Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with
or
.
Download ZIP
A standalone Newick tree reader in Java
Java Perl Shell
Branch: master

README

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

It's a Newick tree parser:

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

This code is *entirely* taken from the TreeJuxtaposer project at:

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

I refactored the code to separate UI drawing from parsing and Tree
creation, so this code is purely for Newick parsing and tree generation.

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

You could do something like this:

    Tree treeoflife;
    int current_depth = 0;

    void setup() {
        BufferedReader r = createReader("treeoflife.tree");
        TreeParser tp = new TreeParser(r);
        treeoflife = tp.tokenize(1, "treeoflife", null);
        int tree_height = treeoflife.getHeight();
        System.out.println("largest tree height is: " + tree_height);
        recursive_print(0, 0);
    }

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

Who uses it?
============

The need for a standalone parser came from the tree explorer at:

    http://exploretree.org/

What license is it available under?
===================================

The TreeJuxtaposer code is under the BSD license, so this code is too.

Who should I contact with a bug report?
=======================================

Since I stripped out anything that wasn't necessary for exploretree, you
could first see if what you need is present in the main TreeJuxtaposer 
source.  If the bug is only in this library, please contact me at 
chris-libnewick@printf.net instead of bugging the TreeJuxtaposer folks.
Something went wrong with that request. Please try again.