See here for how to use JSDuck with Java code:

Unfortunately, as mentioned in that thread, you need to add extra annotations to your java classes:

There is no ant task for it at the moment so if you want to include it in your build you need to use the exec task.

A nice enhancement would be for JSDuck to recognise Java classes to do away with the need for extra annotations.
Alternatively, a script to annotate all your existing targets might be a work around.

Another option could be to roll it into an ant task and get the ant task to add the annotations.
It would probably need to be optional to either modify the actual source or just modify a copy of the source and run JSDuck on the copy.

Anyone fancy stepping up to make the ant task?