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As far as my knowledge goes, I think it is not possible to call the function of a Java class (Java Applet) from Server Side Javascript. As you know the output of the Server Side JavaScript is computed on the server and is forwarded to the browser (the client). At the same time if you assume that there is an applet running on the client m/c downloaded from the server (your server where Server Side JavaScript is running) then these both the programs are running different domains. The applet running in total security of the web browser and other running on the server side. The job of the web server is to provide the class file whenever there is a call to the applet code from within the downloaded page on the client's m/c.
So these two different programs can't communicate. Client Side JavaScript can communicate with the applet variables and functions.