Hi all,  for the last few days, I succeeded in constructing a code that
represents a network and infection transmisson through it.  This is the
first time ever that i wrote a code.  So i am wondering how i validate
my code although it may sound a philosophical question.  And also, I
want someone who are good at java programming to review my code.  I
would really appreciate it if anyone would review my code ??

it has 4 classes.

/**
* DoubletsOrTriplets.java
*/

import java.util.ArrayList;

public class DoubletsOrTriplets {

   String string;
   int value;

   /**
      Constructors
   */
   public DoubletsOrTriplets () {

    string = "";
    value = 0;
   }

   public DoubletsOrTriplets (String otherString) {

    string = otherString;
    value = 0;
   }

   public DoubletsOrTriplets (String otherString, int x) {

    string = otherString;
    value = x;
   }

   /**
   setters
   */

   public void setValue (String otherString, int x) {
    string = otherString;
    value = x;
   }

   public void printSelf () {

    System.out.printf ("%s = %d\n", string, value);

   }

----------------------------------------------------------------------------------------------
/**
* GayEdge.java
*
*/

import java.awt.Color;

import uchicago.src.sim.gui.DrawableEdge;
import uchicago.src.sim.gui.SimGraphics;
import uchicago.src.sim.network.DefaultEdge;
import uchicago.src.sim.network.Node;

/**
* The edge between GayNodes.
*/
public class GayEdge extends DefaultEdge implements DrawableEdge {

 private Color color;

 public GayEdge() {}

 public GayEdge(Node from, Node to, Color color) {
   super(from, to, "");
   this.color = color;
 }

 public void setColor(Color c) {
   color = c;
 }

 public void draw(SimGraphics g, int fromX, int toX, int fromY, int
toY) {
   g.drawDirectedLink(color, fromX, toX, fromY, toY);
 }
}

------------------------------------------------------------------------------------------------------------------
/**
* GayNode.java
*/

import java.awt.Color;
import java.util.ArrayList;

import uchicago.src.sim.gui.RectNetworkItem;
import uchicago.src.sim.network.DefaultDrawableNode;
import uchicago.src.sim.network.DefaultNode;
import uchicago.src.sim.network.Edge;
import uchicago.src.sim.util.Random;

public class GayNode extends DefaultDrawableNode {

   String infectStatus = "s";
   Color color;

   public GayNode (int x, int y) {
    RectNetworkItem rect = new RectNetworkItem(x, y);
    setDrawable(rect);
       infectStatus = "s";
   }

   public void setInfectStatus (String string) {
    infectStatus = string;
   }

   public String getInfectStatus () {
    return infectStatus;
   }

   /**
    * Makes an edge to the specified node and from the specifed node
to
    * thisGayNode if both nodes do not already have edges to each
    * other.  The edges is displayed in the specified color.
    */
   public void makeEdgeToFrom(DefaultNode node, Color color) {
    if (! hasEdgeTo(node)) {
       Edge edge = new GayEdge(this, node, color);
       addOutEdge(edge);
       node.addInEdge(edge);
       Edge otherEdge = new GayEdge(node, this, color);
       node.addOutEdge(otherEdge);
       addInEdge(otherEdge);
    }
   }

   /**
    * Creates a new edge between this GayNode and a node chosen
    * at random from the specified list. This edge is created via
    * <tt>makeEdgeFromTo</tt> and so those conditions must be met as
    * well.
    */
   public void meetRandom(ArrayList list) {
    int index = Random.uniform.nextIntFromTo(0, list.size() - 1);
    GayNode node = (GayNode)list.get(index);
    while (this.equals(node)) {
       index = Random.uniform.nextIntFromTo(0, list.size() - 1);
       node = (GayNode)list.get(index);
    }

    makeEdgeToFrom(node, Color.white);
   }

   public void removePartners() {
    GayNode jNode = (GayNode)getRandomNodeOut();

    // will be null if no outEdges.
    if (jNode != null) {
       removeEdgesTo(jNode);
       jNode.removeEdgesFrom(this);
       removeEdgesFrom(jNode);
       jNode.removeEdgesTo(this);
    }
   }

}

-------------------------------------------------------------------------------------
/**
* GayModel.java
*/

import uchicago.src.reflector.ListPropertyDescriptor;
import uchicago.src.sim.analysis.Histogram;
import uchicago.src.sim.analysis.NetSequenceGraph;
import uchicago.src.sim.analysis.OpenSequenceGraph;
import uchicago.src.sim.analysis.Plot;
import uchicago.src.sim.analysis.PlotModel;
import uchicago.src.sim.engine.BasicAction;
import uchicago.src.sim.engine.Controller;
import uchicago.src.sim.engine.Schedule;
import uchicago.src.sim.engine.SimModelImpl;
import uchicago.src.sim.gui.*;
import uchicago.src.sim.util.Random;
import uchicago.src.sim.analysis.OpenStats;
import uchicago.src.sim.analysis.Sequence;
import java.awt.*;

//import java.util.ArrayList;
//import java.util.Vector;
import java.awt.Color;
import java.util.*;
//import java.lang.Object;

public class GayModel extends SimModelImpl {

   // model variables
   private int              numNodes        = 50;
   private int              initInfNodes    = 5;
   private int              worldXSize      = 400;
   private int              worldYSize      = 400;
   private int              updateEveryN    = 5;
   private int              initialSteps    = 1;
   private int              maxDegree       = 10;
   private int              ss = 0, se1 = 0, se2 = 0, sa1 = 0, sa2 =
0, sa3 = 0, sl = 0;
   private int              e1e1 = 0, e1e2 = 0, e1a1 = 0,e1a2 = 0,
e1a3 = 0, e1l = 0;
   private int              e2e2 = 0, e2a1 = 0, e2a2 = 0, e2a3 = 0,
e2l = 0;
   private int              a1a1 = 0, a1a2 = 0, a1a3 = 0, a1l = 0;
   private int              a2a2 = 0, a2a3 = 0, a2l = 0;
   private int              a3a3 = 0, a3l = 0;
   private int              ll = 0;
   private int              tickCount = 0;
   private double           removeProb      = 0.01;
   private double           partnershipProb = 0.01;
   private double           probFromE1ToE2  = 0.05, probFromA1ToA2 =
0.015, probFromLToS = 0.005;
   private double           transProbAtE    = 0.08,  transProbAtA   =
0.002, transProbAtL = 0.08;
   private double           meanDegree      = 0;

   // arraylists
   private ArrayList agentList = new ArrayList();
   private ArrayList doubletList = new ArrayList();

   // implementation variables
   private String                    layoutType       = "KK";
   private DisplaySurface            surface;
   private Schedule                  schedule;
   private AbstractGraphLayout       graphLayout;
   private Histogram                 degreeDist;
   private boolean                   showHist         = true;
   private NetSequenceGraph          graph, otherGraph;
   private boolean                   showPlot         = false;
   private BasicAction               initialAction;
   private OpenSequenceGraph         seqGraph;
   private boolean                   showPrev         = true;

   public GayModel() {
    Vector vect = new Vector();
    vect.add("Fruch");
    vect.add("KK");
    vect.add("CircleLayout");
    ListPropertyDescriptor pd = new ListPropertyDescriptor("LayoutType",
vect);
    // the name of the property: LayoutType
    // vect - the objects to be displayed in the combo box and passed
    // to the appropriate set method.
    descriptors.put("LayoutType", pd);
   }

   // get and set accessor methods

   public String getLayoutType() {
    return layoutType;
   }

   public void setLayoutType(String type) {
    layoutType = type;
   }

   public boolean getDegreeHist() {
    return showHist;
   }

   public void setDegreeHist(boolean val) {
    showHist = val;
   }

   public boolean getPrevGraph() {
    return showPrev;
   }

   public void setPrevGraph(boolean val) {
    showPrev = val;
   }

   public boolean getPlot() {
    return showPlot;
   }

   public void setPlot(boolean val) {
    showPlot = val;
   }

   public double getRemoveProb() {
    return removeProb;
   }

   public void setRemoveProb(double prob) {
    removeProb = prob;
   }

   public double getPartnershipProb() {
    return partnershipProb;
   }

   public void setPartnershipProb(double prob) {
    partnershipProb = prob;
   }

   public void setNumNodes(int n) {
    numNodes = n;
   }

   public int getNumNodes() {
    return numNodes;
   }

   public int getInitInfNodes() {
    return initInfNodes;
   }

   public void setInitInfNodes(int num) {
    initInfNodes = num;
   }

   public double getProbFromE1ToE2() {
    return probFromE1ToE2;
   }

   public void setProbFromE1ToE2(double prob) {
    probFromE1ToE2 = prob;
   }

   public double getProbFromA1ToA2() {
    return probFromA1ToA2;
   }

   public void setProbFromA1ToA2(double prob) {
    probFromA1ToA2 = prob;
   }

   public double getProbFromLToS() {
    return probFromLToS;
   }

   public void setProbFromLToS(double prob) {
    probFromLToS = prob;
   }

   public double getTransProbAtE() {
    return transProbAtE;
   }

   public void setTransProbAtE(double tp) {
    transProbAtE = tp;
   }

   public double getTransProbAtA() {
    return transProbAtA;
   }

   public void setTransProbAtA(double tp) {
    transProbAtA = tp;
   }

   public double getTransProbAtL() {
    return transProbAtL;
   }

   public void setTransProbAtL(double tp) {
    transProbAtL = tp;
   }

   public int getMaxDegree() {
    return maxDegree;
   }

   public void setMaxDegree(int degree) {
    maxDegree = degree;
   }

   public void setUpdateEveryN(int updates) {
    updateEveryN = updates;
   }

   public int getUpdateEveryN() {
    return updateEveryN;
   }

   public int getStartRemoveAfter() {
    return initialSteps;

   }

   public void setStartRemoveAfter(int steps) {
    initialSteps = steps;
   }

   // arraylist methods
   // print the component of the doublet (or triplet) list
   public void printList (ArrayList list) {
    for (int i = 0; i < list.size(); i++) {
       DoubletsOrTriplets doublet = new  DoubletsOrTriplets();
       doublet = (DoubletsOrTriplets)list.get(i);
       doublet.printSelf();
    }
   }

   // builds the model
   public void buildModel() {
    for (int i = 0; i < (numNodes - initInfNodes); i++) {
       int x = Random.uniform.nextIntFromTo(0, worldXSize - 1);
       int y = Random.uniform.nextIntFromTo(0, worldYSize - 1);
       GayNode node = new GayNode(x, y);
       node.setColor (Color.gray);

       agentList.add(node);
    }
    for (int i = 0; i < initInfNodes; i++) {
       int x = Random.uniform.nextIntFromTo(0, worldXSize - 1);
       int y = Random.uniform.nextIntFromTo(0, worldYSize - 1);
       GayNode node = new GayNode(x, y);
       node.setColor (Color.green);
       node.setInfectStatus ("a1");
       agentList.add(node);
    }

    if (showHist) makeHistogram();
    if (showPlot) makePlot();
    if (showPrev) displayPrevalence();
   }

   private void randomMeeting() {
    for (int i = 0; i < numNodes; i++) {
       GayNode iNode = (GayNode) agentList.get(i);
       double aDouble = Random.uniform.nextDoubleFromTo(0, 1);
       if (partnershipProb > aDouble) {
        iNode.meetRandom(agentList);
       } }
   }
   /**
   it's very possible if the number of edges increases then
infectProbability will increase over 1.
   */

   private void infectPartners () {
    for (int i = 0; i < numNodes; i++) {
       int  ePartners = 0, aPartners = 0, lPartners = 0;
       GayNode iNode = (GayNode) agentList.get(i);
       String aString = iNode.getInfectStatus();
       int degree = iNode.getInDegree();
       if (aString.equals("s") && degree != 0) {
        ArrayList list = iNode.getInNodes();
        for (int j = 0; j < list.size(); j++) {
           GayNode jNode = (GayNode)list.get(j);
           String otherString =  jNode.getInfectStatus();
           if (otherString.equals("e1") || otherString.equals("e2")) {
            ePartners += 1;
           }
           else if (otherString.equals("a1") || otherString.equals("a2") ||
otherString.equals("a3")) {
            aPartners += 1;
           }
           else if (otherString.equals("l")) {
            lPartners += 1;
           }
        }
        //System.out.printf ("ePartners=%d, aPartners = %d, lPartners =
%d\n", ePartners, aPartners, lPartners);

        double infectionPartners = ePartners * transProbAtE  + aPartners *
transProbAtA + lPartners * transProbAtL;
        double safeProb = Random.uniform.nextDoubleFromTo(0, 1);

        //System.out.printf ("infectionPartners = %.4f,  safeProb = %.4f\n",
infectionPartners, safeProb);

        if (infectionPartners > safeProb) {
           iNode.setColor (Color.magenta);
           iNode.setInfectStatus ("e1");
           agentList.add (iNode);
        } } }
   }

   private void randomProgress () {
    for (int i = 0; i < numNodes; i++) {
       GayNode iNode = (GayNode) agentList.get(i);
       String string = iNode.getInfectStatus();
       double aDouble = Random.uniform.nextDoubleFromTo(0, 1);

       if (string.equals("e1") && probFromE1ToE2 > aDouble ) {
        iNode.setColor(Color.blue);
        iNode.setInfectStatus("e2");
       }

       else  if (string.equals("e2") && probFromE1ToE2 > aDouble ) {
        iNode.setColor(Color.green);
        iNode.setInfectStatus("a1");
       }

       else if (string.equals("a1") && probFromA1ToA2 > aDouble ) {
        iNode.setColor(Color.yellow);
        iNode.setInfectStatus("a2");
       }

       else if (string.equals("a2") && probFromA1ToA2 > aDouble ) {
        iNode.setColor(Color.orange);
        iNode.setInfectStatus("a3");
       }

       else if (string.equals("a3") && probFromA1ToA2 > aDouble ) {
        iNode.setColor(Color.red);
        iNode.setInfectStatus("l");
       }

       else if (string.equals("l") && probFromLToS > aDouble ) {
        iNode.setColor(Color.gray);
        iNode.setInfectStatus("s");
       }
       agentList.add (iNode);
    }
   }

   private void removeRandomPartners() {
    for (int i = 0; i < numNodes; i++) {
       GayNode node = (GayNode) agentList.get(i);
       int degree = node.getOutDegree(); // gets outdegree of node
       double aDouble = Random.uniform.nextDoubleFromTo(0, 1);
       if (removeProb > aDouble && degree > 0) {
        node.removePartners();
       }
    }
   }

   public double getMeanDegree() {
    double degree = 0;
    for (int i = 0; i < numNodes; i++) {
       GayNode node = (GayNode) agentList.get(i);
       degree += node.getOutDegree(); // gets outdegree of a node
    }
    meanDegree = degree/(double)numNodes;
    return meanDegree;
   }

   public ArrayList valueDoubletList (ArrayList list) {

    tickCount += 1; // This tick count doesn't reset to zero when I reset
the model.
    System.out.printf("Tick count = %d\n", tickCount);
    list.clear();

    int ss = 0, se1 = 0, se2 = 0, sa1 = 0, sa2 = 0, sa3 = 0, sl = 0;
    int e1e1 = 0, e1e2 = 0, e1a1 = 0,e1a2 = 0, e1a3 = 0, e1l = 0;
    int e2e2 = 0, e2a1 = 0, e2a2 = 0, e2a3 = 0, e2l = 0;
    int a1a1 = 0, a1a2 = 0, a1a3 = 0, a1l = 0;
    int a2a2 = 0, a2a3 = 0, a2l = 0;
    int a3a3 = 0, a3l = 0;
    int ll = 0;

    for (int i  = 0; i < numNodes; i++) {

       GayNode node  = (GayNode) agentList.get(i);
       String string  = node.getInfectStatus();
       ArrayList otherList = node.getOutEdges();

       for ( int j = 0; j < otherList.size(); j++) {

           GayEdge edge =(GayEdge)otherList.get(j);
           GayNode otherNode = (GayNode)edge.getTo();
           String otherString = otherNode.getInfectStatus();

           if (string.equals("s")) {
            if (otherString.equals("s")) { ss += 1; }
            if (otherString.equals("e1")) { se1 += 1; }
            if (otherString.equals("e2")) { se2 += 1; }
            if (otherString.equals("a1")) { sa1 += 1; }
            if (otherString.equals("a2")) { sa2 += 1; }
            if (otherString.equals("a3")) { sa3 += 1; }
            if (otherString.equals("l")) { sl += 1; }
           }
           else if (string.equals("e1")) {
            if (otherString.equals("s")) { se1 += 0; }
            if (otherString.equals("e1")) { e1e1 += 1; }
            if (otherString.equals("e2")) { e1e2 += 1; }
            if (otherString.equals("a1")) { e1a1 += 1; }
            if (otherString.equals("a2")) { e1a2 += 1; }
            if (otherString.equals("a3")) { e1a3 += 1; }
            if (otherString.equals("l")) { e1l += 1; }
           }
           else if (string.equals("e2")) {
            if (otherString.equals("s")) { se2 += 0; }
            if (otherString.equals("e1")) { e1e2 += 0; }
            if (otherString.equals("e2")) { e2e2 += 1; }
            if (otherString.equals("a1")) { e2a1 += 1; }
            if (otherString.equals("a2")) { e2a2 += 1; }
            if (otherString.equals("a3")) { e2a3 += 1; }
            if (otherString.equals("l")) { e2l += 1; }
           }
           else if (string.equals("a1")) {
            if (otherString.equals("s")) { sa1 += 0; }
            if (otherString.equals("e1")) { e1a1 += 0; }
            if (otherString.equals("e2")) { e2a1 += 0; }
            if (otherString.equals("a1")) { a1a1 += 1; }
            if (otherString.equals("a2")) { a1a2 += 1; }
            if (otherString.equals("a3")) { a1a3 += 1; }
            if (otherString.equals("l")) { a1l += 1; }
           }
           else if (string.equals("a2")) {
            if (otherString.equals("s")) { sa2 += 0; }
            if (otherString.equals("e1")) { e1a2 += 0; }
            if (otherString.equals("e2")) { e2a2 += 0; }
            if (otherString.equals("a1")) { a1a2 += 0; }
            if (otherString.equals("a2")) { a2a2 += 1; }
            if (otherString.equals("a3")) { a2a3 += 1; }
            if (otherString.equals("l")) { a2l += 1; }
           }
           else if (string.equals("a3")) {
            if (otherString.equals("s")) { sa3 += 0; }
            if (otherString.equals("e1")) { e1a3 += 0; }
            if (otherString.equals("e2")) { e2a3 += 0; }
            if (otherString.equals("a1")) { a1a3 += 0; }
            if (otherString.equals("a2")) { a2a3 += 0; }
            if (otherString.equals("a3")) { a3a3 += 1; }
            if (otherString.equals("l")) { a3l += 1; }
           }
           else if (string.equals("l")) {
            if (otherString.equals("s")) { sl += 0; }
            if (otherString.equals("e1")) { e1l += 0; }
            if (otherString.equals("e2")) { e2l += 0; }
            if (otherString.equals("a1")) { a1l += 0; }
            if (otherString.equals("a2")) { a2l += 0; }
            if (otherString.equals("a3")) { a3l += 0; }
            if (otherString.equals("l")) { ll += 1; }
           }
        }
       }

          DoubletsOrTriplets doublet1 = new DoubletsOrTriplets ("ss",
ss);
    DoubletsOrTriplets doublet2 = new DoubletsOrTriplets ("se1", se1);
    DoubletsOrTriplets doublet3 = new DoubletsOrTriplets ("se2", se2);
    DoubletsOrTriplets doublet4 = new DoubletsOrTriplets ("sa1", sa1);
    DoubletsOrTriplets doublet5 = new DoubletsOrTriplets ("sa2", sa2);
    DoubletsOrTriplets doublet6 = new DoubletsOrTriplets ("sa3", sa3);
    DoubletsOrTriplets doublet7 = new DoubletsOrTriplets ("sl", sl);
    DoubletsOrTriplets doublet8 = new DoubletsOrTriplets ("e1e1", e1e1);
    DoubletsOrTriplets doublet9 = new DoubletsOrTriplets ("e1e2", e1e2);
    DoubletsOrTriplets doublet10 = new DoubletsOrTriplets ("e1a1", e1a1);
    DoubletsOrTriplets doublet11 = new DoubletsOrTriplets ("e1a2", e1a2);
    DoubletsOrTriplets doublet12 = new DoubletsOrTriplets ("e1a3", e1a3);
    DoubletsOrTriplets doublet13 = new DoubletsOrTriplets ("e1l", e1l);
    DoubletsOrTriplets doublet14 = new DoubletsOrTriplets ("e2e2", e2e2);
    DoubletsOrTriplets doublet15 = new DoubletsOrTriplets ("e2a1", e2a1);
    DoubletsOrTriplets doublet16 = new DoubletsOrTriplets ("e2a2", e2a2);
    DoubletsOrTriplets doublet17 = new DoubletsOrTriplets ("e2a3", e2a3);
    DoubletsOrTriplets doublet18 = new DoubletsOrTriplets ("e2l", e2l);
    DoubletsOrTriplets doublet19 = new DoubletsOrTriplets ("a1a1", a1a1);
    DoubletsOrTriplets doublet20 = new DoubletsOrTriplets ("a1a2", a1a2);
    DoubletsOrTriplets doublet21 = new DoubletsOrTriplets ("a1a3", a1a3);
    DoubletsOrTriplets doublet22 = new DoubletsOrTriplets ("a1l", a1l);
    DoubletsOrTriplets doublet23 = new DoubletsOrTriplets ("a2a2", a2a2);
    DoubletsOrTriplets doublet24 = new DoubletsOrTriplets ("a2a3", a2a3);
    DoubletsOrTriplets doublet25 = new DoubletsOrTriplets ("a2l", a2l);
    DoubletsOrTriplets doublet26 = new DoubletsOrTriplets ("a3a3", a3a3);
    DoubletsOrTriplets doublet27 = new DoubletsOrTriplets ("a3l", a3l);
    DoubletsOrTriplets doublet28 = new DoubletsOrTriplets ("ll", ll);

    list.add (0, doublet1);
    list.add (1, doublet2);
    list.add (2, doublet3);
    list.add (3, doublet4);
    list.add (4, doublet5);
    list.add (5, doublet6);
    list.add (6, doublet7);
    list.add (7, doublet8);
    list.add (8, doublet9);
    list.add (9, doublet10);
    list.add (10, doublet11);
    list.add (11, doublet12);
    list.add (12, doublet13);
    list.add (13, doublet14);
    list.add (14, doublet15);
    list.add (15, doublet16);
    list.add (16, doublet17);
    list.add (17, doublet18);
    list.add (18, doublet19);
    list.add (19, doublet20);
    list.add (20, doublet21);
    list.add (21, doublet22);
    list.add (22, doublet23);
    list.add (23, doublet24);
    list.add (24, doublet25);
    list.add (25, doublet26);
    list.add (26, doublet27);
    list.add (27, doublet28);

    return list;
   }

   class Prevalence implements Sequence {
    public double getSValue() {
       double prevalence = 0;
       int numSusceptible = 0;
       String string;
       for (int i = 0; i < numNodes; i++) {
        GayNode iNode = (GayNode) agentList.get(i);
        string = iNode.getInfectStatus();
        //    System.out.printf("status = %s  ", string);
        if (string.equals("s")) {
           numSusceptible += 1;
        }
       }
       prevalence = ((double)(numNodes - numSusceptible)) /
(double)numNodes;
       //System.out.printf("\nprevalence =%.4f \n", prevalence);
       return prevalence;
    }
   }

   class AvgNumNodes implements Sequence {
    public double getSValue() {
       getMeanDegree();
       return meanDegree;
    }
   }

   public void buildDisplay() {
    if (layoutType.equals("KK")) { // java.lang.String is a subclass of
.Object So .equals is available
       graphLayout = new KamadaGraphLayout(agentList, worldXSize,
worldYSize, surface, updateEveryN);
    } else if (layoutType.equals("Fruch")) {
       graphLayout = new FruchGraphLayout(agentList, worldXSize,
worldYSize, surface, updateEveryN);
    } else if (layoutType.equals("CircleLayout")) {
       graphLayout = new CircularGraphLayout(agentList, worldXSize,
worldYSize);
    }

    // these four lines hook up the graph layouts to the stop, pause, and
    // exit buttons on the toolbar. When stop, pause, or exit is clicked
    // the graph layouts will interrupt their layout as soon as possible.
    Controller c = (Controller) getController();
    c.addStopListener(graphLayout);
    c.addPauseListener(graphLayout);
    c.addExitListener(graphLayout);

    Network2DDisplay display = new Network2DDisplay(graphLayout);
    surface.addDisplayableProbeable(display, "Gay Network");

    // add the display as a Zoomable. This means we can "zoom" in on
    // various parts of the network.
    surface.addZoomable(display);
    //surface.setBackground(Color.white);
    addSimEventListener(surface); //uchicago.src.sim.engine.SimModelImpl
class

   }

   /*
    * Creates a histogram of the degree distribution.
    */
   private void makeHistogram() {

    degreeDist = new Histogram("Degree Distribution", maxDegree + 1, 0,
                  maxDegree + 1, this); // shouldn't the range be double,not int?

    degreeDist.createHistogramItem("Degree Distribution", agentList,
                      "getOutDegree"); // Is "getOutDegree" a data bin src?
    // agentList has nodes as components. The node.getOutDegree is the
getBinValue. ??
   }

   /*
    * Creates a Plot of the Clustering Coefficient, the avg. density,
    * and the component count.
    */
   private void makePlot() {

    graph = new NetSequenceGraph("Network Stats", this,
                    "./net.txt", PlotModel.CSV, agentList);
    graph.setAxisTitles("Time", "Statistic Value");
    graph.setXRange(0, 50);
    graph.setYRange(0, numNodes);
    graph.plotDensity("Density", Color.blue, NetSequenceGraph.SQUARE);
    //graph.plotComponentCount("Component Count", Color.blue,
graph.SQUARE);
    graph.plotClusterCoefficient("Cluster Coef.", Color.red,
NetSequenceGraph.SQUARE);
   }

   private void displayPrevalence() {

    seqGraph = new OpenSequenceGraph (" HIV Prevalence", this,
"./prev.txt", OpenStats.CSV);
    seqGraph.setAxisTitles("Time", "Prevalence");
    seqGraph.setXRange(0, 50);
    seqGraph.setYRange(0, 1.2);
    seqGraph.addSequence("Prevalence", new Prevalence());
    seqGraph.addSequence ("Mean Degree", new AvgNumNodes());

   }

   public void initialAction() {
    randomMeeting();
    graphLayout.updateLayout();
    surface.updateDisplay();
    valueDoubletList(doubletList);
    printList (doubletList);
    if (showHist) degreeDist.step();
    if (showPlot) graph.step();
    if (showPrev) seqGraph.step();
  }

   public void mainAction() {
    randomMeeting();
    removeRandomPartners();
    infectPartners();
    randomProgress();
    valueDoubletList(doubletList);
    printList (doubletList);
    graphLayout.updateLayout();
    surface.updateDisplay();
    if (showHist) degreeDist.step();
    if (showPlot) graph.step();
    if (showPrev) seqGraph.step();

    //System.out.println(NetUtilities.getComponents(agentList).size());

   }
   /**
    * what if we use only main action, in other words, what if
randomMeeting and removeRandomPartners
    * are exercuted simulatneously from the simulation start?
    */
   public void removeInitialAction() {
    schedule.removeAction(initialAction);
    // uchicago.src.sim.engine.ScheduleBase is the superclass of schedule.

    // .revomeAction is one of the methods.
   }

   private void buildSchedule() {
    initialAction = schedule.scheduleActionAt(1, this, "initialAction");
    schedule.scheduleActionAt(initialSteps, this, "removeInitialAction",
                 Schedule.LAST);
    // initialAction and removeInitialAction occurs at the same tick cout,

    // but removeInitialAction occurs after initial action
(Schedule.LAST).
    schedule.scheduleActionBeginning(initialSteps + 1, this,
"mainAction");
    schedule.scheduleActionAtEnd(seqGraph, "writeToFile"); // interface
Recorder.writeToFile()

   }

   public void begin() {
    buildModel();
    buildDisplay();
    buildSchedule();
    graphLayout.updateLayout();
    surface.display();
    if (showHist) degreeDist.display();
    if (showPlot) graph.display();
    if (showPrev) seqGraph.display();
}

   public void setup() {
    Random.createUniform();
    if (surface != null) surface.dispose();
    if (degreeDist != null) degreeDist.dispose();
    if (graph != null) graph.dispose();
    if (seqGraph != null) seqGraph.dispose();
    surface = null;
    schedule = null;
    degreeDist = null;
    graph = null;
    seqGraph = null;
    System.gc(); // runs the garbage collector

    surface = new DisplaySurface(this, "Network Display");
    registerDisplaySurface("Main Display", surface);
    // Registers a DisplaySurface with this model (surface)
    // and associates it with a particular name (Main Display).
    schedule = new Schedule();
    agentList = new ArrayList();
    worldXSize = 500;
    worldYSize = 500;
   }

   public String[] getInitParam() {
    String[] params = {"numNodes", "worldXSize", "worldYSize",
              "updateEveryN", "LayoutType", "RemoveProb", "PartnershipProb",
              "StartRemoveAfter", "MaxDegree", "DegreeHist", "Plot",
"PrevGraph",
                          "initInfNodes", "probFromE1ToE2",
"probFromA1ToA2","probFromLToS",
                          "transProbAtE","transProbAtA",
"transProbAtL"};
    return params;
   }
   // parametera are just dispalyed in alphabetical order.
   public Schedule getSchedule() {
    return schedule;
   }

   public String getName() {
    return "Parameter";
   }

   public static void main(String[] args) {
    uchicago.src.sim.engine.SimInit init =
           new uchicago.src.sim.engine.SimInit();
    GayModel model = new GayModel();
    init.loadModel(model, "", false);
   }
}
--------------------------------------------------------------------------------------------------------------------