The Pi4J project "is intended to provide a friendly object-oriented I/O API and implementation libraries for Java Programmers to access the full I/O capabilities of the Raspberry Pi platform. This project abstracts the low-level native integration and interrupt monitoring to enable Java programmers to focus on implementing their application business logic." http://pi4j.com/index.html
Pi4J (by default) uses an abstract pin numbering scheme to help insulate software from hardware changes. (see Pin Numbering - Raspberry Pi 3 Model B http://pi4j.com/pins/model-3b-rev1.html)
Μπορείτε να αξιοποιήσετε και την ιστοσελίδα με τίτλο Programming the Pi with Eclipse and Java
http://eclipsesource.com/blogs/2014/05/01/programming-the-pi-with-eclipse-and-java/