Cytoscape 2.8.0 API
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

A

AboutDialog - Class in cytoscape.util.swing
About page for web service clients or other plugins.
AboutDialog(Frame, boolean) - Constructor for class cytoscape.util.swing.AboutDialog
Creates new form WSAboutDialog
AboutDialog(Frame, boolean, String, Icon, URL) - Constructor for class cytoscape.util.swing.AboutDialog
Creates a new AboutDialog object.
above - Variable in class cytoscape.visual.ui.editors.continuous.ContinuousMappingEditorPanel
 
ABOVE_VALUE_CHANGED - Static variable in class cytoscape.visual.ui.editors.continuous.ContinuousMappingEditorPanel
 
abovePanel - Variable in class cytoscape.visual.ui.editors.continuous.ContinuousMappingEditorPanel
 
Abs - Class in org.cytoscape.equations.builtins
 
Abs() - Constructor for class org.cytoscape.equations.builtins.Abs
 
AbstractCalculator - Class in cytoscape.visual.calculators
 
AbstractCalculator(String, ObjectMapping, VisualPropertyType) - Constructor for class cytoscape.visual.calculators.AbstractCalculator
Creates a new AbstractCalculator object.
AbstractCalculator.CalculatorUI - Class in cytoscape.visual.calculators
Deprecated. Do not use. This UI was replaced by new VizMap GUI.
AbstractCalculator.CalculatorUI(CyAttributes, JDialog, CyNetwork) - Constructor for class cytoscape.visual.calculators.AbstractCalculator.CalculatorUI
Deprecated.  
AbstractCalculator.CalculatorUI.AttributeSelectorListener - Class in cytoscape.visual.calculators
Deprecated. AttributeSelectorListener listens for events on the JComboBoxes that select the controlling attribute for mappers contained in each calculator.
AbstractCalculator.CalculatorUI.AttributeSelectorListener(JDialog, CyNetwork, int, int, JPanel) - Constructor for class cytoscape.visual.calculators.AbstractCalculator.CalculatorUI.AttributeSelectorListener
Deprecated. Constructs an AttributeSelectorListener for the ObjectMapping at index mapIndex.
AbstractCellEditor - Class in cytoscape.util.swing
 
AbstractCellEditor() - Constructor for class cytoscape.util.swing.AbstractCellEditor
 
AbstractCommandHandler - Class in cytoscape.command
This abstract class provides a convenient (but not necessary) base class for writing CyCommandHandlers.
AbstractCommandHandler(CyCommandNamespace) - Constructor for class cytoscape.command.AbstractCommandHandler
You do not need to call this constructor from you class, but if you don't, you will need to make sure you assign the namespace appropriately.
AbstractDCustomGraphics - Class in cytoscape.visual.customgraphic.impl
 
AbstractDCustomGraphics(String) - Constructor for class cytoscape.visual.customgraphic.impl.AbstractDCustomGraphics
 
AbstractDCustomGraphics(Long, String) - Constructor for class cytoscape.visual.customgraphic.impl.AbstractDCustomGraphics
Create new object for a given ID.
AbstractFunction - Class in org.cytoscape.equations
 
AbstractFunction(ArgDescriptor[]) - Constructor for class org.cytoscape.equations.AbstractFunction
 
AbstractGraphReader - Class in cytoscape.data.readers
 
AbstractGraphReader(String) - Constructor for class cytoscape.data.readers.AbstractGraphReader
Creates a new AbstractGraphReader object.
AbstractLayout - Class in cytoscape.layout
The AbstractLayout provides nice starting point for Layouts written for Cytoscape.
AbstractLayout() - Constructor for class cytoscape.layout.AbstractLayout
The Constructor is null
AbstractMapping - Class in cytoscape.visual.mappings
 
AbstractMapping(Class<?>, String) - Constructor for class cytoscape.visual.mappings.AbstractMapping
 
AbstractParserControl - Class in org.apache.commons.cli.avalon
Class to inherit from so when in future when new controls are added clients will no have to implement them.
AbstractParserControl() - Constructor for class org.apache.commons.cli.avalon.AbstractParserControl
 
AbstractScaler - Class in cytoscape.util
Used to scale a list of values to [a,b]
AbstractScaler() - Constructor for class cytoscape.util.AbstractScaler
 
AbstractTreeTableModel - Class in cytoscape.util.swing
 
AbstractTreeTableModel(Object) - Constructor for class cytoscape.util.swing.AbstractTreeTableModel
Creates a new AbstractTreeTableModel object.
AbstractVisualProperty - Class in cytoscape.visual.properties
 
AbstractVisualProperty() - Constructor for class cytoscape.visual.properties.AbstractVisualProperty
 
acceleratorSet - Variable in class cytoscape.util.CytoscapeAction
 
accept(File) - Method in class cytoscape.util.CyFileFilter
Returns true if this class is capable of processing the specified file.
accept(File, String) - Method in class cytoscape.util.CyFileFilter
Returns true if this class is capable of processing the specified file.
accept(String) - Method in class cytoscape.util.CyFileFilter
Returns true if this class is capable of processing the specified file.
accept(URL, String) - Method in class cytoscape.util.CyFileFilter
Returns true if this class is capable of processing the specified URL
accept(File) - Method in class cytoscape.util.XGMMLFileFilter
Indicates which files the XGMMLFileFilter accepts.
accept(URL, String) - Method in class cytoscape.util.XGMMLFileFilter
 
acceptedClasses - Variable in class cytoscape.visual.mappings.AbstractMapping
 
acceptedDataClasses - Variable in class cytoscape.visual.calculators.AbstractCalculator
The domain classes accepted by the mappings underlying this calculator.
acceptsMultipleArgs() - Method in class org.cytoscape.equations.ArgDescriptor
 
acceptsMultipleArgs() - Method in enum org.cytoscape.equations.ArgType
 
ACos - Class in org.cytoscape.equations.builtins
 
ACos() - Constructor for class org.cytoscape.equations.builtins.ACos
 
ACTION_TITLE - Static variable in class cytoscape.actions.DeleteAction
 
actionButtonMap - Variable in class cytoscape.util.CytoscapeToolBar
 
actionHelp() - Method in class cytoscape.util.CytoscapeAction
DOCUMENT ME!
actionMembersSet - Variable in class cytoscape.util.CytoscapeMenuBar
 
actionMembersSet - Variable in class cytoscape.util.CytoscapeToolBar
 
actionMenuItemMap - Variable in class cytoscape.util.CytoscapeMenuBar
 
actionPerformed(ActionEvent) - Method in class cytoscape.actions.AlignHorizontalAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.AlignVerticalAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.AlphabeticalSelectionAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.AnimatedLayoutAction
Deprecated. DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ApplyLayoutAction
 
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ApplyVisualStyleAction
 
actionPerformed(ActionEvent) - Method in class cytoscape.actions.BackgroundColorAction
Deprecated. Captures User Menu Selection.
actionPerformed(ActionEvent) - Method in class cytoscape.actions.BendSelectedEdgesAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.BirdsEyeViewAction
Deprecated. DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.BookmarkAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.CloneGraphInNewWindowAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.CreateNetworkViewAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.CytoPanelAction
Toggles the cytopanel state.
actionPerformed(ActionEvent) - Method in class cytoscape.actions.DeleteAction
Delete all selected nodes, edges, edges adjacent to the selected nodes, and any nodes/edges passed as arguments.
actionPerformed(ActionEvent) - Method in class cytoscape.actions.DeselectAllAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.DeSelectAllEdgesAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.DeSelectAllNodesAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.DestroyNetworkAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.DestroyNetworkViewAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.EdgeManipulationAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ExitAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ExportAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ExportAsGMLAction
User-initiated action to save the current network in GML format to a user-specified file.
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ExportAsGraphicsAction
 
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ExportAsInteractionsAction
User-initiated action to save the current network in SIF format to a user-specified file.
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ExportAsXGMMLAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ExportEdgeAttributesAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ExportNetworksAsNNFAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ExportNodeAttributesAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ExportVizmapAction
Get file name and execute the saving task
actionPerformed(ActionEvent) - Method in class cytoscape.actions.FitContentAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.GraphObjectSelectionAction
This Should go away
actionPerformed(ActionEvent) - Method in class cytoscape.actions.HelpAboutAction
Show about page.
actionPerformed(ActionEvent) - Method in class cytoscape.actions.HelpContactHelpDeskAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.HelpContentsAction
Merely calls actionPerformed on the CSH.DisplayHelpFromSource object.
actionPerformed(ActionEvent) - Method in class cytoscape.actions.HideSelectedAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.HideSelectedEdgesAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.HideSelectedNodesAction
 
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ImportEdgeAttributesAction
User Initiated Request.
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ImportExpressionMatrixAction
User Initiated Request.
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ImportGraphFileAction
User-initiated action to load a CyNetwork into Cytoscape.
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ImportNodeAttributesAction
User Initiated Request.
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ImportVizmapAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.InvertSelectedEdgesAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.InvertSelectedNodesAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ListFromFileSelectionAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.LoggerAction
 
actionPerformed(ActionEvent) - Method in class cytoscape.actions.MemoryUsageAction
Show memory usage freport.
actionPerformed(ActionEvent) - Method in class cytoscape.actions.NewNetworkAction
create the new network and view
actionPerformed(ActionEvent) - Method in class cytoscape.actions.NewSessionAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.NewWindowSelectedNodesEdgesAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.NewWindowSelectedNodesOnlyAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.OpenSessionAction
Clear current session and open the cys file.
actionPerformed(ActionEvent) - Method in class cytoscape.actions.PluginManagerAction
Gets the lists of plugins and creates the ManagerDialog for users.
actionPerformed(ActionEvent) - Method in class cytoscape.actions.PluginUpdateAction
 
actionPerformed(ActionEvent) - Method in class cytoscape.actions.PreferenceAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.PrintAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ProxyServerAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.RotateSelectedNodesAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.SaveSessionAction
If no current session file exists, open dialog box to ask user a new session file name, otherwise, overwrite the file.
actionPerformed(ActionEvent) - Method in class cytoscape.actions.SaveSessionAsAction
If no current session file exists, open dialog box to save new session, and if it exists, overwrite the file.
actionPerformed(ActionEvent) - Method in class cytoscape.actions.SelectAdjacentEdgesAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.SelectAllAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.SelectAllEdgesAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.SelectAllNodesAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.SelectConnectedNodesAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.SelectFirstNeighborsAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.SetVisualPropertiesAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ShowAllAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ShowCustomGraphicsManagerAction
Display custom graphics manager
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ShowGraphicsDetailsAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.StraightenSelectedEdgesAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ToggleVisualMapperAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.UnHideSelectedAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.UnHideSelectedEdgesAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.UnHideSelectedNodesAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.WebServiceNetworkImportAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ZoomAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.actions.ZoomSelectedAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.EdgeAttributesPopupDetails.OKAction
 
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.EditNetworkTitleDialog
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.ExportAsGraphicsFileChooser
 
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.ExpressionDataPopupTable.OKAction
 
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.GinyEdgeControlDialog.OKAction
 
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.GraphObjectSelection
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.IconPopupButton
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.IconPopupButton.ApplyIconAction
 
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.IconPopupButton.CancelIconAction
 
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.ImportNetworkDialog
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.LabelTextPanel.BoxAction
 
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.NewSlider.MJTextField
 
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.NewStringPopupDialog.CancelAction
 
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.NewStringPopupDialog.OkAction
 
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.plugins.PluginManageDialog
 
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.PopupTextArea.OKAction
 
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.preferences.BookmarkDialog
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.preferences.ProxyServerDialog
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.dialogs.ShrinkExpandGraph
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.layout.Tunable
This method is public as a byproduct of the implementation.
actionPerformed(ActionEvent) - Method in class cytoscape.layout.ui.DynamicLayoutMenu.LayoutAttributeMenuItem
 
actionPerformed(ActionEvent) - Method in class cytoscape.layout.ui.LayoutSettingsDialog
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.layout.ui.SettingsAction
 
actionPerformed(ActionEvent) - Method in class cytoscape.layout.ui.StaticLayoutMenu
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.task.ui.JTask
Capture All Action Events.
actionPerformed(ActionEvent) - Method in class cytoscape.util.CytoscapeAction
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.util.undo.RedoAction
Tries to run redo() on the top edit of the edit stack.
actionPerformed(ActionEvent) - Method in class cytoscape.util.undo.UndoAction
Tries to run undo() on the top edit of the edit stack.
actionPerformed(ActionEvent) - Method in class cytoscape.visual.mappings.discrete.RandomColorListener
User wants to Seed the Discrete Mapper with Random Color Values.
actionPerformed(ActionEvent) - Method in class cytoscape.visual.ui.ObjectPlacerControl
DOCUMENT ME!
actionPerformed(ActionEvent) - Method in class cytoscape.visual.ui.PopupIconChooser.ApplyIconAction
 
actionPerformed(ActionEvent) - Method in class cytoscape.visual.ui.PopupIconChooser.CancelIconAction
 
actionPerformed(ActionEvent) - Method in class cytoscape.visual.ui.VizMapperMainPanel.CopyStyleListener
 
actionPerformed(ActionEvent) - Method in class cytoscape.visual.ui.VizMapperMainPanel.CreateLegendListener
 
activate() - Method in class cytoscape.plugin.CytoscapePlugin
If implemented, then this plugin will be activated after being initialized
add(String, int) - Method in class cytoscape.data.annotation.Annotation
Deprecated. create a new annotation for an entity (typically a gene) of the current species and with respect to the current ontology.
add(OntologyTerm) - Method in class cytoscape.data.annotation.Ontology
Deprecated. DOCUMENT ME!
add(OntologyTerm) - Method in class cytoscape.data.ontology.Ontology
Add a new ontology term to the DAG.
add(String, String) - Method in class cytoscape.data.synonyms.Aliases
Add new alias for an object.
add(String, List<String>) - Method in class cytoscape.data.synonyms.Aliases
Add list of aliases to the existing alias lists.
add(String, String) - Method in class cytoscape.data.synonyms.Thesaurus
DOCUMENT ME!
add(CyLayoutAlgorithm) - Method in class cytoscape.layout.ui.LayoutMenu
DOCUMENT ME!
add(Tunable) - Method in interface cytoscape.util.ModuleProperties
This method is used to add a new Tunable to the LayoutProperties list.
add(Tunable) - Method in class cytoscape.util.ModulePropertiesImpl
This method is used to add a new Tunable to the LayoutProperties list.
add(URL) - Method in class cytoscape.util.RecentlyOpenedTracker
Adds "newURL" to the list of recently opened file names and trims the list if it has exceeded its maximum length.
add(Component) - Method in interface cytoscape.view.cytopanels.CytoPanel
Adds a component to the CytoPanel.
add(Component, int) - Method in interface cytoscape.view.cytopanels.CytoPanel
Adds a component to the CytoPanel at specified index.
add(String, Component) - Method in interface cytoscape.view.cytopanels.CytoPanel
Adds a component to the CytoPanel with a specified title.
add(String, Icon, Component) - Method in interface cytoscape.view.cytopanels.CytoPanel
Adds a component to the CytoPanel with specified title and icon.
add(String, Icon, Component, String) - Method in interface cytoscape.view.cytopanels.CytoPanel
Adds a component to the CytoPanel with specified title, icon, and tool tip.
add(String, Icon, Component, String, int) - Method in interface cytoscape.view.cytopanels.CytoPanel
Adds a component to the CytoPanel with specified title, icon, and tool tip at specified index.
add(Component) - Method in class cytoscape.view.cytopanels.CytoPanelImp
Adds a component to the CytoPanel.
add(Component, int) - Method in class cytoscape.view.cytopanels.CytoPanelImp
Adds a component to the CytoPanel at specified index.
add(String, Component) - Method in class cytoscape.view.cytopanels.CytoPanelImp
Adds a component to the CytoPanel with a specified title.
add(String, Icon, Component) - Method in class cytoscape.view.cytopanels.CytoPanelImp
Adds a component to the CytoPanel with specified title and icon.
add(String, Icon, Component, String) - Method in class cytoscape.view.cytopanels.CytoPanelImp
Adds a component to the CytoPanel with specified title, icon, and tool tip.
add(String, Icon, Component, String, int) - Method in class cytoscape.view.cytopanels.CytoPanelImp
Adds a component to the CytoPanel with specified title, icon, and tool tip at specified index.
add(Component) - Method in class ding.view.ArbitraryGraphicsCanvas
Our implementation of add
addAction(Action) - Method in class cytoscape.util.CytoscapeMenuBar
If the given Action has a present and false inMenuBar property, return; otherwise delegate to addAction( String, Action ) with the value of its preferredMenu property, or null if it does not have that property.
addAction(Action, int) - Method in class cytoscape.util.CytoscapeMenuBar
DOCUMENT ME!
addAction(String, Action) - Method in class cytoscape.util.CytoscapeMenuBar
DOCUMENT ME!
addAction(Action) - Method in class cytoscape.util.CytoscapeToolBar
If the given Action has an absent or false inToolBar property, return; otherwise delegate to addAction( String, Action ) with the value of its preferredButtonGroup property, or null if it does not have that property.
addAction(String, Action) - Method in class cytoscape.util.CytoscapeToolBar
Note that this presently ignores the button group name.
addAction(CytoscapeAction) - Method in class cytoscape.view.CyMenus
Add the menu item.
addAction(CytoscapeAction, int) - Method in class cytoscape.view.CyMenus
Add the menu item in a specific position
addActionListener(ActionListener) - Method in class cytoscape.dialogs.ExportAsGraphicsFileChooser
 
addActionListener(ActionListener) - Method in class cytoscape.dialogs.ExportBitmapOptionsDialog
Add an action for when the "OK" button is pressed.
addAlternateCommonName(String, String) - Method in class cytoscape.data.synonyms.Thesaurus
DOCUMENT ME!
addAnnotation(Annotation) - Method in class cytoscape.data.servers.BioDataServer
DOCUMENT ME!
addAnnotation(Annotation) - Method in interface cytoscape.data.servers.BioDataServerInterface
DOCUMENT ME!
addAnnotation(Annotation) - Method in class cytoscape.data.servers.BioDataServerRmi
if the new annotation is to an already annotated species, curator and type, then simply add (with possible overwriting for identical
addArgument(String) - Method in class cytoscape.command.AbstractCommandHandler
This method adds a new command to the list of command supported by this command handler.
addArgument(String, String) - Method in class cytoscape.command.AbstractCommandHandler
Add a new argument key to a command supported by this command handler.
addArgument(String, String, String) - Method in class cytoscape.command.AbstractCommandHandler
Add a new argument key with a value to a command supported by this command handler.
addArgument(String, Tunable) - Method in class cytoscape.command.AbstractCommandHandler
Add a new argument Tunable to a command supported by this command handler.
addArgument(String) - Method in class org.apache.commons.cli.avalon.CLOption
Mutator of Argument property.
addArguments(ArrayList<String>) - Method in class cytoscape.util.JnlpWriterUtil
 
addAuthor(String, String) - Method in class cytoscape.plugin.PluginInfo
Adds an author to the list of authors.
addButton - Variable in class cytoscape.visual.ui.editors.continuous.ContinuousMappingEditorPanel
 
addButtonActionPerformed(ActionEvent) - Method in class cytoscape.visual.ui.editors.continuous.C2CMappingEditor
 
addButtonActionPerformed(ActionEvent) - Method in class cytoscape.visual.ui.editors.continuous.C2DMappingEditor
 
addButtonActionPerformed(ActionEvent) - Method in class cytoscape.visual.ui.editors.continuous.ContinuousMappingEditorPanel
 
addButtonActionPerformed(ActionEvent) - Method in class cytoscape.visual.ui.editors.continuous.GradientEditorPanel
 
addCalculator(Calculator) - Method in class cytoscape.visual.CalculatorCatalog
Add any calculator to the catalog.
addCalculator(Calculator, Map) - Method in class cytoscape.visual.CalculatorCatalog
 
addCategory(String, List<DownloadableInfo>, PluginManageDialog.PluginInstallStatus) - Method in class cytoscape.dialogs.plugins.PluginManageDialog
Adds a category and it's list of plugins to the appropriate tree (based on Status) in the dialog.
addCategory(String, DownloadableInfo, List<DownloadableInfo>) - Method in class cytoscape.dialogs.plugins.PluginUpdateDialog
DOCUMENT ME
addCellEditorListener(CellEditorListener) - Method in class cytoscape.util.swing.AbstractCellEditor
DOCUMENT ME!
addChangeListener(ChangeListener, VisualPropertyType) - Method in class cytoscape.visual.CalculatorCatalog
DOCUMENT ME!
addChangeListener(ChangeListener) - Method in class cytoscape.visual.calculators.AbstractCalculator
Add a ChangeListener to the calcaultor.
addChangeListener(ChangeListener) - Method in interface cytoscape.visual.calculators.Calculator
Add a ChangeListener to the calcaultor.
addChangeListener(ChangeListener) - Method in interface cytoscape.visual.mappings.ObjectMapping
Add a ChangeListener to the mapping.
addChangeListener(ChangeListener) - Method in class cytoscape.visual.mappings.PassThroughMapping
Empty implementation because PassThroughMapping has no UI.
addChangeListener(ChangeListener) - Method in class cytoscape.visual.SubjectBase
Add a ChangeListener.
addChild(TreeNode) - Method in class cytoscape.dialogs.plugins.TreeNode
Adds newChild to this node if children are allowed.
addChildren(TreeNode[]) - Method in class cytoscape.dialogs.plugins.TreeNode
Adds all children to the child list of this node if children are allowed.
addColumn(ColumnTypes, int) - Method in class cytoscape.view.NetworkTreeTableModel
 
addComponentToSouth(Component) - Method in class cytoscape.view.cytopanels.CytoPanelImp
Add a component to the CytoPanel just below the TabbedPane.
addContainer(int) - Method in class cytoscape.data.annotation.OntologyTerm
Deprecated. DOCUMENT ME!
addContentChangeListener(ContentChangeListener) - Method in class ding.view.DGraphView
DOCUMENT ME!
addContentType(String) - Method in class cytoscape.util.CyFileFilter
Adds a content-type to filter against.
addContextMethod(String, String, String, Object[], ClassLoader) - Method in class ding.view.DGraphView
DOCUMENT ME!
addContextMethod(String, String, String, Object[], ClassLoader) - Method in interface giny.view.GraphView
Context Menu Support
addCustomGraphic(Shape, Paint, byte) - Method in class ding.view.DNodeView
Adds a custom graphic, in draw order, to this DNodeView in a thread-safe way.
addCustomGraphic(CustomGraphic) - Method in class ding.view.DNodeView
Adds a given CustomGraphic, in draw order, to this DNodeView in a thread-safe way.
addCyNetworkListener(CyNetworkListener) - Method in interface cytoscape.CyNetwork
Registers the argument as a listener to this object.
addCyNetworkListener(CyNetworkListener) - Method in class cytoscape.giny.FingCyNetwork
Registers the argument as a listener to this object.
addCytoPanelListener(CytoPanelListener) - Method in interface cytoscape.view.cytopanels.CytoPanel
Adds a CytoPanel listener.
addCytoPanelListener(CytoPanelListener) - Method in class cytoscape.view.cytopanels.CytoPanelImp
Adds a CytoPanel listener.
addCytoscapeAction(CytoscapeAction) - Method in class cytoscape.view.CyMenus
Takes a CytoscapeAction and will add it to the MenuBar or the Toolbar as is appropriate.
addCytoscapeAction(CytoscapeAction, int) - Method in class cytoscape.view.CyMenus
Add the menu item in a specific position
addCytoscapeVersion(String) - Method in class cytoscape.plugin.DownloadableInfo
Contains a list of all the Cytoscape versions this object is compatible with.
addCyWebServiceEventListener(CyWebServiceEventListener) - Method in class cytoscape.data.webservice.CyWebServiceEventSupport
DOCUMENT ME!
addDataDefinitionListener(MultiHashMapDefinitionListener) - Method in interface cytoscape.data.attr.MultiHashMapDefinition
Registers a listener for receiving events having to do with attribute definitions being created and deleted.
addDataListener(MultiHashMapListener) - Method in interface cytoscape.data.attr.MultiHashMap
Registers a listener for receiving events having to do with attribute values being assigned and removed.
addDescription(String, String) - Method in class cytoscape.command.AbstractCommandHandler
This method adds a new description for a command supported by this command handler.
addDownloadable(DownloadableInfo, PluginStatus) - Method in class cytoscape.plugin.PluginTracker
 
addEdge(int) - Method in interface cytoscape.CyNetwork
Add a edge to this Network that already exists in Cytoscape
addEdge(Edge) - Method in interface cytoscape.CyNetwork
Add a edge to this Network that already exists in Cytoscape
addEdge(int) - Method in class cytoscape.giny.FingCyNetwork
Add a edge to this Network that already exists in Cytoscape
addEdge(Edge) - Method in class cytoscape.giny.FingCyNetwork
Add a edge to this Network that already exists in Cytoscape
addEdge(String, Object) - Method in class cytoscape.giny.FingCyNetwork
Adds a edge to this Network, by looking it up via the given attribute and value
addEdgeContextMenuItems(EdgeView, JPopupMenu) - Method in class cytoscape.data.webservice.ui.WebServiceContextMenu
DOCUMENT ME!
addEdgeContextMenuItems(EdgeView, JPopupMenu) - Method in interface ding.view.EdgeContextMenuListener
method for responding to a drop
addEdgeContextMenuListener(EdgeContextMenuListener) - Method in interface cytoscape.view.CyNetworkView
DOCUMENT ME!
addEdgeContextMenuListener(EdgeContextMenuListener) - Method in class ding.view.DGraphView
DOCUMENT ME!
addEdgeContextMenuListener(EdgeContextMenuListener) - Method in class ding.view.InnerCanvas
DOCUMENT ME!
addEdgeMetaChild(int, int) - Method in interface giny.model.RootGraph
Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges.
addEdgeView(int) - Method in class ding.view.DGraphView
Adds EdgeView to the GraphView.
addEdgeView(String, int) - Method in class ding.view.DGraphView
Will thrown an UnsupportedOperationException.
addEdgeView(int) - Method in interface giny.view.GraphView
 
addEdgeView(String, int) - Method in interface giny.view.GraphView
To facilitate adding Custome EdgeViews It is recomended that All Custom Edge Views follow the patterns outlined in PEdgeView and BasicPEdgeView.
addElement(Object) - Method in class cytoscape.util.swing.WidestStringComboBoxModel
Adds the given object to the model.
addError(String) - Method in class cytoscape.command.CyCommandResult
Add an error message to the list of errors for this execution.
addExtension(String) - Method in class cytoscape.util.CyFileFilter
Adds a filetype "dot" extension to filter against.
addFileName(String) - Method in class cytoscape.plugin.PluginInfo
Adds a file to the list of installed files.
addFilter(CyFileFilter) - Method in class cytoscape.data.ImportHandler
Registers a new CyFileFilter.
addFilter(CyFileFilter[]) - Method in class cytoscape.data.ImportHandler
Registers an Array of CyFileFilter Objects.
addGraphics(CyCustomGraphics, URL) - Method in class cytoscape.visual.customgraphic.CustomGraphicsManager
Add a custom graphics to current session.
addGraphPerspectiveChangeListener(GraphPerspectiveChangeListener) - Method in interface giny.model.GraphPerspective
 
addGraphView(GraphView) - Method in class cytoscape.view.GraphViewController
Adds to the set of giny.view.GraphView objects that this GraphViewController keeps synchronized with their giny.model.GraphPerspective objects.
addGraphView(GraphView, GraphViewHandler) - Method in class cytoscape.view.GraphViewController
Adds to the set of giny.view.GraphView objects that this GraphViewController keeps synchronized to their giny.model.GraphPerspective objects.
addGraphViewChangeListener(GraphViewChangeListener) - Method in class ding.view.DGraphView
Add GraphViewChangeListener to linked list of GraphViewChangeListeners.
addGraphViewChangeListener(GraphViewChangeListener) - Method in interface giny.view.GraphView
Adds a new GraphViewChangeListener to this GraphViews list of listeners.
addGroupChangeListener(CyGroupChangeListener) - Static method in class cytoscape.groups.CyGroupManager
Add a new change listener to our list of listeners
addHandle(Point2D) - Method in interface giny.view.Bend
Add a PHandle to the edge at the point specified.
addHandle(int, Point2D) - Method in interface giny.view.Bend
Add a PHandle to the edge at the point and index specified.
addHelpSet(HelpSet) - Static method in class cytoscape.view.CyHelpBroker
 
addInnerEdge(CyEdge) - Method in interface cytoscape.groups.CyGroup
Add an inner edge to the map.
addInnerEdge(CyEdge) - Method in class cytoscape.groups.CyGroupImpl
Add an inner edge to the map.
addItem(Object) - Method in class cytoscape.util.swing.FilterHistoryJList
DOCUMENT ME!
addItemListener(ItemListener) - Method in class cytoscape.util.swing.NetworkSelectorPanel
Installs a new item listener for the embedded combo box.
addItems(String[]) - Method in class cytoscape.dialogs.plugins.PluginUrlDialog
DOCUMENT ME!
addJars(String, ArrayList<String>, String) - Method in class cytoscape.util.JnlpWriterUtil
 
addLayout(CyLayoutAlgorithm, String) - Static method in class cytoscape.layout.CyLayouts
Add a layout to the layout manager's list.
addLicense(PluginInfo, Element) - Static method in class cytoscape.plugin.PluginFileReader
 
addListenerToOk(ActionListener) - Method in class cytoscape.dialogs.plugins.LicenseDialog
 
addLogHandler(CyLogHandler, String, LogLevel) - Method in class cytoscape.logger.CyLogger
Add a new log handler for specific messages
addLogHandler(CyLogHandler, LogLevel) - Method in class cytoscape.logger.CyLogger
Add a new general log handler for all messages
addMapping(String, GMLNode) - Method in class cytoscape.data.readers.GMLNode
Add a mapping from key to node
addMapping(String, Class) - Method in class cytoscape.visual.CalculatorCatalog
Add a mapping to the database of available mappings.
addMapping(ObjectMapping) - Method in class cytoscape.visual.calculators.AbstractCalculator
Add a mapping to the mappings contained by the calculator.
addMessage(String) - Method in class cytoscape.command.CyCommandResult
Add a message to the list of messages that results from this execution.
addMetaChild(Node, Node) - Method in interface giny.model.RootGraph
Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges.
addMetaChild(Node, Edge) - Method in interface giny.model.RootGraph
Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges.
addNetwork(CyNetwork, String, CyNetwork, boolean) - Static method in class cytoscape.Cytoscape
Add a network to Cytoscape's internal list of networks.
addNetwork(String, String) - Method in class cytoscape.view.NetworkPanel
DOCUMENT ME!
addNode(int) - Method in interface cytoscape.CyNetwork
Add a node to this Network that already exists in Cytoscape
addNode(Node) - Method in interface cytoscape.CyNetwork
Add a node to this Network that already exists in Cytoscape
addNode(int) - Method in class cytoscape.giny.FingCyNetwork
Add a node to this Network that already exists in Cytoscape
addNode(Node) - Method in class cytoscape.giny.FingCyNetwork
Add a node to this Network that already exists in Cytoscape
addNode(String, Object) - Method in class cytoscape.giny.FingCyNetwork
Adds a node to this Network, by looking it up via the given attribute and value
addNode(CyNode) - Method in interface cytoscape.groups.CyGroup
Add a new node to this group
addNode(CyNode) - Method in class cytoscape.groups.CyGroupImpl
Add a new node to this group
addNode(CyNode, boolean) - Method in class cytoscape.groups.CyGroupImpl
Add a new node to this group
addNodeAttribute(String) - Static method in class cytoscape.data.NetworkData
Attempts to add a new Attribute name, of Object type for nodes.
addNodeAttribute(String, int) - Static method in class cytoscape.data.NetworkData
Attempts to add a new Attribute name, of given type for nodes.
addNodeContextMenuItems(NodeView, JPopupMenu) - Method in class cytoscape.data.webservice.ui.WebServiceContextMenu
Add this menu to the node context menu.
addNodeContextMenuItems(NodeView, JPopupMenu) - Method in interface ding.view.NodeContextMenuListener
method for responding to a drop
addNodeContextMenuListener(NodeContextMenuListener) - Method in interface cytoscape.view.CyNetworkView
DOCUMENT ME!
addNodeContextMenuListener(NodeContextMenuListener) - Method in class ding.view.DGraphView
DOCUMENT ME!
addNodeContextMenuListener(NodeContextMenuListener) - Method in class ding.view.InnerCanvas
adds a listener to the store of NodeContextMenuListeners
addNodeMetaChild(int, int) - Method in interface giny.model.RootGraph
Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges.
addNodeToParent(TreeNode, TreeNode) - Method in class cytoscape.dialogs.plugins.ManagerModel
Adds node to given parent, fires event
addNodeView(int) - Method in class ding.view.DGraphView
Adds a NodeView object to the GraphView.
addNodeView(String, int) - Method in class ding.view.DGraphView
Will thrown an UnsupportedOperationException.
addNodeView(int, NodeView) - Method in class ding.view.DGraphView
Will thrown an UnsupportedOperationException.
addNodeView(int) - Method in interface giny.view.GraphView
 
addNodeView(String, int) - Method in interface giny.view.GraphView
To facilitate adding Custome NodeViews It is recomended that All Custom Node Views follow the patterns outlined in PNodeView and BasicPNodeView.
addNodeView(int, NodeView) - Method in interface giny.view.GraphView
Add in a NodeView for a Node in the GraphPerspective.
addObject(DownloadableInfo) - Method in class cytoscape.dialogs.plugins.TreeNode
Adds a PluginInfo object to this node.
addOntology(Ontology) - Method in class cytoscape.data.servers.OntologyServer
 
addOntology(URL, OntologyServer.OntologyType, String, String) - Method in class cytoscape.data.servers.OntologyServer
 
addOption(Option) - Method in class org.apache.commons.cli.OptionGroup
add opt to this group
addOption(String, boolean, String) - Method in class org.apache.commons.cli.Options
Add an option that only contains a short-name.
addOption(String, String, boolean, String) - Method in class org.apache.commons.cli.Options
Add an option that contains a short-name and a long-name.
addOption(Option) - Method in class org.apache.commons.cli.Options
Adds an option instance
addOptionGroup(OptionGroup) - Method in class org.apache.commons.cli.Options
Add the specified option group.
addOuterEdge(CyEdge) - Method in interface cytoscape.groups.CyGroup
Add an outer edge to the map.
addOuterEdge(CyEdge) - Method in class cytoscape.groups.CyGroupImpl
Add an outer edge to the map.
addParent(int) - Method in class cytoscape.data.annotation.OntologyTerm
Deprecated. DOCUMENT ME!
addPhoebeCanvasDropListener(PhoebeCanvasDropListener) - Method in class ding.view.InnerCanvas
adds a listener to the store of PhoebeCanvasDropTargetListeners
addPhoebeCanvasDropListener(PhoebeCanvasDropListener) - Method in interface phoebe.PhoebeCanvasDroppable
adds a PhoebeCanvasDropListener to the listener store
addPlugin(DownloadableInfo) - Method in class cytoscape.dialogs.plugins.LicenseDialog
 
addPlugin(String) - Method in class cytoscape.dialogs.preferences.PluginsTableModel
Deprecated. DOCUMENT ME!
addPlugin(URL) - Method in class cytoscape.dialogs.preferences.PluginsTableModel
Deprecated. DOCUMENT ME!
addPlugin(PluginInfo) - Method in class cytoscape.plugin.ThemeInfo
 
addPluginToPropertyString(String) - Method in class cytoscape.dialogs.preferences.PluginsTableModel
Deprecated. DOCUMENT ME!
addPoint(double, BoundaryRangeValues) - Method in class cytoscape.visual.mappings.ContinuousMapping
Adds a New Data Point.
addProperty(String, VisualPropertyType, String) - Method in class cytoscape.data.readers.VisualStyleBuilder
This method actually adds a property to be considered for inclusion into the resulting style.
addProperty(String[]) - Method in class cytoscape.dialogs.preferences.PreferenceTableModel
DOCUMENT ME!
AddRemoveTest - Class in fing.model.test
 
addResult(Object) - Method in class cytoscape.command.CyCommandResult
Add the result for this execution.
addResult(String, Object) - Method in class cytoscape.command.CyCommandResult
Add a result to the result set for this execution.
addScalarArgumentTypes(List<Class>) - Static method in class org.cytoscape.equations.FunctionUtil
Adds Double.class, Long.class, String.class and Boolean.class to "argTypes".
addSelectEventListener(SelectEventListener) - Method in interface cytoscape.CyNetwork
Adds a listener for SelectEvents to this CyNetwork
addSelectEventListener(SelectEventListener) - Method in class cytoscape.data.SelectFilter
If the argument is not already a listener to this object, it is added.
addSelectEventListener(SelectEventListener) - Method in class cytoscape.giny.FingCyNetwork
Adds a listener for SelectEvents to this CyNetwork
addSynonym(Object) - Method in class cytoscape.data.ontology.OntologyTerm
In this implementation, key is the synonym name, and value is the synonym type.
addSynonym(Object, OntologyTerm.SynonymType) - Method in class cytoscape.data.ontology.OntologyTerm
In this implementation, key is the synonym name, and value is the synonym type.
addSynonym(Object) - Method in class cytoscape.data.ontology.Triple
Triple synonym is not supported.
addThesaurus(String, Thesaurus) - Method in class cytoscape.data.servers.BioDataServer
DOCUMENT ME!
addThesaurus(String, Thesaurus) - Method in interface cytoscape.data.servers.BioDataServerInterface
DOCUMENT ME!
addThesaurus(String, Thesaurus) - Method in class cytoscape.data.servers.BioDataServerRmi
DOCUMENT ME!
addToGroup(CyGroup) - Method in class cytoscape.CyNode
Add this node to the specified group.
addTransferComponent(JComponent) - Method in class ding.view.InnerCanvas
DOCUMENT ME!
addTreeModelListener(TreeModelListener) - Method in class cytoscape.dialogs.plugins.ManagerModel
Adds given listener
addTreeModelListener(TreeModelListener) - Method in class cytoscape.util.swing.AbstractTreeTableModel
DOCUMENT ME!
addTunableValueListener(TunableListener) - Method in class cytoscape.layout.Tunable
Method to add a value listener to this Tunable.
addVersion(DownloadableInfo, Element, DownloadableType) - Method in class cytoscape.plugin.PluginFileReader
 
addViewportChangeListener(ViewportChangeListener) - Method in class ding.view.DGraphView
DOCUMENT ME!
addVisualStyle(VisualStyle) - Method in class cytoscape.visual.CalculatorCatalog
DOCUMENT ME!
adjust(float) - Method in enum cytoscape.visual.strokes.PipeStroke.Type
 
adjustColumnPreferredWidths(JTable) - Static method in class cytoscape.util.swing.ColumnResizer
DOCUMENT ME!
ALIAS - Static variable in class cytoscape.data.synonyms.Aliases
Name of the attribute for aliases
Aliases - Class in cytoscape.data.synonyms
Simpler version of Thesaurus.
Aliases(AliasType) - Constructor for class cytoscape.data.synonyms.Aliases
Constructor for the aliases object.
AliasType - Enum in cytoscape.data.synonyms
Type of Aliases.
AlignHorizontalAction - Class in cytoscape.actions
 
AlignHorizontalAction(CyNetworkView) - Constructor for class cytoscape.actions.AlignHorizontalAction
Creates a new AlignHorizontalAction object.
AlignVerticalAction - Class in cytoscape.actions
 
AlignVerticalAction(CyNetworkView) - Constructor for class cytoscape.actions.AlignVerticalAction
Creates a new AlignVerticalAction object.
ALL_ATTRIBUTES_FILTER - Static variable in class cytoscape.data.CyAttributesUtils
An AttributeFilter that produces all attributes--none are filtered out.
allAttributeValuesRemoved(String, String) - Method in interface cytoscape.data.attr.MultiHashMapListener
This listener method gets called as a result of MultiHashMap.removeAllAttributeValues(objectKey, attributeName), but only if objectKey has at least one attribute value bound in attributeName.
AllGraphPerspectiveMethodsTest - Class in fing.model.test
 
allInteractions - Variable in class cytoscape.data.readers.InteractionsReader
A Vector that holds all of the Interactions
allPoints - Variable in class cytoscape.visual.ui.editors.continuous.ContinuousMappingEditorPanel
 
AllRootGraphMethodsTest - Class in fing.model.test
 
almostEqual(float, float) - Static method in class cytoscape.util.MathUtil
 
almostEqual(double, double) - Static method in class cytoscape.util.MathUtil
 
AlphabeticalSelectionAction - Class in cytoscape.actions
 
AlphabeticalSelectionAction() - Constructor for class cytoscape.actions.AlphabeticalSelectionAction
Creates a new AlphabeticalSelectionAction object.
AlreadySelectedException - Exception in org.apache.commons.cli
Thrown when more than one option in an option group has been provided.
AlreadySelectedException(String) - Constructor for exception org.apache.commons.cli.AlreadySelectedException
Construct a new AlreadySelectedException with the specified detail message.
ANCHOR_CENTER - Static variable in class cytoscape.render.stateful.NodeDetails
Specifies that an anchor point lies at the center of a bounding box.
ANCHOR_EAST - Static variable in class cytoscape.render.stateful.NodeDetails
Specifies that an anchor point lies on the east edge of a bounding box, halfway between the north and south edges.
ANCHOR_NORTH - Static variable in class cytoscape.render.stateful.NodeDetails
Specifies that an anchor point lies on the north edge of a bounding box, halfway between the east and west edges.
ANCHOR_NORTHEAST - Static variable in class cytoscape.render.stateful.NodeDetails
Specifies that an anchor point lies on the northeast corner of a bounding box.
ANCHOR_NORTHWEST - Static variable in class cytoscape.render.stateful.NodeDetails
Specifies that an anchor point lies on the northwest corner of a bounding box.
ANCHOR_SOUTH - Static variable in class cytoscape.render.stateful.NodeDetails
Specifies that an anchor point lies on the south edge of a bounding box, halfway between the east and west edges.
ANCHOR_SOUTHEAST - Static variable in class cytoscape.render.stateful.NodeDetails
Specifies that an anchor point lies on the southeast corner of a bounding box.
ANCHOR_SOUTHWEST - Static variable in class cytoscape.render.stateful.NodeDetails
Specifies that an anchor point lies on the southwest corner of a bounding box.
ANCHOR_WEST - Static variable in class cytoscape.render.stateful.NodeDetails
Specifies that an anchor point lies on the west edge of a bounding box, halfway between the north and south edges.
anchorPaint(int, int) - Method in class cytoscape.render.stateful.EdgeDetails
Returns the paint to use when rendering an edge anchor.
anchors(int) - Method in class cytoscape.render.stateful.EdgeDetails
Returns edge anchors to use when rendering this edge.
anchorSize(int, int) - Method in class cytoscape.render.stateful.EdgeDetails
For edges with anchors, the anchors can be rendered as squares.
And - Class in org.cytoscape.equations.builtins
 
And() - Constructor for class org.cytoscape.equations.builtins.And
 
AnimatedLayoutAction - Class in cytoscape.actions
Deprecated. Not apparently used. Shout if you are. Will be removed 5/2008.
AnimatedLayoutAction(CyNetworkView) - Constructor for class cytoscape.actions.AnimatedLayoutAction
Deprecated. Creates a new AnimatedLayoutAction object.
Annotation - Class in cytoscape.data.annotation
Deprecated. Use regular CyAttributes for annotation.
Annotation(String, String, Ontology) - Constructor for class cytoscape.data.annotation.Annotation
Deprecated. Creates a new Annotation object.
Annotation(String, String, String) - Constructor for class cytoscape.data.annotation.Annotation
Deprecated. Creates a new Annotation object.
AnnotationDescription - Class in cytoscape.data.annotation
Deprecated. Use regular CyAttributes for annotation.
AnnotationDescription(String, String, String) - Constructor for class cytoscape.data.annotation.AnnotationDescription
Deprecated.  
AnnotationFlatFileReader - Class in cytoscape.data.annotation.readers
 
AnnotationFlatFileReader(File) - Constructor for class cytoscape.data.annotation.readers.AnnotationFlatFileReader
Creates a new AnnotationFlatFileReader object.
AnnotationFlatFileReader(BufferedReader, Thesaurus, boolean) - Constructor for class cytoscape.data.annotation.readers.AnnotationFlatFileReader
Creates a new AnnotationFlatFileReader object.
AnnotationFlatFileReader(String, Thesaurus) - Constructor for class cytoscape.data.annotation.readers.AnnotationFlatFileReader
Creates a new AnnotationFlatFileReader object.
annotations - Variable in class cytoscape.data.servers.BioDataServerRmi
 
annotationType - Variable in class cytoscape.data.annotation.AnnotationDescription
Deprecated.  
AnnotationXmlReader - Class in cytoscape.data.annotation.readers
 
AnnotationXmlReader(File) - Constructor for class cytoscape.data.annotation.readers.AnnotationXmlReader
Creates a new AnnotationXmlReader object.
Appearance - Class in cytoscape.visual
A class that holds the appearance information for NodeViews and EdgeViews.
Appearance() - Constructor for class cytoscape.visual.Appearance
Creates a new Appearance object.
appendNetwork(CyNetwork) - Method in interface cytoscape.CyNetwork
Appends all of the nodes and edges in the given Network to this Network
appendNetwork(CyNetwork) - Method in class cytoscape.giny.FingCyNetwork
Appends all of the nodes and edges in teh given Network to this Network
applies(LogLevel) - Method in enum cytoscape.logger.LogLevel
 
apply(Appearance, Edge, CyNetwork) - Method in class cytoscape.visual.calculators.AbstractCalculator
DOCUMENT ME!
apply(Appearance, Node, CyNetwork) - Method in class cytoscape.visual.calculators.AbstractCalculator
DOCUMENT ME!
apply(Appearance, Edge, CyNetwork) - Method in interface cytoscape.visual.calculators.Calculator
DOCUMENT ME!
apply(Appearance, Node, CyNetwork) - Method in interface cytoscape.visual.calculators.Calculator
DOCUMENT ME!
apply(Object, VisualPropertyType) - Static method in class cytoscape.visual.ui.VizMapperMainPanel
 
applyAppearance(NodeView, VisualPropertyDependency) - Method in class cytoscape.visual.Appearance
Applies this appearance to the specified NodeView.
applyAppearance(EdgeView, VisualPropertyDependency) - Method in class cytoscape.visual.Appearance
Applies this appearance to the specified EdgeView.
applyAppearances() - Method in class cytoscape.visual.VisualMappingManager
Recalculates and reapplies all of the node, edge, and global visual attributes.
applyBypass(GraphObject, List<VisualPropertyType>) - Method in class cytoscape.visual.Appearance
Applies the visual bypass values specified in the node (edge) attributes for the specified node (edge) to the node (edge).
applyDefaultProperties(Properties, String) - Method in class cytoscape.visual.Appearance
Applies the specified properties as default values for this appearance.
applyDefaultProperties(Properties, String) - Method in interface cytoscape.visual.VisualPropertyDependency
Will search the specified Properties using the specified basedKey for each dependency definition and will update this object according to any properties found.
applyEdgeAppearances() - Method in class cytoscape.visual.VisualMappingManager
Recalculates and reapplies all of the edge appearances.
applyEdgeAppearances(CyNetwork, CyNetworkView) - Method in class cytoscape.visual.VisualMappingManager
Recalculates and reapplies all of the edge appearances.
applyGlobalAppearances() - Method in class cytoscape.visual.VisualMappingManager
Recalculates and reapplies the global visual attributes.
applyGlobalAppearances(CyNetwork, CyNetworkView) - Method in class cytoscape.visual.VisualMappingManager
Recalculates and reapplies the global visual attributes.
applyLayout(CyLayoutAlgorithm) - Method in class cytoscape.ding.DingNetworkView
DOCUMENT ME!
applyLayout(CyLayoutAlgorithm, CyNode[], CyEdge[]) - Method in class cytoscape.ding.DingNetworkView
DOCUMENT ME!
applyLayout(CyLayoutAlgorithm, CyNodeView[], CyEdgeView[]) - Method in class cytoscape.ding.DingNetworkView
DOCUMENT ME!
applyLayout(CyLayoutAlgorithm, int[], int[]) - Method in class cytoscape.ding.DingNetworkView
DOCUMENT ME!
applyLayout(CyLayoutAlgorithm) - Method in interface cytoscape.view.CyNetworkView
Applies the given layout to the entire CyNetworkView
applyLayout(CyLayoutAlgorithm, CyNode[], CyEdge[]) - Method in interface cytoscape.view.CyNetworkView
Applies the given layout to only the given Nodes and Edges.
applyLayout(CyLayoutAlgorithm, CyNodeView[], CyEdgeView[]) - Method in interface cytoscape.view.CyNetworkView
Applies the given layout to only the given NodeViews and EdgeViews.
applyLayout(CyLayoutAlgorithm, int[], int[]) - Method in interface cytoscape.view.CyNetworkView
Applies the given layout to only the given Nodes and Edges.
ApplyLayoutAction - Class in cytoscape.actions
 
ApplyLayoutAction() - Constructor for class cytoscape.actions.ApplyLayoutAction
 
applyLockedLayout(CyLayoutAlgorithm, CyNode[], CyEdge[]) - Method in class cytoscape.ding.DingNetworkView
DOCUMENT ME!
applyLockedLayout(CyLayoutAlgorithm, CyNodeView[], CyEdgeView[]) - Method in class cytoscape.ding.DingNetworkView
DOCUMENT ME!
applyLockedLayout(CyLayoutAlgorithm, int[], int[]) - Method in class cytoscape.ding.DingNetworkView
DOCUMENT ME!
applyLockedLayout(CyLayoutAlgorithm, CyNode[], CyEdge[]) - Method in interface cytoscape.view.CyNetworkView
Applies the given layout to the entire CyNetworkView, but locks the given Nodes and Edges in place.
applyLockedLayout(CyLayoutAlgorithm, CyNodeView[], CyEdgeView[]) - Method in interface cytoscape.view.CyNetworkView
Applies the given layout to the entire CyNetworkView, but locks the given NodeViews and EdgeViews in place.
applyLockedLayout(CyLayoutAlgorithm, int[], int[]) - Method in interface cytoscape.view.CyNetworkView
Applies the given layout to the entire CyNetworkView, but locks the given Nodes and Edges in place.
applyNamingServices(CyNetwork) - Static method in class cytoscape.data.Semantics
Deprecated. 
applyNodeAppearances() - Method in class cytoscape.visual.VisualMappingManager
Recalculates and reapplies all of the node appearances.
applyNodeAppearances(CyNetwork, CyNetworkView) - Method in class cytoscape.visual.VisualMappingManager
Recalculates and reapplies all of the node appearances.
applyProperties(String, Properties, String, CalculatorCatalog) - Method in class cytoscape.visual.EdgeAppearanceCalculator
DOCUMENT ME!
applyProperties(String, Properties, String, CalculatorCatalog) - Method in class cytoscape.visual.GlobalAppearanceCalculator
This method customizes this object by searching the supplied properties object for keys identifying default values and calculators.
applyProperties(Properties, String, ValueParser) - Method in class cytoscape.visual.mappings.AbstractMapping
 
applyProperties(Properties, String, ValueParser) - Method in class cytoscape.visual.mappings.ContinuousMapping
Customizes this object by applying mapping defintions described by the supplied Properties argument.
applyProperties(Properties, String, ValueParser) - Method in class cytoscape.visual.mappings.DiscreteMapping
Customizes this object by applying mapping defintions described by the supplied Properties argument.
applyProperties(Properties, String, ValueParser) - Method in interface cytoscape.visual.mappings.ObjectMapping
 
applyProperties(Properties, String, ValueParser) - Method in class cytoscape.visual.mappings.PassThroughMapping
Customize this object by applying mapping defintions described by the supplied Properties argument.
applyProperties(String, Properties, String, CalculatorCatalog) - Method in class cytoscape.visual.NodeAppearanceCalculator
DOCUMENT ME!
applyToEdgeView(EdgeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.AbstractVisualProperty
DOCUMENT ME!
applyToEdgeView(EdgeView, Object) - Method in class cytoscape.visual.properties.AbstractVisualProperty
 
applyToEdgeView(EdgeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.EdgeColorProp
DOCUMENT ME!
applyToEdgeView(EdgeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.EdgeFontFaceProp
DOCUMENT ME!
applyToEdgeView(EdgeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.EdgeFontSizeProp
DOCUMENT ME!
applyToEdgeView(EdgeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.EdgeLabelColorProp
DOCUMENT ME!
applyToEdgeView(EdgeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.EdgeLabelOpacityProp
DOCUMENT ME!
applyToEdgeView(EdgeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.EdgeLabelProp
DOCUMENT ME!
applyToEdgeView(EdgeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.EdgeLabelWidthProp
DOCUMENT ME!
applyToEdgeView(EdgeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.EdgeLineStyleProp
DOCUMENT ME!
applyToEdgeView(EdgeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.EdgeLineWidthProp
DOCUMENT ME!
applyToEdgeView(EdgeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.EdgeOpacityProp
DOCUMENT ME!
applyToEdgeView(EdgeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.EdgeSourceArrowColorProp
DOCUMENT ME!
applyToEdgeView(EdgeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.EdgeSourceArrowOpacityProp
DOCUMENT ME!
applyToEdgeView(EdgeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.EdgeSourceArrowShapeProp
DOCUMENT ME!
applyToEdgeView(EdgeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.EdgeTargetArrowColorProp
DOCUMENT ME!
applyToEdgeView(EdgeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.EdgeTargetArrowOpacityProp
DOCUMENT ME!
applyToEdgeView(EdgeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.EdgeTargetArrowShapeProp
DOCUMENT ME!
applyToEdgeView(EdgeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.EdgeToolTipProp
 
applyToEdgeView(EdgeView, Object) - Method in interface cytoscape.visual.VisualProperty
Deprecated. Use other the applyToNodeView method with the VisualPropertyDependency arg as null. Will be removed Jan 2011.
applyToEdgeView(EdgeView, Object, VisualPropertyDependency) - Method in interface cytoscape.visual.VisualProperty
 
applyToNodeView(NodeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.AbstractVisualProperty
DOCUMENT ME!
applyToNodeView(NodeView, Object) - Method in class cytoscape.visual.properties.AbstractVisualProperty
 
applyToNodeView(NodeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.NodeBorderColorProp
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applyToNodeView(NodeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.NodeBorderOpacityProp
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applyToNodeView(NodeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.NodeCustomGraphicsPositionProp
Apply Object Position to DNodeView's Custom Graphics.
applyToNodeView(NodeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.NodeCustomGraphicsProp
Apply current Custom Graphics to a node view.
applyToNodeView(NodeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.NodeFillColorProp
DOCUMENT ME!
applyToNodeView(NodeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.NodeFontFaceProp
DOCUMENT ME!
applyToNodeView(NodeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.NodeFontSizeProp
DOCUMENT ME!
applyToNodeView(NodeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.NodeHeightProp
DOCUMENT ME!
applyToNodeView(NodeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.NodeLabelColorProp
DOCUMENT ME!
applyToNodeView(NodeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.NodeLabelOpacityProp
DOCUMENT ME!
applyToNodeView(NodeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.NodeLabelPositionProp
DOCUMENT ME!
applyToNodeView(NodeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.NodeLabelProp
DOCUMENT ME!
applyToNodeView(NodeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.NodeLabelWidthProp
DOCUMENT ME!
applyToNodeView(NodeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.NodeLineStyleProp
DOCUMENT ME!
applyToNodeView(NodeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.NodeLineWidthProp
DOCUMENT ME!
applyToNodeView(NodeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.NodeOpacityProp
DOCUMENT ME!
applyToNodeView(NodeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.NodeShapeProp
DOCUMENT ME!
applyToNodeView(NodeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.NodeShowNestedNetworkProp
DOCUMENT ME!
applyToNodeView(NodeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.NodeSizeProp
DOCUMENT ME!
applyToNodeView(NodeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.NodeToolTipProp
DOCUMENT ME!
applyToNodeView(NodeView, Object, VisualPropertyDependency) - Method in class cytoscape.visual.properties.NodeWidthProp
DOCUMENT ME!
applyToNodeView(NodeView, Object) - Method in interface cytoscape.visual.VisualProperty
Deprecated. Use other the applyToNodeView method with the VisualPropertyDependency arg as null. Will be removed Jan 2011.
applyToNodeView(NodeView, Object, VisualPropertyDependency) - Method in interface cytoscape.visual.VisualProperty
 
ApplyVisualStyleAction - Class in cytoscape.actions
Apply Visual Style for a set of selected networks.
ApplyVisualStyleAction(String) - Constructor for class cytoscape.actions.ApplyVisualStyleAction
Create an action for the specified Visual Style.
applyVizMap(CyEdge) - Method in class cytoscape.ding.DingNetworkView
DOCUMENT ME!
applyVizMap(EdgeView) - Method in class cytoscape.ding.DingNetworkView
DOCUMENT ME!
applyVizMap(CyNode) - Method in class cytoscape.ding.DingNetworkView
DOCUMENT ME!
applyVizMap(NodeView) - Method in class cytoscape.ding.DingNetworkView
DOCUMENT ME!
applyVizMap(CyEdge, VisualStyle) - Method in class cytoscape.ding.DingNetworkView
DOCUMENT ME!
applyVizMap(EdgeView, VisualStyle) - Method in class cytoscape.ding.DingNetworkView
DOCUMENT ME!
applyVizMap(CyNode, VisualStyle) - Method in class cytoscape.ding.DingNetworkView
DOCUMENT ME!
applyVizMap(NodeView, VisualStyle) - Method in class cytoscape.ding.DingNetworkView
DOCUMENT ME!
applyVizMap(CyEdge) - Method in interface cytoscape.view.CyNetworkView
Applies the given edge to the given vizmapper
applyVizMap(EdgeView) - Method in interface cytoscape.view.CyNetworkView
Applies the given edge to the given vizmapper
applyVizMap(CyNode) - Method in interface cytoscape.view.CyNetworkView
Applies the given node to the given vizmapper
applyVizMap(NodeView) - Method in interface cytoscape.view.CyNetworkView
Applies the given node to the given vizmapper
applyVizMap(CyEdge, VisualStyle) - Method in interface cytoscape.view.CyNetworkView
Applies the given edge to the given vizmapper
applyVizMap(EdgeView, VisualStyle) - Method in interface cytoscape.view.CyNetworkView
Applies the given edge to the given vizmapper
applyVizMap(CyNode, VisualStyle) - Method in interface cytoscape.view.CyNetworkView
Applies the given node to the given vizmapper
applyVizMap(NodeView, VisualStyle) - Method in interface cytoscape.view.CyNetworkView
Applies the given node to the given vizmapper
applyVizmapper(VisualStyle) - Method in class cytoscape.ding.DingNetworkView
DOCUMENT ME!
applyVizmapper(VisualStyle) - Method in interface cytoscape.view.CyNetworkView
 
ArbitraryGraphicsCanvas - Class in ding.view
This class extends cytoscape.view.CytoscapeCanvas.
ArbitraryGraphicsCanvas(GraphPerspective, DGraphView, InnerCanvas, Color, boolean, boolean) - Constructor for class ding.view.ArbitraryGraphicsCanvas
Constructor.
areSynonyms(String, String, CyNetwork) - Static method in class cytoscape.data.Semantics
Deprecated. 
ArgDescriptor - Class in org.cytoscape.equations
A class describing a function argument.
ArgDescriptor(ArgType, String, String) - Constructor for class org.cytoscape.equations.ArgDescriptor
 
args - Variable in class cytoscape.CyMain
 
ArgType - Enum in org.cytoscape.equations
An enum specifying a function argument type.
argTypesAreValid(Class[]) - Method in class org.cytoscape.equations.AbstractFunction
 
ARGUMENT_DISALLOWED - Static variable in class org.apache.commons.cli.avalon.CLOptionDescriptor
Flag to say this option does not take arguments
ARGUMENT_OPTIONAL - Static variable in class org.apache.commons.cli.avalon.CLOptionDescriptor
Flag to say that the argument is optional
ARGUMENT_REQUIRED - Static variable in class org.apache.commons.cli.avalon.CLOptionDescriptor
Flag to say that one argument is required
argumentMap - Variable in class cytoscape.command.AbstractCommandHandler
 
ARGUMENTS_REQUIRED_2 - Static variable in class org.apache.commons.cli.avalon.CLOptionDescriptor
Flag to say this option requires 2 arguments
ARowanBugTest - Class in fing.model.test
 
ARowanBugTest() - Constructor for class fing.model.test.ARowanBugTest
 
ArrangeAction - Class in cytoscape.actions
 
ArrangeAction() - Constructor for class cytoscape.actions.ArrangeAction
 
arrangeFrames(CyDesktopManager.Arrange) - Static method in class cytoscape.view.CyDesktopManager
 
ArrayIntEnumerator - Class in cytoscape.util.intr
A utility class which conveniently converts an array of integers into an IntEnumerator (an enumeration of integers).
ArrayIntEnumerator(int[], int, int) - Constructor for class cytoscape.util.intr.ArrayIntEnumerator
No copy of the elements array is made.
ArrayIntIterator - Class in cytoscape.util.intr
A utility class which conveniently converts an array of integers into an IntIterator (an iteration of integers).
ArrayIntIterator(int[], int, int) - Constructor for class cytoscape.util.intr.ArrayIntIterator
No copy of the elements array is made.
ArrayTestMethod1 - Class in cytoscape.geom.rtree.test
 
ArrayTestMethod1() - Constructor for class cytoscape.geom.rtree.test.ArrayTestMethod1
 
ArrayTestMethod2 - Class in cytoscape.geom.rtree.test
 
ArrayTestMethod2() - Constructor for class cytoscape.geom.rtree.test.ArrayTestMethod2
 
ArrayTestMethod3 - Class in cytoscape.geom.rtree.test
 
ArrayTestMethod3() - Constructor for class cytoscape.geom.rtree.test.ArrayTestMethod3
 
ArrayTestMethod4 - Class in cytoscape.geom.rtree.test
 
ArrayTestMethod4() - Constructor for class cytoscape.geom.rtree.test.ArrayTestMethod4
 
ARROW - Static variable in class cytoscape.data.readers.GMLReader
 
Arrow - Interface in cytoscape.render.immed.arrow
 
Arrow - Class in cytoscape.visual
This class is a replacement for the yFiles Arrow class.
Arrow(ArrowShape, Color) - Constructor for class cytoscape.visual.Arrow
New constructor for 2.5 and later:
ARROW - Static variable in class cytoscape.visual.Arrow
DOCUMENT ME!
ARROW_ARROWHEAD - Static variable in class cytoscape.render.immed.GraphGraphics
 
ARROW_BOTH - Static variable in class cytoscape.data.readers.GMLReader
 
ARROW_DELTA - Static variable in class cytoscape.render.immed.GraphGraphics
 
ARROW_DIAMOND - Static variable in class cytoscape.render.immed.GraphGraphics
 
ARROW_DISC - Static variable in class cytoscape.render.immed.GraphGraphics
 
ARROW_FIRST - Static variable in class cytoscape.data.readers.GMLReader
 
ARROW_HALF_BOTTOM - Static variable in class cytoscape.render.immed.GraphGraphics
 
ARROW_HALF_TOP - Static variable in class cytoscape.render.immed.GraphGraphics
 
ARROW_LAST - Static variable in class cytoscape.data.readers.GMLReader
 
ARROW_NONE - Static variable in class cytoscape.data.readers.GMLReader
 
ARROW_NONE - Static variable in class cytoscape.render.immed.GraphGraphics
 
ARROW_TEE - Static variable in class cytoscape.render.immed.GraphGraphics
 
ArrowheadArrow - Class in cytoscape.render.immed.arrow
 
ArrowheadArrow() - Constructor for class cytoscape.render.immed.arrow.ArrowheadArrow
 
ArrowIcon - Class in cytoscape.visual.ui.icon
Icon for arrow shape.
ArrowIcon(ArrowShape, int) - Constructor for class cytoscape.visual.ui.icon.ArrowIcon
Creates a new ArrowIcon object.
ArrowIcon(ArrowShape) - Constructor for class cytoscape.visual.ui.icon.ArrowIcon
Creates a new ArrowIcon object.
ArrowParser - Class in cytoscape.visual.parsers
Parses a String into a yFiles Arrow object.
ArrowParser() - Constructor for class cytoscape.visual.parsers.ArrowParser
 
ArrowShape - Enum in cytoscape.visual
Defines arrow shapes.
This replaces constants defined in Arrow.java.
ArrowShapeParser - Class in cytoscape.visual.parsers
 
ArrowShapeParser() - Constructor for class cytoscape.visual.parsers.ArrowShapeParser
 
ASin - Class in org.cytoscape.equations.builtins
 
ASin() - Constructor for class org.cytoscape.equations.builtins.ASin
 
assignCommonNames(CyNetwork, BioDataServer) - Static method in class cytoscape.data.Semantics
Deprecated. 
assignFile(File) - Method in class cytoscape.dialogs.ExportAsGraphicsFileChooser
 
assignNodeAliases(CyNode, String, BioDataServer) - Static method in class cytoscape.data.Semantics
Deprecated. 
assignSpecies(CyNetwork) - Static method in class cytoscape.data.Semantics
Deprecated. 
asString() - Method in enum org.cytoscape.equations.Token
 
ATan2 - Class in org.cytoscape.equations.builtins
 
ATan2() - Constructor for class org.cytoscape.equations.builtins.ATan2
 
attribNameAsReference(String) - Static method in class org.cytoscape.equations.EquationUtil
 
AttribTopoGraphNode - Class in cytoscape.data
Represents a node in a topological graph.
AttribTopoGraphNode(String, Collection<String>) - Constructor for class cytoscape.data.AttribTopoGraphNode
 
Attribute - Class in cytoscape.bookmarks
Java class for anonymous complex type.
Attribute() - Constructor for class cytoscape.bookmarks.Attribute
 
attribute - Variable in class cytoscape.bookmarks.DataSource
 
ATTRIBUTE_ALREADY_ASSIGNED - Static variable in class cytoscape.data.NetworkData
 
attributeComboBox - Variable in class cytoscape.util.swing.AttributeImportPanel
 
attributeDefined(String) - Method in interface cytoscape.data.attr.MultiHashMapDefinitionListener
This method is called by a MultiHashMapDefinition implementation as a result of a new attribute being defined (MultiHashMapDefinition.defineAttribute()).
attributeDefined(String) - Method in class cytoscape.util.swing.AttributeImportPanel
 
attributeDefined(String) - Method in class cytoscape.visual.ui.VizMapperMainPanel
 
AttributeFilter - Interface in cytoscape.data
Interface for defining CyEdge-based filters used for determining which Edges should be used for a particular operation, such as CyAttributesUtils.copyAttributes().
AttributeImportPanel - Class in cytoscape.util.swing
General GUI component for importing attributes.
Maybe used by Web Service Clients to import attributes.
AttributeImportPanel() - Constructor for class cytoscape.util.swing.AttributeImportPanel
 
AttributeImportPanel(Icon, String, String) - Constructor for class cytoscape.util.swing.AttributeImportPanel
 
AttributeImportQuery - Class in cytoscape.data.webservice
 
AttributeImportQuery(Object, String, String) - Constructor for class cytoscape.data.webservice.AttributeImportQuery
 
attributeLabel - Variable in class cytoscape.util.swing.AttributeImportPanel
 
attributePanel - Variable in class cytoscape.util.swing.AttributeImportPanel
 
attributePanelTitle - Variable in class cytoscape.util.swing.AttributeImportPanel
 
ATTRIBUTES_CHANGED - Static variable in class cytoscape.Cytoscape
This signals when new attributes have been loaded and a few other large scale changes to attributes have been made.
AttributeSaverDialog - Class in cytoscape.data
Dialog box to save various attributes.
AttributeSaverDialog(int) - Constructor for class cytoscape.data.AttributeSaverDialog
Create a dialog box of the specified type.
attributeTypeComboBox - Variable in class cytoscape.util.swing.AttributeImportPanel
 
attributeTypeLabel - Variable in class cytoscape.util.swing.AttributeImportPanel
 
attributeUndefined(String) - Method in interface cytoscape.data.attr.MultiHashMapDefinitionListener
This method is called by a MultiHashMapDefinition implementation as a result of an attribute being undefined (MultiHashMapDefinition.undefineAttribute()).
attributeUndefined(String) - Method in class cytoscape.util.swing.AttributeImportPanel
 
attributeUndefined(String) - Method in class cytoscape.visual.ui.VizMapperMainPanel
 
attributeValueAssigned(String, String, Object[], Object, Object) - Method in interface cytoscape.data.attr.MultiHashMapListener
 
attributeValueRemoved(String, String, Object[], Object) - Method in interface cytoscape.data.attr.MultiHashMapListener
This listener method gets called as a result of MultiHashMap.removeAttributeValue(objectKey, attributeName, keyIntoValue), but only if an attribute value was found [and removed] for specified key.
AttributeValueVisitor - Interface in cytoscape.data
Interface for defining attribute value visitors--operations to perform on each attribute value using CyAttributesUtils.traverseAttributeValues().
attrList - Variable in class cytoscape.util.swing.AttributeImportPanel
 
attrListPanel - Variable in class cytoscape.util.swing.AttributeImportPanel
 
AVAILABLE_FOR_INSTALL - Static variable in class cytoscape.dialogs.plugins.PluginManageDialog
 
availableAttrPanel - Variable in class cytoscape.util.swing.AttributeImportPanel
 
availableAttrScrollPane - Variable in class cytoscape.util.swing.AttributeImportPanel
 
availableMethods - Variable in class cytoscape.data.webservice.WebServiceClientImpl
 
Average - Class in org.cytoscape.equations.builtins
 
Average() - Constructor for class org.cytoscape.equations.builtins.Average
 

B

BACKGROUND - Static variable in class cytoscape.data.writers.XGMMLWriter
 
BackgroundColorAction - Class in cytoscape.actions
Deprecated. Use vizmapper gui to edit background color. Will be removed 5/2008
BackgroundColorAction() - Constructor for class cytoscape.actions.BackgroundColorAction
Deprecated. Constructor.
BackwardSlashStroke - Class in cytoscape.visual.strokes
 
BackwardSlashStroke(float, PipeStroke.Type) - Constructor for class cytoscape.visual.strokes.BackwardSlashStroke
 
BasicCalculator - Class in cytoscape.visual.calculators
BasicCalculator implements some UI features for calculators lower in the object tree.
BasicCalculator(String, ObjectMapping, VisualPropertyType) - Constructor for class cytoscape.visual.calculators.BasicCalculator
Creates a new BasicCalculator object.
BasicCalculator(String, Properties, String, VisualPropertyType) - Constructor for class cytoscape.visual.calculators.BasicCalculator
Creates a new BasicCalculator object.
BasicGraphViewHandler - Class in cytoscape.view
A basic GraphViewHandler that simply reflects GraphPerspective changes on a given GraphView
BasicGraphViewHandler() - Constructor for class cytoscape.view.BasicGraphViewHandler
Constructor
basicHtmlOutput() - Method in class cytoscape.plugin.DownloadableInfo
 
BasicParser - Class in org.apache.commons.cli
The class BasicParser provides a very simple implementation of the flatten method.
BasicParser() - Constructor for class org.apache.commons.cli.BasicParser
 
BasicQuietRTreeTest - Class in cytoscape.geom.rtree.test
 
BasicQuietRTreeTest() - Constructor for class cytoscape.geom.rtree.test.BasicQuietRTreeTest
 
BEGIN - Static variable in class cytoscape.CyNetworkEvent
Indicates that someone is beginning to work with the network.
below - Variable in class cytoscape.visual.ui.editors.continuous.ContinuousMappingEditorPanel
 
BELOW_VALUE_CHANGED - Static variable in class cytoscape.visual.ui.editors.continuous.ContinuousMappingEditorPanel
 
BelowAndAbovePanel - Class in cytoscape.visual.ui.editors.continuous
Drawing and updating below & above values in Gradient Editor.
BelowAndAbovePanel(VisualPropertyType, Color, boolean) - Constructor for class cytoscape.visual.ui.editors.continuous.BelowAndAbovePanel
Creates a new BelowAndAbovePanel object.
BelowAndAbovePanel(VisualPropertyType, boolean) - Constructor for class cytoscape.visual.ui.editors.continuous.BelowAndAbovePanel
Creates a new BelowAndAbovePanel object.
belowPanel - Variable in class cytoscape.visual.ui.editors.continuous.ContinuousMappingEditorPanel
 
Bend - Interface in giny.view
A class that encapsulates the representation of the bend used for a particular EdgeView.
BendSelectedEdgesAction - Class in cytoscape.actions
 
BendSelectedEdgesAction() - Constructor for class cytoscape.actions.BendSelectedEdgesAction
Creates a new BendSelectedEdgesAction object.
BiModalJSplitPane - Class in cytoscape.view.cytopanels
The BiModalJSplitPane class extends JSplitPane to provide two modes: MODE_SHOW_SPLIT: The split in the split pane appears as it normally would, and the user can resize the split pane as needed.
BiModalJSplitPane(JFrame, int, int, Component, Component) - Constructor for class cytoscape.view.cytopanels.BiModalJSplitPane
Constructor.
BinOpNode - Class in org.cytoscape.equations.parse_tree
A node in the parse tree representing a binary operator.
BinOpNode(int, Token, Node, Node) - Constructor for class org.cytoscape.equations.parse_tree.BinOpNode
 
BioDataServer - Class in cytoscape.data.servers
 
BioDataServer(String) - Constructor for class cytoscape.data.servers.BioDataServer
serverName is either an RMI URI, or a manifest file which says what files to load into an in-process server; the manifest, the annotations, and the ontologies, may be files on a filesystem, files in a jar, or files retrieved by HTTP Mod.
BioDataServer() - Constructor for class cytoscape.data.servers.BioDataServer
Creates a new BioDataServer object.
BioDataServerInterface - Interface in cytoscape.data.servers
 
BioDataServerRmi - Class in cytoscape.data.servers
This is the actual class which implements BioDataServer Methods.
BioDataServerRmi() - Constructor for class cytoscape.data.servers.BioDataServerRmi
Creates a new BioDataServerRmi object.
BioDataServerUtil - Class in cytoscape.util
 
BioDataServerUtil() - Constructor for class cytoscape.util.BioDataServerUtil
 
BIOLOGICAL_PROCESS - Static variable in class cytoscape.data.Semantics
Deprecated. 
BiologicalProcessAnnotationReader - Class in cytoscape.cruft.obo
The purpose of this class is to convert a 'gene_association.*' file (for example 'gene_association.sgd') into a crufty old 'bioproc.anno' file that Cytoscape's BioDataServer understands.
BiologicalProcessAnnotationReader(String, Reader) - Constructor for class cytoscape.cruft.obo.BiologicalProcessAnnotationReader
Creates a new BiologicalProcessAnnotationReader object.
BiologicalProcessAnnotationReader(String, Map, Reader) - Constructor for class cytoscape.cruft.obo.BiologicalProcessAnnotationReader
Creates a new BiologicalProcessAnnotationReader object.
BiologicalProcessAnnotationTester - Class in cytoscape.cruft.obo.test
 
BiologicalProcessAnnotationTester() - Constructor for class cytoscape.cruft.obo.test.BiologicalProcessAnnotationTester
 
BirdsEyeView - Class in ding.view
DOCUMENT ME!
BirdsEyeView(DGraphView) - Constructor for class ding.view.BirdsEyeView
Creates a new BirdsEyeView object.
BirdsEyeView(DGraphView, Component) - Constructor for class ding.view.BirdsEyeView
Creates a new BirdsEyeView object.
BirdsEyeViewAction - Class in cytoscape.actions
Deprecated. This class is no longer used since the BirdsEyeView is now always part of the NetworkPanel. BirdsEyeView creation and event handling is done by the BirdsEyeViewHandler and initialized in CytoscapeDesktop This class will be removed 5/2008.
BirdsEyeViewAction() - Constructor for class cytoscape.actions.BirdsEyeViewAction
Deprecated. Creates a new BirdsEyeViewAction object.
BitmapExporter - Class in cytoscape.util.export
Bitmap exporter by the ImageIO class.
BitmapExporter(String, double) - Constructor for class cytoscape.util.export.BitmapExporter
 
BitSetPerformance - Class in cytoscape.util.intr.test
 
BitSetPerformance() - Constructor for class cytoscape.util.intr.test.BitSetPerformance
 
BLACK_ARROW - Static variable in interface giny.view.EdgeView
 
BLACK_CIRCLE - Static variable in interface giny.view.EdgeView
 
BLACK_DELTA - Static variable in interface giny.view.EdgeView
 
BLACK_DIAMOND - Static variable in interface giny.view.EdgeView
 
BLACK_T - Static variable in interface giny.view.EdgeView
 
BList - Class in org.cytoscape.equations.builtins
 
BList() - Constructor for class org.cytoscape.equations.builtins.BList
 
BOOKMARK_PACKAGE_NAME - Static variable in class cytoscape.data.readers.CytoscapeSessionReader
 
BookmarkAction - Class in cytoscape.actions
 
BookmarkAction() - Constructor for class cytoscape.actions.BookmarkAction
Creates a new BookmarkAction object.
BookmarkDialog - Class in cytoscape.dialogs.preferences
 
BookmarkDialog(JFrame) - Constructor for class cytoscape.dialogs.preferences.BookmarkDialog
Creates new BookmarkDialog
BookmarkDialog(JFrame, String) - Constructor for class cytoscape.dialogs.preferences.BookmarkDialog
Creates new BookmarkDialog, set the selection on the given category
BookmarkDialog() - Constructor for class cytoscape.dialogs.preferences.BookmarkDialog
Creates a new BookmarkDialog object.
BookmarkReader - Class in cytoscape.data.readers
 
BookmarkReader() - Constructor for class cytoscape.data.readers.BookmarkReader
Creates a new BookmarkReader object.
Bookmarks - Class in cytoscape.bookmarks
Java class for anonymous complex type.
Bookmarks() - Constructor for class cytoscape.bookmarks.Bookmarks
 
BookmarksUtil - Class in cytoscape.util
Utility methods for getting entries in the bookmark object.
BookmarksUtil() - Constructor for class cytoscape.util.BookmarksUtil
 
BOOLEAN - Static variable in class cytoscape.layout.Tunable
Tunables of type BOOLEAN allow data entry of a boolean value: this is presented to the user as a simple check box.
BooleanConstantNode - Class in org.cytoscape.equations.parse_tree
A node in the parse tree representing an integer constant.
BooleanConstantNode(int, boolean) - Constructor for class org.cytoscape.equations.parse_tree.BooleanConstantNode
 
BooleanList - Class in org.cytoscape.equations
 
BooleanList(boolean[]) - Constructor for class org.cytoscape.equations.BooleanList
 
BooleanParser - Class in cytoscape.visual.parsers
Parses a String into a Boolean object.
BooleanParser() - Constructor for class cytoscape.visual.parsers.BooleanParser
 
BORDER_COLOR - Static variable in interface cytoscape.visual.ui.editors.continuous.VizMapperTrackRenderer
 
borderPaint(int) - Method in class cytoscape.render.stateful.NodeDetails
Returns the paint of the border of the node shape.
borderWidth(int) - Method in class cytoscape.render.stateful.NodeDetails
Returns the border width of the node shape.
bottomPad - Variable in class cytoscape.visual.ui.icon.VisualPropertyIcon
 
bound - Variable in class cytoscape.visual.customgraphic.impl.vector.GradientLayerCustomGraphics
 
BoundaryRangeValues - Class in cytoscape.visual.mappings
This class defines a data object representing the range values associated with a particular domain value, called a boundary value.
BoundaryRangeValues(Object, Object, Object) - Constructor for class cytoscape.visual.mappings.BoundaryRangeValues
Creates a new BoundaryRangeValues object.
BoundaryRangeValues(BoundaryRangeValues) - Constructor for class cytoscape.visual.mappings.BoundaryRangeValues
Creates a new BoundaryRangeValues object.
BoundaryRangeValues() - Constructor for class cytoscape.visual.mappings.BoundaryRangeValues
 
BOX - Static variable in class cytoscape.data.readers.XGMMLReader
 
Bug646Test - Class in fing.model.test
 
Bug646Test() - Constructor for class fing.model.test.Bug646Test
 
BUGFIX - Static variable in class cytoscape.plugin.PluginVersionUtils
 
buildOntologyServer() - Static method in class cytoscape.Cytoscape
This will replace the bioDataServer.
buildStyle() - Method in class cytoscape.data.readers.VisualStyleBuilder
Actually build the style using the provided properties
burstToken(String, boolean) - Method in class org.apache.commons.cli.PosixParser
Breaks token into its constituent parts using the following algorithm.
BUTTON - Static variable in class cytoscape.layout.Tunable
The BUTTON Tunable provides a simple button to be presented to the user: the caller can provide an ActionListener to be called when the button is selected.

C

c1 - Variable in class cytoscape.visual.customgraphic.impl.vector.GradientLayerCustomGraphics
 
c2 - Variable in class cytoscape.visual.customgraphic.impl.vector.GradientLayerCustomGraphics
 
C2CMappingEditor - Class in cytoscape.visual.ui.editors.continuous
Continuous-Continuous mapping editor.
C2CMappingEditor(VisualPropertyType) - Constructor for class cytoscape.visual.ui.editors.continuous.C2CMappingEditor
Creates a new C2CMappingEditor object.
C2DMappingEditor - Class in cytoscape.visual.ui.editors.continuous
Continuous Mapping editor for discrete values, such as Font, Shape, Label Position, etc.
C2DMappingEditor(VisualPropertyType) - Constructor for class cytoscape.visual.ui.editors.continuous.C2DMappingEditor
Creates a new C2DMappingEditor object.
calcSampleVariance(double[]) - Static method in class org.cytoscape.equations.FunctionUtil
 
calculateBackgroundColor(CyNetwork) - Method in class cytoscape.visual.GlobalAppearanceCalculator
Currently no calculators are supported for global visual attributes, so this method simply returns the default background color.
calculateEdgeAppearance(Edge, CyNetwork) - Method in class cytoscape.visual.EdgeAppearanceCalculator
Using the rules defined by the default values and calculators in this object, compute an appearance for the requested Edge in the supplied CyNetwork.
calculateEdgeAppearance(EdgeAppearance, Edge, CyNetwork) - Method in class cytoscape.visual.EdgeAppearanceCalculator
Using the rules defined by the default values and calculators in this object, compute an appearance for the requested Edge in the supplied CyNetwork.
calculateEdgeReverseSelectionColor(CyNetwork) - Method in class cytoscape.visual.GlobalAppearanceCalculator
DOCUMENT ME!
calculateEdgeSelectionColor(CyNetwork) - Method in class cytoscape.visual.GlobalAppearanceCalculator
DOCUMENT ME!
calculateGlobalAppearance(CyNetwork) - Method in class cytoscape.visual.GlobalAppearanceCalculator
Constructs a new GlobalAppearance object containing the values for the known global visual attributes.
calculateGlobalAppearance(GlobalAppearance, CyNetwork) - Method in class cytoscape.visual.GlobalAppearanceCalculator
The supplied GlobalAppearance object will be changed to hold new values for the known global visual attributes.
calculateNodeAppearance(Node, CyNetwork) - Method in class cytoscape.visual.NodeAppearanceCalculator
Using the rules defined by the default values and calculators in this object, compute an appearance for the requested Node in the supplied CyNetwork.
calculateNodeAppearance(NodeAppearance, Node, CyNetwork) - Method in class cytoscape.visual.NodeAppearanceCalculator
Using the rules defined by the default values and calculators in this object, compute an appearance for the requested Node in the supplied CyNetwork.
calculateNodeReverseSelectionColor(CyNetwork) - Method in class cytoscape.visual.GlobalAppearanceCalculator
DOCUMENT ME!
calculateNodeSelectionColor(CyNetwork) - Method in class cytoscape.visual.GlobalAppearanceCalculator
DOCUMENT ME!
calculateRangeValue(Map<String, Object>) - Method in class cytoscape.visual.mappings.AbstractMapping
 
calculateRangeValue(String) - Method in class cytoscape.visual.mappings.continuous.ContinuousRangeCalculator
Calculates Range Value.
calculateRangeValue(Map<String, Object>) - Method in class cytoscape.visual.mappings.ContinuousMapping
Calculates the Range Value.
calculateRangeValue(Map<String, Object>) - Method in class cytoscape.visual.mappings.discrete.DiscreteRangeCalculator
Calculates Range Value.
calculateRangeValue(Map<String, Object>) - Method in class cytoscape.visual.mappings.DiscreteMapping
Calculates the Range Value.
calculateRangeValue(Map<String, Object>) - Method in interface cytoscape.visual.mappings.ObjectMapping
Create a mapped visual representation from the given attribute value.
calculateRangeValue(Map<String, Object>) - Method in class cytoscape.visual.mappings.PassThroughMapping
DOCUMENT ME!
Calculator - Interface in cytoscape.visual.calculators
 
calculator - Variable in class cytoscape.visual.ui.editors.continuous.ContinuousMappingEditorPanel
 
CalculatorCatalog - Class in cytoscape.visual
Stores various types of Calculators from data attributes to an attribute of a specified type.
CalculatorCatalog() - Constructor for class cytoscape.visual.CalculatorCatalog
Creates a new CalculatorCatalog object.
CalculatorCatalog(Properties) - Constructor for class cytoscape.visual.CalculatorCatalog
Creates a new CalculatorCatalog object.
CalculatorCatalogFactory - Class in cytoscape.visual
This class provides a static method for reading a CalculatorCatalog object from file, using parameters specified in a supplied CytoscapeConfig.
CalculatorCatalogFactory() - Constructor for class cytoscape.visual.CalculatorCatalogFactory
 
CalculatorFactory - Class in cytoscape.visual.calculators
This class provides static factory methods for constructing instances of Calculators as specified by arguments and static methods for getting names and labels based on calculator type.
CalculatorFactory() - Constructor for class cytoscape.visual.calculators.CalculatorFactory
 
CalculatorIO - Class in cytoscape.visual
This class defines static methods for reading calculator definitions from a properties object and installing them into a CalculatorCatalog, and for constructing a properties object that describes all the calculators in a CalculatorCatalog.
CalculatorIO() - Constructor for class cytoscape.visual.CalculatorIO
 
call() - Method in class cytoscape.visual.customgraphic.LoadImageTask
 
call() - Method in class cytoscape.visual.customgraphic.SaveImageTask
 
cancel() - Method in interface cytoscape.util.MonitoredTask
Gets called by the CytoscapeProgressMonitor when the user click on the Cancel button.
cancelButton - Variable in class cytoscape.util.swing.AttributeImportPanel
 
cancelButtonActionPerformed(ActionEvent) - Method in class cytoscape.util.swing.AttributeImportPanel
 
cancelCellEditing() - Method in class cytoscape.util.swing.AbstractCellEditor
DOCUMENT ME!
canceled - Variable in class cytoscape.layout.AbstractLayout
 
CANONICAL_NAME - Static variable in class cytoscape.data.Semantics
The name "CANONICAL_NAME" is an historical artifact.
category - Variable in class cytoscape.bookmarks.Bookmarks
 
Category - Class in cytoscape.bookmarks
Java class for anonymous complex type.
Category() - Constructor for class cytoscape.bookmarks.Category
 
Category - Enum in cytoscape.plugin
 
categoryOrDataSource - Variable in class cytoscape.bookmarks.Category
 
CellEditorFactory - Class in cytoscape.visual.ui
 
CellHeightManager - Class in cytoscape.visual.ui
 
CellHeightManager() - Constructor for class cytoscape.visual.ui.CellHeightManager
 
CellRendererFactory - Class in cytoscape.visual.ui
 
CELLULAR_COMPONENT - Static variable in class cytoscape.data.Semantics
Deprecated. 
CellularComponentAnnotationReader - Class in cytoscape.cruft.obo
The purpose of this class is to convert a 'gene_association.*' file (for example 'gene_association.sgd') into a crufty old 'cellcomp.anno' file that Cytoscape's BioDataServer understands.
CellularComponentAnnotationReader(String, Map, Reader) - Constructor for class cytoscape.cruft.obo.CellularComponentAnnotationReader
Creates a new CellularComponentAnnotationReader object.
CellularComponentAnnotationReader(String, Reader) - Constructor for class cytoscape.cruft.obo.CellularComponentAnnotationReader
Creates a new CellularComponentAnnotationReader object.
CellularComponentAnnotationTester - Class in cytoscape.cruft.obo.test
 
CellularComponentAnnotationTester() - Constructor for class cytoscape.cruft.obo.test.CellularComponentAnnotationTester
 
CENTER - Static variable in interface giny.view.Label
Deprecated. 
centerName - Static variable in class cytoscape.visual.LabelPosition
Deprecated.  
centerWindowLocation(Window) - Static method in class cytoscape.util.shadegrown.WindowUtilities
DOCUMENT ME!
centerWindowOnScreen(Window) - Static method in class cytoscape.util.shadegrown.WindowUtilities
DOCUMENT ME!
centerWindowSize(Window) - Static method in class cytoscape.util.shadegrown.WindowUtilities
DOCUMENT ME!
changeEvent - Variable in class cytoscape.visual.CalculatorCatalog
Only one ChangeEvent is needed per catalog instance since the event's only state is the source property.
changeEvent - Variable in class cytoscape.visual.calculators.AbstractCalculator
Only one ChangeEvent is needed per calculator instance since the event's only state is the source property.
changeListeners - Variable in class cytoscape.visual.calculators.AbstractCalculator
keep track of interested UI classes.
changeView(DGraphView) - Method in class ding.view.BirdsEyeView
DOCUMENT ME!
check(VisualPropertyDependency.Definition) - Method in interface cytoscape.visual.VisualPropertyDependency
Checks the state of the specified dependency definition.
CheckBoxFileChooser - Class in cytoscape.actions
Deprecated. This isn't apparently used anywhere. If you are using it, let us know! If you need a file use FileUtil.getFile(). Will be removed 5/2008.
CheckBoxFileChooser(File, String) - Constructor for class cytoscape.actions.CheckBoxFileChooser
Deprecated. Creates a new CheckBoxFileChooser object.
CheckBoxJList - Class in cytoscape.util.swing
This class is based on CheckBoxJList: from SWING HACKS ISBN: 0-596-00907-0 By Joshua Marinacci, Chris Adamson
CheckBoxJList() - Constructor for class cytoscape.util.swing.CheckBoxJList
Creates a new CheckBoxJList object.
checkCalculatorName(String, VisualPropertyType) - Method in class cytoscape.visual.CalculatorCatalog
DOCUMENT ME!
checkCalculatorName(VisualPropertyType, String) - Method in class cytoscape.visual.CalculatorCatalog
DOCUMENT ME!
checkConflictingCalculator(Calculator) - Method in class cytoscape.visual.VisualStyle
Check if contained appearance calculators are using given calculator
checkFileType(BufferedReader) - Method in class cytoscape.data.servers.BioDataServer
 
checkFlag(int) - Method in class cytoscape.layout.Tunable
This method is used to check the value of a flag.
checkMappingName(String) - Method in class cytoscape.visual.CalculatorCatalog
DOCUMENT ME!
checkName(String, Map) - Method in class cytoscape.visual.CalculatorCatalog
 
checkNetworkCount() - Method in class cytoscape.actions.ExportAsXGMMLAction
 
checkNetworkCount() - Method in class cytoscape.actions.ExportNetworksAsNNFAction
 
checkSpecies(BufferedReader, BufferedReader) - Method in class cytoscape.util.BioDataServerUtil
DOCUMENT ME!
checkVisualStyleName(String) - Method in class cytoscape.visual.CalculatorCatalog
DOCUMENT ME!
Child - Class in cytoscape.generated
Java class for anonymous complex type.
Child() - Constructor for class cytoscape.generated.Child
 
child - Variable in class cytoscape.generated.Network
 
chooser - Static variable in class cytoscape.util.CyColorChooser
 
CIRCLE - Static variable in class cytoscape.data.readers.XGMMLReader
 
CIRCLE - Static variable in class cytoscape.visual.Arrow
DOCUMENT ME!
CLArgsParser - Class in org.apache.commons.cli.avalon
Parser for command line arguments.
CLArgsParser(String[], CLOptionDescriptor[], ParserControl) - Constructor for class org.apache.commons.cli.avalon.CLArgsParser
Create a parser that can deal with options and parses certain args.
CLArgsParser(String[], CLOptionDescriptor[]) - Constructor for class org.apache.commons.cli.avalon.CLArgsParser
Create a parser that deals with options and parses certain args.
CLASS_VALUE - Static variable in class org.apache.commons.cli.PatternOptionBuilder
Class class
CLEAN - Static variable in class cytoscape.CytoscapeModifiedNetworkManager
 
clear() - Method in class cytoscape.data.servers.BioDataServer
DOCUMENT ME!
clear() - Method in interface cytoscape.data.servers.BioDataServerInterface
DOCUMENT ME!
clear() - Method in class cytoscape.data.servers.BioDataServerRmi
DOCUMENT ME!
clear - Class in cytoscape.data.servers
 
clear() - Constructor for class cytoscape.data.servers.clear
 
clear(Paint, double, double, double) - Method in class cytoscape.render.immed.GraphGraphics
Clears image area with background paint specified and sets an appropriate transformation of coordinate systems.
clear() - Method in class cytoscape.visual.CalculatorCatalog
DOCUMENT ME!
clear(Graphics) - Method in class cytoscape.visual.ui.editors.continuous.YValueLegendPanel
 
clearAuthorList() - Method in class cytoscape.plugin.PluginInfo
Clears author list.
clearBends() - Method in interface giny.view.EdgeView
 
clearCorruptedElements() - Method in class cytoscape.plugin.PluginTracker
Clears the list of elements and sets the found flag to false.
clearErrorList() - Method in class cytoscape.plugin.PluginManager
Clears the loading error list.
clearFlag(int) - Method in class cytoscape.layout.Tunable
This method can be used to clear a flag for this Tunable
clearPluginList() - Method in class cytoscape.plugin.ThemeInfo
 
clearStatusBar() - Method in class cytoscape.view.CytoscapeDesktop
Clears the Status Bar Message.
clearVector() - Method in class cytoscape.dialogs.preferences.PreferenceTableModel
DOCUMENT ME!
clientData - Variable in class cytoscape.giny.FingCyNetwork
The ClientData map
clientID - Variable in class cytoscape.data.webservice.WebServiceClientImpl
 
clientStub - Variable in class cytoscape.data.webservice.WebServiceClientImpl
 
clone() - Method in class cytoscape.util.CytoscapeAction
The default clone() implementation delegates to the create() method of DataTypeUtilities.getDataTypeFactory( this.getClass() ).
clone() - Method in class cytoscape.visual.Appearance
Returns a clone of this Appearance.
clone() - Method in class cytoscape.visual.calculators.AbstractCalculator
Clone the calculator.
clone() - Method in interface cytoscape.visual.calculators.Calculator
Clone the calculator.
clone() - Method in class cytoscape.visual.EdgeAppearance
 
clone() - Method in class cytoscape.visual.EdgeAppearanceCalculator
Create deep copy of the object.
clone() - Method in class cytoscape.visual.GlobalAppearanceCalculator
Make deep copy of this object
clone() - Method in class cytoscape.visual.mappings.AbstractMapping
 
clone() - Method in class cytoscape.visual.mappings.continuous.ContinuousMappingPoint
Clones the object.
clone() - Method in class cytoscape.visual.mappings.ContinuousMapping
Create deep copy of the object.
clone() - Method in class cytoscape.visual.mappings.DiscreteMapping
Clones the Object.
clone() - Method in interface cytoscape.visual.mappings.ObjectMapping
 
clone() - Method in class cytoscape.visual.mappings.PassThroughMapping
Create clone of this instance.
clone() - Method in class cytoscape.visual.NodeAppearance
 
clone() - Method in class cytoscape.visual.NodeAppearanceCalculator
Create deep copy of the object.
clone() - Method in class cytoscape.visual.ui.icon.NodeIcon
DOCUMENT ME!
clone() - Method in class cytoscape.visual.VisualStyle
Perform deep copy of this VisualStyle.
clone() - Method in interface giny.model.GraphPerspective
 
CloneGraphInNewWindowAction - Class in cytoscape.actions
 
CloneGraphInNewWindowAction() - Constructor for class cytoscape.actions.CloneGraphInNewWindowAction
Creates a new CloneGraphInNewWindowAction object.
CLOption - Class in org.apache.commons.cli.avalon
Basic class describing an instance of option.
CLOption(CLOptionDescriptor) - Constructor for class org.apache.commons.cli.avalon.CLOption
Constructor taking an descriptor
CLOption(String) - Constructor for class org.apache.commons.cli.avalon.CLOption
Constructor taking argument for option.
CLOptionDescriptor - Class in org.apache.commons.cli.avalon
Basic class describing an type of option.
CLOptionDescriptor(String, int, int, String) - Constructor for class org.apache.commons.cli.avalon.CLOptionDescriptor
Constructor.
CLOptionDescriptor(String, int, int, String, int[]) - Constructor for class org.apache.commons.cli.avalon.CLOptionDescriptor
Deprecated. use the version with the array of CLOptionDescriptor's
CLOptionDescriptor(String, int, int, String, CLOptionDescriptor[]) - Constructor for class org.apache.commons.cli.avalon.CLOptionDescriptor
Constructor.
close() - Method in class cytoscape.cruft.obo.BiologicalProcessAnnotationReader
Closes the underlying gene_association file stream as well.
close() - Method in class cytoscape.cruft.obo.CellularComponentAnnotationReader
Closes the underlying gene_association file stream as well.
close() - Method in class cytoscape.cruft.obo.MolecularFunctionAnnotationReader
Closes the underlying gene_association file stream as well.
close() - Method in class cytoscape.cruft.obo.OboOntologyReader
Closes the underlying obo file stream as well.
close() - Method in class cytoscape.cruft.obo.OboOntologyReader2
Closes the underlying obo file stream as well.
close() - Method in class cytoscape.cruft.obo.SynonymReader
Closes the underlying gene_association file stream as well.
CLOSE_EVENT - Static variable in class cytoscape.util.swing.AttributeImportPanel
Will be caught by parent object (usually a dialog.)
closeAllWindows() - Method in class cytoscape.view.CyDesktopManager
 
CLUtil - Class in org.apache.commons.cli.avalon
CLUtil offers basic utility operations for use both internal and external to package.
cName - Static variable in class cytoscape.visual.LabelPosition
Deprecated.  
coarseDetailThreshold - Variable in class cytoscape.ding.CyGraphLOD
 
CodeAndSourceLocation - Class in org.cytoscape.equations
A node in the parse tree representing a binary operator.
CodeAndSourceLocation(Object, int) - Constructor for class org.cytoscape.equations.CodeAndSourceLocation
 
COLLAPSABLE - Static variable in class cytoscape.layout.Tunable
If the COLLAPSABLE flag is set for a GROUP Tunable, then this Group of Tunables should be collapsable, and will be rendered with a button to allow collapse/expand.
color - Static variable in class cytoscape.util.CyColorChooser
 
color - Variable in class cytoscape.visual.ui.icon.VisualPropertyIcon
 
COLOR1 - Static variable in class cytoscape.visual.customgraphic.impl.vector.GradientLayerCustomGraphics
 
COLOR2 - Static variable in class cytoscape.visual.customgraphic.impl.vector.GradientLayerCustomGraphics
 
COLOR_CHANGED - Static variable in class cytoscape.visual.ui.editors.continuous.BelowAndAbovePanel
DOCUMENT ME!
colorButton - Variable in class cytoscape.visual.ui.editors.continuous.ContinuousMappingEditorPanel
 
ColorConverter - Class in cytoscape.visual.converter
 
ColorConverter() - Constructor for class cytoscape.visual.converter.ColorConverter
 
colorLowDetail(int) - Method in class cytoscape.render.stateful.EdgeDetails
Returns the color of edge in low detail rendering mode.
colorLowDetail(int) - Method in class cytoscape.render.stateful.NodeDetails
Returns the color of node in low detail rendering mode.
ColorPaintFactory - Class in cytoscape.visual.customgraphic.paint
 
ColorPaintFactory(Color) - Constructor for class cytoscape.visual.customgraphic.paint.ColorPaintFactory
 
ColorParser - Class in cytoscape.visual.parsers
Parses a String into a Color object.
ColorParser() - Constructor for class cytoscape.visual.parsers.ColorParser
 
ColorRangeValueCalculator - Class in cytoscape.visual.mappings.rangecalculators
 
ColorRangeValueCalculator() - Constructor for class cytoscape.visual.mappings.rangecalculators.ColorRangeValueCalculator
 
ColorScaleTable - Class in cytoscape.dialogs
 
ColorScaleTable(int, int, double[][]) - Constructor for class cytoscape.dialogs.ColorScaleTable
Creates a new ColorScaleTable object.
ColorUtil - Class in cytoscape.util
Color utility class to convert Java color object to string and vice versa.
ColorUtil() - Constructor for class cytoscape.util.ColorUtil
 
columnHeader - Static variable in class cytoscape.dialogs.preferences.PreferenceTableModel
 
ColumnResizer - Class in cytoscape.util.swing
Automatically resize column based on the objects in the cell.
ColumnResizer() - Constructor for class cytoscape.util.swing.ColumnResizer
 
ColumnTypes - Enum in cytoscape.view
 
Combin - Class in org.cytoscape.equations.builtins
 
Combin() - Constructor for class org.cytoscape.equations.builtins.Combin
 
CommandLine - Class in org.apache.commons.cli
Represents list of arguments parsed against a Options descriptor.
CommandLineParser - Interface in org.apache.commons.cli
A class that implements the CommandLineParser interface can parse a String array according to the Options specified and return a CommandLine.
COMMENT - Static variable in class cytoscape.data.readers.GMLReader
 
compare(Object, Object) - Method in class cytoscape.data.readers.GMLNode
DOCUMENT ME!
compile(String, Map<String, Class>) - Method in class org.cytoscape.equations.EqnCompiler
 
completions() - Method in class cytoscape.util.CytoscapeAction
DOCUMENT ME!
compressFast(int, boolean) - Method in class cytoscape.util.ZipUtil
Faster version of compression method.
computeClosedPath(PathIterator, GeneralPath) - Static method in class cytoscape.render.stateful.GraphRenderer
A utility method that converts an open GeneralPath into a closed GeneralPath.
computeEdgeEndpoints(GraphGraphics, float[], byte, byte, float, EdgeAnchors, float[], byte, byte, float, float[], float[]) - Static method in class cytoscape.render.stateful.GraphRenderer
Calculates the edge endpoints given two nodes, any edge anchors, and any arrows.
computeEdgeIntersection(byte, float, float, float, float, float, float, float, float[]) - Method in class cytoscape.render.immed.GraphGraphics
Computes the intersection point between a node outline and a line segment; one point of the line segment lies at the center of the node outline.
computeEdgeIntersection(float, float, float, float, float, float, float[]) - Method in class cytoscape.render.immed.nodeshape.EllipseNodeShape
 
computeEdgeIntersection(float, float, float, float, float, float, float[]) - Method in interface cytoscape.render.immed.nodeshape.NodeShape
Computes the intersection of the node shape with and edge.
Concatenate - Class in org.cytoscape.equations.builtins
 
Concatenate() - Constructor for class org.cytoscape.equations.builtins.Concatenate
 
configure() - Method in class cytoscape.util.MacAppConfig
Configures the Info.plist list with all cytoscape/*.jar files.
ConsoleLogger - Class in cytoscape.logger
The ConsoleLogger is the default log handler for Cytoscape and does nothing much more than issue messages to System.out or System.err, as appropriate.
ConsoleLogger() - Constructor for class cytoscape.logger.ConsoleLogger
 
consoleName - Variable in class cytoscape.util.CytoscapeAction
 
constrained(VisualPropertyDependency) - Method in class cytoscape.visual.properties.AbstractVisualProperty
 
constrained(VisualPropertyDependency) - Method in class cytoscape.visual.properties.EdgeSourceArrowColorProp
 
constrained(VisualPropertyDependency) - Method in class cytoscape.visual.properties.EdgeSourceArrowOpacityProp
 
constrained(VisualPropertyDependency) - Method in class cytoscape.visual.properties.EdgeTargetArrowColorProp
 
constrained(VisualPropertyDependency) - Method in class cytoscape.visual.properties.EdgeTargetArrowOpacityProp
 
constrained(VisualPropertyDependency) - Method in class cytoscape.visual.properties.NodeHeightProp
 
constrained(VisualPropertyDependency) - Method in class cytoscape.visual.properties.NodeSizeProp
 
constrained(VisualPropertyDependency) - Method in class cytoscape.visual.properties.NodeWidthProp
 
constrained(VisualPropertyDependency) - Method in interface cytoscape.visual.VisualProperty
 
constraints - Variable in class cytoscape.dialogs.GridBagGroup
 
construct() - Method in class cytoscape.layout.AbstractLayout
These abstract methods must be overridden.
construct() - Method in class cytoscape.layout.algorithms.GridNodeLayout
DOCUMENT ME!
construct() - Method in class cytoscape.util.SwingWorker
Compute the value to be returned by the get method.
contains(CyNode) - Method in interface cytoscape.groups.CyGroup
Determine if a node is a member of this group
contains(CyNode) - Method in class cytoscape.groups.CyGroupImpl
Determine if a node is a member of this group
containsCustomGraphic(CustomGraphic) - Method in class ding.view.DNodeView
A thread-safe way to determine if this DNodeView contains a given custom graphic.
containsEdge(Edge) - Method in interface giny.model.GraphPerspective
Return true if the given Edge is in this GraphPerspective.
containsEdge(Edge, boolean) - Method in interface giny.model.GraphPerspective
Return true if the given Edge is in this GraphPerspective.
containsEdge(Edge) - Method in interface giny.model.RootGraph
Return true if the given Edge is in this RootGraph.
containsGraphView(GraphView) - Method in class cytoscape.view.GraphViewController
Whether or not the given giny.view.GraphView is kept synchronized with its giny.model.GraphPerspective member by this GraphViewController.
containsNode(Node) - Method in interface giny.model.GraphPerspective
Return true if the given Node is in this GraphPerspective.
containsNode(Node, boolean) - Method in interface giny.model.GraphPerspective
Return true if the given Node is in this GraphPerspective.
containsNode(Node) - Method in interface giny.model.RootGraph
Return true if the given Node is in this RootGraph.
containsPlugin(PluginInfo) - Method in class cytoscape.plugin.ThemeInfo
 
containsTerm(int) - Method in class cytoscape.data.annotation.Ontology
Deprecated. DOCUMENT ME!
containsTerm(String) - Method in class cytoscape.data.ontology.Ontology
 
containsTriple(Term, Term, Term) - Method in class cytoscape.data.ontology.Ontology
See if a triple exists in this ontology.
containsVersion(String) - Method in class cytoscape.plugin.DownloadableInfo
 
content - Variable in class cytoscape.bookmarks.Attribute
 
contentChanged() - Method in interface ding.view.ContentChangeListener
This gets fired upon graph redraw when at least one of the following things change: node unselected, edge unselected, background paint change, node view added, edge view added, node view removed, edge view removed, node view hidden, edge view hidden, node view restored, edge view restored, graph lod changed, node visual property changed, edge visual property changed.
ContentChangeListener - Interface in ding.view
DOCUMENT ME!
contentTypes - Variable in class cytoscape.util.CyFileFilter
 
ContiguousArrowStroke - Class in cytoscape.visual.strokes
 
ContiguousArrowStroke(float) - Constructor for class cytoscape.visual.strokes.ContiguousArrowStroke
 
ContinuousLegend - Class in cytoscape.visual.mappings.continuous
 
ContinuousLegend(String, List, Object, VisualPropertyType) - Constructor for class cytoscape.visual.mappings.continuous.ContinuousLegend
Deprecated. 
ContinuousLegend(List, VisualPropertyType) - Constructor for class cytoscape.visual.mappings.continuous.ContinuousLegend
 
ContinuousMapping - Class in cytoscape.visual.mappings
Implements an interpolation table mapping data to values of a particular class.
ContinuousMapping(Object, byte) - Constructor for class cytoscape.visual.mappings.ContinuousMapping
Deprecated. Use new constructor instead. Will be removed in 10/2011. Controlling attribute name is always required, and now it's a part of constructor argument.
ContinuousMapping(Class<?>, String) - Constructor for class cytoscape.visual.mappings.ContinuousMapping
 
ContinuousMappingEditorPanel - Class in cytoscape.visual.ui.editors.continuous
Abstract class for all Continuous Mapping Editors.
ContinuousMappingEditorPanel(VisualPropertyType) - Constructor for class cytoscape.visual.ui.editors.continuous.ContinuousMappingEditorPanel
Creates new form ContinuousMapperEditorPanel
ContinuousMappingEditorPanel.ThumbMouseListener - Class in cytoscape.visual.ui.editors.continuous
 
ContinuousMappingEditorPanel.ThumbMouseListener() - Constructor for class cytoscape.visual.ui.editors.continuous.ContinuousMappingEditorPanel.ThumbMouseListener
 
ContinuousMappingPoint - Class in cytoscape.visual.mappings.continuous
Encapsulates a ContinuousMapping Point with a single point value and associated BoundaryRangeValues.
ContinuousMappingPoint(double, BoundaryRangeValues) - Constructor for class cytoscape.visual.mappings.continuous.ContinuousMappingPoint
Constructor.
ContinuousMappingReader - Class in cytoscape.visual.mappings.continuous
Reads in ContinuousMapping Properties.
ContinuousMappingReader(Properties, String, ValueParser) - Constructor for class cytoscape.visual.mappings.continuous.ContinuousMappingReader
Constructor.
ContinuousMappingWriter - Class in cytoscape.visual.mappings.continuous
Writes out ContinuousMapping Properties.
ContinuousMappingWriter(List, String, String, Interpolator) - Constructor for class cytoscape.visual.mappings.continuous.ContinuousMappingWriter
Constructor.
ContinuousRangeCalculator - Class in cytoscape.visual.mappings.continuous
Calculates the Range for Continuous Mappers.
ContinuousRangeCalculator(List<ContinuousMappingPoint>, Interpolator, Map) - Constructor for class cytoscape.visual.mappings.continuous.ContinuousRangeCalculator
Constructor.
ContinuousTrackRenderer - Class in cytoscape.visual.ui.editors.continuous
 
ContinuousTrackRenderer(VisualPropertyType, Number, Number) - Constructor for class cytoscape.visual.ui.editors.continuous.ContinuousTrackRenderer
Creates a new ContinuousTrackRenderer object.
controllingAttrName - Variable in class cytoscape.visual.mappings.AbstractMapping
 
convert() - Method in class cytoscape.util.Transform
DOCUMENT ME!
convert(int) - Static method in class cytoscape.visual.LabelPosition
Deprecated. DOCUMENT ME!
convert(String) - Static method in class cytoscape.visual.LabelPosition
Deprecated. DOCUMENT ME!
convertLambdasToPvals() - Method in class cytoscape.data.ExpressionData
Converts all lambdas to p-values.
convertToIcon(Object) - Method in class cytoscape.visual.ui.editors.discrete.CyColorCellRenderer
 
convertToString(Object) - Method in class cytoscape.visual.ui.editors.discrete.CyColorCellRenderer
 
copy(Appearance) - Method in class cytoscape.visual.Appearance
Copies the specified Appearance into this Appearance object.
copy(VisualPropertyDependency) - Method in interface cytoscape.visual.VisualPropertyDependency
Clears the current object and copies the state of the specified VisualPropertyDependency into this object.
copyAttribute(CyAttributes, String, String, String, boolean, StringBuilder) - Static method in class cytoscape.data.CyAttributesUtils
 
copyAttribute(String, String, String, CyAttributes, boolean) - Static method in class cytoscape.data.CyAttributesUtils
Copy a specific attribute of a given object to another object.
copyAttributes(String, String, CyAttributes, boolean) - Static method in class cytoscape.data.CyAttributesUtils
Copy all the attributes of a given object to another object.
copyAttributes(String, String, CyAttributes, AttributeFilter, boolean) - Static method in class cytoscape.data.CyAttributesUtils
Copy all the attributes of a given object that pass a given filter to another object.
copyDefaultAppearance(AppearanceCalculator) - Method in class cytoscape.visual.EdgeAppearanceCalculator
 
copyDefaultAppearance(AppearanceCalculator) - Method in class cytoscape.visual.NodeAppearanceCalculator
 
copyGroup(CyGroup, CyNetwork) - Static method in class cytoscape.groups.CyGroupManager
Create a copy of a group, potentially in a new network, and name the copy automatically.
copyGroup(String, CyGroup, CyNetwork) - Static method in class cytoscape.groups.CyGroupManager
Create a copy of a group, potentially in a new network, and name the copy with the provided new name.
copyInto(int[], int) - Method in class cytoscape.util.intr.MinIntHeap
Deprecated. Use elements() instead.
copyIntoReverseOrder(int[], int) - Method in class cytoscape.util.intr.MinIntHeap
Deprecated. Use orderedElements(boolean) or deleteMin() instead.
copyToAttribs(CyAttributes, TaskMonitor) - Method in class cytoscape.data.ExpressionData
Copies ExpressionData data structure into CyAttributes data structure.
Cos - Class in org.cytoscape.equations.builtins
 
Cos() - Constructor for class org.cytoscape.equations.builtins.Cos
 
Cosh - Class in org.cytoscape.equations.builtins
 
Cosh() - Constructor for class org.cytoscape.equations.builtins.Cosh
 
count() - Method in class cytoscape.data.annotation.Annotation
Deprecated. total number of entities, usually ORFs.
count(int) - Method in class cytoscape.util.intr.IntBTree
Returns the number of entries of the integer x in this tree.
Count - Class in org.cytoscape.equations.builtins
 
Count() - Constructor for class org.cytoscape.equations.builtins.Count
 
CountedIterator - Interface in cytoscape.data.attr
A java.util.Iterator with knowledge of how many elements are remaining.
create() - Method in class cytoscape.util.IndeterminateProgressBar
 
create(T) - Method in interface cytoscape.visual.mappings.CustomGraphicsRangeValueRenderer
 
create(char) - Static method in class org.apache.commons.cli.OptionBuilder
Create an Option using the current settings and with the specified Option char.
create() - Static method in class org.apache.commons.cli.OptionBuilder
Create an Option using the current settings
create(String) - Static method in class org.apache.commons.cli.OptionBuilder
Create an Option using the current settings and with the specified Option char.
createActionButtonMap() - Method in class cytoscape.util.CytoscapeToolBar
Factory method for instantiating the action->button map.
createAlignTab() - Method in class cytoscape.dialogs.PhoebeNodeControl
DOCUMENT ME!
createAttribute() - Method in class cytoscape.bookmarks.ObjectFactory
Create an instance of Attribute
createBasicOntology(URL, String, String) - Method in class cytoscape.data.ontology.OntologyFactory
DOCUMENT ME!
createBookmarks() - Method in class cytoscape.bookmarks.ObjectFactory
Create an instance of Bookmarks
createBottomLeft() - Method in class cytoscape.view.CytoscapeDesktop
 
createCategory() - Method in class cytoscape.bookmarks.ObjectFactory
Create an instance of Category
createChild() - Method in class cytoscape.generated.ObjectFactory
Create an instance of Child
createCircularTab() - Method in class cytoscape.dialogs.PhoebeNodeControl
 
createClass(String) - Static method in class org.apache.commons.cli.TypeHandler
Returns the class whose name is str.
createColorLabel(Color) - Static method in class cytoscape.dialogs.MiscGB
DOCUMENT ME!
createContainer(CyNetworkView) - Method in class cytoscape.view.NetworkViewManager
Contains a CyNetworkView.
createCysession() - Method in class cytoscape.generated.ObjectFactory
Create an instance of Cysession
createCytopanel() - Method in class cytoscape.generated.ObjectFactory
Create an instance of Cytopanel
createCytopanels() - Method in class cytoscape.generated.ObjectFactory
Create an instance of Cytopanels
createDataSource() - Method in class cytoscape.bookmarks.ObjectFactory
Create an instance of DataSource
createDate(String) - Static method in class org.apache.commons.cli.TypeHandler
Returns the date represented by str.
createDefaultVisualStyle() - Method in class cytoscape.visual.CalculatorCatalog
DOCUMENT ME!
createDescription(String) - Method in class cytoscape.bookmarks.ObjectFactory
Create an instance of JAXBElement<String>}
createDesktop() - Method in class cytoscape.generated.ObjectFactory
Create an instance of Desktop
createDesktopSize() - Method in class cytoscape.generated.ObjectFactory
Create an instance of DesktopSize
createDialog(Component) - Method in class cytoscape.actions.CheckBoxFileChooser
Deprecated.  
createDialog(Component) - Method in class cytoscape.actions.ExpFileChooser
Deprecated.  
createDifferenceGraph(List, boolean, String) - Static method in class cytoscape.util.GraphSetUtils
Create a new graph which is the difference of multiple graphs.
createDifferenceGraph2(List, boolean, String) - Static method in class cytoscape.util.GraphSetUtils
The way this works is that the 2nd and optional additional networks will be subtracted from the 1st network.
createEdge() - Method in class cytoscape.generated.ObjectFactory
Create an instance of Edge
createEdge(int, int, boolean) - Method in class cytoscape.giny.FingCyNetwork
This method will create a new edge.
createEdge(Node, Node) - Method in interface giny.model.RootGraph
Create a directed Edge from the given source Node to the given target Node, and return its index.
createEdge(Node, Node, boolean) - Method in interface giny.model.RootGraph
Create an Edge from the given source Node to the given target Node, and return its index.
createEdge(int, int) - Method in interface giny.model.RootGraph
Create a directed Edge from the Node with the given source_index to the Node with the given target_index, and return the new Edge's index.
createEdge(int, int, boolean) - Method in interface giny.model.RootGraph
Create an Edge from the Node with the given source_index to the Node with the given target_index, and return the new Edge's index.
createEdges(int[], int[], boolean) - Method in interface giny.model.RootGraph
Deprecated. Use createEdge(int, int, boolean) instead.
createFile(String) - Static method in class org.apache.commons.cli.TypeHandler
Returns the File represented by str.
createFiles(String) - Static method in class org.apache.commons.cli.TypeHandler
Returns the File[] represented by str.
createGeneOntology(URL, String, String) - Method in class cytoscape.data.ontology.OntologyFactory
DOCUMENT ME!
createGraph() - Method in class cytoscape.data.readers.GMLReader
This will create the graph model objects.
createGraphPerspective(Node[], Edge[]) - Method in interface giny.model.GraphPerspective
Deprecated. Use RootGraph.createGraphPerspective(int[], int[]) instead.
createGraphPerspective(int[], int[]) - Method in interface giny.model.GraphPerspective
Deprecated. Use RootGraph.createGraphPerspective(int[], int[]) instead.
createGraphPerspective(Filter) - Method in interface giny.model.GraphPerspective
Create a new GraphPerspective with all of the Nodes from this one that pass the given filter and all of the Edges from this one that pass the filter (and all Nodes incident on those edges).
createGraphPerspective(int[]) - Method in interface giny.model.GraphPerspective
Create a new GraphPerspective given a list of Nodes.
createGraphPerspective(Node[], Edge[]) - Method in interface giny.model.RootGraph
Create a new GraphPerspective with just the given Nodes and Edges (and all Nodes incident on the given Edges).
createGraphPerspective(int[], int[]) - Method in interface giny.model.RootGraph
Create a new GraphPerspective with just the given Nodes and Edges (and all Nodes incident on the given Edges).
createGroup(String, List<CyNode>, List<CyEdge>, List<CyEdge>, String, CyNetwork) - Static method in class cytoscape.groups.CyGroupManager
Create a new group by specifying all components.
createGroup(String, String, CyNetwork) - Static method in class cytoscape.groups.CyGroupManager
Create a new, empty group.
createGroup(String, List<CyNode>, String, CyNetwork) - Static method in class cytoscape.groups.CyGroupManager
Create a new group with a list of nodes as initial members.
createGroup(CyNode, List<CyNode>, String, CyNetwork) - Static method in class cytoscape.groups.CyGroupManager
Create a new group with a list of nodes as initial members, and a precreated group node.
createGroup(String, String) - Static method in class cytoscape.groups.CyGroupManager
Create a new, empty group.
createGroup(String, List<CyNode>, String) - Static method in class cytoscape.groups.CyGroupManager
Create a new, empty group.
createGroup(CyNode, List<CyNode>, String) - Static method in class cytoscape.groups.CyGroupManager
Create a new group with a list of nodes as initial members, and a precreated group node.
createHiddenEdges() - Method in class cytoscape.generated.ObjectFactory
Create an instance of HiddenEdges
createHiddenNodes() - Method in class cytoscape.generated.ObjectFactory
Create an instance of HiddenNodes
createHorizontalAlignCenter() - Method in class cytoscape.dialogs.PhoebeNodeControl
DOCUMENT ME!
createHorizontalAlignLeft() - Method in class cytoscape.dialogs.PhoebeNodeControl
DOCUMENT ME!
createHorizontalAlignRight() - Method in class cytoscape.dialogs.PhoebeNodeControl
DOCUMENT ME!
createHorizontalDistributeCenter() - Method in class cytoscape.dialogs.PhoebeNodeControl
DOCUMENT ME!
createIdentifier(String, String, String) - Static method in class cytoscape.CyEdge
A static method used to create edge identifiers.
createImage(int, int, double) - Method in class ding.view.DGraphView
Method to return a reference to an Image object, which represents the current network view.
createInfoTag() - Method in class cytoscape.util.JnlpWriterUtil
DOCUMENT ME!
createIntersectionGraph(List, boolean, String) - Static method in class cytoscape.util.GraphSetUtils
Create a new graph which is the intersection of multiple graphs.
createJButton(Action) - Method in class cytoscape.util.CytoscapeToolBar
Factory method for instantiating the buttons in the toolbar.
createJMenu(String) - Method in class cytoscape.util.CytoscapeMenuBar
Factory method for instantiating objects of type JMenu
createJMenuItem(Action) - Method in class cytoscape.util.CytoscapeMenuBar
Factory method for instantiating the menuItems in the menu.
createKVMap(Collection<Tunable>) - Method in class cytoscape.command.AbstractCommandHandler
Execute a given command with a particular set of arguments.
createMapping(byte, Object) - Method in interface cytoscape.visual.mappings.MappingManager
 
createMapping(byte, Object) - Method in class cytoscape.visual.mappings.MappingManagerImpl
 
createMasterPane(NetworkPanel, BiModalJSplitPane) - Method in class cytoscape.view.CytoscapeDesktop
Creates the Master Split Pane.
createNetwork(String) - Static method in class cytoscape.Cytoscape
Creates a new, empty Network.
createNetwork(String, boolean) - Static method in class cytoscape.Cytoscape
Creates a new, empty Network.
createNetwork(String, CyNetwork, boolean) - Static method in class cytoscape.Cytoscape
Creates a new, empty Network.
createNetwork(int[], int[], String) - Static method in class cytoscape.Cytoscape
Creates a new Network.
createNetwork(Collection, Collection, String) - Static method in class cytoscape.Cytoscape
Creates a new Network.
createNetwork(int[], int[], String, CyNetwork) - Static method in class cytoscape.Cytoscape
Creates a new Network, that inherits from the given ParentNetwork.
createNetwork(int[], int[], String, CyNetwork, boolean) - Static method in class cytoscape.Cytoscape
Creates a new Network, that inherits from the given ParentNetwork
createNetwork(Collection, Collection, String, CyNetwork) - Static method in class cytoscape.Cytoscape
Creates a new Network, that inherits from the given ParentNetwork.
createNetwork(Collection, Collection, String, CyNetwork, boolean) - Static method in class cytoscape.Cytoscape
Creates a new Network, that inherits from the given ParentNetwork.
createNetwork(GraphReader, boolean, CyNetwork) - Static method in class cytoscape.Cytoscape
Creates a cytoscape.data.CyNetwork from a reader.
createNetwork() - Method in class cytoscape.generated.ObjectFactory
Create an instance of Network
createNetwork(Collection, Collection) - Method in class cytoscape.giny.CytoscapeFingRootGraph
DOCUMENT ME!
createNetwork(Node[], Edge[]) - Method in class cytoscape.giny.CytoscapeFingRootGraph
Creates a new Network
createNetwork(int[], int[]) - Method in class cytoscape.giny.CytoscapeFingRootGraph
Uses Code copied from ColtRootGraph to create a new Network.
createNetwork(Node[], Edge[]) - Method in interface cytoscape.giny.CytoscapeRootGraph
Uses Code copied from ColtRootGraph to create a new CyNetwork.
createNetwork(Collection, Collection) - Method in interface cytoscape.giny.CytoscapeRootGraph
DOCUMENT ME!
createNetwork(int[], int[]) - Method in interface cytoscape.giny.CytoscapeRootGraph
Uses Code copied from ColtRootGraph to create a new Network.
createNetworkFrame() - Method in class cytoscape.generated.ObjectFactory
Create an instance of NetworkFrame
createNetworkFrames() - Method in class cytoscape.generated.ObjectFactory
Create an instance of NetworkFrames
createNetworkFromFile(String) - Static method in class cytoscape.Cytoscape
Creates a CyNetwork from a file.
createNetworkFromFile(String, boolean) - Static method in class cytoscape.Cytoscape
Creates a CyNetwork from a file.
createNetworkFromURL(URL, boolean) - Static method in class cytoscape.Cytoscape
Creates a CyNetwork from a URL.
createNetworkTree() - Method in class cytoscape.generated.ObjectFactory
Create an instance of NetworkTree
createNetworkView(CyNetwork) - Static method in class cytoscape.Cytoscape
Creates a CyNetworkView, but doesn't do anything with it.
createNetworkView(CyNetwork, String) - Static method in class cytoscape.Cytoscape
Creates a CyNetworkView, but doesn't do anything with it.
createNetworkView(CyNetwork, String, CyLayoutAlgorithm) - Static method in class cytoscape.Cytoscape
Creates a CyNetworkView, but doesn't do anything with it.
createNetworkView(CyNetwork, String, CyLayoutAlgorithm, VisualStyle) - Static method in class cytoscape.Cytoscape
Creates a CyNetworkView that is placed placed in a given visual style and rendered with a given layout algorithm.
CreateNetworkViewAction - Class in cytoscape.actions
 
CreateNetworkViewAction() - Constructor for class cytoscape.actions.CreateNetworkViewAction
Creates a new CreateNetworkViewAction object.
CreateNetworkViewAction(boolean) - Constructor for class cytoscape.actions.CreateNetworkViewAction
Creates a new CreateNetworkViewAction object.
createNewSession() - Static method in class cytoscape.Cytoscape
Clear all networks and attributes and start a new session.
createNode() - Method in class cytoscape.generated.ObjectFactory
Create an instance of Node
createNode() - Method in class cytoscape.giny.FingCyNetwork
This method will create a new node.
createNode() - Method in interface giny.model.RootGraph
Create a new Node in this RootGraph, and return its index.
createNode(Node[], Edge[]) - Method in interface giny.model.RootGraph
Create a new Node in this RootGraph, and return its index.
createNode(GraphPerspective) - Method in interface giny.model.RootGraph
Create a new Node in this RootGraph, and return its index.
createNode(int[], int[]) - Method in interface giny.model.RootGraph
Create a new Node in this RootGraph, and return its index.
createNodes(int) - Method in interface giny.model.RootGraph
Deprecated. Use createNode() instead.
createNumber(String) - Static method in class org.apache.commons.cli.TypeHandler
Create a number from a String.
createObject(String) - Static method in class org.apache.commons.cli.TypeHandler
Create an Object from the classname and empty constructor.
createOntology() - Method in class cytoscape.generated.ObjectFactory
Create an instance of Ontology
createOntologyServer() - Method in class cytoscape.generated.ObjectFactory
Create an instance of OntologyServer
createPadding(int) - Method in class org.apache.commons.cli.HelpFormatter
Return a String of padding of length len.
createPanel() - Method in class cytoscape.generated.ObjectFactory
Create an instance of Panel
createPanels() - Method in class cytoscape.generated.ObjectFactory
Create an instance of Panels
createPanelState(String) - Method in class cytoscape.generated.ObjectFactory
Create an instance of JAXBElement<String>}
createParent() - Method in class cytoscape.generated.ObjectFactory
Create an instance of Parent
createPlugin() - Method in class cytoscape.generated.ObjectFactory
Create an instance of Plugin
createPluginObject(Element) - Method in class cytoscape.plugin.PluginFileReader
Creates the PluginInfo object from the xml element.
createPlugins() - Method in class cytoscape.generated.ObjectFactory
Create an instance of Plugins
createResourcesTag() - Method in class cytoscape.util.JnlpWriterUtil
DOCUMENT ME!
createRightPane(BiModalJSplitPane) - Method in class cytoscape.view.CytoscapeDesktop
Creates the Right Panel.
createRootGraphFromInteractionData() - Method in class cytoscape.data.readers.InteractionsReader
 
createSelectedEdges() - Method in class cytoscape.generated.ObjectFactory
Create an instance of SelectedEdges
createSelectedNodes() - Method in class cytoscape.generated.ObjectFactory
Create an instance of SelectedNodes
createSelectedPanel(String) - Method in class cytoscape.generated.ObjectFactory
Create an instance of JAXBElement<String>}
createServer() - Method in class cytoscape.generated.ObjectFactory
Create an instance of Server
createSessionNote(String) - Method in class cytoscape.generated.ObjectFactory
Create an instance of JAXBElement<String>}
createSessionState() - Method in class cytoscape.generated.ObjectFactory
Create an instance of SessionState
createSettings() - Method in class cytoscape.layout.algorithms.GridNodeLayout
Returns a JPanel to be used as part of the Settings dialog for this layout algorithm.
createStrokedShape(Shape) - Method in class cytoscape.visual.strokes.ShapeStroke
 
createStrokedShape(Shape) - Method in class cytoscape.visual.strokes.ZigzagStroke
 
createTerm(String, String) - Method in class cytoscape.data.ontology.Ontology
Create a new term in this ontology.
createTerm(String, String, Object[]) - Method in class cytoscape.data.ontology.Ontology
DOCUMENT ME!
createThemeObject(Element) - Method in class cytoscape.plugin.PluginFileReader
 
createTopRightPane(NetworkViewManager) - Method in class cytoscape.view.CytoscapeDesktop
Creates the TopRight Pane.
createTreeNodes(DefaultMutableTreeNode, HashMap) - Method in class cytoscape.dialogs.GinyEdgeControlDialog
 
createTreeView(HashMap) - Method in class cytoscape.dialogs.GinyEdgeControlDialog
 
createTriple(Term, Term, Term, String, String) - Method in class cytoscape.data.ontology.Ontology
DOCUMENT ME!
createTunableCollection(Map<String, Object>) - Method in class cytoscape.command.AbstractCommandHandler
Use this method to support the Map version of the execute call if you support Tunables.
createUnionGraph(List, boolean, String) - Static method in class cytoscape.util.GraphSetUtils
Create a new graph which is the union of multiple graphs.
createURL(String) - Static method in class org.apache.commons.cli.TypeHandler
Returns the URL represented by str.
createValue(String, Object) - Static method in class org.apache.commons.cli.TypeHandler
Returns the Object of type obj with the value of str.
createValue(String, Class) - Static method in class org.apache.commons.cli.TypeHandler
Returns the Object of type clazz with the value of str.
createVariable(String, String) - Method in class cytoscape.data.ontology.Ontology
DOCUMENT ME!
createVerticalAlignBottom() - Method in class cytoscape.dialogs.PhoebeNodeControl
DOCUMENT ME!
createVerticalAlignCenter() - Method in class cytoscape.dialogs.PhoebeNodeControl
DOCUMENT ME!
createVerticalAlignTop() - Method in class cytoscape.dialogs.PhoebeNodeControl
DOCUMENT ME!
createVerticalDistributeCenter() - Method in class cytoscape.dialogs.PhoebeNodeControl
DOCUMENT ME!
createViewableNodes() - Method in class cytoscape.generated.ObjectFactory
Create an instance of ViewableNodes
createViewFromCurrentNetwork(CyNetwork) - Static method in class cytoscape.actions.CreateNetworkViewAction
DOCUMENT ME!
CREATOR - Static variable in class cytoscape.data.readers.GMLReader
 
CreditScreen - Class in cytoscape.util
 
CreditScreen() - Constructor for class cytoscape.util.CreditScreen
 
curator - Variable in class cytoscape.data.annotation.Annotation
Deprecated.  
curator - Variable in class cytoscape.data.annotation.AnnotationDescription
Deprecated.  
curator - Variable in class cytoscape.data.annotation.Ontology
Deprecated.  
curator - Variable in class cytoscape.data.annotation.OntologyDescription
Deprecated.  
CURRENTLY_INSTALLED - Static variable in class cytoscape.dialogs.plugins.PluginManageDialog
 
currentNetworkID - Static variable in class cytoscape.Cytoscape
 
currentNetworkID - Variable in class cytoscape.view.CytoscapeDesktop
Current network and view.
currentNetworkViewID - Static variable in class cytoscape.Cytoscape
 
currentNetworkViewID - Variable in class cytoscape.view.CytoscapeDesktop
 
currentSize - Variable in class cytoscape.layout.AbstractLayout
 
CURVED_LINES - Static variable in class cytoscape.data.readers.GMLReader
 
CURVED_LINES - Static variable in interface giny.view.EdgeView
Draws splined curves for edges.
CUSTOM - Static variable in class cytoscape.util.FileUtil
 
CUSTOM_SHAPE_MAX_VERTICES - Static variable in class cytoscape.render.immed.GraphGraphics
This value is currently 100.
CustomGraphic - Class in cytoscape.render.stateful
Represents all the information needed to define a custom graphic for a given NodeView.
CustomGraphic(Shape, PaintFactory) - Constructor for class cytoscape.render.stateful.CustomGraphic
Constructor
CustomGraphic(Shape, Paint, byte) - Constructor for class cytoscape.render.stateful.CustomGraphic
Deprecated. 
customGraphicCount(int) - Method in class cytoscape.render.stateful.NodeDetails
A thread-safe method returning the number of custom graphics associated with a given Node.
customGraphicIterator() - Method in class ding.view.DNodeView
Return a non-null, read-only Iterator over all CustomGraphics contained in this DNodeView.
customGraphicLock() - Method in class ding.view.DNodeView
Obtain the lock used for reading information about custom graphics.
customGraphics(int, int) - Method in class cytoscape.ding.CyGraphLOD
Determines whether or not to render custom graphics on nodes.
customGraphics(int, int) - Method in class cytoscape.render.stateful.GraphLOD
Determines whether or not to render custom graphics on nodes.
customGraphics(int) - Method in class cytoscape.render.stateful.NodeDetails
Return a non-null, read-only Iterator over all CustomGraphics contained in this Node.
customGraphics(int, int) - Method in class ding.view.PrintLOD
DOCUMENT ME!
CustomGraphicsBrowser - Class in cytoscape.visual.customgraphic.ui
Display list of images available as custom graphics
CustomGraphicsBrowser() - Constructor for class cytoscape.visual.customgraphic.ui.CustomGraphicsBrowser
Creates new form CustomGraphicsBrowserPanel
CustomGraphicsCellRenderer - Class in cytoscape.visual.customgraphic.ui
Cell renderer for Custom Graphics Browser.
CustomGraphicsCellRenderer() - Constructor for class cytoscape.visual.customgraphic.ui.CustomGraphicsCellRenderer
 
CustomGraphicsCellRenderer - Class in cytoscape.visual.ui.editors.discrete
 
CustomGraphicsCellRenderer() - Constructor for class cytoscape.visual.ui.editors.discrete.CustomGraphicsCellRenderer
 
CustomGraphicsDetailPanel - Class in cytoscape.visual.customgraphic.ui
 
CustomGraphicsDetailPanel() - Constructor for class cytoscape.visual.customgraphic.ui.CustomGraphicsDetailPanel
Creates new form CustomGraphicsDetailPanel
customGraphicsLock(int) - Method in class cytoscape.render.stateful.NodeDetails
Return the object used for synchronizing custom graphics operations for a given Node.
CustomGraphicsManager - Class in cytoscape.visual.customgraphic
 
CustomGraphicsManager() - Constructor for class cytoscape.visual.customgraphic.CustomGraphicsManager
Creates an image pool object and restore existing images from user resource directory.
CustomGraphicsManagerDialog - Class in cytoscape.visual.customgraphic.ui
Main UI for managing on-memory library of Custom Graphics
CustomGraphicsManagerDialog(Frame, boolean) - Constructor for class cytoscape.visual.customgraphic.ui.CustomGraphicsManagerDialog
Creates new form CustomGraphicsManagerDialog
CustomGraphicsPositionCalculator - Class in ding.view
 
CustomGraphicsPositionCalculator() - Constructor for class ding.view.CustomGraphicsPositionCalculator
 
CustomGraphicsProperty<T> - Interface in cytoscape.visual.customgraphic.impl.vector
 
CustomGraphicsPropertyImpl<T> - Class in cytoscape.visual.customgraphic
 
CustomGraphicsPropertyImpl(T) - Constructor for class cytoscape.visual.customgraphic.CustomGraphicsPropertyImpl
 
CustomGraphicsRangeValueCalculator - Class in cytoscape.visual.mappings.rangecalculators
 
CustomGraphicsRangeValueCalculator() - Constructor for class cytoscape.visual.mappings.rangecalculators.CustomGraphicsRangeValueCalculator
 
CustomGraphicsRangeValueRenderer<T> - Interface in cytoscape.visual.mappings
 
CustomGraphicsUtil - Class in cytoscape.visual.customgraphic
 
CustomGraphicsUtil() - Constructor for class cytoscape.visual.customgraphic.CustomGraphicsUtil
 
CustomMapping - Interface in cytoscape.visual.mappings
User-definable visual mapping.
customNodeShapeExists(byte) - Method in class cytoscape.render.immed.GraphGraphics
Determines whether the specified shape is a custom defined node shape.
CY_NAMESPACE - Static variable in class cytoscape.data.readers.XGMMLReader
 
CY_PROPS - Static variable in class cytoscape.data.readers.CytoscapeSessionReader
 
CyAbstractEdit - Class in cytoscape.util.undo
A small convenience class that can be used to create new edits.
CyAbstractEdit(String) - Constructor for class cytoscape.util.undo.CyAbstractEdit
 
CyAttributes - Interface in cytoscape.data
CyAttributes provides access to network, node, and edge attributes within Cytoscape.
CyAttributesImpl - Class in cytoscape.data
 
CyAttributesImpl() - Constructor for class cytoscape.data.CyAttributesImpl
Creates a new CyAttributesImpl object.
CyAttributesReader - Class in cytoscape.data.readers
 
CyAttributesUtils - Class in cytoscape.data
 
CyAttributesUtils() - Constructor for class cytoscape.data.CyAttributesUtils
 
CyAttributesUtils.AttributeType - Enum in cytoscape.data
 
CyAttributesWriter - Class in cytoscape.data.writers
CyAttributeWriter extracted from AttributeSaverDialog.
CyAttributesWriter(CyAttributes, String, Writer) - Constructor for class cytoscape.data.writers.CyAttributesWriter
Creates a new CyAttributesWriter2 object.
CyCollapsiblePanel - Class in cytoscape.util.swing
The user-triggered collapsable panel containing the component (trigger) in the titled border
CyCollapsiblePanel(JRadioButton) - Constructor for class cytoscape.util.swing.CyCollapsiblePanel
Constructor for an option button controlled collapsable panel.
CyCollapsiblePanel(String) - Constructor for class cytoscape.util.swing.CyCollapsiblePanel
Constructor for a label/button controlled collapsable panel.
CyColorCellRenderer - Class in cytoscape.visual.ui.editors.discrete
CyColorCellRenderer.
CyColorCellRenderer() - Constructor for class cytoscape.visual.ui.editors.discrete.CyColorCellRenderer
 
CyColorCellRenderer.PaintIcon - Class in cytoscape.visual.ui.editors.discrete
 
CyColorCellRenderer.PaintIcon(Paint) - Constructor for class cytoscape.visual.ui.editors.discrete.CyColorCellRenderer.PaintIcon
 
CyColorCellRenderer.PaintIcon(Paint, int, int) - Constructor for class cytoscape.visual.ui.editors.discrete.CyColorCellRenderer.PaintIcon
 
CyColorChooser - Class in cytoscape.util
This is an annoying re-implementation of JColorChooser.showDialog() that remembers recently used colors between invocations of the chooser dialog.
CyColorChooser() - Constructor for class cytoscape.util.CyColorChooser
 
CyColorPropertyEditor - Class in cytoscape.visual.ui.editors.discrete
ColorPropertyEditor.
CyColorPropertyEditor() - Constructor for class cytoscape.visual.ui.editors.discrete.CyColorPropertyEditor
Creates a new CyColorPropertyEditor object.
CyColorPropertyEditor.AsInt - Class in cytoscape.visual.ui.editors.discrete
 
CyColorPropertyEditor.AsInt() - Constructor for class cytoscape.visual.ui.editors.discrete.CyColorPropertyEditor.AsInt
 
CyComboBoxPropertyEditor - Class in cytoscape.visual.ui.editors.discrete
ComboBoxPropertyEditor.
CyComboBoxPropertyEditor() - Constructor for class cytoscape.visual.ui.editors.discrete.CyComboBoxPropertyEditor
Creates a new CyComboBoxPropertyEditor object.
CyComboBoxPropertyEditor.Value - Class in cytoscape.visual.ui.editors.discrete
 
CyComboBoxPropertyEditor.Value(Object, Object) - Constructor for class cytoscape.visual.ui.editors.discrete.CyComboBoxPropertyEditor.Value
 
CyCommandException - Exception in cytoscape.command
The CyCommandException is thrown when a CyCommandHandler encounters an exception condition.
CyCommandException(String) - Constructor for exception cytoscape.command.CyCommandException
Create a CyCommandException with a message, but no results
CyCommandException(Throwable) - Constructor for exception cytoscape.command.CyCommandException
Create a CyCommandException with a root cause but no results
CyCommandException(String, Throwable) - Constructor for exception cytoscape.command.CyCommandException
Create a CyCommandException with a message and a root cause but no results
CyCommandException(String, CyCommandResult) - Constructor for exception cytoscape.command.CyCommandException
Create a CyCommandException with a message and a set of results
CyCommandException(String, Throwable, CyCommandResult) - Constructor for exception cytoscape.command.CyCommandException
Create a CyCommandException with a message, a cause, and a set of results
CyCommandHandler - Interface in cytoscape.command
The CyCommandHandler interface allows a Cytoscape plugin to make it's functions available to other plugins in a loosely-coupled manner (by passing command strings and arguments).
CyCommandManager - Class in cytoscape.command
CyCommandManager is a singleton Cytoscape class that provides a global registry of CyCommands and CyCommandNamespaces.
CyCommandManager() - Constructor for class cytoscape.command.CyCommandManager
 
CyCommandNamespace - Interface in cytoscape.command
A CyCommandNamespace represents a reservation for a group of CyCommands.
CyCommandResult - Class in cytoscape.command
CyCommandResult returns the results from the execution of a command.
CyCommandResult() - Constructor for class cytoscape.command.CyCommandResult
Create a new empty CyCommandResult.
CyCommandResult(String, Map<String, Object>) - Constructor for class cytoscape.command.CyCommandResult
Create a new CyCommandResult with an initial message and execution results.
CyCustomGraphics - Interface in cytoscape.visual.customgraphic
 
CyCustomGraphicsEditor - Class in cytoscape.visual.ui.editors.discrete
 
CyCustomGraphicsEditor() - Constructor for class cytoscape.visual.ui.editors.discrete.CyCustomGraphicsEditor
Creates a new CyLabelPositionLabelEditor object.
CyCustomGraphicsParser - Interface in cytoscape.visual.customgraphic
 
CyCustomGraphicsParserFactory - Interface in cytoscape.visual.customgraphic
 
CyCustomGraphicsParserFactoryImpl - Class in cytoscape.visual.customgraphic.impl
 
CyCustomGraphicsParserFactoryImpl() - Constructor for class cytoscape.visual.customgraphic.impl.CyCustomGraphicsParserFactoryImpl
 
CyCustomGraphicsTableCellRenderer - Class in cytoscape.visual.customgraphic.ui
 
CyCustomGraphicsTableCellRenderer() - Constructor for class cytoscape.visual.customgraphic.ui.CyCustomGraphicsTableCellRenderer
 
CyCustomGraphicsTreeCellRenderer - Class in cytoscape.visual.customgraphic.ui
 
CyCustomGraphicsTreeCellRenderer() - Constructor for class cytoscape.visual.customgraphic.ui.CyCustomGraphicsTreeCellRenderer
 
CyCustomGraphicsTreeNode - Class in cytoscape.visual.customgraphic.ui
 
CyDesktopManager - Class in cytoscape.view
 
CyDesktopManager.Arrange - Enum in cytoscape.view
 
CyDoublePropertyEditor - Class in cytoscape.visual.ui.editors.discrete
 
CyDoublePropertyEditor() - Constructor for class cytoscape.visual.ui.editors.discrete.CyDoublePropertyEditor
Creates a new CyStringPropertyEditor object.
CyEdge - Class in cytoscape
 
CyEdge(RootGraph, int) - Constructor for class cytoscape.CyEdge
Creates a new CyEdge object.
CyEdgeView - Interface in cytoscape.view
 
CyFileFilter - Class in cytoscape.util
A convenience implementation of FileFilter that filters out all files except for those type extensions that it knows about.
CyFileFilter() - Constructor for class cytoscape.util.CyFileFilter
Creates a file filter.
CyFileFilter(String) - Constructor for class cytoscape.util.CyFileFilter
Creates a file filter that accepts files with the given extension.
CyFileFilter(String, String) - Constructor for class cytoscape.util.CyFileFilter
Creates a file filter that accepts the given file type.
CyFileFilter(String[]) - Constructor for class cytoscape.util.CyFileFilter
Creates a file filter from the given string array.
CyFileFilter(String[], String) - Constructor for class cytoscape.util.CyFileFilter
Creates a file filter from the given string array and description.
CyFileFilter(String, String, String) - Constructor for class cytoscape.util.CyFileFilter
Creates a file filter that accepts the given file type.
CyFileFilter(String[], String, String) - Constructor for class cytoscape.util.CyFileFilter
Creates a file filter from the given string array and description.
cyFileFilters - Static variable in class cytoscape.data.ImportHandler
Set of all registered CyFileFilter Objects.
CyFontPropertyEditor - Class in cytoscape.visual.ui.editors.discrete
 
CyFontPropertyEditor() - Constructor for class cytoscape.visual.ui.editors.discrete.CyFontPropertyEditor
 
CyGradientTrackRenderer - Class in cytoscape.visual.ui.editors.continuous
DOCUMENT ME!
CyGradientTrackRenderer(VisualPropertyType, Color, Color, String) - Constructor for class cytoscape.visual.ui.editors.continuous.CyGradientTrackRenderer
Creates a new GradientTrackRenderer object.
CyGraphAllLOD - Class in cytoscape.ding
CyGraphAllLOD is the level of detail (LOD) class used for the "Show Graphics Details" menu item.
CyGraphAllLOD() - Constructor for class cytoscape.ding.CyGraphAllLOD
 
CyGraphLOD - Class in cytoscape.ding
An instance of this class defines the level of detail that goes into a single rendering of a graph.
CyGraphLOD() - Constructor for class cytoscape.ding.CyGraphLOD
Creates a new CyGraphLOD object.
CyGroup - Interface in cytoscape.groups
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 group, and the node that represents the group.
CyGroupChangeListener - Interface in cytoscape.groups
The CyGroupChangeListener interface provides a mechanism for plugins that track group-related events to get notified of global group changes (new groups, etc.).
CyGroupChangeListener.ChangeType - Enum in cytoscape.groups
 
CyGroupImpl - Class in cytoscape.groups
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 group, and the node that represents the group.
CyGroupImpl() - Constructor for class cytoscape.groups.CyGroupImpl
Empty constructor
CyGroupImpl(CyNode, List<CyNode>, List<CyEdge>, List<CyEdge>, CyNetwork) - Constructor for class cytoscape.groups.CyGroupImpl
Constructor to create an empty group.
CyGroupImpl(String) - Constructor for class cytoscape.groups.CyGroupImpl
Constructor to create an empty group
CyGroupImpl(CyNode) - Constructor for class cytoscape.groups.CyGroupImpl
Constructor to create an empty group when the group node is specified.
CyGroupImpl(CyNode, List<CyNode>) - Constructor for class cytoscape.groups.CyGroupImpl
Constructor to create a group with the listed nodes as initial members, and a predetermined CyNode to act as the group Node.
CyGroupImpl(String, List<CyNode>) - Constructor for class cytoscape.groups.CyGroupImpl
Constructor to create a group with the listed nodes as initial members.
CyGroupManager - Class in cytoscape.groups
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 group, and the node that represents the group.
CyGroupManager() - Constructor for class cytoscape.groups.CyGroupManager
 
CyGroupViewer - Interface in cytoscape.groups
The CyGroupViewer interface provides a mechanism for group view implementations to register themselves and get notified of group creation and deletion.
CyGroupViewer.ChangeType - Enum in cytoscape.groups
The change values
CyHelpBroker - Class in cytoscape.view
This class creates the Cytoscape Help Broker for managing the JavaHelp system and help set access
CyInitParams - Interface in cytoscape.init
An interface that describes the initialization parameters needed by cytoscape.
CyLayoutAlgorithm - Interface in cytoscape.layout
 
CyLayouts - Class in cytoscape.layout
CyLayouts is a singleton class that is used to register all available layout algorithms.
CyLogger - Class in cytoscape.logger
 
CyLogger(String) - Constructor for class cytoscape.logger.CyLogger
The constructor to create a CyLogger.
CyLogHandler - Interface in cytoscape.logger
The CyLogHandler interface must be implemented by log handlers for plugins that wish to handle their own logging.
CyMain - Class in cytoscape
This is the main startup class for Cytoscape.
CyMain(String[]) - Constructor for class cytoscape.CyMain
Creates a new CyMain object.
CyMenus - Class in cytoscape.view
Creates the menu and tool bars for a Cytoscape window object.
CyMenus() - Constructor for class cytoscape.view.CyMenus
Creates a new CyMenus object.
cyMenus - Variable in class cytoscape.view.CytoscapeDesktop
The CyMenus object provides access to the all of the menus and toolbars that will be needed.
CyNetwork - Interface in cytoscape
CyNetwork is the primary class for algorithm writing.  All algorithms should take a CyNetwork as input, and do their best to only use the API of CyNetwork.  Plugins that want to affect the display of a graph can look into using CyNetworkView as well.

A CyNetwork can create Nodes or Edges.  Any Nodes or Edges that wish to be added to a CyNetwork first need to be created in Cytoscape. 

The methods that are defined by CyNetwork mostly deal with data integration and flagging of nodes/edges.  All methods that deal with graph traversal are part of the inherited API of the GraphPerspective class.  Links to which can be found at the bottom of the methods list. 

In general, all methods are supported for working with Nodes/Edges as objects, and as indices.
CyNetworkAdapter - Class in cytoscape
Empty implementation of the CyNetworkListener interface, following the adapter pattern useful for defining anonymous inner classes.
CyNetworkAdapter() - Constructor for class cytoscape.CyNetworkAdapter
 
CyNetworkData - Interface in cytoscape
This will be the interface where things like multi-dimensional data are accessed.
CyNetworkEvent - Class in cytoscape
Events of this class are fired from a CyNetwork object when something happens to the network.
CyNetworkEvent(CyNetwork, int) - Constructor for class cytoscape.CyNetworkEvent
Creates a new CyNetworkEvent object.
CyNetworkListener - Interface in cytoscape
Interface for listeners that respond to CyNetwork events.
CyNetworkNaming - Class in cytoscape.util
 
CyNetworkNaming() - Constructor for class cytoscape.util.CyNetworkNaming
 
CyNetworkTitleChange - Class in cytoscape
Class used for passing along information about the network when the network title has changed (firing an event)
CyNetworkTitleChange(String, String) - Constructor for class cytoscape.CyNetworkTitleChange
 
CyNetworkUtilities - Class in cytoscape.data
This class provides static methods that operate on a CyNetwork to perform various useful tasks.
CyNetworkUtilities() - Constructor for class cytoscape.data.CyNetworkUtilities
 
CyNetworkView - Interface in cytoscape.view
CyNetworkView is responsible for actually getting a graph to show up on the screen.

Cytoscape does not currently define specific classes for NodeViews and EdgeViews, the defaults from the GINY graph library (namely phoebe.PNodeView and phoebe.PEdgeView) are most commonly used.
CyNode - Class in cytoscape
 
CyNode(RootGraph, int) - Constructor for class cytoscape.CyNode
Creates a new CyNode object.
CyNodeView - Interface in cytoscape.view
 
CyObjectPositionPropertyEditor - Class in cytoscape.visual.ui.editors.discrete
 
CyObjectPositionPropertyEditor(VisualPropertyType) - Constructor for class cytoscape.visual.ui.editors.discrete.CyObjectPositionPropertyEditor
Creates a new CyLabelPositionLabelEditor object.
CYSESSION - Static variable in class cytoscape.data.readers.CytoscapeSessionReader
 
Cysession - Class in cytoscape.generated
Java class for anonymous complex type.
Cysession() - Constructor for class cytoscape.generated.Cysession
 
CyStartupListener - Class in cytoscape
Implementation of StartupListener interface in install4j API.
CyStartupListener() - Constructor for class cytoscape.CyStartupListener
 
CyStringPropertyEditor - Class in cytoscape.visual.ui.editors.discrete
DOCUMENT ME!
CyStringPropertyEditor() - Constructor for class cytoscape.visual.ui.editors.discrete.CyStringPropertyEditor
Creates a new CyStringPropertyEditor object.
cytoDir - Variable in class cytoscape.util.JnlpWriterUtil
 
Cytopanel - Class in cytoscape.generated
Java class for anonymous complex type.
Cytopanel() - Constructor for class cytoscape.generated.Cytopanel
 
cytopanel - Variable in class cytoscape.generated.Cytopanels
 
CytoPanel - Interface in cytoscape.view.cytopanels
Interface to a CytoPanel.
CytoPanelAction - Class in cytoscape.actions
 
CytoPanelAction(CytoPanelName, boolean, CytoPanelName) - Constructor for class cytoscape.actions.CytoPanelAction
 
CytoPanelContainer - Interface in cytoscape.view.cytopanels
Interface for Container of CytoPanel Objects.
cytoPanelEast - Variable in class cytoscape.view.CytoscapeDesktop
 
CytoPanelImp - Class in cytoscape.view.cytopanels
The CytoPanel class extends JPanel to provide the following functionality: Floating/Docking of Panel.
CytoPanelImp(int, int, CytoPanelState) - Constructor for class cytoscape.view.cytopanels.CytoPanelImp
Constructor.
CytoPanelListener - Interface in cytoscape.view.cytopanels
This listener interface provides the mechanism to respond to CytoPanel Events.
CytoPanelName - Enum in cytoscape.view.cytopanels
An enum that maps names to compass directions.
Cytopanels - Class in cytoscape.generated
Java class for anonymous complex type.
Cytopanels() - Constructor for class cytoscape.generated.Cytopanels
 
cytopanels - Variable in class cytoscape.generated.SessionState
 
cytoPanelSouth - Variable in class cytoscape.view.CytoscapeDesktop
 
cytoPanelSouthWest - Variable in class cytoscape.view.CytoscapeDesktop
 
CytoPanelState - Class in cytoscape.view.cytopanels
CytoPanelState Class.
CytoPanelUtil - Class in cytoscape.view.cytopanels
Contains methods to assist with various tasks performed by the CytoPanel API.
CytoPanelUtil() - Constructor for class cytoscape.view.cytopanels.CytoPanelUtil
 
cytoPanelWest - Variable in class cytoscape.view.CytoscapeDesktop
 
cytoscape - package cytoscape
Core Cytoscape Classes.
Cytoscape - Class in cytoscape
This class, Cytoscape is the primary class in the API.
Cytoscape() - Constructor for class cytoscape.Cytoscape
 
cytoscape.actions - package cytoscape.actions
UI classes that are attached to menu items in the menu or tool bar of the window.
cytoscape.bookmarks - package cytoscape.bookmarks
 
cytoscape.command - package cytoscape.command
 
cytoscape.cruft.obo - package cytoscape.cruft.obo
 
cytoscape.cruft.obo.test - package cytoscape.cruft.obo.test
 
cytoscape.data - package cytoscape.data
Basic data classes used by Cytoscape.
cytoscape.data.annotation - package cytoscape.data.annotation
Classes used to represent generic annotation data in Cytoscape.
cytoscape.data.annotation.readers - package cytoscape.data.annotation.readers
Reader classes for generic annotation data.
cytoscape.data.attr - package cytoscape.data.attr
 
cytoscape.data.attr.util - package cytoscape.data.attr.util
 
cytoscape.data.ontology - package cytoscape.data.ontology
 
cytoscape.data.ontology.readers - package cytoscape.data.ontology.readers
 
cytoscape.data.readers - package cytoscape.data.readers
Reader classes for the basic data types in cytoscape.data.
cytoscape.data.servers - package cytoscape.data.servers
An interface for annotation data providers and various implementations of that interface, including both remote and in-process implementations.
cytoscape.data.synonyms - package cytoscape.data.synonyms
Classes providing synonym funcationality, that is identifying multiple names that refer to the same entity.
cytoscape.data.synonyms.readers - package cytoscape.data.synonyms.readers
Readers for classes in the cytoscape.data.synonyms package.
cytoscape.data.webservice - package cytoscape.data.webservice
 
cytoscape.data.webservice.ui - package cytoscape.data.webservice.ui
 
cytoscape.data.webservice.util - package cytoscape.data.webservice.util
 
cytoscape.data.writers - package cytoscape.data.writers
 
cytoscape.dialogs - package cytoscape.dialogs
UI classes for performing some action, generally more complicated than those contained in the cytoscape.actions package.
cytoscape.dialogs.logger - package cytoscape.dialogs.logger
 
cytoscape.dialogs.plugins - package cytoscape.dialogs.plugins
 
cytoscape.dialogs.preferences - package cytoscape.dialogs.preferences
 
cytoscape.ding - package cytoscape.ding
 
cytoscape.generated - package cytoscape.generated
 
cytoscape.geom.rtree - package cytoscape.geom.rtree
 
cytoscape.geom.rtree.test - package cytoscape.geom.rtree.test
 
cytoscape.geom.spacial - package cytoscape.geom.spacial
 
cytoscape.giny - package cytoscape.giny
 
cytoscape.graph.dynamic - package cytoscape.graph.dynamic
 
cytoscape.graph.dynamic.util - package cytoscape.graph.dynamic.util
 
cytoscape.graph.fixed - package cytoscape.graph.fixed
 
cytoscape.groups - package cytoscape.groups
 
cytoscape.init - package cytoscape.init
 
cytoscape.layout - package cytoscape.layout
Classes providing some kind of graph layout functionality.
cytoscape.layout.algorithms - package cytoscape.layout.algorithms
 
cytoscape.layout.ui - package cytoscape.layout.ui
 
cytoscape.logger - package cytoscape.logger
 
cytoscape.plugin - package cytoscape.plugin
Classes related to Cytoscape plugins.
cytoscape.render.export - package cytoscape.render.export
 
cytoscape.render.immed - package cytoscape.render.immed
 
cytoscape.render.immed.arrow - package cytoscape.render.immed.arrow
 
cytoscape.render.immed.nodeshape - package cytoscape.render.immed.nodeshape
 
cytoscape.render.stateful - package cytoscape.render.stateful
 
cytoscape.task - package cytoscape.task
Cytoscape Task Framework.
cytoscape.task.sample - package cytoscape.task.sample
Sample task, used to illustrate the Task framework.
cytoscape.task.ui - package cytoscape.task.ui
UI code related to task control.
cytoscape.task.util - package cytoscape.task.util
Utility manager for executing tasks.
cytoscape.util - package cytoscape.util
This package contains utility classes which are deemed generally useful, but which do not clearly belong to any other package.
cytoscape.util.export - package cytoscape.util.export
 
cytoscape.util.intr - package cytoscape.util.intr
 
cytoscape.util.intr.test - package cytoscape.util.intr.test
 
cytoscape.util.shadegrown - package cytoscape.util.shadegrown
 
cytoscape.util.swing - package cytoscape.util.swing
 
cytoscape.util.undo - package cytoscape.util.undo
 
cytoscape.view - package cytoscape.view
Classes that provide a window to display a graph and UI components connected to that window, such as the menus.
cytoscape.view.cytopanels - package cytoscape.view.cytopanels
CytoPanels Framework.
cytoscape.visual - package cytoscape.visual
Framework for generalized mappings from graph attributes to visual attributes.
cytoscape.visual.calculators - package cytoscape.visual.calculators
Objects that calculate from the data attributes the value for one visual attribute, such as color, shape, or size.
cytoscape.visual.converter - package cytoscape.visual.converter
 
cytoscape.visual.customgraphic - package cytoscape.visual.customgraphic
 
cytoscape.visual.customgraphic.impl - package cytoscape.visual.customgraphic.impl
 
cytoscape.visual.customgraphic.impl.bitmap - package cytoscape.visual.customgraphic.impl.bitmap
 
cytoscape.visual.customgraphic.impl.vector - package cytoscape.visual.customgraphic.impl.vector
 
cytoscape.visual.customgraphic.paint - package cytoscape.visual.customgraphic.paint
 
cytoscape.visual.customgraphic.ui - package cytoscape.visual.customgraphic.ui
 
cytoscape.visual.mappings - package cytoscape.visual.mappings
The Mappings are used by Calculators to map graph attributes to visual attribute values.
cytoscape.visual.mappings.continuous - package cytoscape.visual.mappings.continuous
Mappings from a continuous numerical input to a particular visual attribute.
cytoscape.visual.mappings.discrete - package cytoscape.visual.mappings.discrete
Mappings from a discrete-valued input to a particular visual attribute.
cytoscape.visual.mappings.rangecalculators - package cytoscape.visual.mappings.rangecalculators
 
cytoscape.visual.parsers - package cytoscape.visual.parsers
Translates visual attribute values to and from their String representation.
cytoscape.visual.properties - package cytoscape.visual.properties
 
cytoscape.visual.strokes - package cytoscape.visual.strokes
The WidthStroke objects in this package should NOT be used directly by anyone other than the LineStyle enum!!!! Seriously, DON'T USE THESE CLASSES!!!
cytoscape.visual.ui - package cytoscape.visual.ui
Top-level UI components for the cytoscape.visual package.
cytoscape.visual.ui.editors.continuous - package cytoscape.visual.ui.editors.continuous
 
cytoscape.visual.ui.editors.discrete - package cytoscape.visual.ui.editors.discrete
 
cytoscape.visual.ui.icon - package cytoscape.visual.ui.icon
 
CYTOSCAPE_EXIT - Static variable in class cytoscape.Cytoscape
 
CYTOSCAPE_INITIALIZED - Static variable in class cytoscape.Cytoscape
 
CytoscapeAction - Class in cytoscape.util
 
CytoscapeAction() - Constructor for class cytoscape.util.CytoscapeAction
 
CytoscapeAction(String) - Constructor for class cytoscape.util.CytoscapeAction
Creates a new CytoscapeAction object.
CytoscapeAction(String, Icon) - Constructor for class cytoscape.util.CytoscapeAction
Creates a new CytoscapeAction object.
CytoscapeDesktop - Class in cytoscape.view
The CytoscapeDesktop is the central Window for working with Cytoscape
CytoscapeDesktop() - Constructor for class cytoscape.view.CytoscapeDesktop
Creates a new CytoscapeDesktop object.
cytoscapeDesktop - Variable in class cytoscape.view.NetworkViewManager
 
CytoscapeFingRootGraph - Class in cytoscape.giny
 
CytoscapeFingRootGraph() - Constructor for class cytoscape.giny.CytoscapeFingRootGraph
Creates a new CytoscapeFingRootGraph object.
CytoscapeInit - Class in cytoscape
Cytoscape Init is responsible for starting Cytoscape in a way that makes sense.
CytoscapeInit() - Constructor for class cytoscape.CytoscapeInit
Creates a new CytoscapeInit object.
CytoscapeMenuBar - Class in cytoscape.util
 
CytoscapeMenuBar() - Constructor for class cytoscape.util.CytoscapeMenuBar
Default constructor.
CytoscapeModifiedNetworkManager - Class in cytoscape
CytoscapeModifiedNetworkManager manages the modified state settings for the networks and listens for PropertyChangeEvents.
CytoscapeModifiedNetworkManager() - Constructor for class cytoscape.CytoscapeModifiedNetworkManager
 
CytoscapePlugin - Class in cytoscape.plugin
A CytoscapePlugin is the new "Global" plugin.
CytoscapePlugin() - Constructor for class cytoscape.plugin.CytoscapePlugin
There are no arguments required or allowed in a CytoscapePlugin constructor.
CytoscapeProgressMonitor - Class in cytoscape.util
CytoscapeProgressMonitor.
CytoscapeProgressMonitor(MonitoredTask) - Constructor for class cytoscape.util.CytoscapeProgressMonitor
Construtor.
CytoscapeProgressMonitor(MonitoredTask, Component) - Constructor for class cytoscape.util.CytoscapeProgressMonitor
Constructor.
cytoscapeRootGraph - Static variable in class cytoscape.Cytoscape
The shared RootGraph between all Networks
CytoscapeRootGraph - Interface in cytoscape.giny
 
CytoscapeSessionReader - Class in cytoscape.data.readers
Reader to load CYtoscape Session file (.cys).
This class unzip cys file and read all files in the archive.
CytoscapeSessionReader(URL, TaskMonitor) - Constructor for class cytoscape.data.readers.CytoscapeSessionReader
Constructor for remote file (specified by an URL)
CytoscapeSessionReader(String, TaskMonitor) - Constructor for class cytoscape.data.readers.CytoscapeSessionReader
Creates a new CytoscapeSessionReader object.
CytoscapeSessionReader(String) - Constructor for class cytoscape.data.readers.CytoscapeSessionReader
Constructor.
Create reader from file name.
CytoscapeSessionReader(URL) - Constructor for class cytoscape.data.readers.CytoscapeSessionReader
Creates a new CytoscapeSessionReader object.
CytoscapeSessionWriter - Class in cytoscape.data.writers
Write session states into files.
Basic functions of this class are:
1.
CytoscapeSessionWriter(String) - Constructor for class cytoscape.data.writers.CytoscapeSessionWriter
Constructor.
CytoscapeToolBar - Class in cytoscape.util
 
CytoscapeToolBar() - Constructor for class cytoscape.util.CytoscapeToolBar
Default constructor delegates to the superclass void constructor and then calls CytoscapeToolBar.initializeCytoscapeToolBar().
CytoscapeVersion - Class in cytoscape
CytoscapeVersion: identify (and describe) successive versions of cytoscape.
CytoscapeVersion() - Constructor for class cytoscape.CytoscapeVersion
 
CyUndo - Class in cytoscape.util.undo
A tiny class for supporting undo in the Cytoscape context.
CyUndo() - Constructor for class cytoscape.util.undo.CyUndo
 
CyWebServiceEvent<P> - Class in cytoscape.data.webservice
Event object used by Web Service Clients and the core.
CyWebServiceEvent(String, CyWebServiceEvent.WSEventType, P) - Constructor for class cytoscape.data.webservice.CyWebServiceEvent
 
CyWebServiceEvent(String, CyWebServiceEvent.WSEventType, P, CyWebServiceEvent.WSEventType) - Constructor for class cytoscape.data.webservice.CyWebServiceEvent
 
CyWebServiceEvent.WSEventType - Enum in cytoscape.data.webservice
 
CyWebServiceEvent.WSResponseType - Enum in cytoscape.data.webservice
Will be used to catch the signal from WS.
CyWebServiceEventListener - Interface in cytoscape.data.webservice
Listener for Web Service Event handling.
CyWebServiceEventSupport - Class in cytoscape.data.webservice
 
CyWebServiceEventSupport() - Constructor for class cytoscape.data.webservice.CyWebServiceEventSupport
Creates a new CyWebServiceEventSupport object.
CyWebServiceException - Exception in cytoscape.data.webservice
 
CyWebServiceException(CyWebServiceException.WSErrorCode) - Constructor for exception cytoscape.data.webservice.CyWebServiceException
 
CyWebServiceException.WSErrorCode - Enum in cytoscape.data.webservice
 

D

DashDotStroke - Class in cytoscape.visual.strokes
 
DashDotStroke(float) - Constructor for class cytoscape.visual.strokes.DashDotStroke
 
dashedEdges(int, int) - Method in class cytoscape.ding.CyGraphLOD
Determines whether or not to honor dashed edges.
dashedEdges(int, int) - Method in class cytoscape.render.stateful.GraphLOD
Determines whether or not to honor dashed edges.
dashedEdges(int, int) - Method in class ding.view.PrintLOD
DOCUMENT ME!
databaseComboBox - Variable in class cytoscape.util.swing.AttributeImportPanel
 
databaseComboBoxActionPerformed(ActionEvent) - Method in class cytoscape.util.swing.AttributeImportPanel
 
databasePanel - Variable in class cytoscape.util.swing.AttributeImportPanel
 
DatabaseSearchResult<R> - Class in cytoscape.data.webservice
 
DatabaseSearchResult(Integer, R, CyWebServiceEvent.WSEventType) - Constructor for class cytoscape.data.webservice.DatabaseSearchResult
 
DATASERVER_CHANGED - Static variable in class cytoscape.Cytoscape
 
DataSource - Class in cytoscape.bookmarks
Java class for anonymous complex type.
DataSource() - Constructor for class cytoscape.bookmarks.DataSource
 
DATE_VALUE - Static variable in class org.apache.commons.cli.PatternOptionBuilder
Date class
DBCrossReferenceReader - Class in cytoscape.data.ontology.readers
Reader for database cross reference file.
DBCrossReferenceReader() - Constructor for class cytoscape.data.ontology.readers.DBCrossReferenceReader
Constructor.
Create a new map for the DB references.
DBCrossReferences - Class in cytoscape.data.ontology
Database cress reference.
DBCrossReferences() - Constructor for class cytoscape.data.ontology.DBCrossReferences
Creates a new DBCrossReferences object.
DBReference - Class in cytoscape.data.ontology
Represents an entry in the database cross reference.
DBReference(String, String, String) - Constructor for class cytoscape.data.ontology.DBReference
Creates a new DBReference object.
DBReference(String, String, String, String, String) - Constructor for class cytoscape.data.ontology.DBReference
Creates a new DBReference object.
DBXrefKeywords - Enum in cytoscape.data.ontology.readers
 
deactivate() - Method in class cytoscape.plugin.CytoscapePlugin
If implemented then this plugin can remove itself from the Menu system, and anything else, when the user decides to deactivate it.
debug(String) - Method in class cytoscape.logger.CyLogger
Log a debug message.
debug(String, Throwable) - Method in class cytoscape.logger.CyLogger
Log a debug message.
DECODE_PROPERTY - Static variable in class cytoscape.data.readers.CyAttributesReader
 
DEF_COMPRESSION_LEVEL - Static variable in class cytoscape.util.ZipUtil
 
DEF_DISPLAY_NAME - Static variable in class cytoscape.data.webservice.WebServiceClientImpl
 
DEF_FONT - Static variable in class cytoscape.visual.ui.FontChooser
 
DEF_NAME - Static variable in class cytoscape.data.webservice.WebServiceClientImpl
 
DEF_RENDERER - Static variable in class cytoscape.visual.ui.CellRendererFactory
 
DEF_SIZE - Static variable in class cytoscape.visual.ui.FontChooser
 
DEF_SNAPSHOT_SIZE - Static variable in class ding.view.DGraphView
 
DEFAULT - Static variable in class cytoscape.visual.LabelPosition
Deprecated.  
DEFAULT_ARG_NAME - Static variable in class org.apache.commons.cli.HelpFormatter
default name for an argument
DEFAULT_DESC_PAD - Static variable in class org.apache.commons.cli.HelpFormatter
??
DEFAULT_EDGE_INTERACTION - Static variable in class cytoscape.data.readers.GMLReader
 
DEFAULT_GRAPH_VIEW_HANDLER - Static variable in class cytoscape.view.GraphViewController
 
DEFAULT_ICON_COLOR - Static variable in class cytoscape.visual.ui.icon.VisualPropertyIcon
Default icon color.
DEFAULT_ICON_SIZE - Static variable in class cytoscape.visual.ui.icon.VisualPropertyIcon
Default icon size for Visual Properties
DEFAULT_LEFT_PAD - Static variable in class org.apache.commons.cli.HelpFormatter
default padding to the left of each line
DEFAULT_LONG_OPT_PREFIX - Static variable in class org.apache.commons.cli.HelpFormatter
default prefix for long Option
DEFAULT_MAX_BRANCHES - Static variable in class cytoscape.geom.rtree.RTree
Deprecated. Use the no-arg constructor.
DEFAULT_MAX_BRANCHES - Static variable in class cytoscape.util.intr.IntBTree
 
DEFAULT_MENU_SPECIFIER - Static variable in class cytoscape.util.CytoscapeMenuBar
 
DEFAULT_NETWORK_METADATA_LABEL - Static variable in class cytoscape.data.readers.MetadataParser
 
DEFAULT_OPT_PREFIX - Static variable in class org.apache.commons.cli.HelpFormatter
default prefix for shortOpts
DEFAULT_POSITION - Static variable in class ding.view.ObjectPositionImpl
 
DEFAULT_SYNTAX_PREFIX - Static variable in class org.apache.commons.cli.HelpFormatter
the string to display at the begining of the usage statement
DEFAULT_WIDTH - Static variable in class org.apache.commons.cli.HelpFormatter
default number of characters per line
DEFAULT_WIN_HEIGHT - Static variable in class cytoscape.view.CyDesktopManager
 
DEFAULT_WIN_WIDTH - Static variable in class cytoscape.view.CyDesktopManager
 
DefaultAppearenceBuilder - Class in cytoscape.visual.ui
Dialog for editing default visual property values.
This is a modal dialog.
DefaultCyCustomGraphicsParser - Class in cytoscape.visual.customgraphic
 
DefaultCyCustomGraphicsParser() - Constructor for class cytoscape.visual.customgraphic.DefaultCyCustomGraphicsParser
 
defaultDesktop - Static variable in class cytoscape.Cytoscape
 
defaultMenuSpecifier - Variable in class cytoscape.util.CytoscapeMenuBar
 
DefaultPluginSiteTitle - Static variable in class cytoscape.dialogs.plugins.PluginManageDialog
 
defaultPluginSiteUrl - Static variable in class cytoscape.dialogs.plugins.PluginManageDialog
 
DefaultViewPanel - Class in cytoscape.visual.ui
Panel to show the default properties visually (as graphics).
defaultVisualStyle - Variable in class cytoscape.view.CytoscapeDesktop
 
defineAttribute(String, byte, byte[]) - Method in interface cytoscape.data.attr.MultiHashMapDefinition
Creates an attribute definition.
defineCustomNodeShape(float[], int, int) - Method in class cytoscape.render.immed.GraphGraphics
The custom node shape that is defined is a polygon specified by the coordinates supplied.
Degrees - Class in org.cytoscape.equations.builtins
 
Degrees() - Constructor for class org.cytoscape.equations.builtins.Degrees
 
delayedFireTableDataChanged() - Method in class cytoscape.util.swing.TreeTableModelAdapter
Invokes fireTableDataChanged after all the pending events have been processed.
delete(int) - Method in class cytoscape.geom.rtree.RTree
Deletes the specified data entry from this tree.
delete(int) - Method in interface cytoscape.geom.spacial.MutableSpacialIndex2D
Deletes the specified data entry from this structure.
delete(DownloadableInfo) - Method in class cytoscape.plugin.PluginManager
Marks the given object for deletion the next time Cytoscape is restarted.
delete() - Method in class cytoscape.plugin.PluginManager
Takes all objects on the "to-delete" list and deletes them.
delete() - Method in class cytoscape.plugin.PluginTracker
Deletes the tracker file.
delete(int) - Method in class cytoscape.util.intr.IntBTree
Deletes at most one entry of the integer x.
DeleteAction - Class in cytoscape.actions
action for deleting selected Cytoscape nodes and edges
DeleteAction() - Constructor for class cytoscape.actions.DeleteAction
action for deleting selected Cytoscape nodes and edges
DeleteAction(GraphObject) - Constructor for class cytoscape.actions.DeleteAction
perform deletion on the input object.
deleteAttribute(String, String) - Method in interface cytoscape.data.CyAttributes
Deletes the id/attributeName pair.
deleteAttribute(String) - Method in interface cytoscape.data.CyAttributes
Deletes the specified attribute.
deleteAttribute(String, String) - Method in class cytoscape.data.CyAttributesImpl
DOCUMENT ME!
deleteAttribute(String) - Method in class cytoscape.data.CyAttributesImpl
DOCUMENT ME!
deleteBookmark(String, Bookmarks, String, DataSource) - Static method in class cytoscape.util.BookmarksUtil
DOCUMENT ME!
deleteBookmark(Bookmarks, String, DataSource) - Static method in class cytoscape.util.BookmarksUtil
DOCUMENT ME!
deleteButton - Variable in class cytoscape.visual.ui.editors.continuous.ContinuousMappingEditorPanel
 
deleteButtonActionPerformed(ActionEvent) - Method in class cytoscape.visual.ui.editors.continuous.C2CMappingEditor
Remove selected slider.
deleteButtonActionPerformed(ActionEvent) - Method in class cytoscape.visual.ui.editors.continuous.C2DMappingEditor
 
deleteButtonActionPerformed(ActionEvent) - Method in class cytoscape.visual.ui.editors.continuous.ContinuousMappingEditorPanel
 
deleteButtonActionPerformed(ActionEvent) - Method in class cytoscape.visual.ui.editors.continuous.GradientEditorPanel
 
deleteEdgeAttribute(String) - Method in class cytoscape.giny.FingCyNetwork
Deletes the attribute with the given name from edge attributes
deleteMin() - Method in class cytoscape.util.intr.MinIntHeap
Deletes and returns the minimum element in this heap.
deleteNodeAttribute(String) - Method in class cytoscape.giny.FingCyNetwork
Deletes the attribute with the given name from node attributes
deletePlugins(String[]) - Method in class cytoscape.dialogs.preferences.PluginsTableModel
Deprecated. DOCUMENT ME!
deleteProperty(String) - Method in class cytoscape.dialogs.preferences.PreferenceTableModel
DOCUMENT ME!
deleteTerm(Term) - Method in class cytoscape.data.ontology.Ontology
Delete a term from DAG (CyNetwork)
DELIMITER - Static variable in class cytoscape.visual.customgraphic.impl.AbstractDCustomGraphics
 
DELTA - Static variable in class cytoscape.visual.Arrow
DOCUMENT ME!
DeltaArrow - Class in cytoscape.render.immed.arrow
 
DeltaArrow() - Constructor for class cytoscape.render.immed.arrow.DeltaArrow
 
dequeue() - Method in class cytoscape.util.intr.IntQueue
Removes and returns the next integer in this queue.
desc - Variable in class cytoscape.util.undo.CyAbstractEdit
 
describe() - Method in class cytoscape.data.servers.BioDataServer
DOCUMENT ME!
describe() - Method in interface cytoscape.data.servers.BioDataServerInterface
DOCUMENT ME!
describe() - Method in class cytoscape.data.servers.BioDataServerRmi
DOCUMENT ME!
describeOptions(CLOptionDescriptor[]) - Static method in class org.apache.commons.cli.avalon.CLUtil
Format options into StringBuffer and return.
description - Variable in class cytoscape.bookmarks.Bookmarks
 
description - Variable in class cytoscape.data.webservice.WebServiceClientImpl
 
descriptionMap - Variable in class cytoscape.command.AbstractCommandHandler
 
DeselectAllAction - Class in cytoscape.actions
 
DeselectAllAction() - Constructor for class cytoscape.actions.DeselectAllAction
Creates a new DeselectAllAction object.
deselectAllEdges(GraphView) - Static method in class cytoscape.actions.GinyUtils
DOCUMENT ME!
deselectAllEdges() - Method in class cytoscape.dialogs.GinyEdgeControlDialog
 
DeSelectAllEdgesAction - Class in cytoscape.actions
 
DeSelectAllEdgesAction() - Constructor for class cytoscape.actions.DeSelectAllEdgesAction
Creates a new DeSelectAllEdgesAction object.
deselectAllNodes(GraphView) - Static method in class cytoscape.actions.GinyUtils
DOCUMENT ME!
DeSelectAllNodesAction - Class in cytoscape.actions
 
DeSelectAllNodesAction() - Constructor for class cytoscape.actions.DeSelectAllNodesAction
Creates a new DeSelectAllNodesAction object.
Desktop - Class in cytoscape.generated
Java class for anonymous complex type.
Desktop() - Constructor for class cytoscape.generated.Desktop
 
desktop - Variable in class cytoscape.generated.SessionState
 
desktop - Static variable in class cytoscape.view.CyDesktopManager
 
desktopSize - Variable in class cytoscape.generated.Desktop
 
DesktopSize - Class in cytoscape.generated
Java class for anonymous complex type.
DesktopSize() - Constructor for class cytoscape.generated.DesktopSize
 
destroy() - Method in class ding.view.BirdsEyeView
DOCUMENT ME!
destroyCurrentNetwork() - Static method in class cytoscape.actions.DestroyNetworkAction
Deprecated. Use Cytoscape.destroyNetwork(Cytoscape.getCurrentNetwork()) instead. Will be gone 11/2008.
destroyNetwork(String) - Static method in class cytoscape.Cytoscape
destroys the given network
destroyNetwork(CyNetwork) - Static method in class cytoscape.Cytoscape
destroys the given network
destroyNetwork(CyNetwork, boolean) - Static method in class cytoscape.Cytoscape
destroys the given network
DestroyNetworkAction - Class in cytoscape.actions
 
DestroyNetworkAction() - Constructor for class cytoscape.actions.DestroyNetworkAction
Creates a new DestroyNetworkAction object.
DestroyNetworkAction(boolean) - Constructor for class cytoscape.actions.DestroyNetworkAction
Creates a new DestroyNetworkAction object.
destroyNetworkView(CyNetworkView) - Static method in class cytoscape.Cytoscape
Destroys the network view.
destroyNetworkView(String) - Static method in class cytoscape.Cytoscape
destroys the networkview, including any layout information
destroyNetworkView(CyNetwork) - Static method in class cytoscape.Cytoscape
destroys the networkview, including any layout information
DestroyNetworkViewAction - Class in cytoscape.actions
 
DestroyNetworkViewAction() - Constructor for class cytoscape.actions.DestroyNetworkViewAction
Creates a new DestroyNetworkViewAction object.
DestroyNetworkViewAction(boolean) - Constructor for class cytoscape.actions.DestroyNetworkViewAction
Creates a new DestroyNetworkViewAction object.
destroyViewFromCurrentNetwork() - Static method in class cytoscape.actions.DestroyNetworkViewAction
Deprecated. Use Cytoscape.destroyNetworkView() instead. Will go 11/2008.
detail(int, int) - Method in class cytoscape.ding.CyGraphLOD
Determines whether or not to render a graph at full detail.
detail(int, int) - Method in class cytoscape.render.stateful.GraphLOD
Determines whether or not to render a graph at full detail.
detail(int, int) - Method in class ding.view.PrintLOD
DOCUMENT ME!
DGraphView - Class in ding.view
DING implementation of the GINY view.
DGraphView(GraphPerspective) - Constructor for class ding.view.DGraphView
Creates a new DGraphView object.
DGraphView.Canvas - Enum in ding.view
Enum to identify ding canvases - used in getCanvas(Canvas canvasId)
DGraphView.ShapeType - Enum in ding.view
 
DIAMOND - Static variable in class cytoscape.data.readers.GMLReader
 
DIAMOND - Static variable in class cytoscape.data.readers.XGMMLReader
 
DIAMOND - Static variable in class cytoscape.visual.Arrow
DOCUMENT ME!
DIAMOND - Static variable in interface giny.view.NodeView
 
DiamondArrow - Class in cytoscape.render.immed.arrow
 
DiamondArrow() - Constructor for class cytoscape.render.immed.arrow.DiamondArrow
 
DiamondNodeShape - Class in cytoscape.render.immed.nodeshape
 
DiamondNodeShape() - Constructor for class cytoscape.render.immed.nodeshape.DiamondNodeShape
 
DIFFERENCE - Static variable in class cytoscape.util.GraphSetUtils
 
DIFFERENCE2 - Static variable in class cytoscape.util.GraphSetUtils
 
differenceEdges(List) - Static method in class cytoscape.util.GraphSetUtils
Determine the set of difference edges.
differenceEdges2(List, int[]) - Static method in class cytoscape.util.GraphSetUtils
Determine the set of difference edges.
differenceNodes(List, int[]) - Static method in class cytoscape.util.GraphSetUtils
Determine the set of difference nodes.
differenceNodes2(List) - Static method in class cytoscape.util.GraphSetUtils
Returns the nodes of the 1st network that are not contained in any of the other networks.
ding.view - package ding.view
 
ding.view.test - package ding.view.test
 
DingCanvas - Class in ding.view
This class is meant to be extended by a class which is meant to exist within the InternalFrameComponent class.
DingCanvas() - Constructor for class ding.view.DingCanvas
 
DingNetworkView - Class in cytoscape.ding
Extended version of DGraphView defined in Ding.
DingNetworkView(CyNetwork, String) - Constructor for class cytoscape.ding.DingNetworkView
Creates a new DingNetworkView object.
DIRECTED_EDGE - Static variable in interface cytoscape.graph.dynamic.DynamicGraph
A nonnegative quantity representing directedness of an edge.
DIRECTED_EDGE - Static variable in interface cytoscape.graph.fixed.FixedGraph
A nonnegative quantity representing directedness of an edge.
disableEdgeSelection() - Method in class ding.view.DGraphView
Disables the ability to select edges.
disableEdgeSelection() - Method in interface giny.view.GraphView
 
disableNodeMovement() - Method in class ding.view.InnerCanvas
 
disableNodeSelection() - Method in class ding.view.DGraphView
Disables the ability to select nodes.
disableNodeSelection() - Method in interface giny.view.GraphView
 
DiscArrow - Class in cytoscape.render.immed.arrow
 
DiscArrow() - Constructor for class cytoscape.render.immed.arrow.DiscArrow
 
DiscreteLegend - Class in cytoscape.visual.mappings.discrete
 
DiscreteLegend(Map, String, VisualPropertyType) - Constructor for class cytoscape.visual.mappings.discrete.DiscreteLegend
Creates a new DiscreteLegend object.
DiscreteMapping - Class in cytoscape.visual.mappings
Implements a lookup table mapping data to values of a particular class.
DiscreteMapping(Object, byte) - Constructor for class cytoscape.visual.mappings.DiscreteMapping
Deprecated. Use new constructor instead. Will be removed in 10/2011. Controlling attribute name is always required, and now it's a part of constructor argument.
DiscreteMapping(Object, String, byte) - Constructor for class cytoscape.visual.mappings.DiscreteMapping
Deprecated. Use new constructor instead. Will be removed in 10/2011. Controlling attribute name is always required, and now it's a part of constructor argument.
DiscreteMapping(Class<?>, String) - Constructor for class cytoscape.visual.mappings.DiscreteMapping
Constructor for Discrete mapping.
DiscreteMappingReader - Class in cytoscape.visual.mappings.discrete
Reads in DiscreteMapping Properties.
DiscreteMappingReader(Properties, String, ValueParser) - Constructor for class cytoscape.visual.mappings.discrete.DiscreteMappingReader
Constructor.
DiscreteMappingWriter - Class in cytoscape.visual.mappings.discrete
Writes DiscreteMapping Properties.
DiscreteMappingWriter(String, String, SortedMap) - Constructor for class cytoscape.visual.mappings.discrete.DiscreteMappingWriter
Constructor.
DiscretePropertySetter - Class in cytoscape.visual.ui
 
DiscreteRangeCalculator<T,V> - Class in cytoscape.visual.mappings.discrete
Range Calculator for the Discrete Mapper.
DiscreteRangeCalculator(SortedMap<T, V>, String) - Constructor for class cytoscape.visual.mappings.discrete.DiscreteRangeCalculator
Constructor.
DiscreteTrackRenderer<T> - Class in cytoscape.visual.ui.editors.continuous
DOCUMENT ME!
DiscreteTrackRenderer(VisualPropertyType, T, T) - Constructor for class cytoscape.visual.ui.editors.continuous.DiscreteTrackRenderer
Creates a new DiscreteTrackRenderer object.
displayCancelButton(boolean) - Method in class cytoscape.task.ui.JTaskConfig
Enables/Disables Display of the Cancel Button.
displayCloseButton(boolean) - Method in class cytoscape.task.ui.JTaskConfig
Enables/Disables Display of the Close Button.
displayName - Variable in class cytoscape.data.webservice.WebServiceClientImpl
 
displayName - Variable in class cytoscape.visual.customgraphic.impl.AbstractDCustomGraphics
 
displayStatus(boolean) - Method in class cytoscape.task.ui.JTaskConfig
Enables/Disables Display of the Status Field.
displayTimeElapsed(boolean) - Method in class cytoscape.task.ui.JTaskConfig
Enables/Disables Display of the Time Elapsed Field.
displayTimeRemaining(boolean) - Method in class cytoscape.task.ui.JTaskConfig
Enables/Disables Display of the Time Remaining Field.
DLayer - Class in cytoscape.visual.customgraphic.impl
 
DLayer(CustomGraphic, int) - Constructor for class cytoscape.visual.customgraphic.impl.DLayer
 
DNA - Static variable in class cytoscape.data.Semantics
Deprecated. 
DNodeView - Class in ding.view
Ding implementation of GINY NodeView.
DOCK - Static variable in class cytoscape.view.cytopanels.CytoPanelState
Dock state of a CytoPanel.
document - Variable in class cytoscape.util.JnlpWriterUtil
 
documentVersion - Variable in class cytoscape.generated.Cysession
 
doLayout() - Method in class cytoscape.layout.AbstractLayout
doLayout on current network view.
doLayout(CyNetworkView) - Method in class cytoscape.layout.AbstractLayout
doLayout on specified network view.
doLayout(CyNetworkView, TaskMonitor) - Method in class cytoscape.layout.AbstractLayout
doLayout on specified network view with specified monitor.
doLayout() - Method in interface cytoscape.layout.CyLayoutAlgorithm
This method performs the layout on the current network using the current network view.
doLayout(CyNetworkView) - Method in interface cytoscape.layout.CyLayoutAlgorithm
This method performs the layout on the current network.
doLayout(CyNetworkView, TaskMonitor) - Method in interface cytoscape.layout.CyLayoutAlgorithm
This method performs the layout on the current network, but assumes that the layout is part of an existing monitored task
doLayout() - Method in class cytoscape.layout.LayoutAdapter
This method performs the layout on the current network using the current network view.
doLayout(CyNetworkView) - Method in class cytoscape.layout.LayoutAdapter
This method performs the layout on the current network.
doLayout(CyNetworkView, TaskMonitor) - Method in class cytoscape.layout.LayoutAdapter
This method performs the layout on the current network, but assumes that the layout is part of an existing monitored task
doLayout() - Method in interface cytoscape.layout.LayoutAlgorithm
Deprecated.  
done() - Method in interface cytoscape.util.MonitoredTask
Returns true if the task is done.
doPostProcessing(CyNetwork) - Method in class cytoscape.data.readers.AbstractGraphReader
Executes post-processing: no-op.
doPostProcessing(CyNetwork) - Method in class cytoscape.data.readers.GMLReader
DOCUMENT ME!
doPostProcessing(CyNetwork) - Method in interface cytoscape.data.readers.GraphReader
Execute whatever post-processing is required.
doPostProcessing(CyNetwork) - Method in class cytoscape.data.readers.InteractionsReader
 
doPostProcessing(CyNetwork) - Method in class cytoscape.data.readers.XGMMLReader
This method does all of our postprocessing after reading and parsing the file
DotStroke - Class in cytoscape.visual.strokes
 
DotStroke(float) - Constructor for class cytoscape.visual.strokes.DotStroke
 
DOUBLE - Static variable in class cytoscape.data.readers.GMLTree
When getting a vector, used to specify the type for the contained objects
DOUBLE - Static variable in class cytoscape.layout.Tunable
Tunables of type DOUBLE allow data entry of double values, possibly bounded between lowerBound and upperBound: if the flag Tunable.USESLIDER is set, and the caller provides both lower and upper bounds, the user is presented with a slider interface.
DOUBLE_TYPE - Static variable in class cytoscape.data.NetworkData
 
DoubleList - Class in org.cytoscape.equations
 
DoubleList(double[]) - Constructor for class org.cytoscape.equations.DoubleList
 
DoubleParser - Class in cytoscape.visual.parsers
Parses a String into a Double object.
DoubleParser() - Constructor for class cytoscape.visual.parsers.DoubleParser
 
DoubleRangeValueCalculator - Class in cytoscape.visual.mappings.rangecalculators
 
DoubleRangeValueCalculator() - Constructor for class cytoscape.visual.mappings.rangecalculators.DoubleRangeValueCalculator
 
doubleToLong(double) - Static method in class org.cytoscape.equations.EquationUtil
 
doubleValue() - Method in class cytoscape.data.readers.GMLNode
Get the value of this node as a Double
download(DownloadableInfo) - Method in class cytoscape.plugin.PluginManager
Downloads given object to the temporary directory.
download(DownloadableInfo, TaskMonitor) - Method in class cytoscape.plugin.PluginManager
Downloads given object to the temporary directory.
download(String, File, TaskMonitor) - Static method in class cytoscape.util.URLUtil
Download the file specified by the url string to the given File object
download(URL) - Static method in class cytoscape.util.URLUtil
Get the the contents of the given URL as a string.
DownloadableInfo - Class in cytoscape.plugin
 
DownloadableInfo() - Constructor for class cytoscape.plugin.DownloadableInfo
 
DownloadableInfo(String) - Constructor for class cytoscape.plugin.DownloadableInfo
 
DownloadableInfo(String, DownloadableInfo) - Constructor for class cytoscape.plugin.DownloadableInfo
 
DownloadableInfo.License - Class in cytoscape.plugin
Fetches and keeps a plugin license if one is available.
DownloadableInfo.License(URL) - Constructor for class cytoscape.plugin.DownloadableInfo.License
 
DownloadableInfo.License(String) - Constructor for class cytoscape.plugin.DownloadableInfo.License
 
DownloadableType - Enum in cytoscape.plugin
 
downloadFromURL(URL, TaskMonitor) - Method in class cytoscape.data.ImportHandler
Download a temporary file from the given URL.
dragEnter(DropTargetDragEvent) - Method in class ding.view.InnerCanvas
default dragEnter handler.
dragExit(DropTargetEvent) - Method in class ding.view.InnerCanvas
default dragExit handler.
dragOver(DropTargetDragEvent) - Method in class ding.view.InnerCanvas
default dragOver handler.
drawCustomGraphicFull(Shape, float, float, Paint) - Method in class cytoscape.render.immed.GraphGraphics
Fills an arbitrary graphical shape with high detail.
drawEdgeFull(byte, float, Paint, byte, float, Paint, float, float, EdgeAnchors, float, float, float, Stroke, Paint) - Method in class cytoscape.render.immed.GraphGraphics
Draws an edge with medium to high detail, depending on parameters specified.
drawEdgeLow(float, float, float, float, Color) - Method in class cytoscape.render.immed.GraphGraphics
This is the method that will render an edge very quickly.
drawNodeFull(byte, float, float, float, float, Paint, float, Paint) - Method in class cytoscape.render.immed.GraphGraphics
Draws a node with medium to high detail, depending on parameters specified.
drawNodeLow(float, float, float, float, Color) - Method in class cytoscape.render.immed.GraphGraphics
This is the method that will render a node very quickly.
drawSelected() - Method in interface giny.view.Bend
Draws any handles previously added.
drawSelected() - Method in interface giny.view.EdgeView
Draws the edge as red and draws any handles previously added.
drawSnapshot(Image, GraphLOD, Paint, double, double, double) - Method in class ding.view.DGraphView
DOCUMENT ME!
drawTextFull(Font, double, String, float, float, float, Paint, boolean) - Method in class cytoscape.render.immed.GraphGraphics
Renders text onto the underlying image with medium to high detail, depending on parameters specified.
drawTextLow(Font, String, float, float, Color) - Method in class cytoscape.render.immed.GraphGraphics
This method will render text very quickly.
drawUnselected() - Method in interface giny.view.Bend
Removes any handles from the display.
drawUnselected() - Method in interface giny.view.EdgeView
Draws the edge as black and removes any handles from the display.
drop(DropTargetDropEvent) - Method in class ding.view.InnerCanvas
default drop handler.
dropActionChanged(DropTargetDragEvent) - Method in class ding.view.InnerCanvas
default dropActionChanged handler.
DropDownMenuButton - Class in cytoscape.util.swing
Button with drop down menu.
DropDownMenuButton(AbstractAction) - Constructor for class cytoscape.util.swing.DropDownMenuButton
Creates a new DropDownMenuButton object.
dump() - Method in class cytoscape.data.synonyms.Thesaurus
DOCUMENT ME!
dupeCount - Variable in class cytoscape.visual.VisualStyle
Keep track of number of times this style has been cloned.
DuplicateCalculatorNameException - Exception in cytoscape.visual
This Exception is thrown when one attempts to add a Calculator to a CalculatorCatalog that already has a Calculator of the same name and interface type.
DuplicateCalculatorNameException(String) - Constructor for exception cytoscape.visual.DuplicateCalculatorNameException
Creates a new DuplicateCalculatorNameException object.
DuplicatePluginClassException - Exception in cytoscape.plugin
 
DuplicatePluginClassException() - Constructor for exception cytoscape.plugin.DuplicatePluginClassException
 
DuplicatePluginClassException(String) - Constructor for exception cytoscape.plugin.DuplicatePluginClassException
 
DuplicatePluginClassException(Throwable) - Constructor for exception cytoscape.plugin.DuplicatePluginClassException
 
DuplicatePluginClassException(String, Throwable) - Constructor for exception cytoscape.plugin.DuplicatePluginClassException
 
DUPLICATES_ALLOWED - Static variable in class org.apache.commons.cli.avalon.CLOptionDescriptor
Flag to say this option may be repeated on the command line
DynamicGraph - Interface in cytoscape.graph.dynamic
A graph whose topology can be modified.
DynamicGraphFactory - Class in cytoscape.graph.dynamic.util
A factory for getting cytoscape.graph.dynamic.DynamicGraph instances.
DynamicLayoutMenu - Class in cytoscape.layout.ui
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 factors such as whether or not nodes are selected, the presence of node or edge attributes, etc.
DynamicLayoutMenu(CyLayoutAlgorithm, boolean) - Constructor for class cytoscape.layout.ui.DynamicLayoutMenu
Creates a new DynamicLayoutMenu object.
DynamicLayoutMenu.LayoutAttributeMenuItem - Class in cytoscape.layout.ui
 
DynamicLayoutMenu.LayoutAttributeMenuItem(String, boolean) - Constructor for class cytoscape.layout.ui.DynamicLayoutMenu.LayoutAttributeMenuItem
 

E

EAST - Static variable in interface giny.view.Label
Deprecated. 
eastName - Static variable in class cytoscape.visual.LabelPosition
Deprecated.  
EDGE - Static variable in class cytoscape.data.readers.GMLReader
 
EDGE - Static variable in class cytoscape.data.readers.XGMMLReader
 
EDGE - Static variable in class cytoscape.data.writers.CytoscapeSessionWriter
 
EDGE - Static variable in class cytoscape.data.writers.XGMMLWriter
 
Edge - Class in cytoscape.generated
Java class for anonymous complex type.
Edge() - Constructor for class cytoscape.generated.Edge
 
edge - Variable in class cytoscape.generated.HiddenEdges
 
edge - Variable in class cytoscape.generated.SelectedEdges
 
Edge - Interface in giny.model
 
EDGE_ANCHOR_MIDPOINT - Static variable in class cytoscape.render.stateful.EdgeDetails
Specifies that an anchor point lies at the midpoint of an edge.
EDGE_ANCHOR_SOURCE - Static variable in class cytoscape.render.stateful.EdgeDetails
Specifies that an anchor point lies at an edge's endpoint at source node.
EDGE_ANCHOR_TARGET - Static variable in class cytoscape.render.stateful.EdgeDetails
Specifies that an anchor point lies at an edge's endpoint at target node.
EDGE_ATTRIBUTE_ADDED - Static variable in class cytoscape.data.NetworkData
 
EDGE_ATTRIBUTE_REMOVED - Static variable in class cytoscape.data.NetworkData
 
EDGE_COLOR_ARROW - Static variable in interface giny.view.EdgeView
 
EDGE_COLOR_CIRCLE - Static variable in interface giny.view.EdgeView
 
EDGE_COLOR_DELTA - Static variable in interface giny.view.EdgeView
 
EDGE_COLOR_DIAMOND - Static variable in interface giny.view.EdgeView
 
EDGE_COLOR_T - Static variable in interface giny.view.EdgeView
 
EDGE_HALF_ARROW_BOTTOM - Static variable in interface giny.view.EdgeView
 
EDGE_HALF_ARROW_TOP - Static variable in interface giny.view.EdgeView
 
EDGE_LINE_TYPE - Static variable in interface giny.view.GraphView
 
EDGE_MAPPING - Static variable in interface cytoscape.visual.mappings.ObjectMapping
Deprecated. 
EDGE_NATURE - Static variable in class cytoscape.data.ImportHandler
Filter Type: EDGE.
EDGE_PAINT - Static variable in interface giny.view.GraphView
 
EDGE_SELECTION_PAINT - Static variable in interface giny.view.GraphView
 
EDGE_SET - Static variable in class cytoscape.data.SelectEvent
Static constant indicating a change to a group of Edges.
EDGE_SOURCE_END_PAINT - Static variable in interface giny.view.GraphView
 
EDGE_SOURCE_END_SELECTED_PAINT - Static variable in interface giny.view.GraphView
 
EDGE_SOURCE_END_TYPE - Static variable in interface giny.view.GraphView
 
EDGE_SUFFIX - Static variable in class cytoscape.data.AttributeSaverDialog
Default suffix for edge attribute files
EDGE_TARGET_END_PAINT - Static variable in interface giny.view.GraphView
 
EDGE_TARGET_END_SELECTED_PAINT - Static variable in interface giny.view.GraphView
 
EDGE_TARGET_END_TYPE - Static variable in interface giny.view.GraphView
 
EDGE_WIDTH - Static variable in interface giny.view.GraphView
 
edgeAnchors(int, int) - Method in class cytoscape.ding.CyGraphLOD
Determines whether or not to honor edge anchors.
EdgeAnchors - Interface in cytoscape.render.immed
Specifies edge anchor points to use when rendering edges in full detail mode.
edgeAnchors(int, int) - Method in class cytoscape.render.stateful.GraphLOD
Determines whether or not to honor edge anchors.
edgeAnchors(int, int) - Method in class ding.view.PrintLOD
DOCUMENT ME!
EdgeAppearance - Class in cytoscape.visual
Objects of this class hold data describing the appearance of an Edge.
EdgeAppearance() - Constructor for class cytoscape.visual.EdgeAppearance
Creates a new EdgeAppearance object.
EdgeAppearanceCalculator - Class in cytoscape.visual
This class calculates the appearance of an Edge.
EdgeAppearanceCalculator() - Constructor for class cytoscape.visual.EdgeAppearanceCalculator
Deprecated. Use VisualStyle.getEdgeAppearanceCalculator() or new EdgeAppearanceCalculator( VisualStyle.getDependency() ); Will be removed Jan 2010.
EdgeAppearanceCalculator(VisualPropertyDependency) - Constructor for class cytoscape.visual.EdgeAppearanceCalculator
Creates a new EdgeAppearanceCalculator object.
EdgeAppearanceCalculator(EdgeAppearanceCalculator) - Constructor for class cytoscape.visual.EdgeAppearanceCalculator
Copy constructor.
EdgeAppearanceCalculator(String, Properties, String, CalculatorCatalog, VisualPropertyDependency) - Constructor for class cytoscape.visual.EdgeAppearanceCalculator
Creates a new EdgeAppearanceCalculator and immediately customizes it by calling applyProperties with the supplied arguments.
edgeArrows(int, int) - Method in class cytoscape.ding.CyGraphLOD
Determines whether or not to render edge arrows.
edgeArrows(int, int) - Method in class cytoscape.render.stateful.GraphLOD
Determines whether or not to render edge arrows.
edgeArrows(int, int) - Method in class ding.view.PrintLOD
DOCUMENT ME!
edgeArrowThreshold - Variable in class cytoscape.ding.CyGraphLOD
 
edgeAttrFiles - Variable in class cytoscape.CyMain
 
edgeAttribute - Variable in class cytoscape.layout.AbstractLayout
 
EDGEATTRIBUTE - Static variable in class cytoscape.layout.Tunable
Tunables of type EDGEATTRIBUTE present a user with a list of the currently defined edge attributes for selection: if the flag Tunable.NUMERICATTRIBUTE is set, only integer or double attributes are shown, and if the Tunable.MULTISELECT flag is set, the user is presented with a list from which multiple values can be selected, otherwise, the user is presented with a combo box.
EdgeAttributesPopupDetails - Class in cytoscape.dialogs
This class provides a detailed list of attribute information for a given edge.
EdgeAttributesPopupDetails(Frame, String, CyAttributes) - Constructor for class cytoscape.dialogs.EdgeAttributesPopupDetails
Creates a new EdgeAttributesPopupDetails object.
EdgeAttributesPopupDetails.OKAction - Class in cytoscape.dialogs
 
EdgeColorProp - Class in cytoscape.visual.properties
 
EdgeColorProp() - Constructor for class cytoscape.visual.properties.EdgeColorProp
 
EdgeContextMenuListener - Interface in ding.view
an interface for responding to PhoebeCanvasDropEvents.
edgeContextMenuListeners - Variable in class ding.view.InnerCanvas
Listeners for edge right-click menu.
edgeCount() - Method in class ding.view.DGraphView
DOCUMENT ME!
edgeCount() - Method in interface giny.view.GraphView
 
edgeCreate(int, int, boolean) - Method in interface cytoscape.graph.dynamic.DynamicGraph
Creates a new edge in this graph, having source node, target node, and directedness specified.
EdgeDetails - Class in cytoscape.render.stateful
Defines the visual properties of an edge.
EdgeDetails() - Constructor for class cytoscape.render.stateful.EdgeDetails
Instantiates edge details with defaults.
edgeExists(Node, Node) - Method in interface giny.model.GraphPerspective
This method returns true if and only if either 1) there exists a directed edge E in this GraphPerspective such that the from node specified is E's source node and the target node specified is E's target node or 2) there exists an undirected edge E in this GraphPerspective such that E's endpoints are the from and to nodes specified.
edgeExists(int, int) - Method in interface giny.model.GraphPerspective
This method returns true if and only if either 1) there exists a directed edge E in this GraphPerspective such that from_node_index is E's source node's index and to_node_index is E's target node's index or 2) there exists an undirected edge E in this GraphPerspective such that E's endpoint nodes have indices from_node_index and to_node_index.
edgeExists(Node, Node) - Method in interface giny.model.RootGraph
Deprecated. Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead; if you decide to use this method anyways: this method returns true if and only if either 1) there exists a directed edge E in this RootGraph such that the from node specified is E's source node and the target node specified is E's target node or 2) there exists an undirected edge E in this RootGraph such that E's endpoints are the from and to nodes specified.
edgeExists(int, int) - Method in interface giny.model.RootGraph
Deprecated. Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead; if you decide to use this method anyways: this method returns true if and only if either 1) there exists a directed edge E in this RootGraph such that from_node_index is E's source node's index and to_node_index is E's target node's index or 2) there exists an undirected edge E in this RootGraph such that E's endpoint nodes have indices from_node_index and to_node_index.
EdgeFontFaceProp - Class in cytoscape.visual.properties
 
EdgeFontFaceProp() - Constructor for class cytoscape.visual.properties.EdgeFontFaceProp
 
EdgeFontSizeProp - Class in cytoscape.visual.properties
 
EdgeFontSizeProp() - Constructor for class cytoscape.visual.properties.EdgeFontSizeProp
 
EdgeLabelColorProp - Class in cytoscape.visual.properties
 
EdgeLabelColorProp() - Constructor for class cytoscape.visual.properties.EdgeLabelColorProp
 
EdgeLabelOpacityProp - Class in cytoscape.visual.properties
 
EdgeLabelOpacityProp() - Constructor for class cytoscape.visual.properties.EdgeLabelOpacityProp
 
EdgeLabelPositionProp - Class in cytoscape.visual.properties
 
EdgeLabelPositionProp() - Constructor for class cytoscape.visual.properties.EdgeLabelPositionProp
 
EdgeLabelProp - Class in cytoscape.visual.properties
 
EdgeLabelProp() - Constructor for class cytoscape.visual.properties.EdgeLabelProp
 
edgeLabels(int, int) - Method in class cytoscape.ding.CyGraphLOD
Determines whether or not to render edge labels.
edgeLabels(int, int) - Method in class cytoscape.render.stateful.GraphLOD
Determines whether or not to render edge labels.
edgeLabels(int, int) - Method in class ding.view.PrintLOD
DOCUMENT ME!
edgeLabelThreshold - Variable in class cytoscape.ding.CyGraphLOD
 
EdgeLabelWidthProp - Class in cytoscape.visual.properties
 
EdgeLabelWidthProp() - Constructor for class cytoscape.visual.properties.EdgeLabelWidthProp
 
EdgeLineStyleProp - Class in cytoscape.visual.properties
 
EdgeLineStyleProp() - Constructor for class cytoscape.visual.properties.EdgeLineStyleProp
 
EdgeLineWidthProp - Class in cytoscape.visual.properties
 
EdgeLineWidthProp() - Constructor for class cytoscape.visual.properties.EdgeLineWidthProp
 
EdgeManipulationAction - Class in cytoscape.actions
 
EdgeManipulationAction(CyNetworkView) - Constructor for class cytoscape.actions.EdgeManipulationAction
Creates a new EdgeManipulationAction object.
edgeMetaChildrenList(Node) - Method in interface giny.model.GraphPerspective
Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges.
edgeMetaChildrenList(int) - Method in interface giny.model.GraphPerspective
Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges.
edgeMetaChildrenList(Node) - Method in interface giny.model.RootGraph
Deprecated. Use getEdgeMetaChildIndicesArray(int) instead.
edgeMetaChildrenList(int) - Method in interface giny.model.RootGraph
Deprecated. Use getEdgeMetaChildIndicesArray(int) instead.
edgeMetaParentsList(int) - Method in interface giny.model.GraphPerspective
Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges.
edgeMetaParentsList(int) - Method in interface giny.model.RootGraph
Deprecated. Use getEdgeMetaParentIndicesArray(int) instead.
EdgeOpacityProp - Class in cytoscape.visual.properties
 
EdgeOpacityProp() - Constructor for class cytoscape.visual.properties.EdgeOpacityProp
 
edgeRemove(int) - Method in interface cytoscape.graph.dynamic.DynamicGraph
Removes the specified edge from this graph.
EDGES - Static variable in class cytoscape.data.AttributeSaverDialog
Constant to specify edges
edges() - Method in interface cytoscape.graph.dynamic.DynamicGraph
Returns an enumeration of all edges currently in this graph.
edges() - Method in interface cytoscape.graph.fixed.FixedGraph
Returns an enumeration of all edges in this graph.
EDGES_CREATED_TYPE - Static variable in class giny.model.RootGraphChangeEvent
 
EDGES_HIDDEN_TYPE - Static variable in class giny.model.GraphPerspectiveChangeEvent
 
EDGES_HIDDEN_TYPE - Static variable in class giny.view.GraphViewChangeEvent
 
EDGES_REMOVED_TYPE - Static variable in class giny.model.RootGraphChangeEvent
 
EDGES_RESTORED_TYPE - Static variable in class giny.model.GraphPerspectiveChangeEvent
 
EDGES_RESTORED_TYPE - Static variable in class giny.view.GraphViewChangeEvent
 
EDGES_SELECTED_TYPE - Static variable in class giny.model.GraphPerspectiveChangeEvent
 
EDGES_SELECTED_TYPE - Static variable in class giny.view.GraphViewChangeEvent
 
EDGES_UNSELECTED_TYPE - Static variable in class giny.model.GraphPerspectiveChangeEvent
 
EDGES_UNSELECTED_TYPE - Static variable in class giny.view.GraphViewChangeEvent
 
edgesAdjacent(int, boolean, boolean, boolean) - Method in interface cytoscape.graph.dynamic.DynamicGraph
Returns a non-repeating enumeration of edges adjacent to a node.
edgesAdjacent(int, boolean, boolean, boolean) - Method in interface cytoscape.graph.fixed.FixedGraph
Returns a non-repeating enumeration of edges adjacent to a node.
edgesConnecting(int, int, boolean, boolean, boolean) - Method in interface cytoscape.graph.dynamic.DynamicGraph
Returns a non-repeating iteration of edges connecting two nodes.
edgesConnecting(int, int, boolean, boolean, boolean) - Method in interface cytoscape.graph.fixed.FixedGraph
Returns a non-repeating iteration of edges connecting two nodes.
edgeSelectionEnabled() - Method in class ding.view.DGraphView
Whether edge selection is enabled.
edgeSelectionEnabled() - Method in interface giny.view.GraphView
 
edgesIterator() - Method in interface giny.model.GraphPerspective
 
edgesIterator() - Method in interface giny.model.RootGraph
Returns an Iterator over all giny.model.Edge objects in this RootGraph.
edgesList() - Method in interface giny.model.GraphPerspective
Returns a list of Edge objects.
edgesList(Node, Node) - Method in interface giny.model.GraphPerspective
Return a new List of the Edges in this GraphPerspective from the first given Node to the second given Node.
edgesList(int, int, boolean) - Method in interface giny.model.GraphPerspective
Deprecated. Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead.
edgesList() - Method in interface giny.model.RootGraph
Returns a list of Edge objects.
edgesList(Node, Node) - Method in interface giny.model.RootGraph
Deprecated. Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead.
edgesList(int, int, boolean) - Method in interface giny.model.RootGraph
Deprecated. Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead.
edgeSource(int) - Method in interface cytoscape.graph.dynamic.DynamicGraph
Determines the source node of an edge.
edgeSource(int) - Method in interface cytoscape.graph.fixed.FixedGraph
Determines the source node of an edge.
EdgeSourceArrowColorProp - Class in cytoscape.visual.properties
 
EdgeSourceArrowColorProp() - Constructor for class cytoscape.visual.properties.EdgeSourceArrowColorProp
 
EdgeSourceArrowOpacityProp - Class in cytoscape.visual.properties
 
EdgeSourceArrowOpacityProp() - Constructor for class cytoscape.visual.properties.EdgeSourceArrowOpacityProp
 
EdgeSourceArrowShapeProp - Class in cytoscape.visual.properties
 
EdgeSourceArrowShapeProp() - Constructor for class cytoscape.visual.properties.EdgeSourceArrowShapeProp
 
edgeTarget(int) - Method in interface cytoscape.graph.dynamic.DynamicGraph
Determines the target node of an edge.
edgeTarget(int) - Method in interface cytoscape.graph.fixed.FixedGraph
Determines the target node of an edge.
EdgeTargetArrowColorProp - Class in cytoscape.visual.properties
 
EdgeTargetArrowColorProp() - Constructor for class cytoscape.visual.properties.EdgeTargetArrowColorProp
 
EdgeTargetArrowOpacityProp - Class in cytoscape.visual.properties
 
EdgeTargetArrowOpacityProp() - Constructor for class cytoscape.visual.properties.EdgeTargetArrowOpacityProp
 
EdgeTargetArrowShapeProp - Class in cytoscape.visual.properties
 
EdgeTargetArrowShapeProp() - Constructor for class cytoscape.visual.properties.EdgeTargetArrowShapeProp
 
EdgeToolTipProp - Class in cytoscape.visual.properties
 
EdgeToolTipProp() - Constructor for class cytoscape.visual.properties.EdgeToolTipProp
 
edgeType(int) - Method in interface cytoscape.graph.dynamic.DynamicGraph
Determines the existence and directedness of an edge.
edgeType(int) - Method in interface cytoscape.graph.fixed.FixedGraph
Determines the existence and directedness of an edge.
EdgeView - Interface in giny.view
 
EditBookmarkDialog - Class in cytoscape.dialogs.preferences
 
EditBookmarkDialog(JDialog, boolean, Bookmarks, String, String, DataSource) - Constructor for class cytoscape.dialogs.preferences.EditBookmarkDialog
Creates new form EditBookmarkDialog
editLabelPosition() - Method in class cytoscape.visual.ui.editors.discrete.CyCustomGraphicsEditor
 
editNetworkTitle(CyNetwork) - Static method in class cytoscape.util.CyNetworkNaming
This will prompt the user to edit the title of a given CyNetork, and after ensuring that the network title is not already in use, this will assign that title to the given CyNetwork
EditNetworkTitleDialog - Class in cytoscape.dialogs
 
EditNetworkTitleDialog(Component, boolean, String) - Constructor for class cytoscape.dialogs.EditNetworkTitleDialog
Creates a new EditNetworkTitleDialog object.
editObjectPosition() - Method in class cytoscape.visual.ui.editors.discrete.CyObjectPositionPropertyEditor
 
editor - Static variable in class cytoscape.visual.ui.editors.continuous.ContinuousMappingEditorPanel
 
EDITOR_WINDOW_CLOSED - Static variable in class cytoscape.visual.ui.editors.continuous.ContinuousMappingEditorPanel
DOCUMENT ME!
EDITOR_WINDOW_OPENED - Static variable in class cytoscape.visual.ui.editors.continuous.ContinuousMappingEditorPanel
DOCUMENT ME!
EditorDisplayer - Enum in cytoscape.visual.ui
Managing value editors in for each data types.
This enum contains both continuous and discrete editors.
EditorDisplayer.EditorType - Enum in cytoscape.visual.ui
Defines editor type.
EditorManager - Interface in cytoscape.visual.ui
 
EditorValueRangeTracer - Class in cytoscape.visual.ui.editors.continuous
 
elements() - Method in class cytoscape.util.intr.IntHash
Returns an enumeration of elements in this hashtable, ordered arbitrarily.
elements() - Method in class cytoscape.util.intr.IntQueue
Returns an enumeration of all elements currently in this queue.
elements() - Method in class cytoscape.util.intr.IntStack
Returns an enumeration of all elements currently on this stack.
elements() - Method in class cytoscape.util.intr.MinIntHeap
Returns an enumeration over all the elements currently in this heap; the order of elements in the returned enumeration is undefined.
ELLIPSE - Static variable in class cytoscape.data.readers.GMLReader
 
ELLIPSE - Static variable in class cytoscape.data.readers.XGMMLReader
 
ELLIPSE - Static variable in interface giny.view.NodeView
 
EllipseNodeShape - Class in cytoscape.render.immed.nodeshape
 
EllipseNodeShape() - Constructor for class cytoscape.render.immed.nodeshape.EllipseNodeShape
 
EMBEDDED_WINDOW - Static variable in interface cytoscape.init.CyInitParams
A gui mode, but where cytoscape is embedded within a different application meaning the usual menus and/or toolbars may not be present.
empty() - Method in class cytoscape.geom.rtree.RTree
Empties this R-tree of all entries.
empty() - Method in interface cytoscape.geom.spacial.MutableSpacialIndex2D
Empties this structure of all entries.
empty() - Method in class cytoscape.util.intr.IntBTree
Empties this structure of all elements.
empty() - Method in class cytoscape.util.intr.IntHash
Removes all elements from this hashtable.
empty() - Method in class cytoscape.util.intr.IntIntHash
Removes all key/value pairs from this hashtable.
empty() - Method in class cytoscape.util.intr.IntQueue
Removes all integers from this queue.
empty() - Method in class cytoscape.util.intr.IntStack
Removes all integers from this stack.
empty() - Method in class cytoscape.util.intr.LongLongHash
Removes all key/value pairs from this hashtable.
empty() - Method in class cytoscape.util.intr.MinIntHeap
Empties this heap of all elements.
enableEdgeSelection() - Method in class ding.view.DGraphView
Enables the ability to select edges.
enableEdgeSelection() - Method in interface giny.view.GraphView
 
enableForNetwork() - Method in class cytoscape.util.CytoscapeAction
Enable the action if the current network exists and is not null.
enableForNetworkAndView() - Method in class cytoscape.util.CytoscapeAction
Enable the action if the current network and view exist and are not null.
enableListeners(boolean) - Method in class cytoscape.visual.ui.VizMapperMainPanel
On/Off listeners.
enableNodeMovement() - Method in class ding.view.InnerCanvas
 
enableNodeSelection() - Method in class ding.view.DGraphView
Enabling the ability to select nodes.
enableNodeSelection() - Method in interface giny.view.GraphView
 
eName - Static variable in class cytoscape.visual.LabelPosition
Deprecated.  
enclosingJar - Variable in class cytoscape.plugin.PluginInfo
 
ENCODE_PROPERTY - Static variable in class cytoscape.data.writers.CyAttributesWriter
 
ENCODE_PROPERTY - Static variable in class cytoscape.data.writers.XGMMLWriter
 
ENCODING - Static variable in class cytoscape.data.writers.XGMMLWriter
 
ENCODING_SCHEME - Static variable in class cytoscape.data.writers.CyAttributesWriter
 
END - Static variable in class cytoscape.CyNetworkEvent
Indicates that someone is done working with the network.
enqueue(int) - Method in class cytoscape.util.intr.IntQueue
Inserts a new integer into this queue.
ensureCapacity(int, int) - Static method in class cytoscape.Cytoscape
Ensure the capacity of Cytoscapce.
ensureCapacity(int, int) - Method in interface giny.model.RootGraph
Deprecated. Please don't call this silly method; implementors: I suggest creating an easter egg and having it take effect when this method is called.
EqnAttrTracker - Class in cytoscape.data.readers
 
EqnAttrTracker() - Constructor for class cytoscape.data.readers.EqnAttrTracker
 
EqnCompiler - Class in org.cytoscape.equations
 
EqnCompiler() - Constructor for class org.cytoscape.equations.EqnCompiler
 
EqnParser - Interface in org.cytoscape.equations
 
EqualDashStroke - Class in cytoscape.visual.strokes
 
EqualDashStroke(float) - Constructor for class cytoscape.visual.strokes.EqualDashStroke
 
equals(Object) - Method in class cytoscape.data.annotation.AnnotationDescription
Deprecated. redefine equals so that instances with the same contents are equal.
equals(Object) - Method in class cytoscape.data.AttribTopoGraphNode
 
equals(Object) - Method in class cytoscape.plugin.DownloadableInfo
Compare the two info objects.
equals(Object) - Method in class cytoscape.util.CytoscapeMenuBar
CytoscapeMenuBars are unique -- this equals() method returns true iff the other object == this.
equals(Object) - Method in class cytoscape.util.CytoscapeToolBar
CytoscapeToolBars are unique -- this equals() method returns true iff the other object == this.
equals(Object) - Method in class cytoscape.visual.LabelPosition
Deprecated. DOCUMENT ME!
equals(Object) - Method in class cytoscape.visual.ui.editors.discrete.CyComboBoxPropertyEditor.Value
 
equals(Object) - Method in class ding.view.ObjectPositionImpl
 
equals(Object) - Method in interface giny.view.ObjectPosition
DOCUMENT ME!
equals(Object) - Method in class org.cytoscape.equations.Equation
 
equalsDifferentObjectVersion(Object) - Method in class cytoscape.plugin.DownloadableInfo
Compares the ID and download URL of the two objects.
equalValue - Variable in class cytoscape.visual.mappings.BoundaryRangeValues
 
Equation - Class in org.cytoscape.equations
 
EquationUtil - Class in org.cytoscape.equations
 
EquationUtil() - Constructor for class org.cytoscape.equations.EquationUtil
 
ERROR - Static variable in interface cytoscape.init.CyInitParams
Error.
error(String) - Method in class cytoscape.logger.CyLogger
Log an error message.
error(String, Throwable) - Method in class cytoscape.logger.CyLogger
Log an error exception message.
Error - Class in org.cytoscape.equations.builtins
 
Error() - Constructor for class org.cytoscape.equations.builtins.Error
 
errorOccurred() - Method in class cytoscape.task.ui.JTask
Returns true if Task Has Encountered An Error.
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.AbstractFunction
Used to invoke this function.
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Abs
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.ACos
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.And
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.ASin
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.ATan2
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Average
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.BList
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Combin
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Concatenate
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Cos
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Cosh
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Count
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Degrees
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Error
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Exp
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.First
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.FList
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.GeoMean
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.HarMean
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.If
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.IList
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Largest
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Last
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Left
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Len
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.ListToString
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Ln
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Log
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Lower
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Max
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Median
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Mid
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Min
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Mod
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Mode
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.NormDist
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Not
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Now
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Nth
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Or
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Permut
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Pi
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Product
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Radians
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Right
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Round
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Sign
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Sin
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Sinh
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.SList
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Sqrt
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.StDev
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Substitute
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Sum
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Tan
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Tanh
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Text
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Today
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Trunc
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Upper
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Value
 
evaluateFunction(Object[]) - Method in class org.cytoscape.equations.builtins.Var
 
evaluateFunction(Object[]) - Method in interface org.cytoscape.equations.Function
Used to invoke this function.
Exec - Class in cytoscape.util
 
Exec() - Constructor for class cytoscape.util.Exec
Creates a new Exec object.
Exec(String[]) - Constructor for class cytoscape.util.Exec
Creates a new Exec object.
execute(String, Map<String, Object>) - Method in interface cytoscape.command.CyCommandHandler
Execute a given command with a particular set of arguments.
execute(String, Collection<Tunable>) - Method in interface cytoscape.command.CyCommandHandler
Execute a given command with a particular set of arguments.
execute(String, String, Map<String, Object>) - Static method in class cytoscape.command.CyCommandManager
Execute a command.
execute(String, String, List<Tunable>) - Static method in class cytoscape.command.CyCommandManager
Execute a command
executeService(CyWebServiceEvent) - Method in interface cytoscape.data.webservice.CyWebServiceEventListener
Execute the service specified in the event object.
executeService(CyWebServiceEvent) - Method in class cytoscape.data.webservice.WebServiceClientImpl
Execute the service through event handling system.
executeTask(Task, JTaskConfig) - Static method in class cytoscape.task.util.TaskManager
Executes the specified task in a new thread, and automatically pops open a JTask UI Component for visually monitoring the task.
EXISTING_FILE_VALUE - Static variable in class org.apache.commons.cli.PatternOptionBuilder
FileInputStream class
exists(int, float[], int) - Method in class cytoscape.geom.rtree.RTree
Determines whether or not a given entry exists in this R-tree structure, and conditionally retrieves the extents of that entry.
exists(int, float[], int) - Method in interface cytoscape.geom.spacial.SpacialIndex2D
Determines whether or not a given entry exists and conditionally retrieves the extents of that entry.
exit(int) - Static method in class cytoscape.Cytoscape
Shuts down Cytoscape, after giving plugins time to react.
ExitAction - Class in cytoscape.actions
 
ExitAction() - Constructor for class cytoscape.actions.ExitAction
Creates a new ExitAction object.
Exp - Class in org.cytoscape.equations.builtins
 
Exp() - Constructor for class org.cytoscape.equations.builtins.Exp
 
ExpFileChooser - Class in cytoscape.actions
Deprecated. Not apparently used anywhere. Shout if you are. Will be removed 5/2008.
ExpFileChooser(File) - Constructor for class cytoscape.actions.ExpFileChooser
Deprecated. Creates a new ExpFileChooser object.
export(CyNetworkView, FileOutputStream) - Method in class cytoscape.util.export.BitmapExporter
 
export(CyNetworkView, FileOutputStream) - Method in interface cytoscape.util.export.Exporter
Export a view as graphics to a stream.
export(CyNetworkView, FileOutputStream) - Method in class cytoscape.util.export.PDFExporter
 
export(CyNetworkView, FileOutputStream) - Method in class cytoscape.util.export.PSExporter
 
export(CyNetworkView, FileOutputStream) - Method in class cytoscape.util.export.SVGExporter
 
ExportAction - Class in cytoscape.actions
 
ExportAction() - Constructor for class cytoscape.actions.ExportAction
Creates a new ExportAction object.
ExportAsGMLAction - Class in cytoscape.actions
 
ExportAsGMLAction() - Constructor for class cytoscape.actions.ExportAsGMLAction
Creates a new ExportAsGMLAction object.
ExportAsGMLAction(boolean) - Constructor for class cytoscape.actions.ExportAsGMLAction
Creates a new ExportAsGMLAction object.
ExportAsGraphicsAction - Class in cytoscape.actions
Action for exporting a network view to bitmap or vector graphics.
ExportAsGraphicsAction() - Constructor for class cytoscape.actions.ExportAsGraphicsAction
 
ExportAsGraphicsAction(String) - Constructor for class cytoscape.actions.ExportAsGraphicsAction
 
ExportAsGraphicsFileChooser - Class in cytoscape.dialogs
Dialog that chooses file to export to.
ExportAsGraphicsFileChooser(CyFileFilter[]) - Constructor for class cytoscape.dialogs.ExportAsGraphicsFileChooser
Deprecated. 
ExportAsGraphicsFileChooser(CyFileFilter[], CyFileFilter) - Constructor for class cytoscape.dialogs.ExportAsGraphicsFileChooser
 
ExportAsInteractionsAction - Class in cytoscape.actions
write out the current graph to the specified file, using the standard interactions format: nodeA edgeType nodeB.
ExportAsInteractionsAction() - Constructor for class cytoscape.actions.ExportAsInteractionsAction
Constructor.
ExportAsXGMMLAction - Class in cytoscape.actions
This action is for exporting network and attributes in XGMML file.
ExportAsXGMMLAction() - Constructor for class cytoscape.actions.ExportAsXGMMLAction
Creates a new ExportAsXGMMLAction object.
ExportAsXGMMLAction(boolean) - Constructor for class cytoscape.actions.ExportAsXGMMLAction
Creates a new ExportAsXGMMLAction object.
ExportBitmapOptionsDialog - Class in cytoscape.dialogs
Options dialog for exporting to bitmap images.
ExportBitmapOptionsDialog(int, int) - Constructor for class cytoscape.dialogs.ExportBitmapOptionsDialog
Creates the options dialog.
ExportEdgeAttributesAction - Class in cytoscape.actions
 
ExportEdgeAttributesAction() - Constructor for class cytoscape.actions.ExportEdgeAttributesAction
Creates a new ExportEdgeAttributesAction object.
Exporter - Interface in cytoscape.util.export
Interface for exporting a network view to a graphics file.
ExportNetworksAsNNFAction - Class in cytoscape.actions
This action is for exporting network and attributes in XGMML file.
ExportNetworksAsNNFAction() - Constructor for class cytoscape.actions.ExportNetworksAsNNFAction
Creates a new ExportNetworksAsNNFAction object.
ExportNetworksAsNNFAction(boolean) - Constructor for class cytoscape.actions.ExportNetworksAsNNFAction
Creates a new ExportNetworksAsNNFAction object.
ExportNodeAttributesAction - Class in cytoscape.actions
 
ExportNodeAttributesAction() - Constructor for class cytoscape.actions.ExportNodeAttributesAction
Creates a new ExportNodeAttributesAction object.
ExportVizmapAction - Class in cytoscape.actions
Export visual styles as a vizmap.props file
ExportVizmapAction() - Constructor for class cytoscape.actions.ExportVizmapAction
Creates a new ExportVizmapAction object.
EXPRESSION_DATA_LOADED - Static variable in class cytoscape.Cytoscape
 
expressionData - Static variable in class cytoscape.Cytoscape
 
ExpressionData - Class in cytoscape.data
This class provides a reader for the common file format for expression data and an interface to access the data.
ExpressionData() - Constructor for class cytoscape.data.ExpressionData
Constructor.
ExpressionData(String) - Constructor for class cytoscape.data.ExpressionData
Constructor.
ExpressionData(String, String) - Constructor for class cytoscape.data.ExpressionData
Constructor.
ExpressionData(String, TaskMonitor) - Constructor for class cytoscape.data.ExpressionData
Constructor.
ExpressionData(String, String, TaskMonitor) - Constructor for class cytoscape.data.ExpressionData
Constructor.
ExpressionDataPopupTable - Class in cytoscape.dialogs
 
ExpressionDataPopupTable(Frame, String[], String, ExpressionData) - Constructor for class cytoscape.dialogs.ExpressionDataPopupTable
Creates a new ExpressionDataPopupTable object.
ExpressionDataPopupTable(Frame, String, String[], ExpressionData) - Constructor for class cytoscape.dialogs.ExpressionDataPopupTable
Creates a new ExpressionDataPopupTable object.
ExpressionDataPopupTable.OKAction - Class in cytoscape.dialogs
 
expressionFiles - Variable in class cytoscape.CyMain
 
ExtensibleMultiHashMapModel - Class in cytoscape.data.attr.util
Deprecated. Use MultiHashMapFactory instead.
ExtensibleMultiHashMapModel() - Constructor for class cytoscape.data.attr.util.ExtensibleMultiHashMapModel
Deprecated.  
extract() - Method in class cytoscape.data.readers.GMLReader
DOCUMENT ME!
extractEdge(List<KeyValue>, String) - Method in class cytoscape.data.readers.GMLReader
 
extractEdgeAttributes(List<KeyValue>, String) - Method in class cytoscape.data.readers.GMLReader
 
extractGraph(List) - Method in class cytoscape.data.readers.GMLReader
 
extractLineStyle(Stroke) - Static method in enum cytoscape.visual.LineStyle
Will attempt to find the LineStyle based on the type of stroke.
extractNode(List) - Method in class cytoscape.data.readers.GMLReader
 
extractNodeAttributes(List, String) - Method in class cytoscape.data.readers.GMLReader
 

F

face - Variable in class cytoscape.visual.ui.FontChooser
 
fatal(String) - Method in class cytoscape.logger.CyLogger
Log a fatal error message.
fatal(String, Throwable) - Method in class cytoscape.logger.CyLogger
Log a fatal exception message.
FConvNode - Class in org.cytoscape.equations.parse_tree
A node in the parse tree representing a conversion to a floating point number
FConvNode(Node) - Constructor for class org.cytoscape.equations.parse_tree.FConvNode
 
FILE_BIOPAX - Static variable in class cytoscape.Cytoscape
 
FILE_BY_SUFFIX - Static variable in class cytoscape.Cytoscape
When creating a network, use one of the standard suffixes to have it parsed correctly
sif -- Simple Interaction File gml -- Graph Markup Languange sbml -- SBML xgmml -- XGMML
FILE_GML - Static variable in class cytoscape.Cytoscape
 
FILE_PSI_MI - Static variable in class cytoscape.Cytoscape
 
FILE_SBML - Static variable in class cytoscape.Cytoscape
 
FILE_SIF - Static variable in class cytoscape.Cytoscape
 
FILE_VALUE - Static variable in class org.apache.commons.cli.PatternOptionBuilder
File class
FILE_XGMML - Static variable in class cytoscape.Cytoscape
 
fileName - Variable in class cytoscape.data.readers.AbstractGraphReader
 
filename - Variable in class cytoscape.generated.Network
 
fileName - Variable in class cytoscape.util.JnlpWriterUtil
 
fileNature - Variable in class cytoscape.util.CyFileFilter
 
FILES_VALUE - Static variable in class org.apache.commons.cli.PatternOptionBuilder
File array class
FileUtil - Class in cytoscape.util
Provides a platform-dependent way to open files.
FileUtil() - Constructor for class cytoscape.util.FileUtil
 
FILL - Static variable in class cytoscape.data.readers.GMLReader
 
fillPaint(int) - Method in class cytoscape.render.stateful.NodeDetails
Returns the paint of the interior of the node shape.
fillPluginInfoObject(DownloadableInfo) - Method in class cytoscape.plugin.PluginProperties
Takes a PluginInfo object (can be null) and fills it in with information that would not come from a properties file like the unique identifier and download url.
Filter - Interface in giny.filter
 
FilterHistoryJList - Class in cytoscape.util.swing
JList with incremntal search & search history.
FilterHistoryJList() - Constructor for class cytoscape.util.swing.FilterHistoryJList
Creates a new FilterHistoryJList object.
findGroup(String) - Static method in class cytoscape.groups.CyGroupManager
Search all groups for the group named 'groupName'
findMin() - Method in class cytoscape.util.intr.MinIntHeap
Returns the minimum element in this heap.
findUpdates() - Method in interface cytoscape.plugin.Installable
 
findUpdates() - Method in class cytoscape.plugin.InstallablePlugin
 
findUpdates() - Method in class cytoscape.plugin.InstallableTheme
 
findUpdates(DownloadableInfo) - Method in class cytoscape.plugin.PluginManager
Get list of plugins that would update the given plugin.
findWrapPos(String, int, int) - Method in class org.apache.commons.cli.HelpFormatter
Finds the next text wrap position after startPos for the text in text with the column width width.
fing.model - package fing.model
 
fing.model.test - package fing.model.test
 
FingCyNetwork - Class in cytoscape.giny
FinhCyNetwork provides an implementation of the CyNetwork interface, as well as the GraphPerspective inteface, and also provides the functionality formally provided by GraphObjAttributes.
FingCyNetwork(FingExtensibleRootGraph, IntIterator, IntIterator) - Constructor for class cytoscape.giny.FingCyNetwork
rootGraphNodeInx need not contain all endpoint nodes corresponding to edges in rootGraphEdgeInx - this is calculated automatically by this constructor.
FingEdgeDepot - Interface in fing.model
Please try to restrain from using this class, or even looking at it.
FingExtensibleGraphPerspective - Class in fing.model
Please try to restrain from using this class.
FingExtensibleGraphPerspective(FingExtensibleRootGraph, IntIterator, IntIterator) - Constructor for class fing.model.FingExtensibleGraphPerspective
rootGraphNodeInx need not contain all endpoint nodes corresponding to edges in rootGraphEdgeInx - this is calculated automatically by this constructor.
FingExtensibleRootGraph - Class in fing.model
Please try to restrain from using this class.
FingExtensibleRootGraph(FingNodeDepot, FingEdgeDepot) - Constructor for class fing.model.FingExtensibleRootGraph
Creates a new FingExtensibleRootGraph object.
FingNodeDepot - Interface in fing.model
Please try to restrain from using this class, or even looking at it.
FingRootGraphFactory - Class in fing.model
This class defines static methods that provide new instances of giny.model.RootGraph objects.
finished() - Method in class cytoscape.util.SwingWorker
Called on the event dispatching thread (not on the worker thread) after the construct method has returned.
fireCyWebServiceEvent(CyWebServiceEvent) - Method in class cytoscape.data.webservice.CyWebServiceEventSupport
DOCUMENT ME!
fireEditingCanceled() - Method in class cytoscape.util.swing.AbstractCellEditor
 
fireEditingStopped() - Method in class cytoscape.util.swing.AbstractCellEditor
 
fireEvent(Object, boolean) - Method in class cytoscape.data.SelectFilter
Fires an event to all registered listeners that represents the operation described by the arguments.
fireEvent(int) - Method in class cytoscape.giny.FingCyNetwork
Fires an event to all listeners registered with this object.
firePropertyChange(String, Object, Object) - Static method in class cytoscape.Cytoscape
DOCUMENT ME!
firePropertyChange(String, Object, Object) - Method in class cytoscape.view.NetworkViewManager
Fires a PropertyChangeEvent
firePropertyChange(Object, Object) - Method in class cytoscape.visual.ui.editors.discrete.CyColorPropertyEditor.AsInt
 
fireStateChanged(VisualPropertyType) - Method in class cytoscape.visual.CalculatorCatalog
 
fireStateChanged() - Method in class cytoscape.visual.calculators.AbstractCalculator
Notifies all listeners that have registered interest for notification on this event type.
fireStateChanged() - Method in class cytoscape.visual.SubjectBase
Notifies all listeners that have registered interest for notification on this event type.
fireTreeNodesAdded(Object, Object[], int[], Object[]) - Method in class cytoscape.dialogs.plugins.ManagerModel
 
fireTreeNodesChanged(Object, Object[], int[], Object[]) - Method in class cytoscape.util.swing.AbstractTreeTableModel
 
fireTreeNodesInserted(Object, Object[], int[], Object[]) - Method in class cytoscape.util.swing.AbstractTreeTableModel
 
fireTreeNodesRemoved(Object, Object[], int[], Object[]) - Method in class cytoscape.dialogs.plugins.ManagerModel
 
fireTreeNodesRemoved(Object, Object[], int[], Object[]) - Method in class cytoscape.util.swing.AbstractTreeTableModel
 
fireTreeStructureChanged(Object, Object[], int[], Object[]) - Method in class cytoscape.dialogs.plugins.ManagerModel
 
fireTreeStructureChanged(Object, Object[], int[], Object[]) - Method in class cytoscape.util.swing.AbstractTreeTableModel
 
First - Class in org.cytoscape.equations.builtins
 
First() - Constructor for class org.cytoscape.equations.builtins.First
 
fitContent() - Method in class ding.view.DGraphView
Resize the network view to the size of the canvas and redraw it.
fitContent() - Method in interface giny.view.GraphView
Fits all Viewable elements onto the Graph
FitContentAction - Class in cytoscape.actions
 
FitContentAction() - Constructor for class cytoscape.actions.FitContentAction
Creates a new FitContentAction object.
fitRatio - Variable in class cytoscape.visual.customgraphic.impl.AbstractDCustomGraphics
 
fitSelected() - Method in class ding.view.DGraphView
DOCUMENT ME!
FixedGraph - Interface in cytoscape.graph.fixed
A graph topology.
FlagAndSelectionHandler - Class in cytoscape.view
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 node and edge views in a GraphView.
FlagAndSelectionHandler(SelectFilter, GraphView) - Constructor for class cytoscape.view.FlagAndSelectionHandler
Standard constructor takes the flag filter and the view that should be synchronized.
FlatInterpolator - Class in cytoscape.visual.mappings
This simple Interpolator returns the value at either the lower or upper boundary of the domain.
FlatInterpolator() - Constructor for class cytoscape.visual.mappings.FlatInterpolator
The default FlatInterpolator returns the range value at the lower boundary.
FlatInterpolator(Integer) - Constructor for class cytoscape.visual.mappings.FlatInterpolator
Constructs a FlatInterpolator which returns the range value at the lower boundary unless the argument 'mode' is equal to FlatInterpolator.UPPER.
flatten(Options, String[], boolean) - Method in class org.apache.commons.cli.BasicParser
A simple implementation of Parser's abstract flatten method.
flatten(Options, String[], boolean) - Method in class org.apache.commons.cli.GnuParser
This flatten method does so using the following rules: If an Option exists for the first character of the arguments entry AND an Option does not exist for the whole argument then add the first character as an option to the processed tokens list e.g.
flatten(Options, String[], boolean) - Method in class org.apache.commons.cli.Parser
Subclasses must implement this method to reduce the arguments that have been passed to the parse method.
flatten(Options, String[], boolean) - Method in class org.apache.commons.cli.PosixParser
An implementation of Parser's abstract flatten method.
FlattenIntVectors - Class in cytoscape.data.annotation
Deprecated. Use regular CyAttributes for annotation.
FlattenIntVectors(Vector) - Constructor for class cytoscape.data.annotation.FlattenIntVectors
Deprecated. Creates a new FlattenIntVectors object.
FList - Class in org.cytoscape.equations.builtins
 
FList() - Constructor for class org.cytoscape.equations.builtins.FList
 
FLOAT - Static variable in class cytoscape.view.cytopanels.CytoPanelState
Float state of a CytoPanel.
FloatConstantNode - Class in org.cytoscape.equations.parse_tree
A node in the parse tree representing an integer constant.
FloatConstantNode(int, double) - Constructor for class org.cytoscape.equations.parse_tree.FloatConstantNode
 
FloatParser - Class in cytoscape.visual.parsers
DOCUMENT ME!
FloatParser() - Constructor for class cytoscape.visual.parsers.FloatParser
 
FloatRangeValueCalculator - Class in cytoscape.visual.mappings.rangecalculators
 
FloatRangeValueCalculator() - Constructor for class cytoscape.visual.mappings.rangecalculators.FloatRangeValueCalculator
 
flush() - Method in class cytoscape.render.export.ImageImposter
This is a no-op.
focusGained(FocusEvent) - Method in class cytoscape.dialogs.ImportNetworkDialog
Listen for focus events in the text field.
focusGained(FocusEvent) - Method in class cytoscape.dialogs.IntegerEntryField.PositiveIntegerListener
 
focusGained(FocusEvent) - Method in class cytoscape.dialogs.JointIntegerEntry.CopyField1To2Listener
 
focusGained(FocusEvent) - Method in class cytoscape.layout.Tunable
This method is public as a byproduct of the implementation.
focusLost(FocusEvent) - Method in class cytoscape.dialogs.ImportNetworkDialog
Listen for focus lost events in the text field.
focusLost(FocusEvent) - Method in class cytoscape.dialogs.IntegerEntryField.PositiveIntegerListener
 
focusLost(FocusEvent) - Method in class cytoscape.dialogs.JointIntegerEntry.CopyField1To2Listener
 
focusLost(FocusEvent) - Method in class cytoscape.layout.Tunable
Document listener routines to handle bounds checking
focusLost(FocusEvent) - Method in class cytoscape.visual.mappings.continuous.PointTextListener
User now clicks outside of Text Box.
focusNetworkNode(String) - Method in class cytoscape.view.NetworkPanel
DOCUMENT ME!
FontCellRenderer - Class in cytoscape.visual.ui.editors.discrete
DOCUMENT ME!
FontCellRenderer() - Constructor for class cytoscape.visual.ui.editors.discrete.FontCellRenderer
 
FontChooser - Class in cytoscape.visual.ui
Defines a generalized font chooser class.
FontChooser() - Constructor for class cytoscape.visual.ui.FontChooser
Create a FontChooser to choose between all fonts available on the system.
FontChooser(Font) - Constructor for class cytoscape.visual.ui.FontChooser
Creates a new FontChooser object.
FontChooser(Font[], Font) - Constructor for class cytoscape.visual.ui.FontChooser
Create a FontChooser to choose between the given array of fonts.
FontConverter - Class in cytoscape.visual.converter
 
FontConverter() - Constructor for class cytoscape.visual.converter.FontConverter
 
fontFaceModel - Variable in class cytoscape.visual.ui.FontChooser
 
FontParser - Class in cytoscape.visual.parsers
Parses a String into a Font object.
FontParser() - Constructor for class cytoscape.visual.parsers.FontParser
 
FontRenderer - Class in cytoscape.visual.ui
FontRenderer describes a class that renders each font name in a FontChooser JList or JComboBox in the face specified.
FontRenderer() - Constructor for class cytoscape.visual.ui.FontRenderer
 
format - Variable in class cytoscape.bookmarks.DataSource
 
ForwardSlashStroke - Class in cytoscape.visual.strokes
 
ForwardSlashStroke(float, PipeStroke.Type) - Constructor for class cytoscape.visual.strokes.ForwardSlashStroke
 
frameID - Variable in class cytoscape.generated.NetworkFrame
 
FuncCallNode - Class in org.cytoscape.equations.parse_tree
A node in the parse tree representing a function call.
FuncCallNode(int, Function, Class, Node[]) - Constructor for class org.cytoscape.equations.parse_tree.FuncCallNode
 
Function - Interface in org.cytoscape.equations
 
FunctionError - Exception in org.cytoscape.equations
 
FunctionError(String, int) - Constructor for exception org.cytoscape.equations.FunctionError
 
FunctionUtil - Class in org.cytoscape.equations
A collection of static methods that may be useful for the implementation of built-in functions.
FunctionUtil() - Constructor for class org.cytoscape.equations.FunctionUtil
 

G

g2d - Variable in class cytoscape.visual.ui.icon.LineTypeIcon
 
g2d - Variable in class cytoscape.visual.ui.icon.NodeIcon
 
GCTest - Class in fing.model.test
 
GCTest() - Constructor for class fing.model.test.GCTest
 
genCode(Stack<CodeAndSourceLocation>) - Method in class org.cytoscape.equations.parse_tree.BinOpNode
 
genCode(Stack<CodeAndSourceLocation>) - Method in class org.cytoscape.equations.parse_tree.BooleanConstantNode
 
genCode(Stack<CodeAndSourceLocation>) - Method in class org.cytoscape.equations.parse_tree.FConvNode
 
genCode(Stack<CodeAndSourceLocation>) - Method in class org.cytoscape.equations.parse_tree.FloatConstantNode
 
genCode(Stack<CodeAndSourceLocation>) - Method in class org.cytoscape.equations.parse_tree.FuncCallNode
 
genCode(Stack<CodeAndSourceLocation>) - Method in class org.cytoscape.equations.parse_tree.IdentNode
 
genCode(Stack<CodeAndSourceLocation>) - Method in class org.cytoscape.equations.parse_tree.Node
 
genCode(Stack<CodeAndSourceLocation>) - Method in class org.cytoscape.equations.parse_tree.SConvNode
 
genCode(Stack<CodeAndSourceLocation>) - Method in class org.cytoscape.equations.parse_tree.StringConstantNode
 
genCode(Stack<CodeAndSourceLocation>) - Method in class org.cytoscape.equations.parse_tree.UnaryOpNode
 
GeneOntology - Class in cytoscape.data.ontology
Gene Ontology object based on general Ontology.
GeneOntology(String, String, String, CyNetwork) - Constructor for class cytoscape.data.ontology.GeneOntology
 
GeneOntology.GOAspect - Enum in cytoscape.data.ontology
 
generateLegendPanel(VisualStyle) - Static method in class cytoscape.visual.ui.LegendDialog
DOCUMENT ME!
GenericNodeCustomGraphicCalculator - Class in cytoscape.visual.calculators
 
GenericNodeCustomGraphicCalculator(String, ObjectMapping, VisualPropertyType) - Constructor for class cytoscape.visual.calculators.GenericNodeCustomGraphicCalculator
 
GeoMean - Class in org.cytoscape.equations.builtins
 
GeoMean() - Constructor for class org.cytoscape.equations.builtins.GeoMean
 
get(int) - Method in class cytoscape.util.intr.IntHash
Determines whether or not the value specified is in this hashtable.
get(int) - Method in class cytoscape.util.intr.IntIntHash
Returns the value bound to the specified key or -1 if no value is currently bound to the specified key.
get(int) - Method in class cytoscape.util.intr.IntObjHash
Returns the value bound to the specified key or null if no value is currently bound to the specified key.
get(int) - Method in class cytoscape.util.intr.IntTHash
Returns the value bound to the specified key or null if no value is currently bound to the specified key.
get(long) - Method in class cytoscape.util.intr.LongLongHash
Returns the value bound to the specified key or -1 if no value is currently bound to the specified key.
get(String) - Method in interface cytoscape.util.ModuleProperties
This method is used to get the Tunable named name from this LayoutProperties.
get(String) - Method in class cytoscape.util.ModulePropertiesImpl
This method is used to get the Tunable named name from this LayoutProperties.
get() - Method in class cytoscape.util.SwingWorker
Return the value created by the construct method.
get(VisualPropertyType) - Method in class cytoscape.visual.Appearance
Gets the appearance for the specified VisualPropertyType.
getAbbreviation() - Method in class cytoscape.data.ontology.DBReference
DOCUMENT ME!
getAcceptedDataClasses() - Method in class cytoscape.visual.mappings.AbstractMapping
 
getAcceptedDataClasses() - Method in interface cytoscape.visual.mappings.ObjectMapping
Return the classes that the ObjectMapping can map from, eg.
getAccessibleMethods() - Method in interface cytoscape.data.webservice.WebServiceClient
Returns all available methods accessible through client stub.
getAccessibleMethods() - Method in class cytoscape.data.webservice.WebServiceClientImpl
DOCUMENT ME!
getActionClass() - Method in enum cytoscape.visual.ui.EditorDisplayer
DOCUMENT ME!
getActionList() - Static method in class cytoscape.util.CytoscapeAction
DOCUMENT ME!
getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) - Method in interface giny.model.GraphPerspective
Returns [RootGraph] indices of all Edges in this GraphPerspective adjacent to the Node at specified [RootGraph] index.
getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) - Method in interface giny.model.RootGraph
Returns indices of all edges adjacent to the node at specified index.
getAdjacentEdgesList(Node, boolean, boolean, boolean) - Method in interface giny.model.GraphPerspective
Deprecated. Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead.
getAffineTransform() - Method in class ding.view.InnerCanvas
Called to get the tranform matrix used by the inner canvas to move the nodes.
getAliases(String) - Method in class cytoscape.data.synonyms.Aliases
 
getAll() - Method in class cytoscape.visual.customgraphic.CustomGraphicsManager
Get a collection of all Custom Graphics in current session.
getAll() - Method in class cytoscape.visual.mappings.DiscreteMapping
gets all map values
getAllAnnotations(AnnotationDescription, String) - Method in class cytoscape.data.servers.BioDataServer
DOCUMENT ME!
getAllAnnotations(AnnotationDescription, String) - Method in interface cytoscape.data.servers.BioDataServerInterface
DOCUMENT ME!
getAllAnnotations(AnnotationDescription, String) - Method in class cytoscape.data.servers.BioDataServerRmi
DOCUMENT ME!
getAllAttributeKeys(String, String, MultiHashMap, MultiHashMapDefinition) - Static method in class cytoscape.data.attr.util.MultiHashMapHelpers
Convenience method for discovering all key sequnces that map into bound values; this method is primarily useful with attribute definitions that have nonzero key spaces.
getAllAttributeKeysAlongPrefix(String, String, Object[], MultiHashMap, MultiHashMapDefinition) - Static method in class cytoscape.data.attr.util.MultiHashMapHelpers
Convenience method for discovering all key sequences having a given prefix that map into bound values; this method is primarily useful with attribute definitions that have nonzero key spaces.
getAllAttributeValues(String, String, MultiHashMap, MultiHashMapDefinition) - Static method in class cytoscape.data.attr.util.MultiHashMapHelpers
Convenience method for discovering all attribute values on an object in a given attribute definition; this method is only useful with attribute definitions that have nonzero key spaces.
getAllAttributeValuesAlongPrefix(String, String, Object[], MultiHashMap, MultiHashMapDefinition) - Static method in class cytoscape.data.attr.util.MultiHashMapHelpers
Convenience method for discovering attribute values along a specified key prefix; this method is only useful with attribute definitions that have nonzero key spaces.
getAllClients() - Static method in class cytoscape.data.webservice.WebServiceClientManager
DOCUMENT ME!
getAllCommonNames(String, String) - Method in class cytoscape.data.servers.BioDataServer
DOCUMENT ME!
getAllCommonNames(String, String) - Method in interface cytoscape.data.servers.BioDataServerInterface
DOCUMENT ME!
getAllCommonNames(String, String) - Method in class cytoscape.data.servers.BioDataServerRmi
DOCUMENT ME!
getAllCommonNames(String) - Method in class cytoscape.data.synonyms.Thesaurus
DOCUMENT ME!
getAllCustomGraphicsType() - Static method in enum cytoscape.visual.VisualPropertyType
 
getAllDescriptions() - Method in class cytoscape.data.ImportHandler
Gets a collection of all registered filter descriptions.
getAllEdgePropertyData(int) - Method in class ding.view.DGraphView
DOCUMENT ME!
getAllEdgePropertyData(int) - Method in interface giny.view.GraphView
 
getAllExtensions() - Method in class cytoscape.data.ImportHandler
Gets a collection of all registered file extensions.
getAllFiles(String, String) - Static method in class cytoscape.util.ZipUtil
Reads zip file, returns a list of all entries that match the given regular expression
getAllFilters() - Method in class cytoscape.data.ImportHandler
Gets a list of all registered filters plus a catch-all super set filter.
getAllFilters(String) - Method in class cytoscape.data.ImportHandler
Gets a list of all registered filters, which are of type: fileNature, plus a catch-all super set filter.
getAllHierarchyPaths(int) - Method in class cytoscape.data.annotation.Ontology
Deprecated. get all unique paths from the termID to the root of the ontology, in reverse order, with the most general classification first, and most specific last.
getAllHierarchyPathsAsNames(String) - Method in class cytoscape.data.annotation.Annotation
Deprecated. DOCUMENT ME!
getAllHierarchyPathsAsNames(int) - Method in class cytoscape.data.annotation.Ontology
Deprecated. DOCUMENT ME!
getAllHierarchyPathsAsVector(int) - Method in class cytoscape.data.annotation.Ontology
Deprecated.  
getAllInteractions() - Method in class cytoscape.data.readers.InteractionsReader
DOCUMENT ME!
getAllLayouts() - Static method in class cytoscape.layout.CyLayouts
Get all of the available layouts.
getAllMeasurements() - Method in class cytoscape.data.ExpressionData
Gets all Measurements.
getAllNamesInGroup(String) - Method in class cytoscape.data.synonyms.Thesaurus
DOCUMENT ME!
getAllNodePropertyData(int) - Method in class ding.view.DGraphView
DOCUMENT ME!
getAllNodePropertyData(int) - Method in interface giny.view.GraphView
 
getAllPoints() - Method in class cytoscape.visual.mappings.ContinuousMapping
Gets all Data Points.
getAllSynonyms(String, CyNetwork) - Static method in class cytoscape.data.Semantics
Deprecated. 
getAllTypes(String) - Method in class cytoscape.data.ImportHandler
Gets descriptions for all registered filters, which are of the type: fileNature.
getAlternateCommonNames(String) - Method in class cytoscape.data.synonyms.Thesaurus
DOCUMENT ME!
getAnchor(int, float[], int) - Method in interface cytoscape.render.immed.EdgeAnchors
Writes an edge anchor point into the array provided, at offset specified.
getAnchor() - Method in class cytoscape.render.stateful.CustomGraphic
Deprecated. 
getAnchor() - Method in class ding.view.ObjectPositionImpl
 
getAnchor() - Method in interface giny.view.ObjectPosition
DOCUMENT ME!
getAnchorNames() - Static method in class cytoscape.visual.LabelPosition
Deprecated. DOCUMENT ME!
getAnchorSelectedPaint() - Method in class ding.view.DGraphView
DOCUMENT ME!
getAnchorSize() - Method in class ding.view.DGraphView
DOCUMENT ME!
getAnchorUnselectedPaint() - Method in class ding.view.DGraphView
DOCUMENT ME!
getAnnotation() - Method in class cytoscape.data.annotation.readers.AnnotationFlatFileReader
DOCUMENT ME!
getAnnotation() - Method in class cytoscape.data.annotation.readers.AnnotationXmlReader
DOCUMENT ME!
getAnnotation() - Method in class cytoscape.data.ontology.OntologyTerm
Always return empty annotation object.
getAnnotation() - Method in class cytoscape.data.ontology.Triple
Always return empty annotation object.
getAnnotation(String, String, String) - Method in class cytoscape.data.servers.BioDataServer
DOCUMENT ME!
getAnnotation(AnnotationDescription) - Method in class cytoscape.data.servers.BioDataServer
DOCUMENT ME!
getAnnotation(String, String, String) - Method in interface cytoscape.data.servers.BioDataServerInterface
DOCUMENT ME!
getAnnotation(AnnotationDescription) - Method in interface cytoscape.data.servers.BioDataServerInterface
DOCUMENT ME!
getAnnotation(String, String, String) - Method in class cytoscape.data.servers.BioDataServerRmi
DOCUMENT ME!
getAnnotation(AnnotationDescription) - Method in class cytoscape.data.servers.BioDataServerRmi
DOCUMENT ME!
getAnnotationCount() - Method in class cytoscape.data.servers.BioDataServer
DOCUMENT ME!
getAnnotationCount() - Method in interface cytoscape.data.servers.BioDataServerInterface
DOCUMENT ME!
getAnnotationCount() - Method in class cytoscape.data.servers.BioDataServerRmi
DOCUMENT ME!
getAnnotationDescriptions() - Method in class cytoscape.data.servers.BioDataServer
DOCUMENT ME!
getAnnotationDescriptions() - Method in interface cytoscape.data.servers.BioDataServerInterface
DOCUMENT ME!
getAnnotationDescriptions() - Method in class cytoscape.data.servers.BioDataServerRmi
DOCUMENT ME!
getArg(String, String, Map<String, Object>) - Method in class cytoscape.command.AbstractCommandHandler
Return the string value of a specific argument from an args map.
getArgAsBoolean(Object) - Static method in class org.cytoscape.equations.FunctionUtil
Assumes that "arg" is a "String", "Boolean", "Long" or a "Double and converts it to "boolean".
getArgAsDouble(Object) - Static method in class org.cytoscape.equations.FunctionUtil
Assumes that "arg" is a "String", "Boolean", "Long" or a "Double and converts it to "double".
getArgAsLong(Object) - Static method in class org.cytoscape.equations.FunctionUtil
Assumes that "arg" is a "String", "Boolean", "Long" or a "Double and converts it to "long".
getArgAsString(Object) - Static method in class org.cytoscape.equations.FunctionUtil
Assumes that "arg" is a "String", "Boolean", "Long" or a "Double and converts it to "double".
getArgList() - Method in class org.apache.commons.cli.CommandLine
Retrieve any left-over non-recognized options and arguments
getArgName() - Method in class org.apache.commons.cli.HelpFormatter
Returns the 'argName'.
getArgName() - Method in class org.apache.commons.cli.Option
Gets the display name for the argument value.
getArgName() - Method in class org.cytoscape.equations.ArgDescriptor
 
getArgNumber() - Method in exception org.cytoscape.equations.FunctionError
 
getArgs() - Method in class cytoscape.CyMain
DOCUMENT ME!
getArgs() - Method in interface cytoscape.init.CyInitParams
Returns the arguments used to trigger the initialization.
getArgs() - Method in class org.apache.commons.cli.CommandLine
Retrieve any left-over non-recognized options and arguments
getArgs() - Method in class org.apache.commons.cli.Option
Returns the number of argument values this Option can take.
getArgType() - Method in class org.cytoscape.equations.ArgDescriptor
 
getArgument() - Method in class org.apache.commons.cli.avalon.CLOption
Retrieve argument to option if it takes arguments.
getArgument(int) - Method in class org.apache.commons.cli.avalon.CLOption
Retrieve indexed argument to option if it takes arguments.
getArgumentById(int) - Method in class org.apache.commons.cli.avalon.CLArgsParser
Retrieve the CLOption with specified id, or null if no command line option is found.
getArgumentByName(String) - Method in class org.apache.commons.cli.avalon.CLArgsParser
Retrieve the CLOption with specified name, or null if no command line option is found.
getArgumentCount() - Method in class org.apache.commons.cli.avalon.CLOption
Get number of arguments.
getArguments(String) - Method in class cytoscape.command.AbstractCommandHandler
Return the arguments for a given command
getArguments(String) - Method in interface cytoscape.command.CyCommandHandler
Return the list of arguments supported by a particular command.
getArguments() - Method in class org.apache.commons.cli.avalon.CLArgsParser
Retrieve a list of options that were parsed from command list.
getArrowShape() - Method in interface cytoscape.render.immed.arrow.Arrow
The Shape of the main Arrow body.
getArrowShape(int) - Static method in enum cytoscape.visual.ArrowShape
DOCUMENT ME!
getArrowShapes() - Static method in class cytoscape.render.immed.GraphGraphics
Get list of arrow heads.
getArrowShapes() - Static method in class ding.view.DGraphView
DOCUMENT ME!
getAspect(String) - Method in class cytoscape.data.ontology.GeneOntology
Returns Aspect/name space of the GO term.
getAttrBundle(String, CyAttributes) - Method in class cytoscape.visual.calculators.AbstractCalculator
Returns a map of attribute names to single values.
getAttrBundle(String) - Method in class cytoscape.visual.calculators.AbstractCalculator
 
getAttribName() - Method in class org.cytoscape.equations.parse_tree.IdentNode
 
getAttribReferences() - Method in class org.cytoscape.equations.Equation
 
getAttribute() - Method in class cytoscape.bookmarks.DataSource
Gets the value of the attribute property.
getAttribute(String, String) - Method in interface cytoscape.data.CyAttributes
Gets an Object value at the specified id/attributeName.
getAttribute(String, String) - Method in class cytoscape.data.CyAttributesImpl
Gets an Object value at the specified id/attributeName.
getAttribute(String, CyAttributes) - Static method in class cytoscape.data.CyAttributesUtils
DOCUMENT ME!
getAttribute(DataSource, String) - Static method in class cytoscape.util.BookmarksUtil
DOCUMENT ME!
getAttributeDescription(String) - Method in interface cytoscape.data.CyAttributes
Gets the human readable description of a specific attribute.
getAttributeDescription(String) - Method in class cytoscape.data.CyAttributesImpl
DOCUMENT ME!
getAttributeKeyspaceDimensionTypes(String) - Method in interface cytoscape.data.attr.MultiHashMapDefinition
Returns information about the dimensionality and types in the key space of specified attribute.
getAttributeKeyspan(String, String, Object[]) - Method in interface cytoscape.data.attr.MultiHashMap
For all key sequences, having specified prefix, that map into bound values on objectKey in attributeName, returns the [unique] representatives from dimension keyPrefix.length + 1.
getAttributeList(String, String) - Method in interface cytoscape.data.CyAttributes
Deprecated. Use getListAttribute() instead. Will be removed 11/2007.
getAttributeList(String, String) - Method in class cytoscape.data.CyAttributesImpl
 
getAttributeMap(String, String) - Method in interface cytoscape.data.CyAttributes
Deprecated. Use getMapAttribute() instead. Will be removed 11/2007.
getAttributeMap(String, String) - Method in class cytoscape.data.CyAttributesImpl
DOCUMENT ME!
getAttributeNames() - Method in interface cytoscape.data.CyAttributes
Gets an array of all attribute names.
getAttributeNames() - Method in class cytoscape.data.CyAttributesImpl
DOCUMENT ME!
getAttributeNamesForObj(String, CyAttributes) - Static method in class cytoscape.data.CyAttributesUtils
Return a non-null List of all the attribute names associated with a given identifier for a given CyAttributes.
getAttributes(String, CyAttributes) - Static method in class cytoscape.data.CyAttributesUtils
DOCUMENT ME!
getAttributeType(String, String) - Static method in class cytoscape.visual.mappings.MappingUtil
This method determines the type of the attribute used for the mapping.
getAttributeTypeString(String, String) - Static method in class cytoscape.visual.mappings.MappingUtil
This method determines the type of the attr used and returns a string representation of it.
getAttributeValue(String, String, Object[]) - Method in interface cytoscape.data.attr.MultiHashMap
Retrieves a bound attribute value from an object.
getAttributeValueType(String) - Method in interface cytoscape.data.attr.MultiHashMapDefinition
Returns the type of attribute values that exist in specified attribute space.
getAuthor() - Method in class cytoscape.plugin.PluginInfo.AuthorInfo
 
getAuthors() - Method in class cytoscape.plugin.PluginInfo
 
getBackground() - Method in class ding.view.DingCanvas
Returns the background color of this component.
getBackgroundColor() - Method in class cytoscape.visual.GlobalAppearance
DOCUMENT ME!
getBackgroundPaint() - Method in class ding.view.DGraphView
Returns the background color on the canvas.
getBackgroundPaint() - Method in interface giny.view.GraphView
 
getBaseKey() - Method in enum cytoscape.visual.mappings.MappingType
DOCUMENT ME!
getBasicInputStream(URL) - Static method in class cytoscape.util.URLUtil
Obtain an InputStream for a given URL.
getBend() - Method in interface giny.view.EdgeView
 
getBirdsEyeViewHandler() - Method in class cytoscape.view.CytoscapeDesktop
DOCUMENT ME!
getBookmarks() - Static method in class cytoscape.Cytoscape
DOCUMENT ME!
getBookmarks() - Method in class cytoscape.data.readers.BookmarkReader
Get loaded bookmark.
getBookmarks(URL) - Static method in class cytoscape.util.BookmarksUtil
DOCUMENT ME!
getBookmarks(File) - Static method in class cytoscape.util.BookmarksUtil
DOCUMENT ME!
getBool() - Method in class cytoscape.util.MutableBool
DOCUMENT ME!
getBoolean(String, boolean) - Method in class cytoscape.ding.CyGraphLOD
Deprecated. Use PropUtil.getBoolean(..) instead. Leaving Feb 2011.
getBoolean(Properties, String, boolean) - Static method in class cytoscape.util.PropUtil
Will return a boolean for the specified property key only if the value exists and if the string matches "true", "false", "yes", or "no" in a case insensitive manner.
getBooleanAttribute(String, String) - Method in interface cytoscape.data.CyAttributes
Gets a Boolean value at the specified id/attributeName.
getBooleanAttribute(String, String) - Method in class cytoscape.data.CyAttributesImpl
DOCUMENT ME!
getBooleanConstant() - Method in class org.cytoscape.equations.Tokeniser
 
getBooleans(Object[]) - Static method in class org.cytoscape.equations.FunctionUtil
Attempts to convert all arguments, including Lists to a uniform array of booleans.
getBorder() - Method in class ding.view.DNodeView
DOCUMENT ME!
getBorder() - Method in interface giny.view.NodeView
 
getBorderPaint() - Method in class ding.view.DNodeView
DOCUMENT ME!
getBorderPaint() - Method in interface giny.view.NodeView
 
getBorderWidth() - Method in class ding.view.DNodeView
DOCUMENT ME!
getBorderWidth() - Method in interface giny.view.NodeView
 
getBounds() - Method in class cytoscape.view.cytopanels.BiModalJSplitPane
Gets the bounds of the applications mainframe.
getBounds() - Method in interface cytoscape.view.cytopanels.CytoPanelContainer
Gets Bounds of Container, relative to parent component.
getBugFixVersion() - Method in class cytoscape.CytoscapeVersion
This method gets the bug fix version for Cytsocape.
getButton() - Method in class cytoscape.dialogs.IconPopupButton
DOCUMENT ME!
getByID(Long) - Method in class cytoscape.visual.customgraphic.CustomGraphicsManager
Get a Custom Graphics by integer ID.
getBypassAttrName() - Method in enum cytoscape.visual.VisualPropertyType
DOCUMENT ME!
getBySourceURL(URL) - Method in class cytoscape.visual.customgraphic.CustomGraphicsManager
Get Custom Graphics by source URL.
getCalculator(VisualPropertyType, String) - Method in class cytoscape.visual.CalculatorCatalog
DOCUMENT ME!
getCalculatorCatalog() - Method in class cytoscape.visual.VisualMappingManager
DOCUMENT ME!
getCalculatorMap(VisualPropertyType) - Method in class cytoscape.visual.CalculatorCatalog
Given a known byte identifier, returns the matching Map structure holding calculators of that type.
getCalculatorNames() - Static method in class cytoscape.visual.GlobalAppearance
 
getCalculators() - Method in class cytoscape.visual.CalculatorCatalog
DOCUMENT ME!
getCalculators(VisualPropertyType) - Method in class cytoscape.visual.CalculatorCatalog
DOCUMENT ME!
getCalculatorTypes() - Method in class cytoscape.visual.CalculatorCatalog
DOCUMENT ME!
getCanonicalName(String, String) - Method in class cytoscape.data.servers.BioDataServer
DOCUMENT ME!
getCanonicalName(String, String) - Method in interface cytoscape.data.servers.BioDataServerInterface
DOCUMENT ME!
getCanonicalName(String, String) - Method in class cytoscape.data.servers.BioDataServerRmi
DOCUMENT ME!
getCanonicalName - Class in cytoscape.data.servers
 
getCanonicalName() - Constructor for class cytoscape.data.servers.getCanonicalName
 
getCanvas() - Method in class ding.view.DGraphView
Method to return a reference to the network canvas.
getCanvas(DGraphView.Canvas) - Method in class ding.view.DGraphView
Method to return a reference to a DingCanvas object, given a canvas id.
getCapShape(double) - Method in interface cytoscape.render.immed.arrow.Arrow
The Shape of the cap that joins the Arrow body with the edge.
getCapShape(double) - Method in class cytoscape.render.immed.arrow.DiscArrow
 
getCategory() - Method in class cytoscape.bookmarks.Bookmarks
Gets the value of the category property.
getCategory() - Method in class cytoscape.plugin.DownloadableInfo
 
getCategory(String, List<Category>) - Static method in class cytoscape.util.BookmarksUtil
Select specific category from a list of categories.
getCategoryOrDataSource() - Method in class cytoscape.bookmarks.Category
Gets the value of the categoryOrDataSource property.
getCategoryText() - Method in enum cytoscape.plugin.Category
 
getCellEditorValue() - Method in class cytoscape.util.swing.AbstractCellEditor
DOCUMENT ME!
getCellHeight() - Static method in class cytoscape.visual.ui.CellHeightManager
 
getCellRenderer(Class<?>) - Method in class cytoscape.visual.ui.CellRendererFactory
 
getCenter() - Method in class ding.view.DGraphView
DOCUMENT ME!
getCheckBoxState() - Method in class cytoscape.actions.CheckBoxFileChooser
Deprecated. method for accessing last state of JCheckBox jcb
getChild(Object, int) - Method in class cytoscape.dialogs.plugins.ManagerModel
Gets child TreeNode from given parent at given index.
getChild() - Method in class cytoscape.generated.Network
Gets the value of the child property.
getChild(Object, int) - Method in class cytoscape.view.NetworkTreeTableModel
 
getChildAt(int) - Method in class cytoscape.dialogs.plugins.TreeNode
Get child from this node's child list at given index.
getChildCount(Object) - Method in class cytoscape.dialogs.plugins.ManagerModel
Gets count of all children under given parent (not including leaves)
getChildCount() - Method in class cytoscape.dialogs.plugins.TreeNode
Get total number of children for this node
getChildCount(Object) - Method in class cytoscape.view.NetworkTreeTableModel
 
getChildlessMetaDescendants(int) - Method in interface giny.model.RootGraph
Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges.
getChildren() - Method in class cytoscape.dialogs.plugins.TreeNode
Gets the list of children for this node
getClass(String, CyAttributes) - Static method in class cytoscape.data.CyAttributesUtils
DOCUMENT ME!
getClassifications() - Method in class cytoscape.data.annotation.Annotation
Deprecated. returns an array of all the classifications in the current annotation
getClassifications(String) - Method in class cytoscape.data.annotation.Annotation
Deprecated. all of the ontology identifiers registered for the specified entity
getClassifications(String, String, String, String) - Method in class cytoscape.data.servers.BioDataServer
DOCUMENT ME!
getClassifications(AnnotationDescription, String) - Method in class cytoscape.data.servers.BioDataServer
DOCUMENT ME!
getClassifications(String, String, String, String) - Method in interface cytoscape.data.servers.BioDataServerInterface
DOCUMENT ME!
getClassifications(AnnotationDescription, String) - Method in interface cytoscape.data.servers.BioDataServerInterface
DOCUMENT ME!
getClassifications(String, String, String, String) - Method in class cytoscape.data.servers.BioDataServerRmi
DOCUMENT ME!
getClassifications(AnnotationDescription, String) - Method in class cytoscape.data.servers.BioDataServerRmi
DOCUMENT ME!
getClassificationsVector(String) - Method in class cytoscape.data.annotation.Annotation
Deprecated. all of the ontology identifiers registered for the specified entity, as a Vector of Integers
getClassLoader() - Static method in class cytoscape.plugin.PluginManager
 
getClassName() - Method in class cytoscape.visual.calculators.AbstractCalculator
This exists so that it can be overridden in legacy classes (GenericNodeSizeCalculator, GenericColorCalculator, GenericArrowCalculator) such that they return the a new class name instead of a legacy class name.
getClient(String) - Static method in class cytoscape.data.webservice.WebServiceClientManager
DOCUMENT ME!
getClientData(String) - Method in interface cytoscape.CyNetwork
Deprecated. Use CyAttributes directly. This method will be removed in May, 2007.
getClientData(String) - Method in class cytoscape.ding.DingNetworkView
DOCUMENT ME!
getClientData(String) - Method in class cytoscape.giny.FingCyNetwork
Deprecated. Get Some client data
getClientData(String) - Method in interface cytoscape.view.CyNetworkView
Get Some client data
getClientDataNames() - Method in interface cytoscape.CyNetwork
Deprecated. Use CyAttributes directly. This method will be removed in May, 2007.
getClientDataNames() - Method in class cytoscape.ding.DingNetworkView
DOCUMENT ME!
getClientDataNames() - Method in class cytoscape.giny.FingCyNetwork
Deprecated. Get a list of all currently available ClientData objects
getClientDataNames() - Method in interface cytoscape.view.CyNetworkView
Get a list of all currently available ClientData objects
getClientID() - Method in interface cytoscape.data.webservice.WebServiceClient
Returns client ID.
getClientID() - Method in class cytoscape.data.webservice.WebServiceClientImpl
DOCUMENT ME!
getClientStub() - Method in interface cytoscape.data.webservice.WebServiceClient
Get client stub object.
getClientStub() - Method in class cytoscape.data.webservice.WebServiceClientImpl
Client stub will be returned from this.
getClientType() - Method in interface cytoscape.data.webservice.WebServiceClient
Returns client type.
getClientType() - Method in class cytoscape.data.webservice.WebServiceClientImpl
DOCUMENT ME!
getCmd() - Method in class cytoscape.util.Exec
DOCUMENT ME!
getCode() - Method in class org.cytoscape.equations.CodeAndSourceLocation
 
getCode() - Method in class org.cytoscape.equations.Equation
 
getColor(String) - Method in class cytoscape.data.readers.GMLReader
Create a color object from the string like it is stored in a gml file
getColor() - Method in class cytoscape.visual.Arrow
DOCUMENT ME!
getColor() - Method in class cytoscape.visual.customgraphic.paint.ColorPaintFactory
 
getColor() - Method in class cytoscape.visual.ui.icon.VisualPropertyIcon
Get color of icon
getColorAsText(Color) - Static method in class cytoscape.util.ColorUtil
Convert Color object into RGB String (e.g., (200,100,120))
getColorHexString(Color) - Method in class cytoscape.data.readers.GMLTree
Get the String representation of the 6 character hexidecimal RGB values i.e.
getColumnClass(int) - Method in class cytoscape.util.swing.AbstractTreeTableModel
DOCUMENT ME!
getColumnClass(int) - Method in interface cytoscape.util.swing.TreeTableModel
Returns the type for column number column.
getColumnClass(int) - Method in class cytoscape.util.swing.TreeTableModelAdapter
DOCUMENT ME!
getColumnClass(int) - Method in class cytoscape.view.NetworkTreeTableModel
 
getColumnCount() - Method in class cytoscape.dialogs.NetworkMetaDataTableModel
DOCUMENT ME!
getColumnCount() - Method in class cytoscape.dialogs.preferences.PluginsTableModel
Deprecated. DOCUMENT ME!
getColumnCount() - Method in class cytoscape.dialogs.preferences.PreferenceTableModel
DOCUMENT ME!
getColumnCount() - Method in interface cytoscape.util.swing.TreeTableModel
Returns the number of availible columns.
getColumnCount() - Method in class cytoscape.util.swing.TreeTableModelAdapter
DOCUMENT ME!
getColumnCount() - Method in class cytoscape.view.NetworkTreeTableModel
 
getColumnCount() - Method in class cytoscape.visual.customgraphic.ui.CyCustomGraphicsTreeNode
 
getColumnName(int) - Method in class cytoscape.dialogs.preferences.PluginsTableModel
Deprecated. DOCUMENT ME!
getColumnName(int) - Method in class cytoscape.dialogs.preferences.PreferenceTableModel
DOCUMENT ME!
getColumnName(int) - Method in interface cytoscape.util.swing.TreeTableModel
Returns the name for column number column.
getColumnName(int) - Method in class cytoscape.util.swing.TreeTableModelAdapter
DOCUMENT ME!
getColumnName(int) - Method in class cytoscape.view.NetworkTreeTableModel
 
getColumnPreferredWidths(JTable) - Static method in class cytoscape.util.swing.ColumnResizer
DOCUMENT ME!
getCommand(String, String) - Static method in class cytoscape.command.CyCommandManager
return a CyCommandHandler by either name or class name.
getCommand() - Method in enum cytoscape.visual.ui.EditorDisplayer
DOCUMENT ME!
getCommandList(String) - Static method in class cytoscape.command.CyCommandManager
Get the list of all commands that are currently registered for the specified namespace.
getCommandMap() - Static method in class cytoscape.command.CyCommandManager
Get the list of all commands that are currently registered, organized by namespaces
getCommands() - Method in class cytoscape.command.AbstractCommandHandler
Return the command or commands supported by this handler
getCommands() - Method in interface cytoscape.command.CyCommandHandler
Return the list of commands supported by this CyCommandHandler.
getCommittedMemory() - Static method in class cytoscape.util.MemoryReporter
 
getCommonName(String, String) - Method in class cytoscape.data.servers.BioDataServer
DOCUMENT ME!
getCommonName(String, String) - Method in interface cytoscape.data.servers.BioDataServerInterface
DOCUMENT ME!
getCommonName(String, String) - Method in class cytoscape.data.servers.BioDataServerRmi
DOCUMENT ME!
getCommonName - Class in cytoscape.data.servers
 
getCommonName() - Constructor for class cytoscape.data.servers.getCommonName
 
getCommonName(String) - Method in class cytoscape.data.synonyms.Thesaurus
DOCUMENT ME!
getCompassDirection() - Method in interface cytoscape.view.cytopanels.CytoPanel
Returns the int indicating the position in the layout.
getCompassDirection() - Method in class cytoscape.view.cytopanels.CytoPanelImp
Returns the int indicating the location within the layout.
getCompassDirection() - Method in enum cytoscape.view.cytopanels.CytoPanelName
 
getCompatibleClass() - Method in enum cytoscape.visual.ui.EditorDisplayer
DOCUMENT ME!
getCompatibleTypes() - Method in class org.cytoscape.equations.ArgDescriptor
 
getCompatibleTypes() - Method in enum org.cytoscape.equations.ArgType
 
getComplementaryColor(Color) - Static method in class cytoscape.util.ColorUtil
 
getComponent() - Method in class ding.view.DGraphView
Returns the InnerCanvas object.
getComponent() - Method in interface giny.view.GraphView
 
getComponentAt(int) - Method in interface cytoscape.view.cytopanels.CytoPanel
Returns the component at index.
getComponentAt(int) - Method in class cytoscape.view.cytopanels.CytoPanelImp
Returns the component at index.
getComponentAt(int, int) - Method in class ding.view.ArbitraryGraphicsCanvas
 
getConditionIndex(String) - Method in class cytoscape.data.ExpressionData
Gets the index value of the specified experimenal conditon.
getConditionNames() - Method in class cytoscape.data.ExpressionData
Gets an Array of All Experimental Conditions.
getConfigDirectory() - Static method in class cytoscape.CytoscapeInit
If .cytoscape directory does not exist, it creates it and returns it
getConfigFile(String) - Static method in class cytoscape.CytoscapeInit
DOCUMENT ME!
getConfigVersionDirectory() - Static method in class cytoscape.CytoscapeInit
Within the .cytoscape directory create a version-specific directory
getConnectingEdgeIndicesArray(int[]) - Method in interface giny.model.GraphPerspective
This will return an array of Edge indices that are the Edges between Nodes or null if even one node index is not in this graph perspective.
getConnectingEdgeIndicesArray(int[]) - Method in interface giny.model.RootGraph
This will return an array of edge indices that are the edges between nodes.
getConnectingEdges(List) - Method in interface giny.model.GraphPerspective
This will return a List of giny.model.Edge objects that are the Edges between Nodes.
getConnectingNodeIndicesArray(int[]) - Method in interface giny.model.GraphPerspective
Deprecated. Use getEdgeSourceIndex(int) and getEdgeTargetIndex(int) instead.
getConnectingNodeIndicesArray(int[]) - Method in interface giny.model.RootGraph
Deprecated. Use getEdgeSourceIndex(int) and getEdgeTargetIndex(int) instead, or use createGraphPerspective(int[], int[]).
getConstraintBox() - Method in class cytoscape.dialogs.JointIntegerEntry
DOCUMENT ME!
getConstraintLabel() - Method in class cytoscape.dialogs.JointIntegerEntry
DOCUMENT ME!
getContainers() - Method in class cytoscape.data.annotation.OntologyTerm
Deprecated. DOCUMENT ME!
getContent() - Method in class cytoscape.bookmarks.Attribute
Gets the value of the content property.
getContentComponent(CyAttributes, String) - Method in class cytoscape.dialogs.EdgeAttributesPopupDetails
 
getContentPane() - Method in class cytoscape.util.swing.CyCollapsiblePanel
This class requires that all content be placed within a designated panel, this method returns that panel.
getContext() - Method in interface cytoscape.visual.customgraphic.RenderingContext
 
getContextMethods(String, boolean) - Method in class ding.view.DGraphView
DOCUMENT ME!
getContextMethods(String, Object[]) - Method in class ding.view.DGraphView
DOCUMENT ME!
getContextMethods(String, boolean) - Method in interface giny.view.GraphView
Context Menu Support
getContextMethods(String, Object[]) - Method in interface giny.view.GraphView
Context Menu Support
getControllingAttributeName() - Method in class cytoscape.visual.mappings.AbstractMapping
 
getControllingAttributeName() - Method in class cytoscape.visual.mappings.continuous.ContinuousMappingReader
Gets Controlling Attribute Name.
getControllingAttributeName() - Method in class cytoscape.visual.mappings.discrete.DiscreteMappingReader
Gets Controlling Attribute Name.
getControllingAttributeName() - Method in interface cytoscape.visual.mappings.ObjectMapping
Get the controlling attribute name
getCoords() - Method in class cytoscape.render.immed.nodeshape.LegacyCustomNodeShape
 
getCount() - Method in class cytoscape.data.readers.InteractionsReader
DOCUMENT ME!
getCreatedEdgeIndices() - Method in class giny.model.RootGraphChangeEvent
 
getCreatedEdges() - Method in class giny.model.RootGraphChangeEvent
 
getCreatedNodeIndices() - Method in class giny.model.RootGraphChangeEvent
 
getCreatedNodes() - Method in class giny.model.RootGraphChangeEvent
 
getCrossReferences() - Method in class cytoscape.data.ontology.GOTerm
DOCUMENT ME!
getCrossReferences() - Method in class cytoscape.data.servers.OntologyServer
 
getCurator() - Method in class cytoscape.data.annotation.Annotation
Deprecated. DOCUMENT ME!
getCurator() - Method in class cytoscape.data.annotation.AnnotationDescription
Deprecated. DOCUMENT ME!
getCurator() - Method in class cytoscape.data.annotation.Ontology
Deprecated. DOCUMENT ME!
getCurator() - Method in class cytoscape.data.annotation.OntologyDescription
Deprecated. DOCUMENT ME!
getCurator() - Method in class cytoscape.data.ontology.GeneOntology
 
getCurator() - Method in class cytoscape.data.ontology.Ontology
 
getCurrent() - Method in interface cytoscape.util.MonitoredTask
Returns the currentProgress parameter.
getCurrentCalculator(VisualStyle) - Method in enum cytoscape.visual.VisualPropertyType
Gets the current calculator for the visual attribute for this type and the specified visual style.
getCurrentCustomGraphics(DNodeView) - Method in class cytoscape.visual.properties.NodeCustomGraphicsProp
 
getCurrentNetwork() - Static method in class cytoscape.Cytoscape
Return the Network that currently has the Focus.
getCurrentNetworkView() - Static method in class cytoscape.Cytoscape
Return the CyNetworkView that currently has the focus.
getCurrentSessionFileName() - Static method in class cytoscape.Cytoscape
Get name of the current session file.
getCustomGraphicsManager() - Method in class cytoscape.visual.VisualMappingManager
 
getCustomGraphicsPosition(CustomGraphic) - Method in class ding.view.DNodeView
 
getCustomGraphicsPositionType(int) - Static method in enum cytoscape.visual.VisualPropertyType
 
getCustomGraphicsType(int) - Static method in enum cytoscape.visual.VisualPropertyType
 
getCustomNodeShape(byte) - Method in class cytoscape.render.immed.GraphGraphics
Returns the vertices of a previously defined custom node shape.
getCustomNodeShapes() - Method in class cytoscape.render.immed.GraphGraphics
DOCUMENT ME!
getCyEdge(Node, Node, String, Object, boolean) - Static method in class cytoscape.Cytoscape
Gets the first CyEdge found between the two nodes (direction does not matter) that has the given value for the given attribute.
getCyEdge(Node, Node, String, Object, boolean, boolean) - Static method in class cytoscape.Cytoscape
Gets the first CyEdge found between the two nodes that has the given value for the given attribute.
getCyEdge(String, String, String, String) - Static method in class cytoscape.Cytoscape
Returns and edge if it exists, otherwise creates a directed edge.
getCyEdgesList() - Static method in class cytoscape.Cytoscape
 
getCyGroup(CyNode) - Static method in class cytoscape.groups.CyGroupManager
getCyGroup is a static method that returns a CyGroup structure when given the CyNode that represents this group.
getCyInitParams() - Static method in class cytoscape.CytoscapeInit
Returns the CyInitParams object used to initialize Cytoscape.
getCyMenus() - Method in class cytoscape.view.CytoscapeDesktop
DOCUMENT ME!
getCyNetworkListeners() - Method in interface cytoscape.CyNetwork
Returns the set of listeners registered with this object.
getCyNetworkListeners() - Method in class cytoscape.giny.FingCyNetwork
Returns the set of listeners registered with this object.
getCyNode(String) - Static method in class cytoscape.Cytoscape
 
getCyNode(String, boolean) - Static method in class cytoscape.Cytoscape
 
getCyNodesList() - Static method in class cytoscape.Cytoscape
 
getCysessionNote() - Method in class cytoscape.data.readers.CytoscapeSessionReader
Extract Session Note test field in cysession.xml
getCytopanel() - Method in class cytoscape.generated.Cytopanels
Gets the value of the cytopanel property.
getCytoPanel(int) - Method in class cytoscape.view.CytoscapeDesktop
Gets a cytoPanel given a Compass direction.
getCytoPanelComponentCount() - Method in interface cytoscape.view.cytopanels.CytoPanel
Returns the number of components in the CytoPanel.
getCytoPanelComponentCount() - Method in class cytoscape.view.cytopanels.CytoPanelImp
Returns the number of components in the CytoPanel.
getCytoPanelMenu() - Method in class cytoscape.view.CyMenus
Deprecated. Will be removed April 2008. Cytopanels no longer have a separate menu (they're in View).
getCytopanels() - Method in class cytoscape.generated.SessionState
Gets the value of the cytopanels property.
getCytoscapeVersion() - Method in class cytoscape.plugin.DownloadableInfo
 
getCytoscapeVersions() - Method in class cytoscape.plugin.DownloadableInfo
 
getCyWebServiceEventSupport() - Static method in class cytoscape.data.webservice.WebServiceClientManager
 
getDag() - Method in class cytoscape.data.ontology.readers.OBOFlatFileReader
DOCUMENT ME!
getDag() - Method in interface cytoscape.data.ontology.readers.OntologyReader
DOCUMENT ME!
getDataSource() - Method in class cytoscape.dialogs.preferences.EditBookmarkDialog
 
getDataSourceList(String, List<Category>) - Static method in class cytoscape.util.BookmarksUtil
Traverse bookmark tree and get a list of data sources from the specified category.
getDataType() - Method in enum cytoscape.visual.VisualPropertyType
DOCUMENT ME!
getDBNames() - Method in class cytoscape.data.ontology.DBCrossReferences
DOCUMENT ME!
getDBReference(String) - Method in class cytoscape.data.ontology.DBCrossReferences
DOCUMENT ME!
getDefault() - Method in class cytoscape.visual.properties.AbstractVisualProperty
 
getDefault() - Method in enum cytoscape.visual.VisualPropertyDependency.Definition
Will return the default state for this Definition.
getDefault(VisualStyle) - Method in enum cytoscape.visual.VisualPropertyType
Gets the current default value for this type in the specified visual style.
getDefaultAppearance() - Method in class cytoscape.visual.EdgeAppearanceCalculator
DOCUMENT ME!
getDefaultAppearance() - Method in class cytoscape.visual.NodeAppearanceCalculator
DOCUMENT ME!
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.AbstractVisualProperty
DOCUMENT ME!
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.EdgeColorProp
DOCUMENT ME!
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.EdgeFontFaceProp
DOCUMENT ME!
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.EdgeFontSizeProp
DOCUMENT ME!
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.EdgeLabelColorProp
DOCUMENT ME!
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.EdgeLabelOpacityProp
DOCUMENT ME!
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.EdgeLabelPositionProp
 
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.EdgeLabelProp
DOCUMENT ME!
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.EdgeLabelWidthProp
DOCUMENT ME!
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.EdgeLineStyleProp
DOCUMENT ME!
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.EdgeLineWidthProp
DOCUMENT ME!
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.EdgeOpacityProp
DOCUMENT ME!
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.EdgeSourceArrowColorProp
DOCUMENT ME!
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.EdgeSourceArrowOpacityProp
DOCUMENT ME!
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.EdgeSourceArrowShapeProp
DOCUMENT ME!
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.EdgeTargetArrowColorProp
DOCUMENT ME!
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.EdgeTargetArrowOpacityProp
DOCUMENT ME!
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.EdgeTargetArrowShapeProp
DOCUMENT ME!
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.EdgeToolTipProp
 
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.NodeBorderColorProp
DOCUMENT ME!
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.NodeBorderOpacityProp
DOCUMENT ME!
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.NodeCustomGraphicsPositionProp
DOCUMENT ME!
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.NodeCustomGraphicsProp
DOCUMENT ME!
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.NodeFillColorProp
DOCUMENT ME!
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.NodeFontFaceProp
DOCUMENT ME!
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.NodeFontSizeProp
DOCUMENT ME!
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.NodeHeightProp
DOCUMENT ME!
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.NodeLabelColorProp
DOCUMENT ME!
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.NodeLabelOpacityProp
DOCUMENT ME!
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.NodeLabelPositionProp
DOCUMENT ME!
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.NodeLabelProp
DOCUMENT ME!
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.NodeLabelWidthProp
DOCUMENT ME!
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.NodeLineStyleProp
DOCUMENT ME!
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.NodeLineWidthProp
DOCUMENT ME!
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.NodeOpacityProp
DOCUMENT ME!
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.NodeShapeProp
DOCUMENT ME!
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.NodeShowNestedNetworkProp
DOCUMENT ME!
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.NodeSizeProp
DOCUMENT ME!
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.NodeToolTipProp
DOCUMENT ME!
getDefaultAppearanceObject() - Method in class cytoscape.visual.properties.NodeWidthProp
DOCUMENT ME!
getDefaultAppearanceObject() - Method in interface cytoscape.visual.VisualProperty
 
getDefaultBackgroundColor() - Method in class cytoscape.visual.GlobalAppearanceCalculator
DOCUMENT ME!
getDefaultColor(String) - Method in class cytoscape.visual.GlobalAppearanceCalculator
Get default color for the given parameter name.
getDefaultEdgeReverseSelectionColor() - Method in class cytoscape.visual.GlobalAppearanceCalculator
DOCUMENT ME!
getDefaultEdgeSelectionColor() - Method in class cytoscape.visual.GlobalAppearanceCalculator
DOCUMENT ME!
getDefaultIcon() - Method in class cytoscape.visual.properties.AbstractVisualProperty
DOCUMENT ME!
getDefaultIcon() - Method in interface cytoscape.visual.VisualProperty
DOCUMENT ME!
getDefaultLayout() - Static method in class cytoscape.layout.CyLayouts
Get the default layout.
getDefaultMenuSpecifier() - Method in class cytoscape.util.CytoscapeMenuBar
DOCUMENT ME!
getDefaultNodeReverseSelectionColor() - Method in class cytoscape.visual.GlobalAppearanceCalculator
DOCUMENT ME!
getDefaultNodeSelectionColor() - Method in class cytoscape.visual.GlobalAppearanceCalculator
DOCUMENT ME!
getDefaultProperties(String) - Method in class cytoscape.visual.Appearance
Returns a Properties object that defines this appearance.
getDefaultProperties(String) - Method in class cytoscape.visual.EdgeAppearance
 
getDefaultProperties(String) - Method in class cytoscape.visual.NodeAppearance
 
getDefaultProperties(String) - Method in interface cytoscape.visual.VisualPropertyDependency
Will return a new Properties object with properties set based on the specified baseKey and any dependency definitions set in this object.
getDefaultPropertyKey() - Method in enum cytoscape.visual.VisualPropertyDependency.Definition
Will return the key used to identify this Definition for use in Properties objects.
getDefaultPropertyKey(String) - Method in enum cytoscape.visual.VisualPropertyType
DOCUMENT ME!
getDefaultPropertyLabel() - Method in enum cytoscape.visual.VisualPropertyType
DOCUMENT ME!
getDefaultTaskConfig() - Static method in class cytoscape.layout.LayoutTask
This method returns a default TaskConfig object.
getDefaultValue() - Method in class cytoscape.visual.customgraphic.CustomGraphicsPropertyImpl
 
getDefaultValue() - Method in interface cytoscape.visual.customgraphic.impl.vector.CustomGraphicsProperty
 
getDefaultValue() - Method in class org.cytoscape.equations.parse_tree.IdentNode
 
getDefaultViewPanel() - Static method in class cytoscape.visual.ui.DefaultViewPanel
 
getDefaultVisualStyle() - Method in interface cytoscape.data.webservice.NetworkImportWebServiceClient
Return default vixual style for this network import client.
getDefinedAttributes() - Method in interface cytoscape.data.attr.MultiHashMapDefinition
Returns all defined attributeNames.
getDegree() - Method in class ding.view.DNodeView
DOCUMENT ME!
getDegree(Node) - Method in interface giny.model.GraphPerspective
Return the number of distinct Edges in this GraphPerspective incident on the given Node.
getDegree(int) - Method in interface giny.model.GraphPerspective
Return the number of distinct Edges in this GraphPerspective incident on the Node with the given index.
getDegree(Node) - Method in interface giny.model.RootGraph
Return the number of distinct Edges incident on the given Node.
getDegree(int) - Method in interface giny.model.RootGraph
Return the number of distinct Edges incident on the Node with the given index.
getDegree() - Method in interface giny.view.NodeView
 
getDependency() - Method in class cytoscape.visual.VisualStyle
 
getDependents() - Method in class cytoscape.data.AttribTopoGraphNode
 
getDependents() - Method in interface cytoscape.util.TopoGraphNode
 
getDescPadding() - Method in class org.apache.commons.cli.HelpFormatter
Returns the 'descPadding'.
getDescription() - Method in class cytoscape.bookmarks.Bookmarks
Gets the value of the description property.
getDescription(String) - Method in class cytoscape.command.AbstractCommandHandler
This method returns a formatted description of the command, including the namespace, command name, plugin-provided description, and arguments.
getDescription(String) - Method in interface cytoscape.command.CyCommandHandler
Get the description/documentation of the command.
getDescription() - Method in class cytoscape.data.annotation.Ontology
Deprecated. DOCUMENT ME!
getDescription() - Method in class cytoscape.data.ExpressionData
Returns a text description of this data object.
getDescription() - Method in class cytoscape.data.ontology.GOTerm
DOCUMENT ME!
getDescription() - Method in class cytoscape.data.ontology.Ontology
DOCUMENT ME!
getDescription() - Method in class cytoscape.data.ontology.OntologyTerm
Return a human-readable description of this term, or the empty string if none is available.
getDescription() - Method in enum cytoscape.data.ontology.readers.OBOTags
DOCUMENT ME!
getDescription() - Method in class cytoscape.data.ontology.Triple
Description for triple is not supported.
getDescription() - Method in interface cytoscape.data.webservice.WebServiceClient
Get description for this client.
getDescription() - Method in class cytoscape.data.webservice.WebServiceClientImpl
DOCUMENT ME!
getDescription() - Method in class cytoscape.dialogs.NetworkMetaDataTableModel
Get Desctiption entry, which will not be included in the table.
getDescription() - Method in class cytoscape.layout.Tunable
Method to return the description for this Tunable.
getDescription() - Method in class cytoscape.plugin.DownloadableInfo
 
getDescription() - Method in class cytoscape.util.CyFileFilter
Returns the human readable description of this filter.
getDescription(String) - Method in class cytoscape.visual.Appearance
Returns a string describing this appearance.
getDescription() - Method in class cytoscape.visual.Appearance
Returns a string describing this appearance with no identifying prefix.
getDescription() - Method in class cytoscape.visual.EdgeAppearanceCalculator
DOCUMENT ME!
getDescription() - Method in class cytoscape.visual.GlobalAppearanceCalculator
Returns a text description of this object's current state.
getDescription() - Method in class cytoscape.visual.NodeAppearanceCalculator
Returns a text description of the current default values and calculator names.
getDescription() - Method in class org.apache.commons.cli.avalon.CLOptionDescriptor
Retrieve textual description.
getDescription() - Method in class org.apache.commons.cli.Option
Retrieve the self-documenting description of this Option
getDescription() - Method in class org.cytoscape.equations.ArgDescriptor
 
getDescriptor() - Method in class org.apache.commons.cli.avalon.CLOption
DOCUMENT ME!
getDesktop() - Static method in class cytoscape.Cytoscape
 
getDesktop() - Method in class cytoscape.generated.SessionState
Gets the value of the desktop property.
getDesktopPane() - Method in class cytoscape.view.NetworkViewManager
DOCUMENT ME!
getDesktopSize() - Method in class cytoscape.generated.Desktop
Gets the value of the desktopSize property.
getDisplayName() - Method in interface cytoscape.data.webservice.WebServiceClient
Returns display name of this client.
getDisplayName() - Method in class cytoscape.data.webservice.WebServiceClientImpl
DOCUMENT ME!
getDisplayName() - Method in enum cytoscape.view.ColumnTypes
 
getDisplayName() - Method in interface cytoscape.visual.customgraphic.CyCustomGraphics
Display name is a simple description of this image object.
getDisplayName() - Method in class cytoscape.visual.customgraphic.impl.AbstractDCustomGraphics
 
getDisplayString() - Method in enum cytoscape.util.ScalingMethod
 
getDocumentVersion() - Method in class cytoscape.generated.Cysession
Gets the value of the documentVersion property.
getDoubleAttribute(String, String) - Method in interface cytoscape.data.CyAttributes
Gets a Double value at the specified id/attributeName.
getDoubleAttribute(String, String) - Method in class cytoscape.data.CyAttributesImpl
DOCUMENT ME!
getDoubles(Object[]) - Static method in class org.cytoscape.equations.FunctionUtil
Attempts to convert all arguments, including Lists to a uniform array of doubles.
getDoubleValue() - Method in class cytoscape.dialogs.NewSlider
DOCUMENT ME!
getDownloadableListByStatus(PluginStatus) - Method in class cytoscape.plugin.PluginTracker
Get the list of all downloadable object by their status.
getDownloadables() - Method in class cytoscape.plugin.PluginFileReader
Retrieves the full list of all downloadable objects in the xml file.
getDownloadables(PluginStatus) - Method in class cytoscape.plugin.PluginManager
Get a list of downloadable objects by status.
getDownloadableURL() - Method in class cytoscape.plugin.DownloadableInfo
 
getDrawPoints() - Method in interface giny.view.Bend
Returns a list of points that define what gets drawn and hence what is visible to the user.
getDupeCount() - Method in class cytoscape.visual.calculators.AbstractCalculator
Get how many times this calculator has been duplicated.
getDupeCount() - Method in class cytoscape.visual.VisualStyle
Get how many times this style has been cloned.
getEdge() - Method in class cytoscape.generated.HiddenEdges
Gets the value of the edge property.
getEdge() - Method in class cytoscape.generated.SelectedEdges
Gets the value of the edge property.
getEdge(String) - Method in class cytoscape.giny.CytoscapeFingRootGraph
DOCUMENT ME!
getEdge(String) - Method in interface cytoscape.giny.CytoscapeRootGraph
DOCUMENT ME!
getEdge(RootGraph, int, String) - Method in interface fing.model.FingEdgeDepot
This either instantiates a new edge or gets one from the recyclery, initializing it with the parameters specified.
getEdge(int) - Method in interface giny.model.GraphPerspective
Return an Edge which is in this GraphPerspective.
getEdge(int) - Method in interface giny.model.RootGraph
Return the Edge with the given index in this RootGraph.
getEdge() - Method in interface giny.view.EdgeView
 
getEdgeAliases() - Method in class cytoscape.data.servers.OntologyServer
 
getEdgeAppearanceCalculator() - Method in class cytoscape.visual.VisualStyle
Get the EdgeAppearanceCalculator for this visual style.
getEdgeAttributeFiles() - Method in class cytoscape.CyMain
DOCUMENT ME!
getEdgeAttributeFiles() - Method in interface cytoscape.init.CyInitParams
A list of Strings that describe edge attribute file locations.
getEdgeAttributes() - Static method in class cytoscape.Cytoscape
Gets Global Edge Attributes
getEdgeAttributesList() - Method in class cytoscape.giny.FingCyNetwork
Return all availble Attributes for the Edges in this CyNetwork
getEdgeAttributeValue(Edge, String) - Method in class cytoscape.giny.FingCyNetwork
Return the requested Attribute for the given Edge
getEdgeAttributeValue(int, String) - Method in class cytoscape.giny.FingCyNetwork
Return the requested Attribute for the given Edge
getEdgeBooleanProperty(int, int) - Method in class ding.view.DGraphView
DOCUMENT ME!
getEdgeBooleanProperty(int, int) - Method in interface giny.view.GraphView
 
getEdgeContextMenuItems(EdgeView) - Method in interface cytoscape.data.webservice.ui.WebServiceClientGUI
Return edge context menu if available.
getEdgeContextMenuItems(EdgeView) - Method in class cytoscape.data.webservice.WebServiceClientImplWithGUI
Returns client dependent context menu for edges
getEdgeCount() - Method in interface giny.model.GraphPerspective
Returns number of active edges in this perspective.
getEdgeCount(Node, Node, boolean) - Method in interface giny.model.GraphPerspective
Count the number of edges from the first Node to the second.
getEdgeCount(int, int, boolean) - Method in interface giny.model.GraphPerspective
Count the number of edges from the Node with index from_index to the Node with index to_index (where this.getIndex( to_node ) == to_index).
getEdgeCount() - Method in interface giny.model.RootGraph
Returns number of edges in this RootGraph.
getEdgeCount(Node, Node, boolean) - Method in interface giny.model.RootGraph
Deprecated. Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead.
getEdgeCount(int, int, boolean) - Method in interface giny.model.RootGraph
Deprecated. Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead.
getEdgeDoubleProperty(int, int) - Method in class ding.view.DGraphView
DOCUMENT ME!
getEdgeDoubleProperty(int, int) - Method in interface giny.view.GraphView
 
getEdgeFloatProperty(int, int) - Method in class ding.view.DGraphView
DOCUMENT ME!
getEdgeFloatProperty(int, int) - Method in interface giny.view.GraphView
 
getEdgeIndex(int) - Method in interface giny.model.GraphPerspective
Deprecated. Use getRootGraphEdgeIndex(int), whose functionality is identical.
getEdgeIndicesArray() - Method in class cytoscape.data.readers.AbstractGraphReader
DOCUMENT ME!
getEdgeIndicesArray() - Method in class cytoscape.data.readers.GMLReader
Part of interace contract
getEdgeIndicesArray() - Method in interface cytoscape.data.readers.GraphReader
Gets an array of edges indices that participate in the newly created graph.
getEdgeIndicesArray() - Method in class cytoscape.data.readers.InteractionsReader
DOCUMENT ME!
getEdgeIndicesArray() - Method in class cytoscape.data.readers.NNFReader
 
getEdgeIndicesArray() - Method in class cytoscape.data.readers.XGMMLReader
 
getEdgeIndicesArray() - Method in interface giny.model.GraphPerspective
Returns an array of length getEdgeCount(); the array contains RootGraph indices of Edge objects in this GraphPerspective, in some undefined order.
getEdgeIndicesArray(int, int, boolean, boolean) - Method in interface giny.model.GraphPerspective
Deprecated. Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead.
getEdgeIndicesArray(int, int, boolean) - Method in interface giny.model.GraphPerspective
Deprecated. Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead.
getEdgeIndicesArray() - Method in interface giny.model.RootGraph
Returns an array of edge indices.
getEdgeIndicesArray(int, int, boolean, boolean) - Method in interface giny.model.RootGraph
Deprecated. Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead.
getEdgeIndicesArray(int, int, boolean) - Method in interface giny.model.RootGraph
Deprecated. Use getAdjacentEdgeIndicesArray(int, boolean, boolean, boolean) instead.
getEdgeIntProperty(int, int) - Method in class ding.view.DGraphView
DOCUMENT ME!
getEdgeIntProperty(int, int) - Method in interface giny.view.GraphView
 
getEdgeLabelAnchor() - Method in interface giny.view.EdgeView
 
getEdgeMetaChildIndicesArray(int) - Method in interface giny.model.GraphPerspective
Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges.
getEdgeMetaChildIndicesArray(int) - Method in interface giny.model.RootGraph
Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges.
getEdgeMetaParentIndicesArray(int) - Method in interface giny.model.GraphPerspective
Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges.
getEdgeMetaParentIndicesArray(int) - Method in interface giny.model.RootGraph
Nodes and Edges comprise an additional directed graph through the contains-a relationship, in which a MetaParent Node contains each of its MetaChild Nodes and Edges.
getEdgeObjectProperty(int, int) - Method in class ding.view.DGraphView
DOCUMENT ME!
getEdgeObjectProperty(int, int) - Method in interface giny.view.GraphView
Return the stored value for the edge for the given property
getEdgePath(byte, float, byte, float, float, float, EdgeAnchors, float, float, GeneralPath) - Method in class cytoscape.render.immed.GraphGraphics
Computes the path that an edge takes; this method is useful if a user interface would allow user selection of edges, for example.
getEdgeReverseSelectionColor() - Method in class cytoscape.visual.GlobalAppearance
DOCUMENT ME!
getEdgeSelectionColor() - Method in class cytoscape.visual.GlobalAppearance
DOCUMENT ME!
getEdgeSourceIndex(int) - Method in interface giny.model.GraphPerspective
Retrieve the index of the Node that is the source of the Edge in this GraphPerspective with the given index.
getEdgeSourceIndex(int) - Method in interface giny.model.RootGraph
Retrieve the index of the Node that is the source of the Edge with the given index.
getEdgeTargetIndex(int) - Method in interface giny.model.GraphPerspective
Retrieve the index of the Node that is the target of the Edge in this GraphPerspective with the given index.
getEdgeTargetIndex(int) - Method in interface giny.model.RootGraph
Retrieve the index of the Node that is the target of the Edge with the given index.
getEdgeView(int) - Method in class ding.view.DGraphView
DOCUMENT ME!
getEdgeView(Edge) - Method in class ding.view.DGraphView
DOCUMENT ME!
getEdgeView(int) - Method in interface giny.view.GraphView
 
getEdgeView(Edge) - Method in interface giny.view.GraphView
 
getEdgeViewCount() - Method in class ding.view.DGraphView
DOCUMENT ME!
getEdgeViewCount() - Method in interface giny.view.GraphView
 
getEdgeViewsIterator() - Method in class ding.view.DGraphView
DOCUMENT ME!
getEdgeViewsIterator() - Method in interface giny.view.GraphView
Return all of the EdgeViews in this GraphView
getEdgeViewsList() - Method in class ding.view.DGraphView
DOCUMENT ME!
getEdgeViewsList(Node, Node) - Method in class ding.view.DGraphView
DOCUMENT ME!
getEdgeViewsList(int, int, boolean) - Method in class ding.view.DGraphView
DOCUMENT ME!
getEdgeViewsList(NodeView) - Method in class ding.view.DNodeView
DOCUMENT ME!
getEdgeViewsList() - Method in interface giny.view.GraphView
Return all of the EdgeViews in this GraphView
getEdgeViewsList(Node, Node) - Method in interface giny.view.GraphView
Note that this will return a list of Edge objects, the other one will return indices
getEdgeViewsList(int, int, boolean) - Method in interface giny.view.GraphView
 
getEdgeViewsList(NodeView) - Method in interface giny.view.NodeView
 
getEdgeVisualPropertyList() - Static method in enum cytoscape.visual.VisualPropertyType
DOCUMENT ME!
getEditingRow() - Method in class cytoscape.util.swing.JTreeTable
DOCUMENT ME!
getEditMenu() - Method in class cytoscape.view.CyMenus
returns the menu with items related to editing the graph.
getEditor(VisualPropertyType, EditorDisplayer.EditorType) - Static method in enum cytoscape.visual.ui.EditorDisplayer
Returns proper editor displayer object based on visual property type.
getEnumValue(String) - Static method in enum cytoscape.util.ScalingMethod
 
getEqnAttrTracker() - Static method in class cytoscape.Cytoscape
 
getEquation(String, String) - Method in interface cytoscape.data.CyAttributes
 
getEquation(String, String) - Method in class cytoscape.data.CyAttributesImpl
 
getEquation() - Method in class org.cytoscape.equations.EqnCompiler
 
getErrorCode() - Method in exception cytoscape.data.webservice.CyWebServiceException
 
getErrorEquation(String, Class, String) - Static method in class org.cytoscape.equations.Equation
A factory method that returns an Equation that always fails at runtime.
getErrorMessage() - Method in enum cytoscape.data.webservice.CyWebServiceException.WSErrorCode
 
getErrorMsg() - Method in interface org.cytoscape.equations.EqnParser
If parse() failed, this will return the last error messages.
getErrorMsg() - Method in class org.cytoscape.equations.Tokeniser
 
getErrors() - Method in class cytoscape.command.CyCommandResult
Return all of the erros from an execution.
getErrorString() - Method in class org.apache.commons.cli.avalon.CLArgsParser
Retrieve an error message that occured during parsing if one existed.
getEventType() - Method in class cytoscape.data.SelectEvent
Returns a boolean identifying the type of event, true the selectes state was set to true, false if it was set to false
getEventType() - Method in class cytoscape.data.webservice.CyWebServiceEvent
 
getException() - Method in class cytoscape.plugin.PluginInquireAction
 
getExpander(WebServiceClient) - Static method in class cytoscape.data.webservice.util.NetworkExpansionMenu
 
getExponent(float) - Static method in class cytoscape.util.MathUtil
 
getExponent(double) - Static method in class cytoscape.util.MathUtil
 
getExportTextAsFont() - Method in class cytoscape.dialogs.ExportAsGraphicsFileChooser
 
getExpressionData() - Static method in class cytoscape.Cytoscape
DOCUMENT ME!
getExpressionFiles() - Method in class cytoscape.CyMain
DOCUMENT ME!
getExpressionFiles() - Method in interface cytoscape.init.CyInitParams
A list of Strings that describe expression matrix file locations.
getExtension(File) - Method in class cytoscape.util.CyFileFilter
Return the extension portion of the file's name.
getExtension(String) - Method in class cytoscape.util.CyFileFilter
DOCUMENT ME!
getExtensionSet() - Method in class cytoscape.util.CyFileFilter
Returns the Set of file extension names.
getExtents(double[]) - Method in class ding.view.DGraphView
Extents of the view.
getExtremeValues() - Method in class cytoscape.data.ExpressionData
Returns a 2D Matrix of Extreme Values.
getFaceComboBox() - Method in class cytoscape.visual.ui.FontChooser
DOCUMENT ME!
getField() - Method in class cytoscape.dialogs.IntegerEntryField
DOCUMENT ME!
getField(String) - Method in class cytoscape.dialogs.JointIntegerEntry
DOCUMENT ME!
getFile() - Method in class cytoscape.dialogs.ImportNetworkDialog
Get first file only.
getFile(String, int) - Static method in class cytoscape.util.FileUtil
Returns a File object, this method should be used instead of rolling your own JFileChooser.
getFile(String, int, CyFileFilter[]) - Static method in class cytoscape.util.FileUtil
Returns a File object, this method should be used instead of rolling your own JFileChooser.
getFile(String, int, CyFileFilter, File) - Static method in class cytoscape.util.FileUtil
Returns a File object, this method should be used instead of rolling your own JFileChooser.
getFile(String, int, CyFileFilter[], String, String) - Static method in class cytoscape.util.FileUtil
Returns a File object, this method should be used instead of rolling your own JFileChooser.
getFileList() - Method in class cytoscape.plugin.PluginInfo
 
getFileMenu() - Method in class cytoscape.view.CyMenus
Returns the menu with items related to file operations.
getFileName() - Method in class cytoscape.data.ExpressionData
Gets the Name of the Expression Data File.
getFilename() - Method in class cytoscape.dialogs.ImportAttributeMatrixDialog
DOCUMENT ME!
getFilename() - Method in class cytoscape.generated.Network
Gets the value of the filename property.
getFileNature() - Method in class cytoscape.util.CyFileFilter
Returns the nature of the file.
getFiles() - Method in class cytoscape.dialogs.ImportNetworkDialog
Get all files selected.
getFiles(String, int, CyFileFilter[]) - Static method in class cytoscape.util.FileUtil
Returns an array of File objects, this method should be used instead of rolling your own JFileChooser.
getFiles(Component, String, int, CyFileFilter[]) - Static method in class cytoscape.util.FileUtil
Returns an array of File objects, this method should be used instead of rolling your own JFileChooser.
getFiles(String, int, CyFileFilter[], String, String) - Static method in class cytoscape.util.FileUtil
Returns a list of File objects, this method should be used instead of rolling your own JFileChooser.
getFiles(String, int, CyFileFilter[], String, String, boolean) - Static method in class cytoscape.util.FileUtil
Returns a list of File objects, this method should be used instead of rolling your own JFileChooser.
getFiles(Component, String, int, CyFileFilter[], String, String, boolean) - Static method in class cytoscape.util.FileUtil
Returns a list of File objects, this method should be used instead of rolling your own JFileChooser.
getFiles(Component, String, int, CyFileFilter[], String, String, boolean, File[]) - Static method in class cytoscape.util.FileUtil
Returns a list of File objects, this method should be used instead of rolling your own JFileChooser.
getFileType(String) - Method in class cytoscape.data.ImportHandler
Gets the name of the filter which is capable of reading the specified file.
getFileType() - Method in class cytoscape.plugin.PluginInfo
 
getFilterField() - Method in class cytoscape.util.swing.FilterHistoryJList
DOCUMENT ME!
getFitRatio() - Method in interface cytoscape.visual.customgraphic.CyCustomGraphics
 
getFitRatio() - Method in class cytoscape.visual.customgraphic.impl.AbstractDCustomGraphics
 
getFlags() - Method in class org.apache.commons.cli.avalon.CLOptionDescriptor
Retrieve flags about option.
getFloat(Properties, String, float) - Static method in class cytoscape.util.PropUtil
Will return a float for the specified property key only if the value exists and is properly formatted as an float.
getFloatConstant() - Method in class org.cytoscape.equations.Tokeniser
 
getFont() - Method in class ding.view.DNodeView
DOCUMENT ME!
getFont() - Method in interface giny.view.Label
Returns the font of this PText.
getFontRenderContextFull() - Method in class cytoscape.render.immed.GraphGraphics
Returns the context that is used by drawTextFull() to produce text shapes to be drawn to the screen.
getFontRenderContextLow() - Method in class cytoscape.render.immed.GraphGraphics
Returns the context that is used by drawTextLow() to produce text shapes to be drawn to the screen.
getFormat() - Method in class cytoscape.bookmarks.DataSource
Gets the value of the format property.
getFrameID() - Method in class cytoscape.generated.NetworkFrame
Gets the value of the frameID property.
getFullName() - Method in class cytoscape.data.ontology.DBReference
DOCUMENT ME!
getFullName() - Method in class cytoscape.data.ontology.GOTerm
DOCUMENT ME!
getFullPath() - Method in class cytoscape.data.ExpressionData
Gets the File representation of the Expression Data Object.
getFullVersion() - Method in class cytoscape.CytoscapeVersion
 
getFunction(String) - Method in interface org.cytoscape.equations.EqnParser
 
getFunctionSummary() - Method in class org.cytoscape.equations.AbstractFunction
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Abs
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.ACos
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.And
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.ASin
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.ATan2
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Average
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.BList
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Combin
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Concatenate
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Cos
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Cosh
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Count
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Degrees
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Error
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Exp
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.First
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.FList
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.GeoMean
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.HarMean
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.If
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.IList
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Largest
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Last
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Left
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Len
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.ListToString
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Ln
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Log
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Lower
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Max
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Median
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Mid
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Min
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Mod
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Mode
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.NormDist
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Not
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Now
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Nth
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Or
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Permut
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Pi
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Product
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Radians
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Right
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Round
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Sign
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Sin
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Sinh
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.SList
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Sqrt
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.StDev
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Substitute
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Sum
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Tan
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Tanh
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Text
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Today
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Trunc
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Upper
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Value
Used to provide help for users.
getFunctionSummary() - Method in class org.cytoscape.equations.builtins.Var
Used to provide help for users.
getFunctionSummary() - Method in interface org.cytoscape.equations.Function
Used to provide help for users.
getGeneDescriptor(String) - Method in class cytoscape.data.ExpressionData
Gets the Gene Descriptor for the specified gene.
getGeneDescriptors() - Method in class cytoscape.data.ExpressionData
Gets an Array of GeneDescriptors.
getGeneDescriptorsVector() - Method in class cytoscape.data.ExpressionData
Gets a Vector Gene Descriptors.
getGeneNames() - Method in class cytoscape.data.ExpressionData
Gets a List of All Gene Names.
getGeneNamesVector() - Method in class cytoscape.data.ExpressionData
Gets a List of All Gene Names.
getGenericURL() - Method in class cytoscape.data.ontology.DBReference
DOCUMENT ME!
getGinyArrow() - Method in enum cytoscape.visual.ArrowShape
Returns arrow type in GINY.
getGinyConstant() - Method in enum giny.view.Justification
 
getGinyConstant() - Method in enum giny.view.Position
 
getGinyName() - Method in enum cytoscape.visual.ArrowShape
Returns name of arrow shape.
getGinyShape() - Method in enum cytoscape.visual.NodeShape
Get GINY shape as integer.
getGlobalAppearanceCalculator() - Method in class cytoscape.visual.VisualStyle
Get the GlobalAppearanceCalculator for this visual style.
getGlobalAppearanceNames() - Static method in class cytoscape.visual.GlobalAppearanceCalculator
Get name of global appearances.
getGlobalPercent(int, int, int) - Method in class cytoscape.util.PercentUtil
Calculates Global Percent Based on Current Step, Current Value, and MaxValue.
getGOTerm(String) - Method in class cytoscape.data.ontology.GeneOntology
 
getGraphFiles() - Method in class cytoscape.CyMain
DOCUMENT ME!
getGraphFiles() - Method in interface cytoscape.init.CyInitParams
A list of Strings that describe graph file locations.
getGraphics() - Method in class cytoscape.render.export.ImageImposter
Returns a copy of the Graphics object that was passed into the constructor.
getGraphicsProps() - Method in class cytoscape.visual.customgraphic.impl.vector.GradientLayerCustomGraphics
 
getGraphicsProps() - Method in interface cytoscape.visual.customgraphic.impl.vector.VectorCustomGraphics
 
getGraphLOD() - Method in class ding.view.DGraphView
DOCUMENT ME!
getGraphPerspective() - Method in class cytoscape.CyNode
DOCUMENT ME!
getGraphPerspective() - Method in interface cytoscape.groups.CyGroup
Get the graph (network) that represents this network
getGraphPerspective() - Method in class cytoscape.groups.CyGroupImpl
Return a CyNetwork that represents the internal components of this group
getGraphPerspective() - Method in class ding.view.DGraphView
Returns the graph model that this view was created for.
getGraphPerspective() - Method in interface giny.model.Node
Deprecated. Don't use this method because the behavior of the returned GraphPerspective with respect to changing meta-children of this Node is ill-defined; use RootGraph.getNodeMetaChildIndicesArray(int) and RootGraph.getEdgeMetaChildIndicesArray(int) instead.
getGraphPerspective() - Method in interface giny.view.GraphView
 
getGraphPerspectiveIndex() - Method in class ding.view.DNodeView
DOCUMENT ME!
getGraphPerspectiveIndex() - Method in interface giny.view.EdgeView
 
getGraphPerspectiveIndex() - Method in interface giny.view.NodeView
 
getGraphView() - Method in class ding.view.DNodeView
DOCUMENT ME!
getGraphView() - Method in interface giny.view.EdgeView
 
getGraphView() - Method in interface giny.view.NodeView
 
getGraphViewController() - Method in class cytoscape.view.CytoscapeDesktop
TO keep things clearer there is one GraphView Controller per CytoscapeDesktop
getGraphViewHandler(GraphView) - Method in class cytoscape.view.GraphViewController
Gets the cytoscape.view.GraphViewHandler for the given giny.view.GraphView
getGraphViewHandlersMap() - Method in class cytoscape.view.GraphViewController
Gets a Map with giny.view.GraphView objects as keys, and cytoscape.view.GraphViewHandler objects as values, two or more different keys can share the same value.
getGraphViews() - Method in class cytoscape.view.GraphViewController
Gets an array of giny.view.GraphView objects that this GraphViewController will keep synchronized with their corresponding giny.model.GraphPerspective objects available through their getGraphPerspective() method
getGreekThreshold() - Method in class ding.view.DNodeView
DOCUMENT ME!
getGreekThreshold() - Method in interface giny.view.Label
Returns the current greek threshold.
getGroup(CyNode) - Static method in class cytoscape.groups.CyGroupManager
getGroup is a static method that returns a CyGroup structure when given a CyNode that is a member of a group.
getGroupList() - Static method in class cytoscape.groups.CyGroupManager
Return the list of all groups
getGroupList(CyNetwork) - Static method in class cytoscape.groups.CyGroupManager
Return the list of all groups for this network
getGroupList(CyGroupViewer) - Static method in class cytoscape.groups.CyGroupManager
Return the list of all groups managed by a particular viewer
getGroupName() - Method in interface cytoscape.groups.CyGroup
Return the name of this group
getGroupName() - Method in class cytoscape.groups.CyGroupImpl
Return the name of this group
getGroupNode() - Method in interface cytoscape.groups.CyGroup
Get the CyNode that represents this group
getGroupNode() - Method in class cytoscape.groups.CyGroupImpl
Get the CyNode that represents this group
getGroups() - Method in class cytoscape.CyNode
Return the list of groups this node is a member of
getGroupViewer(String) - Static method in class cytoscape.groups.CyGroupManager
Return the viewer object for a named viewer
getGroupViewers() - Static method in class cytoscape.groups.CyGroupManager
Return a list of all registered viewers
getGUI() - Method in interface cytoscape.data.webservice.ui.WebServiceClientGUI
Returns GUI for this client.
getGUI() - Method in class cytoscape.data.webservice.WebServiceClientImplWithGUI
DOCUMENT ME!
getHandles() - Method in interface giny.view.Bend
Returns a (new) List of clones of the Point2Ds that locate the handles.
getHeader() - Method in class cytoscape.data.ontology.readers.OBOFlatFileReader
DOCUMENT ME!
getHeader() - Method in interface cytoscape.data.ontology.readers.OntologyReader
DOCUMENT ME!
getHeader(File) - Method in class cytoscape.util.CyFileFilter
Gets header of specified file.
getHeader(URL) - Method in class cytoscape.util.CyFileFilter
 
getHeader(String, VisualPropertyType) - Static method in class cytoscape.visual.mappings.LegendTable
DOCUMENT ME!
getHeight() - Method in class cytoscape.generated.DesktopSize
Gets the value of the height property.
getHeight() - Method in class cytoscape.generated.NetworkFrame
Gets the value of the height property.
getHeight(ImageObserver) - Method in class cytoscape.render.export.ImageImposter
Simply returns the height that was passed into the constructor.
getHeight() - Method in interface cytoscape.visual.customgraphic.CyCustomGraphics
Returns height of current object.
getHeight() - Method in class cytoscape.visual.customgraphic.impl.AbstractDCustomGraphics
 
getHeight() - Method in class ding.view.DNodeView
DOCUMENT ME!
getHeight() - Method in interface giny.view.NodeView
TODO: Reconcile with Border Methods
getHelpActionListener() - Static method in class cytoscape.view.CyHelpBroker
Provides access to an ActionListener that pops up a help dialog.
getHelpBroker() - Static method in class cytoscape.view.CyHelpBroker
Returns the HelpBroker.
getHelpMenu() - Method in class cytoscape.view.CyMenus
Returns the help menu.
getHelpSet() - Static method in class cytoscape.view.CyHelpBroker
Returns the HelpSet.
getHiddenEdgeIndices() - Method in class giny.model.GraphPerspectiveChangeEvent
The integer values in the returned array are RootGraph indices.
getHiddenEdgeIndices() - Method in class giny.view.GraphViewChangeEvent
 
getHiddenEdges() - Method in class cytoscape.generated.Network
Gets the value of the hiddenEdges property.
getHiddenEdges() - Method in class giny.model.GraphPerspectiveChangeEvent
Deprecated. Use getHiddenEdgeIndices() instead; the edges returned by this method may have undefined state.
getHiddenEdges() - Method in class giny.view.GraphViewChangeEvent
 
getHiddenNodeIndices() - Method in class giny.model.GraphPerspectiveChangeEvent
The integer values in the returned array are RootGraph indices.
getHiddenNodeIndices() - Method in class giny.view.GraphViewChangeEvent
 
getHiddenNodes() - Method in class cytoscape.generated.Network
Gets the value of the hiddenNodes property.
getHiddenNodes() - Method in class giny.model.GraphPerspectiveChangeEvent
Deprecated. Use getHiddenNodeIndices() instead; the nodes returned by this method may have undefined state.
getHiddenNodes() - Method in class giny.view.GraphViewChangeEvent
 
getHiddenObject() - Method in class cytoscape.visual.ui.VizMapperProperty
DOCUMENT ME!
getHref() - Method in class cytoscape.bookmarks.DataSource
Gets the value of the href property.
getHref() - Method in class cytoscape.generated.Ontology
Gets the value of the href property.
getIcon(WebServiceClientGUI.IconSize) - Method in interface cytoscape.data.webservice.ui.WebServiceClientGUI
Returns icon for the GUI.
getIcon(WebServiceClientGUI.IconSize) - Method in class cytoscape.data.webservice.WebServiceClientImplWithGUI
DOCUMENT ME!
getIcon(Object) - Method in class cytoscape.visual.properties.AbstractVisualProperty
 
getIcon(Object) - Method in class cytoscape.visual.properties.EdgeColorProp
DOCUMENT ME!
getIcon(Object) - Method in class cytoscape.visual.properties.EdgeFontFaceProp
DOCUMENT ME!
getIcon(Object) - Method in class cytoscape.visual.properties.EdgeFontSizeProp
DOCUMENT ME!
getIcon(Object) - Method in class cytoscape.visual.properties.EdgeLabelColorProp
DOCUMENT ME!
getIcon(Object) - Method in class cytoscape.visual.properties.EdgeLabelOpacityProp
DOCUMENT ME!
getIcon(Object) - Method in class cytoscape.visual.properties.EdgeLabelPositionProp
 
getIcon(Object) - Method in class cytoscape.visual.properties.EdgeLabelProp
DOCUMENT ME!
getIcon(Object) - Method in class cytoscape.visual.properties.EdgeLabelWidthProp
DOCUMENT ME!
getIcon(Object) - Method in class cytoscape.visual.properties.EdgeLineStyleProp
DOCUMENT ME!
getIcon(Object) - Method in class cytoscape.visual.properties.EdgeLineWidthProp
DOCUMENT ME!
getIcon(Object) - Method in class cytoscape.visual.properties.EdgeOpacityProp
DOCUMENT ME!
getIcon(Object) - Method in class cytoscape.visual.properties.EdgeSourceArrowColorProp
DOCUMENT ME!
getIcon(Object) - Method in class cytoscape.visual.properties.EdgeSourceArrowOpacityProp
DOCUMENT ME!
getIcon(Object) - Method in class cytoscape.visual.properties.EdgeSourceArrowShapeProp
DOCUMENT ME!
getIcon(Object) - Method in class cytoscape.visual.properties.EdgeTargetArrowColorProp
DOCUMENT ME!
getIcon(Object) - Method in class cytoscape.visual.properties.EdgeTargetArrowOpacityProp
DOCUMENT ME!
getIcon(Object) - Method in class cytoscape.visual.properties.EdgeTargetArrowShapeProp
DOCUMENT ME!
getIcon(Object) - Method in class cytoscape.visual.properties.EdgeToolTipProp
 
getIcon(Object) - Method in class cytoscape.visual.properties.NodeBorderColorProp
DOCUMENT ME!
getIcon(Object) - Method in class cytoscape.visual.properties.NodeBorderOpacityProp
DOCUMENT ME!
getIcon(Object) - Method in class cytoscape.visual.properties.NodeCustomGraphicsPositionProp
DOCUMENT ME!
getIcon(Object) - Method in class cytoscape.visual.properties.NodeCustomGraphicsProp
 
getIcon(Object) - Method in class cytoscape.visual.properties.NodeFillColorProp
DOCUMENT ME!
getIcon(Object) - Method in class cytoscape.visual.properties.NodeFontFaceProp
DOCUMENT ME!
getIcon(Object) - Method in class cytoscape.visual.properties.NodeFontSizeProp
DOCUMENT ME!
getIcon(Object) - Method in class cytoscape.visual.properties.NodeHeightProp
DOCUMENT ME!
getIcon(Object) - Method in class cytoscape.visual.properties.NodeLabelColorProp
DOCUMENT ME!
getIcon(Object) - Method in class cytoscape.visual.properties.NodeLabelOpacityProp
DOCUMENT ME!
getIcon(Object) - Method in class cytoscape.visual.properties.NodeLabelPositionProp
DOCUMENT ME!
getIcon(Object) - Method in class cytoscape.visual.properties.NodeLabelProp
DOCUMENT ME!
getIcon(Object) - Method in class cytoscape.visual.properties.NodeLabelWidthProp
DOCUMENT ME!
getIcon(Object) - Method in class cytoscape.visual.properties.NodeLineStyleProp
DOCUMENT ME!
getIcon(Object) - Method in class cytoscape.visual.properties.NodeLineWidthProp
DOCUMENT ME!
getIcon(Object) - Method in class cytoscape.visual.properties.NodeOpacityProp
DOCUMENT ME!
getIcon(Object) - Method in class cytoscape.visual.properties.NodeShapeProp
DOCUMENT ME!
getIcon(Object) - Method in class cytoscape.visual.properties.NodeShowNestedNetworkProp
DOCUMENT ME!
getIcon(Object) - Method in class cytoscape.visual.properties.NodeSizeProp
DOCUMENT ME!
getIcon(Object) - Method in class cytoscape.visual.properties.NodeToolTipProp
DOCUMENT ME!
getIcon(Object) - Method in class cytoscape.visual.properties.NodeWidthProp
DOCUMENT ME!
getIcon(int, int, VisualPropertyType) - Static method in class cytoscape.visual.ui.editors.continuous.C2CMappingEditor
DOCUMENT ME!
getIcon(int, int, VisualPropertyType) - Static method in class cytoscape.visual.ui.editors.continuous.C2DMappingEditor
DOCUMENT ME!
getIcon(int, int, VisualPropertyType) - Static method in class cytoscape.visual.ui.editors.continuous.ContinuousMappingEditorPanel
Dynamically generate small icons from continuous mappers.
getIcon(int, int, VisualPropertyType) - Static method in class cytoscape.visual.ui.editors.continuous.GradientEditorPanel
DOCUMENT ME!
getIcon(Object) - Method in interface cytoscape.visual.VisualProperty
 
getIconHeight() - Method in class cytoscape.visual.ui.editors.discrete.CyColorCellRenderer.PaintIcon
 
getIconHeight() - Method in class cytoscape.visual.ui.icon.NodeIcon
 
getIconHeight() - Method in class cytoscape.visual.ui.icon.VisualPropertyIcon
Get height of icon.
getIconName() - Method in class cytoscape.dialogs.IconPopupButton
DOCUMENT ME!
getIconObject() - Method in class cytoscape.dialogs.IconPopupButton
DOCUMENT ME!
getIconSet() - Static method in enum cytoscape.visual.ArrowShape
DOCUMENT ME!
getIconSet() - Static method in enum cytoscape.visual.LineStyle
Returns a map of Icons that can be used for user interfaces.
getIconSet() - Static method in enum cytoscape.visual.NodeShape
DOCUMENT ME!
getIconSet() - Method in class cytoscape.visual.properties.AbstractVisualProperty
DOCUMENT ME!
getIconSet() - Method in class cytoscape.visual.properties.EdgeLineStyleProp
DOCUMENT ME!
getIconSet() - Method in class cytoscape.visual.properties.EdgeSourceArrowShapeProp
DOCUMENT ME!
getIconSet() - Method in class cytoscape.visual.properties.EdgeTargetArrowShapeProp
DOCUMENT ME!
getIconSet() - Method in class cytoscape.visual.properties.NodeCustomGraphicsProp
 
getIconSet() - Method in class cytoscape.visual.properties.NodeLineStyleProp
DOCUMENT ME!
getIconSet() - Method in class cytoscape.visual.properties.NodeShapeProp
DOCUMENT ME!
getIconSet() - Method in interface cytoscape.visual.VisualProperty
DOCUMENT ME!
getIconWidth() - Method in class cytoscape.visual.ui.editors.discrete.CyColorCellRenderer.PaintIcon
 
getIconWidth() - Method in class cytoscape.visual.ui.icon.NodeIcon
 
getIconWidth() - Method in class cytoscape.visual.ui.icon.VisualPropertyIcon
Get width of icon.
getId() - Method in class cytoscape.data.annotation.OntologyTerm
Deprecated. DOCUMENT ME!
getId() - Method in class cytoscape.generated.Child
Gets the value of the id property.
getId() - Method in class cytoscape.generated.Cysession
Gets the value of the id property.
getId() - Method in class cytoscape.generated.Cytopanel
Gets the value of the id property.
getId() - Method in class cytoscape.generated.Edge
Gets the value of the id property.
getId() - Method in class cytoscape.generated.Network
Gets the value of the id property.
getId() - Method in class cytoscape.generated.Node
Gets the value of the id property.
getId() - Method in class cytoscape.generated.Panel
Gets the value of the id property.
getId() - Method in class cytoscape.generated.Parent
Gets the value of the id property.
getId() - Method in class cytoscape.generated.Plugin
Gets the value of the id property.
getID() - Method in class cytoscape.plugin.DownloadableInfo
 
getId() - Method in class org.apache.commons.cli.avalon.CLOption
Deprecated. use getDescriptor().getId() instead
getId() - Method in class org.apache.commons.cli.avalon.CLOptionDescriptor
Retrieve the id for option.
getId() - Method in class org.apache.commons.cli.Option
Returns the id of this Option.
getIdent() - Method in class org.cytoscape.equations.Tokeniser
 
getIdentifier() - Method in class cytoscape.CyEdge
DOCUMENT ME!
getIdentifier() - Method in interface cytoscape.CyNetwork
Can't Change
getIdentifier() - Method in class cytoscape.CyNode
DOCUMENT ME!
getIdentifier() - Method in class cytoscape.giny.FingCyNetwork
DOCUMENT ME!
getIdentifier() - Method in class cytoscape.util.CytoscapeMenuBar
implements CommunityMember
getIdentifier() - Method in interface cytoscape.visual.customgraphic.CyCustomGraphics
Immutable session-unique identifier of image generated in constructor.
getIdentifier() - Method in class cytoscape.visual.customgraphic.impl.AbstractDCustomGraphics
 
getIdentifier() - Method in class ding.view.DGraphView
DOCUMENT ME!
getIdentifier() - Method in interface giny.model.GraphObject
 
getIdentifier() - Method in interface giny.view.GraphView
 
getIDGenerator() - Static method in class cytoscape.visual.customgraphic.IDGenerator
 
getIDListFromAttributeValue(CyAttributesUtils.AttributeType, String, Object) - Static method in class cytoscape.data.CyAttributesUtils
Get list of IDs associated with a specific attribute value.
getIdSet(String) - Method in class cytoscape.data.synonyms.Aliases
Return set of all names for the key (including key itself.)
getIDSet() - Method in class cytoscape.visual.customgraphic.CustomGraphicsManager
 
getImage() - Method in class ding.view.DingCanvas
Returns the image maintained by the canvas.
getImportHandler() - Static method in class cytoscape.Cytoscape
DOCUMENT ME!
getIncompatble() - Method in class org.apache.commons.cli.avalon.CLOptionDescriptor
Deprecated. Use the correctly spelled CLOptionDescriptor.getIncompatible() instead.
getIncompatible() - Method in class org.apache.commons.cli.avalon.CLOptionDescriptor
Get the array of incompatible option ids.
getInDegree(Node) - Method in interface giny.model.GraphPerspective
Return the number of Edges e in this GraphPerspective such that e.getTarget().equals( node ).
getInDegree(int) - Method in interface giny.model.GraphPerspective
Return the number of Edges e in this GraphPerspective such that e.getTarget().equals( node ).
getInDegree(Node, boolean) - Method in interface giny.model.GraphPerspective
Return the number of Edges e in this GraphPerspective such that e.getSource().equals( node ).
getInDegree(int, boolean) - Method in interface giny.model.GraphPerspective
Return the number of Edges e in this GraphPerspective such that e.getSource().equals( node ).
getInDegree(Node) - Method in interface giny.model.RootGraph
Return the number of Edges e such that e.getTarget().equals( node ).
getInDegree(int) - Method in interface giny.model.RootGraph
Return the number of Edges e such that e.getTarget().equals( node ).
getInDegree(Node, boolean) - Method in interface giny.model.RootGraph
Return the number of Edges e such that e.getSource().equals( node ).
getInDegree(int, boolean) - Method in interface giny.model.RootGraph
Return the number of Edges e such that e.getSource().equals( node ).
getIndex(Node) - Method in interface giny.model.GraphPerspective
Return the index of the given Node in the underlying RootGraph.
getIndex(Edge) - Method in interface giny.model.GraphPerspective
Return the index of the given Edge in the underlying RootGraph.
getIndex(Node) - Method in interface giny.model.RootGraph
Return the index of the given Node.
getIndex(Edge) - Method in interface giny.model.RootGraph
Return the index of the given Edge.
getIndexOfChild(Object, Object) - Method in class cytoscape.dialogs.plugins.ManagerModel
Gets the index of the given child node from the given parent node.
getIndexOfChild(TreeNode) - Method in class cytoscape.dialogs.plugins.TreeNode
Gets the index of child from this node's child list.
getIndexOfChild(Object, Object) - Method in class cytoscape.util.swing.AbstractTreeTableModel
DOCUMENT ME!
getInfoObj() - Method in interface cytoscape.plugin.Installable
 
getInfoObj() - Method in class cytoscape.plugin.InstallablePlugin
 
getInfoObj() - Method in class cytoscape.plugin.InstallableTheme
 
getInfoObject(Class) - Static method in class cytoscape.plugin.ManagerUtil
Takes a Class object for a CytoscapePlugin and returns the DownloadableInfo object associated
getInitialAttributeList() - Method in class cytoscape.layout.AbstractLayout
This returns the list of "attributes" that are provided by an algorithm for internal purposes.
getInitialAttributeList() - Method in interface cytoscape.layout.CyLayoutAlgorithm
This returns a (possibly empty) List of Strings that is used for the attribute list in the menu for attribute-based layouts.
getInitialAttributeList() - Method in class cytoscape.layout.LayoutAdapter
This returns a (possibly empty) List of Strings that is used for the attribute list in the menu for attribute-based layouts.
getInnerEdges() - Method in interface cytoscape.groups.CyGroup
Get all of the edges completely contained within this group
getInnerEdges() - Method in class cytoscape.groups.CyGroupImpl
Get all of the edges completely contained within this group
getInputStream(String) - Static method in class cytoscape.util.FileUtil
DOCUMENT ME!
getInputStream(String, TaskMonitor) - Static method in class cytoscape.util.FileUtil
DOCUMENT ME!
getInputStream(URL) - Static method in class cytoscape.util.URLUtil
Gets the an input stream given a URL.
getInputString(String) - Static method in class cytoscape.util.FileUtil
 
getInputString(InputStream) - Static method in class cytoscape.util.FileUtil
 
getInstallable() - Method in class cytoscape.plugin.DownloadableInfo
 
getInstallable() - Method in class cytoscape.plugin.PluginInfo
 
getInstallable() - Method in class cytoscape.plugin.ThemeInfo
 
getInstallLocation() - Method in class cytoscape.plugin.PluginInfo
 
getInstallLocation() - Method in class cytoscape.plugin.ThemeInfo
 
getInstance(String) - Method in interface cytoscape.visual.customgraphic.CyCustomGraphicsParser
 
getInstance(String) - Method in class cytoscape.visual.customgraphic.DefaultCyCustomGraphicsParser
 
getInstance(String) - Method in class cytoscape.visual.customgraphic.URLImageCustomGraphicsParser
Generate Custom Graphics object from a string.
getInstitution() - Method in class cytoscape.plugin.PluginInfo.AuthorInfo
 
getInt() - Method in class cytoscape.dialogs.IntegerEntryField
DOCUMENT ME!
getInt(String) - Method in class cytoscape.dialogs.JointIntegerEntry
DOCUMENT ME!
getInt(String, int) - Method in class cytoscape.ding.CyGraphLOD
Deprecated. Use PropUtil.getInt(..) instead. Leaving Feb 2011.
getInt() - Method in class cytoscape.util.MutableInt
DOCUMENT ME!
getInt(Properties, String, int) - Static method in class cytoscape.util.PropUtil
Will return an integer for the specified property key only if the value exists and is properly formatted as an integer.
getIntAtIndex(int) - Method in class cytoscape.util.intr.IntArray
Returns the value at specified index.
getIntConstant() - Method in class org.cytoscape.equations.Tokeniser
 
getInteger() - Method in class cytoscape.dialogs.IntegerEntryField
DOCUMENT ME!
getInteger(String) - Method in class cytoscape.dialogs.JointIntegerEntry
DOCUMENT ME!
getIntegerAttribute(String, String) - Method in interface cytoscape.data.CyAttributes
Gets an Integer value at the specified id/attributeName.
getIntegerAttribute(String, String) - Method in class cytoscape.data.CyAttributesImpl
DOCUMENT ME!
getIntegerValue() - Method in class cytoscape.dialogs.NewSlider
DOCUMENT ME!
getInteraction() - Method in class cytoscape.generated.Edge
Gets the value of the interaction property.
getInteractionString(CyNetwork) - Static method in class cytoscape.data.writers.InteractionWriter
Returns a SIF formatted string of the specified network.
getInteractionString(CyNetwork, TaskMonitor) - Static method in class cytoscape.data.writers.InteractionWriter
Returns a SIF formatted string of the specified network.
getInteractionType(CyNetwork, Edge) - Static method in class cytoscape.data.Semantics
Returns the interaction type of the given edge.
getInteractionTypes(CyNetwork) - Static method in class cytoscape.data.Semantics
Returns an array containing all of the unique interaction types present in the network.
getInternalFrame(CyNetworkView) - Method in class cytoscape.view.NetworkViewManager
Given a CyNetworkView, returns the internal frame.
getInternalFrameComponent(CyNetworkView) - Method in class cytoscape.view.NetworkViewManager
Given a CyNetworkView, returns the InternalFrameComponent that wraps it.
getInterpolator() - Method in class cytoscape.visual.mappings.continuous.ContinuousMappingReader
Gets Interpolator Object.
getInterpolator() - Method in class cytoscape.visual.mappings.ContinuousMapping
Gets the Mapping Interpolator.
getIOException() - Method in class cytoscape.plugin.PluginInquireAction
 
getItemCount() - Method in class cytoscape.layout.ui.LayoutMenu
DOCUMENT ME!
getJDOMException() - Method in class cytoscape.plugin.PluginInquireAction
 
getJustify() - Method in class cytoscape.visual.LabelPosition
Deprecated. DOCUMENT ME!
getJustify() - Method in class ding.view.DNodeView
Deprecated. 
getJustify() - Method in class ding.view.ObjectPositionImpl
 
getJustify() - Method in interface giny.view.Label
Deprecated. 
getJustify() - Method in interface giny.view.ObjectPosition
DOCUMENT ME!
getJustifyNames() - Static method in class cytoscape.visual.LabelPosition
Deprecated. DOCUMENT ME!
getKey(String) - Method in class cytoscape.data.synonyms.Aliases
Returns true if the object with the alias wxists in the memory (rootGraph).
getKeyAttributeName() - Method in class cytoscape.dialogs.ImportAttributeMatrixDialog
DOCUMENT ME!
getKeyCode() - Method in class cytoscape.util.CytoscapeAction
DOCUMENT ME!
getKeyCyAttrName() - Method in class cytoscape.data.webservice.AttributeImportQuery
 
getKeyModifiers() - Method in class cytoscape.util.CytoscapeAction
DOCUMENT ME!
getKeyNameInWebService() - Method in class cytoscape.data.webservice.AttributeImportQuery
 
getKeySet(String, CyAttributes, ObjectMapping, boolean) - Static method in class cytoscape.visual.ui.MappingKeyFactory
 
getLabel() - Method in class cytoscape.dialogs.IconPopupButton
DOCUMENT ME!
getLabel() - Method in class cytoscape.dialogs.IntegerEntryField
DOCUMENT ME!
getLabel(String) - Method in class cytoscape.dialogs.JointIntegerEntry
DOCUMENT ME!
getLabel(Object) - Method in class cytoscape.util.swing.WidestStringComboBoxModel
Returns the String corresponding to the parameter object for use in calculating the width of popup required.
getLabel() - Method in class ding.view.DNodeView
DOCUMENT ME!
getLabel() - Method in interface giny.view.EdgeView
 
getLabel() - Method in interface giny.view.NodeView
 
getLabelAnchor() - Method in class cytoscape.visual.LabelPosition
Deprecated. DOCUMENT ME!
getLabelOffsetX() - Method in class ding.view.DNodeView
Deprecated. 
getLabelOffsetX() - Method in interface giny.view.EdgeView
 
getLabelOffsetX() - Method in interface giny.view.NodeView
Deprecated. 
getLabelOffsetY() - Method in class ding.view.DNodeView
Deprecated. 
getLabelOffsetY() - Method in interface giny.view.EdgeView
 
getLabelOffsetY() - Method in interface giny.view.NodeView
Deprecated. 
getLabelPosition() - Method in class ding.view.DNodeView
 
getLabelPosition() - Method in interface giny.view.NodeView
Returns current label position as ObjkectPosition object.
getLabelWidth() - Method in class ding.view.DNodeView
 
getLabelWidth() - Method in interface giny.view.EdgeView
 
getLabelWidth() - Method in interface giny.view.NodeView
 
getLastEquationError() - Method in interface cytoscape.data.CyAttributes
Returns any attribute-equation related error message after a call to getAttribute() or getXXXAttribute().
getLastEquationError() - Method in class cytoscape.data.CyAttributesImpl
Returns any attribute-equation related error message after a call to getAttribute() or getXXXAttribute().
getLastErrorMsg() - Method in class org.cytoscape.equations.EqnCompiler
 
getLastKeyModified() - Method in class cytoscape.visual.mappings.DiscreteMapping
Gets the Last Modified Key.
getLastRenderDetail() - Method in class ding.view.InnerCanvas
DOCUMENT ME!
getLayerObject() - Method in class cytoscape.visual.customgraphic.impl.DLayer
 
getLayerObject() - Method in interface cytoscape.visual.customgraphic.Layer
 
getLayers() - Method in interface cytoscape.visual.customgraphic.CyCustomGraphics
Get layers belongs to this object.
getLayers() - Method in class cytoscape.visual.customgraphic.impl.AbstractDCustomGraphics
 
getLayout(String) - Static method in class cytoscape.layout.CyLayouts
Get the layout named "name".
getLayoutAlgorithm() - Method in class cytoscape.data.readers.AbstractGraphReader
Return the CyLayoutAlgorithm used to layout the graph
getLayoutAlgorithm() - Method in class cytoscape.data.readers.GMLReader
getLayoutAlgorithm is called to get the Layout Algorithm that will be used to layout the resulting graph.
getLayoutAlgorithm() - Method in interface cytoscape.data.readers.GraphReader
Returns the CyLayoutAlgorithm used to layout the graph
getLayoutAlgorithm() - Method in class cytoscape.data.readers.XGMMLReader
getLayoutAlgorithm is called to get the Layout Algorithm that will be used to layout the resulting graph.
getLayoutMenu() - Method in class cytoscape.view.CyMenus
Returns the menu with items realted to layout actions.
getLeafCount() - Method in class cytoscape.dialogs.plugins.TreeNode
Gets the total (recursively) of all leaves under this node.
getLeftChild() - Method in class org.cytoscape.equations.parse_tree.BinOpNode
 
getLeftChild() - Method in class org.cytoscape.equations.parse_tree.BooleanConstantNode
 
getLeftChild() - Method in class org.cytoscape.equations.parse_tree.FConvNode
 
getLeftChild() - Method in class org.cytoscape.equations.parse_tree.FloatConstantNode
 
getLeftChild() - Method in class org.cytoscape.equations.parse_tree.FuncCallNode
 
getLeftChild() - Method in class org.cytoscape.equations.parse_tree.IdentNode
 
getLeftChild() - Method in class org.cytoscape.equations.parse_tree.Node
 
getLeftChild() - Method in class org.cytoscape.equations.parse_tree.SConvNode
 
getLeftChild() - Method in class org.cytoscape.equations.parse_tree.StringConstantNode
 
getLeftChild() - Method in class org.cytoscape.equations.parse_tree.UnaryOpNode
 
getLeftPadding() - Method in class org.apache.commons.cli.HelpFormatter
Returns the 'leftPadding'.
getLegend(VisualPropertyType) - Method in class cytoscape.visual.mappings.AbstractMapping
 
getLegend(VisualPropertyType) - Method in class cytoscape.visual.mappings.ContinuousMapping
 
getLegend(VisualPropertyType) - Method in class cytoscape.visual.mappings.DiscreteMapping
DOCUMENT ME!
getLegend(VisualPropertyType) - Method in interface cytoscape.visual.mappings.ObjectMapping
 
getLegend(VisualPropertyType) - Method in class cytoscape.visual.mappings.PassThroughMapping
DOCUMENT ME!
getLegend(int, int, VisualPropertyType) - Static method in class cytoscape.visual.ui.editors.continuous.C2CMappingEditor
DOCUMENT ME!
getLegend(int, int, VisualPropertyType) - Static method in class cytoscape.visual.ui.editors.continuous.C2DMappingEditor
DOCUMENT ME!
getLegend(int, int) - Method in class cytoscape.visual.ui.editors.continuous.ContinuousTrackRenderer
DOCUMENT ME!
getLegend(int, int) - Method in class cytoscape.visual.ui.editors.continuous.CyGradientTrackRenderer
DOCUMENT ME!
getLegend(int, int) - Method in class cytoscape.visual.ui.editors.continuous.DiscreteTrackRenderer
 
getLegend(int, int, VisualPropertyType) - Static method in class cytoscape.visual.ui.editors.continuous.GradientEditorPanel
DOCUMENT ME!
getLengthOfTask() - Method in interface cytoscape.util.MonitoredTask
Returns the lenghtOfTask parameter.
getLevel() - Method in enum cytoscape.logger.LogLevel
 
getLibJars() - Method in class cytoscape.util.JnlpWriterUtil
DOCUMENT ME!
getLicense() - Method in class cytoscape.plugin.DownloadableInfo.License
Get the license text as a string.
getLicenseText() - Method in class cytoscape.plugin.DownloadableInfo
 
getLineStyle() - Method in class cytoscape.visual.strokes.DashDotStroke
 
getLineStyle() - Method in class cytoscape.visual.strokes.EqualDashStroke
 
getLineStyle() - Method in class cytoscape.visual.strokes.LongDashStroke
 
getLineStyle() - Method in class cytoscape.visual.strokes.ShapeStroke
 
getLineStyle() - Method in class cytoscape.visual.strokes.SolidStroke
 
getLineStyle() - Method in interface cytoscape.visual.strokes.WidthStroke
 
getLineStyle() - Method in class cytoscape.visual.strokes.ZeroStroke
 
getLineStyle() - Method in class cytoscape.visual.strokes.ZigzagStroke
 
getLineType() - Method in interface giny.view.EdgeView
 
getList() - Method in class cytoscape.data.readers.GMLReader
Returns a list containing the gml object tree
getListAttribute(String, String) - Method in interface cytoscape.data.CyAttributes
Gets a 'simple' list of attributes for the id/attributeName pair.
getListAttribute(String, String) - Method in class cytoscape.data.CyAttributesImpl
 
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class cytoscape.visual.customgraphic.ui.CustomGraphicsCellRenderer
 
getListCellRendererComponent(JList, Object, int, boolean, boolean) - Method in class cytoscape.visual.ui.FontRenderer
DOCUMENT ME!
getListElementType(String) - Method in interface cytoscape.data.CyAttributes
Gets the member data type of the specified simple list attribute.
getListElementType(String) - Method in class cytoscape.data.CyAttributesImpl
Gets the member data type of the specified simple list attribute.
getListenerList(VisualPropertyType) - Method in class cytoscape.visual.CalculatorCatalog
 
getLoadingErrors() - Method in class cytoscape.plugin.PluginManager
/** Returns list of loading exceptions.
getLoadSubMenu() - Method in class cytoscape.view.CyMenus
Returns the submenu with items related to loading objects.
getLocation() - Method in class phoebe.PhoebeCanvasDropEvent
 
getLocationOfExternalFrame(Dimension, Rectangle, Dimension, int, boolean) - Static method in class cytoscape.view.cytopanels.CytoPanelUtil
Gets Location of External Frame, based on current UI Dimensions.
getLocationOnScreen() - Method in class cytoscape.view.cytopanels.BiModalJSplitPane
Gets the location of the applications mainframe.
getLocationOnScreen() - Method in interface cytoscape.view.cytopanels.CytoPanelContainer
Gets Location of Container, in screen coordinates.
getLock() - Method in class ding.view.DGraphView
 
getLogger() - Static method in class cytoscape.logger.ConsoleLogger
 
getLogger(String) - Static method in class cytoscape.logger.CyLogger
Get a logger with the specified name
getLogger(Class) - Static method in class cytoscape.logger.CyLogger
Get a logger for the specified class
getLogger() - Static method in class cytoscape.logger.CyLogger
Get the default ("cytoscape") logger
getLoggerDialog() - Static method in class cytoscape.dialogs.logger.LoggerDialog