In short, there's not much in the base java API to support DSP that I'm aware of. Also of consideration is how the data is being inputted, such as, as a file, a stream, an array, or some other format. If you're interacting with the hardware directly, you'll need special drivers so I'd investigate the hardware and see if the API that connects to the hardware provides any of these features.
Most of the basic DSP algorithms are simple to implement (*assuming you use one of the well-known fast algorithms*) even if you don't understand them such as the FFT. Although it does require some optimization. For example, you wouldn't want to compute the same FFT matrix hundreds or dozens of times.
I once wrote a paper on the FFT (shameless plug) that may give you some guidence although you'll want to skip the later sections of the proof of Fourier Analysis:
There are many 3rd party packages that perform DSP calculations, although since I can't suggest one in particular I would just search google for them and see which one appeals to you most. [ November 07, 2005: Message edited by: Scott Selikoff ]