ah, the dreaded PortInUseException...
you don't want to see it, but often when working with Serial in Java/Processing, you do.
two tips for getting around it.
the first tip:
http://www.arduino.cc/cgi-bin/yabb2/YaBB.pl?num=1262317780
basically --
make a new folder in the root/var folder called 'lock', with super-user privileges (sudo),
set permissions on that folder to read/write for the current user.
apparently the PortInUseException stems from the RXTX lib trying to write a serial lock file to that folder and failing. the above clears it up.
however, sometimes trying to run an application using Serial on system startup sporadically tosses a PortInUseException.
i'm not sure what causes this, but you can work around it with the second tip:
https://forum.processing.org/topic/recover-from-portinuseexception
note, this also allows, for example, the ability to have one program connected to the serial port, have another launch and fail to connect, the first closes, and the second automatically picks up the serial port as soon as it's made available by the closure of the first.