Cytoscape 2.6.2 (c) 2006,2007 ISB, MSKCC, UCSD

Package cytoscape

Core Cytoscape Classes.

See:
          Description

Interface Summary
CyNetwork CyNetwork is the primary class for algorithm writing.
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.


www.cytoscape.org