Recently I've found that all of my scene objects are in left-handed coordinates, but Java 3D uses right-hand coordinates. There is a solution: flipping the scene Z-axis and reverting the triangles winding order. But this will be a horrible mess. It seems that if I can somehow flip the view horizontally it will do the job needed. How can I achieve this? Applying Transform3D somewhere, some kind of offscreen rendering or...?
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You can try changing the view by rotating it on the Z axis by 180 degrees. This is assuming your using a SimpleUniverse.