Java has built in support for most .wav/.aiff files using the javax.sound.* classes:
import javax.sound.sampled.AudioFormat;
import javax.sound.sampled.AudioInputStream;
import javax.sound.sampled.AudioSystem;
You can see how I read in sample data from a file here:
Around line 801, I start to convert the stream to bytes, etc.
One thing the built in Java libraries don't have, is support for reading in special "chunks" of a .wav file.
I created a library called riff-wav-for-java that parses .wav files. If you look at line 862 of that link I posted, you'll see how I grab loop points from files. You could probably use that library to grab byte data, but I didn't really make a friendly API for that (kind of abandoned it since I only needed it for loop points).
Anyways, there's also the "Java Media Framework (JMF)", which is apparently the successor to the Java Sound libraries, but I don't have any experience with it.
You can also check Stack Overflow for what other people are doing. I don't have a ton of experience messing with audio in Java (as I've only really used audio in Java for this project).
Good luck! Sounds like an interesting project you have planned.