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I've been Googling this for about an hour with no luck. I have absolutely no idea where to start. What I need is to find the coordinates of a specific window (one that is NOT part of the Java program) and be able to assign them to a integer. Right now I don't think it's possible, but if anyone knows how, I would much appreciate it if you could explain it.
Java programs don't have access to external processes (except for streams from processes created by your java program). The only solution here is JNI (or JNA. Though I've personally never used this, it's suppose to make linking Java and native code easier).
If you had access to the other program's source code you could get that program to open a socket which you could use to communicate between your Java program and the other program.