|
Cytoscape 2.8.0 API | |||||||||
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| Deprecated Interfaces | |
|---|---|
| cytoscape.layout.LayoutAlgorithm
Use CyLayoutAlgorithm instead. Will be removed June, 2008 |
|
| Deprecated Classes | |
|---|---|
| cytoscape.visual.calculators.AbstractCalculator.CalculatorUI
Do not use. This UI was replaced by new VizMap GUI. |
|
| cytoscape.actions.AnimatedLayoutAction
Not apparently used. Shout if you are. Will be removed 5/2008. |
|
| cytoscape.data.annotation.Annotation
Use regular CyAttributes for annotation. |
|
| cytoscape.data.annotation.AnnotationDescription
Use regular CyAttributes for annotation. |
|
| 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 CytoscapeDesktop
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.data.annotation.FlattenIntVectors
Use regular CyAttributes for annotation. |
|
| cytoscape.visual.ui.LabelPlacerGraphic
|
|
| cytoscape.visual.LabelPosition
|
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| cytoscape.visual.parsers.LabelPositionParser
|
|
| cytoscape.visual.parsers.ObjectToString
will be removed in May 2011. Use ValueToStringConverterManager.manager.toString(obj) instead. |
|
| cytoscape.data.annotation.Ontology
Use regular CyAttributes for annotation. |
|
| cytoscape.data.annotation.OntologyDescription
Use regular CyAttributes for annotation. |
|
| cytoscape.data.annotation.OntologyTerm
Use regular CyAttributes for annotation. |
|
| 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 Methods | |
|---|---|
| cytoscape.data.Semantics.applyNamingServices(CyNetwork)
|
|
| 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.data.Semantics.areSynonyms(String, String, CyNetwork)
|
|
| cytoscape.data.Semantics.assignCommonNames(CyNetwork, BioDataServer)
|
|
| cytoscape.data.Semantics.assignNodeAliases(CyNode, String, BioDataServer)
|
|
| cytoscape.data.Semantics.assignSpecies(CyNetwork)
|
|
| 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.Semantics.getAllSynonyms(String, CyNetwork)
|
|
| cytoscape.render.stateful.CustomGraphic.getAnchor()
|
|
| 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.ding.CyGraphLOD.getBoolean(String, boolean)
Use PropUtil.getBoolean(..) instead. Leaving Feb 2011. |
|
| 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. |
|
| 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. |
|
| org.apache.commons.cli.avalon.CLOption.getId()
use getDescriptor().getId() instead |
|
| org.apache.commons.cli.avalon.CLOptionDescriptor.getIncompatble()
Use the correctly spelled CLOptionDescriptor.getIncompatible() instead. |
|
| cytoscape.ding.CyGraphLOD.getInt(String, int)
Use PropUtil.getInt(..) instead. Leaving Feb 2011. |
|
| giny.view.Label.getJustify()
|
|
| ding.view.DNodeView.getJustify()
|
|
| giny.view.NodeView.getLabelOffsetX()
|
|
| ding.view.DNodeView.getLabelOffsetX()
|
|
| giny.view.NodeView.getLabelOffsetY()
|
|
| ding.view.DNodeView.getLabelOffsetY()
|
|
| cytoscape.visual.mappings.MappingType.getMappingType(String)
Will be removed 5/2008 |
|
| giny.model.GraphPerspective.getNodeIndex(int)
Use getRootGraphNodeIndex(int), whose functionality is identical. |
|
| giny.view.NodeView.getNodeLabelAnchor()
|
|
| ding.view.DNodeView.getNodeLabelAnchor()
|
|
| 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. |
|
| 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. |
|
| cytoscape.util.Misc.getRGBText(Color)
Will be removed April, 2011. Use ColorUtil.getColorAsText instead. |
|
| 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.data.Semantics.getSpeciesInNetwork(CyNetwork)
|
|
| cytoscape.visual.parsers.ObjectToString.getStringValue(Object)
|
|
| cytoscape.view.NetworkViewManager.getTabbedPane()
Tabbed view is no longer used. Will be removed Aug 2008. |
|
| giny.view.Label.getTextAnchor()
|
|
| ding.view.DNodeView.getTextAnchor()
|
|
| cytoscape.visual.calculators.AbstractCalculator.getUI(CyAttributes, JDialog, CyNetwork)
will be removed in the next release (2.8 or 3.0) |
|
| cytoscape.visual.calculators.Calculator.getUI(JDialog, CyNetwork)
replaced by new VizMap GUI components. Will be removed in 2.8 or 3.0 |
|
| cytoscape.visual.calculators.AbstractCalculator.getUI(JDialog, CyNetwork)
Will be removed next release (2.8 or 3.0) |
|
| cytoscape.visual.mappings.ObjectMapping.getUI(JDialog, CyNetwork)
|
|
| cytoscape.visual.mappings.AbstractMapping.getUI(JDialog, CyNetwork)
|
|
| 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. |
|
| 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.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.util.Misc.parseRGBText(String)
will be removed in April, 2011. use ColorUtil.parseColorText 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.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.visual.mappings.ObjectMapping.setControllingAttributeName(String, CyNetwork, boolean)
Will be removed in 2.8. Use setControllingAttributeName(final String controllingAttrName) instead. |
|
| cytoscape.visual.mappings.AbstractMapping.setControllingAttributeName(String, CyNetwork, boolean)
|
|
| 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. |
|
| giny.view.Label.setJustify(int)
|
|
| ding.view.DNodeView.setJustify(int)
|
|
| giny.view.NodeView.setLabelOffsetX(double)
|
|
| ding.view.DNodeView.setLabelOffsetX(double)
|
|
| giny.view.NodeView.setLabelOffsetY(double)
|
|
| ding.view.DNodeView.setLabelOffsetY(double)
|
|
| giny.view.NodeView.setNodeLabelAnchor(int)
|
|
| ding.view.DNodeView.setNodeLabelAnchor(int)
|
|
| 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) |
|
| giny.view.Label.setTextAnchor(int)
|
|
| ding.view.DNodeView.setTextAnchor(int)
|
|
| cytoscape.view.CyMenus.setVisualMapperItemsEnabled(boolean)
Will be removed April 2008. Item state is now handled by Actions directly. Don't use this. |
|
| cytoscape.view.CytoscapeDesktop.setVisualStyle(VisualStyle)
use VisualMappingManager.setVisualStyle(VisualStyle style) instead. |
|
| 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 | |
|---|---|
| org.apache.commons.cli.avalon.CLOptionDescriptor(String, int, int, String, int[])
use the version with the array of CLOptionDescriptor's |
|
| cytoscape.visual.mappings.continuous.ContinuousLegend(String, List, Object, VisualPropertyType)
|
|
| cytoscape.visual.mappings.ContinuousMapping(Object, byte)
Use new constructor instead. Will be removed in 10/2011. Controlling attribute name is always required, and now it's a part of constructor argument. |
|
| cytoscape.render.stateful.CustomGraphic(Shape, Paint, byte)
|
|
| cytoscape.visual.mappings.DiscreteMapping(Object, byte)
Use new constructor instead. Will be removed in 10/2011. Controlling attribute name is always required, and now it's a part of constructor argument. |
|
| cytoscape.visual.mappings.DiscreteMapping(Object, String, byte)
Use new constructor instead. Will be removed in 10/2011. Controlling attribute name is always required, and now it's a part of constructor argument. |
|
| cytoscape.visual.EdgeAppearanceCalculator()
Use VisualStyle.getEdgeAppearanceCalculator() or new EdgeAppearanceCalculator( VisualStyle.getDependency() ); Will be removed Jan 2010. |
|
| cytoscape.dialogs.ExportAsGraphicsFileChooser(CyFileFilter[])
|
|
| 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.visual.mappings.PassThroughMapping(Object)
Use new constructor instead. Will be removed in 10/2011. Controlling attribute name is always required, and now it's a part of constructor argument. |
|
| cytoscape.visual.mappings.PassThroughMapping(Object, byte)
Use new constructor instead. Will be removed in 10/2011. Controlling attribute name is always required, and now it's a part of constructor argument. |
|
| cytoscape.visual.mappings.PassThroughMapping(Object, String)
Use new constructor instead. Will be removed in 10/2011. Controlling attribute name is always required, and now it's a part of constructor argument. |
|
| 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.geom.rtree.RTree(int)
Use the no-arg constructor instead. |
|
| 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 |
|
|
Cytoscape 2.8.0 API | |||||||||
| PREV NEXT | FRAMES NO FRAMES | |||||||||