Package cytoscape

Core Cytoscape Classes.

See:
Description

Interface Summary

CyNetwork	CyNetwork is the primary class for algorithm writing. All algorithms should take a CyNetwork as input, and do their best to only use the API of CyNetwork. Plugins that want to affect the display of a graph can look into using CyNetworkView as well. A CyNetwork can create Nodes or Edges. Any Nodes or Edges that wish to be added to a CyNetwork first need to be created in Cytoscape. The methods that are defined by CyNetwork mostly deal with data integration and flagging of nodes/edges. All methods that deal with graph traversal are part of the inherited API of the GraphPerspective class. Links to which can be found at the bottom of the methods list. In general, all methods are supported for working with Nodes/Edges as objects, and as indices.
CyNetworkData	This will be the interface where things like multi-dimensional data are accessed.
CyNetworkListener	Interface for listeners that respond to CyNetwork events.

Class Summary

CyEdge
CyMain	This is the main startup class for Cytoscape.
CyNetworkAdapter	Empty implementation of the CyNetworkListener interface, following the adapter pattern useful for defining anonymous inner classes.
CyNetworkEvent	Events of this class are fired from a CyNetwork object when something happens to the network.
CyNetworkTitleChange	Class used for passing along information about the network when the network title has changed (firing an event)
CyNode
CyStartupListener	Implementation of StartupListener interface in install4j API.
Cytoscape	This class, Cytoscape is the primary class in the API.
CytoscapeInit	Cytoscape Init is responsible for starting Cytoscape in a way that makes sense.
CytoscapeModifiedNetworkManager	CytoscapeModifiedNetworkManager manages the modified state settings for the networks and listens for PropertyChangeEvents.
CytoscapeVersion	CytoscapeVersion: identify (and describe) successive versions of cytoscape.

Package cytoscape Description

Core Cytoscape Classes.

Cytoscape is a software pacakge designed to enable the vizualization and analysis of networks. While commonly used for biological networks, it is designed to be able to accomodate any field which requires a junction between graph theory and associated data.

The Cytoscape API is designed to be easy to use, and intuitive. Which means that most method names are fairly boring, and follow Java standards, so there are a lot of get/set methods. More information on using the classes can be found at http://www.cytoscape.org/alpha.html .

In general, the most commonly used classes will be found in the cytoscape package. So:

import cytoscape.*;

will be sufficent for many of your classes. The class cytoscape.Cytoscape is where CyNodes and CyEdges are created. This is done via the getCyNode and getCyEdge methods. Note that Cytoscape does its best to not create duplicate nodes and edges. All of the nodes and edges are then accessable from Cytoscape. To actually do things like run algorithms a CyNetwork is required. The createNetwork series of methods will get you started in that directions.

Generally, working with CyNetworks is the preffered method of interacting with Cytoscape. CyNetwork contains many methods for easily writing Graph algoroithms, and for the smooth integration of data. More information can be found in the Developer documentation.