Question

I’m having problems converting a binary rooted tree to newick format.
The full explanation for such a format can be found: http://code.google.com/p/mrsrf/wiki/NewickTree

An example of a newick format would be as follows:

for a tree T such as http://www.cs.mcgill.ca/~cs251/OldCourses/1997/topic8/images/completetreetwo.gif
the newick representation would be: (((8,9),(10,11)),((12,13),(14,15)))

the internal node will become the commas while the leaves will be retained.

such trees have internal nodes which will always have 2 children.

I have a problem using recursion to come out with this newick format.
The output contains far too many nodes and braces.

Any comments to resolve this problem is appreciated or even an iterative algorithm would be welcomed


import java.util.Stack;

public class Tree {

....

public String inOrderNewick(Node root, String output) throws ItemNotFoundException {
    if (root.hasChild()) {
        output += "(";
        output += inOrderNewick(root.child1, output);
        output += ",";
        output += inOrderNewick(root.child2, output);
        output += ")";
        return output;
    } else {
        return root.getSeq();
    }    

}

//edit: implemented the change as advised.
but the desired output for a tree is ((S3,(S1,S2)),(S4,S5))
where the actual output is (((S3,((S3,(S1,S2)),(((S3,((S3,(S1,S2)),(S4,S5))

This tells me that there are logic errors.
Perhaps there is a need to have flags?

Answer 1

Maybe you have a flaw in understanding recursion. You don’t need the “output” argument. When you compute a subtree you don’t need the representation of the previous nodes. Make it like this:

public String inOrderNewick(Node root) throws ItemNotFoundException {
    if (root.hasChild()) {
        String output = "";
        output += "(";
        output += inOrderNewick(root.child1);
        output += ",";
        output += inOrderNewick(root.child2);
        output += ")";
        return output;
    } else {
        return root.getSeq();
    }
}