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Packages |
| 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.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.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.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 contains the core interfaces that define the basic network and
table data types that constitute the foundation of 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.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.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 packages everything relating to tasks in Cytoscape. |
| 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. |