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 

The program needs to interact with the League of Legends client. (not ingame, just the client). I want to be able to click around in the League of Legends client without java taking over control of my mouse.