Creating API Reference

Is there an application that generates API reference from .java files? I'm working with an application that has many custom java classes, and their API reference is in the same format as that of the Java API reference. I was wondering if there was anything that can generate all of this automatically?

Do you mean something besides javadoc?
Javadoc will do all that you asked. You can added additional notes and information to the docs by inserting /**...*/ style comments just before the methods or classes you are documenting. If you don't insert any notes, javadoc will just document the method and parameters.
-Freeman

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