I\'m not sure if this is possible, especially since Java runs through a VM, but can I call gnuplot from within Java? Perhaps I could have Java open a terminal and input
You can launch any external application using the "exec" commands.
http://java.sun.com/javase/6/docs/api/java/lang/Runtime.html
See this page for a few examples. http://www.rgagnon.com/javadetails/java-0014.html
EDIT: I forgot about ProcessBuilder. Michael Borgwardt's answer is a more robust solution.