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I'd take a look at how Micro Manager does it. This is a software package written in java for use with microscopes, and many of the common microscope automation systems rely on RS-232 communication. I don't know for sure if the java layer has direct access to the serial port, but you can read up on it here: http://valelab.ucsf.edu/~MM/MMwiki/index.php/Micro-Manager_Programming_Guide