[OBO-Edit Working Group] OBO-Edit release 2-b41

[Nomi H. <nlh...@gm...>]

This release is not very different from b40, but I wanted to make sure  
everyone had access to the very latest version before our WEEK OF  
TESTING AND DOCUMENTATION begins on Monday, June 30.  You can enter  
your testing/documenting plans on the wiki page, http://wiki.geneontology.org/index.php/OBO-Edit:_Documentation_Week

You can download b41 from https://sourceforge.net/project/showfiles.php?group_id=36855&package_id=148487

	Nomi

Changes in 2.000-b41:
- Got links in Graph Editor to look a bit better.  The dotted line is
less dotty and the arrows on the links are easier to see (particularly
the vertical and near-vertical ones).  It's not perfect yet, but I
think it's somewhat better.
- Background of Ontology Tree Editor turns pale gray when you're in  
local
selection mode (like in OE1).
- Improved Graph Editor rendering time by decreasing number of  
iterations it
goes through while calculating the layout.  It originally did 10 double
passes.  1 seems to work almost as well as 10 (and of course it's much
quicker).  Simple graphs come out almost exactly the same.  Huge hairy  
ones
are huge and hairy whether you do 1 iteration or 20.
- If you're running a script in batch mode (e.g. OBO2OBO0) and you  
have config
files in the old config directory (~/.oboeditbeta), you were getting a  
popup
dialog asking if you wanted your config files copied to the new config
directory, which you don't want in batch mode.  Now it checks to see  
if you're
in batch mode before popping up that dialog (and the default is that all
applications ARE batch mode unless, like OBO-Edit, they specify  
otherwise
using Preferences.setBatchMode(false)).
- Jen modified the Graphviz Viewer so that it no longer displays  
disjoint
relationships. This is a good thing because they were getting in the  
way of
having a clearly displayed graph. Display of disjoint relationships is  
not yet
optional but it could be fairly easily if people wanted that.