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Cytoscape 3.1.1 API | |||||||||
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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.true if this filter accepts the given element from
context.
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.Transformer's
parameters.
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.TaskManager to tell us that the task iterator has completed.
Annotations.org.cytoscape.view.model.NetworkView.filter to the list of children.
element.
source from context.
AppsFinishedStartingEvent.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.
Bounded object.
CyColumn of the CyTable cell
CyColumn that descendants will operate on.
RowsSetListener is provided for.
ColumnNameChangedEvents.Equation class
Filter that computes the set-union or set-intersection of the
Filters it contains.CompositeFilter combines the results of its
contained Filters.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
CompositeFilter that selects elements of type
elementType from an object of type contextType.
DataSource
JAXBElement<String>}
ElementTransformer with the same id as this
factory.
Filter with the same id as this factory.
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.
id.
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.
transformer.
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, if you want to allow your component to be retrieved
from the CytoPanel by its identifier.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.ElementTransformers.Equation to another.
Equation.
transformer to the context.
transformers to the context.
transformers to the context, via
source.
Tasks in a TaskIterator provided
by a TaskFactory.
Tasks in a TaskIterator provided
by a TaskFactory.
Filters.TaskObservers.Font values.Filter at the given index.
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.
AvailableCommands.
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.
CommandExecutorTaskFactory which can be used
to execute commands.
Tunables
read from the TaskFactory.
Transformer is
compatible with.
TransformerSource is
compatible with.
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.
CyEdges.
CyNetwork.DEFAULT_ATTRS namespace specified by columnName and are in
the specified state.
List of elements from the given context.
Transformer is
compatible with.
TransformerSource is
compatible with.
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.
Transformer.
Transformer produced by this factory.
Transformer this factory produces
views for.
URL for the image to be displayed
URL.
GUITunableHandler.
JTextField, JFileChooser, JLabel, JList ...)
Filters contained by
this CompositeFilter.
CyWriterFactory for the appropriate filter.
NamedTransformer.
Transformer.
CyNetworkTableManager.getTables(org.cytoscape.model.CyNetwork, java.lang.Class).
CyNetwork.
Task.
CyNetworks this group is in.
CyNodes.
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().
List values .
PresentationWriterManager.
CyProperty objects defined for this session.
PropertyEditor object for this data type.
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.
CyRows.
CyProperty.SavePolicy of the CyProperty.
CyProperty.SavePolicy of the CyProperty.
CyProperty.SavePolicy of the CyProperty.
CySession object
Shape object
Shape
Annotation for this arrow.
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.
FinishStatus instance that indicates success.
CyTable.
CyTable that this row belongs to.
CyTable objects.
CyNetwork.class, CyNode.class, or
CyEdge.class.
TaskManager.
List of Transformers contained within this
NamedTransformer.
TransformerSource for the given contextType.
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.
SessionAboutToBeLoadedEvent when it is fired.
Transformer to indicate that its settings have
changed in some way.
Tunable annotations.
HolisticTransformers.IdentDescriptor and provides minimal type translation
(from Integer to Long).
CustomGraphicLayer that
paints an image on a node.filter within the list of children,
or -1 if filter is not in that list.
filter at the given index within the list of children.
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.Transformers with a user-defined name.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.FinishStatus object that indicates cancellation.
FinishStatus object that indicates failure.
NodeShape values.Task that notifies its observers when it is finished
executing.Transformers and
Filters.Transformers and
Filters.Transformers
provided by the core.Transformers to
Cytoscape.CyGroups.CyNetworkView.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.
Transformers.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.
Filter at the given index from the list of children
and returns in.
RemovedEdgesEvents.RemovedNodesEvents.CySubNetwork but not from the CyRootNetwork.
Transformer's
parameters.
CySubNetwork but not from the CyRootNetwork.
RenderingEngineAboutToBeRemovedEvent.RowsCreatedEventRowsDeletedEventCyRow that was set and what it was set to.RowsSetEventTask begins execution.
Task begins execution.
Task begins execution.
SearchFinishedEvent.CySession is about to be
loaded or created should implement this listener.CySessionManager at beginning of the
CySessionManager.getCurrentSession() method.CySession is about to be
created should listen to this event.SessionLoadCancelledEvents.CySessionManager.setCurrentSession(CySession, String)
method and is used to notify interested parties in the change
of state.SessionLoadedEvents.SessionSaveCancelledEvents.SessionSavedEvents.upper) and
lower bound (lower) of the Bounded Object.
SetCurrentNetworkEvents.SetCurrentNetworkViewEvents.RenderingEngine has been set as current.SetCurrentRenderingEngineEvent.VisualStyle as the current one.
URL to fetch the image from.
lowerStrict.
SetNetworkPointerEvents.Task.
SetSelectedNetworksEvents.SetSelectedNetworkViewsEvents.val item of type T as selected in the ListSingleSelection.
T items as selected in the ListMultipleSelection object.
Annotation for this arrow.
Annotation
CyNode
TaskIterator to set itself on the newly added Task.
Task.
upperStrict.
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.ObservableTask when it is finished executing.
Tasks.Tasks found in the TaskIterator provided by a TaskFactory.Task's implementation run method
to inform users of the status of its execution.showMessage method to indicate the severity of the message.ObservableTask finishes
executing.JPanel that summarizes
currently executing tasks.String representation of this node.
Equation.
AffineTransform.
Transformer factories.Transformer parameters.Transformers
supplied by the core.Transformer.Double, Long, Boolean or String.
- TreeNode - Interface in org.cytoscape.equations
- The interface for a node within the Equation parse tree.
- TreeTableModel - Interface in org.cytoscape.util.swing
- TreeTableModel is the model used by a JTreeTable.
- TreeTableModelAdapter - Class in org.cytoscape.util.swing
- This 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.work
- An 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. - TunableGravityOrderer - Class in org.cytoscape.work
- This class provides a comparator to order the
Tunables based on their
gravity value. - TunableGravityOrderer() -
Constructor for class org.cytoscape.work.TunableGravityOrderer
-
- TunableHandler - Interface in org.cytoscape.work
- Interface 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.work
- A 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.work
- This 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.work
- TunableRecorder 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.work
- An API for setting tunable fields and methods with predetermined
values in the Tasks found in the specified TaskIterator.
- TunableUIHelper - Interface in org.cytoscape.work.swing
-
- TunableValidator - Interface in org.cytoscape.work
- If implemented, this interface is used to apply a test to the modified values of a Tunable.
- TunableValidator.ValidationState - Enum in org.cytoscape.work
- The states the the validator can return.
- type -
Variable in class org.cytoscape.view.layout.EdgeWeighter
-
UnsetNetworkPointerEvents.Tunable annotation.
T.
View.VisualPropertyEditor but need to know
the visual property you are editing (eg to check if the user
inputted a value in the visual property's range), implement this interface
in addition to VisualPropertyEditor.VisualMappingManager,
it fires this event.VisualStyle is set to a network view through
VisualMappingManager.setVisualStyle(VisualStyle, org.cytoscape.view.model.CyNetworkView).PropertyChangeEvent.VizMapEventHandlers.VisualStyle object.VizmapReader
for the input.CyWriterFactory that allows a VisualStyle to
be specified and written.CyWriterManager specific to writing VisualStyle objects.VisualProperty that the RowsSetListener is provided for.
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Cytoscape 3.1.1 API | |||||||||
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