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Antialiasing has become much more difficult to implement with the programmable openGL pipeline in openGL 3. And as of now, no-one knows a really good solution to the problem. Therefore the jogl3 backend allows you to render at twice the resolution (4 times as many pixels) and scale down to your window. This gives quite good and correct anti-aliasing, however is 4 times as expensive for the fragment shader. Especially combined with rendering transparent objects or rendering with many lights this can become a performance problem. Therefore it is turned off by default.

Here's how to toggle anti-aliasing:

JRViewer vr;
Scene scene = vr.getPlugin(Scene.class);
scene.getRootAppearance().setAttribute(CommonAttributes.ANTIALIASING_ENABLED, false);
scene.getRootAppearance().setAttribute(CommonAttributes.ANTI_ALIASING_FACTOR, 2);