You need to do some socket programming. How do you know file types, sizes, whatever else? Depends what protocol you choose to implement. If your iOS device only needs to send data, probably the quickest win would be to use an HTTP client to upload stuff to a Java-based server.
Have a look at this Apple guide for making basic HTTP requests or check out a third-party library like ASI. YMMV.
If all you need in the Java app is a minimal upload handler, check out Netty. You can get a simple server going with very little effort.
HTTP's just a suggestion, although the quantity of good client & server libraries makes it a reasonable choice unless you have a special requirement it can't satisfy. If you want to roll your own protocol to push files back & forth, that's cool too. You'll need to familiarize yourself with socket programming on the respective platforms though.