How can I display file in a special tool?

My task is to display a 3D protein structure in a special tool. How can I use Java application to pass the structure file to the tool?
Thanks

If you know the path to the tool, I have some code at artcomputer.se/java. Look for the ProcessTracker.
The main point is that you need to track both the output and error streams, ot the tool might be blocked.

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