There will be several methods used to grade your projects. Your projects will be graded by running them on a number of test files with pre-generated correct (we hope) output. Your output will have all punctuation, blank lines, and non-newline whitespace stripped before diffing similarly cleaned files.
Some of your data structures may be included with the TAs own testing code to test their efficiency and correctness.
Some text output cannot always be graded by simply diffing because there is no guarantee that we will have the same output. In these cases your project's output will be pre-processed. In the case of the B+ tree, for instance, this program will verify that each node has the correct number of keys, that they are correctly ordered, and that all the correct data is at the leaves (and any other rules I may have left out).
Thanks to the miracle of automation you should expect your projects to be run on very very large inputs.