|
Deprecated Methods |
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.giny.FingCyNetwork.addFlagEventListener(FlagEventListener)
As of 2.3, replaced by FingCyNetwork.addSelectEventListener(SelectEventListener) |
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.NodeAppearance.applyAppearance(NodeView, boolean)
use applyAppearance(nodeView) instead - now we always optimize.
will be removed 10/2007 |
cytoscape.dialogs.MiscGB.buttonAndColor(JDialog, MutableColor, JLabel, String)
No one uses this so don't start. Will be removed 12/2006. |
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.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.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.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.Cytoscape.createNetwork(String, int, boolean, BioDataServer, String)
It will be removed in April 2007 Use CyNetwork
createNetworkFromFile(String location, boolean create_view)
instead. File type is no longer needed as ImportHandler now
manages all file types. |
cytoscape.CyNetwork.flagAllEdges()
As of 2.3, replaced by CyNetwork.selectAllEdges() |
cytoscape.giny.FingCyNetwork.flagAllEdges()
As of 2.3, replaced by FingCyNetwork.selectAllEdges() |
cytoscape.CyNetwork.flagAllNodes()
As of 2.3, replaced by CyNetwork.selectAllNodes() |
cytoscape.giny.FingCyNetwork.flagAllNodes()
As of 2.3, replaced by FingCyNetwork.selectAllNodes() |
cytoscape.CytoscapeInit.getArgs()
Use Properties (getProperties()) instead of args for
accessing initialization information. This method will be
removed April 2007. |
cytoscape.CytoscapeConfig.getArgs()
Will be removed October 2006. Use methods in CytoscapeInit instead. |
cytoscape.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.CytoscapeInit.getBioDataServer()
This method will be removed April 2007. Use
getProperty("bioDataServer") instead. |
cytoscape.CytoscapeVersion.getBriefHistory()
See cytoscape.org for history. Will be removed 10/2007 |
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.CytoscapeInit.getConfigDirectoy()
This method is only deprecated because it is misspelled. Just
use the correctly spelled method: getConfigDirectory(). This
method will be removed 12/2006. |
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.CytoscapeInit.getDefaultSpeciesName()
Will be removed April 2007. Use getProperty(
"defaultSpeciesName" ) instead. |
cytoscape.CytoscapeInit.getDefaultVisualStyle()
Will be removed April 2007. Use getProperties().getProperty(
"defaultVisualStyle" ) instead. |
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.CytoscapeInit.getEdgeAttributes()
Will be removed April 2007. No one appears to be using this
method, so don't start. |
cytoscape.data.readers.AbstractGraphReader.getEdgeAttributes()
Use Cytoscape.getEdgeAttributes() instead. Will be removed Dec 2006. |
cytoscape.data.readers.GraphReader.getEdgeAttributes()
Use Cytoscape.getEdgeAttributes() instead. Will be removed Dec 2006. |
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.giny.FingCyNetwork.getExpressionData()
@see{getNetworkData}
Returns the expression data object associated with this network.
Will be removed Feb 2007. |
cytoscape.CytoscapeInit.getExpressionFiles()
Will be removed April 2007. No one appears to be using this
method, so don't start. |
cytoscape.CyNetwork.getFlaggedEdgeIndicesArray()
As of 2.3, replaced by CyNetwork.getSelectedEdges() |
cytoscape.giny.FingCyNetwork.getFlaggedEdgeIndicesArray()
As of 2.3, replaced by FingCyNetwork.getSelectedEdges() |
cytoscape.CyNetwork.getFlaggedEdges()
As of 2.3, replaced by CyNetwork.getSelectedEdges() |
cytoscape.giny.FingCyNetwork.getFlaggedEdges()
As of 2.3, replaced by FingCyNetwork.getSelectedEdges() |
cytoscape.CyNetwork.getFlaggedNodeIndicesArray()
As of 2.3, replaced by CyNetwork.getSelectedNodes() |
cytoscape.giny.FingCyNetwork.getFlaggedNodeIndicesArray()
As of 2.3, replaced by FingCyNetwork.getSelectedNodes() |
cytoscape.CyNetwork.getFlaggedNodes()
As of 2.3, replaced by CyNetwork.getSelectedNodes() |
cytoscape.giny.FingCyNetwork.getFlaggedNodes()
As of 2.3, replaced by FingCyNetwork.getSelectedNodes() |
cytoscape.CyNetwork.getFlagger()
As of 2.3, replaced by CyNetwork.getSelectFilter() |
cytoscape.giny.FingCyNetwork.getFlagger()
As of 2.3, replaced by FingCyNetwork.getSelectFilter() |
cytoscape.CytoscapeInit.getGraphFiles()
Will be removed April 2007. No one appears to be using this
method, so don't start. |
cytoscape.CytoscapeInit.getHelp()
This method will be removed April 2007. No one appears to use
this method, so don't start. |
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.CytoscapeInit.getNodeAttributes()
Will be removed April 2007. No one appears to be using this
method, so don't start. |
cytoscape.data.readers.AbstractGraphReader.getNodeAttributes()
Use Cytoscape.getNodeAttributes() instead. Will be removed Dec 2006. |
cytoscape.data.readers.GraphReader.getNodeAttributes()
Use Cytoscape.getNodeAttributes() instead. Will be removed Dec 2006. |
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.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.CytoscapeConfig.getProperties()
Will be removed October 2006. Use methods in CytoscapeInit instead. |
cytoscape.visual.calculators.AbstractCalculator.getProperties(String)
Just use getProperties() - baseKey is already known by the calculator. This will
be removed 10/2007. |
cytoscape.CytoscapeInit.getPropertiesLocation()
This method will be removed April 2007. |
cytoscape.CytoscapeInit.getProperty(String)
Use getProperties().getProperty( ) instead. Since this method
never made it into a release, it will be removed Summer 2006. |
cytoscape.data.readers.AbstractGraphReader.getRootGraph()
Use Cytoscape.getRootGraph() instead. Will be removed Dec 2006. |
cytoscape.data.readers.GraphReader.getRootGraph()
Use Cytoscape.getRootGraph() instead. Will be removed Dec 2006. |
cytoscape.CytoscapeInit.getSecondaryViewThreshold()
Will be removed April 2007. Use getProperty(
"secondaryViewThreshold" ) instead. |
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.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.CalculatorCatalog.getType(Calculator)
Use calc.getType() instead. Will be removed 10/2007. |
cytoscape.data.readers.GMLTree.getVector(String, String, int)
use anonymous String arrays instead |
cytoscape.CytoscapeInit.getViewThreshold()
Will be removed April 2007. Use getProperty( "viewThreshold" )
instead. |
cytoscape.CytoscapeInit.getViewType()
Will be removed April 2007. Use
CytoscapeDesktop.parseViewType(CytoscapeInit.getProperties().getProperty("viewType")); |
cytoscape.view.CytoscapeDesktop.getVizMapManager()
Use Cytoscape.getVisualMappingManager() instead. This will be
removed at 03/2007 (possibly sooner). |
cytoscape.CytoscapeInit.getVizmapPropertiesLocation()
Will be removed April 2007. Use getProperties().getProperty(
"TODO" ) instead. |
cytoscape.CyNetwork.isFlagged(Edge)
As of 2.3, replaced by CyNetwork.isSelected(Edge) |
cytoscape.giny.FingCyNetwork.isFlagged(Edge)
As of 2.3, replaced by FingCyNetwork.isSelected(Edge) |
cytoscape.CyNetwork.isFlagged(Node)
As of 2.3, replaced by CyNetwork.isSelected(Node) |
cytoscape.giny.FingCyNetwork.isFlagged(Node)
As of 2.3, replaced by FingCyNetwork.isSelected(Node) |
cytoscape.CytoscapeInit.isHeadless()
This method will be removed April 2007. Use getMode()
instead. |
cytoscape.Cytoscape.loadAttributes(String[], String[], boolean, BioDataServer, String)
Use loadAttributes(nodeAttrLocations,edgeAttrLocations)
instead. BioDataServer, canonicalize, and species are no
longer used. Will be removed 10/2007. |
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.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.CytoscapeInit.noCanonicalization()
Will be removed April 2007. Use getProperty(
"canonicalizeNames" ) instead. |
cytoscape.CyNetwork.putClientData(String, Object)
Use CyAttributes directly. This method will be
removed in May, 2007. |
cytoscape.giny.FingCyNetwork.putClientData(String, Object)
Networks can support client data. |
cytoscape.data.readers.AbstractGraphReader.read(boolean)
Use read() instead. Will be removed Dec 2006. |
cytoscape.data.readers.GraphReader.read(boolean)
Use read() instead. Will be removed Dec 2006. |
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.CyNetwork.removeFlagEventListener(FlagEventListener)
As of 2.3, replaced by CyNetwork.removeSelectEventListener(SelectEventListener) |
cytoscape.giny.FingCyNetwork.removeFlagEventListener(FlagEventListener)
As of 2.3, replaced by FingCyNetwork.removeSelectEventListener(SelectEventListener) |
cytoscape.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.calculators.EdgeArrowCalculator.set(byte, String, String)
DON'T USE. Only exists to support deprecated code.
Will be removed 10/2007 |
cytoscape.visual.calculators.NodeSizeCalculator.set(byte, String, String)
DON'T USE. Only exists to support deprecated code.
Will be removed 10/2007 |
cytoscape.visual.calculators.NodeColorCalculator.set(byte, String, String)
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.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.CytoscapeInit.setDefaultSpeciesName()
Will be removed April 2007. This doesn't do anything. To set
the default species name use
getProperties().setProperty("defaultSpeciesName", newName),
which you were presumably doing already. |
cytoscape.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.giny.FingCyNetwork.setExpressionData(ExpressionData)
Sets the expression data object associated with this network.
Will be removed Feb 2007. |
cytoscape.CyNetwork.setFlagged(Edge, boolean)
As of 2.3, replaced by CyNetwork.setSelectedEdgeState(Edge,boolean) |
cytoscape.giny.FingCyNetwork.setFlagged(Edge, boolean)
As of 2.3, replaced by FingCyNetwork.setSelectedEdgeState(Collection,boolean) |
cytoscape.CyNetwork.setFlagged(Node, boolean)
As of 2.3, replaced by CyNetwork.setSelectedNodeState(Node,boolean) |
cytoscape.giny.FingCyNetwork.setFlagged(Node, boolean)
As of 2.3, replaced by FingCyNetwork.setSelectedNodeState(Collection,boolean) |
cytoscape.CyNetwork.setFlaggedEdges(Collection, boolean)
As of 2.3, replaced by CyNetwork.setSelectedEdgeState(Collection,boolean) |
cytoscape.giny.FingCyNetwork.setFlaggedEdges(Collection, boolean)
As of 2.3, replaced by FingCyNetwork.setSelectedEdgeState(Collection,boolean) |
cytoscape.CyNetwork.setFlaggedEdges(int[], boolean)
As of 2.3, replaced by CyNetwork.setSelectedEdgeState(Collection,boolean) |
cytoscape.giny.FingCyNetwork.setFlaggedEdges(int[], boolean)
As of 2.3, replaced by FingCyNetwork.setSelectedEdgeState(Collection,boolean) |
cytoscape.CyNetwork.setFlaggedNodes(Collection, boolean)
As of 2.3, replaced by CyNetwork.setSelectedNodeState(Collection,boolean) |
cytoscape.giny.FingCyNetwork.setFlaggedNodes(Collection, boolean)
As of 2.3, replaced by FingCyNetwork.setSelectedNodeState(Collection,boolean) |
cytoscape.CyNetwork.setFlaggedNodes(int[], boolean)
As of 2.3, replaced by CyNetwork.setSelectedNodeState(Collection,boolean) |
cytoscape.giny.FingCyNetwork.setFlaggedNodes(int[], boolean)
As of 2.3, replaced by FingCyNetwork.setSelectedNodeState(Collection,boolean) |
cytoscape.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.NodeAppearanceCalculator.setNodeShapeCalculator(NodeShapeCalculator)
Use setCalculator(calc) instead. This method will be removed Sept 2007. |
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.CytoscapeInit.setProperty(String, String)
Use getProperties().setProperty( ) instead. Since this method
never made it into a release, it will be removed Summer 2006. |
cytoscape.CytoscapeInit.setSecondaryViewThreshold(int)
Will be removed April 2007. Use getProperties().setProperty(
"secondaryViewThreshold", thresh ) instead. |
cytoscape.view.CyNetworkView.setSelected(CyEdge[])
this method is not working, use CyNetwork.setSelectedEdgeState(Collection, boolean) |
cytoscape.view.CyNetworkView.setSelected(CyNode[])
this method is not working, use Cytoscape.CyNetwork#setSelectedNodeState(Collection, boolean) |
cytoscape.view.CyNetworkView.setSelected(EdgeView[])
this method is not working, use CyNetwork.setSelectedEdgeState(Collection, boolean) |
cytoscape.view.CyNetworkView.setSelected(NodeView[])
this method is not working, use Cytoscape.CyNetwork#setSelectedNodeState(Collection, boolean) |
cytoscape.Cytoscape.setSpecies()
This will be removed Feb 2007. |
cytoscape.CytoscapeInit.setViewThreshold(int)
Will be removed April 2007. Use setProperty( "viewThreshold",
thresh ) instead. |
cytoscape.CytoscapeInit.suppressView()
This method will be removed April 2007. No one appears to use
this method, so don't start. |
cytoscape.CyNetwork.unFlagAllEdges()
As of 2.3, replaced by CyNetwork.unselectAllEdges() |
cytoscape.giny.FingCyNetwork.unFlagAllEdges()
As of 2.3, replaced by FingCyNetwork.unselectAllEdges() |
cytoscape.CyNetwork.unFlagAllNodes()
As of 2.3, replaced by CyNetwork.unselectAllNodes() |
cytoscape.giny.FingCyNetwork.unFlagAllNodes()
As of 2.3, replaced by FingCyNetwork.unselectAllNodes() |
cytoscape.CytoscapeInit.useView()
This method will be removed April 2007. Use getMode()
instead. |
cytoscape.dialogs.preferences.PreferenceValueDialog.validatedPluginData(Component, String)
no longer used by anyting. Will leave this world Dec 2007. |