Cytoscape 3.1.0 API

Cytoscape Swing App API (swing-app-api) 3.1.0 API

This document represents the API specification for Cytoscape 3.0 using a Java Swing front-end.

See: Description

Packages 
Package Description
org.cytoscape.app
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.
org.cytoscape.app.event  
org.cytoscape.app.swing
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.
org.cytoscape.application
This package provides Cytoscape version number, application-wide setting, basic access to current network, selected networks, views and rendering engines.
org.cytoscape.application.events
This package provides application events/listeners, including Cytoscape startup/shutdown, setCurrentNetwork/setCurrentNetworkView/ setSelectedNetwork.
org.cytoscape.application.swing
This package defines the various interfaces, abstract classes, and enums that represent the Cytoscape Swing Application API.
org.cytoscape.application.swing.events
This package defines the various events fired by the Cytoscape Swing Application API.
org.cytoscape.command
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.
org.cytoscape.command.util
Tunable classes useful for command applications
org.cytoscape.equations
Various types and utility methods relating to attribute equations.
org.cytoscape.event
This package contains the basic interfaces necessary for defining, firing, and listening for Cytoscape events.
org.cytoscape.filter
Provides interfaces for constructing and executing Transformers and Filters.
org.cytoscape.filter.model
Provides interfaces and classes for defining Transformers and Filters.
org.cytoscape.filter.predicates
General purpose predicates used to perform comparisons against numbers and strings.
org.cytoscape.filter.transformers
Provides interfaces for working with the Transformers provided by the core.
org.cytoscape.filter.view
Provides interfaces for contributing user interfaces for Transformers to Cytoscape.
org.cytoscape.group
This package provides an API for creating and managing groups in Cytoscape.
org.cytoscape.group.data
An api for configuring CyGroups.
org.cytoscape.group.events
This package contains the various events and listeners related to group management, creation, and destruction.
org.cytoscape.io
Handle import/export of Cytoscape data structures to/from local files/remote URLs.
org.cytoscape.io.datasource
API to provide data files as a bundle.
org.cytoscape.io.read
Handle importing Cytoscape data (network, attributes, session, properties, etc) from files/URLs.
org.cytoscape.io.util
A small number of utilities related to IO.
org.cytoscape.io.webservice
Interfaces for SOAP/REST web service clients, web services that return results as networks or tables, or query results.
org.cytoscape.io.webservice.client
Provides an abstract class for all web service clients, i.e.
org.cytoscape.io.webservice.events
This package defines events/listeners related to data query/import from web services.
org.cytoscape.io.webservice.swing
Web Service Clients with Swing GUI.
org.cytoscape.io.write
This package provides factory interfaces to be used by anyone wishing to provide export or writing capabilities to the rest of Cytoscape.
org.cytoscape.model
This package has the core interfaces of network and table data structures that are foundational to Cytoscape.
org.cytoscape.model.events
This package contains the event interfaces necessary for communicating with the classes in org.cytoscape.model.
org.cytoscape.model.subnetwork
This package contains rootnetwork and subnetwork extensions to the CyNetwork interface that provide a more complex meta-network data model.
org.cytoscape.property
This package provides a general property service interface for providing access to different types of property objects as OSGi services.
org.cytoscape.property.bookmark
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.
org.cytoscape.service.util
This package contains a simple utility for registering OSGi services without requiring use of the OSGi API.
org.cytoscape.session
This package contains the interfaces and classes necessary to capturing, storing, and retrieving the state of a Cytoscape session.
org.cytoscape.session.events
This package contains the interfaces and classes necessary to capturing, session change events.
org.cytoscape.task
This package provides base classes for common task factory types as well as their associated task types found in Cytoscape.
org.cytoscape.task.analyze  
org.cytoscape.task.create
This package provides a variety of task factory interfaces for creating new instances of network and other objects.
org.cytoscape.task.destroy
This package includes a set of task factory interfaces for deleting or or destroying objects within Cytoscape.
org.cytoscape.task.edit
This package include a set of task factory interfaces that allow the modification or editing of various objects within Cytoscape.
org.cytoscape.task.hide
This package includes a set of task factory interfaces showing and hiding nodes and edges within network views.
org.cytoscape.task.read
This package contains a set of task factory interfaces for reading various Cytoscape objects from files and URLs.
org.cytoscape.task.select
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.
org.cytoscape.task.visualize
This package include a set of task factory interfaces used to manipulate the visualizations of network views.
org.cytoscape.task.write
This package contains a set of task factory interfaces used for exporting or writing a variety of Cytoscape objects to files.
org.cytoscape.util.swing
This package contains misc helper classes for Cytoscape Desktop application.
org.cytoscape.view.layout
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.
org.cytoscape.view.model
Module for View Models and Visual Properties.
org.cytoscape.view.model.events
Definitions for View-Model related events and their listeners.
org.cytoscape.view.presentation
API set for rendering engines (visualizers).
org.cytoscape.view.presentation.annotations
This package provides support for graphical annotations associated with a Cytoscape CyNetworkView.
org.cytoscape.view.presentation.customgraphics
This package provides an API for augmenting a RenderingEngines node rendering with custom graphics.
org.cytoscape.view.presentation.events
Event implementations and listener interfaces for the Presentation layer.
org.cytoscape.view.presentation.property
Implementations of basic VisualProperty objects and VisualLexicons.
org.cytoscape.view.presentation.property.values
Interfaces for VisualPropertyValues -- ArrowShape, LineType and NodeShape
org.cytoscape.view.vizmap
Visual Mapping basic API module.
org.cytoscape.view.vizmap.events
Events for Visual Mappings.
org.cytoscape.view.vizmap.gui
This package provides access to GUI component of VizMap GUI, and interfaces of mapping related managers.
org.cytoscape.view.vizmap.gui.editor
Provides editors for Visual Properties and editor managers for VizMap GUI.
org.cytoscape.view.vizmap.gui.event
Provides events and listeners of LexiconState, visual style switch and vizMap event, as well as VizMap event handler manager.
org.cytoscape.view.vizmap.gui.util
Create discrete mapping for a given set of attribute values
org.cytoscape.view.vizmap.mappings
APIs for different mapping functions -- continuous mapping, discrete mapping and pass through mapping.
org.cytoscape.work
This package defines the task framework, where tasks are units of work.
org.cytoscape.work.swing
This packages provides Swing-specific specialisations of concepts from work-api This includes TaskFactory, TaskManager, and TaskIterator.
org.cytoscape.work.swing.undo
This packages provides Swing-specific extensions for undo support.
org.cytoscape.work.undo
Cytoscape's undo framework.
org.cytoscape.work.util
Various supporting classes for Cytoscape the work (Task) framework.
Cytoscape 3.1.0 API

Copyright 2011 Cytoscape Consortium. All rights reserved.