Keep in mind that Adobe Air is an environment. Even if you would be able to make your app communicate from Java to Adobe Air, it would still require the Adobe runtime to work. If you want to reuse the same codebase for Adobe Air and Java, I would take a look at http://haxe.org/
Haxe is very similar to ActionScript, you should be able to quickly port your library code from AS3 to Haxe. It will then allow you to compile .swc and .jar libraries from it so you can reuse your library in Air and Java.