The best way to get started with Structure101 for Java and Restructure101 for Java is to just download and point it at your code. Your best friends here are the Evaluator's Guide, our online demos, and the product documentation.
It is important to note that they are based on a JSE (single VM) view of the world. If your start point is more JEE (lots of lovely ears and wars, etc.), see this description of some of the issues and differences.
Structure101 for Java and Restructure101 for Java parse byte code, not source. The correlation between source code and byte code is extremely close, but there are a couple of places where you might want to be aware of the distinctions.
I was using IDEA and Eclipse to analyze the dependencies in my code. However, I now use Structure101 because it has way more in this area, all wrapped in an easy-to-use and understand interface.
Igor Spasic
Lead, Jodd Open Source Utility Library
Overall, we trust you will find Structure101 for Java and Restructure101 for Java: