If you are only interested in Java programs, you can use the following Java-specific APIs:

• Program Element Facts for Java AST – The Program Element Facts (PEFs) representing the Java AST.
• Java Query API – Selected analysis predicates for Java Program Element Facts.
• Java Transformation API – Selected transformation predicates for Java Program Element Facts.

However, we recommend to check whether the functionality you want can be implemented with the language-independent API. Using it wherever possible will reduce the amount of Java-specific code and will ease porting your analyses and transformations to other languages.