What's this?
============

It's a Newick tree parser:

   http://en.wikipedia.org/wiki/Newick_format

This code is based on the libnewicktree project:

   https://github.com/cjb/libnewicktree
   
which is in turn *entirely* taken from the TreeJuxtaposer project at:

   http://olduvai.sourceforge.net/tj/index.shtml

How can I use it?
================

You could do something like this:

    File treeFile = new File("my_newick_tree_file");
    Tree tree = TreeParser.readTree(treeFile);
    int tree_height = tree.getHeight();
    System.out.println("largest tree height is: " + tree_height);
    recursivePrint(tree, 0, 0);

    void recursivePrint (Tree tree, int currkey, int currdepth) {
        TreeNode currNode = tree.getNodeByKey(currkey);
        int numChildren = currNode.numberChildren();
        for (int i = 0; i < numChildren; i++) {
            int childkey = currNode.getChild(i).key;
            TreeNode childnode = tree.getNodeByKey(childkey);
            System.out.println("child name is: " + childnode.getName() + " depth is: " + currdepth);
            recursive_print(childkey, currdepth+1);
        }
    }