Calling OS-native code from Java is a little bit difficult. Depending on your way of thought this might be good or bad. You might consider this good, because Java apps are supposed to run on many different platforms. So the more difficult calling OS-native code, the less platform-dependent apps are written.
Anyways. The low-level method of calling OS-native code from Java apps is JNI. It is difficult. You have to write native code (most probably in C/C++) to be able to call OS-native code.
There are APIs available that make it easier to call OS-native code. One instance is JNIWrapper by TeamDev ( www.jniwrapper.com/pages/jniwrapper/overview). You might also want to consider using ComfyJ ( ( http://www.jniwrapper.com/pages/comfyj/overview). Open source alternatives are also available but I can't remember them right now.