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 Cytoscape or corelibs. Public methods found in 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 |
BiNGO |
BioPAX |
CPDBClient |
CytoSQL |
EntrezGeneAttributeImportUI |
IDMapping |
JRubyEngine |
KEGGBrowser |
KGMLReader |
MCODE3 |
NCBIClient |
PICRClient2 |
PPINetworksEvolutionPlugin |
PSI-MI |
PSIQUICUniversalClient |
RDFScape |
RFilters |
SBMLReader |
SFLDLoader |
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 |