Apache Commons Math Transform library.

Does anybody have any experience working with this library? I'm trying to use the Fast Fourier Transform class on an audio sequence, so I can get the frequencies, but I have no idea where to begin... I've successfully loaded an audio file with AudioInputStream, but I really have no idea how to go about using this with the FFT.

What I want to eventually do is compare two songs to see if they're similar, and I know I need to get the FFTs in order to do this, so I was wondering if anyone could help explain what's going on (with the FFT), how I go about doing this, or just pointing me in the way of a tutorial or examples. The Apache Commons Math Transform documentation isn't much of a help to me... I kind of need examples to go off of.