Index: /BH13SPARQLBuilder/src/org/biohackathon/SPARQLBuilder/OWL/OWLClassGraph.java
===================================================================
--- /BH13SPARQLBuilder/src/org/biohackathon/SPARQLBuilder/OWL/OWLClassGraph.java (revision 67)
+++ /BH13SPARQLBuilder/src/org/biohackathon/SPARQLBuilder/OWL/OWLClassGraph.java (revision 82)
@@ -55,29 +55,8 @@
         divcut = - 2.0;
     }
-    
-    /*
-    public void generateGraph(List<List<ClassLink>> paths){
-        ListIterator<List<ClassLink>> pit = paths.listIterator();
-        while( pit.hasNext() ){
-            List<ClassLink> cls = pit.next();
-            String start = startClass;
-            ListIterator<ClassLink> cit = cls.listIterator();
-            while ( cit.hasNext() ){
-                // KOKO
-            }
-        }
-    }
-   */
-    
-    public Path[] getPaths(OWLQueryBuilderImpl qb, int mode, boolean countLink){
+        
+    public Path[] getPaths(RDFSchemaAnalyzer rdfsa, boolean countLink){
         List<List<ClassLink>> paths = null;
-        if ( mode <= 1){
-            paths = searchPaths(qb, mode, countLink);
-        }else if ( mode == 2 ){
-            paths = searchPathsWithCut(qb);        
-        }else{
-            System.err.println("Mode is not correct");
-            return null;
-        }
+        paths = searchPaths(rdfsa, countLink);
         Path[] patharray = new Path[paths.size()];
         ListIterator<List<ClassLink>> pit = paths.listIterator();
@@ -102,5 +81,5 @@
     }
         
-    private List<List<ClassLink>> searchPaths(OWLQueryBuilderImpl qb, int mode, boolean countLinks){
+    private List<List<ClassLink>> searchPaths(RDFSchemaAnalyzer rdfsa, boolean countLinks){
         List<List<ClassLink>> paths = new ArrayList<>();
         ClassLink crrLink = new ClassLink(null,startClass,Direction.both,0,0,0,0,0);
@@ -114,10 +93,5 @@
                   LinkAndPath crrlp = lit.next();
                   ClassLink[] classLinks = null;
-                  // Mode
-                  if ( mode == 0 ){
-                      classLinks = qb.getNextClass(null, crrlp.classLink.getLinkedClassURI(), limit, countLinks);
-                  }else if ( mode == 1 ){
-                      classLinks = qb.getNextClassViaInstanceLink(null, crrlp.classLink.getLinkedClassURI(), limit); 
-                  }else{ System.err.println("Mode is not correct."); }
+                  classLinks = rdfsa.getNextClass(null, crrlp.classLink.getLinkedClassURI(), limit, countLinks);
                   for ( int j = 0 ; j < classLinks.length; j++ ){
                       List<ClassLink> crrpath = new LinkedList<>(crrlp.path);
@@ -140,5 +114,6 @@
         return paths;  
     }
-    
+
+/*    
     private List<List<ClassLink>> searchPathsWithCut(OWLQueryBuilderImpl qb){
         List<List<ClassLink>> paths = new ArrayList<>();
@@ -194,5 +169,7 @@
         return paths;  
     }
-    
+*/
+    
+/*    
     private boolean decideConvergence(ClassLink classLink){
         double con = getValueForConvergence(classLink.getNumOfOriginInstances(), 
@@ -204,5 +181,7 @@
         return false;
     }
-    
+*/
+    
+/*    
     private boolean decideDivergence(ClassLink classLink){
         double con = getValueForConvergence(classLink.getNumOfOriginInstances(), 
@@ -214,5 +193,7 @@
         return false;
     }
-
+*/
+    
+/*    
     private double getValueForConvergence(int numOfOriginInstances, int numOfLinkedInstances, int numOfLinks){
         //return (double) numOfLinks / (double) numOfLinkedInstances ;
@@ -220,3 +201,4 @@
         return Math.log((double)numOfOriginInstances) - Math.log((double)numOfLinkedInstances); 
     }
+    */
 }