Cytoscape Swing App API (swing-app-api) 3.9.0 API
This document represents the API specification for Cytoscape 3.0 using a Java Swing front-end.
Getting Started
Resources for getting started with Cytoscape App development:- Cytoscape App Ladder (overview of setting up development environment)
- Introduction to Cytoscape App Development (tutorial for getting started using the API)
- Cytoscape 3 App Cookbook (API usage examples)
- Cytoscape App Samples (github repo of example Apps)
- cytoscape-app-dev (Google Group for asking questions about Cytoscape App development)
Cytoscape 3 is build on the OSGi framework. The Cytoscape API is divided into several bundles, each of which requires its own maven dependency. Use the tabs below to see which packages are contained within each bundle.
Package
Description
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
Various types and utility methods relating to attribute equations.
This package contains the basic interfaces necessary for defining, firing,
and listening for Cytoscape events.
Provides interfaces for constructing and executing
Transformers and
Filters.Provides interfaces and classes for defining
Transformers and
Filters.General purpose predicates used to perform comparisons against numbers
and strings.
Provides interfaces for working with the
Transformers
provided by the core.Provides interfaces for contributing user interfaces for
Transformers to
Cytoscape.This package provides an API for creating and managing
groups in Cytoscape.
An api for configuring
CyGroups.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
CyNetworkView.This package provides an API for augmenting a
RenderingEngines
node rendering with custom graphics.Event implementations and listener interfaces for the Presentation layer.
Implementations of basic VisualProperty objects and VisualLexicons.
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 specialisations of concepts from work-api
This includes
TaskFactory, TaskManager,
and TaskIterator.This packages provides Swing-specific extensions for undo support.
Cytoscape's undo framework.
Various supporting classes for Cytoscape the work (Task) framework.