In the Winter of 2010 a message was sent to all plugin authors who had submitted a plugin to the Cytoscape website requesting access to their source code so that the Cytoscape team could analyze which methods were being used and how widely they were being used.  The following table lists the Cytoscape methods used.  A table even further below lists the plugins that were analyzed.

Cytoscape methods are defined as any public (or accessible) method that is found in [[http://chianti.ucsd.edu/svn/cytoscape/trunk/|Cytoscape]] or [[http://chianti.ucsd.edu/svn/corelibs/|corelibs]].  Public methods found in  [[http://chianti.ucsd.edu/svn/coreplugins/|coreplugins]] were not considered because those APIs are generally inaccessible to external users.

||'''Num Times Used'''||'''Num Plugins Using'''||'''Method Name'''||
||697||81||cytoscape.Cytoscape.getDesktop||
||591||41||cytoscape.CyNode.getIdentifier||
||491||61||cytoscape.Cytoscape.getCurrentNetwork||
||418||56||cytoscape.Cytoscape.getCurrentNetworkView||
||394||59||cytoscape.Cytoscape.getNodeAttributes||
||255||15||cytoscape.layout.Tunable.getValue||
||236||30||cytoscape.task.TaskMonitor.setStatus||
||236||29||giny.model.Node.getIdentifier||
||233||39||cytoscape.CyNetwork.getIdentifier||
||222||8||cytoscape.layout.Tunable.valueChanged||
||217||28||cytoscape.data.CyAttributes.setAttribute||
||207||30||cytoscape.task.TaskMonitor.setPercentCompleted||
||188||47||cytoscape.Cytoscape.getEdgeAttributes||
||186||39||cytoscape.data.CyAttributes.getType||
||151||33||cytoscape.CyEdge.getIdentifier||
||144||28||cytoscape.logger.CyLogger.getLogger||
||124||27||giny.view.NodeView.getNode||
||115||30||cytoscape.Cytoscape.getCyNode||
||105||33||cytoscape.Cytoscape.getVisualMappingManager||
||96||33||cytoscape.data.CyAttributes.getAttributeNames||
||93||31||cytoscape.task.util.TaskManager.executeTask||
||91||12||cytoscape.logger.CyLogger.debug||
||91||23||cytoscape.CyNetwork.nodesIterator||
||90||7||cytoscape.layout.Tunable.getName||
||89||27||cytoscape.CyNetwork.getNodeCount||
||89||13||cytoscape.visual.mappings.DiscreteMapping.putMapValue||
||81||20||giny.view.NodeView.getYPosition||
||80||20||cytoscape.task.TaskMonitor.setException||
||78||20||giny.view.NodeView.getXPosition||
||77||6||cytoscape.layout.LayoutProperties.get||
||76||18||cytoscape.visual.NodeAppearanceCalculator.setCalculator||
||74||2||cytoscape.command.CyCommandResult.addMessage||
||72||30||cytoscape.Cytoscape.createNetwork||
||70||15||cytoscape.logger.CyLogger.error||
||69||7||cytoscape.data.CyAttributes.deleteAttribute||
||69||15||cytoscape.Cytoscape.getNetworkAttributes||
||68||11||cytoscape.logger.CyLogger.info||
||68||16||giny.model.Edge.getIdentifier||
||67||12||cytoscape.visual.NodeAppearanceCalculator.getDefaultAppearance||
||66||21||cytoscape.CyNode.getRootGraphIndex||
||66||14||cytoscape.Cytoscape.getNetwork||
||66||23||cytoscape.CyNetwork.getTitle||
||66||26||cytoscape.view.CyNetworkView.getNodeView||
||65||29||cytoscape.task.ui.JTaskConfig.displayStatus||
||63||30||cytoscape.data.CyAttributes.getStringAttribute||
||61||13||cytoscape.data.CyAttributes.hasAttribute||
||60||28||cytoscape.task.ui.JTaskConfig.displayCancelButton||
||58||15||cytoscape.Cytoscape.getRootGraph||
||58||25||cytoscape.CyNetwork.getSelectedNodes||
||56||20||cytoscape.CyNetwork.addNode||
||55||23||cytoscape.task.ui.JTaskConfig.setAutoDispose||
||55||6||giny.model.GraphObject.getIdentifier||
||52||21||cytoscape.visual.VisualMappingManager.getCalculatorCatalog||
||51||20||cytoscape.CyEdge.getSource||
||51||20||cytoscape.CyEdge.getTarget||
||50||9||cytoscape.visual.mappings.ContinuousMapping.addPoint||
||50||22||cytoscape.task.ui.JTaskConfig.displayCloseButton||
||49||15||giny.model.Edge.getSource||
||48||14||giny.view.NodeView.getWidth||
||48||22||cytoscape.view.CyNetworkView.redrawGraph||
||48||17||cytoscape.data.CyAttributes.getListAttribute||
||47||20||cytoscape.CytoscapeInit.getProperties||
||46||20||cytoscape.Cytoscape.getNetworkSet||
||46||16||cytoscape.CyNetwork.nodesList||
||46||26||cytoscape.data.CyAttributes.getDoubleAttribute||
||46||15||giny.model.Edge.getTarget||
||46||19||cytoscape.CyNetwork.setSelectedNodeState||
||44||17||cytoscape.view.CyNetworkView.updateView||
||44||15||cytoscape.data.CyAttributes.setListAttribute||
||43||10||giny.view.NodeView.getHeight||
||42||15||giny.view.EdgeView.getEdge||
||41||12||cytoscape.view.CytoscapeDesktop.getCytoPanel||
||40||5||cytoscape.data.CyAttributes.setUserVisible||
||40||6||cytoscape.logger.CyLogger.warn||
||40||21||cytoscape.CyNetwork.addEdge||
||40||23||cytoscape.data.CyAttributes.getIntegerAttribute||
||39||17||giny.view.NodeView.setXPosition||
||38||8||cytoscape.visual.EdgeAppearanceCalculator.getDefaultAppearance||
||37||7||giny.view.NodeView.getOffset||
||36||9||ding.view.DGraphView.getCanvas||
||36||15||giny.view.NodeView.setYPosition||
||36||8||cytoscape.data.CyAttributes.getAttribute||
||36||2||cytoscape.visual.mappings.DiscreteMapping.getMapValue||
||36||8||cytoscape.groups.CyGroup.getGroupNode||
||36||8||giny.view.NodeView.setOffset||
||35||20||cytoscape.view.CyNetworkView.getNetwork||
||35||11||cytoscape.Cytoscape.getCyEdge||
||35||14||cytoscape.CyNetwork.getEdgeCount||
||35||21||cytoscape.Cytoscape.getPropertyChangeSupport||
||34||9||giny.model.Node.getRootGraphIndex||
||34||19||cytoscape.visual.VisualStyle.getName||
||34||12||cytoscape.visual.EdgeAppearanceCalculator.setCalculator||
||33||21||cytoscape.visual.VisualMappingManager.setVisualStyle||
||32||14||cytoscape.CyNetwork.edgesIterator||
||31||14||cytoscape.Cytoscape.getNullNetwork||
||31||16||cytoscape.util.OpenBrowser.openURL||
||29||14||cytoscape.CyNetwork.unselectAllNodes||
||29||14||cytoscape.visual.VisualStyle.getNodeAppearanceCalculator||
||29||18||cytoscape.view.cytopanels.CytoPanel.add||
||29||8||cytoscape.groups.CyGroup.getNodes||
||29||22||cytoscape.data.CyAttributes.getBooleanAttribute||
||29||17||cytoscape.visual.CalculatorCatalog.getVisualStyle||
||28||15||cytoscape.Cytoscape.getNullNetworkView||
||28||9||cytoscape.layout.Tunable.setValue||
||27||6||cytoscape.CyNetwork.getNode||
||27||12||cytoscape.CyEdge.getRootGraphIndex||
||26||21||cytoscape.Cytoscape.createNetworkView||
||25||6||cytoscape.CyNetwork.getIndex||
||24||13||cytoscape.view.cytopanels.CytoPanel.indexOfComponent||
||23||4||cytoscape.groups.CyGroup.getGroupName||
||23||8||cytoscape.Cytoscape.getNetworkView||
||23||12||cytoscape.visual.VisualStyle.getEdgeAppearanceCalculator||
||23||12||cytoscape.CyNetwork.edgesList||
||23||12||cytoscape.view.CyNetworkView.getNodeViewsIterator||
||21||1||cytoscape.command.CyCommandResult.addResult||
||21||6||cytoscape.visual.mappings.DiscreteMapping.setControllingAttributeName||
||21||5||cytoscape.groups.CyGroup.setState||
||21||12||cytoscape.visual.VisualMappingManager.getVisualStyle||
||21||11||cytoscape.data.CyAttributes.getUserVisible||
||20||5||cytoscape.groups.CyGroup.getViewer||
||20||9||cytoscape.view.cytopanels.CytoPanel.remove||
||20||13||cytoscape.visual.CalculatorCatalog.addVisualStyle||
||20||11||cytoscape.CyNetwork.setSelectedEdgeState||
||20||11||cytoscape.view.cytopanels.CytoPanel.setSelectedIndex||
||20||3||cytoscape.layout.CyLayouts.addLayout||
||19||9||cytoscape.view.CyNetworkView.getEdgeView||
||19||10||cytoscape.CyNetwork.getEdge||
||19||4||giny.view.NodeView.getRootGraphIndex||
||19||7||cytoscape.groups.CyGroupManager.createGroup||
||19||4||cytoscape.layout.Tunable.add||
||18||3||giny.model.GraphPerspective.getNodeCount||
||18||1||cytoscape.data.annotation.Ontology.getTerm||
||18||10||cytoscape.task.ui.JTaskConfig.displayTimeElapsed||
||18||4||cytoscape.CyNetwork.containsNode||
||17||6||cytoscape.Cytoscape.destroyNetwork||
||17||2||cytoscape.util.intr.IntEnumerator.numRemaining||
||17||14||cytoscape.Cytoscape.getSwingPropertyChangeSupport||
||17||2||cytoscape.util.intr.IntEnumerator.nextInt||
||16||4||cytoscape.layout.Tunable.addTunableValueListener||
||16||9||cytoscape.view.CyNetworkView.fitContent||
||16||6||cytoscape.view.cytopanels.CytoPanel.getCytoPanelComponentCount||
||16||2||ding.view.DNodeView.getHeight||
||16||6||cytoscape.data.webservice.CyWebServiceEvent.getEventType||
||15||2||cytoscape.layout.Tunable.getType||
||15||9||cytoscape.CyNetwork.unselectAllEdges||
||15||2||ding.view.DNodeView.getWidth||
||15||6||cytoscape.groups.CyGroupManager.removeGroup||
||15||9||cytoscape.view.CyNetworkView.getSelectedNodes||
||15||7||cytoscape.CyNetwork.getAdjacentEdgeIndicesArray||
||15||5||cytoscape.data.CyAttributes.getMultiHashMapDefinition||
||15||4||cytoscape.groups.CyGroupManager.getCyGroup||
||14||4||cytoscape.groups.CyGroup.getState||
||14||5||cytoscape.data.SelectEvent.getTargetType||
||14||1||cytoscape.data.CyAttributes.setAttributeDescription||
||14||6||cytoscape.groups.CyGroupManager.getGroupList||
||14||6||cytoscape.data.webservice.CyWebServiceEvent.getParameter||
||14||5||cytoscape.view.CyNetworkView.getComponent||
||14||4||cytoscape.layout.Tunable.setLowerBound||
||14||1||cytoscape.command.CyCommandException.getArg||
||13||6||cytoscape.data.webservice.WebServiceClientManager.getCyWebServiceEventSupport||
||13||1||cytoscape.Cytoscape.getOntologyServer||
||13||1||cytoscape.layout.LayoutProperties.add||
||13||8||cytoscape.layout.CyLayouts.getDefaultLayout||
||13||6||cytoscape.CyNetwork.getAdjacentEdgesList||
||13||7||cytoscape.data.CyAttributes.getMultiHashMap||
||13||4||giny.view.EdgeView.getBend||
||12||9||cytoscape.visual.VisualStyle.getGlobalAppearanceCalculator||
||12||3||cytoscape.CyNode.getGroups||
||12||8||cytoscape.CyNetwork.getSelectedEdges||
||12||9||cytoscape.view.CyNetworkView.getIdentifier||
||12||3||giny.view.GraphViewChangeEvent.getType||
||12||8||cytoscape.view.CyNetworkView.applyVizmapper||
||12||3||cytoscape.groups.CyGroupManager.findGroup||
||12||4||cytoscape.logger.CyLogger.warning||
||12||1||cytoscape.data.annotation.Annotation.getClassifications||
||12||3||ding.view.DGraphView.xformComponentToNodeCoords||
||12||6||cytoscape.task.ui.JTaskConfig.setModal||
||11||5||cytoscape.view.CyNetworkView.getNodeViewCount||
||11||9||cytoscape.visual.GlobalAppearanceCalculator.setDefaultBackgroundColor||
||11||5||cytoscape.CyNetwork.getConnectingEdges||
||11||9||cytoscape.layout.CyLayouts.getLayout||
||11||3||cytoscape.view.CyNetworkView.addGraphViewChangeListener||
||11||3||giny.view.GraphView.getGraphPerspective||
||11||7||cytoscape.Cytoscape.getCyEdgesList||
||11||6||cytoscape.visual.mappings.ContinuousMapping.setControllingAttributeName||
||11||5||cytoscape.view.CyNetworkView.setVisualStyle||
||10||3||cytoscape.layout.LayoutProperties.initializeProperties||
||10||2||cytoscape.task.TaskMonitor.setEstimatedTimeRemaining||
||10||4||cytoscape.layout.LayoutProperties.getTunablePanel||
||10||3||ding.view.DGraphView.getPickedNodeView||
||10||5||cytoscape.util.CyNetworkNaming.getSuggestedNetworkTitle||
||10||1||cytoscape.command.CyCommandResult.addError||
||10||6||cytoscape.visual.VisualMappingManager.applyAppearances||
||10||4||cytoscape.util.undo.CyUndo.getUndoableEditSupport||
||10||4||giny.view.GraphView.getNodeViewsIterator||
||10||5||giny.view.NodeView.setSelected||
||10||4||cytoscape.view.CyNetworkView.getTitle||
||10||1||cytoscape.command.CyCommandManager.reserveNamespace||
||10||1||cytoscape.data.synonyms.Aliases.add||
||9||4||cytoscape.Cytoscape.getCyNodesList||
||9||3||cytoscape.visual.mappings.DiscreteMapping.addChangeListener||
||9||4||cytoscape.data.webservice.WebServiceClientManager.getClient||
||9||1||cytoscape.visual.mappings.DiscreteMapping.getControllingAttributeName||
||9||7||cytoscape.Cytoscape.getImportHandler||
||9||3||cytoscape.groups.CyGroup.getOuterEdges||
||9||2||cytoscape.layout.Tunable.setImmutable||
||9||2||ding.view.InnerCanvas.getGraphics||
||9||2||cytoscape.data.CyAttributes.setUserEditable||
||9||5||cytoscape.layout.LayoutProperties.revertProperties||
||9||3||cytoscape.layout.LayoutProperties.updateValues||
||9||2||cytoscape.data.annotation.Annotation.add||
||8||6||cytoscape.Cytoscape.getNetworkViewMap||
||8||1||cytoscape.logger.CyLogger.isDebugging||
||8||2||cytoscape.groups.CyGroup.getNodeIterator||
||8||5||cytoscape.view.CyNetworkView.getEdgeViewsIterator||
||8||1||cytoscape.util.plugins.communication.Message.getContent||
||8||1||cytoscape.view.cytopanels.CytoPanel.getComponentAt||
||8||5||cytoscape.CyNetwork.getEdgeTargetIndex||
||8||4||cytoscape.CyNetwork.getEdgeIndicesArray||
||8||1||cytoscape.visual.mappings.DiscreteMapping.putAll||
||8||4||cytoscape.groups.CyGroupManager.isaGroup||
||8||1||cytoscape.data.CyAttributesImpl.getType||
||8||1||cytoscape.visual.mappings.InterpolatorFactory.newInterpolator||
||8||1||com.nerius.math.xform.AffineTransform3D.transformArr||
||8||1||cytoscape.data.CyAttributesImpl.getStringAttribute||
||8||5||cytoscape.CyNetwork.getEdgeSourceIndex||
||8||7||cytoscape.view.CyNetworkView.addNodeContextMenuListener||
||8||1||cytoscape.view.CyNetworkView.getEdgeViewsList||
||8||6||cytoscape.layout.CyLayoutAlgorithm.doLayout||
||8||4||cytoscape.layout.CyLayoutAlgorithm.getName||
||7||2||cytoscape.util.URLUtil.getInputStream||
||7||4||cytoscape.actions.GinyUtils.deselectAllNodes||
||7||1||cytoscape.data.annotation.Annotation.getSpecies||
||7||3||giny.view.NodeView.isSelected||
||7||1||cytoscape.visual.NodeAppearanceCalculator.getDefaultNodeFillColor||
||7||5||cytoscape.visual.mappings.ContinuousMapping.setInterpolator||
||7||3||giny.model.GraphPerspective.getEdgeCount||
||7||2||cytoscape.Cytoscape.getExpressionData||
||7||4||cytoscape.util.URLUtil.getBasicInputStream||
||7||1||cytoscape.data.annotation.Annotation.getType||
||7||1||cytoscape.data.annotation.Annotation.getCurator||
||7||3||cytoscape.view.CyNetworkView.applyLayout||
||7||3||cytoscape.groups.CyGroup.getInnerEdges||
||6||3||cytoscape.layout.CyLayoutAlgorithm.updateSettings||
||6||4||cytoscape.CyNetwork.restoreEdge||
||6||2||ding.view.InnerCanvas.repaint||
||6||4||cytoscape.view.cytopanels.CytoPanelImp.indexOfComponent||
||6||4||cytoscape.CyNetwork.hideNode||
||6||3||cytoscape.CyNetwork.setTitle||
||6||3||cytoscape.Cytoscape.loadAttributes||
||6||5||cytoscape.visual.NodeAppearanceCalculator.setNodeSizeLocked||
||6||5||cytoscape.visual.VisualStyle.setEdgeAppearanceCalculator||
||6||2||cytoscape.layout.Tunable.getTunablePanel||
||6||6||cytoscape.visual.VisualStyle.setNodeAppearanceCalculator||
||6||1||cytoscape.util.IndeterminateProgressBar.setVisible||
||6||6||cytoscape.data.webservice.CyWebServiceEvent.getSource||
||6||5||cytoscape.Cytoscape.createNetworkFromFile||
||6||2||phoebe.PhoebeCanvasDropEvent.getLocation||
||6||6||cytoscape.CyNetwork.addSelectEventListener||
||6||3||cytoscape.view.CyNetworkView.getZoom||
||6||1||cytoscape.data.CyAttributesImpl.getAttributeNames||
||6||5||cytoscape.data.writers.CytoscapeSessionWriter.writeSessionToDisk||
||6||5||cytoscape.data.CyAttributes.setMapAttribute||
||6||1||cytoscape.view.CyNetworkView.removeGraphViewChangeListener||
||6||5||cytoscape.data.CyAttributes.getMapAttribute||
||6||3||cytoscape.groups.CyGroupViewer.getViewerName||
||6||3||cytoscape.plugin.PluginManager.getPluginManager||
||5||4||cytoscape.visual.VisualMappingManager.setNetworkView||
||5||1||cytoscape.util.intr.IntIntHash.put||
||5||5||cytoscape.view.cytopanels.CytoPanelImp.add||
||5||3||cytoscape.data.attr.MultiHashMapDefinition.getAttributeKeyspaceDimensionTypes||
||5||4||cytoscape.CyNetwork.hideEdge||
||5||5||cytoscape.view.CyNetworkView.getVisualStyle||
||5||2||cytoscape.giny.CytoscapeRootGraph.getIndex||
||5||2||giny.view.NodeView.getGraphPerspectiveIndex||
||5||2||cytoscape.data.attr.MultiHashMapDefinition.getAttributeValueType||
||5||1||cytoscape.data.CyAttributesUtils.getVisibleAttributeNames||
||5||1||cytoscape.data.readers.TextFileReader.read||
||5||4||ding.view.DGraphView.addNodeContextMenuListener||
||5||5||cytoscape.data.ImportHandler.addFilter||
||5||2||cytoscape.giny.CytoscapeRootGraph.getNode||
||5||1||giny.view.GraphView.getNodeView||
||5||2||giny.model.GraphPerspective.nodesIterator||
||5||4||cytoscape.view.cytopanels.CytoPanelImp.setSelectedIndex||
||5||3||cytoscape.visual.mappings.DiscreteMapping.getAll||
||5||4||cytoscape.util.CyFileFilter.addExtension||
||5||1||cytoscape.data.readers.TextFileReader.getText||
||5||3||ding.view.DingCanvas.add||
||5||3||cytoscape.view.CyNetworkView.setZoom||
||5||3||ding.view.InnerCanvas.addPhoebeCanvasDropListener||
||5||2||ding.view.InnerCanvas.removeMouseListener||
||5||1||cytoscape.data.readers.TextHttpReader.getText||
||5||2||ding.view.InnerCanvas.removeMouseMotionListener||
||5||4||cytoscape.view.CyNetworkView.addEdgeContextMenuListener||
||5||1||cytoscape.data.annotation.Annotation.setOntology||
||5||2||cytoscape.CyNetwork.getSelectFilter||
||5||1||cytoscape.data.ExpressionData.getConditionNames||
||5||1||cytoscape.editor.editors.BasicCytoscapeEditor.ConnectSelectedNodesAction.setEnabled||
||5||4||cytoscape.util.CyFileFilter.setDescription||
||5||1||cytoscape.util.CytoscapeAction.initialize||
||5||2||cytoscape.CyNetwork.createGraphPerspective||
||5||2||cytoscape.data.SelectEvent.getEventType||
||5||4||cytoscape.CyNetwork.restoreNode||
||5||1||cytoscape.data.readers.TextHttpReader.read||
||4||4||giny.view.NodeView.setWidth||
||4||3||cytoscape.CyEdge.setIdentifier||
||4||2||giny.view.NodeView.getGraphView||
||4||3||ding.view.DGraphView.fitContent||
||4||1||cytoscape.init.CyInitParams.getMode||
||4||2||cytoscape.task.ui.JTaskConfig.setMillisToPopup||
||4||1||cytoscape.visual.Arrow.getShape||
||4||1||cytoscape.data.annotation.Ontology.add||
||4||2||cytoscape.util.undo.CyAbstractEdit.redo||
||4||2||giny.view.NodeView.setSelectedPaint||
||4||3||cytoscape.layout.CyLayoutAlgorithm.getSettings||
||4||4||cytoscape.data.readers.CytoscapeSessionReader.read||
||4||2||cytoscape.view.CyMenus.addAction||
||4||2||cytoscape.CyNode.isaGroup||
||4||2||cytoscape.CytoscapeInit.getConfigFile||
||4||3||cytoscape.data.CyAttributesUtils.getAttribute||
||4||2||cytoscape.data.ExpressionData.getNumberOfConditions||
||4||1||cytoscape.CyNetwork.edgeExists||
||4||3||ding.view.InnerCanvas.getHeight||
||4||3||cytoscape.CyNode.setIdentifier||
||4||3||phoebe.PhoebeCanvasDropEvent.getTransferable||
||4||4||cytoscape.groups.CyGroupManager.registerGroupViewer||
||4||4||cytoscape.task.ui.JTaskConfig.setOwner||
||4||3||cytoscape.visual.calculators.Calculator.getMappings||
||4||1||cytoscape.giny.CytoscapeRootGraph.getEdge||
||4||1||cytoscape.visual.calculators.Calculator.getMapping||
||4||2||cytoscape.util.undo.CyAbstractEdit.undo||
||4||1||cytoscape.view.CyMenus.addCytoscapeAction||
||4||2||cytoscape.CyNetwork.hideEdges||
||4||1||cytoscape.visual.NodeAppearanceCalculator.getNodeFillColorCalculator||
||4||1||ding.view.DEdgeView.addHandle||
||4||3||ding.view.DGraphView.getPickedEdgeView||
||4||1||cytoscape.visual.calculators.Calculator.getVisualPropertyType||
||4||4||cytoscape.CyNetwork.isSelected||
||4||2||ding.view.DingCanvas.repaint||
||4||4||giny.view.NodeView.setHeight||
||4||3||giny.view.NodeView.setUnselectedPaint||
||4||3||cytoscape.data.writers.InteractionWriter.writeInteractions||
||4||3||cytoscape.CyNetwork.getConnectingEdgeIndicesArray||
||4||1||cytoscape.visual.EdgeAppearanceCalculator.getEdgeTargetArrowCalculator||
||4||2||cytoscape.editor.editors.BasicCytoscapeEditor.ConnectSelectedNodesAction.setPreferredMenu||
||4||1||cytoscape.visual.NodeAppearanceCalculator.getNodeShapeCalculator||
||4||4||cytoscape.groups.CyGroupManager.getGroupViewer||
||4||1||cytoscape.visual.GlobalAppearanceCalculator.getDefaultEdgeSelectionColor||
||4||4||giny.model.GraphPerspective.neighborsList||
||4||1||cytoscape.visual.GlobalAppearanceCalculator.getDefaultNodeSelectionColor||
||4||4||cytoscape.data.readers.AbstractGraphReader.getHeader||
||4||1||giny.model.Edge.isDirected||
||4||2||giny.model.GraphPerspective.getNodeIndicesArray||
||4||3||ding.view.InnerCanvas.getWidth||
||3||2||cytoscape.CyNode.removeFromGroup||
||3||2||giny.view.NodeView.setNodePosition||
||3||1||cytoscape.data.ExpressionData.getNumberOfGenes||
||3||3||giny.view.NodeView.setBorderPaint||
||3||1||cytoscape.visual.calculators.GenericNodeColorCalculator.getMappings||
||3||3||giny.view.GraphViewChangeEvent.getSelectedNodes||
||3||1||cytoscape.actions.SelectShortestPathsPlugin.NewWindowShortestPathsAction.setEnabled||
||3||1||cytoscape.util.swing.ColumnResizer.adjustColumnPreferredWidths||
||3||2||cytoscape.visual.NodeAppearanceCalculator.setDefaultAppearance||
||3||1||ding.view.ViewChangeEdit.post||
||3||2||cytoscape.data.mRNAMeasurement.getRatio||
||3||2||cytoscape.CyNetwork.restoreEdges||
||3||1||cytoscape.view.CyNetworkView.applyVizMap||
||3||3||cytoscape.CyNetwork.getNodeIndicesArray||
||3||2||ding.view.InnerCanvas.getAffineTransform||
||3||2||cytoscape.groups.CyGroupManager.addGroupChangeListener||
||3||3||cytoscape.visual.VisualStyle.setGlobalAppearanceCalculator||
||3||1||cytoscape.visual.calculators.GenericEdgeArrowCalculator.getMappings||
||3||3||cytoscape.Cytoscape.createNewSession||
||3||3||cytoscape.visual.VisualStyle.getDependency||
||3||3||cytoscape.visual.mappings.PassThroughMapping.setControllingAttributeName||
||3||2||ding.view.DNodeView.addCustomGraphic||
||3||2||cytoscape.visual.NodeAppearance.setNodeSizeLocked||
||3||3||cytoscape.view.CytoscapeDesktop.getCyMenus||
||3||2||cytoscape.CyNode.addToGroup||
||3||1||cytoscape.util.intr.IntIntHash.get||
||3||3||cytoscape.view.cytopanels.CytoPanel.addCytoPanelListener||
||3||1||cytoscape.visual.calculators.GenericNodeShapeCalculator.getMappings||
||3||2||cytoscape.groups.CyGroup.contains||
||3||2||cytoscape.data.ExpressionData.getMeasurements||
||3||3||cytoscape.CyNode.setNestedNetwork||
||3||1||ding.view.DingCanvas.setBackground||
||3||3||giny.view.GraphViewChangeEvent.getUnselectedNodes||
||3||1||cytoscape.layout.Tunable.getDescription||
||3||1||cytoscape.visual.NodeAppearance.setFillColor||
||3||2||cytoscape.util.URLUtil.getURLConnection||
||3||2||cytoscape.layout.Tunable.getLowerBound||
||3||2||cytoscape.visual.GlobalAppearanceCalculator.getDefaultNodeReverseSelectionColor||
||3||1||cytoscape.view.CyNetworkView.getEdgeViewCount||
||3||1||cytoscape.util.IndeterminateProgressBar.pack||
||3||2||cytoscape.view.cytopanels.CytoPanel.getState||
||3||2||ding.view.InnerCanvas.addMouseMotionListener||
||3||2||cytoscape.CyNetwork.restoreNodes||
||3||1||cytoscape.command.CyCommandResult.successful||
||3||3||ding.view.DNodeView.removeCustomGraphic||
||3||1||cytoscape.data.webservice.CyWebServiceException.getErrorCode||
||3||2||cytoscape.visual.parsers.ObjectToString.getStringValue||
||3||3||cytoscape.layout.CyLayouts.getAllLayouts||
||3||1||cytoscape.data.annotation.Ontology.getType||
||3||2||ding.view.InnerCanvas.addKeyListener||
||3||2||cytoscape.actions.GinyUtils.deselectAllEdges||
||3||3||giny.view.GraphView.getEdgeViewCount||
||3||3||giny.view.GraphView.getNodeViewCount||
||3||2||cytoscape.data.webservice.WebServiceClientManager.registerClient||
||3||3||cytoscape.data.webservice.AttributeImportQuery.getParameter||
||3||2||cytoscape.command.CyCommandResult.getErrors||
||3||1||cytoscape.data.annotation.Ontology.getCurator||
||3||3||cytoscape.CyNetwork.removeSelectEventListener||
||3||2||giny.model.Edge.getRootGraphIndex||
||3||2||giny.model.GraphPerspective.nodesList||
||3||1||cytoscape.view.InternalFrameComponent.getWidth||
||3||3||cytoscape.data.webservice.AttributeImportQuery.getKeyCyAttrName||
||3||1||giny.model.GraphPerspective.getAdjacentEdgesList||
||3||3||cytoscape.visual.VisualMappingManager.applyNodeAppearances||
||3||1||cytoscape.visual.NodeAppearanceCalculator.getDefaultNodeShape||
||3||2||ding.view.DGraphView.addEdgeContextMenuListener||
||3||1||cytoscape.CyNetwork.hideNodes||
||3||1||cytoscape.view.CyNetworkView.showGraphObjects||
||3||2||cytoscape.view.CyNetworkView.hideGraphObjects||
||3||2||ding.view.InnerCanvas.addMouseListener||
||3||1||cytoscape.util.SwingWorker.start||
||3||2||ding.view.InnerCanvas.removeKeyListener||
||3||1||cytoscape.data.webservice.WebServiceClient.execute||
||2||2||cytoscape.groups.CyGroup.addNode||
||2||2||cytoscape.visual.mappings.DiscreteMapping.removeChangeListener||
||2||2||giny.view.NodeView.setToolTip||
||2||1||cytoscape.groups.CyGroup.addOuterEdge||
||2||1||giny.model.Edge.setIdentifier||
||2||1||ding.view.DEdgeView.getHandles||
||2||1||cytoscape.view.CyNetworkView.hideGraphObject||
||2||1||cytoscape.cythesaurus.service.CyThesaurusServiceClient.isServiceAvailable||
||2||1||cytoscape.CyNetwork.getDegree||
||2||1||cytoscape.groups.CyGroupManager.removeGroupChangeListener||
||2||2||cytoscape.visual.NodeAppearanceCalculator.getCalculator||
||2||1||giny.view.GraphView.getSelectedNodes||
||2||2||cytoscape.data.SelectEvent.getTarget||
||2||2||cytoscape.editor.editors.BasicCytoscapeEditor.ConnectSelectedNodesAction.setPreferredIndex||
||2||2||cytoscape.data.readers.GMLReader.getList||
||2||2||giny.model.GraphPerspective.createGraphPerspective||
||2||1||giny.view.EdgeView.clearBends||
||2||2||cytoscape.view.CyNetworkView.getSelectedNodeIndices||
||2||1||cytoscape.visual.mappings.ContinuousMapping.addChangeListener||
||2||2||cytoscape.view.CytoscapeDesktop.setStatusBarMsg||
||2||1||cytoscape.data.attr.CountedIterator.next||
||2||1||cytoscape.Cytoscape.getDetailsSlider||
||2||2||giny.view.GraphView.updateView||
||2||2||cytoscape.util.CytoscapeAction.setPreferredMenu||
||2||1||cytoscape.data.attr.CountedIterator.hasNext||
||2||2||giny.model.GraphPerspective.getDegree||
||2||1||cytoscape.view.PropertySheetView.getTunables||
||2||1||cytoscape.bookmarks.Bookmarks.getCategory||
||2||1||cytoscape.dialogs.SetNestedNetworkDialog.setVisible||
||2||2||cytoscape.Cytoscape.destroyNetworkView||
||2||1||cytoscape.data.ExpressionData.getMeasurement||
||2||1||cytoscape.data.ontology.GeneOntology.getAspect||
||2||2||cytoscape.data.readers.GraphReader.read||
||2||2||ding.view.InnerCanvas.setEnabled||
||2||1||cytoscape.util.CytoscapeAction.setAcceleratorCombo||
||2||1||ding.view.DGraphView.setZoom||
||2||1||cytoscape.actions.LoadNetworkTask.loadURL||
||2||2||cytoscape.data.readers.GraphReader.getNodeIndicesArray||
||2||2||cytoscape.layout.LayoutProperties.getTunables||
||2||1||cytoscape.data.CyAttributes.getUserEditable||
||2||2||ding.view.DGraphView.setPrintingTextAsShape||
||2||2||cytoscape.task.ui.JTaskConfig.displayTimeRemaining||
||2||2||cytoscape.visual.EdgeAppearanceCalculator.getCalculator||
||2||1||giny.view.GraphView.hideGraphObject||
||2||2||cytoscape.data.readers.GraphReader.getEdgeIndicesArray||
||2||2||cytoscape.view.CyNetworkView.getSelectedEdges||
||2||2||ding.view.InnerCanvas.print||
||2||1||cytoscape.util.swing.CheckBoxJList.setSelectedItems||
||2||1||giny.model.GraphPerspective.getEdgeIndicesArray||
||2||1||ding.view.DGraphView.disableEdgeSelection||
||2||1||cytoscape.data.annotation.OntologyTerm.addContainer||
||2||1||cytoscape.groups.CyGroupManager.getGroupViewers||
||2||1||cytoscape.giny.CytoscapeRootGraph.edgesIterator||
||2||1||cytoscape.view.CyNetworkView.getGraphPerspective||
||2||1||cytoscape.dialogs.NetworkMetaDataDialog.setVisible||
||2||1||cytoscape.util.FileUtil.setPreferredMenu||
||2||2||cytoscape.CyNetwork.containsEdge||
||2||2||cytoscape.visual.NodeAppearanceCalculator.calculateNodeAppearance||
||2||2||cytoscape.CytoscapeInit.getCyInitParams||
||2||2||cytoscape.layout.Tunable.initializeProperties||
||2||2||cytoscape.layout.Tunable.getPanel||
||2||1||ding.view.DGraphView.getZoom||
||2||2||cytoscape.view.CyMenus.getToolBar||
||2||2||cytoscape.view.CytoscapeDesktop.clearStatusBar||
||2||2||cytoscape.ding.DingNetworkView.setGraphLOD||
||2||1||cytoscape.data.annotation.Ontology.containsTerm||
||2||1||cytoscape.bookmarks.DataSource.getHref||
||2||1||cytoscape.visual.GlobalAppearanceCalculator.getDefaultEdgeReverseSelectionColor||
||2||1||cytoscape.ding.DingNetworkView.fitSelected||
||2||1||cytoscape.visual.CalculatorCatalog.getVisualStyleNames||
||2||1||cytoscape.command.CyCommandManager.getNamespaceList||
||2||1||cytoscape.Cytoscape.getBookmarks||
||2||2||cytoscape.util.CytoscapeToolBar.add||
||2||2||giny.view.GraphViewChangeEvent.isNodesUnselectedType||
||2||1||ding.view.DGraphView.getNodeViewsIterator||
||2||2||cytoscape.data.webservice.CyWebServiceException.printStackTrace||
||2||2||cytoscape.data.readers.GMLWriter.writeGML||
||2||1||phoebe.PhoebeCanvasDropEvent.getSource||
||2||1||cytoscape.logger.CyLogger.setDebug||
||2||1||cytoscape.view.CyNetworkView.showGraphObject||
||2||1||cytoscape.view.cytopanels.CytoPanel.getSelectedComponent||
||2||1||cytoscape.coreplugins.biopax.util.CytoscapeWrapper.activateBioPaxPlugInTab||
||2||1||cytoscape.util.ModuleProperties.get||
||2||2||cytoscape.data.webservice.WebServiceClient.getClientID||
||2||2||cytoscape.data.readers.AbstractGraphReader.getNetworkName||
||2||2||giny.model.GraphPerspectiveChangeEvent.isEdgesHiddenType||
||2||1||cytoscape.util.ProxyHandler.getProxyServer||
||2||1||cytoscape.data.annotation.OntologyTerm.getParentsAndContainers||
||2||1||cytoscape.giny.CytoscapeRootGraph.nodesIterator||
||2||1||cytoscape.coreplugins.biopax.view.BioPaxContainer.showLegend||
||2||2||giny.model.GraphPerspectiveChangeEvent.getHiddenEdgeIndices||
||2||1||cytoscape.layout.Tunable.get||
||2||2||cytoscape.groups.CyGroupManager.setGroupViewer||
||2||1||cytoscape.util.BookmarksUtil.getAttribute||
||2||1||cytoscape.cythesaurus.service.CyThesaurusServiceClient.supportedTgtIDTypes||
||2||2||giny.model.GraphPerspectiveChangeEvent.isNodesHiddenType||
||2||1||cytoscape.view.PropertySheetView.getTunablePanel||
||2||2||giny.model.GraphPerspectiveChangeEvent.getHiddenNodeIndices||
||2||1||cytoscape.view.cytopanels.CytoPanel.getSelectedIndex||
||2||2||cytoscape.util.export.Exporter.export||
||2||1||cytoscape.data.annotation.OntologyTerm.addParent||
||2||2||cytoscape.CyNetwork.addGraphPerspectiveChangeListener||
||2||2||cytoscape.view.cytopanels.CytoPanelImp.remove||
||2||1||ding.view.DGraphView.disableNodeSelection||
||2||1||cytoscape.util.IndeterminateProgressBar.setLocation||
||2||2||cytoscape.util.CytoscapeAction.actionPerformed||
||2||1||cytoscape.view.PropertySheetView.add||
||2||2||cytoscape.Cytoscape.getCurrentSessionFileName||
||2||2||cytoscape.visual.VisualStyle.setName||
||2||1||giny.view.EdgeView.setSelectedPaint||
||2||1||cytoscape.view.cytopanels.CytoPanelImp.getState||
||2||1||cytoscape.data.webservice.CyWebServiceEvent.getNextMove||
||2||1||cytoscape.bookmarks.DataSource.getName||
||2||1||cytoscape.coreplugins.biopax.view.BioPaxContainer.getInstance||
||2||2||giny.model.GraphPerspective.getRootGraphNodeIndex||
||2||1||cytoscape.cythesaurus.service.CyThesaurusServiceClient.supportedSrcIDTypes||
||2||2||cytoscape.CyNetwork.neighborsList||
||2||2||cytoscape.util.CyNetworkNaming.getSuggestedSubnetworkTitle||
||2||2||giny.view.GraphViewChangeEvent.isNodesSelectedType||
||2||1||ding.view.DingCanvas.remove||
||2||1||cytoscape.command.CyCommandManager.getCommandList||
||2||2||ding.view.DNodeView.getCustomGraphicCount||
||2||2||giny.view.NodeView.getLabel||
||2||2||cytoscape.data.writers.XGMMLWriter.write||
||2||2||giny.model.GraphPerspective.isNeighbor||
||2||2||cytoscape.CyNetwork.neighborsArray||
||2||1||cytoscape.Cytoscape.setCurrentSessionFileName||
||2||2||cytoscape.data.CyAttributes.getAttributeDescription||
||2||2||cytoscape.data.readers.GMLParser.printList||
||2||1||cytoscape.Cytoscape.isCancelled||
||2||1||cytoscape.data.annotation.Annotation.getMap||
||2||2||cytoscape.CyNetwork.getClientData||
||2||2||cytoscape.visual.NodeAppearanceCalculator.getCalculators||
||2||1||ding.view.InnerCanvas.add||
||2||2||ding.view.InnerCanvas.removePhoebeCanvasDropListener||
||1||1||cytoscape.visual.NodeAppearance.setFont||
||1||1||cytoscape.dialogs.plugins.TreeNode.addChild||
||1||1||ding.view.DingCanvas.getComponent||
||1||1||ding.view.InnerCanvas.mouseDragged||
||1||1||cytoscape.ding.DingNetworkView.setPrintingTextAsShape||
||1||1||cytoscape.plugin.PluginException.getMessage||
||1||1||cytoscape.data.SelectEvent.getSource||
||1||1||cytoscape.CyNetwork.getRootGraph||
||1||1||cytoscape.render.stateful.GraphLOD.edgeArrows||
||1||1||cytoscape.util.swing.DropDownMenuButton.setIcon||
||1||1||cytoscape.visual.EdgeAppearance.setLabel||
||1||1||cytoscape.layout.CyLayoutAlgorithm.setLayoutAttribute||
||1||1||cytoscape.actions.ImportNodeAttributesAction.actionPerformed||
||1||1||cytoscape.actions.ImportExpressionMatrixAction.actionPerformed||
||1||1||cytoscape.visual.EdgeAppearanceCalculator.getEdgeFontSizeCalculator||
||1||1||cytoscape.CyNetwork.unFlagAllNodes||
||1||1||cytoscape.graph.fixed.FixedGraph.edges||
||1||1||cytoscape.visual.NodeAppearanceCalculator.setNodeFillColorCalculator||
||1||1||cytoscape.util.swing.NetworkSelectorPanel.getSelectedNetwork||
||1||1||cytoscape.visual.EdgeAppearanceCalculator.getEdgeColorCalculator||
||1||1||cytoscape.util.swing.DropDownMenuButton.setText||
||1||1||cytoscape.CytoscapeInit.getMRUD||
||1||1||cytoscape.visual.mappings.ObjectMapping.getControllingAttributeName||
||1||1||cytoscape.visual.LabelPosition.setOffsetY||
||1||1||cytoscape.visual.EdgeAppearanceCalculator.getEdgeLabelCalculator||
||1||1||cytoscape.render.stateful.GraphLOD.customGraphics||
||1||1||cytoscape.data.webservice.CyWebServiceException.getMessage||
||1||1||giny.model.Node.setIdentifier||
||1||1||cytoscape.graph.fixed.FixedGraph.edgesAdjacent||
||1||1||cytoscape.CyEdge.isDirected||
||1||1||cytoscape.visual.NodeAppearance.setWidth||
||1||1||cytoscape.ding.DingNetworkView.applyLayout||
||1||1||cytoscape.visual.NodeAppearanceCalculator.getNodeWidthCalculator||
||1||1||cytoscape.visual.NodeAppearanceCalculator.getNodeHeightCalculator||
||1||1||cytoscape.task.ui.JTask.haltRequested||
||1||1||ding.view.DGraphView.addNodeView||
||1||1||ding.view.InnerCanvas.getBackground||
||1||1||cytoscape.util.plugins.communication.PluginsCommunicationSupport.addMessageListener||
||1||1||cytoscape.view.CyMenus.getNewNetworkMenu||
||1||1||giny.view.EdgeView.setStroke||
||1||1||cytoscape.util.plugins.communication.Message.getId||
||1||1||cytoscape.visual.NodeAppearanceCalculator.setNodeShapeCalculator||
||1||1||cytoscape.data.ExpressionData.hasSignificanceValues||
||1||1||ding.view.DNodeView.setWidth||
||1||1||cytoscape.cythesaurus.service.CyThesaurusServiceClient.mapID||
||1||1||giny.model.GraphPerspective.edgesIterator||
||1||1||cytoscape.command.CyCommandManager.getCommand||
||1||1||cytoscape.render.stateful.GraphLOD.nodeBorders||
||1||1||cytoscape.visual.calculators.GenericNodeShapeCalculator.addChangeListener||
||1||1||giny.view.EdgeView.getUnselectedPaint||
||1||1||cytoscape.view.CytoscapeDesktop.setEnabled||
||1||1||ding.view.DNodeView.customGraphicIterator||
||1||1||cytoscape.view.CyNetworkView.removeEdgeContextMenuListener||
||1||1||cytoscape.visual.calculators.GenericNodeColorCalculator.addChangeListener||
||1||1||cytoscape.editor.actions.DeleteAction.setPreferredIndex||
||1||1||cytoscape.data.attr.MultiHashMap.getAttributeKeyspan||
||1||1||cytoscape.graph.fixed.FixedGraph.edgesConnecting||
||1||1||cytoscape.graph.fixed.FixedGraph.nodeExists||
||1||1||cytoscape.CyNetwork.selectAllNodes||
||1||1||cytoscape.visual.LabelPosition.setJustify||
||1||1||cytoscape.layout.Tunable.setUpperBound||
||1||1||cytoscape.view.CyNetworkView.setVisualMapperEnabled||
||1||1||ding.view.DGraphView.getNodeViewCount||
||1||1||cytoscape.visual.NodeAppearance.setLabelColor||
||1||1||cytoscape.partitionNetwork.PartitionNetworkPlugin.PartitionNetworkAction.setPreferredMenu||
||1||1||cytoscape.coreplugins.biopax.action.NetworkListener.registerNetwork||
||1||1||cytoscape.data.annotation.Ontology.getAllHierarchyPaths||
||1||1||cytoscape.util.swing.NetworkSelectorPanel.setBorder||
||1||1||ding.view.DGraphView.enableNodeSelection||
||1||1||cytoscape.data.webservice.AttributeImportQuery.getKeyNameInWebService||
||1||1||cytoscape.command.CyCommandException.createKVMap||
||1||1||cytoscape.data.readers.GraphReader.doPostProcessing||
||1||1||cytoscape.util.IndeterminateProgressBar.setLocationRelativeTo||
||1||1||cytoscape.editor.actions.DeleteAction.setPreferredMenu||
||1||1||cytoscape.render.stateful.NodeDetails.getTunablePanel||
||1||1||cytoscape.util.export.SVGExporter.export||
||1||1||cytoscape.CyNetwork.isNeighbor||
||1||1||cytoscape.data.CyAttributes.getAttributeMap||
||1||1||cytoscape.visual.calculators.GenericNodeShapeCalculator.removeChangeListener||
||1||1||ding.view.DEdgeView.removeAllHandles||
||1||1||cytoscape.ding.DingNetworkView.fitContent||
||1||1||cytoscape.dialogs.SetNestedNetworkDialog.getSelectedNetwork||
||1||1||cytoscape.ding.DingNetworkView.redrawGraph||
||1||1||cytoscape.data.webservice.DatabaseSearchResult.getResultSize||
||1||1||cytoscape.data.attr.MultiHashMapDefinition.defineAttribute||
||1||1||cytoscape.actions.GinyUtils.unHideAll||
||1||1||cytoscape.visual.EdgeAppearanceCalculator.getEdgeFontFaceCalculator||
||1||1||cytoscape.visual.VisualStyle.getControllingAttributeName||
||1||1||cytoscape.util.swing.CheckBoxJList.clearSelection||
||1||1||cytoscape.ding.DingNetworkView.addNodeView||
||1||1||cytoscape.editor.actions.NewNetworkAction.setPreferredMenu||
||1||1||cytoscape.util.CytoscapeProgressMonitor.setVisible||
||1||1||ding.view.DGraphView.getGraphLOD||
||1||1||cytoscape.visual.EdgeAppearanceCalculator.getEdgeLineTypeCalculator||
||1||1||cytoscape.visual.NodeShape.setNodeAppearanceCalculator||
||1||1||cytoscape.util.intr.IntObjHash.put||
||1||1||cytoscape.coreplugins.biopax.action.ExportAsBioPAXAction.setPreferredMenu||
||1||1||cytoscape.Cytoscape.getSelectionMode||
||1||1||cytoscape.ding.DingNetworkView.getNodeViewsIterator||
||1||1||cytoscape.util.swing.CheckBoxJList.setModel||
||1||1||ding.view.DingCanvas.getBackground||
||1||1||cytoscape.coreplugins.biopax.action.ExportAsBioPAXAction.setEnabled||
||1||1||cytoscape.render.stateful.GraphLOD.renderEdges||
||1||1||cytoscape.actions.SelectShortestPathsPlugin.NewWindowShortestPathsAction.setAcceleratorCombo||
||1||1||cytoscape.CyNetwork.setFlagged||
||1||1||cytoscape.util.swing.CheckBoxJList.setSelectionMode||
||1||1||cytoscape.render.stateful.GraphLOD.edgeAnchors||
||1||1||ding.view.DGraphView.edgeCount||
||1||1||ding.view.InnerCanvas.remove||
||1||1||cytoscape.data.ExpressionData.getFileName||
||1||1||cytoscape.CyNode.getNestedNetwork||
||1||1||cytoscape.data.webservice.WebServiceClient.getClientStub||
||1||1||cytoscape.coreplugins.biopax.view.BioPaxContainer.getNetworkListener||
||1||1||cytoscape.util.swing.CheckBoxJList.getSelectedValues||
||1||1||cytoscape.giny.CytoscapeRootGraph.getNodeCount||
||1||1||cytoscape.util.BioDataServerUtil.getTaxonMap||
||1||1||cytoscape.view.NatureProtocolsWorkflowPanel.NewWorkflowPanelAction.setPreferredMenu||
||1||1||cytoscape.visual.EdgeAppearanceCalculator.getDefaultEdgeTargetArrow||
||1||1||cytoscape.command.CyCommandResult.getMessages||
||1||1||cytoscape.actions.ZoomSelectedAction.actionPerformed||
||1||1||cytoscape.coreplugins.biopax.util.ParentFinder.getCurrentParentsList||
||1||1||cytoscape.data.readers.XGMMLException.getMessage||
||1||1||cytoscape.visual.CalculatorCatalog.removeVisualStyle||
||1||1||cytoscape.layout.Tunable.setModuleType||
||1||1||cytoscape.ding.DingNetworkView.addEdgeView||
||1||1||cytoscape.filters.FilterPluginToolBarAction.putValue||
||1||1||cytoscape.visual.VisualPropertyType.setDefault||
||1||1||cytoscape.coreplugins.biopax.MapBioPaxToCytoscape.initAttributes||
||1||1||cytoscape.view.InternalFrameComponent.getSize||
||1||1||cytoscape.util.plugins.communication.Message.getType||
||1||1||cytoscape.visual.NodeAppearance.setLabelPosition||
||1||1||cytoscape.data.readers.GraphReader.getLayoutAlgorithm||
||1||1||cytoscape.actions.FitContentAction.actionPerformed||
||1||1||cytoscape.layout.Tunable.updateValue||
||1||1||ding.view.InnerCanvas.update||
||1||1||cytoscape.util.intr.IntObjHash.get||
||1||1||cytoscape.data.webservice.ui.WebServiceClientGUI.getIcon||
||1||1||cytoscape.Cytoscape.exit||
||1||1||giny.view.NodeView.getDegree||
||1||1||cytoscape.data.CyAttributesUtils.traverseAttributeValues||
||1||1||cytoscape.command.CyCommandException.getCommands||
||1||1||cytoscape.bookmarks.DataSource.getAttribute||
||1||1||cytoscape.util.swing.DropDownMenuButton.getHeight||
||1||1||cytoscape.filters.FilterMenuItemAction.setAcceleratorCombo||
||1||1||cytoscape.visual.calculators.GenericNodeColorCalculator.removeChangeListener||
||1||1||cytoscape.view.InternalFrameComponent.print||
||1||1||ding.view.DGraphView.addEdgeView||
||1||1||cytoscape.util.CytoscapeToolBar.validate||
||1||1||cytoscape.command.CyCommandManager.execute||
||1||1||cytoscape.data.annotation.Annotation.getNames||
||1||1||cytoscape.visual.NodeAppearanceCalculator.setNodeLabelCalculator||
||1||1||cytoscape.visual.EdgeAppearance.setColor||
||1||1||ding.view.DGraphView.drawSnapshot||
||1||1||cytoscape.plugin.CytoscapePlugin.propertyChange||
||1||1||cytoscape.plugin.PluginManager.getClassLoader||
||1||1||giny.view.EdgeView.getGraphView||
||1||1||ding.view.DGraphView.enableEdgeSelection||
||1||1||cytoscape.util.CyColorChooser.showDialog||
||1||1||cytoscape.actions.SelectShortestPathsPlugin.NewWindowShortestPathsAction.setPreferredMenu||
||1||1||cytoscape.view.CytoscapeDesktop.getFrames||
||1||1||cytoscape.command.CyCommandException.getMessage||
||1||1||cytoscape.util.swing.JStatusBar.setCenterLabel||
||1||1||cytoscape.data.CyAttributes.setAttributeList||
||1||1||cytoscape.visual.GlobalAppearanceCalculator.getDefaultBackgroundColor||
||1||1||cytoscape.layout.LayoutProperties.saveProperties||
||1||1||cytoscape.command.CyCommandHandler.getSettings||
||1||1||cytoscape.data.CyAttributes.setAttributeMap||
||1||1||giny.view.NodeView.getUnselectedPaint||
||1||1||cytoscape.visual.EdgeAppearanceCalculator.setEdgeTargetArrowCalculator||
||1||1||cytoscape.view.cytopanels.CytoPanel.removeAll||
||1||1||ding.view.DGraphView.getEdgeViewsIterator||
||1||1||cytoscape.graph.fixed.FixedGraph.edgeSource||
||1||1||cytoscape.data.attr.MultiHashMap.setAttributeValue||
||1||1||cytoscape.visual.NodeAppearance.setHeight||
||1||1||cytoscape.data.attr.MultiHashMap.getAttributeValue||
||1||1||cytoscape.visual.NodeAppearanceCalculator.getNodeBorderColorCalculator||
||1||1||cytoscape.visual.NodeAppearanceCalculator.getNodeFontSizeCalculator||
||1||1||cytoscape.filters.FilterMenuItemAction.setPreferredMenu||
||1||1||cytoscape.visual.EdgeAppearanceCalculator.getEdgeSourceArrowCalculator||
||1||1||cytoscape.visual.ui.editors.continuous.GradientEditorPanel.getIcon||
||1||1||cytoscape.data.servers.BioDataServer.getAnnotationDescriptions||
||1||1||cytoscape.coreplugins.biopax.BioPaxFilter.getHeader||
||1||1||cytoscape.bookmarks.Attribute.getName||
||1||1||cytoscape.visual.calculators.BasicCalculator.addChangeListener||
||1||1||giny.view.GraphView.getEdgeViewsIterator||
||1||1||cytoscape.visual.NodeAppearance.setBorderColor||
||1||1||giny.view.NodeView.setShape||
||1||1||cytoscape.data.FlagEvent.getTarget||
||1||1||cytoscape.command.CyCommandHandler.getTunables||
||1||1||cytoscape.view.CyNetworkView.removeEdgeView||
||1||1||cytoscape.visual.LabelPosition.setOffsetX||
||1||1||cytoscape.util.swing.DropDownMenuButton.setComponentPopupMenu||
||1||1||cytoscape.CytoscapeVersion.getFullVersion||
||1||1||cytoscape.util.swing.CheckBoxJList.addMouseListener||
||1||1||cytoscape.visual.EdgeAppearanceCalculator.getEdgeToolTipCalculator||
||1||1||ding.view.DGraphView.addViewportChangeListener||
||1||1||cytoscape.util.plugins.communication.Message.getSender||
||1||1||cytoscape.data.webservice.ui.UnifiedNetworkImportDialog.dispose||
||1||1||cytoscape.graph.fixed.FixedGraph.nodes||
||1||1||cytoscape.view.InternalFrameComponent.addComponentListener||
||1||1||cytoscape.CyMain.main||
||1||1||giny.view.NodeView.setBorderWidth||
||1||1||cytoscape.bookmarks.DataSource.getFormat||
||1||1||cytoscape.visual.NodeAppearanceCalculator.getNodeLineTypeCalculator||
||1||1||cytoscape.visual.NodeAppearance.setLabel||
||1||1||cytoscape.view.InternalFrameComponent.getHeight||
||1||1||cytoscape.util.swing.DropDownMenuButton.setToolTipText||
||1||1||cytoscape.data.mRNAMeasurement.getSignificance||
||1||1||cytoscape.coreplugins.biopax.util.BioPaxVisualStyleUtil.getBioPaxVisualStyle||
||1||1||cytoscape.util.swing.JStatusBar.setLeftLabel||
||1||1||cytoscape.data.SelectFilter.addSelectEventListener||
||1||1||giny.view.EdgeView.setSourceEdgeEndPaint||
||1||1||cytoscape.data.annotation.Ontology.getTerms||
||1||1||cytoscape.visual.NodeShape.getGinyShape||
||1||1||ding.view.DGraphView.getExtents||
||1||1||cytoscape.Cytoscape.loadExpressionData||
||1||1||cytoscape.layout.Tunable.setClientStub||
||1||1||cytoscape.graph.fixed.FixedGraph.edgeType||
||1||1||cytoscape.visual.ui.LegendDialog.generateLegendPanel||
||1||1||giny.view.EdgeView.setUnselectedPaint||
||1||1||cytoscape.visual.EdgeAppearanceCalculator.getCalculators||
||1||1||ding.view.InnerCanvas.reshape||
||1||1||cytoscape.visual.NodeAppearanceCalculator.getNodeFontFaceCalculator||
||1||1||cytoscape.data.webservice.WebServiceClient.getProps||
||1||1||cytoscape.util.swing.JStatusBar.setRightLabel||
||1||1||cytoscape.visual.EdgeAppearance.setToolTip||
||1||1||cytoscape.util.plugins.communication.PluginsCommunicationSupport.sendMessage||
||1||1||cytoscape.render.stateful.GraphLOD.dashedEdges||
||1||1||cytoscape.coreplugins.biopax.util.LayoutUtil.doLayout||
||1||1||cytoscape.util.intr.IntStack.elements||
||1||1||cytoscape.bookmarks.Attribute.getContent||
||1||1||cytoscape.filters.FilterPluginToolBarAction.setPreferredMenu||
||1||1||cytoscape.data.annotation.Annotation.getOntology||
||1||1||cytoscape.visual.NodeAppearance.setSize||
||1||1||cytoscape.CyNetwork.appendNetwork||
||1||1||cytoscape.view.CyMenus.getOperationsMenu||
||1||1||cytoscape.util.swing.WidestStringProvider.resetWidest||
||1||1||cytoscape.graph.fixed.FixedGraph.edgeTarget||
||1||1||cytoscape.util.swing.DropDownMenuButton.setMargin||
||1||1||cytoscape.groups.CyGroup.removeNode||
||1||1||cytoscape.Cytoscape.setCurrentNetwork||
||1||1||cytoscape.visual.Arrow.getColor||
||1||1||cytoscape.coreplugins.biopax.util.CytoscapeWrapper.initBioPaxPlugInUI||
||1||1||cytoscape.Cytoscape.getBioDataServer||
||1||1||cytoscape.actions.LoadNetworkTask.loadFile||
||1||1||cytoscape.cythesaurus.service.CyThesaurusServiceClient.serviceVersion||
||1||1||cytoscape.data.CyAttributes.getName||
||1||1||cytoscape.cythesaurus.service.CyThesaurusServiceClient.openMappingResourceConfigDialog||
||1||1||cytoscape.dialogs.plugins.TreeNode.getTitle||
||1||1||cytoscape.actions.ImportEdgeAttributesAction.actionPerformed||
||1||1||cytoscape.visual.NodeAppearanceCalculator.setDefaultNodeLabelColor||
||1||1||cytoscape.groups.CyGroup.addInnerEdge||
||1||1||cytoscape.visual.VisualMappingManager.fireStateChanged||
||1||1||cytoscape.layout.Tunable.removeTunableValueListener||
||1||1||cytoscape.util.swing.ColumnResizer.getColumnPreferredWidths||
||1||1||cytoscape.visual.NodeAppearanceCalculator.getNodeToolTipCalculator||
||1||1||cytoscape.view.cytopanels.CytoPanelImp.addCytoPanelListener||
||1||1||cytoscape.command.CyCommandHandler.getDescription||
||1||1||cytoscape.data.ontology.GeneOntology.getGOTerm||
||1||1||ding.view.DGraphView.nodeCount||
||1||1||giny.view.GraphView.fitContent||
||1||1||cytoscape.visual.NodeAppearanceCalculator.getNodeSizeLocked||
||1||1||cytoscape.data.CyAttributes.getAttributeList||
||1||1||cytoscape.render.stateful.GraphLOD.detail||
||1||1||cytoscape.data.webservice.util.NetworkExpansionMenu.getExpander||
||1||1||cytoscape.CyNetwork.removeEdge||
||1||1||cytoscape.visual.NodeAppearanceCalculator.getNodeLabelCalculator||
||1||1||giny.view.EdgeView.setTargetEdgeEndPaint||
||1||1||cytoscape.coreplugins.biopax.action.ExportAsBioPAXAction.enableForNetwork||
||1||1||giny.view.GraphView.getIdentifier||
||1||1||cytoscape.visual.mappings.ObjectMapping.setNodeAppearanceCalculator||
||1||1||cytoscape.CytoscapeInit.getDefaultVisualStyle||
||1||1||ding.view.DingCanvas.getComponentCount||
||1||1||cytoscape.render.stateful.GraphLOD.textAsShape||
||1||1||cytoscape.groups.CyGroupViewer.groupCreated||

||'''Plugin Name'''||
||AdvancedNetworkMerge||
||AffinityPropagationPlugin||
||AttrTransformingPlugin||
||AutomaticLayout||
||BiNGO||
||BioMartClient||
||BioPAX||
||BubbleRouter||
||CPDBClient||
||CoryneRegNetPlugin||
||CustomGraphicsDemo||
||CyGoose||
||CytoSQL||
||CytoscapeEditor2||
||DualLayout||
||EdgeBundlerPlugin||
||EntrezGeneAttributeImportUI||
||ExcentricLabelsPlugin||
||GradientNodeViewPlugin||
||GroovyEnginePlugin||
||IDMapping||
||JRubyEngine||
||JavaScriptEngine||
||JythonEnginePlugin||
||KEGGBrowser||
||KGMLReader||
||LayoutRegion||
||MCODE3||
||ManualLayout||
||NCBIClient||
||NatureProtocolsWorkflow||
||NetLink||
||PICRClient2||
||PPINetworksEvolutionPlugin||
||PSI-MI||
||PSIQUICUniversalClient||
||PartitionNetwork||
||PropertySheetPlugin||
||PythonEnginePlugin||
||QuickFind||
||RDFScape||
||RFilters||
||SBMLReader||
||SFLDLoader||
||ScriptEngineManager||
||SelectShortestPathPlugin||
||SessionForWebPlugin||
||ShortestPath2||
||TableImport||
||addParentNeighbors||
||batchTool||
||bionetbuilder||
||blast2simGraph||
||browser||
||cPath||
||cPath2||
||centiscape||
||chemViz||
||cluego||
||clusterExplorerPlugin||
||clusterMaker||
||coma||
||commandTool||
||common-attrs||
||coreCommands||
||droplugin||
||dynamicXpr||
||edgeLengthPlugin||
||edgeLister||
||epitrace||
||fern||
||filters||
||fluxviz||
||gpml||
||gramophone||
||groupTool||
||hiderslider||
||linkout||
||metaNodePlugin2||
||namedSelection||
||nemo||
||netatlas||
||perturbation-analyzer||
||reconn||
||reorient||
||reposition||
||sampleGroupViewer||
||sampleLayout||
||sbmlreader2||
||string||
||structureViz||
||subgraphCreator||
||tunableSampler||