Deprecated API

Contents

• Deprecated Interfaces
• Deprecated Classes
• Deprecated Fields
• Deprecated Methods
• Deprecated Constructors

Deprecated Interfaces

cytoscape.layout.LayoutAlgorithm
Use CyLayoutAlgorithm instead. Will be removed June, 2008

Deprecated Classes

cytoscape.actions.AnimatedLayoutAction
Not apparently used. Shout if you are. Will be removed 5/2008.

cytoscape.actions.BackgroundColorAction
Use vizmapper gui to edit background color. Will be removed 5/2008

cytoscape.actions.BirdsEyeViewAction
This class is no longer used since the BirdsEyeView is now always part of the NetworkPanel. BirdsEyeView creation and event handling is done by the BirdsEyeViewHandler and initialized in This class will be removed 5/2008.

cytoscape.actions.CheckBoxFileChooser
This isn't apparently used anywhere. If you are using it, let us know! If you need a file use FileUtil.getFile(). Will be removed 5/2008.

cytoscape.actions.ExpFileChooser
Not apparently used anywhere. Shout if you are. Will be removed 5/2008.

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

cytoscape.visual.parsers.ParserFactory
Use VisualPropertyType.getValueParser() instead. Will be removed 5/2008.

cytoscape.dialogs.preferences.PluginsTableModel
This class is no longer used in cytoscape. If you are using it, let us know and we'll figure something out. Otherwise, this will be removed December 2007.

Deprecated Fields

cytoscape.plugin.InstallablePlugin.MATCH_JAR_REGEXP
This was only ever used internally, so now it is package protected and part of JarUtil. Use that one as an alternative. Will be removed Jan 2010.

Deprecated Methods

cytoscape.view.CytoscapeDesktop.addEdit(UndoableEdit)
Use CyUndo.getUndoableEditSupport().postEdit(edit) instead. Will be removed March 2008.

cytoscape.visual.VisualProperty.applyToEdgeView(EdgeView, Object)
Use other the applyToNodeView method with the VisualPropertyDependency arg as null. Will be removed Jan 2011.

cytoscape.visual.VisualProperty.applyToNodeView(NodeView, Object)
Use other the applyToNodeView method with the VisualPropertyDependency arg as null. Will be removed Jan 2011.

cytoscape.util.intr.MinIntHeap.copyInto(int[], int)
Use elements() instead.

cytoscape.util.intr.MinIntHeap.copyIntoReverseOrder(int[], int)
Use orderedElements(boolean) or deleteMin() instead.

giny.model.RootGraph.createEdges(int[], int[], boolean)
Use createEdge(int, int, boolean) instead.

giny.model.GraphPerspective.createGraphPerspective(int[], int[])
Use RootGraph.createGraphPerspective(int[], int[]) instead.

giny.model.GraphPerspective.createGraphPerspective(Node[], Edge[])
Use RootGraph.createGraphPerspective(int[], int[]) instead.

giny.model.RootGraph.createNodes(int)
Use createNode() instead.

cytoscape.actions.DestroyNetworkAction.destroyCurrentNetwork()
Use Cytoscape.destroyNetwork(Cytoscape.getCurrentNetwork()) instead. Will be gone 11/2008.

cytoscape.actions.DestroyNetworkViewAction.destroyViewFromCurrentNetwork()
Use Cytoscape.destroyNetworkView() instead. Will go 11/2008.

giny.model.RootGraph.edgeExists(int, int)
Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead; if you decide to use this method anyways: this method returns true if and only if either 1) there exists a directed edge E in this RootGraph such that from_node_index is E's source node's index and to_node_index is E's target node's index or 2) there exists an undirected edge E in this RootGraph such that E's endpoint nodes have indices from_node_index and to_node_index.

giny.model.RootGraph.edgeExists(Node, Node)
Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead; if you decide to use this method anyways: this method returns true if and only if either 1) there exists a directed edge E in this RootGraph such that the from node specified is E's source node and the target node specified is E's target node or 2) there exists an undirected edge E in this RootGraph such that E's endpoints are the from and to nodes specified.

giny.model.RootGraph.edgeMetaChildrenList(int)
Use getEdgeMetaChildIndicesArray(int) instead.

giny.model.RootGraph.edgeMetaChildrenList(Node)
Use getEdgeMetaChildIndicesArray(int) instead.

giny.model.RootGraph.edgeMetaParentsList(int)
Use getEdgeMetaParentIndicesArray(int) instead.

giny.model.RootGraph.edgesList(int, int, boolean)
Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead.

giny.model.GraphPerspective.edgesList(int, int, boolean)
Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead.

giny.model.RootGraph.edgesList(Node, Node)
Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead.

giny.model.RootGraph.ensureCapacity(int, int)
Please don't call this silly method; implementors: I suggest creating an easter egg and having it take effect when this method is called.

giny.model.GraphPerspective.getAdjacentEdgesList(Node, boolean, boolean, boolean)
Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead.

cytoscape.data.CyAttributes.getAttributeList(String, String)
Use getListAttribute() instead. Will be removed 11/2007.

cytoscape.data.CyAttributes.getAttributeMap(String, String)
Use getMapAttribute() instead. Will be removed 11/2007.

cytoscape.CyNetwork.getClientData(String)
Use CyAttributes directly. This method will be removed in May, 2007.

cytoscape.giny.FingCyNetwork.getClientData(String)
Get Some client data

cytoscape.CyNetwork.getClientDataNames()
Use CyAttributes directly. This method will be removed in May, 2007.

cytoscape.giny.FingCyNetwork.getClientDataNames()
Get a list of all currently available ClientData objects

giny.model.RootGraph.getConnectingNodeIndicesArray(int[])
Use getEdgeSourceIndex(int) and getEdgeTargetIndex(int) instead, or use createGraphPerspective(int[], int[]).

giny.model.GraphPerspective.getConnectingNodeIndicesArray(int[])
Use getEdgeSourceIndex(int) and getEdgeTargetIndex(int) instead.

cytoscape.view.CyMenus.getCytoPanelMenu()
Will be removed April 2008. Cytopanels no longer have a separate menu (they're in View).

giny.model.RootGraph.getEdgeCount(int, int, boolean)
Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead.

giny.model.RootGraph.getEdgeCount(Node, Node, boolean)
Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead.

giny.model.GraphPerspective.getEdgeIndex(int)
Use getRootGraphEdgeIndex(int), whose functionality is identical.

giny.model.RootGraph.getEdgeIndicesArray(int, int, boolean)
Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead.

giny.model.GraphPerspective.getEdgeIndicesArray(int, int, boolean)
Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead.

giny.model.RootGraph.getEdgeIndicesArray(int, int, boolean, boolean)
Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead.

giny.model.GraphPerspective.getEdgeIndicesArray(int, int, boolean, boolean)
Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead.

giny.model.Node.getGraphPerspective()
Don't use this method because the behavior of the returned GraphPerspective with respect to changing meta-children of this Node is ill-defined; use RootGraph.getNodeMetaChildIndicesArray(int) and RootGraph.getEdgeMetaChildIndicesArray(int) instead.

cytoscape.view.CytoscapeDesktop.getHelpBroker()
Will be removed April 2008. Use CyHelpBroker.getHelpBroker() instead.

cytoscape.view.CytoscapeDesktop.getHelpSet()
Will be removed April 2008. Use CyHelpBroker.getHelpSet() instead.

giny.model.GraphPerspectiveChangeEvent.getHiddenEdges()
Use getHiddenEdgeIndices() instead; the edges returned by this method may have undefined state.

giny.model.GraphPerspectiveChangeEvent.getHiddenNodes()
Use getHiddenNodeIndices() instead; the nodes returned by this method may have undefined state.

cytoscape.visual.mappings.MappingType.getMappingType(String)
Will be removed 5/2008

giny.model.GraphPerspective.getNodeIndex(int)
Use getRootGraphNodeIndex(int), whose functionality is identical.

cytoscape.visual.NodeAppearanceCalculator.getNodeSizeLocked()
Use VisualStyle.getDependency().check(VisualPropertyDependency.Definition.NODE_SIZE_LOCKED) instead. Will be removed Jan 2011.

cytoscape.visual.NodeAppearance.getNodeSizeLocked()
Use VisualStyle.getDependency().check(VisualPropertyDependency.Definition.NODE_SIZE_LOCKED) instead. Will be removed Jan 2011.

cytoscape.visual.parsers.ParserFactory.getParser(Class)
Use VisualPropertyType.getValueParser() instead. Will be removed 5/2008.

cytoscape.visual.parsers.ParserFactory.getParser(Object)
Use VisualPropertyType.getValueParser() instead. Will be removed 5/2008.

giny.model.RootGraphChangeEvent.getRemovedEdges()
Use getRemovedEdgeIndices() instead; the edges returned by this method may have undefined state.

giny.model.RootGraphChangeEvent.getRemovedNodes()
Use getRemovedNodeIndices() instead; the nodes returned by this method may have undefined state.

giny.model.GraphPerspectiveChangeEvent.getSelectedEdgeIndices()
Nowhere in GraphPerspective is there functionality that specifies edge selection logic.

giny.model.GraphPerspectiveChangeEvent.getSelectedEdges()
Nowhere in GraphPerspective is there functionality that specifies edge selection logic.

giny.model.GraphPerspectiveChangeEvent.getSelectedNodeIndices()
Nowhere in GraphPerspective is there functionality that specifies node selection logic.

giny.model.GraphPerspectiveChangeEvent.getSelectedNodes()
Nowhere in GraphPerspective is there functionality that specifies node selection logic.

cytoscape.view.NetworkViewManager.getTabbedPane()
Tabbed view is no longer used. Will be removed Aug 2008.

giny.model.GraphPerspectiveChangeEvent.getUnselectedEdgeIndices()
Nowhere in GraphPerspective is there functionality that specifies edge un-selection logic.

giny.model.GraphPerspectiveChangeEvent.getUnselectedEdges()
Nowhere in GraphPerspective is there functionality that specifies edge un-selection logic.

giny.model.GraphPerspectiveChangeEvent.getUnselectedNodeIndices()
Nowhere in GraphPerspective is there functionality that specifies node un-selection logic.

giny.model.GraphPerspectiveChangeEvent.getUnselectedNodes()
Nowhere in GraphPerspective is there functionality that specifies node un-selection logic.

cytoscape.view.CytoscapeDesktop.getViewType()
View type is no longer used, so just don't use this method. Will be gone August 2008.

giny.model.GraphPerspective.hideEdges(List)
Use hideEdge(Edge) or hideEdges(int[]) instead.

giny.model.GraphPerspective.hideNodes(List)
Use hideNode(Node) or hideNodes(int[]) instead.

cytoscape.view.CyMenus.initCytoPanelMenus()
Will be removed April 2008. Cytopanels are initialized in the Display* actions. Do not use.

giny.model.GraphPerspectiveChangeEvent.isEdgesSelectedType()
Nowhere in GraphPerspective is there functionality that specifies edge selection logic.

giny.model.GraphPerspectiveChangeEvent.isEdgesUnselectedType()
Nowhere in GraphPerspective is there functionality that specifies edge un-selection logic.

giny.model.RootGraph.isNeighbor(int, int)
Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead; if you decide to use this method anyways, please note that the definition of "node neighbor" is such: Node A is a "node neighbor" of node B if and only if there exists an edge [directed or undirected] E such that A is E's target and B is E's source, or A is E's source and B is E's target; this method then returns true if and only if node at index a_node_index is a "node neighbor" of node at index another_node_index in this RootGraph.

giny.model.RootGraph.isNeighbor(Node, Node)
Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead; if you decide to use this method anyways, please note that the definition of "node neighbor" is such: Node A is a "node neighbor" of node B if and only if there exists an edge [directed or undirected] E such that A is E's target and B is E's source, or A is E's source and B is E's target; this method then returns true if and only if a_node is a "node neighbor" of another_node in this RootGraph.

giny.model.GraphPerspectiveChangeEvent.isNodesSelectedType()
Nowhere in GraphPerspective is there functionality that specifies node selection logic.

giny.model.GraphPerspectiveChangeEvent.isNodesUnselectedType()
Nowhere in GraphPerspective is there functionality that specifies node un-selection logic.

cytoscape.data.readers.InteractionsReader.layout(CyNetworkView)
Use getLayoutAlgorithm() instead. Gone 5/2008.

cytoscape.visual.CalculatorCatalogFactory.loadCalculatorCatalog(String)
The vmName parameter is no longer used - just use loadCalculatorCatalog(). Will be removed 10/06.

giny.model.RootGraph.metaParentsList(Edge)
Use getEdgeMetaParentIndicesArray(int) instead.

giny.model.RootGraph.metaParentsList(Node)
Use getNodeMetaParentIndicesArray(int) instead.

giny.model.RootGraph.neighborsList(Node)
Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead; if you decide to use this method anyways, please note that the definition of "node neighbor" is such: Node A is a "node neighbor" of node B if and only if there exists an edge [directed or undirected] E such that A is E's target and B is E's source, or A is E's source and B is E's target; this method then returns a non-repeating list of all nodes N in this RootGraph such that N is a "node neighbor" of node, the input parameter.

giny.model.RootGraph.nodeMetaChildrenList(Node)
Use getNodeMetaChildIndicesArray(int) instead.

giny.model.RootGraph.nodeMetaParentsList(int)
Use getNodeMetaParentIndicesArray(int) instead.

cytoscape.view.CytoscapeDesktop.parseViewType(String)
View types are no longer support so stop using this. Will be removed August 2008.

cytoscape.CyNetwork.putClientData(String, Object)
Use CyAttributes directly. This method will be removed in May, 2007.

cytoscape.giny.FingCyNetwork.putClientData(String, Object)
Networks can support client data.

cytoscape.data.readers.InteractionsReader.read(boolean)
Will be removed 5/2008

cytoscape.util.ZipUtil.readFile(String, String)

giny.model.RootGraph.removeEdges(int[])
Use removeEdge(int) instead.

giny.model.RootGraph.removeEdges(List)
Use removeEdge(Edge) or removeEdges(int[]) instead.

giny.model.RootGraph.removeNodes(int[])
Use removeNode(int) instead.

giny.model.RootGraph.removeNodes(List)
Use removeNode(Node) or removeNodes(int[]) instead.

giny.model.GraphPerspective.restoreEdges(List)
Use restoreEdges(int[]) instead.

giny.model.GraphPerspective.restoreNodes(int[], boolean)
Use restoreNodes(int[]) and restoreEdges(int[]) instead; to get edges incident to specified nodes, use RootGraph.getConnectingEdgeIndicesArray(int[]).

giny.model.GraphPerspective.restoreNodes(List)
Use restoreNode(Node) restoreNodes(int[]) instead.

giny.model.GraphPerspective.restoreNodes(List, boolean)
Use restoreNodes(int[]) and restoreEdges(int[]) instead; to get edges incident to specified nodes, use RootGraph.getConnectingEdgeIndicesArray(int[]).

cytoscape.data.CyAttributes.setAttributeList(String, String, List)
Use setListAttribute() instead. Will be removed 11/2007.

cytoscape.data.CyAttributes.setAttributeMap(String, String, Map)
Use setMapAttribute() instead. Will be removed 11/2007.

giny.model.Node.setGraphPerspective(GraphPerspective)
Don't use this method because the behavior of the input GraphPerspective with respect to changing meta-children of this Node is ill-defined; use RootGraph.addNodeMetaChild(int, int) and RootGraph.addEdgeMetaChild(int, int) instead.

cytoscape.visual.NodeAppearanceCalculator.setNodeSizeLocked(boolean)
Use VisualStyle.getDependency().set(VisualPropertyDependency.Definition.NODE_SIZE_LOCKED,b) instead. Will be removed Jan 2011.

cytoscape.visual.NodeAppearance.setNodeSizeLocked(boolean)
Use VisualStyle.getDependency().set(VisualPropertyDependency.Definition.NODE_SIZE_LOCKED,b) instead. Will be removed Jan 2011.

cytoscape.view.CyMenus.setNodesRequiredItemsEnabled()
Will be removed April 2008. Item state is now handled by Actions directly. Don't use this.

cytoscape.view.CyMenus.setOverviewEnabled(boolean)
Will be removed April 2008. Item state is now handled by Actions directly. Don't use this.

cytoscape.view.CyNetworkView.setSelected(CyEdge[])
this method is not working, use CyNetwork.setSelectedEdgeState(Collection, boolean)

cytoscape.view.CyNetworkView.setSelected(CyNode[])
this method is not working, use Cytoscape.CyNetwork#setSelectedNodeState(Collection, boolean)

cytoscape.view.CyNetworkView.setSelected(EdgeView[])
this method is not working, use CyNetwork.setSelectedEdgeState(Collection, boolean)

cytoscape.view.CyNetworkView.setSelected(NodeView[])
this method is not working, use Cytoscape.CyNetwork#setSelectedNodeState(Collection, boolean)

cytoscape.view.CyMenus.setVisualMapperItemsEnabled(boolean)
Will be removed April 2008. Item state is now handled by Actions directly. Don't use this.

cytoscape.view.NetworkViewManager.stateChanged(ChangeEvent)
Will no longer support ChangeListener. Will be removed August 2008.

cytoscape.dialogs.preferences.PreferenceValueDialog.validatedPluginData(Component, String)
no longer used by anyting. Will leave this world Dec 2007.

cytoscape.view.NetworkViewManager.windowGainedFocus(WindowEvent)
Will no longer support WindowFocusListener. Will be removed August 2008.

cytoscape.view.NetworkViewManager.windowLostFocus(WindowEvent)
Will no longer support WindowFocusListener. Will be removed August 2008.

Deprecated Constructors

cytoscape.visual.EdgeAppearanceCalculator()
Use VisualStyle.getEdgeAppearanceCalculator() or new EdgeAppearanceCalculator( VisualStyle.getDependency() ); Will be removed Jan 2010.

cytoscape.view.NetworkViewManager(CytoscapeDesktop, int)
view_type is no longer used. Use the other constructor. Will be removed Aug 2008.

cytoscape.visual.NodeAppearanceCalculator()
Use VisualStyle.getNodeAppearanceCalculator() or new NodeAppearancCalculator( VisualStyle.getDependency() ) instead. Will be removed January 2011.

cytoscape.dialogs.preferences.PreferenceValueDialog(Dialog, String, String, PreferencesDialog, TableModel, String, boolean)
includeBrowse is not longer supported. Use the other constructor instead. Will be removed 5/2008.

cytoscape.layout.Tunable(String, String, int, Object, Object, Object, int, boolean)
Use the IMMUTABLE flag directly rather than this special constructor.

cytoscape.data.readers.VisualStyleBuilder(String, Map, Map, Map)
this should no longer be used and is not functional. Use VisualStyleBuilder(String) instead and then call addProperty for each value