Matlab Arduino GUI Interface

I am building an a GUI to interface between matlab and arduino. This will have a few different commands.

One button with turn on power to a couple digital inputs and monitor them. Another button will take in a couple sets of data and store them into an array and then graph them. Another object will monitor a senor and alarm the user that the monitor has been interrupted.

Now when working with an MATlab GUI it calls each part individually what I am wondering is with each button press does it change the sketch of the arduino program. Because I need the monitor to be continually monitoring the system?

Does this make sense?

So you are communicating via serial over USB? Where are the buttons? Where are things being displayed?

I am communicating through serial. The buttons are all in the MATLab GUI.

What do you mean by change the sketch?