2006.

cytoscape.Cytoscape.getNodeAttributeValue(Node, String)
Use CyAttributes directly. This method will be removed in September, 2006.

cytoscape.Cytoscape.getNodeNetworkData()
Use Cytoscape.getNodeAttributes() instead. This method will be removed in September, 2006.

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.setEdgeAttributeValue(Edge, String, Object)
Use CyAttributes directly. This method will be removed in September, 2006.

cytoscape.Cytoscape.setEdgeAttributeValue(Edge, String, Object)
Use CyAttributes directly. This method will be removed in September, 2006.

cytoscape.CyNetwork.setEdgeAttributeValue(int, String, Object)
Use CyAttributes directly. This method will be removed in September, 2006.

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

cytoscape.view.CytoscapeDesktop.setInteractivity(boolean)

cytoscape.CyNetwork.setNewGraphFrom(CyNetwork, boolean)

cytoscape.CyNetwork.setNodeAttributeValue(int, String, Object)
Use CyAttributes directly. This method will be removed in September, 2006.

cytoscape.CyNetwork.setNodeAttributeValue(Node, String, Object)
Use CyAttributes directly. This method will be removed in September, 2006.

cytoscape.Cytoscape.setNodeAttributeValue(Node, String, Object)
Use CyAttributes directly. This method will be removed in September, 2006.

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()