A brief summary of day 1:
I'm currently focusing on crating the tree classes. getTree and storeTree are the two I'm working on now. Currently I'm relying on the forester package for my parsers. This package is part of the biojava library. I'm currently implementing newick, nexus and phyloxml parsers. More will come as time permits, but these three are the priority right now.
storeTree, as the name suggests, is the class that defines how a tree object is stored in the library. It mainly defines a tree objects and holds information such as parent-child relationships, number of nodes, branch lengths and leafs.
getTree deals with the parsers and outlines functions that call the appropriate parser. It will probably end up interacting heavily with storeTree.