Hi Padma
Its possible to integrate a java application running in the other server with enterprise portal.In portal i think there is a IView template call Java application template.Using this generally we can do this.But in you case what type of a java application is it?Just a class or webapplication or a server side application.This you can also acheive using a webdynpro applications as these are very flexible with integration into EP.In webdynpro you can use suspend and resume plugs to navigate from one application to other application.I have given my ideas how to implement.But integration mainly depends upon your landscape and version compatibilities and type of the application you need to integrate.
Hope this answer helps you in implementation.
Regards
Kalyan
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