TouchGraph provides a set of interfaces for graph visualization using force-based layout and focus+context techniques. For now only older code is available, but we are planning to release new versions as well. indirect dep of biojava ( thru jgrapht ) ebuild coming.
I had already done an ebuild but not committed it yet. It is now at... http://overlays.gentoo.org/svn/proj/java/java-overlay/dev-java/touchgraph-graphlayout/touchgraph-graphlayout-1.22.ebuild
In gentoo-x86.