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Sounds like your coding got ahead of your design.
If you need to have Swing update the GUI while in a long running background task, use the SwingUtilities invoke... methods to call the Swing...

Look for some sample code here or on other forums that use Thread or SwingWorker. Or read the Java Tutorial.
Basically you create a Thread with a Runnable and put a call to your long running code...

GUI lockups are usually caused by having your code execute on Swing's Event Dispatcher Thread.
If you have a long task you want to run, you need to have it execute on its own thread and leave the...