|
Cytoscape 2.6.0 (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 |
|
| 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.EdgeLineTypeCalculator.calculateEdgeLineType(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.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.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. |
|
| cytoscape.view.NetworkPanel.fireFocus(String)
No longer used. If you need to fire focus, call CytoscapeDesktop.setFocus(). will be removed 11/2008. |
|
| cytoscape.visual.EdgeAppearance.get(byte)
Use Appearance.get(VisualPropertyType) instead. Will be removed 5/2008. |
|
| cytoscape.visual.NodeAppearance.get(byte)
Use Appearance.get(VisualPropertyType) instead. Will be removed 5/2008. |
|
| 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. |
|
| 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 |
|
| cytoscape.visual.NodeAppearance.getFillColor()
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.getFont()
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.NodeAppearance.getFontSize()
Use Appearance.get(VisualPropertyType) instead. Will be removed 5/2008. |
|
| cytoscape.visual.Arrow.getGinyArrow()
Will be removed 5/2008 |
|
| 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. |
|
| cytoscape.visual.EdgeAppearance.getLabel()
Use Appearance.get(VisualPropertyType) instead. Will be removed 5/2008. |
|
| cytoscape.visual.NodeAppearance.getLabel()
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.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.ContinuousMapping.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.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 |
|
| 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.AbstractCalculator.getPropertyLabel()
Will be removed 5/2008 |
|
| cytoscape.visual.calculators.Calculator.getPropertyLabel()
Will be removed 5/2008 |
|
| cytoscape.visual.calculators.CalculatorFactory.getPropertyLabel(byte)
Use VisualPropertyType.getPropertyLabel(). Will be removed 4/2008 |
|
| 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.EdgeAppearance.getToolTip()
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.VisualPropertyType.getType()
Will be removed 5/2008 |
|
| cytoscape.visual.calculators.AbstractCalculator.getType()
Will be removed 5/2008 |
|
| cytoscape.visual.calculators.Calculator.getType()
Will be removed 5/2008 |
|
| cytoscape.visual.calculators.AbstractCalculator.getTypeName()
Will be removed 5/2008 |
|
| cytoscape.visual.calculators.Calculator.getTypeName()
Will be removed 5/2008 |
|
| cytoscape.visual.calculators.CalculatorFactory.getTypeName(byte)
Use VisualPropertyType.getName() instead. Gone 5/2008. |
|
| 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. |
|
| cytoscape.view.CyMenus.initCytoPanelMenus()
Will be removed April 2008. Cytopanels are initialized in the Display* actions. Do not use. |
|
| cytoscape.plugin.PluginInfo.isLicenseRequired()
See DownloadableInfo.isLicenseRequired() will be removed June 2008 |
|
| cytoscape.plugin.PluginInfo.isNewerPluginVersion(PluginInfo)
See DownloadableInfo.isNewerObjectVersion(DownloadableInfo)} will be removed June 2008
Compare the version of the object to the given object. |
|
| 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. |
|
| 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. |
|
| 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 |
|
| cytoscape.visual.EdgeAppearance.set(byte, Object)
Use Appearance.set(VisualPropertyType,Object) instead. Will be removed 5/2008. |
|
| cytoscape.visual.NodeAppearance.set(byte, Object)
Use Appearance.set(VisualPropertyType,Object) instead. Will be removed 5/2008. |
|
| cytoscape.visual.calculators.NodeColorCalculator.set(VisualPropertyType)
DON'T USE. Only exists to support deprecated code. Will be removed 10/2007 |
|
| cytoscape.visual.calculators.NodeSizeCalculator.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.EdgeAppearance.setFont(Font)
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.setFontSize(float)
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.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.EdgeAppearance.setLabel(String)
Use Appearance.set(VisualPropertyType,Object) instead. Will be removed 5/2008. |
|
| cytoscape.visual.NodeAppearance.setLabel(String)
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.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.EdgeAppearance.setToolTip(String)
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.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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