As you are probably aware, lots of people, including the writers at Naked Security, are advising you to turn off Java in your browser for security reasons.
So, let me clarify.
They're configured separately.
Apologies if you already know this. But the names are a bit confusing.
I'll keep this article short and simple by not going into too much detail about the differences here.
On the other hand, Java, made by Oracle, is a software package installed separately from your browser.
It can be used for creating and running all sorts of regular-style software: web servers, code editors, word processors and much more. These are called applications, just like any other application such as Microsoft Word or Apple iMovie.
In fact, you probably won't miss much without applet support. Lots of Facebook users, for example, report being able to use their favourite addons such as games without Java.
Nevertheless, there have been several recent and widely-abused bugs in the applet part of Java that make your browser insecure.
So we are recommending that you turn off Java in your browser.
And that's it.
But let me reiterate: we aren't recommending that. And if you do, you won't get rid of Java, which is probably what you want.
In case you're wondering, Java was originally called Oak, after a tree outside the inventor's office. It was renamed Java after the island, because lots of coffee comes from there, and programmers run on coffee.