Best methodology for daemon testing?

One of our teams has a suite of functional tests (I don't believe they're specifically coded as JUnits).  The test methodology is:

1. Build their Java application A
2. Start application A (I'm not sure offhand if it runs in a Tomcat container, or if it just runs as a java -jar executable).  A opens a listening socket.
3. Send a test input deck through A via the socket and analyze/verify the results.

What we would like to do is obtain IDEA coverage statistics from A as it executes the test deck.  Assuming that A can be started as a result of an Ant script that is being executed as part of a Teamcity build configuration, what steps do we need to take in order to get the coverage analyzer to perform its magic?