Index: /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/OWLClassGraph.java
===================================================================
--- /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/OWLClassGraph.java (revision 281)
+++ /SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/OWLClassGraph.java (revision 283)
@@ -10,8 +10,9 @@
  */
 import java.util.*;
-
-public class OWLClassGraph extends LabeledMultiDigraph{
+import java.io.Serializable;
+
+public class OWLClassGraph extends LabeledMultiDigraph implements Serializable{
     int nsteps = 4;
-    int limit = 100;
+    //int limit = 100;
     
     List<String> nodeType;
@@ -52,5 +53,5 @@
         nodeType = new LinkedList<String>();
     }
-        
+    
     public OWLClassGraph(RDFSchemaAnalyzer rdfsa){ // for experiment
         super();
@@ -220,9 +221,10 @@
             addNode(classes[i].getClassURI());
             nodeType.add("class");
+            nodeweight.add(classes[i].getNumOfInstances());           
         }
         // setEdges
         for (int i = 0 ; i < classes.length; i++ ){
             try{
-                ClassLink[] classLinks = rdfsa.getNextClass(null, classes[i].getClassURI(), limit, true);
+                ClassLink[] classLinks = rdfsa.getNextClass(null, classes[i].getClassURI(), 10000, true);
                 for (int j = 0 ; j < classLinks.length; j++){
                     Integer n = labelednodes.get(classLinks[j].getLinkedClassURI());
@@ -242,5 +244,5 @@
                 System.err.println(e);
             }
-        }       
+        }
     }
 
@@ -249,5 +251,4 @@
         this.sparqlEndpoint = sparqlEndpoint;
         visited = new HashSet<Integer>();
-        //edgeweight = new LinkedList<Map<Integer,Integer>>();
         nodeweight = new LinkedList<Integer>();
         // setNodes for all classes
@@ -261,5 +262,4 @@
            addNode(classes[i].getClassURI());
            nodeType.add("class");
-           //edgeweight.add(new HashMap<Integer,Integer>());
            nodeweight.add(classes[i].getNumOfInstances());
         }
@@ -275,5 +275,5 @@
                 Integer crr = nit.next();
                 try{
-                    ClassLink[] classLinks = rdfsa.getNextClass(null, labels.get(crr), limit, true);
+                    ClassLink[] classLinks = rdfsa.getNextClass(null, labels.get(crr), 10000, true);
                     for (int j = 0 ; j < classLinks.length; j++){
                         Integer nn = labelednodes.get(classLinks[j].getLinkedClassURI());
@@ -294,4 +294,7 @@
             nodes = nextnodes;
             visited.addAll(nodes);
+            if ( visited.size() > labelednodes.size()){
+                System.out.println();
+            }
         }
         // cut visited
@@ -337,19 +340,5 @@
             if ( c1 < 0.5 && c2 < 0.5 ){ chk = false;}
             double prob2 = 1.0 - c1;
-                    //((double) ( crr.getNumOfOriginClassInstances())/ 
-                    //(double) (  nodeweight.get(labelednodes.get(prev.getLinkedClassURI())) ));
-            //if ( prob2 > 1.0 || prob2 < 0 ){
-            //    System.out.println("Prob2 > 1 or Prob2 < 0");
-            //    System.out.println(prev.getLinkedClassURI());
-                //classes[labelednodes.get(prev.getLinkedClassURI())].getNumOfInstances();
-            //    System.out.println(prev.getPropertyURI());
-            //}
             double prob3 = 1.0 - Math.pow(prob2, (double) prev.getNumOfLinkedClassInstances());
-            //if ( prob3 > 1.0 ){
-            //    System.out.println("Prob3 > 1");
-            //    System.out.println(prev.getLinkedClassURI());
-                //classes[labelednodes.get(prev.getLinkedClassURI())].getNumOfInstances();
-            //    System.out.println(prev.getPropertyURI());
-            //}
             prob = prob * prob3 ;
             prev = crr;