<p>I have a project to build a voting desktop application for a class in Java. While security isn't the focus of the project, I would like to be as realistic as I can. What are some of the primary tools to integrate security into a Java application.</p>

<p>Edit: I'm not primarily worried about physical security, we are simply building an application not a whole system. I want to ensure votes are recorded correctly and not able to be changed or read by someone else.</p>

It really depends on what kind of security you are looking to integrate.  Do you want security to ensure that the user isn't running any debuggers or such to flip bits in your application to change the votes?  Do you want to ensure that the user doesn't install logging software to keep track of who voted for who?  Do you want to ensure that the person who is supposed to be voting is actually voting?  Security is a very broad subject, and it's hard to give an answer without knowing what exactly you are looking for.