The Firmata Arduino library has an example called SimpleDigitalFirmata which implements the callbacks to listen for commands from the computer, then sets the digital pins correspondingly.
It also appears to send the input state of the digital pins back to the computer, but I've tried fiddling with this and it doesn't behave as I'd expect, so this will need more looking into.
I think we certainly have the beginnings of what could become a Firmata API in Java. The existing code could do with a clean up though! 
It's worth noting, the Firmata library doesnt provide any methods for communicating values or strings, so these would have to be implemented using the sysex commands. If all you need is the ability to pass strings back and forth, then Firmata might be overkill.