Index: SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/OWLClassGraph.java
===================================================================
--- SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/OWLClassGraph.java (revision 173)
+++ SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/OWLClassGraph.java (revision 177)
@@ -58,4 +58,5 @@
         NavigableSet<Path> sortedpath = new TreeSet<Path>();
         ListIterator<List<ClassLink>> pit = paths.listIterator();
+        int j = 0;
         while ( pit.hasNext() ){
             Path path = new Path();
@@ -73,4 +74,5 @@
             path.setWidth(min);
             sortedpath.add(path);
+            j++;
         }
         Path[] patharray = new Path[paths.size()];
@@ -94,12 +96,6 @@
               while ( lit.hasNext() ){
                   LinkAndPath crrlp = lit.next();
-                  /*if ( crrlp.classLink.getLinkedClassURI().equals("http://www.biopax.org/release/biopax-level3.owl#Pathway") ){
-                      System.out.println("here!");
-                  }*/
                   ClassLink[] classLinks = rdfsa.getNextClass(null, crrlp.classLink.getLinkedClassURI(), limit, countLinks);
                   for ( int j = 0 ; j < classLinks.length; j++ ){
-                      /*if ( classLinks[j].getLinkedClassURI().endsWith("http://www.biopax.org/release/biopax-level3.owl#BiochemicalReaction") ){
-                          ClassLink cltmp = classLinks[j];
-                      }*/
                       List<ClassLink> crrpath = new LinkedList<>(crrlp.path);
                       crrpath.add(classLinks[j]);
@@ -116,17 +112,12 @@
                            crrlp.classLink.getDirection() != classLinks[j].getDirection() &&
                            crrlp.originalClassURI.equals( classLinks[j].getLinkedClassURI()) ){
-                              System.out.println("P1");
+                              //System.out.println("P1");
                               continue;
                           }
                           if ( checkPruning(crrlp.classLink, classLinks[j]) ){
-                              System.out.println("P2");
+                              //System.out.println("P2");
                               continue;
                           }
                       }
-                      /*
-                      if ( classLinks[j].getDirection() != Direction.reverse ){
-                         System.out.println("here b"); 
-                      }*/
-
                       nextlp.add(new LinkAndPath(classLinks[j], crrpath, crrlp.classLink.getLinkedClassURI()));
                   }
Index: SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/QueryPathGenerator.java
===================================================================
--- SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/QueryPathGenerator.java (revision 167)
+++ SPARQLBuilderWWW/src/java/org/biohackathon/SPARQLBuilder/OWL/QueryPathGenerator.java (revision 177)
@@ -67,5 +67,5 @@
     public QueryPathGenerator(String sparqlEndpoint){
         factory = new RDFSchemaAnalyzerFactory(CDIR);
-        setSPARQLendpoint(sparqlEndpoint);      
+        setSPARQLendpoint(sparqlEndpoint);
     }