I think I understand what you are trying to do.
If you are in your final year, I would concentrate on your project, that is, use the most familiar tool to you to achieve a good final year project. If you try to learn a new skill such as java, you are introducing a new element of risk into your project, and you may find yourself in trouble towards the end of the year with a half built solution that may be rushed and not as good as it could be.
If you know what you need to do in Matlab, then I reckon that you should use that tool. At the end of the day you will be marked on the success of your project, not the coding tool that you have used to build it.
You can always pick up java afterwards in your own time without the burden of a project and its deadline.
Hope that this helps.