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| Deprecated Interfaces | |
|---|---|
| cytoscape.view.NetworkView
This interface defines methods for displaying a graph without specifying the details of the UI components surrounding the graph display. |
|
| 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.data.FlagEvent
As of 2.3, replaced with SelectEvent |
|
| cytoscape.data.FlagFilter
As of 2.3, replaced with SelectFilter |
|
| cytoscape.foo.GraphConverter
Please avoid looking at or using this code -- this code is going away in the next Cytoscape release (the one after 2.1). |
|
| cytoscape.data.GraphObjAttributes
Use CyAttributes instead. |
|
| Deprecated Fields | |
|---|---|
| cytoscape.data.Semantics.ALIASES
Use CyNode.getIdentifier() instead.
This attribute will be removed in April, 2007. |
|
| 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. |
|
| Deprecated Methods | |
|---|---|
| cytoscape.data.GraphObjAttributes.add(GraphObjAttributes)
Method is no longer needed in the Cytoscape core, and no equivalent method will be provided. |
|
| cytoscape.data.GraphObjAttributes.add(String, HashMap)
Method is no longer needed in the Cytoscape core, and no equivalent method will be provided. |
|
| cytoscape.data.GraphObjAttributes.add(String, String, double)
Use CyAttributes.setAttribute(String, String, Double) instead. |
|
| cytoscape.data.GraphObjAttributes.add(String, String, Object)
Storing arbitrary Java objects as attribute values will no longer be supported in CyAttributes. However, you will be able to store arbitrarily complex trees of Boolean, Integer, Double, and String Objects. For details, refer to CyAttributes. |
|
| cytoscape.data.GraphObjAttributes.addClassMap(HashMap)
Method is no longer needed in the Cytoscape core, and no equivalent method will be provided. |
|
| cytoscape.giny.FingCyNetwork.addFlagEventListener(FlagEventListener)
As of 2.3, replaced by FingCyNetwork.addSelectEventListener(SelectEventListener) |
|
| cytoscape.data.GraphObjAttributes.addNameMap(HashMap)
Method is no longer needed in the Cytoscape core, and no equivalent method will be provided. |
|
| cytoscape.data.GraphObjAttributes.addNameMapping(String, Object)
Method is no longer needed in the Cytoscape core, and no equivalent method will be provided. |
|
| cytoscape.data.GraphObjAttributes.addObjectMap(HashMap)
Method is no longer needed in the Cytoscape core, and no equivalent method will be provided. |
|
| cytoscape.data.GraphObjAttributes.append(String, String, Object)
Use CyAttributes.setAttributeList(String, String, java.util.List)
for equivalent functionality. |
|
| cytoscape.CyNetwork.beginActivity(String)
|
|
| cytoscape.giny.FingCyNetwork.beginActivity(String)
This method should be called before reading or changing the data held in this network object. A CyNetworkEvent of type CyNetworkEvent.BEGIN will be fired to all listeners attached to this object, *only* if this is the first begin of a nested stack of begin/end methods. No event will be fired if a previous beginActivity call hasn't been closed by a matching endActivity call. The argument is simply a String that is useful for identifying the caller of this method. This is provided for debugging purposes, in case an algorithm forgets to provide a matching end method for each begin. |
|
| cytoscape.Cytoscape.clearCytoscape()
WARNING: this should only be used under special circumstances. |
|
| cytoscape.data.GraphObjAttributes.clearNameMap()
Method is no longer needed in the Cytoscape core, and no equivalent method will be provided. |
|
| cytoscape.data.GraphObjAttributes.clearObjectMap()
Method is no longer needed in the Cytoscape core, and no equivalent method will be provided. |
|
| cytoscape.data.GraphObjAttributes.countIdentical(String)
Method is no longer needed in the Cytoscape core, and no equivalent method will be provided. |
|
| 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.data.GraphObjAttributes.deduceClass(String)
Method is no longer needed in the Cytoscape core, and no equivalent method will be provided. |
|
| cytoscape.data.GraphObjAttributes.deleteAttribute(String)
Use CyAttributes.deleteAttribute(String) instead. |
|
| cytoscape.data.GraphObjAttributes.deleteAttribute(String, String)
Use CyAttributes.deleteAttribute(String, String) instead. |
|
| cytoscape.data.GraphObjAttributes.deleteAttributeValue(String, String, Object)
Method is no longer needed in the Cytoscape core, and no equivalent method will be provided. |
|
| 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.giny.FingCyNetwork.endActivity(String)
This method should be called when an algorithm is finished reading or changing the data held in this network object. A CyNetworkEvent of type CyNetworkEvent.END will be fired to listeners attached to this object, *only* if this is the last end in a nested block of begin/end calls. The argument is a String for identifying the caller of this method. |
|
| 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.giny.FingCyNetwork.flagAllEdges()
As of 2.3, replaced by FingCyNetwork.selectAllEdges() |
|
| cytoscape.CyNetwork.flagAllNodes()
As of 2.3, replaced by CyNetwork.selectAllNodes() |
|
| cytoscape.giny.FingCyNetwork.flagAllNodes()
As of 2.3, replaced by FingCyNetwork.selectAllNodes() |
|
| cytoscape.CyNetwork.forceClear(String)
|
|
| cytoscape.giny.FingCyNetwork.forceClear(String)
This method is provided as a failsafe in case an algorithm fails to close its beginActivity calls without matching endActivity calls. If the current state is not clear, this method resets this object to the state of no activity and fires a CyNetworkEvent of type CyNetworkEvent.END to all registered listeners. If the current state is clear (i.e., there are no calls to beginActivity without matching endActivity calls), then this method does nothing. The argument is a String for identifying the caller of this method. |
|
| cytoscape.data.GraphObjAttributes.get(String, String)
Use CyAttributes instead. It provides several
getter methods for retrieving Boolean, Integer, Double and String values. |
|
| cytoscape.CytoscapeInit.getArgs()
Use Properties (getProperties()) instead of args for accessing initialization information. This method will be removed April 2007. |
|
| cytoscape.CytoscapeConfig.getArgs()
Will be removed October 2006. Use methods in CytoscapeInit instead. |
|
| cytoscape.data.GraphObjAttributes.getArrayValues(String, String)
There is no one method in CyAttributes that provides
this functionality, but it can be recreated via several calls. |
|
| cytoscape.data.GraphObjAttributes.getAttribute(String)
Use CyAttributesUtils.getAttribute(String, CyAttributes)
instead. |
|
| cytoscape.data.GraphObjAttributes.getAttributeNames()
Use CyAttributes.getAttributeNames() instead. |
|
| cytoscape.data.GraphObjAttributes.getAttributes(String)
use CyAttributeUtils.getAttributes(String,CyAttributes). |
|
| 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.data.GraphObjAttributes.getCanonicalName(Object)
Use CyNode.getIdentifier() or
CyEdge.getIdentifier() instead. |
|
| cytoscape.data.GraphObjAttributes.getClass(String)
Use CyAttributesUtils.getClass(String,CyAttributes) instead. |
|
| cytoscape.data.GraphObjAttributes.getClassMap()
Method is no longer needed in the Cytoscape core, and no equivalent method will be provided. |
|
| 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 |
|
| 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.CytoscapeInit.getDefaultSpeciesName()
Will be removed April 2007. Use getProperty( "defaultSpeciesName" ) instead. |
|
| 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.getDefaultVisualStyle()
Will be removed April 2007. Use getProperties().getProperty( "defaultVisualStyle" ) instead. |
|
| cytoscape.data.GraphObjAttributes.getDoubleValue(String, String)
Use CyAttributes.getDoubleAttribute(String, String) 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.CytoscapeInit.getEdgeAttributes()
Will be removed April 2007. No one appears to be using this method, so don't start. |
|
| cytoscape.CyNetwork.getEdgeAttributes()
Use Cytoscape.getEdgeAttributes() instead. This
method will be removed in September, 2006. |
|
| cytoscape.giny.FingCyNetwork.getEdgeAttributes()
Use Cytoscape.getEdgeAttributes() instead. This
method will be removed in September, 2006. |
|
| cytoscape.Cytoscape.getEdgeAttributesList()
Use CyAttributes directly. This method will be
removed in September, 2006. |
|
| cytoscape.CyNetwork.getEdgeAttributesList()
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(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.giny.FingCyNetwork.getExpressionData()
@see{getNetworkData} Returns the expression data object associated with this network. |
|
| 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.giny.FingCyNetwork.getFlaggedEdgeIndicesArray()
As of 2.3, replaced by FingCyNetwork.getSelectedEdges() |
|
| cytoscape.CyNetwork.getFlaggedEdges()
As of 2.3, replaced by CyNetwork.getSelectedEdges() |
|
| cytoscape.giny.FingCyNetwork.getFlaggedEdges()
As of 2.3, replaced by FingCyNetwork.getSelectedEdges() |
|
| cytoscape.CyNetwork.getFlaggedNodeIndicesArray()
As of 2.3, replaced by CyNetwork.getSelectedNodes() |
|
| cytoscape.giny.FingCyNetwork.getFlaggedNodeIndicesArray()
As of 2.3, replaced by FingCyNetwork.getSelectedNodes() |
|
| cytoscape.CyNetwork.getFlaggedNodes()
As of 2.3, replaced by CyNetwork.getSelectedNodes() |
|
| cytoscape.giny.FingCyNetwork.getFlaggedNodes()
As of 2.3, replaced by FingCyNetwork.getSelectedNodes() |
|
| cytoscape.CyNetwork.getFlagger()
As of 2.3, replaced by CyNetwork.getSelectFilter() |
|
| cytoscape.giny.FingCyNetwork.getFlagger()
As of 2.3, replaced by FingCyNetwork.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.data.GraphObjAttributes.getGraphObject(String)
Use Cytoscape.getCyNode(String) or
Cytoscape.getCyEdge(String, String, String, String) instead. |
|
| cytoscape.CyNetwork.getGraphPerspective()
|
|
| cytoscape.giny.FingCyNetwork.getGraphPerspective()
This is a GraphPerspective now! Therefore treat it as such. This method will not be changed and will simply return itself, recasted as a GraphPerspective |
|
| cytoscape.CytoscapeInit.getHelp()
This method will be removed April 2007. No one appears to use this method, so don't start. |
|
| cytoscape.data.GraphObjAttributes.getIntegerValue(String, String)
Use CyAttributes.getIntegerAttribute(String, String)
instead. |
|
| 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.data.GraphObjAttributes.getList(String, String)
Use CyAttributes.getAttributeList(String, String)
instead. |
|
| cytoscape.data.GraphObjAttributes.getNameMap()
Use GraphPerspective.nodesIterator() or
GraphPerspective.edgesIterator() instead. |
|
| cytoscape.giny.FingCyNetwork.getNeedsLayout()
|
|
| 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.CytoscapeInit.getNodeAttributes()
Will be removed April 2007. No one appears to be using this method, so don't start. |
|
| cytoscape.CyNetwork.getNodeAttributes()
Use Cytoscape.getNodeAttributes() instead. This
method will be removed in September, 2006. |
|
| cytoscape.giny.FingCyNetwork.getNodeAttributes()
Use Cytoscape.getNodeAttributes() instead. 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()
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(Edge[])
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.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.Cytoscape.getNodeAttributeValue(Node, 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.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.data.GraphObjAttributes.getObjectCount(String)
There is no one method in CyAttributes that provides
this functionality, but it can be recreated via several calls. |
|
| cytoscape.data.GraphObjAttributes.getObjectMap()
Method is no longer needed in the Cytoscape core, and no equivalent method will be provided. |
|
| cytoscape.data.GraphObjAttributes.getObjectNames(String)
Use MultiHashMap.getObjectKeys(String)
instead. |
|
| 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.giny.FingCyNetwork.getRootGraph()
use @link{Cytoscape.getRootGraph()} instead |
|
| cytoscape.CytoscapeInit.getSecondaryViewThreshold()
Will be removed April 2007. Use getProperty( "secondaryViewThreshold" ) instead. |
|
| cytoscape.data.GraphObjAttributes.getStringArrayValues(String, String)
Use CyAttributes.getAttributeList(String, String)
instead. |
|
| cytoscape.data.GraphObjAttributes.getStringValue(String, String)
Use CyAttributes.getStringAttribute(String, String)
instead. |
|
| cytoscape.data.GraphObjAttributes.getSummary()
Method is no longer needed in the Cytoscape core, and no equivalent method will be provided. |
|
| cytoscape.data.GraphObjAttributes.getUniqueStringValues(String)
There is no one method in CyAttributes that provides
this functionality, but it can be recreated via several calls. |
|
| cytoscape.data.GraphObjAttributes.getUniqueValues(String)
There is no one method in CyAttributes that provides
this functionality, but it can be recreated via several calls. |
|
| cytoscape.data.GraphObjAttributes.getValue(String, String)
Use CyAttributes instead. It provides several
getter methods for retrieving Boolean, Integer, Double and String values. |
|
| cytoscape.data.readers.GMLTree.getVector(String, String, int)
use anonymous String arrays 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.data.GraphObjAttributes.hasAttribute(String)
Use CyAttributes.getType(String) instead. |
|
| cytoscape.data.GraphObjAttributes.hasAttribute(String, String)
Use CyAttributes.hasAttribute(String, String) instead. |
|
| cytoscape.CyNetwork.isFlagged(Edge)
As of 2.3, replaced by CyNetwork.isSelected(Edge) |
|
| cytoscape.giny.FingCyNetwork.isFlagged(Edge)
As of 2.3, replaced by FingCyNetwork.isSelected(Edge) |
|
| cytoscape.CyNetwork.isFlagged(Node)
As of 2.3, replaced by CyNetwork.isSelected(Node) |
|
| cytoscape.giny.FingCyNetwork.isFlagged(Node)
As of 2.3, replaced by FingCyNetwork.isSelected(Node) |
|
| cytoscape.CytoscapeInit.isHeadless()
This method will be removed April 2007. Use getMode() instead. |
|
| cytoscape.CyNetwork.isStateClear()
|
|
| cytoscape.giny.FingCyNetwork.isStateClear()
This method returns true if the current state of this object is clear; that is, if every beginActivity call has been followed by a matching endActivity call, so that one can reasonably assume that no one is currently working with the network. |
|
| cytoscape.CytoscapeInit.noCanonicalization()
Will be removed April 2007. Use getProperty( "canonicalizeNames" ) instead. |
|
| cytoscape.data.GraphObjAttributes.numberOfAttributes()
Use CyAttributes.getAttributeNames().length instead. |
|
| cytoscape.data.GraphObjAttributes.processFileHeader(String)
Use CyAttributesReader instead. |
|
| 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.GraphObjAttributes.readAttributesFromFile(File)
Method is no longer needed in the Cytoscape core, and no equivalent method will be provided. |
|
| cytoscape.data.GraphObjAttributes.readAttributesFromFile(String)
Use CyAttributesReader instead. |
|
| cytoscape.CyProject.readProjectFile(String)
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.removeFlagEventListener(FlagEventListener)
As of 2.3, replaced by CyNetwork.removeSelectEventListener(SelectEventListener) |
|
| cytoscape.giny.FingCyNetwork.removeFlagEventListener(FlagEventListener)
As of 2.3, replaced by FingCyNetwork.removeSelectEventListener(SelectEventListener) |
|
| cytoscape.data.GraphObjAttributes.removeNameMapping(String)
Method is no longer needed in the Cytoscape core, and no equivalent method will be provided. |
|
| cytoscape.data.GraphObjAttributes.removeObjectMapping(Object)
Method is no longer needed in the Cytoscape core, and no equivalent method will be provided. |
|
| cytoscape.data.GraphObjAttributes.set(GraphObjAttributes)
Method is no longer needed in the Cytoscape core, and no equivalent method will be provided. |
|
| cytoscape.data.GraphObjAttributes.set(String, HashMap)
Method is no longer needed in the Cytoscape core, and no equivalent method will be provided. |
|
| cytoscape.data.GraphObjAttributes.set(String, String, double)
Use CyAttributes.setAttribute(String, String, Double) instead. |
|
| cytoscape.data.GraphObjAttributes.set(String, String, Object)
Storing arbitrary Java objects as attribute values will no longer be supported in CyAttributes. However, you will be able to store arbitrarily complex trees of Boolean, Integer, Double, and String Objects. For details, refer to CyAttributes. |
|
| cytoscape.data.GraphObjAttributes.setCategory(String, String)
Method is no longer needed in the Cytoscape core, and no equivalent method will be provided. |
|
| cytoscape.data.GraphObjAttributes.setClass(String, Class)
Method is no longer needed in the Cytoscape core, and no equivalent method will be provided. |
|
| 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.giny.FingCyNetwork.setEdgeAttributes(GraphObjAttributes)
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(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.giny.FingCyNetwork.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.giny.FingCyNetwork.setFlagged(Edge, boolean)
As of 2.3, replaced by FingCyNetwork.setSelectedEdgeState(Collection,boolean) |
|
| cytoscape.CyNetwork.setFlagged(Node, boolean)
As of 2.3, replaced by CyNetwork.setSelectedNodeState(Collection,boolean) |
|
| cytoscape.giny.FingCyNetwork.setFlagged(Node, boolean)
As of 2.3, replaced by FingCyNetwork.setSelectedNodeState(Collection,boolean) |
|
| cytoscape.CyNetwork.setFlaggedEdges(Collection, boolean)
As of 2.3, replaced by CyNetwork.setSelectedEdgeState(Collection,boolean) |
|
| cytoscape.giny.FingCyNetwork.setFlaggedEdges(Collection, boolean)
As of 2.3, replaced by FingCyNetwork.setSelectedEdgeState(Collection,boolean) |
|
| cytoscape.CyNetwork.setFlaggedEdges(int[], boolean)
As of 2.3, replaced by CyNetwork.setSelectedEdgeState(Collection,boolean) |
|
| cytoscape.giny.FingCyNetwork.setFlaggedEdges(int[], boolean)
As of 2.3, replaced by FingCyNetwork.setSelectedEdgeState(Collection,boolean) |
|
| cytoscape.CyNetwork.setFlaggedNodes(Collection, boolean)
As of 2.3, replaced by CyNetwork.setSelectedNodeState(Collection,boolean) |
|
| cytoscape.giny.FingCyNetwork.setFlaggedNodes(Collection, boolean)
As of 2.3, replaced by FingCyNetwork.setSelectedNodeState(Collection,boolean) |
|
| cytoscape.CyNetwork.setFlaggedNodes(int[], boolean)
As of 2.3, replaced by CyNetwork.setSelectedNodeState(Collection,boolean) |
|
| cytoscape.giny.FingCyNetwork.setFlaggedNodes(int[], boolean)
As of 2.3, replaced by FingCyNetwork.setSelectedNodeState(Collection,boolean) |
|
| cytoscape.giny.FingCyNetwork.setGraphPerspective(GraphPerspective)
|
|
| cytoscape.giny.FingCyNetwork.setNeedsLayout(boolean)
|
|
| cytoscape.CyNetwork.setNewGraphFrom(CyNetwork, boolean)
|
|
| cytoscape.giny.FingCyNetwork.setNewGraphFrom(CyNetwork, boolean)
|
|
| cytoscape.giny.FingCyNetwork.setNodeAttributes(GraphObjAttributes)
This method will be removed in September, 2006. |
|
| cytoscape.CyNetwork.setNodeAttributeValue(int, 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.CyNetwork.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.data.GraphObjAttributes.setTaskMonitor(TaskMonitor)
|
|
| 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.giny.FingCyNetwork.unFlagAllEdges()
As of 2.3, replaced by FingCyNetwork.unselectAllEdges() |
|
| cytoscape.CyNetwork.unFlagAllNodes()
As of 2.3, replaced by CyNetwork.unselectAllNodes() |
|
| cytoscape.giny.FingCyNetwork.unFlagAllNodes()
As of 2.3, replaced by FingCyNetwork.unselectAllNodes() |
|
| cytoscape.CytoscapeInit.useView()
This method will be removed April 2007. Use getMode() instead. |
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