If you need to parse existing source code, use JavaParser. It gives you visitor-based access to the AST. You can write new code, but many things are a pain (e.g. referencing other classes)
If you need to generate source code use CodeModel. It lets you programmatically create classes, packages, methods etc, and it's very easy to use. However, I don't think it can import existing code.
Both are pretty awesome in their respective domains.
