|
Cytoscape 2.6.2 (c) 2006,2007 ISB, MSKCC, UCSD | ||||||||
| PREV NEXT | FRAMES NO FRAMES | ||||||||
| Deprecated Interfaces | |
|---|---|
| cytoscape.visual.calculators.EdgeArrowCalculator
Use Calculator instead. Will be removed 10/2007 |
|
| cytoscape.visual.calculators.EdgeColorCalculator
Use Calculator instead. Will be removed 10/2007 |
|
| cytoscape.visual.calculators.EdgeFontFaceCalculator
Use Calculator instead. Will be removed 10/2007 |
|
| cytoscape.visual.calculators.EdgeFontSizeCalculator
Use Calculator instead. Will be removed 10/2007 |
|
| cytoscape.visual.calculators.EdgeLabelCalculator
Use Calculator instead. Will be removed 10/2007 |
|
| cytoscape.visual.calculators.EdgeLineTypeCalculator
Use Calculator instead. Will be removed 10/2007 |
|
| cytoscape.visual.calculators.EdgeToolTipCalculator
Use Calculator instead. Will be removed 10/2007 |
|
| cytoscape.layout.LayoutAlgorithm
Use CyLayoutAlgorithm instead. Will be removed June, 2008 |
|
| cytoscape.visual.calculators.NodeColorCalculator
Use Calculator instead. Will be removed 10/2007 |
|
| cytoscape.visual.calculators.NodeFontFaceCalculator
Use Calculator instead. Will be removed 10/2007 |
|
| cytoscape.visual.calculators.NodeFontSizeCalculator
Use Calculator instead. Will be removed 10/2007 |
|
| cytoscape.visual.calculators.NodeLabelCalculator
Use Calculator instead. Will be removed 10/2007 |
|
| cytoscape.visual.calculators.NodeLabelColorCalculator
Use Calculator instead. Will be removed 10/2007 |
|
| cytoscape.visual.calculators.NodeLineTypeCalculator
Use Calculator instead. Will be removed 10/2007 |
|
| cytoscape.visual.calculators.NodeShapeCalculator
Use Calculator instead. Will be removed 10/2007 |
|
| cytoscape.visual.calculators.NodeSizeCalculator
Use Calculator instead. Will be removed 10/2007 |
|
| cytoscape.visual.calculators.NodeToolTipCalculator
Use Calculator instead. Will be removed 10/2007 |
|
| 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.visual.mappings.continuous.ContinuousUI
Will be removed 5/2008 |
|
| cytoscape.visual.ui.DefaultPanel
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.servers.ui.GeneOntologyWizard
will be removed in May 2008 |
|
| cytoscape.visual.calculators.GenericEdgeArrowCalculator
Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008. |
|
| cytoscape.visual.calculators.GenericEdgeColorCalculator
Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008. |
|
| cytoscape.visual.calculators.GenericEdgeFontFaceCalculator
Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008. |
|
| cytoscape.visual.calculators.GenericEdgeFontSizeCalculator
Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008. |
|
| cytoscape.visual.calculators.GenericEdgeLabelCalculator
Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008. |
|
| cytoscape.visual.calculators.GenericEdgeLabelColorCalculator
Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008. |
|
| cytoscape.visual.calculators.GenericEdgeLineStyleCalculator
Will be removed 5/2008 |
|
| cytoscape.visual.calculators.GenericEdgeLineTypeCalculator
Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008. |
|
| cytoscape.visual.calculators.GenericEdgeLineWidthCalculator
Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008. |
|
| cytoscape.visual.calculators.GenericEdgeSourceArrowCalculator
Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008. |
|
| cytoscape.visual.calculators.GenericEdgeSourceArrowColorCalculator
Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008. |
|
| cytoscape.visual.calculators.GenericEdgeSourceArrowShapeCalculator
Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008. |
|
| cytoscape.visual.calculators.GenericEdgeTargetArrowCalculator
Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008. |
|
| cytoscape.visual.calculators.GenericEdgeTargetArrowColorCalculator
Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008. |
|
| cytoscape.visual.calculators.GenericEdgeTargetArrowShapeCalculator
Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008. |
|
| cytoscape.visual.calculators.GenericEdgeToolTipCalculator
Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008. |
|
| cytoscape.visual.calculators.GenericNodeBorderColorCalculator
Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008. |
|
| cytoscape.visual.calculators.GenericNodeColorCalculator
Use BasicCalculator(VisualPropertyType,...) instead. Will be removed 5/2008. Will be hidden, although probably not removed, in 5/2008. |
|
| cytoscape.visual.calculators.GenericNodeFillColorCalculator
Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008. |
|
| cytoscape.visual.calculators.GenericNodeFontFaceCalculator
Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008. |
|
| cytoscape.visual.calculators.GenericNodeFontSizeCalculator
Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008. |
|
| cytoscape.visual.calculators.GenericNodeHeightCalculator
Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008. |
|
| cytoscape.visual.calculators.GenericNodeLabelCalculator
Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008. |
|
| cytoscape.visual.calculators.GenericNodeLabelColorCalculator
Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008. |
|
| cytoscape.visual.calculators.GenericNodeLabelPositionCalculator
Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008. |
|
| cytoscape.visual.calculators.GenericNodeLineStyleCalculator
Will be removed 5/2008 |
|
| cytoscape.visual.calculators.GenericNodeLineTypeCalculator
Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008. |
|
| cytoscape.visual.calculators.GenericNodeLineWidthCalculator
Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008. |
|
| cytoscape.visual.calculators.GenericNodeShapeCalculator
Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008. |
|
| cytoscape.visual.calculators.GenericNodeSizeCalculator
Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008. |
|
| cytoscape.visual.calculators.GenericNodeToolTipCalculator
Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008. |
|
| cytoscape.visual.calculators.GenericNodeUniformSizeCalculator
Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008. |
|
| cytoscape.visual.calculators.GenericNodeWidthCalculator
Use BasicCalculator(VisualPropertyType,...) instead. Will be hidden, although probably not removed, in 5/2008. |
|
| cytoscape.visual.ui.IconSupport
Will be removed 5/2008 |
|
| cytoscape.visual.LineType
Will be removed 5/2008. Use LineStyle and LineWidth instead. |
|
| cytoscape.visual.ui.MiscDialog
This class has been enhanced and renamed to IconSupport. This will be removed 10/2007. |
|
| cytoscape.visual.parsers.ParserFactory
Use VisualPropertyType.getValueParser() instead. Will be removed 5/2008. |
|
| cytoscape.giny.PhoebeNetworkView
You should be using DingNetworkView instead. This will be removed in whatever major release follows 2.4. |
|
| 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. |
|
| cytoscape.visual.ShapeNodeRealizer
Will be removed 5/2008. Use enum NodeShape instead. |
|
| cytoscape.visual.ui.ValueDisplayer
Will be removed 5/2008 |
|
| cytoscape.visual.ui.VizMapAttrTab
Will be removed 5/2008. Use New Vizmapper UI instead. |
|
| cytoscape.visual.ui.VizMapFontTab
Will be removed 5/2008 |
|
| cytoscape.visual.ui.VizMapTab
Will be removed 5/2008 |
|
| cytoscape.visual.ui.VizMapUI
Will be removed 5/2008. Use VizMapperMainPanel instead. |
|
| cytoscape.visual.ui.VizUIUtilities
|
|
| Deprecated Methods | |
|---|---|
| cytoscape.visual.CalculatorCatalog.addChangeListener(ChangeListener, byte)
Will be removed 5/2008 |
|
| ding.view.DNodeView.addCustomGraphic(Shape, Paint, int)
use addCustomGraphic(Shape,Paint,byte).
The entire index-based custom graphic API has been deprecated. This includes all the methods that refer to custom graphics using indices: public int addCustomGraphic(Shape s, Paint p, int index); public void removeCustomGraphic(int index); public Paint getCustomGraphicPaint(int index); public Shape getCustomGraphicShape(int index); public int getCustomGraphicCount();To keep things completetly backwards compatible and to avoid introducing bugs, the new API methods are completely independent from the the old API methods. Thus, a custom graphic added using the new API will not be accessible from the old API and visa versa. The reason for the deprecation is:
|
|
| cytoscape.view.CytoscapeDesktop.addEdit(UndoableEdit)
Use CyUndo.getUndoableEditSupport().postEdit(edit) instead. Will be removed March 2008. |
|
| cytoscape.visual.EdgeAppearance.applyAppearance(EdgeView, boolean)
Use applyAppearance(edgeView) instead - now we always optimize. Will be removed 10/2007 |
|
| cytoscape.data.readers.GMLReader.applyMaps(String, String)
Don't use this. Gone 2/2009. |
|
| cytoscape.visual.calculators.EdgeArrowCalculator.calculateEdgeArrow(Edge, CyNetwork)
Use Calculator.apply() instead. Will be removed 10/2007 |
|
| cytoscape.visual.calculators.EdgeColorCalculator.calculateEdgeColor(Edge, CyNetwork)
Use Calculator.apply() instead. Will be removed 10/2007 |
|
| cytoscape.visual.calculators.EdgeFontFaceCalculator.calculateEdgeFontFace(Edge, CyNetwork)
Use Calculator.apply() instead. Will be removed 10/2007 |
|
| cytoscape.visual.calculators.EdgeFontSizeCalculator.calculateEdgeFontSize(Edge, CyNetwork)
Use Calculator.apply() instead. Will be removed 10/2007 |
|
| cytoscape.visual.calculators.EdgeLabelCalculator.calculateEdgeLabel(Edge, CyNetwork)
Use Calculator.apply() instead. Will be removed 10/2007 |
|
| cytoscape.visual.calculators.GenericEdgeLineTypeCalculator.calculateEdgeLineType(Edge, CyNetwork)
Will be removed 5/2008 |
|
| cytoscape.visual.calculators.EdgeLineTypeCalculator.calculateEdgeLineType(Edge, CyNetwork)
Use Calculator.apply() instead. Will be removed 10/2007 |
|
| cytoscape.visual.calculators.EdgeToolTipCalculator.calculateEdgeToolTip(Edge, CyNetwork)
Use Calculator.apply() instead. Will be removed 10/2007 |
|
| cytoscape.visual.calculators.NodeColorCalculator.calculateNodeColor(Node, CyNetwork)
Use Calculator.apply() instead. Will be removed 10/2007 |
|
| cytoscape.visual.calculators.NodeFontFaceCalculator.calculateNodeFontFace(Node, CyNetwork)
Use Calculator.apply() instead. Will be removed 10/2007 |
|
| cytoscape.visual.calculators.NodeFontSizeCalculator.calculateNodeFontSize(Node, CyNetwork)
Use Calculator.apply() instead. Will be removed 10/2007 |
|
| cytoscape.visual.calculators.NodeLabelCalculator.calculateNodeLabel(Node, CyNetwork)
Use Calculator.apply() instead. Will be removed 10/2007 |
|
| cytoscape.visual.calculators.NodeLabelColorCalculator.calculateNodeLabelColor(Node, CyNetwork)
Use Calculator.apply() instead. Will be removed 10/2007 |
|
| cytoscape.visual.calculators.NodeLineTypeCalculator.calculateNodeLineType(Node, CyNetwork)
Use Calculator.apply() instead. Will be removed 10/2007 |
|
| cytoscape.visual.calculators.GenericNodeLineTypeCalculator.calculateNodeLineType(Node, CyNetwork)
Will be removed 5/2008 |
|
| cytoscape.visual.calculators.NodeShapeCalculator.calculateNodeShape(Node, CyNetwork)
Use Calculator.apply() instead. Will be removed 10/2007 |
|
| cytoscape.visual.calculators.NodeSizeCalculator.calculateNodeSize(Node, CyNetwork)
Use Calculator.apply() instead. Will be removed 10/2007 |
|
| cytoscape.visual.calculators.NodeToolTipCalculator.calculateNodeToolTip(Node, CyNetwork)
Use Calculator.apply() instead. Will be removed 10/2007 |
|
| cytoscape.visual.GlobalAppearanceCalculator.calculateSloppySelectionColor(CyNetwork)
Will be removed 5/2008 |
|
| cytoscape.visual.CalculatorCatalog.checkCalculatorName(byte, String)
Will be removed 5/2008 |
|
| cytoscape.visual.CalculatorCatalog.checkCalculatorName(String, byte)
Will be removed 5/2008 |
|
| 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.plugin.CytoscapePlugin.describe()
|
|
| 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.GraphPerspective.edgesList(int, int, boolean)
Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead. |
|
| giny.model.RootGraph.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. |
|
| cytoscape.view.NetworkPanel.fireFocus(String)
No longer used. If you need to fire focus, call CytoscapeDesktop.setFocus(). will be removed 11/2008. |
|
| cytoscape.visual.NodeAppearance.get(byte)
Use Appearance.get(VisualPropertyType) instead. Will be removed 5/2008. |
|
| cytoscape.visual.EdgeAppearance.get(byte)
Use Appearance.get(VisualPropertyType) instead. Will be removed 5/2008. |
|
| giny.model.GraphPerspective.getAdjacentEdgesList(Node, boolean, boolean, boolean)
Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead. |
|
| cytoscape.visual.ui.MiscDialog.getArrowIcons()
Use IconSupport instead. This will be removed 10/2007. |
|
| cytoscape.visual.ui.MiscDialog.getArrowToStringHashMap(int)
Use IconSupport instead. This will be removed 10/2007. |
|
| 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.visual.NodeAppearance.getBorderColor()
Use Appearance.get(VisualPropertyType) instead. Will be removed 5/2008. |
|
| cytoscape.visual.NodeAppearance.getBorderLineType()
Use Appearance.get(VisualPropertyType) instead. Will be removed 5/2008. |
|
| cytoscape.CytoscapeVersion.getBriefHistory()
See cytoscape.org for history. Will be removed 10/2007 |
|
| cytoscape.visual.CalculatorCatalog.getCalculator(byte, String)
Will be removed 5/2008 |
|
| cytoscape.visual.CalculatorCatalog.getCalculators(byte)
Will be removed 5/2008 |
|
| 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.visual.EdgeAppearance.getColor()
Use Appearance.get(VisualPropertyType) instead. Will be removed 5/2008. |
|
| giny.model.GraphPerspective.getConnectingNodeIndicesArray(int[])
Use getEdgeSourceIndex(int) and getEdgeTargetIndex(int) instead. |
|
| giny.model.RootGraph.getConnectingNodeIndicesArray(int[])
Use getEdgeSourceIndex(int) and getEdgeTargetIndex(int) instead, or use createGraphPerspective(int[], int[]). |
|
| ding.view.DNodeView.getCustomGraphicCount()
use getNumCustomGraphics().
Note that the new API methods work independent of the old API methods.
See addCustomGraphic(Shape,Paint,int)
for details. |
|
| ding.view.DNodeView.getCustomGraphicPaint(int)
use cytoscape.render.stateful.CustomGraphic.getPaint().
Note that the new API methods work independent of the old API methods.
See addCustomGraphic(Shape,Paint,int)
for details. |
|
| ding.view.DNodeView.getCustomGraphicShape(int)
use cytoscape.render.stateful.CustomGraphic.getShape().
Note that the new API methods work independent of the old API methods.
See addCustomGraphic(Shape,Paint,int)
for details. |
|
| cytoscape.view.CyMenus.getCytoPanelMenu()
Will be removed April 2008. Cytopanels no longer have a separate menu (they're in View). |
|
| cytoscape.visual.GlobalAppearanceCalculator.getDefaultSloppySelectionColor()
Will be removed 5/2008 |
|
| cytoscape.plugin.PluginInfo.getDownloadUrl()
See DownloadableInfo.getDownloadableURL()} will be removed June 2008 |
|
| 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.GraphPerspective.getEdgeIndicesArray(int, int, boolean)
Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead. |
|
| giny.model.RootGraph.getEdgeIndicesArray(int, int, 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.RootGraph.getEdgeIndicesArray(int, int, boolean, boolean)
Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead. |
|
| cytoscape.visual.NodeAppearance.getFillColor()
Use Appearance.get(VisualPropertyType) instead. Will be removed 5/2008. |
|
| cytoscape.visual.NodeAppearance.getFont()
Use Appearance.get(VisualPropertyType) instead. Will be removed 5/2008. |
|
| cytoscape.visual.EdgeAppearance.getFont()
Use Appearance.get(VisualPropertyType) instead. Will be removed 5/2008. |
|
| cytoscape.visual.NodeAppearance.getFontSize()
Use Appearance.get(VisualPropertyType) instead. Will be removed 5/2008. |
|
| cytoscape.visual.EdgeAppearance.getFontSize()
Use Appearance.get(VisualPropertyType) instead. Will be removed 5/2008. |
|
| cytoscape.visual.Arrow.getGinyArrow()
Will be removed 5/2008 |
|
| 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.visual.mappings.LegendTable.getHeader()
Will be removed 5/2008 |
|
| cytoscape.visual.NodeAppearance.getHeight()
Use Appearance.get(VisualPropertyType) instead. Will be removed 5/2008. |
|
| 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.NodeAppearance.getLabel()
Use Appearance.get(VisualPropertyType) instead. Will be removed 5/2008. |
|
| cytoscape.visual.EdgeAppearance.getLabel()
Use Appearance.get(VisualPropertyType) instead. Will be removed 5/2008. |
|
| cytoscape.visual.NodeAppearance.getLabelColor()
Use Appearance.get(VisualPropertyType) instead. Will be removed 5/2008. |
|
| cytoscape.visual.EdgeAppearance.getLabelColor()
Use Appearance.get(VisualPropertyType) instead. Will be removed 5/2008. |
|
| cytoscape.visual.NodeAppearance.getLabelPosition()
Use Appearance.get(VisualPropertyType) instead. Will be removed 5/2008. |
|
| cytoscape.visual.mappings.PassThroughMapping.getLegend(String, byte)
Use getLegend(VisualPropertyType) instead. Gone 5/2008. |
|
| cytoscape.visual.mappings.ObjectMapping.getLegend(String, byte)
Use getLegend(VisualPropertyType) instead. Gone 5/2008. |
|
| cytoscape.visual.mappings.DiscreteMapping.getLegend(String, byte)
Use getLegend(VisualPropertyType) instead. Gone 5/2008. |
|
| cytoscape.visual.mappings.ContinuousMapping.getLegend(String, byte)
Use getLegend(VisualPropertyType) instead. Gone 5/2008. |
|
| cytoscape.plugin.PluginInfo.getLicenseText()
See DownloadableInfo.getLicenseText() will be removed June 2008 |
|
| cytoscape.visual.EdgeAppearance.getLineType()
Use Appearance.get(VisualPropertyType) instead. Will be removed 5/2008. |
|
| cytoscape.data.readers.GMLReader.getLineType(int)
Don't use this. Set the line width directly. Gone 5/2008. |
|
| cytoscape.visual.ui.MiscDialog.getLineTypeIcons()
Use IconSupport instead. This will be removed 10/2007. |
|
| cytoscape.visual.ui.MiscDialog.getLineTypeToStringHashMap()
Use IconSupport instead. This will be removed 10/2007. |
|
| cytoscape.visual.EdgeAppearance.getLineWidth()
Use Appearance.get(VisualPropertyType) instead. Will be removed 5/2008. |
|
| cytoscape.visual.mappings.MappingType.getMappingType(String)
Will be removed 5/2008 |
|
| cytoscape.visual.Arrow.getName()
Will be removed 5/2008 |
|
| giny.model.GraphPerspective.getNodeIndex(int)
Use getRootGraphNodeIndex(int), whose functionality is identical. |
|
| cytoscape.visual.NodeAppearance.getNodeShape()
Use Appearance.get(VisualPropertyType) instead. Will be removed 5/2008. |
|
| 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. |
|
| cytoscape.plugin.PluginInfo.getPluginVersion()
See DownloadableInfo.getObjectVersion() will be removed June 2008 |
|
| cytoscape.visual.calculators.AbstractCalculator.getProperties(String)
Just use getProperties() - baseKey is already known by the calculator. This will be removed 10/2007. |
|
| cytoscape.visual.calculators.Calculator.getPropertyLabel()
Will be removed 5/2008 |
|
| cytoscape.visual.calculators.AbstractCalculator.getPropertyLabel()
Will be removed 5/2008 |
|
| cytoscape.visual.calculators.CalculatorFactory.getPropertyLabel(byte)
Use VisualPropertyType.getPropertyLabel(). Will be removed 4/2008 |
|
| 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.visual.NodeAppearance.getShape()
Use Appearance.get(VisualPropertyType) instead. Will be removed 5/2008. |
|
| cytoscape.visual.ui.MiscDialog.getShapeByteToStringHashMap()
Use IconSupport instead. This will be removed 10/2007. |
|
| cytoscape.visual.ui.MiscDialog.getShapeIcons()
Use IconSupport instead. This will be removed 10/2007. |
|
| cytoscape.visual.NodeAppearance.getSize()
Use Appearance.get(VisualPropertyType) instead. Will be removed 5/2008. |
|
| cytoscape.visual.GlobalAppearance.getSloppySelectionColor()
Will be removed 5/2008 |
|
| cytoscape.visual.EdgeAppearance.getSourceArrow()
Use Appearance.get(VisualPropertyType) instead. Will be removed 5/2008. |
|
| cytoscape.visual.ui.MiscDialog.getStringToArrowHashMap(int)
Use IconSupport instead. This will be removed 10/2007. |
|
| cytoscape.visual.ui.MiscDialog.getStringToLineTypeHashMap()
Use IconSupport instead. This will be removed 10/2007. |
|
| cytoscape.visual.ui.MiscDialog.getStringToShapeByteHashMap()
Use IconSupport instead. This will be removed 10/2007. |
|
| cytoscape.view.NetworkViewManager.getTabbedPane()
Tabbed view is no longer used. Will be removed Aug 2008. |
|
| cytoscape.visual.EdgeAppearance.getTargetArrow()
Use Appearance.get(VisualPropertyType) instead. Will be removed 5/2008. |
|
| cytoscape.visual.NodeAppearance.getToolTip()
Use Appearance.get(VisualPropertyType) instead. Will be removed 5/2008. |
|
| cytoscape.visual.EdgeAppearance.getToolTip()
Use Appearance.get(VisualPropertyType) instead. Will be removed 5/2008. |
|
| cytoscape.visual.VisualPropertyType.getType()
Will be removed 5/2008 |
|
| cytoscape.visual.calculators.Calculator.getType()
Will be removed 5/2008 |
|
| cytoscape.visual.calculators.AbstractCalculator.getType()
Will be removed 5/2008 |
|
| cytoscape.visual.calculators.Calculator.getTypeName()
Will be removed 5/2008 |
|
| cytoscape.visual.calculators.AbstractCalculator.getTypeName()
Will be removed 5/2008 |
|
| cytoscape.visual.calculators.CalculatorFactory.getTypeName(byte)
Use VisualPropertyType.getName() instead. Gone 5/2008. |
|
| 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.plugin.PluginInfo.getUrl()
See DownloadableInfo.getObjectUrl()} will be removed June 2008 |
|
| cytoscape.view.CytoscapeDesktop.getViewType()
View type is no longer used, so just don't use this method. Will be gone August 2008. |
|
| cytoscape.visual.VisualPropertyType.getVisualPorpertyType(byte)
Will be removed 5/2008. |
|
| cytoscape.view.CytoscapeDesktop.getVizMapUI()
use getVizMapperUI() isntead. |
|
| cytoscape.visual.NodeAppearance.getWidth()
Use Appearance.get(VisualPropertyType) instead. Will be removed 5/2008. |
|
| 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. |
|
| cytoscape.plugin.PluginInfo.isLicenseRequired()
See DownloadableInfo.isLicenseRequired() will be removed June 2008 |
|
| 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. |
|
| cytoscape.plugin.PluginInfo.isNewerPluginVersion(PluginInfo)
See DownloadableInfo.isNewerObjectVersion(DownloadableInfo)} will be removed June 2008
Compare the version of the object to the given object. |
|
| 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.parsers.NodeShapeParser.isValidShape(byte)
Will be removed 5/2008 |
|
| cytoscape.data.readers.InteractionsReader.layout(CyNetworkView)
Use getLayoutAlgorithm() instead. Gone 5/2008. |
|
| cytoscape.data.readers.GraphReader.layout(GraphView)
Use getLayoutAlgorithm().doLayout(view) instead. Will be removed 5/2008. |
|
| cytoscape.data.readers.AbstractGraphReader.layout(GraphView)
Use getLayoutAlgorithm().doLayout(view) instead. Will be removed 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.GraphPerspective.neighborsList(Node)
Use neighborsArray(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. |
|
| cytoscape.visual.calculators.CalculatorFactory.newCalculator(String, Properties, String, String)
Use othe newCalculator - we don't need the base interface class name any more. Will be removed 10/2007. |
|
| cytoscape.visual.calculators.CalculatorFactory.newDefaultCalculator(byte, String, ObjectMapping)
Use new BasicCalculator(name,mapper,type) instead. Gone 5/2008. |
|
| giny.model.RootGraph.nodeMetaChildrenList(Node)
Use getNodeMetaChildIndicesArray(int) instead. |
|
| giny.model.RootGraph.nodeMetaParentsList(int)
Use getNodeMetaParentIndicesArray(int) instead. |
|
| cytoscape.visual.parsers.NodeShapeParser.parseNodeShape(String)
Will be removed 5/2008 |
|
| 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.visual.CalculatorCatalog.removeCalculator(byte, String)
Will be removed 5/2008 |
|
| ding.view.DNodeView.removeCustomGraphic(int)
use removeCustomGraphic(CustomGraphic).
Note that the new API methods work independent of the old API methods.
See addCustomGraphic(Shape,Paint,int)
for details. |
|
| 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.NodeAppearance.set(byte, Object)
Use Appearance.set(VisualPropertyType,Object) instead. Will be removed 5/2008. |
|
| cytoscape.visual.EdgeAppearance.set(byte, Object)
Use Appearance.set(VisualPropertyType,Object) instead. Will be removed 5/2008. |
|
| cytoscape.visual.calculators.NodeSizeCalculator.set(VisualPropertyType)
DON'T USE. Only exists to support deprecated code. Will be removed 10/2007 |
|
| cytoscape.visual.calculators.NodeColorCalculator.set(VisualPropertyType)
DON'T USE. Only exists to support deprecated code. Will be removed 10/2007 |
|
| cytoscape.visual.calculators.EdgeArrowCalculator.set(VisualPropertyType)
DON'T USE. Only exists to support deprecated code. Will be removed 10/2007 |
|
| 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. |
|
| cytoscape.visual.NodeAppearance.setBorderColor(Color)
Use Appearance.set(VisualPropertyType,Object) instead. Will be removed 5/2008. |
|
| cytoscape.visual.NodeAppearance.setBorderLineType(LineType)
Use Appearance.set(VisualPropertyType,Object) instead. Will be removed 5/2008. |
|
| cytoscape.visual.EdgeAppearance.setColor(Color)
Use Appearance.set(VisualPropertyType,Object) instead. Will be removed 5/2008. |
|
| cytoscape.visual.GlobalAppearanceCalculator.setDefaultSloppySelectionColor(Color)
Will be removed 5/2008 |
|
| cytoscape.data.readers.GMLReader.setEdgeMaps(VisualMappingManager)
Don't use this. Gone 2/2009. |
|
| cytoscape.visual.NodeAppearance.setFillColor(Color)
Use Appearance.set(VisualPropertyType,Object) instead. Will be removed 5/2008. |
|
| cytoscape.visual.NodeAppearance.setFont(Font)
Use Appearance.set(VisualPropertyType,Object) instead. Will be removed 5/2008. |
|
| cytoscape.visual.EdgeAppearance.setFont(Font)
Use Appearance.set(VisualPropertyType,Object) instead. Will be removed 5/2008. |
|
| cytoscape.visual.NodeAppearance.setFontSize(float)
Use Appearance.set(VisualPropertyType,Object) instead. Will be removed 5/2008. |
|
| cytoscape.visual.EdgeAppearance.setFontSize(float)
Use Appearance.set(VisualPropertyType,Object) instead. Will be removed 5/2008. |
|
| 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.NodeAppearance.setHeight(double)
Use Appearance.set(VisualPropertyType,Object) instead. Will be removed 5/2008. |
|
| cytoscape.visual.NodeAppearance.setJustHeight(double)
Use Appearance.set(VisualPropertyType,Object) instead. Will be removed 5/2008. |
|
| cytoscape.visual.NodeAppearance.setJustWidth(double)
Use Appearance.set(VisualPropertyType,Object) instead. Will be removed 5/2008. Sets only the height variable. |
|
| cytoscape.visual.NodeAppearance.setLabel(String)
Use Appearance.set(VisualPropertyType,Object) instead. Will be removed 5/2008. |
|
| cytoscape.visual.EdgeAppearance.setLabel(String)
Use Appearance.set(VisualPropertyType,Object) instead. Will be removed 5/2008. |
|
| cytoscape.visual.NodeAppearance.setLabelColor(Color)
Use Appearance.set(VisualPropertyType,Object) instead. Will be removed 5/2008. |
|
| cytoscape.visual.EdgeAppearance.setLabelColor(Color)
Use Appearance.set(VisualPropertyType,Object) instead. Will be removed 5/2008. |
|
| cytoscape.visual.NodeAppearance.setLabelPosition(LabelPosition)
Use Appearance.set(VisualPropertyType,Object) instead. Will be removed 5/2008. |
|
| cytoscape.plugin.PluginInfo.setLicense(String, boolean)
See DownloadableInfo.setLicense(String, boolean) will be removed June 2008
Sets the license information for the plugin. Not required. |
|
| cytoscape.plugin.PluginInfo.setLicense(URL)
See DownloadableInfo#setLicense(String) will be removed June 2008
Sets the license information for the plugin. Not required. |
|
| cytoscape.visual.EdgeAppearance.setLineType(LineType)
Use Appearance.set(VisualPropertyType,Object) instead. Will be removed 5/2008. |
|
| cytoscape.visual.EdgeAppearance.setLineWidth(Float)
Use Appearance.set(VisualPropertyType,Object) instead. Will be removed 5/2008. |
|
| cytoscape.data.readers.GMLReader.setNodeMaps(VisualMappingManager)
Don't use this. Gone 2/2009. |
|
| cytoscape.visual.NodeAppearance.setNodeShape(NodeShape)
Use Appearance.set(VisualPropertyType,Object) instead. Will be removed 5/2008. |
|
| 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.plugin.PluginInfo.setPluginVersion(double)
See DownloadableInfo.setObjectVersion(double)} will be removed June 2008
Sets the version of the plugin. Defaults to 0.1 |
|
| 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.visual.NodeAppearance.setShape(byte)
Use Appearance.set(VisualPropertyType,Object) instead. Will be removed 5/2008. |
|
| cytoscape.visual.NodeAppearance.setSize(double)
Use Appearance.set(VisualPropertyType,Object) instead. Will be removed 5/2008. |
|
| cytoscape.visual.GlobalAppearance.setSloppySelectionColor(Color)
Will be removed 5/2008 |
|
| cytoscape.visual.EdgeAppearance.setSourceArrow(Arrow)
Use Appearance.set(VisualPropertyType,Object) instead. Will be removed 5/2008. |
|
| cytoscape.visual.EdgeAppearance.setTargetArrow(Arrow)
Use Appearance.set(VisualPropertyType,Object) instead. Will be removed 5/2008. |
|
| cytoscape.visual.NodeAppearance.setToolTip(String)
Use Appearance.set(VisualPropertyType,Object) instead. Will be removed 5/2008. |
|
| cytoscape.visual.EdgeAppearance.setToolTip(String)
Use Appearance.set(VisualPropertyType,Object) instead. Will be removed 5/2008. |
|
| cytoscape.view.CytoscapeDesktop.setupVizMapper()
use VizMapperMainPanel instead. |
|
| cytoscape.view.CyMenus.setVisualMapperItemsEnabled(boolean)
Will be removed April 2008. Item state is now handled by Actions directly. Don't use this. |
|
| cytoscape.visual.NodeAppearance.setWidth(double)
Use Appearance.set(VisualPropertyType,Object) instead. Will be removed 5/2008. |
|
| 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. |
|
|
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