guidata handles + started using Matlab classes - why do I have to update (pass by value/reference?)

Hi all,

A LOT has been written about guidata and handles, but I couldn't find exactly the answer to my question. So I'm learning to use object-oriented programming in Matlab and I am making a GUI and in the end of the gui (I call it MainFigureWindow) OpeningFcn(hObject, eventdata, handles, varargin) I/we have:

handles.guiDataFile = 'someStuff.txt';
handles.utils = utilities(handles); % utilities is a class
handles.myMachineClass = myMachineClass( parameter1, parameter2, handles );
guidata(hObject,handles); % saving my "global variables"

Notice that I pass "handles" into the classes, so I always have access to my "global variable" (I'm sure you understand what I mean, although maybe technically it's not really a "global variable")... Then I have (simplified) my first class (utilities.m)-definition:

classdef utilities < handle % a handle class (pass by reference)
    properties
       ourHandles
    end
    methods % non-static, only for this particular GUI
      function obj = utilities(ourHndls) % constructor
          % pass by reference or pass by value? Seems like pass by value, how to get pass by reference?
          obj.ourHandles = ourHndls;
      end % constructor

And I have my second class-definition (i.e. "myMachineClass.m" in this simplified example):

classdef myMachineClass < handle % a handle class (pass by reference)
    % ==================================================
    properties % default public
        ourHandles
        MachNum % empty [] default value, use constructor
    end
    function obj = myMachineClass(ourHndls) % constructor
        % pass by reference or pass by value? Seems like pass by value, how to get pass by reference?
        obj.ourHandles = ourHndls;
    end % constructor

I use "handles.myUtilityFunctions = utilities(handles);" and "handles.myMachineClass = myMachineClass( parameter1, parameter2, handles );" so I should have access to all data everywhere...

In the GUI I have 3 checkboxes. The user must confirm some output and after the 3 checkboxes are all checked, the program continues to the next stage. Each checkbox callback function (in the main GUI-file) is like (num1_Ok_checkbox_Callback, num2_Ok_checkbox_Callback and num3_Ok_checkbox_Callback are the same, I don't want to show all - I'm just calling the utility function to check the "Value" of all 3 checkboxes):

function num1_Ok_checkbox_Callback(hObject, eventdata, handles)
handles.utils.checkAllcheckboxes()

Now we're leaving the main GUI ".m"-file and going into the utility ".m"-file (namely the "checkAllcheckboxes"-function):

          function checkUVWcheckboxes(obj)
              if obj.ourHandles.num1_Ok_checkbox.Value & ...
                      obj.ourHandles.num2_Ok_checkbox.Value & ...
                      obj.ourHandles.num3_Ok_checkbox.Value
                  obj.ourHandles.some_confirmed_text.String = "OK, confirmed!"
                  obj.updateListboxes();
              else
                  obj.ourHandles.some_confirmed_text.String = "You did not confirm yet"
              end

The program works pretty ok, so far. But now I want to update a listbox so I'm checking the "obj.ourHandles" - which in my opinion SHOULD correspond 100% to the "handles"-variable in the "main .m GUI"-file. But it doesn't... It seems like the obj.ourHandles-object contains references to almost everything, including "handles.guiDataFile", i.e. remember from my OpeningFcn:

    handles.guiDataFile = 'someStuff.txt';
    handles.utils = utilities(handles); % utilities is a class
    handles.myMachineClass = myMachineClass( parameter1, parameter2, handles );

I cannot see the "handles.utils" nor "handles.myMachineClass", which I think is weird - because when I can see "handles.guiDataFile" it means the "guidata(hObject,handles)" worked - but not fully, i.e. at least to some degree... This behaviour, I don't understand... However, after reading a lot - searching in the forums, I discovered this temporary "solution":

    readSavedVars = guidata(obj.ourHandles.MainFigureWindow);

Now I can type "readSavedVars.utils" and "readSavedVars.myMachineClass" and suddenly I have access again to the two new class-objects I've made and want access to... It is a solution, but I would prefer not having to use "readSavedVars = guidata(obj.ourHandles.MainFigureWindow);" to access the original "handles"-data.

My question is: Why is it that I have to use "readSavedVars = guidata(...)" when I've saved obj.ourHandles which should contain the same data as "handles"? Is it something about pass-by-value / pass-by-reference? In that case, I wish to have my class constructors save the "handles"-variable (to ourHandles) as a pass-by-reference, how would I accomplish this?

I hope someone can help me understand this better and I hope you think I've explained this properly with this minimal example, thanks!