interface windows w/ microcontroller??

I'm stumped on how to make this work. I need for a Java program to be able to talk to a microcontroller that will in turn move two motors. I would prefer to do this w/ USB but I'd settle for parallel port if need be.
The microcontroller is a Basic stamp that I can download PBasic code to run on it fine, but in order to hook it up w/ input while the stamp is running the code...I need to be able to feed it a high or low voltage to an IO pin right? I mean are there microcontrollers out there that can download code and take inputs via a USB cable? Any ideas on the matter would be greatly appreciated.
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