|
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. |
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
|
cytoscape.visual.ui.DefaultPanel
|
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
|
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
|
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
|
cytoscape.visual.LineType
|
cytoscape.visual.ui.MiscDialog
This class has been enhanced and renamed to IconSupport.
This will be removed 10/2007. |
cytoscape.visual.OldStyleCalculatorIO
Use CalculatorIO instead. 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
|
cytoscape.visual.ui.ValueDisplayer
|
cytoscape.visual.ui.VizMapAttrTab
|
cytoscape.visual.ui.VizMapFontTab
|
cytoscape.visual.ui.VizMapTab
|
cytoscape.visual.ui.VizMapUI
|
|
Deprecated Methods |
cytoscape.visual.CalculatorCatalog.addChangeListener(ChangeListener, byte)
|
cytoscape.visual.CalculatorCatalog.addEdgeArrowCalculator(EdgeArrowCalculator)
Use addCalculator(calc) instead. Will be removed 10/2007. |
cytoscape.visual.CalculatorCatalog.addEdgeColorCalculator(EdgeColorCalculator)
Use addCalculator(calc) instead. Will be removed 10/2007. |
cytoscape.visual.CalculatorCatalog.addEdgeFontFaceCalculator(EdgeFontFaceCalculator)
Use addCalculator(calc) instead. Will be removed 10/2007. |
cytoscape.visual.CalculatorCatalog.addEdgeFontSizeCalculator(EdgeFontSizeCalculator)
Use addCalculator(calc) instead. Will be removed 10/2007. |
cytoscape.visual.CalculatorCatalog.addEdgeLabelCalculator(EdgeLabelCalculator)
Use addCalculator(calc) instead. Will be removed 10/2007. |
cytoscape.visual.CalculatorCatalog.addEdgeLineTypeCalculator(EdgeLineTypeCalculator)
Use addCalculator(calc) instead. Will be removed 10/2007. |
cytoscape.visual.CalculatorCatalog.addEdgeToolTipCalculator(EdgeToolTipCalculator)
Use addCalculator(calc) instead. Will be removed 10/2007. |
cytoscape.view.CytoscapeDesktop.addEdit(UndoableEdit)
Use CyUndo.getUndoableEditSupport().postEdit(edit) instead. Will be removed March 2008. |
cytoscape.visual.CalculatorCatalog.addNodeColorCalculator(NodeColorCalculator)
Use addCalculator(calc) instead. Will be removed 10/2007. |
cytoscape.visual.CalculatorCatalog.addNodeFontFaceCalculator(NodeFontFaceCalculator)
Use addCalculator(calc) instead. Will be removed 10/2007. |
cytoscape.visual.CalculatorCatalog.addNodeFontSizeCalculator(NodeFontSizeCalculator)
Use addCalculator(calc) instead. Will be removed 10/2007. |
cytoscape.visual.CalculatorCatalog.addNodeLabelCalculator(NodeLabelCalculator)
Use addCalculator(calc) instead. Will be removed 10/2007. |
cytoscape.visual.CalculatorCatalog.addNodeLabelColorCalculator(NodeLabelColorCalculator)
Use addCalculator(calc) instead. Will be removed 10/2007. |
cytoscape.visual.CalculatorCatalog.addNodeLineTypeCalculator(NodeLineTypeCalculator)
Use addCalculator(calc) instead. Will be removed 10/2007. |
cytoscape.visual.CalculatorCatalog.addNodeShapeCalculator(NodeShapeCalculator)
Use addCalculator(calc) instead. Will be removed 10/2007. |
cytoscape.visual.CalculatorCatalog.addNodeSizeCalculator(NodeSizeCalculator)
Use addCalculator(calc) instead. Will be removed 10/2007. |
cytoscape.visual.CalculatorCatalog.addNodeToolTipCalculator(NodeToolTipCalculator)
Use addCalculator(calc) instead. Will be removed 10/2007. |
cytoscape.visual.EdgeAppearance.applyAppearance(EdgeView, boolean)
Use applyAppearance(edgeView) instead - now we always
optimize. Will be removed 10/2007 |
cytoscape.visual.calculators.EdgeArrowCalculator.calculateEdgeArrow(Edge, CyNetwork)
Use Calculator.apply() instead. Will be removed 10/2007 |
cytoscape.visual.EdgeAppearanceCalculator.calculateEdgeColor(Edge, CyNetwork)
Use calculateEdgeAppearance() instead. This method will be
removed Sept. 2007. |
cytoscape.visual.calculators.EdgeColorCalculator.calculateEdgeColor(Edge, CyNetwork)
Use Calculator.apply() instead. Will be removed 10/2007 |
cytoscape.visual.EdgeAppearanceCalculator.calculateEdgeFont(Edge, CyNetwork)
Use calculateEdgeAppearance() instead. This method will be
removed Sept. 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.EdgeAppearanceCalculator.calculateEdgeLabel(Edge, CyNetwork)
Use calculateEdgeAppearance() instead. This method will be
removed Sept. 2007. |
cytoscape.visual.calculators.EdgeLabelCalculator.calculateEdgeLabel(Edge, CyNetwork)
Use Calculator.apply() instead. Will be removed 10/2007 |
cytoscape.visual.EdgeAppearanceCalculator.calculateEdgeLineType(Edge, CyNetwork)
Use calculateEdgeAppearance() instead. This method will be
removed Sept. 2007. |
cytoscape.visual.calculators.GenericEdgeLineTypeCalculator.calculateEdgeLineType(Edge, CyNetwork)
|
cytoscape.visual.calculators.EdgeLineTypeCalculator.calculateEdgeLineType(Edge, CyNetwork)
Use Calculator.apply() instead. Will be removed 10/2007 |
cytoscape.visual.EdgeAppearanceCalculator.calculateEdgeSourceArrow(Edge, CyNetwork)
Use calculateEdgeAppearance() instead. This method will be
removed Sept. 2007. |
cytoscape.visual.EdgeAppearanceCalculator.calculateEdgeTargetArrow(Edge, CyNetwork)
Use calculateEdgeAppearance() instead. This method will be
removed Sept. 2007. |
cytoscape.visual.EdgeAppearanceCalculator.calculateEdgeToolTip(Edge, CyNetwork)
Use calculateEdgeAppearance() instead. This method will be
removed Sept. 2007. |
cytoscape.visual.calculators.EdgeToolTipCalculator.calculateEdgeToolTip(Edge, CyNetwork)
Use Calculator.apply() instead. Will be removed 10/2007 |
cytoscape.visual.NodeAppearanceCalculator.calculateNodeBorderColor(Node, CyNetwork)
Use calculateNodeAppearance() and get the value from the
NodeAppearance. This method will be removed Sept 2007. |
cytoscape.visual.calculators.NodeColorCalculator.calculateNodeColor(Node, CyNetwork)
Use Calculator.apply() instead. Will be removed 10/2007 |
cytoscape.visual.NodeAppearanceCalculator.calculateNodeFillColor(Node, CyNetwork)
Use calculateNodeAppearance() and get the value from the
NodeAppearance. This method will be removed Sept 2007. |
cytoscape.visual.NodeAppearanceCalculator.calculateNodeFont(Node, CyNetwork)
Use calculateNodeAppearance() and get the value from the
NodeAppearance. This method will be removed Sept 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.NodeAppearanceCalculator.calculateNodeHeight(Node, CyNetwork)
Use calculateNodeAppearance() and get the value from the
NodeAppearance. This method will be removed Sept 2007. |
cytoscape.visual.NodeAppearanceCalculator.calculateNodeLabel(Node, CyNetwork)
Use calculateNodeAppearance() and get the value from the
NodeAppearance. This method will be removed Sept 2007. |
cytoscape.visual.calculators.NodeLabelCalculator.calculateNodeLabel(Node, CyNetwork)
Use Calculator.apply() instead. Will be removed 10/2007 |
cytoscape.visual.NodeAppearanceCalculator.calculateNodeLabelColor(Node, CyNetwork)
Use calculateNodeAppearance() and get the value from the
NodeAppearance. This method will be removed Sept 2007. |
cytoscape.visual.calculators.NodeLabelColorCalculator.calculateNodeLabelColor(Node, CyNetwork)
Use Calculator.apply() instead. Will be removed 10/2007 |
cytoscape.visual.NodeAppearanceCalculator.calculateNodeLineType(Node, CyNetwork)
Use calculateNodeAppearance() and get the value from the
NodeAppearance. This method will be removed Sept 2007. |
cytoscape.visual.calculators.GenericNodeLineTypeCalculator.calculateNodeLineType(Node, CyNetwork)
|
cytoscape.visual.calculators.NodeLineTypeCalculator.calculateNodeLineType(Node, CyNetwork)
Use Calculator.apply() instead. Will be removed 10/2007 |
cytoscape.visual.NodeAppearanceCalculator.calculateNodeShape(Node, CyNetwork)
Use calculateNodeAppearance() and get the value from the
NodeAppearance. This method will be removed Sept 2007. |
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.NodeAppearanceCalculator.calculateNodeToolTip(Node, CyNetwork)
Use calculateNodeAppearance() and get the value from the
NodeAppearance. This method will be removed Sept 2007. |
cytoscape.visual.calculators.NodeToolTipCalculator.calculateNodeToolTip(Node, CyNetwork)
Use Calculator.apply() instead. Will be removed 10/2007 |
cytoscape.visual.NodeAppearanceCalculator.calculateNodeWidth(Node, CyNetwork)
Use calculateNodeAppearance() and get the value from the
NodeAppearance. This method will be removed Sept 2007. |
cytoscape.visual.GlobalAppearanceCalculator.calculateSloppySelectionColor(CyNetwork)
|
cytoscape.visual.CalculatorCatalog.checkCalculatorName(byte, String)
|
cytoscape.visual.CalculatorCatalog.checkCalculatorName(String, byte)
|
cytoscape.visual.CalculatorCatalog.checkEdgeArrowCalculatorName(String)
Use checkCalculatorName(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.checkEdgeColorCalculatorName(String)
Use checkCalculatorName(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.checkEdgeFontFaceCalculatorName(String)
Use checkCalculatorName(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.checkEdgeFontSizeCalculatorName(String)
Use checkCalculatorName(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.checkEdgeLabelCalculatorName(String)
Use checkCalculatorName(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.checkEdgeLineTypeCalculatorName(String)
Use checkCalculatorName(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.checkEdgeToolTipCalculatorName(String)
Use checkCalculatorName(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.OldStyleCalculatorIO.checkForCalculators(Properties, CalculatorCatalog)
Use CalculatorIO instead. Will be removed 10/2007 |
cytoscape.visual.CalculatorCatalog.checkNodeColorCalculatorName(String)
Use checkCalculatorName(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.checkNodeFontFaceCalculatorName(String)
Use checkCalculatorName(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.checkNodeFontSizeCalculatorName(String)
Use checkCalculatorName(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.checkNodeLabelCalculatorName(String)
Use checkCalculatorName(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.checkNodeLabelColorCalculatorName(String)
Use checkCalculatorName(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.checkNodeLineTypeCalculatorName(String)
Use checkCalculatorName(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.checkNodeShapeCalculatorName(String)
Use checkCalculatorName(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.checkNodeSizeCalculatorName(String)
Use checkCalculatorName(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.checkNodeToolTipCalculatorName(String)
Use checkCalculatorName(type,name) instead. Will be removed
10/2007. |
cytoscape.plugin.CytoscapePlugin.describe()
|
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)
|
cytoscape.visual.CalculatorCatalog.getCalculators(byte)
|
cytoscape.CytoscapeInit.getClassLoader()
Will be removed December 2007.
Use PluginManager.getClassLoader() instead. |
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.EdgeAppearanceCalculator.getDefaultEdgeColor()
Use getDefaultAppearance() instead. This method will be
removed Sept. 2007. |
cytoscape.visual.EdgeAppearanceCalculator.getDefaultEdgeFont()
Use getDefaultAppearance() instead. This method will be
removed Sept. 2007. |
cytoscape.visual.EdgeAppearanceCalculator.getDefaultEdgeFontFace()
Use getDefaultAppearance() instead. This method will be
removed Sept. 2007. |
cytoscape.visual.EdgeAppearanceCalculator.getDefaultEdgeFontSize()
Use getDefaultAppearance() instead. This method will be
removed Sept. 2007. |
cytoscape.visual.EdgeAppearanceCalculator.getDefaultEdgeLabel()
Use getDefaultAppearance() instead. This method will be
removed Sept. 2007. |
cytoscape.visual.EdgeAppearanceCalculator.getDefaultEdgeLineType()
Use getDefaultAppearance() instead. This method will be
removed Sept. 2007. |
cytoscape.visual.EdgeAppearanceCalculator.getDefaultEdgeSourceArrow()
Use getDefaultAppearance() instead. This method will be
removed Sept. 2007. |
cytoscape.visual.EdgeAppearanceCalculator.getDefaultEdgeTargetArrow()
Use getDefaultAppearance() instead. This method will be
removed Sept. 2007. |
cytoscape.visual.EdgeAppearanceCalculator.getDefaultEdgeToolTip()
Use getDefaultAppearance() instead. This method will be
removed Sept. 2007. |
cytoscape.visual.NodeAppearanceCalculator.getDefaultNodeBorderColor()
Use setDefaultAppearance() instead. This method will be
removed Sept 2007. |
cytoscape.visual.NodeAppearanceCalculator.getDefaultNodeFillColor()
Use setDefaultAppearance() instead. This method will be
removed Sept 2007. |
cytoscape.visual.NodeAppearanceCalculator.getDefaultNodeFont()
Use setDefaultAppearance() instead. This method will be
removed Sept 2007. |
cytoscape.visual.NodeAppearanceCalculator.getDefaultNodeFontFace()
Use setDefaultAppearance() instead. This method will be
removed Sept 2007. |
cytoscape.visual.NodeAppearanceCalculator.getDefaultNodeFontSize()
Use setDefaultAppearance() instead. This method will be
removed Sept 2007. |
cytoscape.visual.NodeAppearanceCalculator.getDefaultNodeHeight()
Use setDefaultAppearance() instead. This method will be
removed Sept 2007. |
cytoscape.visual.NodeAppearanceCalculator.getDefaultNodeLabel()
Use setDefaultAppearance() instead. This method will be
removed Sept 2007. |
cytoscape.visual.NodeAppearanceCalculator.getDefaultNodeLabelColor()
Use setDefaultAppearance() instead. This method will be
removed Sept 2007. |
cytoscape.visual.NodeAppearanceCalculator.getDefaultNodeLineType()
Use setDefaultAppearance() instead. This method will be
removed Sept 2007. |
cytoscape.visual.NodeAppearanceCalculator.getDefaultNodeShape()
Use setDefaultAppearance() instead. This method will be
removed Sept 2007. |
cytoscape.visual.NodeAppearanceCalculator.getDefaultNodeToolTip()
Use setDefaultAppearance() instead. This method will be
removed Sept 2007. |
cytoscape.visual.NodeAppearanceCalculator.getDefaultNodeWidth()
Use setDefaultAppearance() instead. This method will be
removed Sept 2007. |
cytoscape.visual.GlobalAppearanceCalculator.getDefaultSloppySelectionColor()
|
cytoscape.visual.CalculatorCatalog.getEdgeArrowCalculator(String)
Use getCalculator(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.getEdgeArrowCalculators()
Use getCalculators(type) instead. Will be removed 10/2007. |
cytoscape.visual.EdgeAppearanceCalculator.getEdgeColorCalculator()
Use getCalculator(type) instead. This method will be removed
Sept. 2007. |
cytoscape.visual.CalculatorCatalog.getEdgeColorCalculator(String)
Use getCalculator(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.getEdgeColorCalculators()
Use getCalculators(type) instead. Will be removed 10/2007. |
cytoscape.visual.EdgeAppearanceCalculator.getEdgeFontFaceCalculator()
Use getCalculator(type) instead. This method will be removed
Sept. 2007. |
cytoscape.visual.CalculatorCatalog.getEdgeFontFaceCalculator(String)
Use getCalculator(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.getEdgeFontFaceCalculators()
Use getCalculators(type) instead. Will be removed 10/2007. |
cytoscape.visual.EdgeAppearanceCalculator.getEdgeFontSizeCalculator()
Use getCalculator(type) instead. This method will be removed
Sept. 2007. |
cytoscape.visual.CalculatorCatalog.getEdgeFontSizeCalculator(String)
Use getCalculator(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.getEdgeFontSizeCalculators()
Use getCalculators(type) instead. Will be removed 10/2007. |
cytoscape.visual.EdgeAppearanceCalculator.getEdgeLabelCalculator()
Use getCalculator(type) instead. This method will be removed
Sept. 2007. |
cytoscape.visual.CalculatorCatalog.getEdgeLabelCalculator(String)
Use getCalculator(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.getEdgeLabelCalculators()
Use getCalculators(type) instead. Will be removed 10/2007. |
cytoscape.visual.EdgeAppearanceCalculator.getEdgeLineTypeCalculator()
Use getCalculator(type) instead. This method will be removed
Sept. 2007. |
cytoscape.visual.CalculatorCatalog.getEdgeLineTypeCalculator(String)
Use getCalculator(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.getEdgeLineTypeCalculators()
Use getCalculators(type) instead. Will be removed 10/2007. |
cytoscape.visual.EdgeAppearanceCalculator.getEdgeSourceArrowCalculator()
Use getCalculator(type) instead. This method will be removed
Sept. 2007. |
cytoscape.visual.EdgeAppearanceCalculator.getEdgeTargetArrowCalculator()
Use getCalculator(type) instead. This method will be removed
Sept. 2007. |
cytoscape.visual.EdgeAppearanceCalculator.getEdgeToolTipCalculator()
Use getCalculator(type) instead. This method will be removed
Sept. 2007. |
cytoscape.visual.CalculatorCatalog.getEdgeToolTipCalculator(String)
Use getCalculator(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.getEdgeToolTipCalculators()
Use getCalculators(type) instead. Will be removed 10/2007. |
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()
|
cytoscape.visual.mappings.LegendTable.getHeader()
|
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.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.visual.mappings.ObjectMapping.getLegend(String, byte)
Use getLegend(VisualPropertyType) instead. Gone 5/2008. |
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)
|
cytoscape.visual.Arrow.getName()
|
cytoscape.visual.NodeAppearanceCalculator.getNodeBorderColorCalculator()
Use getCalculator(type) instead. This method will be removed
Sept 2007. |
cytoscape.visual.CalculatorCatalog.getNodeColorCalculator(String)
Use getCalculator(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.getNodeColorCalculators()
Use getCalculators(type) instead. Will be removed 10/2007. |
cytoscape.visual.NodeAppearanceCalculator.getNodeFillColorCalculator()
Use getCalculator(type) instead. This method will be removed
Sept 2007. |
cytoscape.visual.NodeAppearanceCalculator.getNodeFontFaceCalculator()
Use getCalculator(type) instead. This method will be removed
Sept 2007. |
cytoscape.visual.CalculatorCatalog.getNodeFontFaceCalculator(String)
Use getCalculator(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.getNodeFontFaceCalculators()
Use getCalculators(type) instead. Will be removed 10/2007. |
cytoscape.visual.NodeAppearanceCalculator.getNodeFontSizeCalculator()
Use getCalculator(type) instead. This method will be removed
Sept 2007. |
cytoscape.visual.CalculatorCatalog.getNodeFontSizeCalculator(String)
Use getCalculator(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.getNodeFontSizeCalculators()
Use getCalculators(type) instead. Will be removed 10/2007. |
cytoscape.visual.NodeAppearanceCalculator.getNodeHeightCalculator()
Use getCalculator(type) instead. This method will be removed
Sept 2007. |
cytoscape.visual.NodeAppearanceCalculator.getNodeLabelCalculator()
Use getCalculator(type) instead. This method will be removed
Sept 2007. |
cytoscape.visual.CalculatorCatalog.getNodeLabelCalculator(String)
Use getCalculator(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.getNodeLabelCalculators()
Use getCalculators(type) instead. Will be removed 10/2007. |
cytoscape.visual.NodeAppearanceCalculator.getNodeLabelColorCalculator()
Use getCalculator(type) instead. This method will be removed
Sept 2007. |
cytoscape.visual.CalculatorCatalog.getNodeLabelColorCalculator(String)
Use getCalculator(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.getNodeLabelColorCalculators()
Use getCalculators(type) instead. Will be removed 10/2007. |
cytoscape.visual.NodeAppearanceCalculator.getNodeLineTypeCalculator()
Use getCalculator(type) instead. This method will be removed
Sept 2007. |
cytoscape.visual.CalculatorCatalog.getNodeLineTypeCalculator(String)
Use getCalculator(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.getNodeLineTypeCalculators()
Use getCalculators(type) instead. Will be removed 10/2007. |
cytoscape.visual.NodeAppearance.getNodeShape()
Use Appearance.get(VisualPropertyType) instead. Will be removed 5/2008. |
cytoscape.visual.NodeAppearanceCalculator.getNodeShapeCalculator()
Use getCalculator(type) instead. This method will be removed
Sept 2007. |
cytoscape.visual.CalculatorCatalog.getNodeShapeCalculator(String)
Use getCalculator(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.getNodeShapeCalculators()
Use getCalculators(type) instead. Will be removed 10/2007. |
cytoscape.visual.CalculatorCatalog.getNodeSizeCalculator(String)
Use getCalculator(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.getNodeSizeCalculators()
Use getCalculators(type) instead. Will be removed 10/2007. |
cytoscape.visual.NodeAppearanceCalculator.getNodeToolTipCalculator()
Use getCalculator(type) instead. This method will be removed
Sept 2007. |
cytoscape.visual.CalculatorCatalog.getNodeToolTipCalculator(String)
Use getCalculator(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.getNodeToolTipCalculators()
Use getCalculators(type) instead. Will be removed 10/2007. |
cytoscape.visual.NodeAppearanceCalculator.getNodeWidthCalculator()
Use getCalculator(type) instead. This method will be removed
Sept 2007. |
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.CytoscapeInit.getPluginURLs()
Will be removed December 2007.
Use PluginManager.getPluginURLs() instead. |
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()
|
cytoscape.visual.calculators.Calculator.getPropertyLabel()
|
cytoscape.visual.calculators.CalculatorFactory.getPropertyLabel(byte)
Use VisualPropertyType.getPropertyLabel(). Will be removed 4/2008 |
cytoscape.CytoscapeInit.getResourcePlugins()
Will be removed December 2007.
Use PluginManager.getResourcePlugins() instead. |
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()
|
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.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()
|
cytoscape.visual.calculators.AbstractCalculator.getType()
|
cytoscape.visual.calculators.Calculator.getType()
|
cytoscape.visual.CalculatorCatalog.getType(Calculator)
Use calc.getType() instead. Will be removed 10/2007. |
cytoscape.visual.calculators.AbstractCalculator.getTypeName()
|
cytoscape.visual.calculators.Calculator.getTypeName()
|
cytoscape.visual.calculators.CalculatorFactory.getTypeName(byte)
Use VisualPropertyType.getName() instead. Gone 5/2008. |
cytoscape.visual.VisualPropertyType.getVisualPorpertyType(byte)
|
cytoscape.view.CytoscapeDesktop.getVizMapManager()
Use Cytoscape.getVisualMappingManager() instead. This will be
removed at 03/2007 (possibly sooner). |
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.visual.parsers.NodeShapeParser.isValidShape(byte)
|
cytoscape.data.readers.InteractionsReader.layout(CyNetworkView)
Use getLayoutAlgorithm() instead. Gone 5/2008. |
cytoscape.data.readers.AbstractGraphReader.layout(GraphView)
Use getLayoutAlgorithm().doLayout(view) instead. Will be removed 5/2008. |
cytoscape.data.readers.GraphReader.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.OldStyleCalculatorIO.loadCalculators(Properties, CalculatorCatalog)
Use CalculatorIO instead. Will be removed 10/2007 |
cytoscape.CytoscapeInit.loadPlugin(Class, String)
Will be removed December 2007.
Will not be replaced by a public method, PluginManager handles all loading now. |
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)
|
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)
|
cytoscape.visual.CalculatorCatalog.removeCalculator(byte, String)
|
cytoscape.visual.CalculatorIO.removeDuplicate(Calculator, CalculatorCatalog)
WTF? Use CalculatorCatalog.removeCalculator() Will be removed
10/2007 |
cytoscape.visual.CalculatorCatalog.removeEdgeArrowCalculator(String)
Use removeCalculator(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.removeEdgeColorCalculator(String)
Use removeCalculator(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.removeEdgeFontFaceCalculator(String)
Use removeCalculator(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.removeEdgeFontSizeCalculator(String)
Use removeCalculator(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.removeEdgeLabelCalculator(String)
Use removeCalculator(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.removeEdgeLineTypeCalculator(String)
Use removeCalculator(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.removeEdgeToolTipCalculator(String)
Use removeCalculator(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.removeNodeColorCalculator(String)
Use removeCalculator(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.removeNodeFontFaceCalculator(String)
Use removeCalculator(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.removeNodeFontSizeCalculator(String)
Use removeCalculator(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.removeNodeLabelCalculator(String)
Use removeCalculator(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.removeNodeLabelColorCalculator(String)
Use removeCalculator(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.removeNodeLineTypeCalculator(String)
Use removeCalculator(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.removeNodeShapeCalculator(String)
Use removeCalculator(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.removeNodeSizeCalculator(String)
Use removeCalculator(type,name) instead. Will be removed
10/2007. |
cytoscape.visual.CalculatorCatalog.removeNodeToolTipCalculator(String)
Use removeCalculator(type,name) instead. Will be removed
10/2007. |
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.EdgeArrowCalculator.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.NodeColorCalculator.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.Cytoscape.setCurrentNetwork(String)
This will be removed Feb 2007. |
cytoscape.Cytoscape.setCurrentNetworkView(String)
This will be removed Feb 2007. |
cytoscape.visual.EdgeAppearanceCalculator.setDefaultEdgeColor(Color)
Use setDefaultAppearance() instead. This method will be
removed Sept. 2007. |
cytoscape.visual.EdgeAppearanceCalculator.setDefaultEdgeFont(Font)
Use setDefaultAppearance() instead. This method will be
removed Sept. 2007. |
cytoscape.visual.EdgeAppearanceCalculator.setDefaultEdgeFontFace(Font)
Use setDefaultAppearance() instead. This method will be
removed Sept. 2007. |
cytoscape.visual.EdgeAppearanceCalculator.setDefaultEdgeFontSize(float)
Use setDefaultAppearance() instead. This method will be
removed Sept. 2007. |
cytoscape.visual.EdgeAppearanceCalculator.setDefaultEdgeLabel(String)
Use setDefaultAppearance() instead. This method will be
removed Sept. 2007. |
cytoscape.visual.EdgeAppearanceCalculator.setDefaultEdgeLineType(LineType)
Use setDefaultAppearance() instead. This method will be
removed Sept. 2007. |
cytoscape.visual.EdgeAppearanceCalculator.setDefaultEdgeSourceArrow(Arrow)
Use setDefaultAppearance() instead. This method will be
removed Sept. 2007. |
cytoscape.visual.EdgeAppearanceCalculator.setDefaultEdgeTargetArrow(Arrow)
Use setDefaultAppearance() instead. This method will be
removed Sept. 2007. |
cytoscape.visual.EdgeAppearanceCalculator.setDefaultEdgeToolTip(String)
Use setDefaultAppearance() instead. This method will be
removed Sept. 2007. |
cytoscape.visual.NodeAppearanceCalculator.setDefaultNodeBorderColor(Color)
Use getDefaultAppearance() and then set that. This method
will be removed Sept 2007. |
cytoscape.visual.NodeAppearanceCalculator.setDefaultNodeFillColor(Color)
Use getDefaultAppearance() and then set that. This method
will be removed Sept 2007. |
cytoscape.visual.NodeAppearanceCalculator.setDefaultNodeFont(Font)
Use getDefaultAppearance() and then set that. This method
will be removed Sept 2007. |
cytoscape.visual.NodeAppearanceCalculator.setDefaultNodeFontFace(Font)
Use getDefaultAppearance() and then set that. This method
will be removed Sept 2007. |
cytoscape.visual.NodeAppearanceCalculator.setDefaultNodeFontSize(float)
Use getDefaultAppearance() and then set that. This method
will be removed Sept 2007. |
cytoscape.visual.NodeAppearanceCalculator.setDefaultNodeHeight(double)
Use getDefaultAppearance() and then set that. This method
will be removed Sept 2007. |
cytoscape.visual.NodeAppearanceCalculator.setDefaultNodeLabel(String)
Use getDefaultAppearance() and then set that. This method
will be removed Sept 2007. |
cytoscape.visual.NodeAppearanceCalculator.setDefaultNodeLabelColor(Color)
Use getDefaultAppearance() and then set that. This method
will be removed Sept 2007. |
cytoscape.visual.NodeAppearanceCalculator.setDefaultNodeLineType(LineType)
Use getDefaultAppearance() and then set that. This method
will be removed Sept 2007. |
cytoscape.visual.NodeAppearanceCalculator.setDefaultNodeShape(byte)
Use getDefaultAppearance() and then set that. This method
will be removed Sept 2007. |
cytoscape.visual.NodeAppearanceCalculator.setDefaultNodeToolTip(String)
Use getDefaultAppearance() and then set that. This method
will be removed Sept 2007. |
cytoscape.visual.NodeAppearanceCalculator.setDefaultNodeWidth(double)
Use getDefaultAppearance() and then set that. This method
will be removed Sept 2007. |
cytoscape.visual.GlobalAppearanceCalculator.setDefaultSloppySelectionColor(Color)
|
cytoscape.visual.EdgeAppearanceCalculator.setEdgeColorCalculator(EdgeColorCalculator)
Use setCalculator(calc) instead. This method will be removed
Sept. 2007. |
cytoscape.visual.EdgeAppearanceCalculator.setEdgeFontFaceCalculator(EdgeFontFaceCalculator)
Use setCalculator(calc) instead. This method will be removed
Sept. 2007. |
cytoscape.visual.EdgeAppearanceCalculator.setEdgeFontSizeCalculator(EdgeFontSizeCalculator)
Use setCalculator(calc) instead. This method will be removed
Sept. 2007. |
cytoscape.visual.EdgeAppearanceCalculator.setEdgeLabelCalculator(EdgeLabelCalculator)
Use setCalculator(calc) instead. This method will be removed
Sept. 2007. |
cytoscape.visual.EdgeAppearanceCalculator.setEdgeLineTypeCalculator(EdgeLineTypeCalculator)
Use setCalculator(calc) instead. This method will be removed
Sept. 2007. |
cytoscape.visual.EdgeAppearanceCalculator.setEdgeSourceArrowCalculator(EdgeArrowCalculator)
Use setCalculator(calc) instead. This method will be removed
Sept. 2007. |
cytoscape.visual.EdgeAppearanceCalculator.setEdgeTargetArrowCalculator(EdgeArrowCalculator)
Use setCalculator(calc) instead. This method will be removed
Sept. 2007. |
cytoscape.visual.EdgeAppearanceCalculator.setEdgeToolTipCalculator(EdgeToolTipCalculator)
Use setCalculator(calc) instead. This method will be removed
Sept. 2007. |
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.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.visual.NodeAppearanceCalculator.setNodeBorderColorCalculator(NodeColorCalculator)
Use setCalculator(calc) instead. This method will be removed
Sept 2007. |
cytoscape.visual.NodeAppearanceCalculator.setNodeFillColorCalculator(NodeColorCalculator)
Use setCalculator(calc) instead. This method will be removed
Sept 2007. |
cytoscape.visual.NodeAppearanceCalculator.setNodeFontFaceCalculator(NodeFontFaceCalculator)
Use setCalculator(calc) instead. This method will be removed
Sept 2007. |
cytoscape.visual.NodeAppearanceCalculator.setNodeFontSizeCalculator(NodeFontSizeCalculator)
Use setCalculator(calc) instead. This method will be removed
Sept 2007. |
cytoscape.visual.NodeAppearanceCalculator.setNodeHeightCalculator(NodeSizeCalculator)
Use setCalculator(calc) instead. This method will be removed
Sept 2007. |
cytoscape.visual.NodeAppearanceCalculator.setNodeLabelCalculator(NodeLabelCalculator)
Use setCalculator(calc) instead. This method will be removed
Sept 2007. |
cytoscape.visual.NodeAppearanceCalculator.setNodeLabelColorCalculator(NodeLabelColorCalculator)
Use setCalculator(calc) instead. This method will be removed
Sept 2007. |
cytoscape.visual.NodeAppearanceCalculator.setNodeLineTypeCalculator(NodeLineTypeCalculator)
Use setCalculator(calc) instead. This method will be removed
Sept 2007. |
cytoscape.visual.NodeAppearance.setNodeShape(NodeShape)
Use Appearance.set(VisualPropertyType,Object) instead. Will be removed 5/2008. |
cytoscape.visual.NodeAppearanceCalculator.setNodeShapeCalculator(NodeShapeCalculator)
Use setCalculator(calc) instead. This method will be removed
Sept 2007. |
cytoscape.view.CyMenus.setNodesRequiredItemsEnabled()
Will be removed April 2008. Item state is now handled by Actions directly. Don't use this. |
cytoscape.visual.NodeAppearanceCalculator.setNodeToolTipCalculator(NodeToolTipCalculator)
Use setCalculator(calc) instead. This method will be removed
Sept 2007. |
cytoscape.visual.NodeAppearanceCalculator.setNodeWidthCalculator(NodeSizeCalculator)
Use setCalculator(calc) instead. This method will be removed
Sept 2007. |
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) |
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)
|
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.dialogs.preferences.PreferenceValueDialog.validatedPluginData(Component, String)
no longer used by anyting. Will leave this world Dec 2007. |