I've got the openTree functions working in the getTree class. openTree takes in a tree file and returns an array of phylogeny objects. These objects can be accessed by storeTree.
The csv parsers seem to be working as well. I'm thinking about replacing these with parsers from the GeoTools library. There's tons of stuff there, so I'll need to spend time picking out what I need for phyloGeoRef.
A side note, I'm having some problems with git and github so if you're watching the repo I wouldn't rely on anything that shows up there until I give the OK on this blog.
UPDATE: everything in the github repo should be good to go now :-)