The above picture was the old version (not good). Below is the "new" version (much better because the black bars are removed). The "upstream" and "downstream" calculations are performed by taking the starting node and walking along the circle in increments of 0.02 * PI degrees (i.e. 100 points on the circle). If any part is smaller than that (hope not), it might get skipped. The AutoGeneRegulatoryTool now has two functions -- allPartsLinear and allPartsCircular -- one is used for linear arrangement of parts and the other for circular.
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