# Classes and Interfaces in #CytoScape

_{# Classes and Interfaces in #CytoScape - 956 results found.}

Name	Description	Type	Package	Framework
AboutDialog	About page for web service clients or other plugins.	Class	cytoscape.util.swing	CytoScape
Abs		Class	org.cytoscape.equations.builtins	CytoScape
AbstractCalculator		Class	cytoscape.visual.calculators	CytoScape
AbstractCellEditor		Class	cytoscape.util.swing	CytoScape
AbstractCommandHandler	This abstract class provides a convenient (but not necessary) base class for writing CyCommandHandlers.	Class	cytoscape.command	CytoScape
AbstractDCustomGraphics		Class	cytoscape.visual.customgraphic.impl	CytoScape
AbstractFunction		Class	org.cytoscape.equations	CytoScape
AbstractGraphReader		Class	cytoscape.data.readers	CytoScape
AbstractLayout	The AbstractLayout provides nice starting point for Layouts written for Cytoscape.	Class	cytoscape.layout	CytoScape
AbstractMapping		Class	cytoscape.visual.mappings	CytoScape
AbstractParserControl	Class to inherit from so when in future when new controls are added clients will no have to implement them.	Class	org.apache.commons.cli.avalon	CytoScape
AbstractScaler	Used to scale a list of values to [a,b]Constructor SummaryAbstractScaler()	Class	cytoscape.util	CytoScape
AbstractTreeTableModel		Class	cytoscape.util.swing	CytoScape
AbstractVisualProperty		Class	cytoscape.visual.properties	CytoScape
ACos		Class	org.cytoscape.equations.builtins	CytoScape
AddRemoveTest		Class	fing.model.test	CytoScape
Aliases	Simpler version of Thesaurus.	Class	cytoscape.data.synonyms	CytoScape
AliasType	enum AliasTypeextends Enum Aliases are always belongs to one of these types.	Class	cytoscape.data.synonyms	CytoScape
AlignHorizontalAction	See Also:Serialized FormFields inherited from class javax.	Class	cytoscape.actions	CytoScape
AlignVerticalAction	See Also:Serialized FormFields inherited from class javax.	Class	cytoscape.actions	CytoScape
AllGraphPerspectiveMethodsTest		Class	fing.model.test	CytoScape
AllRootGraphMethodsTest		Class	fing.model.test	CytoScape
AlphabeticalSelectionAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
AlreadySelectedException	Thrown when more than one option in an option groupAuthor:John Keyes ( john at integralsource.	Class	org.apache.commons.cli	CytoScape
And		Class	org.cytoscape.equations.builtins	CytoScape
AnimatedLayoutAction	See Also:Serialized FormFields inherited from class javax.	Class	cytoscape.actions	CytoScape
Annotation	Store any number of classifications for named entities, each of which is from a specified species, and where the classifications are all terms from an	Class	cytoscape.data.annotation	CytoScape
AnnotationDescription	Distinguish among different ontologies, by curator and type.	Class	cytoscape.data.annotation	CytoScape
AnnotationFlatFileReader		Class	cytoscape.data.annotation.readers	CytoScape
AnnotationXmlReader		Class	cytoscape.data.annotation.readers	CytoScape
Appearance	A class that holds the appearance information for NodeViews and EdgeViews.	Class	cytoscape.visual	CytoScape
ApplyLayoutAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
ApplyVisualStyleAction	Apply Visual Style for a set of selected networks.	Class	cytoscape.actions	CytoScape
ArbitraryGraphicsCanvas	This class extends cytoscape.	Class	ding.view	CytoScape
ArgDescriptor	A class describing a function argument.	Class	org.cytoscape.equations	CytoScape
ArgType	enum ArgTypeextends EnumAn enum specifying a function argument type.	Class	org.cytoscape.equations	CytoScape
ARowanBugTest		Class	fing.model.test	CytoScape
ArrangeAction		Class	cytoscape.actions	CytoScape
ArrayIntEnumerator	A utility class which conveniently converts an array of integers into an IntEnumerator (an enumeration of integers).	Class	cytoscape.util.intr	CytoScape
ArrayIntIterator	A utility class which conveniently converts an array of integers into an IntIterator (an iteration of integers).	Class	cytoscape.util.intr	CytoScape
ArrayTestMethod1		Class	cytoscape.geom.rtree.test	CytoScape
ArrayTestMethod2		Class	cytoscape.geom.rtree.test	CytoScape
ArrayTestMethod3		Class	cytoscape.geom.rtree.test	CytoScape
ArrayTestMethod4		Class	cytoscape.geom.rtree.test	CytoScape
Arrow		Interface	cytoscape.render.immed.arrow	CytoScape
Arrow	This class is a replacement for the yFiles Arrow class.	Class	cytoscape.visual	CytoScape
ArrowheadArrow		Class	cytoscape.render.immed.arrow	CytoScape
ArrowIcon	Icon for arrow shape.	Class	cytoscape.visual.ui.icon	CytoScape
ArrowParser	Parses a String into a yFiles Arrow object.	Class	cytoscape.visual.parsers	CytoScape
ArrowShape	enum ArrowShapeextends EnumDefines arrow shapes.	Class	cytoscape.visual	CytoScape
ArrowShapeParser		Class	cytoscape.visual.parsers	CytoScape
ASin		Class	org.cytoscape.equations.builtins	CytoScape
ATan2		Class	org.cytoscape.equations.builtins	CytoScape
AttribTopoGraphNode	Represents a node in a topological graph.	Class	cytoscape.data	CytoScape
Attribute	Java class for anonymous complex type.	Class	cytoscape.bookmarks	CytoScape
AttributeFilter	Interface for defining CyEdge-based filters used for determining which Edges should be used for a particular operation, such as	Interface	cytoscape.data	CytoScape
AttributeImportPanel	General GUI component for importing attributes.	Class	cytoscape.util.swing	CytoScape
AttributeImportQuery		Class	cytoscape.data.webservice	CytoScape
AttributeSaverDialog	Dialog box to save various attributes.	Class	cytoscape.data	CytoScape
AttributeValueVisitor	Interface for defining attribute value visitors--operations to perform on each attribute value using CyAttributesUtils.	Interface	cytoscape.data	CytoScape
Average		Class	org.cytoscape.equations.builtins	CytoScape
BackgroundColorAction	Prompts User for New Background Color.	Class	cytoscape.actions	CytoScape
BackwardSlashStroke	Nested Class SummaryNested classes/interfaces inherited from class cytoscape.	Class	cytoscape.visual.strokes	CytoScape
BasicCalculator		Class	cytoscape.visual.calculators	CytoScape
BasicGraphViewHandler	A basic GraphViewHandler that simply reflects GraphPerspective changes on a given GraphView	Class	cytoscape.view	CytoScape
BasicParser	The class BasicParser provides a very simple implementation of the flatten method.	Class	org.apache.commons.cli	CytoScape
BasicQuietRTreeTest		Class	cytoscape.geom.rtree.test	CytoScape
BelowAndAbovePanel	Drawing and updating below & above values in Gradient Editor.	Class	cytoscape.visual.ui.editors.continuous	CytoScape
Bend	A class that encapsulates the representation of the bend used for a particular EdgeView.	Interface	giny.view	CytoScape
BendSelectedEdgesAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
BiModalJSplitPane	The BiModalJSplitPane class extends JSplitPane to provide two modes: MODE_SHOW_SPLIT: The split in the split pane appears as it normally	Class	cytoscape.view.cytopanels	CytoScape
BinOpNode	A node in the parse tree representing a binary operator.	Class	org.cytoscape.equations.parse_tree	CytoScape
BioDataServer		Class	cytoscape.data.servers	CytoScape
BioDataServerInterface		Interface	cytoscape.data.servers	CytoScape
BioDataServerRmi	This is the actual class which implements BioDataServer Methods.	Class	cytoscape.data.servers	CytoScape
BioDataServerUtil		Class	cytoscape.util	CytoScape
BiologicalProcessAnnotationReader	The purpose of this class is to convert a 'gene_association.	Class	cytoscape.cruft.obo	CytoScape
BiologicalProcessAnnotationTester		Class	cytoscape.cruft.obo.test	CytoScape
BirdsEyeView		Class	ding.view	CytoScape
BirdsEyeViewAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
BitmapExporter	Bitmap exporter by the ImageIO class.	Class	cytoscape.util.export	CytoScape
BitSetPerformance		Class	cytoscape.util.intr.test	CytoScape
BList		Class	org.cytoscape.equations.builtins	CytoScape
BookmarkAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
BookmarkDialog		Class	cytoscape.dialogs.preferences	CytoScape
BookmarkReader		Class	cytoscape.data.readers	CytoScape
Bookmarks	Java class for anonymous complex type.	Class	cytoscape.bookmarks	CytoScape
BookmarksUtil	Utility methods for getting entries in the bookmark object.	Class	cytoscape.util	CytoScape
BooleanConstantNode	A node in the parse tree representing an integer constant.	Class	org.cytoscape.equations.parse_tree	CytoScape
BooleanList		Class	org.cytoscape.equations	CytoScape
BooleanParser	Parses a String into a Boolean object.	Class	cytoscape.visual.parsers	CytoScape
BoundaryRangeValues	This class defines a data object representing the range values associated with a particular domain value, called a boundary value.	Class	cytoscape.visual.mappings	CytoScape
Bug646Test		Class	fing.model.test	CytoScape
C2CMappingEditor	Continuous-Continuous mapping editor.	Class	cytoscape.visual.ui.editors.continuous	CytoScape
C2DMappingEditor	Continuous Mapping editor for discrete values, such as Font, Shape, Label Position, etc.	Class	cytoscape.visual.ui.editors.continuous	CytoScape
Calculator		Interface	cytoscape.visual.calculators	CytoScape
CalculatorCatalog	Stores various types of Calculators from data attributes to an attribute of a specified type.	Class	cytoscape.visual	CytoScape
CalculatorCatalogFactory	This class provides a static method for reading a CalculatorCatalog object from file, using parameters specified in a supplied CytoscapeConfig.	Class	cytoscape.visual	CytoScape
CalculatorFactory	This class provides static factory methods for constructing instances of Calculators as specified by arguments and static methods for getting names	Class	cytoscape.visual.calculators	CytoScape
CalculatorIO	This class defines static methods for reading calculator definitions from a properties object and installing them into a CalculatorCatalog, and for	Class	cytoscape.visual	CytoScape
Category	Java class for anonymous complex type.	Class	cytoscape.bookmarks	CytoScape
Category	enum Categoryextends EnumEnum Constant SummaryANALYSIS	Class	cytoscape.plugin	CytoScape
CellEditorFactory		Class	cytoscape.visual.ui	CytoScape
CellHeightManager		Class	cytoscape.visual.ui	CytoScape
CellRendererFactory		Class	cytoscape.visual.ui	CytoScape
CellularComponentAnnotationReader	The purpose of this class is to convert a 'gene_association.	Class	cytoscape.cruft.obo	CytoScape
CellularComponentAnnotationTester		Class	cytoscape.cruft.obo.test	CytoScape
CheckBoxFileChooser		Class	cytoscape.actions	CytoScape
CheckBoxJList	This class is based on CheckBoxJList: from SWING HACKS ISBN: 0-596-00907-0	Class	cytoscape.util.swing	CytoScape
Child	Java class for anonymous complex type.	Class	cytoscape.generated	CytoScape
CLArgsParser	Parser for command line arguments.	Class	org.apache.commons.cli.avalon	CytoScape
clear		Class	cytoscape.data.servers	CytoScape
CloneGraphInNewWindowAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
CLOption	Basic class describing an instance of option.	Class	org.apache.commons.cli.avalon	CytoScape
CLOptionDescriptor	Basic class describing an type of option.	Class	org.apache.commons.cli.avalon	CytoScape
CLUtil	CLUtil offers basic utility operations for use both internal and external to package.	Class	org.apache.commons.cli.avalon	CytoScape
CodeAndSourceLocation	A node in the parse tree representing a binary operator.	Class	org.cytoscape.equations	CytoScape
ColorConverter		Class	cytoscape.visual.converter	CytoScape
ColorPaintFactory		Class	cytoscape.visual.customgraphic.paint	CytoScape
ColorParser	Parses a String into a Color object.	Class	cytoscape.visual.parsers	CytoScape
ColorRangeValueCalculator		Class	cytoscape.visual.mappings.rangecalculators	CytoScape
ColorScaleTable		Class	cytoscape.dialogs	CytoScape
ColorUtil	Color utility class to convert Java color object to string and vice versa.	Class	cytoscape.util	CytoScape
ColumnResizer	Automatically resize column based on the objects in the cell.	Class	cytoscape.util.swing	CytoScape
ColumnTypes	enum ColumnTypesextends EnumEnum Constant SummaryEDGES	Class	cytoscape.view	CytoScape
Combin		Class	org.cytoscape.equations.builtins	CytoScape
CommandLine	Represents list of arguments parsed against a Options descriptor.	Class	org.apache.commons.cli	CytoScape
CommandLineParser	A class that implements the CommandLineParser interface can parse a String array according to the Options specified	Interface	org.apache.commons.cli	CytoScape
Concatenate		Class	org.cytoscape.equations.builtins	CytoScape
ConsoleLogger	The ConsoleLogger is the default log handler for Cytoscape and does nothing much more than issue messages to System.	Class	cytoscape.logger	CytoScape
ContentChangeListener		Interface	ding.view	CytoScape
ContiguousArrowStroke	Fields inherited from class cytoscape.	Class	cytoscape.visual.strokes	CytoScape
ContinuousLegend		Class	cytoscape.visual.mappings.continuous	CytoScape
ContinuousMapping	class.	Class	cytoscape.visual.mappings	CytoScape
ContinuousMappingEditorPanel	Abstract class for all Continuous Mapping Editors.	Class	cytoscape.visual.ui.editors.continuous	CytoScape
ContinuousMappingPoint	Encapsulates a ContinuousMapping Point with a single point value and associated BoundaryRangeValues.	Class	cytoscape.visual.mappings.continuous	CytoScape
ContinuousMappingReader	Reads in ContinuousMapping Properties.	Class	cytoscape.visual.mappings.continuous	CytoScape
ContinuousMappingWriter	Writes out ContinuousMapping Properties.	Class	cytoscape.visual.mappings.continuous	CytoScape
ContinuousRangeCalculator	Calculates the Range for Continuous Mappers.	Class	cytoscape.visual.mappings.continuous	CytoScape
ContinuousTrackRenderer		Class	cytoscape.visual.ui.editors.continuous	CytoScape
Cos		Class	org.cytoscape.equations.builtins	CytoScape
Cosh		Class	org.cytoscape.equations.builtins	CytoScape
Count		Class	org.cytoscape.equations.builtins	CytoScape
CountedIterator	A java.	Interface	cytoscape.data.attr	CytoScape
CreateNetworkViewAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
CreditScreen		Class	cytoscape.util	CytoScape
CustomGraphic	Represents all the information needed to define a custom graphic for a given NodeView.	Class	cytoscape.render.stateful	CytoScape
CustomGraphicsBrowser	Display list of images available as custom graphicsAuthor:konoSee Also:Serialized Form	Class	cytoscape.visual.customgraphic.ui	CytoScape
CustomGraphicsCellRenderer	Cell renderer for Custom Graphics Browser.	Class	cytoscape.visual.customgraphic.ui	CytoScape
CustomGraphicsCellRenderer		Class	cytoscape.visual.ui.editors.discrete	CytoScape
CustomGraphicsDetailPanel		Class	cytoscape.visual.customgraphic.ui	CytoScape
CustomGraphicsManager		Class	cytoscape.visual.customgraphic	CytoScape
CustomGraphicsManagerDialog	Main UI for managing on-memory library of Custom GraphicsAuthor:konoSee Also:Serialized Form	Class	cytoscape.visual.customgraphic.ui	CytoScape
CustomGraphicsPositionCalculator		Class	ding.view	CytoScape
CustomGraphicsProperty		Interface	cytoscape.visual.customgraphic.impl.vector	CytoScape
CustomGraphicsPropertyImpl		Class	cytoscape.visual.customgraphic	CytoScape
CustomGraphicsRangeValueCalculator		Class	cytoscape.visual.mappings.rangecalculators	CytoScape
CustomGraphicsRangeValueRenderer		Interface	cytoscape.visual.mappings	CytoScape
CustomGraphicsUtil		Class	cytoscape.visual.customgraphic	CytoScape
CustomMapping	User-definable visual mapping.	Interface	cytoscape.visual.mappings	CytoScape
CyAbstractEdit	A small convenience class that can be used to create new edits.	Class	cytoscape.util.undo	CytoScape
CyAttributes	CyAttributes provides access to network, node, and edge attributes within Cytoscape.	Interface	cytoscape.data	CytoScape
CyAttributesImpl		Class	cytoscape.data	CytoScape
CyAttributesReader		Class	cytoscape.data.readers	CytoScape
CyAttributesUtils		Class	cytoscape.data	CytoScape
CyAttributesWriter	CyAttributeWriter extracted from AttributeSaverDialog.	Class	cytoscape.data.writers	CytoScape
CyCollapsiblePanel	The user-triggered collapsable panel containing the component (trigger) in the titled borderSee Also:Serialized Form	Class	cytoscape.util.swing	CytoScape
CyColorCellRenderer	CyColorCellRenderer.	Class	cytoscape.visual.ui.editors.discrete	CytoScape
CyColorChooser	This is an annoying re-implementation of JColorChooser.	Class	cytoscape.util	CytoScape
CyColorPropertyEditor	ColorPropertyEditor.	Class	cytoscape.visual.ui.editors.discrete	CytoScape
CyComboBoxPropertyEditor	ComboBoxPropertyEditor.	Class	cytoscape.visual.ui.editors.discrete	CytoScape
CyCommandException	The CyCommandException is thrown when a CyCommandHandler encounters an exception condition.	Class	cytoscape.command	CytoScape
CyCommandHandler	The CyCommandHandler interface allows a Cytoscape plugin to make it's functions available to other plugins in a loosely-coupled manner (by passing command	Interface	cytoscape.command	CytoScape
CyCommandManager	CyCommandManager is a singleton Cytoscape class that provides a global registry of CyCommands and CyCommandNamespaces.	Class	cytoscape.command	CytoScape
CyCommandNamespace	A CyCommandNamespace represents a reservation for a group of CyCommands.	Interface	cytoscape.command	CytoScape
CyCommandResult	CyCommandResult returns the results from the execution of a command.	Class	cytoscape.command	CytoScape
CyCustomGraphics		Interface	cytoscape.visual.customgraphic	CytoScape
CyCustomGraphicsEditor	Fields inherited from class com.	Class	cytoscape.visual.ui.editors.discrete	CytoScape
CyCustomGraphicsParser		Interface	cytoscape.visual.customgraphic	CytoScape
CyCustomGraphicsParserFactory		Interface	cytoscape.visual.customgraphic	CytoScape
CyCustomGraphicsParserFactoryImpl		Class	cytoscape.visual.customgraphic.impl	CytoScape
CyCustomGraphicsTableCellRenderer		Class	cytoscape.visual.customgraphic.ui	CytoScape
CyCustomGraphicsTreeCellRenderer		Class	cytoscape.visual.customgraphic.ui	CytoScape
CyCustomGraphicsTreeNode	Fields inherited from class org.	Class	cytoscape.visual.customgraphic.ui	CytoScape
CyDesktopManager		Class	cytoscape.view	CytoScape
CyDoublePropertyEditor	Fields inherited from class com.	Class	cytoscape.visual.ui.editors.discrete	CytoScape
CyEdge		Class	cytoscape	CytoScape
CyEdgeView	Fields inherited from interface giny.	Interface	cytoscape.view	CytoScape
CyFileFilter	A convenience implementation of FileFilter that filters out all files except for those type extensions that it knows about.	Class	cytoscape.util	CytoScape
CyFontPropertyEditor	Fields inherited from class com.	Class	cytoscape.visual.ui.editors.discrete	CytoScape
CyGradientTrackRenderer		Class	cytoscape.visual.ui.editors.continuous	CytoScape
CyGraphAllLOD	CyGraphAllLOD is the level of detail (LOD) class used for the "Show Graphics Details" menu item.	Class	cytoscape.ding	CytoScape
CyGraphLOD	An instance of this class defines the level of detail that goes into a single rendering of a graph.	Class	cytoscape.ding	CytoScape
CyGroup	The CyGroup interface provides the methods for a group model that maintains the list of nodes belonging to a group, the parent of a particular	Interface	cytoscape.groups	CytoScape
CyGroupChangeListener	The CyGroupChangeListener interface provides a mechanism for plugins that track group-related events to get notified of global group changes (new groups, etc.	Interface	cytoscape.groups	CytoScape
CyGroupImpl	The CyGroup class provides the implementation for a group model that maintains the list of nodes belonging to a group, the parent of a particular	Class	cytoscape.groups	CytoScape
CyGroupManager	The CyGroup class provides the implementation for a group model that maintains the list of nodes belonging to a group, the parent of a particular	Class	cytoscape.groups	CytoScape
CyGroupViewer	The CyGroupViewer interface provides a mechanism for group view implementations to register themselves and get notified of group creation and deletion.	Interface	cytoscape.groups	CytoScape
CyHelpBroker	This class creates the Cytoscape Help Broker for managing the JavaHelp system and help set access	Class	cytoscape.view	CytoScape
CyInitParams	An interface that describes the initialization parameters needed by cytoscape.	Interface	cytoscape.init	CytoScape
CyLayoutAlgorithm		Interface	cytoscape.layout	CytoScape
CyLayouts		Class	cytoscape.layout	CytoScape
CyLogger		Class	cytoscape.logger	CytoScape
CyLogHandler	The CyLogHandler interface must be implemented by log handlers for plugins that wish to handle their own logging.	Interface	cytoscape.logger	CytoScape
CyMain	This is the main startup class for Cytoscape.	Class	cytoscape	CytoScape
CyMenus	Creates the menu and tool bars for a Cytoscape window object.	Class	cytoscape.view	CytoScape
CyNetwork	CyNetwork is the primary class for algorithm writing.	Interface	cytoscape	CytoScape
CyNetworkAdapter	Empty implementation of the CyNetworkListener interface, following the adapter pattern useful for defining anonymous inner classes.	Class	cytoscape	CytoScape
CyNetworkData		Interface	cytoscape	CytoScape
CyNetworkEvent	Events of this class are fired from a CyNetwork object when something happens to the network.	Class	cytoscape	CytoScape
CyNetworkListener	Interface for listeners that respond to CyNetwork events.	Interface	cytoscape	CytoScape
CyNetworkNaming		Class	cytoscape.util	CytoScape
CyNetworkTitleChange	Class used for passing along information about the network when the network title has changed (firing an event)	Class	cytoscape	CytoScape
CyNetworkUtilities	This class provides static methods that operate on a CyNetwork to perform various useful tasks.	Class	cytoscape.data	CytoScape
CyNetworkView	CyNetworkView is responsible for actually getting a graph to show up on the screen.	Interface	cytoscape.view	CytoScape
CyNode		Class	cytoscape	CytoScape
CyNodeView	Fields inherited from interface giny.	Interface	cytoscape.view	CytoScape
CyObjectPositionPropertyEditor	Fields inherited from class com.	Class	cytoscape.visual.ui.editors.discrete	CytoScape
Cysession	Java class for anonymous complex type.	Class	cytoscape.generated	CytoScape
CyStartupListener	arguments passed from file assocations set by install4j for Mac OS.	Class	cytoscape	CytoScape
CyStringPropertyEditor	Fields inherited from class com.	Class	cytoscape.visual.ui.editors.discrete	CytoScape
Cytopanel	Java class for anonymous complex type.	Class	cytoscape.generated	CytoScape
CytoPanel	Interface to a CytoPanel.	Interface	cytoscape.view.cytopanels	CytoScape
CytoPanelAction		Class	cytoscape.actions	CytoScape
CytoPanelContainer	Interface for Container of CytoPanel Objects.	Interface	cytoscape.view.cytopanels	CytoScape
CytoPanelImp	The CytoPanel class extends JPanel to provide the following functionality: Floating/Docking of Panel.	Class	cytoscape.view.cytopanels	CytoScape
CytoPanelListener	This listener interface provides the mechanism to respond to CytoPanel Events.	Interface	cytoscape.view.cytopanels	CytoScape
CytoPanelName	enum CytoPanelNameextends EnumAn enum that maps names to compass directions.	Class	cytoscape.view.cytopanels	CytoScape
Cytopanels	Java class for anonymous complex type.	Class	cytoscape.generated	CytoScape
CytoPanelState	CytoPanelState Class.	Class	cytoscape.view.cytopanels	CytoScape
CytoPanelUtil	Contains methods to assist with various tasks performed by the CytoPanel API.	Class	cytoscape.view.cytopanels	CytoScape
Cytoscape	This class, Cytoscape is the primary class in the API.	Class	cytoscape	CytoScape
CytoscapeAction		Class	cytoscape.util	CytoScape
CytoscapeDesktop	The CytoscapeDesktop is the central Window for working with CytoscapeSee Also:Serialized Form	Class	cytoscape.view	CytoScape
CytoscapeFingRootGraph	Fields inherited from interface cytoscape.	Class	cytoscape.giny	CytoScape
CytoscapeInit	Cytoscape Init is responsible for starting Cytoscape in a way that makes The comments below are more hopeful than accurate.	Class	cytoscape	CytoScape
CytoscapeMenuBar		Class	cytoscape.util	CytoScape
CytoscapeModifiedNetworkManager	CytoscapeModifiedNetworkManager manages the modified state settings for the networks and listens for PropertyChangeEvents.	Class	cytoscape	CytoScape
CytoscapePlugin	A CytoscapePlugin is the new "Global" plugin.	Class	cytoscape.plugin	CytoScape
CytoscapeProgressMonitor	CytoscapeProgressMonitor.	Class	cytoscape.util	CytoScape
CytoscapeRootGraph		Interface	cytoscape.giny	CytoScape
CytoscapeSessionReader	Reader to load CYtoscape Session file (.	Class	cytoscape.data.readers	CytoScape
CytoscapeSessionWriter	Write session states into files.	Class	cytoscape.data.writers	CytoScape
CytoscapeToolBar		Class	cytoscape.util	CytoScape
CytoscapeVersion	CytoscapeVersion: identify (and describe) successive versions of cytoscape.	Class	cytoscape	CytoScape
CyUndo	A tiny class for supporting undo in the Cytoscape context.	Class	cytoscape.util.undo	CytoScape
CyWebServiceEvent	Event object used by Web Service Clients and the core.	Class	cytoscape.data.webservice	CytoScape
CyWebServiceEventListener	Listener for Web Service Event handling.	Interface	cytoscape.data.webservice	CytoScape
CyWebServiceEventSupport		Class	cytoscape.data.webservice	CytoScape
CyWebServiceException		Class	cytoscape.data.webservice	CytoScape
DashDotStroke	Fields inherited from class java.	Class	cytoscape.visual.strokes	CytoScape
DatabaseSearchResult		Class	cytoscape.data.webservice	CytoScape
DataSource	Java class for anonymous complex type.	Class	cytoscape.bookmarks	CytoScape
DBCrossReferenceReader	Reader for database cross reference file.	Class	cytoscape.data.ontology.readers	CytoScape
DBCrossReferences	Database cress reference.	Class	cytoscape.data.ontology	CytoScape
DBReference	Represents an entry in the database cross reference.	Class	cytoscape.data.ontology	CytoScape
DBXrefKeywords	enum DBXrefKeywordsextends EnumEnum Constant SummaryABBREVIATION	Class	cytoscape.data.ontology.readers	CytoScape
DefaultAppearenceBuilder	Dialog for editing default visual property values.	Class	cytoscape.visual.ui	CytoScape
DefaultCyCustomGraphicsParser		Class	cytoscape.visual.customgraphic	CytoScape
DefaultViewPanel	Panel to show the default properties visually (as graphics).	Class	cytoscape.visual.ui	CytoScape
Degrees		Class	org.cytoscape.equations.builtins	CytoScape
DeleteAction	action for deleting selected Cytoscape nodes and edgesVersion:1.	Class	cytoscape.actions	CytoScape
DeltaArrow		Class	cytoscape.render.immed.arrow	CytoScape
DeselectAllAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
DeSelectAllEdgesAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
DeSelectAllNodesAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
Desktop	Java class for anonymous complex type.	Class	cytoscape.generated	CytoScape
DesktopSize	Java class for anonymous complex type.	Class	cytoscape.generated	CytoScape
DestroyNetworkAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
DestroyNetworkViewAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
DGraphView	DING implementation of the GINY view.	Class	ding.view	CytoScape
DiamondArrow		Class	cytoscape.render.immed.arrow	CytoScape
DiamondNodeShape		Class	cytoscape.render.immed.nodeshape	CytoScape
DingCanvas	This class is meant to be extended by a class which is meant to exist within the InternalFrameComponent class.	Class	ding.view	CytoScape
DingNetworkView	Nested Class SummaryNested classes/interfaces inherited from class ding.	Class	cytoscape.ding	CytoScape
DiscArrow		Class	cytoscape.render.immed.arrow	CytoScape
DiscreteLegend		Class	cytoscape.visual.mappings.discrete	CytoScape
DiscreteMapping	data value is extracted from a bundle of attributes by using a specified dataFields inherited from class cytoscape.	Class	cytoscape.visual.mappings	CytoScape
DiscreteMappingReader	Reads in DiscreteMapping Properties.	Class	cytoscape.visual.mappings.discrete	CytoScape
DiscreteMappingWriter	Writes DiscreteMapping Properties.	Class	cytoscape.visual.mappings.discrete	CytoScape
DiscretePropertySetter		Class	cytoscape.visual.ui	CytoScape
DiscreteRangeCalculator	Range Calculator for the Discrete Mapper.	Class	cytoscape.visual.mappings.discrete	CytoScape
DiscreteTrackRenderer		Class	cytoscape.visual.ui.editors.continuous	CytoScape
DLayer		Class	cytoscape.visual.customgraphic.impl	CytoScape
DotStroke	Fields inherited from class cytoscape.	Class	cytoscape.visual.strokes	CytoScape
DoubleList		Class	org.cytoscape.equations	CytoScape
DoubleParser	Parses a String into a Double object.	Class	cytoscape.visual.parsers	CytoScape
DoubleRangeValueCalculator		Class	cytoscape.visual.mappings.rangecalculators	CytoScape
DownloadableInfo		Class	cytoscape.plugin	CytoScape
DownloadableType	enum DownloadableTypeextends EnumEnum Constant SummaryFILE	Class	cytoscape.plugin	CytoScape
DropDownMenuButton	Button with drop down menu.	Class	cytoscape.util.swing	CytoScape
DuplicateCalculatorNameException	This Exception is thrown when one attempts to add a Calculator to a CalculatorCatalog that already has a Calculator of the same name and	Class	cytoscape.visual	CytoScape
DuplicatePluginClassException	See Also:Serialized FormConstructor SummaryDuplicatePluginClassException()	Class	cytoscape.plugin	CytoScape
DynamicGraph	A graph whose topology can be modified.	Interface	cytoscape.graph.dynamic	CytoScape
DynamicGraphFactory	A factory for getting cytoscape.	Class	cytoscape.graph.dynamic.util	CytoScape
DynamicLayoutMenu	A DynamicLayoutMenu is a more complicated layout menu that constructs layout menu items on-the-fly based on the capabilities of the layout algorithm and environment	Class	cytoscape.layout.ui	CytoScape
Edge	Java class for anonymous complex type.	Class	cytoscape.generated	CytoScape
Edge		Interface	giny.model	CytoScape
EdgeAnchors		Interface	cytoscape.render.immed	CytoScape
EdgeAppearance	Objects of this class hold data describing the appearance of an Edge.	Class	cytoscape.visual	CytoScape
EdgeAppearanceCalculator	This class calculates the appearance of an Edge.	Class	cytoscape.visual	CytoScape
EdgeAttributesPopupDetails	This class provides a detailed list of attribute information for a givenSee Also:Serialized Form	Class	cytoscape.dialogs	CytoScape
EdgeColorProp	Fields inherited from class cytoscape.	Class	cytoscape.visual.properties	CytoScape
EdgeContextMenuListener	an interface for responding to PhoebeCanvasDropEvents.	Interface	ding.view	CytoScape
EdgeDetails	Defines the visual properties of an edge.	Class	cytoscape.render.stateful	CytoScape
EdgeFontFaceProp	Fields inherited from class cytoscape.	Class	cytoscape.visual.properties	CytoScape
EdgeFontSizeProp	Fields inherited from class cytoscape.	Class	cytoscape.visual.properties	CytoScape
EdgeLabelColorProp	Fields inherited from class cytoscape.	Class	cytoscape.visual.properties	CytoScape
EdgeLabelOpacityProp	Fields inherited from class cytoscape.	Class	cytoscape.visual.properties	CytoScape
EdgeLabelPositionProp	Fields inherited from class cytoscape.	Class	cytoscape.visual.properties	CytoScape
EdgeLabelProp	Fields inherited from class cytoscape.	Class	cytoscape.visual.properties	CytoScape
EdgeLabelWidthProp	Fields inherited from class cytoscape.	Class	cytoscape.visual.properties	CytoScape
EdgeLineStyleProp	Fields inherited from class cytoscape.	Class	cytoscape.visual.properties	CytoScape
EdgeLineWidthProp	Fields inherited from class cytoscape.	Class	cytoscape.visual.properties	CytoScape
EdgeManipulationAction	See Also:Serialized FormFields inherited from class javax.	Class	cytoscape.actions	CytoScape
EdgeOpacityProp	Fields inherited from class cytoscape.	Class	cytoscape.visual.properties	CytoScape
EdgeSourceArrowColorProp	Fields inherited from class cytoscape.	Class	cytoscape.visual.properties	CytoScape
EdgeSourceArrowOpacityProp	Fields inherited from class cytoscape.	Class	cytoscape.visual.properties	CytoScape
EdgeSourceArrowShapeProp	Fields inherited from class cytoscape.	Class	cytoscape.visual.properties	CytoScape
EdgeTargetArrowColorProp	Fields inherited from class cytoscape.	Class	cytoscape.visual.properties	CytoScape
EdgeTargetArrowOpacityProp	Fields inherited from class cytoscape.	Class	cytoscape.visual.properties	CytoScape
EdgeTargetArrowShapeProp	Fields inherited from class cytoscape.	Class	cytoscape.visual.properties	CytoScape
EdgeToolTipProp	Fields inherited from class cytoscape.	Class	cytoscape.visual.properties	CytoScape
EdgeView		Interface	giny.view	CytoScape
EditBookmarkDialog		Class	cytoscape.dialogs.preferences	CytoScape
EditNetworkTitleDialog		Class	cytoscape.dialogs	CytoScape
EditorDisplayer	enum EditorDisplayerextends EnumManaging value editors in for each data types.	Class	cytoscape.visual.ui	CytoScape
EditorManager		Interface	cytoscape.visual.ui	CytoScape
EditorValueRangeTracer		Class	cytoscape.visual.ui.editors.continuous	CytoScape
EllipseNodeShape		Class	cytoscape.render.immed.nodeshape	CytoScape
EqnAttrTracker	Constructor SummaryEqnAttrTracker()Methods inherited from class java.	Class	cytoscape.data.readers	CytoScape
EqnCompiler		Class	org.cytoscape.equations	CytoScape
EqnParser		Interface	org.cytoscape.equations	CytoScape
EqualDashStroke	Fields inherited from class java.	Class	cytoscape.visual.strokes	CytoScape
Equation		Class	org.cytoscape.equations	CytoScape
EquationUtil		Class	org.cytoscape.equations	CytoScape
Error		Class	org.cytoscape.equations.builtins	CytoScape
Exec		Class	cytoscape.util	CytoScape
ExitAction		Class	cytoscape.actions	CytoScape
Exp		Class	org.cytoscape.equations.builtins	CytoScape
ExpFileChooser	adds a JCheckBox at the bottom of the chooser, asking whether to copy expression data to attributes.	Class	cytoscape.actions	CytoScape
ExportAction		Class	cytoscape.actions	CytoScape
ExportAsGMLAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
ExportAsGraphicsAction	Action for exporting a network view to bitmap or vector graphics.	Class	cytoscape.actions	CytoScape
ExportAsGraphicsFileChooser	Dialog that chooses file to export to.	Class	cytoscape.dialogs	CytoScape
ExportAsInteractionsAction	write out the current graph to the specified file, using the standard interactions format: nodeA edgeType nodeB.	Class	cytoscape.actions	CytoScape
ExportAsXGMMLAction	This action is for exporting network and attributes in XGMML file.	Class	cytoscape.actions	CytoScape
ExportBitmapOptionsDialog	Options dialog for exporting to bitmap images.	Class	cytoscape.dialogs	CytoScape
ExportEdgeAttributesAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
Exporter	Interface for exporting a network view to a graphics file.	Interface	cytoscape.util.export	CytoScape
ExportNetworksAsNNFAction	This action is for exporting network and attributes in XGMML file.	Class	cytoscape.actions	CytoScape
ExportNodeAttributesAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
ExportVizmapAction	Export visual styles as a vizmap.	Class	cytoscape.actions	CytoScape
ExpressionData	This class provides a reader for the common file format for expression data and an interface to access the data.	Class	cytoscape.data	CytoScape
ExpressionDataPopupTable		Class	cytoscape.dialogs	CytoScape
ExtensibleMultiHashMapModel	Please try to restrain from using this class.	Class	cytoscape.data.attr.util	CytoScape
FConvNode		Class	org.cytoscape.equations.parse_tree	CytoScape
FileUtil	Provides a platform-dependent way to open files.	Class	cytoscape.util	CytoScape
Filter		Interface	giny.filter	CytoScape
FilterHistoryJList	JList with incremntal search & search history.	Class	cytoscape.util.swing	CytoScape
FingCyNetwork	FinhCyNetwork provides an implementation of the CyNetwork interface, as well as the GraphPerspective inteface, and also provides the	Class	cytoscape.giny	CytoScape
FingEdgeDepot	Please try to restrain from using this class, or even looking at it.	Interface	fing.model	CytoScape
FingExtensibleGraphPerspective	Please try to restrain from using this class.	Class	fing.model	CytoScape
FingExtensibleRootGraph	Please try to restrain from using this class.	Class	fing.model	CytoScape
FingNodeDepot	Please try to restrain from using this class, or even looking at it.	Interface	fing.model	CytoScape
FingRootGraphFactory	This class defines static methods that provide new instances of giny.	Class	fing.model	CytoScape
First		Class	org.cytoscape.equations.builtins	CytoScape
FitContentAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
FixedGraph	Edges and nodes are non-negative integers; a given node and a given edge in a single graph can be the same integer.	Interface	cytoscape.graph.fixed	CytoScape
FlagAndSelectionHandler	This class synchronizes the flagged status of nodes and edges as held by a SelectFilter object of a network with the selection status of the corresponding	Class	cytoscape.view	CytoScape
FlatInterpolator	This simple Interpolator returns the value at either the lower or upper boundary of the domain.	Class	cytoscape.visual.mappings	CytoScape
FlattenIntVectors	given a vector which nests other vectors, each resolving eventually to a list of Integers, flatten it out into a simple 1-level-deep	Class	cytoscape.data.annotation	CytoScape
FList		Class	org.cytoscape.equations.builtins	CytoScape
FloatConstantNode	A node in the parse tree representing an integer constant.	Class	org.cytoscape.equations.parse_tree	CytoScape
FloatParser		Class	cytoscape.visual.parsers	CytoScape
FloatRangeValueCalculator		Class	cytoscape.visual.mappings.rangecalculators	CytoScape
FontCellRenderer		Class	cytoscape.visual.ui.editors.discrete	CytoScape
FontChooser	Defines a generalized font chooser class.	Class	cytoscape.visual.ui	CytoScape
FontConverter		Class	cytoscape.visual.converter	CytoScape
FontParser	Parses a String into a Font object.	Class	cytoscape.visual.parsers	CytoScape
FontRenderer	FontRenderer describes a class that renders each font name in a JList or JComboBox in the face specified.	Class	cytoscape.visual.ui	CytoScape
ForwardSlashStroke	Nested Class SummaryNested classes/interfaces inherited from class cytoscape.	Class	cytoscape.visual.strokes	CytoScape
FuncCallNode	A node in the parse tree representing a function call.	Class	org.cytoscape.equations.parse_tree	CytoScape
Function		Interface	org.cytoscape.equations	CytoScape
FunctionError		Class	org.cytoscape.equations	CytoScape
FunctionUtil	A collection of static methods that may be useful for the implementation of built-in functions.	Class	org.cytoscape.equations	CytoScape
GCTest		Class	fing.model.test	CytoScape
GeneOntology	Gene Ontology object based on general Ontology.	Class	cytoscape.data.ontology	CytoScape
GenericNodeCustomGraphicCalculator	Nested Class SummaryNested classes/interfaces inherited from class cytoscape.	Class	cytoscape.visual.calculators	CytoScape
GeoMean		Class	org.cytoscape.equations.builtins	CytoScape
getCanonicalName		Class	cytoscape.data.servers	CytoScape
getCommonName		Class	cytoscape.data.servers	CytoScape
GinyEdgeControlDialog	present a JTree with edge attributes names as top level nodes, and attribute values as child nodes; any node/s, once selected, are operated on by buttons in the bottom	Class	cytoscape.dialogs	CytoScape
GinyUtils	Utility operations for selection and hiding/unhiding nodes and edges in a Giny GraphView.	Class	cytoscape.actions	CytoScape
GlobalAppearance	Objects of this class hold data describing global appearance attributes ofConstructor SummaryGlobalAppearance()	Class	cytoscape.visual	CytoScape
GlobalAppearanceCalculator	This class calculates global visual attributes such as the background color of the graph window.	Class	cytoscape.visual	CytoScape
GMLException	Exception for GML Reader.	Class	cytoscape.data.readers	CytoScape
GMLFileFilter	FileFilter for Reading in GML Files.	Class	cytoscape.util	CytoScape
GMLNode	This class represents a GMLNode.	Class	cytoscape.data.readers	CytoScape
GMLParser	The purpose of this class is to translate GML into an object tree, and print out an object tree into GML	Class	cytoscape.data.readers	CytoScape
GMLReader	This class is responsible for converting a gml object tree into cytoscape objects New features to the current version: 1.	Class	cytoscape.data.readers	CytoScape
GMLTag	enum GMLTagextends EnumEnum Constant SummaryARROW	Class	cytoscape.data.readers	CytoScape
GMLTree	This class wraps around GMLNode and provides various methods for constructing a tree structure given other data.	Class	cytoscape.data.readers	CytoScape
GMLWriter	The purpse of this class is to translate cytoscape data structures into a gml object tree, we can then use the gml parser to write this tree out into a	Class	cytoscape.data.readers	CytoScape
GnuParser	The class GnuParser provides an implementation of theVersion:$Revision: 155404 $Author:John Keyes (john at integralsource.	Class	org.apache.commons.cli	CytoScape
GOTerm	A Gene Ontology term.	Class	cytoscape.data.ontology	CytoScape
GradientEditorPanel		Class	cytoscape.visual.ui.editors.continuous	CytoScape
GradientLayerCustomGraphics	Proof of concept code to generate Custom Graphics dynamically as vector graphics.	Class	cytoscape.visual.customgraphic.impl.vector	CytoScape
GradientOvalLayer	Fields inherited from class cytoscape.	Class	cytoscape.visual.customgraphic.impl.vector	CytoScape
GradientPaintFactory		Class	cytoscape.visual.customgraphic.paint	CytoScape
GradientRoundRectangleLayer	Fields inherited from class cytoscape.	Class	cytoscape.visual.customgraphic.impl.vector	CytoScape
GraphGraphics	The purpose of this class is to make the proper calls on a Graphics2D object to efficiently render nodes, labels, and edges.	Class	cytoscape.render.immed	CytoScape
GraphicsParser		Class	cytoscape.visual.parsers	CytoScape
GraphLOD	An instance of this class defines the level of detail that goes into a single rendering of a graph.	Class	cytoscape.render.stateful	CytoScape
GraphObject		Interface	giny.model	CytoScape
GraphObjectSelection		Class	cytoscape.dialogs	CytoScape
GraphObjectSelectionAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
GraphPerspective	TODO: Remove deprecated methods and add generics parameters.	Interface	giny.model	CytoScape
GraphPerspectiveChangeEvent	The event source must be the GraphPerspective that changed.	Class	giny.model	CytoScape
GraphPerspectiveChangeListener		Interface	giny.model	CytoScape
GraphReader	Interface for Reading in Cytoscape Graphs.	Interface	cytoscape.data.readers	CytoScape
GraphRenderer	This class contains a chunk of procedural code that stitches together several external modules in an effort to efficiently render graphs.	Class	cytoscape.render.stateful	CytoScape
GraphSetUtils		Class	cytoscape.util	CytoScape
GraphView		Interface	giny.view	CytoScape
GraphViewChangeEvent	The event source must be the GraphPerspective that changed.	Class	giny.view	CytoScape
GraphViewChangeListener		Interface	giny.view	CytoScape
GraphViewController		Class	cytoscape.view	CytoScape
GraphViewHandler	This interface represents an object that handles a change in a giny.	Interface	cytoscape.view	CytoScape
GridBagGroup		Class	cytoscape.dialogs	CytoScape
GridNodeLayout	The GridNodeLayout provides a very simple layout, suitable as the default layout for Cytoscape data readers.	Class	cytoscape.layout.algorithms	CytoScape
HalfBottomArrow		Class	cytoscape.render.immed.arrow	CytoScape
HalfTopArrow		Class	cytoscape.render.immed.arrow	CytoScape
Haltable	A hook for requesting that a running process be halted.	Interface	cytoscape.task	CytoScape
HarMean		Class	org.cytoscape.equations.builtins	CytoScape
HelpAboutAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
HelpContactHelpDeskAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
HelpContentsAction	Really just a wrapper for the CSH.	Class	cytoscape.actions	CytoScape
HelpFormatter	A formatter of help messages for the current command line optionsAuthor:Slawek Zachcial, John Keyes (john at integralsource.	Class	org.apache.commons.cli	CytoScape
HexagonNodeShape		Class	cytoscape.render.immed.nodeshape	CytoScape
HiddenEdges	Java class for anonymous complex type.	Class	cytoscape.generated	CytoScape
HiddenNodes	Java class for anonymous complex type.	Class	cytoscape.generated	CytoScape
HideEdgeListener	Adds EdgeView and EdgeView vizmap bypass listeners to network views as the views are created.	Class	cytoscape.visual.ui	CytoScape
HideNodeListener	Adds NodeView and EdgeView vizmap bypass listeners to network views as the views are created.	Class	cytoscape.visual.ui	CytoScape
HideSelectedAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
HideSelectedEdgesAction		Class	cytoscape.actions	CytoScape
HideSelectedNodesAction		Class	cytoscape.actions	CytoScape
IconPopupButton		Class	cytoscape.dialogs	CytoScape
IconTableCellRenderer		Class	cytoscape.view	CytoScape
IdentDescriptor		Class	org.cytoscape.equations.interpreter	CytoScape
IdentNode	A node in the parse tree representing an attribute reference.	Class	org.cytoscape.equations.parse_tree	CytoScape
IDGenerator		Class	cytoscape.visual.customgraphic	CytoScape
If		Class	org.cytoscape.equations.builtins	CytoScape
IList		Class	org.cytoscape.equations.builtins	CytoScape
ImageImposter	The primary purpose of this class is to enable an arbitrary Graphics object to receive rendering calls from a	Class	cytoscape.render.export	CytoScape
ImageUtil		Class	cytoscape.visual.customgraphic	CytoScape
ImplementsGraphTest		Class	fing.model.test	CytoScape
ImportAttributeMatrixDialog	This class prompts the user for data for entry of the attribute matrix, which includes expression data as a use case.	Class	cytoscape.dialogs	CytoScape
ImportEdgeAttributesAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
ImportExpressionMatrixAction	User has requested loading of an Expression Matrix File.	Class	cytoscape.actions	CytoScape
ImportGraphFileAction	Imports a graph of arbitrary type.	Class	cytoscape.actions	CytoScape
ImportHandler	Central registry for all Cytoscape import classes.	Class	cytoscape.data	CytoScape
ImportNetworkDialog		Class	cytoscape.dialogs	CytoScape
ImportNodeAttributesAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
ImportVizmapAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
IndeterminateProgressBar	This class creates a dialog with a JProgressBar in indeterminate state.	Class	cytoscape.util	CytoScape
InnerCanvas	The GUI component for drawing networks.	Class	ding.view	CytoScape
InnerCanvasEvent	See Also:Serialized FormFields inherited from class java.	Class	ding.view	CytoScape
InnerCanvasListener		Interface	ding.view	CytoScape
Installable		Interface	cytoscape.plugin	CytoScape
InstallablePlugin		Class	cytoscape.plugin	CytoScape
InstallableTheme		Class	cytoscape.plugin	CytoScape
Instruction	enum Instructionextends EnumEnum Constant SummaryAREF	Class	org.cytoscape.equations.interpreter	CytoScape
IntArray	A dynamically growing array of integers.	Class	cytoscape.util.intr	CytoScape
IntBTree	An in-memory B+-tree that stores integers.	Class	cytoscape.util.intr	CytoScape
IntBTreeConstructionTuner		Class	cytoscape.util.intr.test	CytoScape
IntBTreePerformance		Class	cytoscape.util.intr.test	CytoScape
IntBTreeQueryTuner		Class	cytoscape.util.intr.test	CytoScape
IntegerEntryField		Class	cytoscape.dialogs	CytoScape
IntEnumerator	An enumeration over a list of 32 bit integers.	Interface	cytoscape.util.intr	CytoScape
Interaction	Interaction.	Class	cytoscape.data	CytoScape
InteractionsReader	Reader for graphs in the interactions file format.	Class	cytoscape.data.readers	CytoScape
InteractionWriter	A few utility methods to assist in writing SIF files.	Class	cytoscape.data.writers	CytoScape
InternalFrameComponent	This class manages the JLayeredPane that resides in each internal frame of cytoscape.	Class	cytoscape.view	CytoScape
Interpolator	This interface defines an interpolation function that takes two pairs of (domain,range) values plus a target domain value, and calculates an	Interface	cytoscape.visual.mappings	CytoScape
InterpolatorFactory	Provides static factory methods for constructing known interpolators from a recognized name, for example from a properties object.	Class	cytoscape.visual.mappings	CytoScape
Interpreter		Class	org.cytoscape.equations.interpreter	CytoScape
IntHash	An insert-only hashtable that has non-negative 32 bit integer keys; no satellite data is stored in this hashtable.	Class	cytoscape.util.intr	CytoScape
IntHashPerformance		Class	cytoscape.util.intr.test	CytoScape
IntIntHash	An insert-only hashtable that has non-negative 32 bit integer keys and non-negative 32 bit integer values.	Class	cytoscape.util.intr	CytoScape
IntIterator	An iteration over a list of 32 bit integers.	Interface	cytoscape.util.intr	CytoScape
IntObjHash	An insert-only hashtable that has non-negative 32 bit integer keys and non-null object values.	Class	cytoscape.util.intr	CytoScape
IntQueue	A first-in, first-out container of 32 bit integers.	Class	cytoscape.util.intr	CytoScape
IntStack	A first-in, last-out container of 32 bit integers.	Class	cytoscape.util.intr	CytoScape
IntTHash	An insert-only hashtable that has non-negative 32 bit integer keys and non-null object values.	Class	cytoscape.util.intr	CytoScape
InvalidDownloadable		Class	cytoscape.plugin	CytoScape
InvertSelectedEdgesAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
InvertSelectedNodesAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
JErrorPanel	Common UI element for displaying errors and stack traces.	Class	cytoscape.task.ui	CytoScape
JnlpWriterUtil		Class	cytoscape.util	CytoScape
JointIntegerEntry		Class	cytoscape.dialogs	CytoScape
JStatusBar	Simple status bar with 3 fields.	Class	cytoscape.util.swing	CytoScape
JTask	Common UI element for visually monitoring task progress.	Class	cytoscape.task.ui	CytoScape
JTaskConfig	Used to configure the JTask UI component.	Class	cytoscape.task.ui	CytoScape
JTreeTable	This example shows how to create a simple JTreeTable component, by using a JTree as a renderer (and editor) for the cells in a particular column in the	Class	cytoscape.util.swing	CytoScape
Justification	enum Justificationextends EnumEnum Constant SummaryJUSTIFY_CENTER	Class	giny.view	CytoScape
KeyValue	Key and Value pair in GML file.	Class	cytoscape.data.readers	CytoScape
Label		Interface	giny.view	CytoScape
LabelPlacerGraphic	A drag and drop graphic that allows users to set the placement Deprecated.	Class	cytoscape.visual.ui	CytoScape
LabelPosition	Deprecated.	Class	cytoscape.visual	CytoScape
LabelPositionParser	Parses a String into a LabelPosition object.	Class	cytoscape.visual.parsers	CytoScape
LabelTextPanel		Class	cytoscape.dialogs	CytoScape
Largest		Class	org.cytoscape.equations.builtins	CytoScape
Last		Class	org.cytoscape.equations.builtins	CytoScape
Layer	Wrapper for actual implementations of layers.	Interface	cytoscape.visual.customgraphic	CytoScape
LayoutAdapter	LayoutAdapter provides a very minimal interface to implement a layout algorithm.	Class	cytoscape.layout	CytoScape
LayoutAlgorithm		Interface	cytoscape.layout	CytoScape
LayoutMenu	A DynamicLayoutMenu is a more complicated layout menu that constructs layout menu items on-the-fly based on the capabilities of the layout algorithm and environment	Class	cytoscape.layout.ui	CytoScape
LayoutMenuManager		Class	cytoscape.layout.ui	CytoScape
LayoutProperties	The LayoutProperties class is a helper class to support the management of settings and properties for layout algorithms that implement	Class	cytoscape.layout	CytoScape
LayoutSettingsDialog	The LayoutSettingsDialog is a dialog that provides an interface into all of the various settings for layout algorithms.	Class	cytoscape.layout.ui	CytoScape
LayoutTask	A wrapper for applying a layout in a task.	Class	cytoscape.layout	CytoScape
Left		Class	org.cytoscape.equations.builtins	CytoScape
LegacyCustomNodeShape		Class	cytoscape.render.immed.nodeshape	CytoScape
LegendDialog		Class	cytoscape.visual.ui	CytoScape
LegendTable		Class	cytoscape.visual.mappings	CytoScape
Len		Class	org.cytoscape.equations.builtins	CytoScape
LicenseDialog		Class	cytoscape.dialogs.plugins	CytoScape
LinearNumberInterpolator	This subclass of NumberInterpolator further assumes a linear interpolation, and calculates the fractional distance of the target domain value from	Class	cytoscape.visual.mappings	CytoScape
LinearNumberToColorInterpolator	The class provides a linear interpolation between color values.	Class	cytoscape.visual.mappings	CytoScape
LinearNumberToNumberInterpolator	The class assumes that the supplied range objects are Numbers, and returns a linearly interplated value according to the value of frac.	Class	cytoscape.visual.mappings	CytoScape
LineStyle	enum LineStyleextends EnumEnum Constant SummaryBACKWARD_SLASH	Class	cytoscape.visual	CytoScape
LineStyleParser	Parses a String into a yFiles shape, which is represented by a byte identifier.	Class	cytoscape.visual.parsers	CytoScape
LineTypeIcon		Class	cytoscape.visual.ui.icon	CytoScape
ListFromFileSelectionAction	Select nodes from a text list of node IDs.	Class	cytoscape.actions	CytoScape
ListToString		Class	org.cytoscape.equations.builtins	CytoScape
Ln		Class	org.cytoscape.equations.builtins	CytoScape
loadAnnotation	load an annotation into an rmi biodata server.	Class	cytoscape.data.servers	CytoScape
loadAnnotationFromFlatFiles	load an annotation into an rmi biodata server.	Class	cytoscape.data.servers	CytoScape
LoadImageTask		Class	cytoscape.visual.customgraphic	CytoScape
LoadNetworkTask	Task to load a new network.	Class	cytoscape.actions	CytoScape
loadThesaurus	load an thesaurus into an rmi biodata server.	Class	cytoscape.data.servers	CytoScape
Log		Class	org.cytoscape.equations.builtins	CytoScape
LoggerAction	Created by IntelliJ IDEA.	Class	cytoscape.actions	CytoScape
LoggerDialog		Class	cytoscape.dialogs.logger	CytoScape
LogLevel	enum LogLevelextends EnumThe levels of logged messages	Class	cytoscape.logger	CytoScape
LongDashStroke	Fields inherited from class java.	Class	cytoscape.visual.strokes	CytoScape
LongEnumerator	An enumeration over a list of 64 bit integers.	Interface	cytoscape.util.intr	CytoScape
LongList		Class	org.cytoscape.equations	CytoScape
LongLongHash	An insert-only hashtable that has non-negative 64 bit integer keys and non-negative 64 bit integer values.	Class	cytoscape.util.intr	CytoScape
Lower		Class	org.cytoscape.equations.builtins	CytoScape
MacAppConfig	Configures the Mac OS X Info.	Class	cytoscape.util	CytoScape
ManagerException	Thrown to indicate PluginManager errorsAuthor:skillcoyneSee Also:Serialized Form	Class	cytoscape.plugin	CytoScape
ManagerModel	Fairly similar to DefaultTreeModel but I wanted to add some extra functionality to removing/adding nodes and use my own node objects	Class	cytoscape.dialogs.plugins	CytoScape
ManagerUtil		Class	cytoscape.plugin	CytoScape
MapperAndAttribute		Class	cytoscape.visual.ui	CytoScape
MappingFactory	This class provides a static factory method for constructing an instance of ObjectMapping as specified by a Properties object and other arguments.	Class	cytoscape.visual.mappings	CytoScape
MappingKeyFactory		Class	cytoscape.visual.ui	CytoScape
MappingManager		Interface	cytoscape.visual.mappings	CytoScape
MappingManagerImpl		Class	cytoscape.visual.mappings	CytoScape
MappingType	enum MappingTypeextends EnumDefines visual mapping types.	Class	cytoscape.visual.mappings	CytoScape
MappingUtil	Provides simple utility methods for the Mapping classes.	Class	cytoscape.visual.mappings	CytoScape
MathUtil		Class	cytoscape.util	CytoScape
Max		Class	org.cytoscape.equations.builtins	CytoScape
Median		Class	org.cytoscape.equations.builtins	CytoScape
MemoryReporter	A class used to track JVM memory usage.	Class	cytoscape.util	CytoScape
MemoryUsageAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
MetadataEntries	enum MetadataEntriesextends EnumEntries in the network metadata.	Class	cytoscape.data.readers	CytoScape
MetadataParser	Manipulates network metadata for loading and saving.	Class	cytoscape.data.readers	CytoScape
Mid		Class	org.cytoscape.equations.builtins	CytoScape
Min		Class	org.cytoscape.equations.builtins	CytoScape
MinIntHeap	A heap is an implementation of a priority queue.	Class	cytoscape.util.intr	CytoScape
MinIntHeapPerformance		Class	cytoscape.util.intr.test	CytoScape
MinMaxDialog		Class	cytoscape.visual.ui.editors.continuous	CytoScape
MinMaxDouble	find the min and max of a 1- or 2-d aarray of doubles.	Class	cytoscape.util	CytoScape
MinMaxInt	find the min and max of a 1- or 2-d array of ints.	Class	cytoscape.util	CytoScape
Misc		Class	cytoscape.util	CytoScape
MiscGB	We DO need to replace this with swing-layout! Miscellaneous static GridBagLayout utilities	Class	cytoscape.dialogs	CytoScape
MissingArgumentException	Thrown when an option requiring an argument is not provided with an argument.	Class	org.apache.commons.cli	CytoScape
MissingOptionException	Thrown when a required option has not been provided.	Class	org.apache.commons.cli	CytoScape
Mod		Class	org.cytoscape.equations.builtins	CytoScape
Mode		Class	org.cytoscape.equations.builtins	CytoScape
ModuleProperties		Interface	cytoscape.util	CytoScape
ModulePropertiesImpl		Class	cytoscape.util	CytoScape
MolecularFunctionAnnotationReader	The purpose of this class is to convert a 'gene_association.	Class	cytoscape.cruft.obo	CytoScape
MolecularFunctionAnnotationTester		Class	cytoscape.cruft.obo.test	CytoScape
MonitoredTask		Interface	cytoscape.util	CytoScape
mRNAMeasurement		Class	cytoscape.data	CytoScape
MultiHashMap	This interface consists of the API specification to bind attribute values to objects.	Interface	cytoscape.data.attr	CytoScape
MultiHashMapDefinition	This interface contains the API specification for creating attribute definitions.	Interface	cytoscape.data.attr	CytoScape
MultiHashMapDefinitionListener		Interface	cytoscape.data.attr	CytoScape
MultiHashMapFactory	This class provides access to implementations of MultiHashMap and MultiHashMapDefinition.	Class	cytoscape.data.attr.util	CytoScape
MultiHashMapHelpers	This class contains static utilitarian methods that return information pertaining to attributes.	Class	cytoscape.data.attr.util	CytoScape
MultiHashMapListener		Interface	cytoscape.data.attr	CytoScape
MutableBool		Class	cytoscape.util	CytoScape
MutableInt		Class	cytoscape.util	CytoScape
MutableSpacialIndex2D	A spacial index for objects in two dimensions, with support for insertions and deletions.	Interface	cytoscape.geom.spacial	CytoScape
MutableString		Class	cytoscape.util	CytoScape
NestedNetworkChangeEvent	This event will be fired when nested network is created/removed.	Class	giny.model	CytoScape
NestedNetworkChangeEventListener	Listener for nested network change events.	Interface	giny.model	CytoScape
NestedNetworkListener	Adds NodeView and EdgeView vizmap bypass listeners to network views as the views are created.	Class	cytoscape.visual.ui	CytoScape
NestedNetworkReader	Special interface for Graph readers which read nested networks from a file.	Interface	cytoscape.data.readers	CytoScape
NestedNetworkViewUpdater	This class manages images that represent nested networks.	Class	cytoscape.util	CytoScape
Network	Java class for anonymous complex type.	Class	cytoscape.generated	CytoScape
NetworkData	There is an event fired anytime that a value is modified, you need to be listener to the attribute name though.	Class	cytoscape.data	CytoScape
NetworkExpansionMenu		Class	cytoscape.data.webservice.util	CytoScape
NetworkFrame	Java class for anonymous complex type.	Class	cytoscape.generated	CytoScape
NetworkFrames	Java class for anonymous complex type.	Class	cytoscape.generated	CytoScape
NetworkImportWebServiceClient		Interface	cytoscape.data.webservice	CytoScape
NetworkMetaDataDialog	Dialog for editing network metadata in RDF.	Class	cytoscape.dialogs	CytoScape
NetworkMetaDataTableModel	Table model for the Network Metadata Dialog.	Class	cytoscape.dialogs	CytoScape
NetworkPanel	GUI component for managing network list in current session.	Class	cytoscape.view	CytoScape
NetworkSelectorPanel		Class	cytoscape.util.swing	CytoScape
NetworkTree	Java class for anonymous complex type.	Class	cytoscape.generated	CytoScape
NetworkTreeNode	See Also:Serialized FormFields inherited from class javax.	Class	cytoscape.view	CytoScape
NetworkTreeTableModel	Inner class that extends the AbstractTreeTableModelFields inherited from class cytoscape.	Class	cytoscape.view	CytoScape
NetworkViewManager		Class	cytoscape.view	CytoScape
NewMappingBuilder	Constructor SummaryNewMappingBuilder()Methods inherited from class java.	Class	cytoscape.visual.ui	CytoScape
NewNetworkAction	creates a new network and associates an editor with itVersion:1.	Class	cytoscape.actions	CytoScape
NewSessionAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
NewSlider		Class	cytoscape.dialogs	CytoScape
NewStringPopupDialog	NewStringPopupDialog: a dialog that is used for creating a new string.	Class	cytoscape.dialogs	CytoScape
NewWindowSelectedNodesEdgesAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
NewWindowSelectedNodesOnlyAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
NNFFileFilter	File filter for Nested Network Format (NNF).	Class	cytoscape.util	CytoScape
NNFParser	Parser for NNF files.	Class	cytoscape.data.readers	CytoScape
NNFReader	Graph file reader for NNF files.	Class	cytoscape.data.readers	CytoScape
NoArrow		Class	cytoscape.render.immed.arrow	CytoScape
Node	Java class for anonymous complex type.	Class	cytoscape.generated	CytoScape
Node		Interface	giny.model	CytoScape
Node	A node in the parse tree.	Class	org.cytoscape.equations.parse_tree	CytoScape
NodeAppearance	Objects of this class hold data describing the appearance of a Node.	Class	cytoscape.visual	CytoScape
NodeAppearanceCalculator	This class calculates the appearance of a Node.	Class	cytoscape.visual	CytoScape
NodeBorderColorProp	Fields inherited from class cytoscape.	Class	cytoscape.visual.properties	CytoScape
NodeBorderOpacityProp	Fields inherited from class cytoscape.	Class	cytoscape.visual.properties	CytoScape
NodeContextMenuListener	an interface for responding to PhoebeCanvasDropEvents.	Interface	ding.view	CytoScape
NodeCustomGraphicsPositionProp	Fields inherited from class cytoscape.	Class	cytoscape.visual.properties	CytoScape
NodeCustomGraphicsProp	Fields inherited from class cytoscape.	Class	cytoscape.visual.properties	CytoScape
NodeDetails	Defines visual properties of a node modulo the node size and location Even though this class is not declared abstract, in most situations it	Class	cytoscape.render.stateful	CytoScape
NodeFillColorProp	Fields inherited from class cytoscape.	Class	cytoscape.visual.properties	CytoScape
NodeFontFaceProp	Fields inherited from class cytoscape.	Class	cytoscape.visual.properties	CytoScape
NodeFontSizeProp	Fields inherited from class cytoscape.	Class	cytoscape.visual.properties	CytoScape
NodeHeightProp	Fields inherited from class cytoscape.	Class	cytoscape.visual.properties	CytoScape
NodeIcon	Icon for node shapes.	Class	cytoscape.visual.ui.icon	CytoScape
NodeLabelColorProp	Fields inherited from class cytoscape.	Class	cytoscape.visual.properties	CytoScape
NodeLabelOpacityProp	Fields inherited from class cytoscape.	Class	cytoscape.visual.properties	CytoScape
NodeLabelPositionProp	Fields inherited from class cytoscape.	Class	cytoscape.visual.properties	CytoScape
NodeLabelProp	Fields inherited from class cytoscape.	Class	cytoscape.visual.properties	CytoScape
NodeLabelWidthProp	Fields inherited from class cytoscape.	Class	cytoscape.visual.properties	CytoScape
NodeLineStyleProp	Fields inherited from class cytoscape.	Class	cytoscape.visual.properties	CytoScape
NodeLineWidthProp	Fields inherited from class cytoscape.	Class	cytoscape.visual.properties	CytoScape
NodeOpacityProp	Fields inherited from class cytoscape.	Class	cytoscape.visual.properties	CytoScape
NodeShape	An interface defining the methods necessary to render a node shape in GraphGraphics.	Interface	cytoscape.render.immed.nodeshape	CytoScape
NodeShape	enum NodeShapeextends EnumSince:Cytoscape 2.	Class	cytoscape.visual	CytoScape
NodeShapeConverter		Class	cytoscape.visual.converter	CytoScape
NodeShapeParser	Parses a String into a yFiles shape, which is represented by a byte identifier.	Class	cytoscape.visual.parsers	CytoScape
NodeShapeProp	Fields inherited from class cytoscape.	Class	cytoscape.visual.properties	CytoScape
NodeShapeRangeValueCalculator		Class	cytoscape.visual.mappings.rangecalculators	CytoScape
NodeShowNestedNetworkProp	Fields inherited from class cytoscape.	Class	cytoscape.visual.properties	CytoScape
NodeSizeProp	Fields inherited from class cytoscape.	Class	cytoscape.visual.properties	CytoScape
NodeToolTipProp	Fields inherited from class cytoscape.	Class	cytoscape.visual.properties	CytoScape
NodeView	Any and all questions should be directed to me.	Interface	giny.view	CytoScape
NodeWidthProp	Fields inherited from class cytoscape.	Class	cytoscape.visual.properties	CytoScape
NormDist		Class	org.cytoscape.equations.builtins	CytoScape
NoRTreeQueryPerformance		Class	cytoscape.geom.rtree.test	CytoScape
Not		Class	org.cytoscape.equations.builtins	CytoScape
NotAPluginException	Thrown to indicate that a class cannot be used as a plugin becuase it does not extend CytoscapePlugin.	Class	cytoscape.plugin	CytoScape
Now		Class	org.cytoscape.equations.builtins	CytoScape
Nth		Class	org.cytoscape.equations.builtins	CytoScape
NullCustomGraphics	Null object for Custom Graphics.	Class	cytoscape.visual.customgraphic	CytoScape
NumberInterpolator	This partial implementation of Interpolator assumes that the domain values are some kind of number, and extracts the values into ordinary	Class	cytoscape.visual.mappings	CytoScape
ObjectFactory	This object contains factory methods for each Java content interface and Java element interface	Class	cytoscape.bookmarks	CytoScape
ObjectFactory	This object contains factory methods for each Java content interface and Java element interface	Class	cytoscape.generated	CytoScape
ObjectMapping	Mappings should implement this interface.	Interface	cytoscape.visual.mappings	CytoScape
ObjectPlacerControl		Class	cytoscape.visual.ui	CytoScape
ObjectPlacerGraphic		Class	cytoscape.visual.ui	CytoScape
ObjectPosition	Interface representing relative location of graphics objects, such as labels or custom graphics.	Interface	giny.view	CytoScape
ObjectPositionCellRenderer		Class	cytoscape.visual.ui.editors.discrete	CytoScape
ObjectPositionConverter		Class	cytoscape.visual.converter	CytoScape
ObjectPositionImpl		Class	ding.view	CytoScape
ObjectPositionParser		Class	cytoscape.visual.parsers	CytoScape
ObjectToString	This class contains a method that does the reverse of the various parsing classes in this package, i.	Class	cytoscape.visual.parsers	CytoScape
OBOFlatFileReader	This is a general OBO (Open Biomedical Ontologies: http://obo.	Class	cytoscape.data.ontology.readers	CytoScape
OBOHeaderTags	enum OBOHeaderTagsextends EnumEnum Constant SummaryAUTO_GENERATED_BY	Class	cytoscape.data.ontology.readers	CytoScape
OboOntologyReader	The purpose of this class is to convert a 'gene_ontology.	Class	cytoscape.cruft.obo	CytoScape
OboOntologyReader2	The purpose of this class is to convert a 'gene_ontology.	Class	cytoscape.cruft.obo	CytoScape
OboOntologyTester		Class	cytoscape.cruft.obo.test	CytoScape
OBOTags	enum OBOTagsextends EnumTags used in OBO file:	Class	cytoscape.data.ontology.readers	CytoScape
OctagonNodeShape		Class	cytoscape.render.immed.nodeshape	CytoScape
Ontology	Contains a collection of OntologyTerms, each of which may have pointers to other terms, creating a hierarchical controlled vocabulary.	Class	cytoscape.data.annotation	CytoScape
Ontology	General Ontology class which implements interface from BioJava project.	Class	cytoscape.data.ontology	CytoScape
Ontology	Java class for anonymous complex type.	Class	cytoscape.generated	CytoScape
OntologyDescription	Distinguish among different ontologies, by curator and type.	Class	cytoscape.data.annotation	CytoScape
OntologyFactory		Class	cytoscape.data.ontology	CytoScape
OntologyFlatFileReader		Class	cytoscape.data.annotation.readers	CytoScape
OntologyReader	Interface for all ontology file readers.	Interface	cytoscape.data.ontology.readers	CytoScape
OntologyServer	Ontology Server which manages ontologies, aliases, and bookmarks.	Class	cytoscape.data.servers	CytoScape
OntologyServer	Java class for anonymous complex type.	Class	cytoscape.generated	CytoScape
OntologyTerm	Represents one node in an ontology, which is a hierarchical classification of entities using a controlled vocabulary.	Class	cytoscape.data.annotation	CytoScape
OntologyTerm	Simple in-memory implementation of an ontology term based on BioJava's This implementation uses CyNetwork and CyAttributes as its actual data	Class	cytoscape.data.ontology	CytoScape
OntologyXmlReader		Class	cytoscape.data.annotation.readers	CytoScape
OpenBrowser		Class	cytoscape.util	CytoScape
OpenSessionAction	Call the session reader and read everything in the zip archive.	Class	cytoscape.actions	CytoScape
Option	Describes a single command-line option.	Class	org.apache.commons.cli	CytoScape
OptionBuilder	OptionBuilder allows the user to create Options using descriptive Details on the Builder pattern can be found at	Class	org.apache.commons.cli	CytoScape
OptionGroup	A group of mutually exclusive options.	Class	org.apache.commons.cli	CytoScape
Options	Main entry-point into the library.	Class	org.apache.commons.cli	CytoScape
OptionValidator	Validates an Option string.	Class	org.apache.commons.cli	CytoScape
Or		Class	org.cytoscape.equations.builtins	CytoScape
PaintFactory	Factory for creating paint object for a rectangulaer bounds.	Interface	cytoscape.render.stateful	CytoScape
Panel	Java class for anonymous complex type.	Class	cytoscape.generated	CytoScape
Panels	Java class for anonymous complex type.	Class	cytoscape.generated	CytoScape
ParallelogramNodeShape		Class	cytoscape.render.immed.nodeshape	CytoScape
ParallelStroke	Fields inherited from class cytoscape.	Class	cytoscape.visual.strokes	CytoScape
Parent	Java class for anonymous complex type.	Class	cytoscape.generated	CytoScape
ParseException	Base for Exceptions thrown during parsing of a command-line.	Class	org.apache.commons.cli	CytoScape
Parser	Parser creates CommandLines.	Class	org.apache.commons.cli	CytoScape
Parser	A singleton EqnParserConstructor SummaryParser()	Class	org.cytoscape.equations	CytoScape
ParserControl	ParserControl is used to control particular behaviour of the parser.	Interface	org.apache.commons.cli.avalon	CytoScape
PassThroughMapping	Defines a mapping from a bundle of data attributes to a visual attribute.	Class	cytoscape.visual.mappings	CytoScape
PatternOptionBuilder	Allows Options to be created from a single String.	Class	org.apache.commons.cli	CytoScape
PDFExporter	PDF exporter by the iText library.	Class	cytoscape.util.export	CytoScape
PercentUtil	Helper Class for Calculating Percentage of Multi-Step Processes.	Class	cytoscape.util	CytoScape
Permut		Class	org.cytoscape.equations.builtins	CytoScape
PersistImageTask		Class	cytoscape.visual.customgraphic	CytoScape
PhoebeCanvasDropEvent	forwards the drop event and its locationSee Also:Serialized Form	Class	phoebe	CytoScape
PhoebeCanvasDropListener	an interface for responding to PhoebeCanvasDropEvents.	Interface	phoebe	CytoScape
PhoebeCanvasDroppable	interface for maintaining listeners for PhoebeCanvasDropEvents.	Interface	phoebe	CytoScape
PhoebeNodeControl	An Adobe style node organizer.	Class	cytoscape.dialogs	CytoScape
Pi		Class	org.cytoscape.equations.builtins	CytoScape
PipeStroke		Class	cytoscape.visual.strokes	CytoScape
Plugin	Java class for anonymous complex type.	Class	cytoscape.generated	CytoScape
PluginException		Class	cytoscape.plugin	CytoScape
PluginFileReader		Class	cytoscape.plugin	CytoScape
PluginIndex		Class	cytoscape.dialogs.plugins	CytoScape
PluginInfo		Class	cytoscape.plugin	CytoScape
PluginInquireAction	Object should be implmeneted by anyone using the PluginManager#inquireThread(String, PluginInquireAction) method to get plugins from a given site.	Class	cytoscape.plugin	CytoScape
PluginManageDialog		Class	cytoscape.dialogs.plugins	CytoScape
PluginManager		Class	cytoscape.plugin	CytoScape
PluginManagerAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
PluginManagerInquireTask		Class	cytoscape.plugin	CytoScape
PluginProperties	This class reads the plugin.	Class	cytoscape.plugin	CytoScape
Plugins	Java class for anonymous complex type.	Class	cytoscape.generated	CytoScape
PluginsTableModel	See Also:Serialized FormFields inherited from class javax.	Class	cytoscape.dialogs.preferences	CytoScape
PluginStatus	enum PluginStatusextends EnumEnum Constant SummaryCURRENT	Class	cytoscape.plugin	CytoScape
PluginTracker		Class	cytoscape.plugin	CytoScape
PluginUpdateAction		Class	cytoscape.actions	CytoScape
PluginUpdateDialog		Class	cytoscape.dialogs.plugins	CytoScape
PluginUrlDialog		Class	cytoscape.dialogs.plugins	CytoScape
PluginVersionUtils		Class	cytoscape.plugin	CytoScape
PluginXml	enum PluginXmlextends EnumEnum Constant SummaryAUTHOR	Class	cytoscape.plugin	CytoScape
PointTextListener	Listens for a User Initiated Change in any of the JTextFields in the Continuous Mapper UI.	Class	cytoscape.visual.mappings.continuous	CytoScape
PopupFontChooser		Class	cytoscape.visual.ui	CytoScape
PopupIconChooser	PopupIconChooser borrows all of its functionality from IconPopupButton.	Class	cytoscape.visual.ui	CytoScape
PopupObjectPositionChooser		Class	cytoscape.visual.ui	CytoScape
PopupStringChooser	An input dialog for strings, ints, and doubles.	Class	cytoscape.visual.ui	CytoScape
PopupTextArea		Class	cytoscape.dialogs	CytoScape
Position	enum Positionextends EnumConstants represent position of graphics objects.	Class	giny.view	CytoScape
PosixParser	The class PosixParser provides an implementation of theVersion:$Revision: 155404 $Author:John Keyes (john at integralsource.	Class	org.apache.commons.cli	CytoScape
PreferenceAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
PreferencesDialog		Class	cytoscape.dialogs.preferences	CytoScape
PreferenceTableModel		Class	cytoscape.dialogs.preferences	CytoScape
PreferenceValueDialog		Class	cytoscape.dialogs.preferences	CytoScape
PrimesGenerator		Class	cytoscape.util.intr.test	CytoScape
PrintAction		Class	cytoscape.actions	CytoScape
PrintLOD		Class	ding.view	CytoScape
Product		Class	org.cytoscape.equations.builtins	CytoScape
PropUtil	A stateless utility class that makes it easy to parse int and boolean values from a Properties object.	Class	cytoscape.util	CytoScape
ProxyHandler		Class	cytoscape.util	CytoScape
ProxyServerAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
ProxyServerDialog		Class	cytoscape.dialogs.preferences	CytoScape
PSExporter		Class	cytoscape.util.export	CytoScape
Radians		Class	org.cytoscape.equations.builtins	CytoScape
RandomColorListener	User wants to Seed the Discrete Mapper with Random Color Values.	Class	cytoscape.visual.mappings.discrete	CytoScape
RangeValueCalculator		Interface	cytoscape.visual.mappings	CytoScape
RangeValueCalculatorFactory		Interface	cytoscape.visual.mappings	CytoScape
RangeValueCalculatorFactoryImpl	Constructor SummaryRangeValueCalculatorFactoryImpl()>	Class	cytoscape.visual.mappings	CytoScape
RecentlyOpenedTracker	A class to keep track of a short list of recently opened URLs.	Class	cytoscape.util	CytoScape
RectangleNodeShape		Class	cytoscape.render.immed.nodeshape	CytoScape
RedoAction	An action that calls redo for the most recent edit in the undoable edit stack.	Class	cytoscape.util.undo	CytoScape
RedrawTask		Class	cytoscape.visual.ui	CytoScape
RenderingContext		Interface	cytoscape.visual.customgraphic	CytoScape
RepeatedAllRootGraphMethodsTest		Class	fing.model.test	CytoScape
RestoreImageTask		Class	cytoscape.visual.customgraphic	CytoScape
Right		Class	org.cytoscape.equations.builtins	CytoScape
RootGraph	A graph model consisting of nodes and the edges between them.	Interface	giny.model	CytoScape
RootGraphAddRemoveTest		Class	fing.model.test	CytoScape
RootGraphChangeEvent	The event source must be the RootGraph that changed.	Class	giny.model	CytoScape
RootGraphChangeListener		Interface	giny.model	CytoScape
RootGraphPerformanceTest		Class	fing.model.test	CytoScape
RotateSelectedNodesAction	Rotates the given selection by the specified amount.	Class	cytoscape.actions	CytoScape
Round		Class	org.cytoscape.equations.builtins	CytoScape
RoundedRectangleNodeShape		Class	cytoscape.render.immed.nodeshape	CytoScape
RTree	An in-memory R-tree over real numbers in two dimensions.	Class	cytoscape.geom.rtree	CytoScape
RTreeQueryPerformance		Class	cytoscape.geom.rtree.test	CytoScape
RTreeSerializationPerformance		Class	cytoscape.geom.rtree.test	CytoScape
RTreeUpdatePerformance		Class	cytoscape.geom.rtree.test	CytoScape
RunBareBones	Illustrates how to execute a sample task via the TaskManager.	Class	cytoscape.task.sample	CytoScape
RunSampleTask	Runs the Sample Task and demonstrate various UI options.	Class	cytoscape.task.sample	CytoScape
SampleTask	Sample Task, used to illustrate the Task Framework.	Class	cytoscape.task.sample	CytoScape
SanityTest		Class	ding.view.test	CytoScape
SaveImageTask		Class	cytoscape.visual.customgraphic	CytoScape
SaveSessionAction	Save Session action.	Class	cytoscape.actions	CytoScape
SaveSessionAsAction	Same as SaveSessionAction, but always opens file chooser.	Class	cytoscape.actions	CytoScape
Scaler		Interface	cytoscape.util	CytoScape
ScalerFactory		Class	cytoscape.util	CytoScape
ScalingMethod	enum ScalingMethodextends EnumEnum Constant SummaryLINEAR_LOWER	Class	cytoscape.util	CytoScape
SConvNode		Class	org.cytoscape.equations.parse_tree	CytoScape
SelectAdjacentEdgesAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
SelectAllAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
SelectAllEdgesAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
SelectAllNodesAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
SelectConnectedNodesAction	select every node connected to the current selected edges.	Class	cytoscape.actions	CytoScape
SelectedEdges	Java class for anonymous complex type.	Class	cytoscape.generated	CytoScape
SelectedNodes	Java class for anonymous complex type.	Class	cytoscape.generated	CytoScape
SelectEvent	Events that are fired when the selected state of a Node or Edge, or a group of Nodes or Edges, is changed.	Class	cytoscape.data	CytoScape
SelectEventListener	Listener for SelectEvents fired by a SelectFilter object.	Interface	cytoscape.data	CytoScape
SelectFilter	This class implements the ability to set the selected state of every node or edge in a GraphPerspective.	Class	cytoscape.data	CytoScape
SelectFirstNeighborsAction	select every first neighbor (directly connected nodes) of the currentlySee Also:Serialized Form	Class	cytoscape.actions	CytoScape
SelectionModeAction		Class	cytoscape.actions	CytoScape
Semantics	This class defines names for certain data attributes that are commonly used within Cytoscape.	Class	cytoscape.data	CytoScape
SeparateArrowStroke	Fields inherited from class cytoscape.	Class	cytoscape.visual.strokes	CytoScape
Server	Java class for anonymous complex type.	Class	cytoscape.generated	CytoScape
SessionState	Java class for anonymous complex type.	Class	cytoscape.generated	CytoScape
SetNestedNetworkDialog		Class	cytoscape.dialogs	CytoScape
SettingsAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.layout.ui	CytoScape
SetVisualPropertiesAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
ShapeCellRenderer		Class	cytoscape.visual.ui.editors.discrete	CytoScape
ShapeStroke		Class	cytoscape.visual.strokes	CytoScape
ShowAllAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
ShowCustomGraphicsManagerAction	Display Custom Graphics Manager GUI.	Class	cytoscape.actions	CytoScape
ShowGraphicsDetailsAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
ShrinkExpandGraph	This class shifts the nodes to shrink or expand the graph: it averages the coordinates of all the nodes to find the center	Class	cytoscape.dialogs	CytoScape
ShrinkExpandGraphUI		Class	cytoscape.dialogs	CytoScape
SIFFileFilter	FileFilter for Reading in Cytoscape SIF Files.	Class	cytoscape.util	CytoScape
Sign		Class	org.cytoscape.equations.builtins	CytoScape
Sin		Class	org.cytoscape.equations.builtins	CytoScape
SineWaveStroke	Fields inherited from class cytoscape.	Class	cytoscape.visual.strokes	CytoScape
Sinh		Class	org.cytoscape.equations.builtins	CytoScape
SList		Class	org.cytoscape.equations.builtins	CytoScape
SolidStroke	Fields inherited from class java.	Class	cytoscape.visual.strokes	CytoScape
SpacialEntry2DEnumerator	An enumeration over a set of entries in a SpacialIndex2D structure.	Interface	cytoscape.geom.spacial	CytoScape
SpacialIndex2D	A spacial index for objects in two dimensions.	Interface	cytoscape.geom.spacial	CytoScape
Sqrt		Class	org.cytoscape.equations.builtins	CytoScape
StaticLayoutMenu	StaticLayoutMenu provides a simple menu item to be added to a layoutSee Also:Serialized Form	Class	cytoscape.layout.ui	CytoScape
status		Class	cytoscape.data.servers	CytoScape
StDev		Class	org.cytoscape.equations.builtins	CytoScape
StraightenSelectedEdgesAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
StringConstantNode	A node in the parse tree representing an integer constant.	Class	org.cytoscape.equations.parse_tree	CytoScape
StringList		Class	org.cytoscape.equations	CytoScape
StringParser	simply returning the supplied argument.	Class	cytoscape.visual.parsers	CytoScape
StringRangeValueCalculator		Class	cytoscape.visual.mappings.rangecalculators	CytoScape
StringUtils	Misc Utilities for Formatting Times and Strings.	Class	cytoscape.task.ui	CytoScape
StringWrap		Class	cytoscape.task.util	CytoScape
SubjectBase	Abstract Base Class for Subject in the Subject / Observer Pattern.	Class	cytoscape.visual	CytoScape
Substitute		Class	org.cytoscape.equations.builtins	CytoScape
Sum		Class	org.cytoscape.equations.builtins	CytoScape
SVGExporter	SVG exporter by the batik library.	Class	cytoscape.util.export	CytoScape
SwingWorker	This is the 3rd version of SwingWorker (also known as SwingWorker 3), an abstract class that you subclass to	Class	cytoscape.util	CytoScape
SynonymReader	The purpose of this class is to convert a 'gene_association.	Class	cytoscape.cruft.obo	CytoScape
SynonymTester		Class	cytoscape.cruft.obo.test	CytoScape
Taggable		Interface	cytoscape.visual.customgraphic	CytoScape
Tan		Class	org.cytoscape.equations.builtins	CytoScape
Tanh		Class	org.cytoscape.equations.builtins	CytoScape
Task	Represents a task that can be terminated prematurely by the same entity that started the task - tasks are started with	Interface	cytoscape.task	CytoScape
TaskManager	Utility class used to execute tasks and visually monitor their progress.	Class	cytoscape.task.util	CytoScape
TaskMonitor	Interface for monitoring the progress of a task.	Interface	cytoscape.task	CytoScape
TeeArrow		Class	cytoscape.render.immed.arrow	CytoScape
Text		Class	org.cytoscape.equations.builtins	CytoScape
TextFileReader		Class	cytoscape.data.readers	CytoScape
TextHttpReader		Class	cytoscape.data.readers	CytoScape
TextJarReader		Class	cytoscape.data.readers	CytoScape
TexturePaintFactory		Class	cytoscape.visual.customgraphic.paint	CytoScape
ThemeInfo	Nested Class SummaryNested classes/interfaces inherited from class cytoscape.	Class	cytoscape.plugin	CytoScape
Thesaurus	todo (pshannon, 25 oct 2002): there may be multiple canonicalNames for the same common name.	Class	cytoscape.data.synonyms	CytoScape
ThesaurusFlatFileReader	Read synonyms from flat file.	Class	cytoscape.data.synonyms.readers	CytoScape
Today		Class	org.cytoscape.equations.builtins	CytoScape
ToggleVisualMapperAction	This class implements two menu items that allow enabling and disabling theSee Also:Serialized Form	Class	cytoscape.actions	CytoScape
Token	enum Tokenextends EnumEnum Constant SummaryAMPERSAND	Class	org.cytoscape.equations	CytoScape
Tokeniser		Class	org.cytoscape.equations	CytoScape
TopoGraphNode	Represents a node in a topological graph.	Interface	cytoscape.util	CytoScape
TopologicalSort	See for example http://en.	Class	cytoscape.util	CytoScape
TrackerException	See Also:Serialized FormConstructor SummaryTrackerException()	Class	cytoscape.plugin	CytoScape
Transform		Class	cytoscape.util	CytoScape
TreeCellRenderer		Class	cytoscape.dialogs.plugins	CytoScape
TreeCellRenderer		Class	cytoscape.view	CytoScape
TreeNode	See Also:Serialized FormFields inherited from class javax.	Class	cytoscape.dialogs.plugins	CytoScape
TreeTableModel	TreeTableModel is the model used by a JTreeTable.	Interface	cytoscape.util.swing	CytoScape
TreeTableModelAdapter	This is a wrapper class takes a TreeTableModel and implements the table model interface.	Class	cytoscape.util.swing	CytoScape
TriangleNodeShape		Class	cytoscape.render.immed.nodeshape	CytoScape
TriangleThumbRenderer		Class	cytoscape.visual.ui.editors.continuous	CytoScape
Triple	Extract partial graph structure.	Class	cytoscape.data.ontology	CytoScape
Trunc		Class	org.cytoscape.equations.builtins	CytoScape
Tunable	Tunables are typed objects that maintain properties and an easy way to generate a settings panel to allow user manipulation	Class	cytoscape.layout	CytoScape
TunableListener	The TunableListener interface provides a way to encapsulate CyLayoutAlgorithm property and settings values.	Interface	cytoscape.layout	CytoScape
TypeHandler	This is a temporary implementation.	Class	org.apache.commons.cli	CytoScape
UnaryOpNode	A node in the parse tree representing a unary operator application.	Class	org.cytoscape.equations.parse_tree	CytoScape
Undo	Rudimentary support for undo.	Class	undo	CytoScape
UndoAction	An action that calls undo for the most recent edit in the undoable edit stack.	Class	cytoscape.util.undo	CytoScape
UnHideSelectedAction	See Also:Serialized FormFields inherited from class javax.	Class	cytoscape.actions	CytoScape
UnHideSelectedEdgesAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
UnHideSelectedNodesAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
UnifiedNetworkImportDialog	Default GUI component for network import web service clients.	Class	cytoscape.data.webservice.ui	CytoScape
UnrecognizedOptionException	Exception thrown during parsing signalling an unrecognizedVersion:$Revision: 155404 $Author:bob mcwhiter (bob @ werken.	Class	org.apache.commons.cli	CytoScape
Upper		Class	org.cytoscape.equations.builtins	CytoScape
URLImageCustomGraphics	Fields inherited from class cytoscape.	Class	cytoscape.visual.customgraphic.impl.bitmap	CytoScape
URLImageCustomGraphicsParser	Create instance of URLImageCustomGraphics object from String.	Class	cytoscape.visual.customgraphic	CytoScape
URLUtil		Class	cytoscape.util	CytoScape
Value		Class	org.cytoscape.equations.builtins	CytoScape
ValueParser		Interface	cytoscape.visual.parsers	CytoScape
ValueSelectDialog	Visual Property selector for discrete valuesAuthor:konoSee Also:Serialized Form	Class	cytoscape.visual.ui	CytoScape
ValueToStringConverter	Provide special type of toString for the given class.	Interface	cytoscape.visual.converter	CytoScape
ValueToStringConverterManager	Replacement for ObjectToString.	Class	cytoscape.visual.converter	CytoScape
Var		Class	org.cytoscape.equations.builtins	CytoScape
VectorCustomGraphics		Interface	cytoscape.visual.customgraphic.impl.vector	CytoScape
VeeNodeShape		Class	cytoscape.render.immed.nodeshape	CytoScape
VerticalSlashStroke	Nested Class SummaryNested classes/interfaces inherited from class cytoscape.	Class	cytoscape.visual.strokes	CytoScape
ViewableNodes	Java class for anonymous complex type.	Class	cytoscape.generated	CytoScape
ViewChangeEdit	A Ding specific undoable edit.	Class	ding.view	CytoScape
ViewportChangeListener		Interface	ding.view	CytoScape
VisualMappingManager	Top-level class for controlling the visual appearance of nodes and edges according to data attributes, as well as some global visual attributes.	Class	cytoscape.visual	CytoScape
VisualProperty	Represents a visual property.	Interface	cytoscape.visual	CytoScape
VisualPropertyDependency	Define dependency of visual properties.	Interface	cytoscape.visual	CytoScape
VisualPropertyIcon	Icon created from Shape object passed from rendering engine.	Class	cytoscape.visual.ui.icon	CytoScape
VisualPropertyType	enum VisualPropertyTypeextends EnumEnum for calculator types.	Class	cytoscape.visual	CytoScape
VisualStyle	This class encapsulates a full set of visual mapping specifications for Cytoscape.	Class	cytoscape.visual	CytoScape
VisualStyleBuilder	Based on the graph/node/edge view information, build new Visual Style.	Class	cytoscape.data.readers	CytoScape
VizMapBypassNetworkListener	Adds NodeView and EdgeView vizmap bypass listeners to network views as the views are created.	Class	cytoscape.visual.ui	CytoScape
VizMapperMainPanel	New VizMapper UI main panel.	Class	cytoscape.visual.ui	CytoScape
VizMapperProperty		Class	cytoscape.visual.ui	CytoScape
VizMapperTrackRenderer		Interface	cytoscape.visual.ui.editors.continuous	CytoScape
WebServiceClient	Web service client wrapper for Cytoscape.	Interface	cytoscape.data.webservice	CytoScape
WebServiceClientGUI	Web service client which has custom component should implements this interface.	Interface	cytoscape.data.webservice.ui	CytoScape
WebServiceClientImpl	Abstract class for all web service clients.	Class	cytoscape.data.webservice	CytoScape
WebServiceClientImplWithGUI		Class	cytoscape.data.webservice	CytoScape
WebServiceClientManager	Web Service Client Manager manages available web service clients in Cytoscape.	Class	cytoscape.data.webservice	CytoScape
WebServiceContextMenu	Context menu for web service clients.	Class	cytoscape.data.webservice.ui	CytoScape
WebServiceContextMenuListener		Class	cytoscape.data.webservice.ui	CytoScape
WebServiceNetworkImportAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
WebServiceThemeInstall		Class	cytoscape.data.webservice.util	CytoScape
WebstartException	This exception is used when methods that can't be used from the PluginManager if webstart is running are called.	Class	cytoscape.plugin	CytoScape
WidestStringComboBoxModel	This ComboBoxModel tracks the widest string getLabel(Object anObject) should be overridden to derive the String from	Class	cytoscape.util.swing	CytoScape
WidestStringComboBoxPopupMenuListener	Listener that can be attached to a JComboBox.	Class	cytoscape.util.swing	CytoScape
WidestStringProvider	Marker interface to decouple WidestStringComboBoxPopupMenuListener from WidestStringComboBoxModel.	Interface	cytoscape.util.swing	CytoScape
WidthStroke	A simple extension of Stroke that allows Stroke objects to be coupled with LineStyle enum values and allows the width of the	Interface	cytoscape.visual.strokes	CytoScape
WindowUtilities	WindowUtilities keeps track of open windows and may close down the JVM when all primary windows are closed (see #setExitJVMWhenAllWindowsClose	Class	cytoscape.util.shadegrown	CytoScape
WSImportResultDialog		Class	cytoscape.data.webservice.ui	CytoScape
XGMMLException	Exception for XGMML Reader.	Class	cytoscape.data.readers	CytoScape
XGMMLFileFilter	FileFilter for Reading in XGMML Files.	Class	cytoscape.util	CytoScape
XGMMLReader	This version is Metanode-compatible.	Class	cytoscape.data.readers	CytoScape
XGMMLWriter	Write network and attributes in XGMML format and marshall it in a streme.	Class	cytoscape.data.writers	CytoScape
YValueLegendPanel		Class	cytoscape.visual.ui.editors.continuous	CytoScape
ZeroStroke	Rather than handle strokes of width 0 for all implementations of WidthStroke, use this wrapper class that, when the width is less than or equal to 0 a	Class	cytoscape.visual.strokes	CytoScape
ZigzagStroke		Class	cytoscape.visual.strokes	CytoScape
ZipUtil	Compression-related methods mainly for Session Writer.	Class	cytoscape.util	CytoScape
ZoomAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape
ZoomSelectedAction	See Also:Serialized FormFields inherited from class cytoscape.	Class	cytoscape.actions	CytoScape

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