This is the Cytoscape App API, which supports development of Cytoscape 3.X apps in a manner similar to apps developed in Cytoscape 2.X.
This is the Cytoscape Swing App API, which supports development of Cytoscape 3.X apps in a manner similar to apps developed in Cytoscape 2.X and provides full access to the Swing specific services of the Cytoscape API in addition to all other services provided in Cytoscape App API.
This package provides Cytoscape version number, application-wide setting, basic access to current network, selected networks, views and rendering engines.
This package provides application events/listeners, including Cytoscape startup/shutdown, setCurrentNetwork/setCurrentNetworkView/ setSelectedNetwork.
This package defines the various interfaces, abstract classes, and enums that represent the Cytoscape Swing Application API.
This package defines the various events fired by the Cytoscape Swing Application API.
Interface to support execution of tasks as commands, including the ability to get a list of namespaces, commands, and arguments, and then execute those commands with a set of arguments.
Tunable classes useful for command applications
This package provides an interface to OpenCL from Cytoscape core and Cytoscape apps.
Various types and utility methods relating to attribute equations.
This package contains the basic interfaces necessary for defining, firing, and listening for Cytoscape events.
General purpose predicates used to perform comparisons against numbers and strings.
Provides interfaces for working with the
provided by the core.
Provides interfaces for contributing user interfaces for
This package provides an API for creating and managing groups in Cytoscape.
An api for configuring
This package contains the various events and listeners related to group management, creation, and destruction.
Handle import/export of Cytoscape data structures to/from local files/remote URLs.
API to provide data files as a bundle.
Handle importing Cytoscape data (network, attributes, session, properties, etc) from files/URLs.
A small number of utilities related to IO.
Interfaces for SOAP/REST web service clients, web services that return results as networks or tables, or query results.
Provides an abstract class for all web service clients, i.e.
This package defines events/listeners related to data query/import from web services.
Web Service Clients with Swing GUI.
This package provides factory interfaces to be used by anyone wishing to provide export or writing capabilities to the rest of Cytoscape.
This package provides a mechanism for executing remote jobs from within Cytoscape.
This package has the core interfaces of network and table data structures that are foundational to Cytoscape.
This package contains the event interfaces necessary for communicating with the classes in org.cytoscape.model.
This package contains rootnetwork and subnetwork extensions to the CyNetwork interface that provide a more complex meta-network data model.
This package provides a general property service interface for providing access to different types of property objects as OSGi services.
This package provides a set of utility methods to manipulate the bookmarks XML format which is used to store and categorize collections of URL bookmarks pointing to data sources.
This package contains a simple utility for registering OSGi services without requiring use of the OSGi API.
This package contains the interfaces and classes necessary to capturing, storing, and retrieving the state of a Cytoscape session.
This package contains the interfaces and classes necessary to capturing, session change events.
This package provides base classes for common task factory types as well as their associated task types found in Cytoscape.
This package provides a variety of task factory interfaces for creating new instances of network and other objects.
This package includes a set of task factory interfaces for deleting or or destroying objects within Cytoscape.
This package include a set of task factory interfaces that allow the modification or editing of various objects within Cytoscape.
This package includes a set of task factory interfaces showing and hiding nodes and edges within network views.
This package contains a set of task factory interfaces for reading various Cytoscape objects from files and URLs.
This package includes a set of task factory interfaces for selecting, de-selecting and inverting selections of nodes, edges, or combinations of both based on specific criteria.
This package include a set of task factory interfaces used to manipulate the visualizations of network views.
This package contains a set of task factory interfaces used for exporting or writing a variety of Cytoscape objects to files.
This package contains misc helper classes for Cytoscape Desktop application.
This package provides access to the available layout algorithms, as well as provides abstract layout classes and layout information containers for the convenience of implementing other layout algorithms.
Module for View Models and Visual Properties.
Definitions for View-Model related events and their listeners.
API set for rendering engines (visualizers).
This package provides support for graphical annotations associated with a Cytoscape
This package provides an API for augmenting a
node rendering with custom graphics.
Event implementations and listener interfaces for the Presentation layer.
Interfaces for VisualPropertyValues -- ArrowShape, LineType and NodeShape
Visual Mapping basic API module.
Events for Visual Mappings.
This package provides access to GUI component of VizMap GUI, and interfaces of mapping related managers.
Provides editors for Visual Properties and editor managers for VizMap GUI.
Provides events and listeners of LexiconState, visual style switch and vizMap event, as well as VizMap event handler manager.
Create discrete mapping for a given set of attribute values
APIs for different mapping functions -- continuous mapping, discrete mapping and pass through mapping.
This package defines the task framework, where tasks are units of work.
This packages provides Swing-specific extensions for undo support.
Cytoscape's undo framework.
Various supporting classes for Cytoscape the work (Task) framework.