Use Arrays.sort to sort an array : Array Reflection Utilities « Collections « Java Tutorial

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import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Scanner;

public class Anagrams2 {
  public static void main(String[] args) {
    int minGroupSize = Integer.parseInt(args[1]);

    // Read words from file and put into simulated multimap
    Map<String, List<String>> m = new HashMap<String, List<String>>();
    try {
      Scanner s = new Scanner(new File(args[0]));
      while (s.hasNext()) {
        String word = s.next();
        String alpha = alphabetize(word);
        List<String> l = m.get(alpha);
        if (l == null)
          m.put(alpha, l = new ArrayList<String>());
        l.add(word);
      }
    } catch (IOException e) {
      System.err.println(e);
      System.exit(1);
    }

    // Make a List of all permutation groups above size threshold
    List<List<String>> winners = new ArrayList<List<String>>();
    for (List<String> l : m.values())
      if (l.size() >= minGroupSize)
        winners.add(l);

    // Sort permutation groups according to size
    Collections.sort(winners, new Comparator<List<String>>() {
      public int compare(List<String> o1, List<String> o2) {
        return o2.size() - o1.size();
      }
    });

    // Print permutation groups
    for (List<String> l : winners) {
      System.out.println(l.size() + ": " + l);
    }
  }

  private static String alphabetize(String s) {
    char[] a = s.toCharArray();
    Arrays.sort(a);
    return new String(a);
  }
}