Deprecated API

Deprecated Classes

cytoscape.CyProject
Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.

cytoscape.CytoscapeConfig
Will be removed October 2006. Use methods in CytoscapeInit instead.

cytoscape.CytoscapeObj
Will be removed October 2006. Use static methods in Cytoscape.java instead.

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

cytoscape.util.MutableColor
No one uses this, so don't start. Just use Color directly. This will be removed 12/2006.

Deprecated Fields

cytoscape.data.Semantics.ALIASES
Use CyNode.getIdentifier() instead. This attribute will be removed in April, 2007.

cytoscape.Cytoscape.ATTRIBUTES_CHANGED
this event should not be used, it is not fired

cytoscape.data.Semantics.CANONICAL_NAME
Use CyNode.getIdentifier() instead. This attribute will be removed in April, 2007.

cytoscape.data.Semantics.COMMON_NAME
Use CyNode.getIdentifier() instead. This attribute will be removed in April, 2007.

cytoscape.data.Semantics.IDENTIFIER
Use CyNode.getIdentifier() instead. This attribute will be removed in April, 2007.

cytoscape.data.Semantics.LABEL
Use CyNode.getIdentifier() instead. This attribute will be removed in April, 2007.

Deprecated Methods

cytoscape.CyNetwork.beginActivity(String)

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

cytoscape.Cytoscape.createNetwork(String, int, boolean, BioDataServer, String)
It will be removed in April 2007 Use CyNetwork createNetworkFromFile(String location, boolean create_view) instead. File type is no longer needed as ImportHandler now manages all file types.

cytoscape.Cytoscape.createNetworkFromProject(CyProject, BioDataServer)
Will be removed Oct 2006. This is not apparently used, so don't start. This functionality has been subsumed by Cytoscape Sessions.

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.Cytoscape.disableSquiggle()
Squiggle is gone and we don't expect the functionality to return. if this causes major problems, let us know. This method will be removed Sept 2006.

cytoscape.Cytoscape.enableSquiggle()
Squiggle is gone and we don't expect the functionality to return. if this causes major problems, let us know. This method will be removed Sept 2006.

cytoscape.CyNetwork.endActivity(String)

cytoscape.Cytoscape.exit()
Use exit(returnVal) instead. This will be removed in Sept 2006.

cytoscape.CyNetwork.flagAllEdges()
As of 2.3, replaced by CyNetwork.selectAllEdges()

cytoscape.CyNetwork.flagAllNodes()
As of 2.3, replaced by CyNetwork.selectAllNodes()

cytoscape.CyNetwork.forceClear(String)

cytoscape.CytoscapeConfig.getArgs()
Will be removed October 2006. Use methods in CytoscapeInit instead.

cytoscape.CytoscapeInit.getArgs()
Use Properties (getProperties()) instead of args for accessing initialization information. This method will be removed April 2007.

cytoscape.CyProject.getBioDataDirectory()
Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.

cytoscape.CytoscapeInit.getBioDataServer()
This method will be removed April 2007. Use getProperty("bioDataServer") instead.

cytoscape.CytoscapeObj.getBioDataServer()
Will be removed October 2006. Use static methods in Cytoscape.java instead.

cytoscape.CyProject.getCanonicalize()
Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.

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

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

cytoscape.CytoscapeInit.getConfigDirectoy()
This method is only deprecated because it is misspelled. Just use the correctly spelled method: getConfigDirectory(). This method will be removed 12/2006.

cytoscape.CytoscapeObj.getConfiguration()
Will be removed October 2006. Use methods in CytoscapeInit.java instead.

cytoscape.Cytoscape.getCytoscapeObj()

cytoscape.CyProject.getDefaultLayoutStrategy()
Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.

cytoscape.CyProject.getDefaultSpeciesName()
Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.

cytoscape.CytoscapeInit.getDefaultSpeciesName()
Will be removed April 2007. Use getProperty( "defaultSpeciesName" ) instead.

cytoscape.CytoscapeInit.getDefaultVisualStyle()
Will be removed April 2007. Use getProperties().getProperty( "defaultVisualStyle" ) instead.

cytoscape.CyProject.getEdgeAttributeFilenames()
Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.

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

cytoscape.CytoscapeInit.getEdgeAttributes()
Will be removed April 2007. No one appears to be using this method, so don't start.

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()

cytoscape.CyProject.getExpressionFilename()
Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.

cytoscape.CytoscapeInit.getExpressionFiles()
Will be removed April 2007. No one appears to be using this method, so don't start.

cytoscape.CyNetwork.getFlaggedEdgeIndicesArray()
As of 2.3, replaced by CyNetwork.getSelectedEdges()

cytoscape.CyNetwork.getFlaggedEdges()
As of 2.3, replaced by CyNetwork.getSelectedEdges()

cytoscape.CyNetwork.getFlaggedNodeIndicesArray()
As of 2.3, replaced by CyNetwork.getSelectedNodes()

cytoscape.CyNetwork.getFlaggedNodes()
As of 2.3, replaced by CyNetwork.getSelectedNodes()

cytoscape.CyNetwork.getFlagger()
As of 2.3, replaced by CyNetwork.getSelectFilter()

cytoscape.CyProject.getGeometryFilename()
Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.

cytoscape.CytoscapeInit.getGraphFiles()
Will be removed April 2007. No one appears to be using this method, so don't start.

cytoscape.CyNetwork.getGraphPerspective()

cytoscape.CytoscapeInit.getHelp()
This method will be removed April 2007. No one appears to use this method, so don't start.

cytoscape.CyProject.getInteractionsFilename()
Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.

cytoscape.CyProject.getNodeAttributeFilenames()
Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.

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

cytoscape.CytoscapeInit.getNodeAttributes()
Will be removed April 2007. No one appears to be using this method, so don't start.

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.CyProject.getNumberOfEdgeAttributeFiles()
Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.

cytoscape.CyProject.getNumberOfNodeAttributeFiles()
Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.

cytoscape.CyProject.getOtherArgs()
Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.

cytoscape.CyProject.getProjectFilename()
Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.

cytoscape.CyProject.getProjectPropsFileName()
Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.

cytoscape.CyProject.getProjectVizmapPropsFileName()
Will be removed October 2006. CyProject is not used in any way in the core. Cytoscape Sessions now encapsulate all of this functionality.

cytoscape.CytoscapeConfig.getProperties()
Will be removed October 2006. Use methods in CytoscapeInit instead.

cytoscape.CytoscapeInit.getPropertiesLocation()
This method will be removed April 2007.

cytoscape.CytoscapeInit.getProperty(String)
Use getProperties().getProperty( ) instead. Since this method never made it into a release, it will be removed Summer 2006.

cytoscape.CytoscapeInit.getSecondaryViewThreshold()
Will be removed April 2007. Use getProperty( "secondaryViewThreshold" ) instead.

cytoscape.CytoscapeInit.getViewThreshold()
Will be removed April 2007. Use getProperty( "viewThreshold" ) instead.

cytoscape.CytoscapeInit.getViewType()
Will be removed April 2007. Use CytoscapeDesktop.parseViewType(CytoscapeInit.getProperties().getProperty("viewType"));

cytoscape.view.CytoscapeDesktop.getVizMapManager()
Use Cytoscape.getVisualMappingManager() instead. This will be removed at 03/2007 (possibly sooner).

cytoscape.CytoscapeInit.getVizmapPropertiesLocation()
Will be removed April 2007. Use getProperties().getProperty( "TODO" ) instead.

cytoscape.CyNetwork.isFlagged(Edge)
As of 2.3, replaced by CyNetwork.isSelected(Edge)

cytoscape.CyNetwork.isFlagged(Node)
As of 2.3, replaced by CyNetwork.isSelected(Node)

cytoscape.CytoscapeInit.isHeadless()
This method will be removed April 2007. Use getMode() instead.

cytoscape.Cytoscape.isSquiggleEnabled()
Squiggle is gone and we don't expect the functionality to return. if this causes major problems, let us know. This method will be removed Sept 2006.

cytoscape.CyNetwork.isStateClear()

cytoscape.CytoscapeInit.noCanonicalization()
Will be removed April 2007. Use getProperty( "canonicalizeNames" ) instead.

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

cytoscape.CyNetwork.removeFlagEventListener(FlagEventListener)
As of 2.3, replaced by CyNetwork.removeSelectEventListener(SelectEventListener)

cytoscape.Cytoscape.setCurrentNetwork(String)

cytoscape.Cytoscape.setCurrentNetworkView(String)

cytoscape.CytoscapeInit.setDefaultSpeciesName()
Will be removed April 2007. This doesn't do anything. To set the default species name use getProperties().setProperty("defaultSpeciesName", newName), which you were presumably doing already.

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.CyNetwork.setFlagged(Edge, boolean)
As of 2.3, replaced by CyNetwork.setSelectedEdgeState(Collection,boolean)

cytoscape.CyNetwork.setFlagged(Node, boolean)
As of 2.3, replaced by CyNetwork.setSelectedNodeState(Collection,boolean)

cytoscape.CyNetwork.setFlaggedEdges(Collection, boolean)
As of 2.3, replaced by CyNetwork.setSelectedEdgeState(Collection,boolean)

cytoscape.CyNetwork.setFlaggedEdges(int[], boolean)
As of 2.3, replaced by CyNetwork.setSelectedEdgeState(Collection,boolean)

cytoscape.CyNetwork.setFlaggedNodes(Collection, boolean)
As of 2.3, replaced by CyNetwork.setSelectedNodeState(Collection,boolean)

cytoscape.CyNetwork.setFlaggedNodes(int[], boolean)
As of 2.3, replaced by CyNetwork.setSelectedNodeState(Collection,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.CytoscapeInit.setProperty(String, String)
Use getProperties().setProperty( ) instead. Since this method never made it into a release, it will be removed Summer 2006.

cytoscape.CytoscapeInit.setSecondaryViewThreshold(int)
Will be removed April 2007. Use getProperties().setProperty( "secondaryViewThreshold", thresh ) instead.

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.Cytoscape.setSpecies()
argh!...

cytoscape.CytoscapeInit.setViewThreshold(int)
Will be removed April 2007. Use setProperty( "viewThreshold", thresh ) instead.

cytoscape.CytoscapeInit.suppressView()
This method will be removed April 2007. No one appears to use this method, so don't start.

cytoscape.CyNetwork.unFlagAllEdges()
As of 2.3, replaced by CyNetwork.unselectAllEdges()

cytoscape.CyNetwork.unFlagAllNodes()
As of 2.3, replaced by CyNetwork.unselectAllNodes()

cytoscape.CytoscapeInit.useView()
This method will be removed April 2007. Use getMode() instead.