API_usage

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