Java 7 and biofabric

[bifx...@gmail.com]

Hello,

I am working on Mac OS 10.8 and noticed that since  the Java7 upgrade, the select rectangle and zoom somehow ceased to work. I have a small network of 2,000 nodes and less than 15,000 edges.
I tested on my own downloaded copy of BioFabric and the 2 online versions (low/high memory) via  java webstart.

Has anybody else experienced the same issue?

thanks,

Isabelle

[Bill Longabaugh]

I have to admit that the select rectangle function has always seemed to be a little "picky" on the Mac, regardless of the Java version. I think there might be a bug in there somewhere that I need to track down. One thing I find is that it seems to have problems selecting rectangles in the upper left corner of the network.

That being said, I have not tried it using Java7, which is different from all previous Mac Java implementations in that it comes from Oracle, not from Apple. So there are quite a few cases of differences between the two that people run into, though this is the first I have heard about for BioFabric. Does the rectangle not draw, or does the procedure exit just after drawing only the first point but not the second? What happens if you try to do the rectangle zoom after you have already zoomed in a ways using the Zoom In button?

One thing that may help is to try using an _extremely_ steady hand when doing the two clicks to define the rectangle, as that seems to help with rectangle weirdness on Java 5 and 6. Wiggling the mouse during a click makes it not register as a click. Failing that, you can also use command-mouse drag to move around in the network, and Control-1 will max-zoom to the point under the mouse. You may also specify from the Java Preferences utility in Applications::Utilities which Java you want to use (at least you used to be able to do that), and maybe be able to get back to Java 6.

If I can manage to track down a Mac running 10.8 and try out the Oracle Java7 upgrade, I will see what I can find.

Sorry for the inconvenience.

Bill

[bifx...@gmail.com]

Hi Bill!
this is a minor issue, no worries. I just noticed this while preparing the page to present the interactive network as a suppl material for our paper.

So, sometimes the rectangle does not draw, sometimes it does, but instead of zooming, it just greys out the rest of the network and highlights an arbitrary number of nodes  to the right of the selected region (that is larger than the rectangle selection). I see no change in behaviour after zooming in using the Zoom button.
On my Mac the Java Preferences seem to have vanished from the Applications::Utilities and the System preferences seem to configure applet settings with the runtime location set by default to http://java.sun.com/products/autodl/j2se version 1.7.0_25.

I don't think the zoom is essential since the bottom left-hand window already provides that functionality. I'll check again at the next Java update...

cheers,
Isabelle

[William Longabaugh]

Isabelle:

The behavior you are describing is for the rubber-box drag selection,
which highlights nodes and grays out the rest of the network. It's what
happens when you drag a box out when the boxed zoom has not been
activated. The implication is that the boxed zoom function is exiting
before the box drawing is done. I'll try to take a look when I get the
chance to get to a 10.8 Mac.

Thanks for the bug report.

Bill

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