How to interact with an application using java without taking control of the mouse?

I am currently making a program in java that does some simple automation to make my life easier. The problem is that the bot takes over my mouse. (I am using Robot). I want the bot to be able to click and do stuff in the background so I can still use my mouse while the bot is running. I want to be able to run the application in it's own window through java sort of how RSBOT does it. Please help