How to implement simple graphics editor for custom file types?

I would like to implement simple graph editor with my own file type. It can be either binary or text (not decided yet, probably YAML), but it's text representation will not be visible. User will be allowed to manipulate graph primitives on screen, then save it to file.

I have already implemented simple file type, which draws something hardcoded. 

Now, how to implement something like MVC?

What should I imlement/override first? Document? VirtualFile? FileDocumentManager?

Please mention just a sketch....