The simplest answer is: don't worry about it. Make sure you choose the "Full" installer on the download page, which doesn't require you to have Java already.

If you are using Omniscope Online, or the "Light" download, you'll need Java 5 or better; we recommend using the latest version from http://www.java.com.

And if you have Vista and aren't using the "Full" installation, make sure you have Java 6u3 (1.6.0_03) or later.