Personally I dislike GUIDE, especially for anything more complex than an axes and two buttons. The differences between AppDesigner and a programmatic GUI are mainly that one is class based and the other is function based. See below for my guide to avoid GUIDE.
One thing to keep in mind is that the I stands for interface. That means the meat of your program is the program itself. The GUI is just to allow a user to run your program. So things like saving mat files is not a difference for any of the three options.
One closing note: situations that require global variables are extremely rare.
My small guide to avoid GUIDE:
- Make a figure (with f=figure;) and look into the doc for figure which properties you want to turn off (you probably want to set Menu and Toolbar to 'none')
- Create buttons and axes and everything you need with functions like uicontrol and axes. Save the handles to each element to fields of a struct (like handles.mybutton=uicontrol(___);)
- When you've finished loading all data (and saving it to fields of your handles struct), and creating all the buttons, save your handles struct to the guidata of your figure like this guidata(handles.f,handles);. (You can also use getappdata and setappdata)
- You can set the Callback property of many objects. If you do, use a function name with an @ in front, or a char array that can be evaluated to valid code. (like @MyFunction or 'disp(''you pushed the button'')')
- Callback functions will be called with two arguments: the first is a handle to the callback object, the second is eventdata that may contain special information. To get access to your data, just use handles=guidata(gcbo);. You can replace the gcbo function with the name of the first input to your callback function if you prefer.
- More information about callbacks can be found in multiple places in the doc, for example here.
