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.