Add more JUnit test cases to improve overall coverage

[gkapfham]

There are currently only a few test cases for either the examples or the main system. We should add test cases in order to increase the coverage of the examples and the main tool. In accomplishing this task, we should also think about using automated test data generation tools that help to increase code coverage. Finally, it is important to make sure that the test cases are all integrated into the tool's build system.