#331 Adding the unfinished paths to root vis in D3. Have a lot done, but the D3 stuff for populating in stages needs revision; it was never needed for the ontology view, so it was never testable really. I will sort it out, but I need to save the code. Only changing the new paths to root file, but the ontology one should be updated later; then everything refactored?
#331 Confused about adding new edges and nodes. Found soemthing online, but might require big changes, so I am committing this as a checkpoint.
#331 Sorted out graph updates, for the most part. I knew how to update properties, but not population fo the graph. A stackoverflow answer had the grand secret, of always using the arrays pulled out of the graph object, since arrays passed in or otherwise created clobber vital properties. Boo D3, thanks stack overflow.
#331 Have more progress. Remaining work is highly visible when run.
#331 Fixed edge layout misbehavior. Did not get help from the documentation or examples unfortunately. Fixed some other issues as well. More to do.
#331 Put edges below nodes. Fixed edge endpoints to be in center of rectangles. May have to adjust those yet again or make conditional when I refactor the ontology and concept graphs together.
Merge branch 'master' into issue331_d3_paths_to_root
#331 Have term neighborhood working fairly well. Re-organized initialization code to accoutn for new drop down menu for different viz options. Still need to make mappings neighborhood, and when I swap between path to root and term neighbourhood, it breaks badly.
#331 Cleaned up a lot of comments, and crufty unhelpful commented out code.
#331 Re-arranged order of some functions to make overall program easier to navigate. This will make it harder when combining and refactoring with the ontology view, but I can reorganize that view in a similar fashion prior to refactoring, to make it easier. It also breaks our history a bit.
#331 Fixed mode selection problem by reinitializing more. Reorganzied some more functions.
#330 Test commit
Added menu icon
Added two buttons to layout menu
Added circle layout function
#330 Added smooth transaction to circle layout
#330 Added transaction back to force-directed layout
#330 Adjusted layout menu, changed force parameters, and fixed node posittion when transitioning back to force layout
#330 Fixed central node layout
Google AppEngine changes required absolutely no Java 6 code in the uploaded package. Luckily, we only had a few unused server side libraries that I was able to remove. I updated  the app engine jars as well, and cleaned up the config.