The problem isn't with the comments, it's with throwing everything into one big main() method. Why throw away code when with a little bit more work you can give it some real power?

import java.util.ArrayList;
import java.util.Comparator;
import java.util.List;

import perlforjava.control.Looper;
import perlforjava.functions.Arrays;
import perlforjava.functions.Mapper;
import perlforjava.lang.Block;

/**
 * The Schwartzian Transform written in Java.
 */
public class TheSchwartz {

    private ArrayList list;

    /**
     * Comparator to sort by length.
     */
    public final static Comparator BY_LENGTH;
    
    /**
     * Comparator to sort alphabetically.
     */    
    public final static Comparator ALPHABETICALLY;
    
    /**
     * Static initializer
     */
    static {
        BY_LENGTH = new Comparator() {
            public int compare(Object a, Object b) {
                return ((Integer) ((List) a).get(1)).compareTo(
                    ((Integer) ((List) b).get(1)));
            }
        };
        ALPHABETICALLY = new Comparator() {
            public int compare(Object a, Object b) {
                String s1 = a.toString().substring(1);
                String s2 = b.toString().substring(1);
                return s1.compareTo(s2);
            }
        };        
    }

    /**
     * Simple Constructor. 
     * 
     * @param list
     */
    public TheSchwartz(ArrayList list) {
        this.list = list;
    }

    /**
     * Workhorse function. Sorting by passed in Comparator
     * 
     * @return
     */
    public ArrayList sort(Comparator sortBy) {
    
        List out = Mapper.map(new Block() {
                // pull the first element from each List and return it
                protected Object process(Object elem) {
                    return ((List) elem).get(0);
                }
            }, Arrays.sort(
                // run the comparison of Integer values to determine o
+rder
                sortBy,
            // map each string into an ArrayList of string => length
            Mapper.map(new Block() {
                protected Object process(Object elem) {
                    ArrayList temp = new ArrayList();
                    temp.add(elem);
                    temp.add(new Integer(((String) elem).length()));
                    return temp;
                }
            }, list)));
        return (ArrayList)out;
    }

    public static void main(String[] args) {

        // Create a new List of values to sort
        ArrayList in = new ArrayList();
        in.add("fu");
        in.add("duhh");
        in.add("birdy");
        in.add("sea");

        /* Sort based upon length of string by mapping each string to
           a List where the first element is the string and the second
+ is
           its length. Sort on the latter and return a new List of str
+ings. */

        TheSchwartz merlyn = new TheSchwartz(in);
        List outByLength = merlyn.sort(TheSchwartz.BY_LENGTH);

        System.out.println("By Length:");

        // Loop over the results to view them
        Looper.foreach(outByLength, new Block() {
            protected Object process(Object elem) {
                System.out.println("ELEM " + elem.toString());
                return null;
            }
        });
        
        System.out.println("\nAlphabetically:");
        
        List outAlphabetically = merlyn.sort(TheSchwartz.ALPHABETICALL
+Y);

            // Loop over the results to view them
            Looper.foreach(outAlphabetically, new Block() {
                protected Object process(Object elem) {
                    System.out.println("ELEM " + elem.toString());
                    return null;
                }
            });        
        
    }
}
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Fun post.

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