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You could use ROS messages as the abstraction enabler. If your non-java code is already a ROS node, just create pub/sub or service messages to exchange the data. If it's not already a ROS node, wrap it in code that makes it a ROS node (which is good design for non-trivial code anyway). In effect, the messages then define your API.
I did this for a java/c++ project; rosjava integrated with/into an external project, c++ for robot control on my end. ROS communication worked without a hitch, as expected.