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Views are about to be removed from a CyNetworkView, this event will be fired.Views are about to be removed from a CyNetworkView, this event will be fired.CyAppAdapter reference provided as an
argument to the constructor.
CyEvent that can be used by events.CyPayloadEvent that can be used by events.CySwingAppAdapter reference provided as an
argument to the constructor.
Function implementations.Functions from function argument descriptors.
TunableHandler.TunableHandlers that deal with
Tunables that annotate a field.
TunableHandlers that deal with
Tunables that use getter and setter methods.
CyNetworks.CyNetwork.CyNetwork
CyNetworkViews.Node type.
CyRow.CyTable.CyTable.
AbstractTaskManager object by setting
its TunableInterceptor.
TunableHandlers that deal with
Tunables that annotate a field.
TunableHandlers that deal with
Tunables that use getter and setter methods.
RowsSetListener
for a particular column and VisualProperty.VisualPropertyValue.GUITunableHandler.
GUITunableHandler that listens to THIS tunable handler.
GUITunableHandler.
GUITunableHandler that depends on THIS tunable handler.
AddedEdgesEvents.CySubNetwork.
CyEdge in both this subnetwork
AND in the CyRootNetwork.
AddedNodesEvents.CySubNetwork.
CyNode in both this subnetwork
AND in the CyRootNetwork.
RenderingEngine to this manager.
CySubNetwork.
CySubNetwork which can have a different save policy from that of this root network,
as long as the root network's policy is not SavePolicy.DO_NOT_SAVE.
CySubNetwork containing the specified CyNodes and
CyEdges.
CySubNetwork containing the specified CyNodes and
CyEdges.
VisualProperty to the tree.
VisualStyle to this manager.
CyGroup.ArrowShape values.CyFileFilter that can
either be used directly or extended to provide different acceptance criteria.Boolean values.CyNetworkView from one of the networks just read.
Task.
TaskManager when the user chooses to cancel the
Task.
Task is currently doing in the run() method.
GUITunableHandler that this tunable handler listens to makes
a change.
GUITunableHandler that this tunable handler listens to makes
a change.
GUITunableHandler with the others.
GUITunableHandler with the others.
CyColumn of the CyTable cell
CyColumn that descendants will operate on.
RowsSetListener is provided for.
ColumnNameChangedEvents.Equation class
Tunable annotation.BoundaryRangeValues.VisualPropertys.Tunable allows switching
of mutually exclusive nested children, else false.
Tunable allows switching
of mutually exclusive nested children, else false.
Attribute
Bookmarks
Category
DataSource
JAXBElement<String>}
CyNode.
CyNode.
Icon object for the given VisualProperty value.
CyNetwork object.
CyNetwork object.
CyNetworkView from a CyNetwork object.
CyNetwork object where the associated default tables are private.
CyNetwork object where the associated default tables are private.
CyNetwork that will be passed
into any task created by it.
CyNetworkView
CyRow that will be passed into any task created by it.
CyColumn and a primary key that will be
used to create tasks.
CyColumn that will be used to create tasks.
CyTable that will be used to create tasks.
Tasks.
TunableHandler for a field annotated as a Tunable
if this factory can produce an appropriate handler for this type of field.
TunableHandler for a method annotated as a Tunable
if this factory can produce an appropriate handler for this type of method.
CySession object to the
specified OutputStream.
CyTable object to the
specified OutputStream.
RenderingEngine object to the specified OutputStream.
VisualStyle
objects to the specified OutputStream.
CyNode.CyNetwork to restrict
the edges that match a query.CyGroup objects.CyNetwork objects that are read as part
of the Task.CyNetworkReader
for the input.CyNetworkView objects.CyWriterFactory that allows a
CyNetworkView or CyNetwork to be specified
and written to an OutputStream.CyWriterManager specific to writing
CyNetworkView objects.CyPropertyReader
for the input.CyWriterFactory that allows a property Object to
be specified and written.CyWriterManager specific to writing property objects.org.cytoscape.property.session.Cysession object.CySessionReader
for the input.CyWriterFactory that allows a CySession to
be specified and written.CyWriterManager specific to writing CySession objects.CyShutdownEvent.CyStartEvent.CyNetwork that is contained within a parent
CyNetwork.CyAppAdapter that
serves as a Java-only api providing access to core
Cytoscape functionality.CyTable objects.CyTables.CyTable objects.CyTableReader
for the input.CyWriterFactory that allows a CyTable to
be specified and written.CyWriterManager specific to writing CyTable objects.CytoPanel.CytoPanelComponent has been selected.CytoPanelComponentSelectedEvent.CytoPanels uses compass directions
to describe their location within the application.CytoPanel.CytoPanelStateChangedEvents.CyWriterFactory services for specific DataCategories
and provides a mechanism for choosing the CyWriterFactory given a particular
file type.DataImportFinishedEvent.DataSource.Tunable.
Tunable.
JDialog configuration
object and expects the dialog parent to be a Window.VisualPropertys.Double values.MenuListener that is used to describe
dynamic submenus.Bend values.Equation to another.
Equation.
Tasks in a TaskIterator provided
by a TaskFactory.
Font values.ApplyPreferredLayoutTaskFactory.
ApplyVisualStyleTaskFactory.
CloneNetworkTaskFactory.
CollapseGroupTaskFactory.
ConnectSelectedNodesTaskFactory.
CreateNetworkViewTaskFactory.
DeleteColumnTaskFactory.
DeleteSelectedNodesAndEdgesTaskFactory.
DeleteTableTaskFactory.
DeselectAllEdgesTaskFactory.
DeselectAllNodesTaskFactory.
DeselectAllTaskFactory.
DestroyNetworkTaskFactory.
DestroyNetworkViewTaskFactory.
EditNetworkTitleTaskFactory.
ExpandGroupTaskFactory.
ExportNetworkImageTaskFactory.
ExportNetworkViewTaskFactory.
ExportSelectedTableTaskFactory.
ExportTableTaskFactory.
ExportVizmapTaskFactory.
GroupNodesTaskFactory.
HideSelectedEdgesTaskFactory.
HideSelectedNodesTaskFactory.
HideSelectedTaskFactory.
InvertSelectedEdgesTaskFactory.
InvertSelectedNodesTaskFactory.
LoadNetworkFileTaskFactory.
LoadNetworkURLTaskFactory.
LoadTableFileTaskFactory.
LoadTableURLTaskFactory.
LoadVizmapFileTaskFactory.
MapGlobalToLocalTableTaskFactory.
MapTableToNetworkTablesTaskFactory.
NewEmptyNetworkViewFactory.
NewNetworkSelectedNodesAndEdgesTaskFactory.
NewNetworkSelectedNodesOnlyTaskFactory.
NewSessionTaskFactory.
OpenSessionTaskFactory.
RenameColumnTaskFactory.
SaveSessionAsTaskFactory.
SelectAdjacentEdgesTaskFactory.
SelectAllEdgesTaskFactory.
SelectAllNodesTaskFactory.
SelectAllTaskFactory.
SelectConnectedNodesTaskFactory.
SelectFirstNeighborsNodeViewTaskFactory.
SelectFirstNeighborsTaskFactory.
SelectFirstNeighborsTaskFactory.
SelectFirstNeighborsTaskFactory.
SelectFromFileListTaskFactory.
UnGroupNodesTaskFactory.
UnGroupTaskFactory.
UnHideAllEdgesTaskFactory.
UnHideAllNodesTaskFactory.
UnHideAllTaskFactory.
RenderingEngines registered in this manager.
VisualLexicons.
CyFileFilters known to this CyWriter manager.
CyFileFilters that define the available
output types.
CyNodes and CyEdges.
Rectangle2D
GUITunableHandlers that this tunable handler listens to.
GUITunableHandlers that this tunable handler listens to.
Equation.
column.
column.
RowSetRecords whose specified column value is set.
Tunables
read from the TaskFactory.
CyProperty of type Properties.
CySession object describing the current
state of Cytoscape.
CyApplicationManager.
CyEventHelper.
CyGroupAggregationManager.
CyGroupFactory.
CyGroupManager.
CyLayoutAlgorithmManager.
CyNetworkFactory.
CyNetworkManager.
CyNetworkViewFactory.
CyNetworkViewManager.
CyNetworkReaderManager.
CyNetworkViewWriterManager.
CyPropertyReaderManager.
CyPropertyWriterManager.
CyRootNetworkManager.
CyServiceRegistrar.
CySessionManager.
CySessionReaderManager.
CySessionWriterManager.
CySwingApplication.
CyTableFactory.
CyTableManager.
CyTableReaderManager.
CyTableWriterManager.
CyVersion.
DataCategory of this data.
DataSourceManager.
JComboBox type editor
VisualLexicon from a default engine factory.
VisualStyle.
GUITunableHandler that this tunable handler depends on.
GUITunableHandler that this tunable handler depends on.
Tunable's description.
Tunable's description.
DialogTaskManager.
CyNetwork.DEFAULT_ATTRS namespace specified by columnName and are in
the specified state.
CyNetwork.
CyNode that represents this group
in the network.
Tunable's groups or nesting hierarchy.
Tunable's groups or nesting hierarchy.
CyGroups this node is in.
CyGroups this node is in for
a particular network.
TunableHandler objects that have been found to process
the fields and methods annotated with Tunable.
URL.
GUITunableHandler.
JTextField, JFileChooser, JLabel, JList ...)
CyWriterFactory for the appropriate filter.
CyNetworkTableManager.getTables(org.cytoscape.model.CyNetwork, java.lang.Class).
Task.
CyNetworks this group is in.
CyNetwork.DEFAULT_ATTRS namespace specified by columnName and are in
the specified state.
Paint to be used to
fill the Shape.
TexturePaint to be used as
an image to fill a node
Paint to fill the shape with.
PanelTaskManager.
Tunable.getParams().
Tunable.getParams().
PresentationWriterManager.
CyProperty objects defined for this session.
PropertyEditor object for this data type.
Range of this VisualProperty.
InputStream this method will attempt to find a InputStreamReaderFactory
that can read the stream, will set the InputStream for the factory and
will return the reader.
InputStream this method will attempt to find a InputStreamReaderFactory
that can read the stream, will set the InputStream for the factory and
will return the reader.
InputStream this method will attempt to find a InputStreamReaderFactory
that can read the stream, will set the InputStream for the factory and
will return the reader.
RenderingEngine associated with the deleted presentation.
RenderingEngineManager.
CyRootNetwork that contains this CySubNetwork.
CyRow of the data that was set.
JTree.
CyProperty.SavePolicy of the CyProperty.
CyProperty.SavePolicy of the CyProperty.
CyProperty.SavePolicy of the CyProperty.
CySession object
Shape
Tunable associated with
this GUITunableHandler.
Handler
(or path for a FileHandler, or selected item(s)
for ListMultipleSelection ListSingleSelection, ...)
StreamUtil.
Stroke to use to outline the
Shape provided by the PaintedShape.getShape() method above.
Paint to use to color the
Stroke returned by PaintedShape.getStroke().
CySubNetworks contained in this root network.
CyTable that this row belongs to.
CyTable objects.
TaskManager.
Tunable.
Tunable.
UndoableEditSupport associated with this UndoSupport instance.
UndoManager associated with this UndoSupport instance.
UndoSupport.
URLConnection for a given URL.
Tunables.
Tunable or null if no field / get method has been associated with this handler.
Tunable or null if no field / get method has been associated with this handler.
node,
at column number column.
Equation.
VisualMappingFunctionFactory.
VisualMappingFunctionFactory.
VisualMappingFunctionFactory.
VisualMappingManager.
VisualPropertyEditor for the given VisualProperty.
VisualStyleFactory.
VisualStyle objects.
VisualStyle to be removed from manager.
CyWriter Task that will attempt to write the specified network to the
specified file of the specified file type.
CyWriter Task that will attempt to write the specified network to the
specified output steam of the specified file type.
CyWriter Task that will attempt to write the specified view to the
specified file of the specified file type.
CyWriter Task that will attempt to write the specified view to the
specified output steam of the specified file type.
CyWriter Task that will attempt to write the specified property
object to the specified file of the specified file type.
CyWriter Task that will attempt to write the specified property
object to the specified output stream of the specified file type.
CyWriter Task that will attempt to write the specified session to the
specified file of the specified file type.
CyWriter Task that will attempt to write the specified session to the
specified output stream of the specified file type.
CyWriter Task that will attempt to write the specified table to the
specified file of the specified file type.
CyWriter Task that will attempt to write the specified table to the
specified output stream of the specified file type.
CyWriter Task that will attempt to write the specified view to the
specified file of the specified file type.
CyWriter Task that will attempt to write the specified view to the
specified output stream of the specified file type.
CyWriter Task that will attempt to write the specified vizmap to the
specified file of the specified file type.
CyWriter Task that will attempt to write the specified vizmap to the
specified output stream of the specified file type.
GroupAboutToBeDestroyedEventGroupAboutToBeRemovedEventGroupAboutToCollapseEventGroupAddedEventGroupAddedToNetworkEventGroupCollapsedEventGroupEdgesAddedEventGroupEdgesRemovedEventGroupNodesAddedEventGroupNodesRemovedEventTunableHandler with added functionality to support
the construction of a Swing-based UI.CyRows are changed.
TablePrivacyChangedListener.
Tunable annotations.
IdentDescriptor and provides minimal type translation
(from Integer to Long).
CustomGraphicLayer that
paints an image on a node.Integer values.node,
at column number column is editable.
CyGroup in
a particular CyNetwork.
List.
LexiconStateChangedEvent.LineType values.EventListenerList associated with this AbstractTreeTableModel.
Tunable.
Tunable.
T : one or more items can be selected.T : only 1 item can be selected.AbstractEdgeViewTask.edgeView.
NetworkAboutToBeDestroyedEventNetworkAddedEventNetworkDestroyedEventCyNetworkView is about to be destroyed, this event will be fired.CyNetworkView is added to a CyNetworkViewManager, this event will be fired.CyNetworkView is destroyed, this event will be fired.NodeShape values.CyGroups.RenderingEngines
node rendering with custom graphics.TaskFactory, TaskManager,
and TaskIterator.Shape that has an arbitrary
fill Paint and Stroke.Paint values.JPanel that will contain the GUI representation of the TunableHandler.
PreferencesUpdatedEvent.CyWriterFactory that allows a View
rendered by the specified RenderingEngine to
be specified and written.CyWriterManager specific to writing View objects.CyTable cell
PropertyUpdatedEvent.VisualPropertys.TaskManager.
RemovedEdgesEvents.RemovedNodesEvents.CySubNetwork but not from the CyRootNetwork.
CySubNetwork but not from the CyRootNetwork.
RenderingEngineAboutToBeRemovedEvent.RowsCreatedEventCyRow that was set and what it was set to.RowsSetEventTask begins execution.
Task begins execution.
Task begins execution.
SearchFinishedEvent.CySessionManager at beginning of the
CySessionManager.getCurrentSession() method.CySession is about to be
created listen to this event.CySessionManager.setCurrentSession(CySession, String)
method and is used to notify interested parties in the change
of state.SessionLoadedEvents.SessionSavedEvents.SetCurrentNetworkEvents.SetCurrentNetworkViewEvents.RenderingEngine has been set as current.SetCurrentRenderingEngineEvent.VisualStyle as the current one.
SetNetworkPointerEvents.Task.
SetSelectedNetworksEvents.SetSelectedNetworkViewsEvents.val item of type T as selected in the ListSingleSelection.
T items as selected in the ListMultipleSelection object.
Task is currently doing.
TaskIterator to set itself on the newly added Task.
Task.
Tunable.
Tunable.
v as the value of the Bounded Object.
Bounded object.
node,
at column number column.
String values.UndoSupport instead.TableAboutToBeDeletedEventCyTableManager.TableAddedEvent.TableDeletedEventTablePrivacyChangedEvent.Thread along with a user interface to
display its progress, provide a means for the user to
cancel the Task, and show information
about any Exceptions thrown during its
execution.TaskIterator.Tasks.Tasks found in the TaskIterator provided by a TaskFactory.Tasks to modify its user interface.String representation of this node.
Equation.
AffineTransform.
Double, Long, Boolean or String.
TreeNode - Interface in org.cytoscape.equationsThe interface for a node within the Equation parse tree.TreeTableModel - Interface in org.cytoscape.util.swingTreeTableModel is the model used by a JTreeTable.TreeTableModelAdapter - Class in org.cytoscape.util.swingThis is a wrapper class takes a TreeTableModel and implements
the table model interface.TreeTableModelAdapter(TreeTableModel, JTree) -
Constructor for class org.cytoscape.util.swing.TreeTableModelAdapter
Creates a new TreeTableModelAdapter object.
TRIANGLE -
Static variable in class org.cytoscape.view.presentation.property.NodeShapeVisualProperty
Triangular shape.
Tunable - Annotation Type in org.cytoscape.workAn annotation type that can be applied to public fields or a methods
in a Task object that allows the Task to be configured
with user supplied information.TunableHandler - Interface in org.cytoscape.workInterface for classes that deal with reading out and writing back
Tunables and their properties.tunableHandlerFactories -
Variable in class org.cytoscape.work.AbstractTunableInterceptor
A list of TunableHandlerFactory services that have been registered.
TunableHandlerFactory<T extends TunableHandler> - Interface in org.cytoscape.workA factory service to create a TunableHandler for a single type of object,
determined by the type of the field or the return value of the getter method in the
appropriate methods.tunableMutator -
Variable in class org.cytoscape.work.AbstractTaskManager
The single tunable mutator that will be used by this task manager.
TunableMutator<T extends TunableHandler,S> - Interface in org.cytoscape.workThis is a type of tunable interceptor that reads and
modifies the values annotated with the Tunable
annotation.TunableRecorder<T extends TunableHandler> - Interface in org.cytoscape.workTunableRecorder is a special type of tunable interceptor that
reads the state of the tunables but does not modify the
value of the tunables.tunableRecorders -
Variable in class org.cytoscape.work.AbstractTaskManager
The list of tunable recorders that will be used by this task manager.
TunableSetter - Interface in org.cytoscape.workAn API for setting tunable fields and methods with predetermined
values in the Tasks found in the specified TaskIterator.TunableValidator - Interface in org.cytoscape.workIf implemented, this interface is used to apply a test to the modified values of a Tunable.TunableValidator.ValidationState - Enum in org.cytoscape.workThe states the the validator can return.type -
Variable in class org.cytoscape.view.layout.EdgeWeighter
U
- undo -
Variable in class org.cytoscape.view.layout.AbstractLayoutTask
- Undo support for the task.
- undo() -
Method in class org.cytoscape.view.layout.LayoutEdit
-
- undo() -
Method in class org.cytoscape.work.undo.AbstractCyEdit
- The method that performs the undo.
- undoSupport -
Variable in class org.cytoscape.view.layout.AbstractLayoutAlgorithm
- An undo support object available for use
- UndoSupport - Interface in org.cytoscape.work.undo
- A simple interface that posts edits to the Cytoscape undo stack.
- UnGroupNodesTaskFactory - Interface in org.cytoscape.task.edit
- This interface provides a task iterator ungrouping a selection of nodes from a node view.
- UnGroupTaskFactory - Interface in org.cytoscape.task.edit
- This interface provides a task iterator ungrouping a group from a network view.
- UnHideAllEdgesTaskFactory - Interface in org.cytoscape.task.hide
- This interface provides a task iterator for unhiding all edges.
- UnHideAllNodesTaskFactory - Interface in org.cytoscape.task.hide
- This interface provides a task iterator for unhiding all nodes.
- UnHideAllTaskFactory - Interface in org.cytoscape.task.hide
- This interface provides a task iterator for unhiding everything
(all nodes and edges).
- unLock() -
Method in class org.cytoscape.view.layout.LayoutNode
- Register this node as being "unlocked".
- unregisterAllServices(Object) -
Method in interface org.cytoscape.service.util.CyServiceRegistrar
- This method unregisters an object as all OSGi service
interfaces that the object implements.
- unregisterService(Object, Class) -
Method in interface org.cytoscape.service.util.CyServiceRegistrar
- This method unregisters an object as an OSGi service
for the specified service interface.
- UnsetNetworkPointerEvent - Class in org.cytoscape.model.events
- Used to track removing of nested networks from nodes.
- UnsetNetworkPointerEvent(CyNode, CyNetwork) -
Constructor for class org.cytoscape.model.events.UnsetNetworkPointerEvent
- Constructs event.
- UnsetNetworkPointerListener - Interface in org.cytoscape.model.events
- Listener for
UnsetNetworkPointerEvents. - unsilenceEventSource(Object) -
Method in interface org.cytoscape.event.CyEventHelper
- This method will allow events fired from the specified source
object to be propagated to listeners.
- update() -
Method in class org.cytoscape.work.swing.AbstractGUITunableHandler
- The default implementation is a no-op.
- update() -
Method in interface org.cytoscape.work.swing.GUITunableHandler
- This method should be implemented to update the user interface in such a way that other tunable
handlers we listen to have changed, this tunable handler can display the appropriate inforamtion.
- updateEnableState() -
Method in class org.cytoscape.application.swing.AbstractCyAction
- Triggers the enable state of the action to be updated based
on the enableFor state of the action and the state of the
system.
- updateEnableState() -
Method in class org.cytoscape.application.swing.ActionEnableSupport
- Updates the enable state for the specified action/menuListener/menuItem
for the specified enableFor description and the state of the system.
- updateEnableState() -
Method in interface org.cytoscape.application.swing.CyAction
- Forces the action to update its enable state based on the criteria defined for
the action.
- UpdateNetworkPresentationEvent - Class in org.cytoscape.view.model.events
- If something has been changed in the view model, presentation layer should
catch the event and update its visualization.
- UpdateNetworkPresentationEvent(CyNetworkView) -
Constructor for class org.cytoscape.view.model.events.UpdateNetworkPresentationEvent
- Event for updating (redrawing) presentation.
- UpdateNetworkPresentationListener - Interface in org.cytoscape.view.model.events
- Listener for UpdateNetworkPresentationEvent.
- updateUI() -
Method in class org.cytoscape.util.swing.JTreeTable
- Overridden to message super and forward the method to the tree.
- updateView() -
Method in interface org.cytoscape.view.model.CyNetworkView
- Cascading event for the presentation layer for updating presentation.
- URL_PATTERN -
Static variable in interface org.cytoscape.io.util.StreamUtil
-
- urlPattern -
Static variable in interface org.cytoscape.util.swing.FileUtil
- A string that defines a simplified java regular expression for a URL.
- USE_ALPHABETIC_ORDER -
Static variable in interface org.cytoscape.util.swing.GravityTracker
-
- useCheckBoxMenuItem -
Variable in class org.cytoscape.application.swing.AbstractCyAction
- Indicates whether to use a checkbox menu item.
- useCheckBoxMenuItem() -
Method in class org.cytoscape.application.swing.AbstractCyAction
- Returns whether or not a checkbox menu item should be used.
- useCheckBoxMenuItem() -
Method in interface org.cytoscape.application.swing.CyAction
- Returns whether or not a checkbox menu item should be used.
V
- validateAndApplyTunables(Object) -
Method in interface org.cytoscape.work.swing.PanelTaskManager
- Validates any pending changes to the tunables in the given context
object.
- validateAndWriteBack(Object) -
Method in interface org.cytoscape.work.TunableMutator
- This method is called to validate and then set the values for
fields and methods annotated with the
Tunable annotation.
- validateArgTypes(Class[]) -
Method in class org.cytoscape.equations.AbstractFunction
- Returns the return type of this function.
- validateArgTypes(Class<?>[]) -
Method in interface org.cytoscape.equations.Function
-
- valueChanged(ListSelectionEvent) -
Method in class org.cytoscape.util.swing.CheckBoxJList
-
- ValueEditor<V> - Interface in org.cytoscape.view.vizmap.gui.editor
- Provides a GUI Editor for a data type.
- valueForPathChanged(TreePath, Object) -
Method in class org.cytoscape.util.swing.AbstractTreeTableModel
- Should be overridden.
- valueOf(String) -
Static method in enum org.cytoscape.application.swing.CytoPanelName
- Returns the enum constant of this type with the specified name.
- valueOf(String) -
Static method in enum org.cytoscape.application.swing.CytoPanelState
- Returns the enum constant of this type with the specified name.
- valueOf(String) -
Static method in enum org.cytoscape.equations.ArgType
- Returns the enum constant of this type with the specified name.
- valueOf(String) -
Static method in enum org.cytoscape.group.data.AttributeHandlingType
- Returns the enum constant of this type with the specified name.
- valueOf(String) -
Static method in enum org.cytoscape.io.DataCategory
- Returns the enum constant of this type with the specified name.
- valueOf(String) -
Static method in enum org.cytoscape.model.CyEdge.Type
- Returns the enum constant of this type with the specified name.
- valueOf(String) -
Static method in enum org.cytoscape.model.CyTable.Mutability
- Returns the enum constant of this type with the specified name.
- valueOf(String) -
Static method in enum org.cytoscape.model.CyTableFactory.InitialTableSize
- Returns the enum constant of this type with the specified name.
- valueOf(String) -
Static method in enum org.cytoscape.model.SavePolicy
- Returns the enum constant of this type with the specified name.
- valueOf(String) -
Static method in enum org.cytoscape.property.CyProperty.SavePolicy
- Returns the enum constant of this type with the specified name.
- valueOf(String) -
Static method in enum org.cytoscape.view.layout.WeightTypes
- Returns the enum constant of this type with the specified name.
- valueOf(String) -
Static method in enum org.cytoscape.view.vizmap.gui.editor.ContinuousEditorType
- Returns the enum constant of this type with the specified name.
- valueOf(String) -
Static method in enum org.cytoscape.work.TunableValidator.ValidationState
- Returns the enum constant of this type with the specified name.
- values() -
Static method in enum org.cytoscape.application.swing.CytoPanelName
- Returns an array containing the constants of this enum type, in
the order they are declared.
- values() -
Static method in enum org.cytoscape.application.swing.CytoPanelState
- Returns an array containing the constants of this enum type, in
the order they are declared.
- values() -
Static method in enum org.cytoscape.equations.ArgType
- Returns an array containing the constants of this enum type, in
the order they are declared.
- values() -
Static method in enum org.cytoscape.group.data.AttributeHandlingType
- Returns an array containing the constants of this enum type, in
the order they are declared.
- values() -
Static method in enum org.cytoscape.io.DataCategory
- Returns an array containing the constants of this enum type, in
the order they are declared.
- values() -
Static method in enum org.cytoscape.model.CyEdge.Type
- Returns an array containing the constants of this enum type, in
the order they are declared.
- values() -
Static method in enum org.cytoscape.model.CyTable.Mutability
- Returns an array containing the constants of this enum type, in
the order they are declared.
- values() -
Static method in enum org.cytoscape.model.CyTableFactory.InitialTableSize
- Returns an array containing the constants of this enum type, in
the order they are declared.
- values() -
Static method in enum org.cytoscape.model.SavePolicy
- Returns an array containing the constants of this enum type, in
the order they are declared.
- values() -
Static method in enum org.cytoscape.property.CyProperty.SavePolicy
- Returns an array containing the constants of this enum type, in
the order they are declared.
- values() -
Static method in enum org.cytoscape.view.layout.WeightTypes
- Returns an array containing the constants of this enum type, in
the order they are declared.
- values() -
Method in class org.cytoscape.view.model.DiscreteRange
- Returns a Set of all the values for this DiscreteRange.
- values() -
Static method in enum org.cytoscape.view.vizmap.gui.editor.ContinuousEditorType
- Returns an array containing the constants of this enum type, in
the order they are declared.
- values() -
Static method in enum org.cytoscape.work.TunableValidator.ValidationState
- Returns an array containing the constants of this enum type, in
the order they are declared.
- ValueTranslator<V,T> - Interface in org.cytoscape.view.vizmap.mappings
- Translate given table value to a Visual Property value.
- version -
Variable in class org.cytoscape.property.bookmark.Bookmarks
-
- VERSION_PROPERTY_NAME -
Static variable in interface org.cytoscape.application.CyVersion
- Deprecated.
- VERSION_REGEX -
Static variable in interface org.cytoscape.application.CyVersion
- The regular expression used to test the property version string.
- view -
Variable in class org.cytoscape.task.AbstractNetworkViewTask
- The network view that descendants of this class will operate on.
- View<S> - Interface in org.cytoscape.view.model
- The base interface that defines methods used to set visual properties
for nodes, edges, and networks.
- ViewChangeRecord<T> - Class in org.cytoscape.view.model.events
- A utility class used to describe one change to a
View. - ViewChangeRecord(View<T>, VisualProperty<?>, Object) -
Constructor for class org.cytoscape.view.model.events.ViewChangeRecord
- Constructor.
- viewExists(CyNetwork) -
Method in interface org.cytoscape.view.model.CyNetworkViewManager
- Determines whether a network view for the specified network is known to
the network view manager.
- viewVisualStyleMap(Map<CyNetworkView, String>) -
Method in class org.cytoscape.session.CySession.Builder
- Returns an instance of Builder that has at least been configured with the specified network view visual style
name map.
- VirtualColumnInfo - Interface in org.cytoscape.model
- Information object for columns that stores extra Virtual Column information
if applicable.
- Visualizable - Interface in org.cytoscape.view.model
- Marker interface for data types used by higher-level Visual Properties such as NODE, EDGE, or NETWORK.
- VisualLexicon - Interface in org.cytoscape.view.model
- A RenderingEngine should provide one, immutable lexicon implementing this interface.
- VisualLexiconNode - Class in org.cytoscape.view.model
- A node in the visual property tree (lexicon).
- VisualLexiconNode(VisualProperty<?>, VisualLexiconNode) -
Constructor for class org.cytoscape.view.model.VisualLexiconNode
- Constructs this VisualLexiconNode.
- VisualMappingFunction<K,V> - Interface in org.cytoscape.view.vizmap
- This class defines how an attribute gets mapped to a visual property.
It takes two values:
Attribute value: node name(Strings), expression values(Numbers), ...
Visual Property: node size(Numbers), edge color(Color), node
shape(NodeShape), ...
This provides the mapping function from converting the attribute to the
visual property. - VisualMappingFunctionChangedEvent - Class in org.cytoscape.view.vizmap.events
- VisualMappingFunctions should fire this event when the contents of the mapping
modified.
- VisualMappingFunctionChangedEvent(VisualMappingFunction, Collection<VisualMappingFunctionChangeRecord>) -
Constructor for class org.cytoscape.view.vizmap.events.VisualMappingFunctionChangedEvent
-
- VisualMappingFunctionChangedListener - Interface in org.cytoscape.view.vizmap.events
-
- VisualMappingFunctionChangeRecord - Class in org.cytoscape.view.vizmap.events
-
- VisualMappingFunctionChangeRecord() -
Constructor for class org.cytoscape.view.vizmap.events.VisualMappingFunctionChangeRecord
-
- VisualMappingFunctionFactory - Interface in org.cytoscape.view.vizmap
- Factory for VisualMappingFunctions.
- VisualMappingManager - Interface in org.cytoscape.view.vizmap
- Manager for VisualStyles.
- VisualProperty<T> - Interface in org.cytoscape.view.model
- An object which represents a type of visual entity, such as node color, size, etc.
- VisualPropertyDependency<T> - Class in org.cytoscape.view.vizmap
- Represents a set of Visual Properties to be set by their parent value if
dependency is enabled.
- VisualPropertyDependency(String, String, Set<VisualProperty<T>>, VisualLexicon) -
Constructor for class org.cytoscape.view.vizmap.VisualPropertyDependency
- Constructor.
- VisualPropertyDependencyFactory<T> - Interface in org.cytoscape.view.vizmap
-
- VisualPropertyEditor<T> - Interface in org.cytoscape.view.vizmap.gui.editor
- Facade of all editor-related objects for a Visual Property.
- VisualPropertyUtil - Class in org.cytoscape.view.presentation.property
- Utility functions for traversing visual lexicon tree.
- VisualPropertyValue - Interface in org.cytoscape.view.presentation.property.values
- Object used as a Visual Property value.
- VisualStyle - Interface in org.cytoscape.view.vizmap
- A VisualStyle is a collection of VisualMappingFunctions and default values
that define how a set of attributes is mapped to visual properties of View objects.
- VisualStyleAboutToBeRemovedEvent - Class in org.cytoscape.view.vizmap.events
- This event will be fired when VisualStyle object is removed from
VisualMappingManager.
- VisualStyleAboutToBeRemovedEvent(VisualMappingManager, VisualStyle) -
Constructor for class org.cytoscape.view.vizmap.events.VisualStyleAboutToBeRemovedEvent
- Create an event for the removed VisualStyle.
- VisualStyleAboutToBeRemovedListener - Interface in org.cytoscape.view.vizmap.events
- Listener for VisualStyleAboutToBeRemovedEvent.
- VisualStyleAddedEvent - Class in org.cytoscape.view.vizmap.events
- When new VisualStyle is added to the
VisualMappingManager,
it fires this event. - VisualStyleAddedEvent(VisualMappingManager, VisualStyle) -
Constructor for class org.cytoscape.view.vizmap.events.VisualStyleAddedEvent
- Creates an event for the newly created style.
- VisualStyleAddedListener - Interface in org.cytoscape.view.vizmap.events
- Listener for VisualStyleAddedEvent.
- VisualStyleChangedEvent - Class in org.cytoscape.view.vizmap.events
- When contents (default values or mappings) of an existing
VisualStyle is modified, this event should be fired.
- VisualStyleChangedEvent(VisualStyle, Collection<VisualStyleChangeRecord>) -
Constructor for class org.cytoscape.view.vizmap.events.VisualStyleChangedEvent
- Constructor of this event.
- VisualStyleChangedListener - Interface in org.cytoscape.view.vizmap.events
-
- VisualStyleChangeRecord - Class in org.cytoscape.view.vizmap.events
-
- VisualStyleChangeRecord() -
Constructor for class org.cytoscape.view.vizmap.events.VisualStyleChangeRecord
-
- VisualStyleFactory - Interface in org.cytoscape.view.vizmap
- Factory for VisualStyles.
- visualStyles(Set<VisualStyle>) -
Method in class org.cytoscape.session.CySession.Builder
- Returns an instance of Builder that has at least been configured with the specified properties.
- VisualStyleSetEvent - Class in org.cytoscape.view.vizmap.events
- Event fired when a
VisualStyle is set to a network view through
VisualMappingManager.setVisualStyle(VisualStyle, org.cytoscape.view.model.CyNetworkView). - VisualStyleSetEvent(VisualMappingManager, VisualStyle, CyNetworkView) -
Constructor for class org.cytoscape.view.vizmap.events.VisualStyleSetEvent
- Creates the event.
- VisualStyleSetListener - Interface in org.cytoscape.view.vizmap.events
- Listener for VisualStyleSetEvent.
- VizMapEventHandler - Interface in org.cytoscape.view.vizmap.gui.event
- Handler for Vizmap-GUI-local
PropertyChangeEvent. - VizMapEventHandlerManager - Interface in org.cytoscape.view.vizmap.gui.event
- Manages
VizMapEventHandlers. - VizMapGUI - Interface in org.cytoscape.view.vizmap.gui
-
The top-level GUI component of VizMap GUI.
- VizmapReader - Interface in org.cytoscape.io.read
- An extension of the Task interface that returns a
VisualStyle object. - VizmapReaderManager - Interface in org.cytoscape.io.read
- An object that registers all InputStreamReaderFactory singletons,
processes specified input to determine the appropriate factory to
use and then returns an instance of the correct
VizmapReader
for the input. - VizmapWriterFactory - Interface in org.cytoscape.io.write
- A specialization of
CyWriterFactory that allows a VisualStyle to
be specified and written. - VizmapWriterManager - Interface in org.cytoscape.io.write
- A
CyWriterManager specific to writing VisualStyle objects. - vp -
Variable in class org.cytoscape.application.swing.AbstractViewUpdater
- The
VisualProperty that the RowsSetListener is provided for.
- vp -
Variable in class org.cytoscape.view.vizmap.mappings.AbstractVisualMappingFunction
- Visual Property used in this mapping.
W
- WebServiceClient - Interface in org.cytoscape.io.webservice
- Thin wrapper for SOAP/REST web service clients.
- WebServiceGUI - Interface in org.cytoscape.io.webservice.swing
- Cytoscape's unified UI for accessing web services.
- WebServiceGUIClient - Interface in org.cytoscape.io.webservice.swing
- An interface that allows web service clients to provide
their own GUI component.
- WeightTypes - Enum in org.cytoscape.view.layout
- An enum describing different weighting strategies.
- writeOut() -
Method in interface org.cytoscape.io.util.RecentlyOpenedTracker
- Writes the list of recently opened files to the file specified by the
constructor argument.
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