All Classes and Interfaces
Class
Description
When column
Views are about to be removed from a CyTableView, this event will be fired.Listener for
AboutToRemoveColumnViewEvent.Fired before an edge is actually removed so that listeners
have a chance to clean up before the edge object disappears.
Listener for AboutToRemoveEdgeEvents.
When edge
Views are about to be removed from a CyNetworkView, this event will be fired.Listener for AboutToRemoveEdgeViewsEvent.
Fired before a node is actually removed so that listeners
have a chance to clean up before the node object disappears.
Listener for AboutToRemoveNodeEvents.
When node
Views are about to be removed from a CyNetworkView, this event will be fired.Listener for AboutToRemoveNodeViewsEvent.
When row
Views are about to be removed from a CyTableView, this event will be fired.Listener for
AboutToRemoveRowViewsEvent.A bounded number object whose bounds values cannot be modified
An abstract, convenience implementation of a Cell Editor that
really only adds event listener support.
An abstract implementation of CyProperty<Properties> that attempts to read the specified
properties file first from the jar file running this code and then appends any properties
found in the local configuration directory to that properties object.
An abstract implementation of the CyAction interface.
A simple BundleActivator with convenience methods for registering
OSGi services and either getting references to single services or
registering interest in all services of a specified type.
Deprecated.
(As of Cytoscape 3.7)
Support for simple apps will be removed in a future version
of Cytoscape, please provide an OSGi bundle app instead.
A small class used to create new undoable edits.
A base implementation of
CyEvent that can be used by events.This can be used as a base class for custom implementations of
CyJobA base implementation of
CyPayloadEvent that can be used by events.Deprecated.
(As of Cytoscape 3.7)
Support for simple apps will be removed in a future version
of Cytoscape, please provide an OSGi bundle app instead.
The base class for all tasks that need to operate on an edge view and possibly its associated network view.
An EdgeViewTaskFactory that is always ready to produce a TaskIterator.
Base class for all
Function implementations.Base class for the various Swing implementations of
TunableHandler.TODO: Missing documentation
The AbstractLayoutAlgorithm provides a basic implementation of a layout TaskFactory.
This is a basic implementation of a LayoutAlgorithm Task that does some
bookkeeping, but primarily delegates to the doLayout() method.
The base class for all tasks that need to operate on a Collection of
CyNetworks.An NetworkCollectionTaskFactory that is always ready to produce a TaskIterator.
This abstract implementation of
NetworkSearchTaskFactory makes the method AbstractNetworkSearchTaskFactory.getQueryComponent()
optional.Base class for all tasks that need to operate on a
CyNetwork.A NetworkTaskFactory that is always ready to produce a TaskIterator.
The base class for all tasks that need to operate on a Collection of
CyNetworkViews.A NetworkViewCollectionTaskFactory that is always ready to produce a TaskIterator.
A base class for task factories that need to add a functionality to the network view
considering a given location (for example adding a node where a mouse was clicked).
The base class for all tasks that need to operate on a network view.
A NetworkViewTaskFactory that is always ready to produce a TaskIterator.
A node in the parse tree.
The base class for all tasks that need to operate on a node view and possibly its associated network view.
A NodeViewTaskFactory that is always ready to produce a TaskIterator.
This is an even more helpful implementation of a LayoutAlgorithm Task
that extends AbstractPartitionLayoutTask and does the work of partitioning
the CyNetworkView so that partitions may be laid out individually.
This is a more helpful implementation of a LayoutAlgorithm Task
that extends AbstractBasicLayoutTask and does the work of partitioning
the CyNetworkView so that partitions may be laid out individually.
The base class for all tasks that need to operate on a Collection of
CyRootNetworks.A
RootNetworkCollectionTaskFactory that is always ready to produce a TaskIterator.Base class for all tasks that need to operate on a
CyRow.A base class for Tasks that need to operate on a single CyTable cell.
A TableCellTaskFactory that is always ready to produce a TaskIterator.
A base class for Tasks that need to operate on an entire CyTable column.
A TableColumnTaskFactory that is always ready to produce a TaskIterator.
A base class for Tasks that need to operate on an entire
CyTable.A TableTaskFactory that is always ready to produce a TaskIterator.
A base class for tasks that need to be able to access the TaskIterator that contains them.
A TaskFactory that is always ready to produce a TaskIterator.
Provides access to a TunableInterceptor to all derived classes and a
utility method to determine if an object has been annotated with Tunables.
An abstract, convenience implementation of ToolBarComponent.
A convenience base class for Transformers.
An abstract implementation of the TreeTableModel interface, handling the list
of listeners.
Provides the standard implementation for most of the methods declared by the
TunableHandler interface.
An abstract base class for TunableRecorder and TunableMutator implementations.
A convenience base class for ValidatableTransformers.
A utility class that provides an implementation of
RowsSetListener
for a particular column and VisualProperty.Reusable template implementation of VisualLexicon.
A base class for visual mapping functions where all fields are immutable.
An abstract implementation of VisualProperty that omits the methods dealing
with serializing data.
Abstract implementation of Visual Property Editor.
Base class for all
VisualPropertyValue.Abstract class for all web service clients.
Abstract base class for web service clients with Swing GUI.
A class that allows the enabled state of an Action of JMenuItem to managed in
a consistent way.
When column
View is added to a CyTableView, this event will be fired.Listener for
AddedColumnViewEvent.An event fired when an edge is added to a network.
Listener for
AddedEdgesEvents.When edge View is added to a CyNetworkView, this event will be fired.
Listener for AddedEdgeViewsEvent.
Event for upper layers.
Listener for
AddedNodesEvents.When node View is added to a CyNetworkView, this event will be fired.
Listener for AddedNodeViewsEvent.
When row
View is added to a CyTableView, this event will be fired.Listener for
AddedRowViewsEvent.The Aggregator interface acts as a service interface for
different methods of aggregating attribute data for the
nodes in a
CyGroup.Provides a TaskIterator to analyze a collection of networks.
This is the base interface for all Annotations.
An interface describing a factory used to create
Annotations.The annotation manager is responsible for managing all of the
annotations currently assigned to a particular
org.cytoscape.view.model.NetworkView.This interface provides a task iterator for applying the preferred layout.
Marker interface which provides a task iterator for applying a visual style to views.
An event that occurs when the Cytoscape core has started, and any
installed apps have either finished starting or failed to start.
Listener for the
AppsFinishedStartingEvent.A class describing a function argument.
An enum specifying a function argument type.
This is the interface for an arrow annotation.
This enum is used to indicate how the arrow is anchored to the
source or target.
This enum is used to indicate which end of the arrow the
operation is referring to.
Marker interface representing edge end shape (arrow).
Visual Property for
ArrowShape values.Java class for anonymous complex type.
The AttributeHandlingType enum contains the list of all of the
different ways that attributes can be aggregated.
TODO: Missing documentation
A user-triggered collapsible panel containing the component (trigger) in the
titled border
This is meant to be an basic implementation of
CyFileFilter that can
either be used directly or extended to provide different acceptance criteria.A convenience implementation of TunableHandlerFactory that will construct a TunableHandler
of the specified type given the TunableHandler in question has at least two constructors, one
with Field, Object, Tunable parameters and the other with Method, Method, Object, Tunable parameters.
Basic Implementation of VisualLexicon.
Definition of Edge Bends.
Factory to create an instance of Bend.
Java class for anonymous complex type.
A set of utility methods to manipulate the bookmarks.
Visual Property for
Boolean values.This class defines a data object representing the range values associated
with a particular domain value, called a boundary value.
Classes which wish to listen for changes in AbstractBounded objects
(BoundedDouble, BoundedFloat, etc.) should implement this interface
and add themselves as observers (listeners) to the object.
A Double object which has low and up bounds
A Float object which has low and up bounds.
An Integer object which has low and up bounds.
A Long object which has low and up bounds.
The BoundedText annotation is a ShapeAnnotation that also implements
Text.
Java class for anonymous complex type.
Visual Property for CellFormat values.
This class is based on CheckBoxJList: from SWING HACKS
ISBN: 0-596-00907-0
By Joshua Marinacci, Chris Adamson
This interface provides a task iterator for network cloning.
Encapsulates compiled code with the location in the original source equation.
This interface provides a task iterator collapsing selection of nodes from a node view.
JButton that opens a Color Chooser when clicked and shows the previously set color as an icon.
This event signals that a column has been created.
Listener for ColumnCreatedEvents.
This event signals that a column has been deleted.
Listener for ColumnDeletedEvents.
This event signals that a columns name has been changed.
Listener for
ColumnNameChangedEvents.Automatically resize column based on the objects in the cell.
Event fired when a
VisualStyle is set to a column view through
TableVisualMappingManager.setVisualStyle(View, VisualStyle).Listener for ColumnVisualStyleSetEvent.
TODO: Missing documentation
Determines how a
CompositeFilter combines the results of its
contained Filters.This interface provides a task iterator for connecting selected nodes.
An annotation designed to signal that the annotated field contains
fields and methods that are annotated with the
Tunable annotation.An enum describing the possible types of continuous editors.
An interface describing a continuous mapping from attribute value
to visual property.
A factory for creating TableCellRenderers for a particular ContinuousMappingEditor.
A basic interface used to display continuous mapping editors.
Encapsulates a ContinuousMapping Point with a single point value and
associated
BoundaryRangeValues.Defines a continuous range of values for
VisualPropertys.This interface provides a task iterator for creating network views.
This interface defines the minimum interface to
add a custom graphics to a
CyNode.Custom graphic layer interface that allows a custom graphics implementation to draw directly onto the
CyNetworkView's Graphics2D object.An interface that describes how an action should be placed within
the menus and/or toolbars of the Swing application.
Deprecated.
(As of Cytoscape 3.7)
Support for simple apps will be removed in a future version
of Cytoscape, please provide an OSGi bundle app instead.
Application-wide setting will be accessible through this interface.
Basic access to current and/or currently selected networks,
views and rendering engines in an instance of Cytoscape.
Provides functionality associated with an OpenCL memory object.
An interface to the OpenCL Context object.
Represents functionality associated with a single OpenCL device.
The OpenCL list of device types.
CyCLFactory is the service that provides access to the OpenCL interface in Cytoscape.
This provides an interface to OpenCL Kernels
Specifies the amount of local memory in an argument of a kernel call.
Interface to the OpenCL platforms available on this computer.
Interface to an OpenCL program, including methods to get an OpenCL kernel
by name and to get build information after the program has been created (see
CyCLDevice addProgram method).This is an annoying re-implementation of JColorChooser.showDialog() that remembers
recently used colors between invocations of the chooser dialog.
This defines a color chooser that allows users to choose colors from a
palette and (optionally) change palettes.
This defines a color chooser that allows users to choose colors from a
palette and (optionally) change palettes.
This class describes a column in a CyTable.
An implementation of JComboBox that displays a list of CyColumns with their namespace icons.
A factory for creating
CyColumnIdentifier objects.Service that allows UI presentation to be given for a column namespace.
This class provides access to registered CyColumnPresentation service objects.
An Swing control that allows the user to select a set of CyColumn objects.
This interface is meant for internal use, it should not be used by Apps.
A snapshot of information about a CyColumn and its associated visual property values.
Base interface for all Custom Graphics.
Just an extension of
CyCustomGraphics which provides a way for the custom graphics instance
to define itself as a set of properties.
Factory to create
CyCustomGraphics2 objects.This interface provides the factory to create
CyCustomGraphics objects.An interface for objects that require an explicit clean up at the end of
their lifecycle.
An object that represents an edge within a network of nodes (vertices)
and edges.
The Type enum is used by methods in
CyNetwork to restrict
the edges that match a query.A factory interface used to produce a CyMenuItem (JMenuItem) that
will be added to the context menu for the specified edge view.
All Cytoscape events should extend this interface.
The basic event handling interface for Cytoscape.
An interface that captures the metadata description of a file type
so that files of the specified type can be handled correctly by the
application and the user interface.
An interface extended by various reader and writer factories.
An object that represents a group of nodes and edges.
The CyGroupAggregationManager provides a mechanism to add new
Aggregators to the group aggregation mechanism.
An interface describing a factory used for creating
CyGroup objects.The CyGroupManager maintains information about all of the groups
an instance of Cytoscape.
The CyGroupSettingsManager is responsible for providing an interface
to all of the possible settings controlling
CyGroups, including
the default settings and group specific settings.The
DoubleClickAciton enum provides the options for
what to do when the user double-clicks on either a group node
or a node that's a member of a group.The
CyGroupSettingsManager.GroupViewType enum provides the options for
how to visualize a group.Deprecated.
JavaHelp no longer used in Cytoscape as of 3.4.
CyIdentifiable is an interface that indicates that the implementing
object can be considered a key into a table.
A
CyJob represents all of the state information necessary to
marshal and unmarshal data, submit jobs, query job status, and fetch
results.CyJobData presents a general interface to sending data to and receiving
data from a job.
The main interface for the marshalling and unmarshalling
of data to be exchanged with remote services.
The
CyJobExecutionService is a stateless service that can be used to provide
remote job services, including the execution, cancellation, status checking, and retrieval
of results.CyJobManager is responsible for managing all currently running
CyJobs, including polling for changes in the
Status of the job and notifying the
CyJobMonitor provided by the App of the change in status.Apps are expected to implement this interface to receive notifications
about job completions.
This object stores information about the status of a
CyJob, including
the actual job status (CyJobStatus.Status) and any message returned
from the remote execution.This enum contains the primary status returned from the remote execution.
This interface provides some very basic JSON representations of Cytoscape objects.
A task factory specifically for layout algorithms.
This class provides access to the available layout algorithms.
The basic interface that any class interested in a particular
type of event should implement.
A simple wrapper class that allows a JMenuItem to be associated with
a gravity value which defines where in a menu the item should fall.
CyNetwork is the primary interface for representing a network (graph)
data structure in Cytoscape.
A singleton factory object used for instantiating CyNetwork
objects.
Basic access to networks and view in an instance of Cytoscape.
A utility that helps with the creation of unique network names.
An extension of the Task interface that returns an array of
CyNetwork objects that are read as part
of the Task.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
CyNetworkReader
for the input.Provides access to all network-table relationships.
Additional methods for CyNetworkView.
A factory interface used to produce a CyMenuItem (JMenuItem) that
will be added to the context menu for the specified network view.
Interface for managing CyNetworkViews within the desktop where they reside.
Factory for
CyNetworkView objects.Used to configure the behavior of
CyNetworkView objects created using
the CyNetworkViewFactoryFactory service.
A singleton factory that is used to create
CyNetworkViewFactory objects.Callback interface for use with
CyNetworkView instances that are created
from CyNetworkViewFactoryProvider factories.Basic access to network views in an instance of Cytoscape.
An immutable snapshot of a
CyNetworkView created using the
CyNetworkView.createSnapshot() method.A specialization of
CyWriterFactory that allows a
CyNetworkView or CyNetwork to be specified
and written to an OutputStream.A
CyWriterManager specific to writing
CyNetworkView objects.An object that represents a node (vertex) within a network
of nodes and edges.
A factory interface used to produce a CyMenuItem (JMenuItem) that
will be added to the context menu for the specified node view.
An extension of CyEvent specifically for payload events.
A general property service interface for providing access to different types
of property objects as OSGi services.
SavePolicy specifies how the CyProperty will be saved, or if it will not be saved.
An extension of the Task interface that returns a property
object.
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
CyPropertyReader
for the input.A specialization of
CyWriterFactory that allows a property Object to
be specified and written.A
CyWriterManager specific to writing property objects.CyRootNetwork is an interface for managing Cytoscape's
meta-network implementation.
A manager that provides access to the CyRootNetwork
objects associated with CyNetwork objects.
This interface represents one row in a CyTable.
A snapshot of information about a CyRow and its associated visual property values.
An interface to hide the OSGi dependencies needed to register
services dynamically at runtime.
Implementation of
CyServiceRegistrar.A session is an immutable snapshot of the data contents of Cytoscape.
A implementation of the builder pattern used to construct immutable instances of CySession objects.
This class primarily acts as a listener and tracks the state of
the Cytoscape application.
An extension of the Task interface that returns a
org.cytoscape.property.session.Cysession object.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
CySessionReader
for the input.A specialization of
CyWriterFactory that allows a CySession to
be specified and written.A
CyWriterManager specific to writing CySession objects.A service that will shutdown Cytoscape cleanly.
An event fired immediately before Cytoscape will be shutdown.
The listener for the
CyShutdownEvent.An event fired immediately before Cytoscape will be shutdown to determine if the shutdown action should be aborted.
The listener for the
CyShutdownRequestedEvent.An event fired after Cytoscape startup mostly complete (but not necessarily 100 percent).
The listener for the
CyStartEvent.Deprecated.
(As of Cytoscape 3.7)
Support for simple apps will be removed in a future version
of Cytoscape, please provide an OSGi bundle app instead.
This interface provides basic access to the Swing objects that
constitute this application.
A simple representation of a table object consisting of rows
and columns.
Mutability of the table specifies whether or not it is able to be deleted..
An interface describing a factory used for creating
CyTable objects.A description of the initial size of the table.
A singleton object for managing registered
CyTables.A snapshot of information about a relationship shared between a CyTable
instance and an associated CyNetworks.
An extension of the Task interface that returns an array of
CyTable objects.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
CyTableReader
for the input.A collection of state-less, static utility methods provided to
simplify querying of table objects.
Additional methods for table views.
Factory for
CyTableView objects.
A singleton factory that is used to create
CyTableViewFactory objects.Basic access to table views in an instance of Cytoscape.
A snapshot of information about a CyTable and its associated visual property values.
A specialization of
CyWriterFactory that allows a CyTable to
be specified and written.A
CyWriterManager specific to writing CyTable objects.Interface to a CytoPanel.
An interface that allows a component to be registered as a service
that will then be added to the appropriate
CytoPanel.Implement this interface rather than
CytoPanelComponent, if you want to allow your component to be retrieved
from the CytoPanel by its identifier.The event fired to indicate that a
CytoPanelComponent has been selected.The listener for handling
CytoPanelComponentSelectedEvent.An enum that describes
CytoPanels uses compass directions
to describe their location within the application.The different display states available for a
CytoPanel.An event to indicate that a CytoPanel has changed state.
A listener for handling
CytoPanelStateChangedEvents.This contains the name of the user log.
An interface providing access to version information about this
version of the Cytoscape application.
A marker interface used to identify tasks involved in
writing data.
A marker interface used to identify factories that
create CyWriter instances.
A CyWriterManager aggregates
CyWriterFactory services for specific DataCategories
and provides a mechanism for choosing the CyWriterFactory given a particular
file type.An enum that captures the types of data the IO package can read and write.
An event indicating that data has been successfully imported.
Listener for
DataImportFinishedEvent.Immutable data source object, which represents one data file associated with an URL.
Java class for anonymous complex type.
Entry point to access all data sources implemented as OSGi services.
A timer that can be used to ensure that time-consuming tasks, usually triggered
by events, do not run too often.
Basic implementation of
DataSource.Deprecated.
Deprecated.
Visual Property to represent abstract concept such as Node or Edge.
This interface provides a task iterator for deleting a column.
This interface provides a task iterator for deleting selected nodes and edges.
This interface provides a task iterator for deleting a table.
This interface provides a task iterator for deselecting all of the edges.
This interface provides a task iterator for deselecting all of the nodes.
This interface provides a task iterator for deselecting all of the items.
This interface provides a task iterator for destruction of networks.
This interface provides a task iterator that destroys a network view.
TODO: Missing documentation
An interface describing a discrete mapping from attribute value
to visual property.
Generates Discrete mapping for a set of attribute values and a Visual
Property.
Defines a discrete range of values for
VisualPropertys.Visual Property for
Double values.Button with drop down menu.
An extension of
MenuListener that is used to describe
dynamic submenus.TODO: Missing documentation
Visual Property for Edge
Bend values.This class implements a wrapper for a List of CyEdges that
can be used by the Tunables mechanism.
Enumerator returned when querying a
NetworkSpacialIndex2D, used to iterate over the results of the query.Marker interface for edge stacking.
Visual Property for
EdgeStacking values.A task factory that creates one or more tasks that operate on the specified View<CyEdge> within
the specified CyNetworkView.
The EdgeWeighter class.
This interface provides a task iterator for editing a network's title.
Manages all editor objects for the VizMap GUI.
A transformer that transforms its input one element at a time and pushes
the results into the given sink.
A factory for creating
ElementTransformers.The class representing an equation.
Compiler that compiles equations to byte (non-Java) code.
Parser for a string representing an equation.
Tokeniser for a string representing an equation.
Various static utility methods relating to equations.
This interface provides a task iterator expanding a group from a node view.
This interface provides a task iterator for exporting networks as image.
This interface provides a task iterator for exporting network views.
This interface provides a task iterator for exporting network views.
This interface provides a task iterator for exporting the current
table.
This task factory provides a task iterator for writing a specified
table to a specified file.
This interface provides a task iterator for exporting the vizmap visual style.
Used to hold extension(s) of acceptable file types and a short description of
them.
Provides a platform-dependent way to open files.
A transformer that decides whether to accept or reject elements.
A factory for creating
Filters.Indicates the status of a task iterator when it has finished for
TaskObservers.Fit network visualization to the given container.
Listener for FitContentEvent.
Fit only selected graph object views to the container.
Listener for FitSelectedEvent.
Visual Property for
Font values.The basic description of a Function.
A class describing an error in a function.
A collection of static methods that may be useful for the implementation of built-in functions.
This interface sepecifies a tracker that will be used to insert items (submenus, menu items
and separators) into a menu based on their "gravity" or "weight".
This event signals that a group is about to be destroyed -- i.e.
Listener for
GroupAboutToBeDestroyedEventThis event signals that a group is about to be removed from a network, but
not completely deleted.
Listener for
GroupAboutToBeRemovedEventThis event signals that a group is either about to be expanded or collapsed in
a particular network.
Listener for
GroupAboutToCollapseEventThis event signals that a new group has been added.
Listener for
GroupAddedEventThis event signals that an existing group has been added to a new network.
Listener for
GroupAddedToNetworkEventThe GroupAnnotation is a container for a collection of
annotations that should be grouped together.
This event signals that a group has either been expanded or collapsed in
a particular network.
Listener for
GroupCollapsedEventThis event signals that edges have been added to the network.
Listener for
GroupEdgesAddedEventThis event signals that edges have been removed from the network.
Listener for
GroupEdgesRemovedEventThis event signals that edges have been added to the network.
Listener for
GroupNodesAddedEventThis event signals that edges have been removed from the network.
Listener for
GroupNodesRemovedEventThis interface provides a task iterator for grouping nodes.
An extension of
TunableHandler with added functionality to support
the construction of a Swing-based UI.A specialization fo TunableHandlerFactory for GUITunableHandler.
Defines a handle, an anchor point in the edge.
Factory of the handle object.
This interface provides a task iterator for hiding selected edges.
This interface provides a task iterator for hiding selected nodes.
This interface provides a task iterator for hiding all of the selected
items.
This interface provides a task iterator for hiding the given nodes and edges.
This interface provides a task iterator for hiding unselected edges.
This interface provides a task iterator for hiding unselected nodes.
This interface provides a task iterator for hiding unselected nodes and edges.
A transformer that takes its input altogether, transforms it, and pushes
the results into the given sink.
A factory for creating
HolisticTransformers.Interface that provides constants for simple icons that can be used by Cytoscape and third party apps in order to
create a more consistent GUI.
Used to hold a current value for an equation's variable reference.
This annotation positions an image on on the screen.
This interface defines a
CustomGraphicLayer that
paints an image on a node.This interface provides a task iterator for importing a table data in a network data table.
A super interface that allows the input stream to be set for reader
task factories.
Visual Property for
Integer values.Listens for changes in the system-level state of interactivity.
Executes the code represented by an equation.
This interface provides a task iterator for inverting the selected edges.
This interface provides a task iterator for inverting the selected nodes.
A class that creates and manages hierarchies of JMenu objects.
TODO: Missing documentation
This interface is intended to facilitate retrieving valid JSON strings from
ObservableTask.getResults(Class).Simple status bar with 3 fields.
This example shows how to create a simple JTreeTable component, by using a
JTree as a renderer (and editor) for the cells in a particular column in the
JTable.
An ENUM that provides information about text justification.
Marker interface for node label background shapes.
The LayoutEdge class.
An undoable edit that will undo and redo of a layout algorithm applied to a
network view.
The LayoutNode class.
The LayoutPartition class contains all of the information about a
single graph partition, where a partition is defined as all nodes
in a graph that connect only to each other.
Simple immutable object which represents a point (x, y, z).
Tell listeners a enabled/disabled visual properties.
Listener for
LexiconStateChangedEvent.Marker interface for line types.
Visual Property for
LineType values.Classes which wish to listen for changes in ListSelection objects
(ListSingleSelection, ListMultipleSelection) should implement this interface
and add themselves as observers (listeners) to the object.
Generic editor for discrete values, such as Shape, Line Type, etc.
List with items of type
T : one or more items can be selected.A ListSelection object.
List with items of type
T : only 1 item can be selected.This interface provides a task iterator for loading networks from multiple files at once.
This interface provides a task iterator for loading networks from a file.
This interface provides a task iterator for loading a URL into a network.
This interface provides a task iterator for importing the attribute file to one of network tables(Node,Edge or Network Table).
This interface provides a task iterator for importing an attribute URL to one of network tables(Node,Edge or Network Table).
An interface for loading styles from files.
Class that provides useful methods to help create standard and consistent UI on the current Look and Feel and OS.
This interface provides a task iterator for mapping a global to a local table.
This is a special
VisualPropertyValue that allows a VisualProperty value
to be specified as depending on one or more CyColumns.Manages factories to create actual mappings (discrete/passthrough/continuous).
TODO: Missing documentation
This class inserts menu items and separators in a menu based on their "gravity".
This interface provides a task iterator for merging two data tables.
There have been some issues with JOptionPane not working correctly when triggered from
a command or automation script.
A chain of
Transformers with a user-defined name.This event signals that a network is about to be destroyed.
Listener for
NetworkAboutToBeDestroyedEventThis event signals that a network has been added.
Listener for
NetworkAddedEventProduces a task iterator for the specified collection of networks.
This event signals that a Network has been destroyed.
Listener for
NetworkDestroyedEvent
This service is used to create images for a given
CyNetworkView.Marker interface for web service clients that have ability to import network data.
Task Factory that has to be implemented in order to create and register a Network Search provider.
Stores the location and rectangular boundary of nodes in a 2D representation of a network.
A task factory that creates one or more tasks that operate on the specified CyNetwork.
When a
CyNetworkView is about to be destroyed, this event will be fired.Listener for NetworkViewAboutToBeDestroyedEvent.
When a
CyNetworkView is added to a CyNetworkViewManager, this event will be fired.Listener for NetworkViewAddedEvent.
A task factory that creates one or more tasks that operate on the specified
collection of network views.
When a
CyNetworkView is destroyed, this event will be fired.Listener for NetworkViewDestroyedEvent.
An extension of TaskFactory that provides support for
tasks that need to know the a location within a CyNetworkView to
perform their task.
A task factory that creates one or more tasks that operate on the specified CyNetworkView.
An interface for creating new, empty network views.
This interface provides a task iterator for creating networks
from selected nodes and edges.
This interface provides a task iterator for creating networks
from selected nodes only.
This interface provides a task iterator for creating a new session.
This class implements a wrapper for a List of CyNodes that
can be used by the Tunables mechanism.
Marker interface for node shapes.
Visual Property for
NodeShape values.Enumerator returned when querying a
NetworkSpacialIndex2D, used to iterate over the results of the query.A task factory that creates a task that operates on the specified View<CyNode> within
the specified CyNetworkView.
A CyNetwork with no corresponding view.
An empty/null data type marker interface for Visual Properties holding no actual data.
Visual Property for root.
This object contains factory methods for each
Java content interface and Java element interface
generated in the org.cytoscape.property.bookmark package.
ObjectPosition is the value that is used by Position VisualProperties.
Visual Property for
ObjectPosition values.A
Task that notifies its observers when it is finished
executing.A utility provided as an OSGi service for opening
a web browser.
This interface provides a task iterator for loading a session.
Visual Property for
Paint values.This interface provides a consistent way for various providers (ColorBrewer,
ColourLovers, etc.) to provide color palettes to Cytoscape routines.
This interface provides a consistent way for various providers (ColorBrewer,
ColourLovers, etc.) to provide color palettes to Cytoscape routines.
The PaletteProviderManager provides a way for palette providers
to register themselves.
This is an interface for defining types of palettes.
A specialization of a TaskManager that creates a JPanel configuration
object and expects its execution context to be another JPanel.
This class also provides static methods that are used to partition a network.
An interface describing a passthrough or identity mapping from attribute value
to visual property.
This class inserts menu items and separators in a menu based on their "gravity".
An ENUM that provides values for the various anchors that
may be used for text, customgraphics, etc.
Various predicates that can be used to test conditions in
Transformers.An event indicating that system preferences have been updated.
A listener for the
PreferencesUpdatedEvent.A specialization of
CyWriterFactory that allows a View
rendered by the specified RenderingEngine to
be specified and written.A
CyWriterManager specific to writing View objects.Utility class to provide access to basic set of Visual Properties.
This event signals that a CyProperty is updated.
Listener interface for
PropertyUpdatedEvent.An annotation type that can be applied to a method which returns a
String that will be used for the title of a Tunable user interface dialog
window.
Defines a range of values for
VisualPropertys.Manages list of recently opened files.
Just a signal in case anyone wants to
resync after an edge has been removed.
Listener for
RemovedEdgesEvents.Just a signal in case anyone wants to
resync after a node has been removed.
Listener for
RemovedNodesEvents.This interface provides a task iterator for renaming a column.
RenderingEngine is an interface for all visualizers which renders.
When presentation (rendered graphics) is destroyed, this event should be
fired.
Listener for
RenderingEngineAboutToBeRemovedEvent.When new presentation is created, its factory always creates a RenderingEngine).
Listener for RenderingEngineAddedEvent.
A factory class to create visualization for a given view model.
Manager for network RenderingEngine objects.
Interface to indicate that an app wants to have a UI helper
provided.
Produces a task iterator for the specified collection of root-networks.
This class implements a wrapper for a List of table rows that
can be used by the Tunables mechanism.
This event signals that rows have been created.
Listener for
RowsCreatedEventThis event signals that rows have been Deleted.
Listener for
RowsDeletedEventHolds a record of a
CyRow that was set and what it was set to.This event signals that rows have been set.
Listener for
RowsSetEventA task factory that creates one or more tasks that operate on the specified CyRow.
The SavePolicy of an object specifies whether or not it will be saved.
This interface provides a task iterator for saving a session in a
specified file.
This interface provides a task iterator for saving a session.
An event that indicates a search has completed.
Listener for
SearchFinishedEvent.Marker interface for web service clients sending search query
and getting arbitrary search result.
This interface provides a task iterator for selecting adjacent edges.
This interface provides a task iterator for selecting all of the edges.
This interface provides a task iterator for selecting all of the nodes.
This interface provides a task iterator for selecting all of the items.
This interface provides a task iterator for selecting connected nodes.
This interface provides a task iterator for selecting connected nodes.
Event that signals when the selection state of nodes and/or edges has changed within a network.
Listener for
SelectedNodesAndEdgesEventThis interface provides a task iterator for selecting neighbor nodes.
This interface provides a task iterator for selecting the first neighbors.
This interface provides a task iterator for selecting items based on a file.
Reserved keywords for OSGi service properties (meta data).
This event is fired right before Cytoscape begins to load a session.
Any object that needs to know that a
CySession is about to be
loaded or created should implement this listener.This event is fired synchronously by the
CySessionManager at beginning of the
CySessionManager.getCurrentSession() method.Any object that needs to know that a
CySession is about to be
created should listen to this event.Deprecated.
Just listen to
SessionLoadedEvent instead now.Deprecated.
Use
SessionLoadedListener instead.This event is fired after a new session has been set in the
CySessionManager.setCurrentSession(CySession, String)
method and is used to notify interested parties in the change of state.A listener for
SessionLoadedEvents.This event is fired when a session save task is cancelled, which can also happen because of exceptions.
A listener for
SessionSaveCancelledEvents.TODO: Missing documentation
A listener for
SessionSavedEvents.An event signaling that the a network has been set to current.
A listener for
SetCurrentNetworkEvents.An event indicating that a network view has been set to current.
A listener for
SetCurrentNetworkViewEvents.This event signals that a
RenderingEngine has been set as current.Listener for
SetCurrentRenderingEngineEvent.An event signaling that the a table has been set to current.
A listener for
SetCurrentTableEvents.TODO: Missing documentation
TODO: Missing documentation
Used to track setting of nested networks on nodes.
Listener for
SetNetworkPointerEvents.An event indicating the a collection of networks has been selected.
A listener for
SetSelectedNetworksEvents.An event that indicates that a collection of network views has been selected.
A listener for
SetSelectedNetworkViewsEvents.A Shape annotation supports annotations that can be drawn and filled
on the graphics canvas.
A simple implementation of CyProperty suitable for general purpose use.
A specialization for GUITunableHandlers.
Size constants for scalar and vector data types.
Contains additional info about a
View<CyEdge> obtained from a CyNetworkViewSnapshot.Contains additional info about a
View<CyNode> obtained from a CyNetworkViewSnapshot.Stores the location and rectangular boundary of objects
(typically
View<CyNode> objects)
in 2D space.Enumerator returned when querying a
SpacialIndex2D, used to iterate over the results of the query.Creates a
JPanel that is shown
at the bottom of the Cytoscape Desktop.
NOTE: this is not meant to be implemented
by App developers.A stateless utility class that provides special handling to support
InputStreams and URLConnections over the network.
The service implementing StringToModel provides a common mechanism for converting
command arguments into Cytoscape model elements.
Visual Property for
String values.A
Transformer that contains a CompositeFilter that it uses to filter its output.This singleton class returns unique, positive SUID (session unique ID) values.
This utility class provides methods to save and restore SUIDs that
are sent to remote execution environments across sessions.
In general, developers should NOT use this interface or the classes
it provides access to to post edits and should use
UndoSupport instead.A marker interface that indicates that the TaskManager in question will
execute the tasks found in the TaskFactory synchronously with the current thread,
blocking code execution until all tasks finish.
This event signals that a table is about to be deleted.
Listener for
TableAboutToBeDeletedEventThis event will be fired when new table is added to
CyTableManager.Listener for
TableAddedEvent.A task factory that creates one or more tasks that operate on the specified CyColumn
along with primary key.
A task factory that creates one or more tasks that operate on the specified CyColumn.
This event signals that a table has been deleted.
Listener for
TableDeletedEventMaker interface for web service clients that have ability to import table data.
Visual Property for TableMode values.
This event is fired when a table privacy is changed from public
to private or vice versa.
Listener interface for handling
TablePrivacyChangedEvent.A task factory that creates one or more tasks that operate on the specified CyTable.
TODO: Missing documentation
TODO: Missing documentation
An interface that allows a component to be registered as a service that will then be added
to a Table Panel's toolbar.
When a
CyTableView is about to be destroyed, this event will be fired.Listener for
TableViewAboutToBeDestroyedEvent.When a
CyTableView is added to a CyTableViewManager, this event will be fired.Listener for TableViewAddedEvent.
This event is fired when a
VisualProperty value
is set or removed from a View.Listener for TableViewChangedEvent.
When a
CyTableView is destroyed, this event will be fired.Listener for TableViewDestroyedEvent.
Manager for
VisualStyles applied to table columns.This interface specifies a unit of work to be executed
asynchronously in its own
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.Returns an instance of a
TaskIterator.A TaskIterator provides the functionality of sequencing
Tasks.Used by a
Task's implementation run method
to inform users of the status of its execution.Used by the
showMessage and setStatusMessage methods to indicate the severity of the message.An observer that gets notified when an
ObservableTask finishes
executing.Deprecated.
A text annotation is a simple text string that is displayed on
the network canvas.
Renders any text/font as an icon.
An extension of JToolTip that supports text wrapping.
This interface is meant to be implemented by task factories that provides tasks which switches something on and off.
Represents the interpretation of a substring of an equation string.
An interface that allows a component to be registered as a service
that will then be added to the ToolBar.
Transforms a stream of elements from a particular context.
A class that contains and manages a list of Transformers.
The base interface for all
Transformer factories.Listens for changes to
Transformer parameters.A class for creating and executing Transformers.
Identifiers of the
Transformers
supplied by the core.Collects the results of a transformation.
Provides a sequence of elements from a context.
A factory for making UI panels to configure a specific
Transformer.The interface for a node within the Equation parse tree.
TreeTableModel is the model used by a JTreeTable.
This is a wrapper class takes a TreeTableModel and implements
the table model interface.
This class provides a comparator to order the
Tunables based on their
gravity value.Interface for classes that deal with reading out and writing back
Tunables and their properties.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.This is a type of tunable interceptor that reads and
modifies the values annotated with the
Tunable
annotation.An extension of
TunableHandler with added functionality to support
converting to/from a String.A specialization of TunableHandlerFactory for TunablePropertyHandler.
This is a type of tunable interceptor that converts the values
annotated with
Tunable annotations to and from a Properties object.Factory to create TunablePropertySerializer instances.
TunableRecorder is a special type of tunable interceptor that
reads the state of the tunables but does not modify the
value of the tunables.
An API for setting tunable fields and methods with predetermined
values in the Tasks found in the specified TaskIterator.
If implemented, this interface is used to apply a test to the modified values of a Tunable.
The states the the validator can return.
A simple interface that posts edits to the Cytoscape undo stack.
This interface provides a task iterator ungrouping a selection of nodes from a node view.
This interface provides a task iterator ungrouping a group from a network view.
This interface provides a task iterator for unhiding all edges.
This interface provides a task iterator for unhiding all nodes.
This interface provides a task iterator for unhiding everything
(all nodes and edges).
This interface provides a task iterator for unhiding selected edges.
This interface provides a task iterator for unhiding selected nodes.
This interface provides a task iterator for unhiding the given nodes and edges.
Used to track removing of nested networks from nodes.
Listener for
UnsetNetworkPointerEvents.If something has been changed in the view model, presentation layer should
catch the event and update its visualization.
Listener for UpdateNetworkPresentationEvent.
Support for a user initiated action
A marker interface that can be added to any
Transformer to indicate
that the transformer may be invalid in certain contexts.A warning message that will appear in the UI when a Transformer is invalid.
Provides a GUI Editor for a data type.
Translate given table value to a Visual Property value.
The base interface that defines methods used to set visual properties
for nodes, edges, and networks.
This event is fired when a
VisualProperty value
is set or removed from a View.Listener for ViewChangedEvent.
A utility class used to describe one change to a
View.Information object for columns that stores extra Virtual Column information
if applicable.
Marker interface for data types used by higher-level Visual Properties such as NODE, EDGE, or NETWORK.
A RenderingEngine should provide one, immutable lexicon implementing this interface.
A node in the visual property tree (lexicon).
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.
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.
VisualMappingFunctions should fire this event when the contents of the mapping are modified.
This listener is used by the
VisualStyle implementation, so a style can be
notified when its visual mappings are changed.This is used to create a
VisualMappingFunctionChangedEvent.Factory for VisualMappingFunctions.
Manager for VisualStyles.
An object which represents a type of visual entity, such as node color, size, etc.
Represents a set of Visual Properties to be set by their parent value if
dependency is enabled.
Visual property dependencies should fire this event when
VisualPropertyDependency.setDependency(boolean)
is called with a different value.This listener is used by the
VisualStyle implementation, so a style can be
notified when VisualPropertyDependency.setDependency(boolean) is called on any of its
visual property dependencies.TODO: Missing documentation
Facade of all editor-related objects for a Visual Property.
If you are writing a
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.Utility functions for traversing visual lexicon tree.
Object used as a Visual Property value.
Provides a GUI Editor for a data type.
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.
This event will be fired when VisualStyle object is removed from
VisualMappingManager.
Listener for VisualStyleAboutToBeRemovedEvent.
When new VisualStyle is added to the
VisualMappingManager,
it fires this event.Listener for VisualStyleAddedEvent.
When contents (default values or mappings) of an existing
VisualStyle is modified, this event should be fired.
TODO: Missing documentation
This is used to create a
VisualStyleChangedEvent.Factory for VisualStyles.
Event fired when a
VisualStyle is set to a network view through
VisualMappingManager.setVisualStyle(VisualStyle, org.cytoscape.view.model.CyNetworkView).Listener for VisualStyleSetEvent.
Handler for Vizmap-GUI-local
PropertyChangeEvent.Manages
VizMapEventHandlers.Deprecated.
An extension of the Task interface that returns a
VisualStyle object.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.A specialization of
CyWriterFactory that allows a VisualStyle to
be specified and written.A
CyWriterManager specific to writing VisualStyle objects.Thin wrapper for SOAP/REST web service clients.
Cytoscape's unified UI for accessing web services.
An interface that allows web service clients to provide
their own GUI component.
An enum describing different weighting strategies.