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You could handle the presentation aspects with a combination of FXML and controllers etc., or you could code the UI entirely in Java code using a kind of builder pattern described in the PragmaticCoding article I linked above. Another alternative is to use a framework like Afterburner.fx which uses it's own "convention over configuration" approach to building and structuring your presentation code.
Unfortunately I'd like to say I have implemented them in my MaterialFX library but I still haven't done it Definitely on the ROADMAP though
Actually, there is Have you ever wondered why JavaFX controls are made in Java code and not FXML, even custom ones (like this here from Gluon)