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Acyclic edges for same node are drawn on one another. AT5G35750 in TAIR is good example of this. They need to be separated out.
Have a removeDuplicates() function in SticksRenderer that is currently disabled, but does generate acyclic edges of different sizes. However the current issue causing probems is that the visibility of a second acyclic edge is not shown - even though EdgeView objects seem to be correct. Somewhere in JMOL/Jnet lies the problem. The search for the visibility fix is ongoing.