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Could anyone please suggest a Java or JavaScript library to layout a graph. The main requirement is that it should support graph layout algorithm taking into account a node size.

I myself found a list of Java libraries to work with graphs and already tried JUNG, but I wasn't been able to find any graph layout implementations for JUNG that would take into account a node size. As a result some nodes happen to be too close so they're overlapping.

P.S.: I think it should be pointed out that I only look for a library to layout the graph (i.e. determine its nodes positions). Calculated node positions will be then transfered from the server to a client requested the layout using http.
P.P.S.: a JavaScript library would be as good. I already tried arbor.js and it didn't work out for me because it doesn't take into account a node size.

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The nodes seems to be repelling. I didn't yet have time to check it out, but I'm certainly gonna give it a try.
Unfortunately there seems to be no way to extract node coordinates and specify nodes size. In this case they aren't overlapping only because of their repulsion.

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