Good Java graph algorithm library?

If you were using JGraph, you should give a try to JGraphT which is designed for algorithms. One of its features is visualization using the JGraph library. It's still developed, but pretty stable. I analyzed the complexity of JGraphT algorithms some time ago. Some of them aren't the quickest, but if you're going to implement them on your own and need to display your graph, then it might be the best choice. I really liked using its API, when I quickly had to write an app that was working on graph and displaying it later.

Summary:

• JGraphT if you are more interested in data structures and algorithms.
• JGraph if your primary focus is visualization.
• Jung, yWorks, and BFG are other things people tried using.
• Prefuse is a no no since one has to rewrite most of it.
• Google Guava if you need good datastructures only.
• Apache Commons Graph. Currently dormant, but provides implementations for many algorithms. See https://issues.apache.org/jira/browse/SANDBOX-458 for a list of implemented algorithms, also compared with Jung, GraphT, Prefuse, jBPT

Check out JGraphT for a very simple and powerful Java graph library that is pretty well done and, to allay any confusion, is different than JGraph. Some sample code:

UndirectedGraph<String, DefaultEdge> g =
        new SimpleGraph<String, DefaultEdge>(DefaultEdge.class);

    String v1 = "v1";
    String v2 = "v2";
    String v3 = "v3";
    String v4 = "v4";

    // add the vertices
    g.addVertex(v1);
    g.addVertex(v2);
    g.addVertex(v3);
    g.addVertex(v4);

    // add edges to create a circuit
    g.addEdge(v1, v2);
    g.addEdge(v2, v3);
    g.addEdge(v3, v4);
    g.addEdge(v4, v1);

JUNG is a good option for visualisation, and also has a fairly good set of available graph algorithms, including several different mechanisms for random graph creation, rewiring, etc. I've also found it to be generally fairly easy to extend and adapt where necessary.

In a university project I toyed around with yFiles by yWorks and found it had pretty good API.

JDSL (Data Structures Library in Java) should be good enough if you're into graph algorithms - http://www.cs.brown.edu/cgc/jdsl/

For visualization our group had some success with prefuse. We extended it to handle architectural floorplates and bubble diagraming, and it didn't complain too much. They have a new Flex toolkit out too called Flare that uses a very similar API.

UPDATE: I'd have to agree with the comment, we ended up writing a lot of custom functionality/working around prefuse limitations. I can't say that starting from scratch would have been better though as we were able to demonstrate progress from day 1 by using prefuse. On the other hand if we were doing a second implementation of the same stuff, I might skip prefuse since we'd understand the requirements a lot better.

Try Annas its an open source graph package which is easy to get to grips with

http://annas.googlecode.com

I don't know if I'd call it production-ready, but there's jGABL.

If you are actually looking for Charting libraries and not for Node/Edge Graph libraries I would suggest splurging on Big Faceless Graph library (BFG). It's way easier to use than JFreeChart, looks nicer, runs faster, has more output options, really no comparison.