Add HierarchicalGraphView

[trajar]

The hierarchical graph api was removed in Geph 0.9.x, but represented a valuable api not widely available in other open source graph libraries. This implementation incorporates the hierarchical classes by abstracting the graph view, rather than core graph, and allows the UI to determine which nodes are collapsed/expanded (and therefore visible) for layouts and interaction. The core graph api remains unchanged.

[trajar]

Please let me know if you have any questions or issues with the proposed changes. The unit tests represent a good example of how to use the hierarchical view.

[eduramiba]

Hi, thanks for the pull request, we need to review it.

[trajar]

What is the status of Gephi and thoughts on this PR? 0.9.0 was released over a year ago.

[eduramiba]

@trajar Hi, this pull request is quite big and it needs a deep code and tests review plus a performance comparison with current graphstore, so it can take a lot of time.

For performance benchmarks, the current code (https://github.com/gephi/graphstore/tree/master/store-benchmark) is not compiling at the moment. It would be very helpful to have them fixed first.

[trajar]

@eduramiba Good to know, didn't realize the benchmarks were failing or otherwise blocking a review. Looks like beyond the compile issues, there were issues with string vs. integer node and edge id model types that may have been due to previous changes/default with the Configuration api. I've made the changes and code is committed -- all appears to be compiling and running successfully.

As for the commit and impact to core performance, I don't anticipate it to be too impactful as the hierarchical API was added as an extended view and leaves much of the core graph non-view api intact. Admittedly, the most disruptive changes are consolidated common view logic in #AbstractGraphView and then subclassing out the specific impl and hierarchical implementations. Let me know if you have any questions.

[eduramiba]

Thanks a lot for fixing the benchmark tests! That will be very useful for reviewing this pull request and future changes :)

[penyuan]

Thanks to all the developers behind Gephi, what a great program!

Sorry if I am being a pain with this comment, but I make heavy use of hierarchical topologies in my graphs and can't use Gephi effectively without that function. In fact, I often have to resort to yEd (which is sadly closed source and not-preferable) just to view my graphs hierarchically.

I read this thread and other issues (#1100 and #128), but I see that "All checks have passed" for this patch, is there an update on if and when it will be merged? Sorry I'm not a Java programmer, but would be happy to help do some testing if it can be merged!