Have started using JgraphT on my latest project and am excited to report that I really like it. It allows me to build directed (and undirected) graphs of my own class instances without changing my code. Plus it includes algorithms for shortest path and transitive closures, as well as breadth and depth first iterators. And the gravy on top is its support for writing DOT files which can be imported into OmniGraffle. Brilliant...
Java Object Graphs
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