Java and Serial Port
There are com-port libraries available for java.
RXTX seems to be one of the most prominent.
Here is a long discussion about how to use RXTX and an alternative, called JavaComm.
Here is a question on StackExchange asking essentially exactly what you are asking.

Note: I'm assuming you want to write a java application to do what you describe (otherwise, why would the application being java-based be relevant?)
If not, please update your question.

Edit:
If you're in control of the USB-serial converter, you could use the jD2XX library, which wraps the FTDI D2XX driver API.
This is an excellent API, but it will only work with FTDI usb-serial converters.