The current project I\'m working on requires me to write a tool which runs functional tests on a web application, and outputs method coverage data, recording which test case
Have you looked at existing coverage tools (Cobertura, Clover, Emma, ...). I'm not sure if one of them is able to link the coverage data to test cases, but at least with Cobertura, which is open-source, you might be able to do the following:
If you need a merged report, I guess it shouldn't be too hard to generate it from the set of saved files, using the cobertura API.