Programmatic Method of Handling Matlab Dialog Windows

I have a rather large Matlab program that is GUI based. I am looking into creating automated tests for it, as the current way of checking for bugs before a release is simply using all its functionality like a user would.

I would rather not use a GUI testing program that just records clicks and what not, so I was thinking of adding testing code that would call the button callbacks directly. The problem that I have run into with this is that we have a lot of warndlg and msgbox popups, and I would like my tester code to be able to see these.

Is there any way for Matlab code to tell if a function it called created a warndlg or msgbox? If so, is there any way to click 'ok' on these popups?

In a similar vein, is it possible to handle popups that block code execution (using uiwait or an inputdlg)?

If it matters I didn't use GUIDE, and all the GUI elements are created programmatically