Just store the vector locations of the boxes, the 2d line will have the start lie within the question and the end within an answer (if not it's not valid)
validating point lies in a box:
endpoint (vector) > x1 & endpoint (vector) > y1
&
endpoint < x2 & endpoint < y2
rinse, repeat (there may already be this sort of thing, C# has intersect for rectangles for instance)
View model, linked list of questions & answers, kvp array linking pointers for questions and answers? Pretty simple model (containing the objects)
It's not really suited to MVC as there will likely be binding from the view and controller, so MVVM seems more suited (I think iOS is more MVVM in it's MVC implementation though as MVC should be stateless)
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