no run button

import java.util.*;
import java.io.*;
import java.sql.*;


public class PF {

    private static boolean neato = false;
    private static boolean showTransitionCount = true;



    public static void main(String[] Args){
                System.out.println("I am here");

        (new PF()).go();
    }

    private void goX() {

        String students[] = { "class", "studentA", "studentB", "studentC" };
        int n = students.length;

        Pathfinder pf[] = new Pathfinder[n];

        pf[0] = new Pathfinder();

        System.out.println("reading log file");
        pf[0].readLogfile("example/log.txt");

        for (int i = 1; i < n; i++) pf[i] = new Pathfinder(pf[0]);
        for (int i = 1; i < n; i++) pf[i].restrictTo(students[i]);
        for (int i = 0; i < n; i++) pf[i].setFrequencies();
        for (int i = 0; i < n; i++) pf[i].MCN();

        for (int i = 0; i < n; i++) pf[i].outputGraph("example\\" + students[i]);

}


    private void go1() {
        Pathfinder pf = new Pathfinder();

        System.out.println("starting...");
        pf.readLogfile("iisdata/visit.txt");
        System.out.println("data read");
        pf.setFrequencies();
        System.out.println("frequencies set");
        pf.MCN();
        System.out.println("MCN computed");
        pf.outputGraph("iisdata/visit");
        System.out.println("XML written");
    }


    private void go() {
        int[] classNumber = { 4 };
        String[] date =     {"2001-10-19"};

        for (int i = 0; i < classNumber.length; i++) {
            doClass(classNumber[i],date[i]);
        }
    }

        private void doClass(int classNumber, String dateRestriction) {
        RawData rd = new RawData();

        String[] nodeNames = rd.getNodeNames("%",classNumber, dateRestriction);
        String[] studentNames = rd.getStudentNames("%", classNumber, dateRestriction);
        int n = studentNames.length;

        System.out.print("Class " + classNumber + ", " + dateRestriction + " has " + n + " students");
        System.out.println(" and " + nodeNames.length + " nodes.");

        Pathfinder[] pf = new Pathfinder[n + 1]; // for all students and the class

        Hashtable invNodeNames = new Hashtable();

        for (int i = 0; i < nodeNames.length; i++) {
            invNodeNames.put(nodeNames[i].toLowerCase(),new Integer(i));
        }

        for (int i = 0; i < n+1; i++) {
            double[][] s;

            if (i < n) {
                System.out.print(studentNames[i] + " ");
                s = rd.getTransitionMatrix(classNumber, dateRestriction, studentNames[i], invNodeNames);
            } else {
                System.out.println("all students");
                s = rd.getTransitionMatrix(classNumber, dateRestriction, "%", invNodeNames);
            }

            pf[i] = new Pathfinder();
            pf[i].setFrequencies(s);
            pf[i].setNames(nodeNames);
            pf[i].MCN();

            if (i < n) {
                pf[i].outputGraph("data/" + "/" + classNumber + "_" + studentNames[i] + "_" + dateRestriction,showTransitionCount,neato);
            } else {
                pf[i].outputGraph("data/" + "/" + classNumber + "_" + "CLASS_" + dateRestriction,showTransitionCount,neato);
            }

        }
        System.out.println();

        try {

            //finally generating the comaprison output into a tab delimited file
            System.out.println("Writing comparison file");

            String filename = "data/" + "/" + classNumber + "_" + "CLASS_" + dateRestriction + ".txt";
            PrintWriter outFile = new PrintWriter(new BufferedWriter(new FileWriter(filename)));

            outFile.write("Comparing each student to the whole class\n\n");

            for (int i = 0; i < n; i++) {
                double sim = pf[i].sim(pf[n]);
                outFile.write(studentNames[i] + "\t" + sim + "\n");
            }

            outFile.write("\nComparing all student to each other\n\n");

            outFile.write("\t");
            for (int i = 0; i < n; i++) {
                outFile.write(studentNames[i] + "\t");
            }
            outFile.write("\n");

            double[][] matrix = new double[n][n];

            for (int i = 0; i < n; i++) {
                outFile.write(studentNames[i] + "\t");
                for (int j = 0; j < n; j++) {
                    double sim = pf[i].sim(pf[j]);
                    outFile.write(sim + "\t");
                    matrix[i][j] = sim;
                    if (sim <= 0) matrix[i][j] = -1;
                }
                outFile.write("\n");
            }
            outFile.close();


            //now we treat similarities as frequencies and use pathfinder again
            //that's probably silly, but...
            /* ling uncomments   */
            System.out.println("doing the pathfinder for the big thing");
            Pathfinder p = new Pathfinder();
            System.out.println("setting frequencies");
            p.setFrequencies(matrix);
            System.out.println("setting names");
            p.setNames(studentNames);
            System.out.println("MCN...");
            p.MCN();
            System.out.println("MCN done!");


            p.outputGraph("data/" + "/" + classNumber + "_allstudents_" + dateRestriction,showTransitionCount, neato, 10);


            //now we do the real clustering
//ling          for (int k = 1; k <= 3; k++) {

                int k=3;
                System.out.println("clustering with k = " + k);
                ClusterAlg clusterAlg = new ClusterAlg(k,studentNames);
                for(int i = 0; i < n; i++) {
                    clusterAlg.addPNF(pf[i]);
                }

                float v = 0, worstV = 0;
                v = clusterAlg.cluster();
                worstV += clusterAlg.worstClusterValue();

                Pathfinder centroid[] = clusterAlg.getCentroids();
                for (int i = 0; i < k; i++) {
                    centroid[i].outputGraph("data/" + "/" + classNumber +"_C_"+k+"_"+(i+1)+"_"+ dateRestriction,showTransitionCount, neato, 10);
                }
                System.out.println("k = " + k + " -> " + v + " -- " + worstV);
                System.out.println(clusterAlg);
//          }
/*ling end          */


        } catch (Exception e) {
            System.out.println(e);
        }
    }





}