X-Git-Url: http://demsky.eecs.uci.edu/git/?a=blobdiff_plain;f=Robust%2Fsrc%2FAnalysis%2FSSJava%2FHierarchyGraph.java;h=d7900939e6d4d6e4f221838c2113f8177527ce35;hb=47cc527f574f19b71e92fceac668fb8c0655b13b;hp=50744f0140b6c3b1d0ef224a8950ef0f2c744925;hpb=9e11ce79473fe199b045066b384fdfed8eb022ea;p=IRC.git

diff --git a/Robust/src/Analysis/SSJava/HierarchyGraph.java b/Robust/src/Analysis/SSJava/HierarchyGraph.java
index 50744f01..d7900939 100644
--- a/Robust/src/Analysis/SSJava/HierarchyGraph.java
+++ b/Robust/src/Analysis/SSJava/HierarchyGraph.java
@@ -8,15 +8,17 @@ import java.util.HashSet;
 import java.util.Iterator;
 import java.util.Map;
 import java.util.Set;
+import java.util.Stack;
 
 import IR.Descriptor;
 import IR.FieldDescriptor;
-import IR.VarDescriptor;
 
 public class HierarchyGraph {
 
   Descriptor desc;
 
+  boolean isSCgraph;
+
   String name;
 
   // graph structure
@@ -26,6 +28,8 @@ public class HierarchyGraph {
   Map<Descriptor, HNode> mapDescToHNode;
   Map<HNode, Set<Descriptor>> mapHNodeToDescSet;
   Map<HNode, HNode> mapHNodeToCurrentHNode; // tracking which node corresponds to the initial node
+  Map<String, HNode> mapHNodeNameToCurrentHNode; // tracking which node corresponds to the initial
+                                                 // node
   Map<HNode, Set<HNode>> mapMergeNodetoMergingSet;
 
   // data structures for a combination node
@@ -34,9 +38,11 @@ public class HierarchyGraph {
   Map<Set<HNode>, HNode> mapCombineNodeSetToCombinationNode;
   Map<Set<HNode>, Set<HNode>> mapCombineNodeSetToOutgoingNodeSet;
 
-  Set<HNode> nodeSet;
+  Map<HNode, Set<HNode>> mapNormalNodeToSCNodeReachToSet;
 
-  public static int seed = 0;
+  Map<Set<HNode>, Set<HNode>> mapCombineNodeSetToFirstNodeOfChainSet;
+
+  Set<HNode> nodeSet;
 
   // for the lattice generation
   Map<HNode, Integer> mapHNodeToUniqueIndex;
@@ -61,6 +67,21 @@ public class HierarchyGraph {
 
     mapHNodeToCurrentHNode = new HashMap<HNode, HNode>();
 
+    mapHNodeNameToCurrentHNode = new HashMap<String, HNode>();
+
+    mapNormalNodeToSCNodeReachToSet = new HashMap<HNode, Set<HNode>>();
+
+    mapCombineNodeSetToFirstNodeOfChainSet = new HashMap<Set<HNode>, Set<HNode>>();
+
+    isSCgraph = false;
+  }
+
+  public void setSCGraph(boolean in) {
+    isSCgraph = in;
+  }
+
+  public boolean isSCGraph() {
+    return isSCgraph;
   }
 
   public Descriptor getDesc() {
@@ -97,10 +118,18 @@ public class HierarchyGraph {
     return mapHNodeToCurrentHNode;
   }
 
+  public Map<String, HNode> getMapHNodeNameToCurrentHNode() {
+    return mapHNodeNameToCurrentHNode;
+  }
+
   public void setMapHNodeToCurrentHNode(Map<HNode, HNode> mapHNodeToCurrentHNode) {
     this.mapHNodeToCurrentHNode = mapHNodeToCurrentHNode;
   }
 
+  public void setMapHNodeNameToCurrentHNode(Map<String, HNode> mapHNodeNameToCurrentHNode) {
+    this.mapHNodeNameToCurrentHNode = mapHNodeNameToCurrentHNode;
+  }
+
   public Map<Descriptor, HNode> getMapDescToHNode() {
     return mapDescToHNode;
   }
@@ -128,22 +157,25 @@ public class HierarchyGraph {
     if (possibleCycleSet.size() > 0) {
 
       if (possibleCycleSet.size() == 1) {
+        // System.out.println("possibleCycleSet=" + possibleCycleSet + "  from src=" + srcHNode
+        // + " dstHNode=" + dstHNode);
         if (dstHNode.isSharedNode()) {
           // it has already been assigned shared node.
         } else {
           dstHNode.setSharedNode(true);
+          // System.out.println("$$$setShared=" + dstHNode);
         }
         return;
       }
 
-      HNode newMergeNode = mergeNodes(possibleCycleSet, false);
+      // System.out.println("--- CYCLIC VALUE FLOW: " + srcHNode + " -> " + dstHNode);
+      HNode newMergeNode = mergeNodes(possibleCycleSet);
       newMergeNode.setSharedNode(true);
-      System.out.println("### INTRODUCE A NEW MERGE NODE: " + newMergeNode);
-      System.out.println("### CYCLIC VALUE FLOW: " + srcHNode + " -> " + dstHNode);
+
     } else {
       getIncomingNodeSet(dstHNode).add(srcHNode);
       getOutgoingNodeSet(srcHNode).add(dstHNode);
-      System.out.println("add an edge " + srcHNode + " -> " + dstHNode);
+      // System.out.println("add an edge " + srcHNode + " -> " + dstHNode);
     }
 
   }
@@ -153,10 +185,16 @@ public class HierarchyGraph {
   }
 
   public void addEdge(Descriptor src, Descriptor dst) {
-    HNode srcHNode = getHNode(src);
-    HNode dstHNode = getHNode(dst);
 
-    addEdge(srcHNode, dstHNode);
+    if (src.equals(LocationInference.LITERALDESC)) {
+      // in this case, we do not need to add a source hnode
+      // just add a destination hnode
+      getHNode(dst);
+    } else {
+      HNode srcHNode = getHNode(src);
+      HNode dstHNode = getHNode(dst);
+      addEdge(srcHNode, dstHNode);
+    }
 
   }
 
@@ -167,9 +205,20 @@ public class HierarchyGraph {
   public HNode getHNode(Descriptor d) {
     if (!mapDescToHNode.containsKey(d)) {
       HNode newNode = new HNode(d);
+
       if (d instanceof FieldDescriptor) {
         newNode.setSkeleton(true);
       }
+
+      if (d.equals(LocationInference.TOPDESC)) {
+        newNode.setSkeleton(true);
+      }
+
+      String symbol = d.getSymbol();
+      if (symbol.startsWith(LocationInference.PCLOC) || symbol.startsWith(LocationInference.RLOC)) {
+        newNode.setSkeleton(true);
+      }
+
       mappingDescriptorToHNode(d, newNode);
       nodeSet.add(newNode);
     }
@@ -219,6 +268,7 @@ public class HierarchyGraph {
     skeletonGraph.setMapHNodeToDescSet(getMapHNodeToDescSet());
     skeletonGraph.setMapHNodetoMergeSet(getMapHNodetoMergeSet());
     skeletonGraph.setMapHNodeToCurrentHNode(getMapHNodeToCurrentHNode());
+    skeletonGraph.setMapHNodeNameToCurrentHNode(getMapHNodeNameToCurrentHNode());
 
     return skeletonGraph;
 
@@ -264,21 +314,16 @@ public class HierarchyGraph {
 
   }
 
-  public void simplifyHierarchyGraph() {
-    removeRedundantEdges();
-    combineRedundantNodes(false);
-  }
-
-  public void simplifySkeletonCombinationHierarchyGraph() {
+  public void simplifyHierarchyGraph(LocationInference infer) {
     removeRedundantEdges();
-    combineRedundantNodes(true);
+    combineRedundantNodes(infer);
   }
 
-  public void combineRedundantNodes(boolean onlyCombinationNodes) {
+  public void combineRedundantNodes(LocationInference infer) {
     // Combine field/parameter nodes who have the same set of incoming/outgoing edges.
     boolean isUpdated = false;
     do {
-      isUpdated = combineTwoRedundatnNodes(onlyCombinationNodes);
+      isUpdated = combineTwoRedundatnNodes(infer);
     } while (isUpdated);
   }
 
@@ -296,12 +341,16 @@ public class HierarchyGraph {
     return mapHNodeToOutgoingSet.get(node);
   }
 
-  private boolean combineTwoRedundatnNodes(boolean onlyCombinationNodes) {
+  private boolean combineTwoRedundatnNodes(LocationInference infer) {
     for (Iterator iterator = nodeSet.iterator(); iterator.hasNext();) {
       HNode node1 = (HNode) iterator.next();
 
-      if ((onlyCombinationNodes && (!node1.isCombinationNode()))
-          || (!onlyCombinationNodes && (!node1.isSkeleton()))) {
+      // if ((onlyCombinationNodes && (!node1.isCombinationNode()))
+      // || (!onlyCombinationNodes && (!node1.isSkeleton()))) {
+      // continue;
+      // }
+
+      if (!node1.isSkeleton()) {
         continue;
       }
 
@@ -311,11 +360,16 @@ public class HierarchyGraph {
       for (Iterator iterator2 = nodeSet.iterator(); iterator2.hasNext();) {
         HNode node2 = (HNode) iterator2.next();
 
-        if ((onlyCombinationNodes && (!node2.isCombinationNode()))
-            || (!onlyCombinationNodes && (!node2.isSkeleton()))) {
+        // if ((onlyCombinationNodes && (!node2.isCombinationNode()))
+        // || (!onlyCombinationNodes && (!node2.isSkeleton()))) {
+        // continue;
+        // }
+
+        if (!node2.isSkeleton()) {
           continue;
         }
 
+        // System.out.println("node1=" + node1 + " vs node2=" + node2);
         if (!isEligibleForMerging(node1, node2)) {
           continue;
         }
@@ -325,14 +379,26 @@ public class HierarchyGraph {
           Set<HNode> incomingNodeSet2 = getIncomingNodeSet(node2);
           Set<HNode> outgoingNodeSet2 = getOutgoingNodeSet(node2);
 
+          // System.out.println(node1 + " " + node2 + " MERGING incoming?=" + incomingNodeSet1
+          // + " vs " + incomingNodeSet2);
+          // System.out.println(node1 + " " + node2 + " MERGING outgoing?=" + outgoingNodeSet1
+          // + " vs " + outgoingNodeSet2);
+
           if (incomingNodeSet1.equals(incomingNodeSet2)
               && outgoingNodeSet1.equals(outgoingNodeSet2)) {
             // need to merge node1 and node2
-
+            // System.out.println("MERGE!!!!!!!!!!!!!");
+            // ///////////////
+            // merge two nodes only if every hierarchy graph in the inheritance hierarchy
+            // that includes both nodes allows the merging of them...
             Set<HNode> mergeSet = new HashSet<HNode>();
             mergeSet.add(node1);
             mergeSet.add(node2);
-            mergeNodes(mergeSet, onlyCombinationNodes);
+            infer.isValidMergeInheritanceCheck(desc, mergeSet);
+
+            // ///////////////
+
+            mergeNodes(mergeSet);
             return true;
           }
 
@@ -345,8 +411,6 @@ public class HierarchyGraph {
 
   private boolean isEligibleForMerging(HNode node1, HNode node2) {
 
-    System.out.println("********isEligibleForMerging=" + node1 + " " + node2);
-
     if (node1.isSharedNode() || node2.isSharedNode()) {
 
       // if either of nodes is a shared node,
@@ -358,36 +422,22 @@ public class HierarchyGraph {
 
       for (Iterator iterator = descSet.iterator(); iterator.hasNext();) {
         Descriptor desc = (Descriptor) iterator.next();
-        if (!isPrimitive(desc)) {
+        if (!LocationInference.isPrimitive(desc)) {
           return false;
         }
       }
-      System.out.println("******** true");
-      return true;
-    }
-    return false;
-  }
-
-  private boolean isPrimitive(Descriptor desc) {
-
-    if (desc instanceof FieldDescriptor) {
-      return ((FieldDescriptor) desc).getType().isPrimitive();
-    } else if (desc instanceof VarDescriptor) {
-      return ((VarDescriptor) desc).getType().isPrimitive();
-    } else if (desc instanceof InterDescriptor) {
       return true;
     }
-
-    return false;
+    return true;
   }
 
   private void addEdgeWithNoCycleCheck(HNode srcHNode, HNode dstHNode) {
     getIncomingNodeSet(dstHNode).add(srcHNode);
     getOutgoingNodeSet(srcHNode).add(dstHNode);
-    System.out.println("addEdgeWithNoCycleCheck src=" + srcHNode + " -> " + dstHNode);
+    // System.out.println("addEdgeWithNoCycleCheck src=" + srcHNode + " -> " + dstHNode);
   }
 
-  private HNode mergeNodes(Set<HNode> set, boolean onlyCombinationNodes) {
+  private HNode mergeNodes(Set<HNode> set) {
 
     Set<HNode> incomingNodeSet = new HashSet<HNode>();
     Set<HNode> outgoingNodeSet = new HashSet<HNode>();
@@ -400,12 +450,9 @@ public class HierarchyGraph {
 
     String nodeName;
     boolean isMergeNode = false;
-    if (onlyCombinationNodes) {
-      nodeName = "Comb" + (seed++);
-    } else {
-      nodeName = "Node" + (seed++);
-      isMergeNode = true;
-    }
+    nodeName = "MNode" + (LocationInference.locSeed++);
+    isMergeNode = true;
+
     HNode newMergeNode = new HNode(nodeName);
     newMergeNode.setMergeNode(isMergeNode);
 
@@ -414,16 +461,22 @@ public class HierarchyGraph {
 
     // if the input set contains a skeleton node, need to set a new merge node as skeleton also
     boolean hasSkeleton = false;
+    boolean hasShared = false;
     for (Iterator iterator = set.iterator(); iterator.hasNext();) {
       HNode inNode = (HNode) iterator.next();
       if (inNode.isSkeleton()) {
         hasSkeleton = true;
-        break;
+      }
+      if (inNode.isSharedNode()) {
+        hasShared = true;
       }
     }
-    System.out.println("--Set merging node=" + newMergeNode + " as a skeleton=" + set
-        + " hasSkeleton=" + hasSkeleton);
+    // System.out.println("-----Set merging node=" + newMergeNode + " as a skeleton=" + set
+    // + " hasSkeleton=" + hasSkeleton + " CUR DESC=" + desc);
     newMergeNode.setSkeleton(hasSkeleton);
+    newMergeNode.setSharedNode(hasShared);
+
+    // System.out.println("-----MERGING NODE=" + set + " new node=" + newMergeNode);
 
     for (Iterator iterator = set.iterator(); iterator.hasNext();) {
       HNode node = (HNode) iterator.next();
@@ -459,35 +512,42 @@ public class HierarchyGraph {
         mergedSkeletonNode.add(merged);
       }
     }
-    mapMergeNodetoMergingSet.put(newMergeNode, mergedSkeletonNode);
-    for (Iterator iterator = mergedSkeletonNode.iterator(); iterator.hasNext();) {
+
+    // mapMergeNodetoMergingSet.put(newMergeNode, mergedSkeletonNode);
+    // for (Iterator iterator = set.iterator(); iterator.hasNext();) {
+    mapMergeNodetoMergingSet.put(newMergeNode, set);
+    for (Iterator iterator = set.iterator(); iterator.hasNext();) {
       HNode mergedNode = (HNode) iterator.next();
       addMapHNodeToCurrentHNode(mergedNode, newMergeNode);
     }
-    System.out.println("\n###mergedSkeletonNode=" + mergedSkeletonNode);
-    System.out.println("###MERGING NODE=" + set + " new node=" + newMergeNode);
 
     for (Iterator iterator = set.iterator(); iterator.hasNext();) {
       HNode hNode = (HNode) iterator.next();
-      System.out.println("old=" + hNode + "----->newNode=" + getCurrentHNode(hNode));
+      // System.out.println("old=" + hNode + "----->newNode=" + getCurrentHNode(hNode));
     }
 
+    // System.out.println();
+
     return newMergeNode;
   }
 
   private void addMapHNodeToCurrentHNode(HNode curNode, HNode newNode) {
+
     if (curNode.isMergeNode()) {
       Set<HNode> mergingSet = getMergingSet(curNode);
       mergingSet.add(curNode);
-      System.out.println("addMapHNodeToCurrentHNode curNode=" + curNode + " meringSet="
-          + mergingSet);
+      // System.out.println("-------addMapHNodeToCurrentHNode curNode=" + curNode + " meringSet="
+      // + mergingSet + " newNode=" + newNode);
       for (Iterator iterator = mergingSet.iterator(); iterator.hasNext();) {
         HNode mergingNode = (HNode) iterator.next();
         mapHNodeToCurrentHNode.put(mergingNode, newNode);
+        mapHNodeNameToCurrentHNode.put(mergingNode.getName(), newNode);
       }
     } else {
       mapHNodeToCurrentHNode.put(curNode, newNode);
+      mapHNodeNameToCurrentHNode.put(curNode.getName(), newNode);
     }
+
   }
 
   public HNode getCurrentHNode(HNode node) {
@@ -497,6 +557,10 @@ public class HierarchyGraph {
     return mapHNodeToCurrentHNode.get(node);
   }
 
+  public HNode getCurrentHNode(String nodeName) {
+    return mapHNodeNameToCurrentHNode.get(nodeName);
+  }
+
   private Set<HNode> getMergingSet(HNode mergeNode) {
     Set<HNode> mergingSet = new HashSet<HNode>();
     Set<HNode> mergedNode = mapMergeNodetoMergingSet.get(mergeNode);
@@ -552,6 +616,68 @@ public class HierarchyGraph {
 
   }
 
+  public Set<HNode> getReachableSCNodeSet(HNode startNode) {
+    // returns the set of hnodes which is reachable from the startNode and is either SC node or a
+    // node which is directly connected to the SC nodes
+    Set<HNode> reachable = new HashSet<HNode>();
+    Set<HNode> visited = new HashSet<HNode>();
+    visited.add(startNode);
+    recurReachableNodeSet(startNode, visited, reachable);
+    return reachable;
+  }
+
+  public Set<HNode> getSCNodeReachToSet(HNode node) {
+    if (!mapNormalNodeToSCNodeReachToSet.containsKey(node)) {
+      mapNormalNodeToSCNodeReachToSet.put(node, new HashSet<HNode>());
+    }
+    return mapNormalNodeToSCNodeReachToSet.get(node);
+  }
+
+  private void recurReachableNodeSet(HNode node, Set<HNode> visited, Set<HNode> reachable) {
+
+    Set<HNode> outSet = getOutgoingNodeSet(node);
+    for (Iterator iterator = outSet.iterator(); iterator.hasNext();) {
+      HNode out = (HNode) iterator.next();
+
+      if (!visited.contains(out)) {
+        visited.add(out);
+        Set<HNode> reachableFromSCNodeSet = reachableFromSCNode(out);
+        mapNormalNodeToSCNodeReachToSet.put(out, reachableFromSCNodeSet);
+        if (out.isSkeleton() || out.isCombinationNode() || reachableFromSCNodeSet.size() > 0) {
+          reachable.add(out);
+        } else {
+          visited.add(out);
+          recurReachableNodeSet(out, visited, reachable);
+        }
+
+      }
+
+    }
+
+  }
+
+  private Set<HNode> reachableFromSCNode(HNode node) {
+    Set<HNode> visited = new HashSet<HNode>();
+    visited.add(node);
+    Set<HNode> reachable = new HashSet<HNode>();
+    recurReachableFromSCNode(node, reachable, visited);
+    return reachable;
+  }
+
+  private void recurReachableFromSCNode(HNode node, Set<HNode> reachable, Set<HNode> visited) {
+    Set<HNode> inNodeSet = getIncomingNodeSet(node);
+    for (Iterator iterator = inNodeSet.iterator(); iterator.hasNext();) {
+      HNode inNode = (HNode) iterator.next();
+      if (inNode.isSkeleton() || inNode.isCombinationNode()) {
+        visited.add(inNode);
+        reachable.add(inNode);
+      } else if (!visited.contains(inNode)) {
+        visited.add(inNode);
+        recurReachableFromSCNode(inNode, reachable, visited);
+      }
+    }
+  }
+
   public Set<HNode> getDirectlyReachableSkeletonCombinationNodeFrom(HNode node,
       Set<HNode> combinationNodeSet) {
     Set<HNode> reachable = new HashSet<HNode>();
@@ -655,8 +781,10 @@ public class HierarchyGraph {
   }
 
   public HNode getCombinationNode(Set<HNode> combineSet) {
+    assert isSCGraph();
     if (!mapCombineNodeSetToCombinationNode.containsKey(combineSet)) {
-      String name = "COMB" + (seed++);
+      String name = "COMB" + (LocationInference.locSeed++);
+      System.out.println("-NEW COMB NODE=" + name);
       HNode node = new HNode(name);
       node.setCombinationNode(true);
       nodeSet.add(node);
@@ -683,9 +811,48 @@ public class HierarchyGraph {
     Set<Set<HNode>> keySet = simpleHierarchyGraph.getCombineNodeSet();
     for (Iterator iterator = keySet.iterator(); iterator.hasNext();) {
       Set<HNode> combineSet = (Set<HNode>) iterator.next();
-      System.out.println("--combineSet=" + combineSet);
       HNode combinationNode = getCombinationNode(combineSet);
-      System.out.println("--combinationNode=" + combinationNode);
+      System.out.println("\n@INSERT COMBINATION NODE FOR combineSet=" + combineSet
+          + "  --combinationNode=" + combinationNode);
+      System.out.println("      --hierarchynodes="
+          + simpleHierarchyGraph.getCombinationNodeSetByCombineNodeSet(combineSet));
+
+      Set<HNode> simpleHNodeSet =
+          simpleHierarchyGraph.getCombinationNodeSetByCombineNodeSet(combineSet);
+
+      // check whether a hnode in the simple hierarchy graph is the first node of the chain
+      // if all incoming combination nodes to the hnode have a different combination set from the
+      // hnode, it is the first node of the chain
+      for (Iterator iterator2 = simpleHNodeSet.iterator(); iterator2.hasNext();) {
+        HNode simpleHNode = (HNode) iterator2.next();
+        boolean isFirstNodeOfChain = true;
+        Set<HNode> incomingNodeSet = simpleHierarchyGraph.getIncomingNodeSet(simpleHNode);
+        for (Iterator iterator3 = incomingNodeSet.iterator(); iterator3.hasNext();) {
+          HNode inNode = (HNode) iterator3.next();
+          if (inNode.isCombinationNode()) {
+            Set<HNode> inNodeCombineSet =
+                simpleHierarchyGraph.getCombineSetByCombinationNode(inNode);
+            if (inNodeCombineSet.equals(combineSet)) {
+              isFirstNodeOfChain = false;
+              break;
+            }
+          }
+        }
+        simpleHNode.setDirectCombinationNode(isFirstNodeOfChain);
+        if (isFirstNodeOfChain) {
+          simpleHierarchyGraph.addFirstNodeOfChain(combineSet, simpleHNode);
+          System.out.println("IT IS THE FIRST NODE OF THE CHAIN:" + simpleHNode);
+          // System.out.println("--->INCOMING NODES=");
+          // Set<HNode> inNodeSet = simpleHierarchyGraph.getIncomingNodeSet(simpleHNode);
+          // for (Iterator iterator3 = inNodeSet.iterator(); iterator3.hasNext();) {
+          // HNode inNode = (HNode) iterator3.next();
+          // System.out.println("          inNode=" + inNode + "   combineSet="
+          // + simpleHierarchyGraph.getCombineSetByCombinationNode(inNode) + " SKELETON TO SET="
+          // + simpleHierarchyGraph.getSkeleteNodeSetReachTo(inNode));
+          // }
+        }
+      }
+
       // add an edge from a skeleton node to a combination node
       for (Iterator iterator2 = combineSet.iterator(); iterator2.hasNext();) {
         HNode inSkeletonNode = (HNode) iterator2.next();
@@ -699,6 +866,7 @@ public class HierarchyGraph {
           srcNode = getHNode(inSkeletonNode.getDescriptor());
         }
         // System.out.println("--srcNode=" + srcNode);
+        System.out.println("     ADD EDGE SRC=" + srcNode + " -> " + combinationNode);
         addEdgeWithNoCycleCheck(srcNode, combinationNode);
       }
 
@@ -719,66 +887,43 @@ public class HierarchyGraph {
         }
       }
 
-      System.out.println("--");
+      // System.out.println("--");
 
     }
 
   }
 
-  private void addCombinationNode(HNode curNode, Set<HNode> reachToSet, Set<HNode> reachableSet) {
-    if (!mapSkeletonNodeSetToCombinationNode.containsKey(reachToSet)) {
-      // need to create a new combination node
-      String nodeName = "Comb" + (seed++);
-      HNode newCombinationNode = new HNode(nodeName);
-      newCombinationNode.setCombinationNode(true);
-
-      nodeSet.add(newCombinationNode);
-      mapSkeletonNodeSetToCombinationNode.put(reachToSet, newCombinationNode);
-
-      for (Iterator iterator = reachToSet.iterator(); iterator.hasNext();) {
-        HNode reachToNode = (HNode) iterator.next();
-        addEdge(reachToNode, newCombinationNode);
-      }
+  public Set<HNode> getSkeleteNodeSetReachToNoTransitive(HNode node) {
 
-    }
+    Set<HNode> reachToSet = new HashSet<HNode>();
+    Set<HNode> visited = new HashSet<HNode>();
+    // visited.add(node);
+    recurSkeletonReachTo(node, reachToSet, visited);
 
-    HNode combinationNode = mapSkeletonNodeSetToCombinationNode.get(reachToSet);
-    for (Iterator iterator = reachableSet.iterator(); iterator.hasNext();) {
-      HNode reachableNode = (HNode) iterator.next();
-      addEdge(combinationNode, reachableNode);
-    }
+    // obsolete!
+    // if a node reaches to one of elements in the reachToSet, we do not need to keep it
+    // because the node is not directly connected to the combination node
+    // removeRedundantReachToNodes(reachToSet);
 
+    return removeTransitivelyReachToSet(reachToSet);
+    // return reachToSet;
   }
 
-  private Set<HNode> getSkeleteNodeSetReachTo(HNode node) {
+  public Set<HNode> getSkeleteNodeSetReachTo(HNode node) {
 
     Set<HNode> reachToSet = new HashSet<HNode>();
     Set<HNode> visited = new HashSet<HNode>();
+    // visited.add(node);
     recurSkeletonReachTo(node, reachToSet, visited);
 
+    // obsolete!
     // if a node reaches to one of elements in the reachToSet, we do not need to keep it
     // because the node is not directly connected to the combination node
+    // removeRedundantReachToNodes(reachToSet);
 
-    removeRedundantReachToNodes(reachToSet);
-
-    return reachToSet;
-  }
-
-  private void removeRedundantReachToNodes(Set<HNode> reachToSet) {
-
-    Set<HNode> toberemoved = new HashSet<HNode>();
-    for (Iterator iterator = reachToSet.iterator(); iterator.hasNext();) {
-      HNode cur = (HNode) iterator.next();
-
-      for (Iterator iterator2 = reachToSet.iterator(); iterator2.hasNext();) {
-        HNode dst = (HNode) iterator2.next();
-        if (!cur.equals(dst) && reachTo(cur, dst)) {
-          // it is redundant
-          toberemoved.add(cur);
-        }
-      }
-    }
-    reachToSet.removeAll(toberemoved);
+    // TODO
+    return removeTransitivelyReachToSet(reachToSet);
+    // return reachToSet;
   }
 
   private void recurSkeletonReachTo(HNode node, Set<HNode> reachToSet, Set<HNode> visited) {
@@ -788,6 +933,7 @@ public class HierarchyGraph {
       HNode inNode = (HNode) iterator.next();
 
       if (inNode.isSkeleton()) {
+        visited.add(inNode);
         reachToSet.add(inNode);
       } else if (!visited.contains(inNode)) {
         visited.add(inNode);
@@ -845,9 +991,15 @@ public class HierarchyGraph {
     clone.setMapHNodeToDescSet(getMapHNodeToDescSet());
     clone.setMapHNodetoMergeSet(getMapHNodetoMergeSet());
     clone.setMapHNodeToCurrentHNode(getMapHNodeToCurrentHNode());
+    clone.setMapHNodeNameToCurrentHNode(getMapHNodeNameToCurrentHNode());
+
     return clone;
   }
 
+  public void setMapCombineNodeSetToCombinationNode(Map<Set<HNode>, HNode> in) {
+    mapCombineNodeSetToCombinationNode = in;
+  }
+
   public Map<HNode, Set<HNode>> getMapHNodetoMergeSet() {
     return mapMergeNodetoMergingSet;
   }
@@ -871,12 +1023,48 @@ public class HierarchyGraph {
       HNode node = (HNode) iterator.next();
       if (!node.isSkeleton()) {
         Set<HNode> reachToSet = getSkeleteNodeSetReachTo(node);
+        // Set<HNode> tempSet = removeTransitivelyReachToSet(reachToSet);
+        // System.out.println("ALL REACH SET=" + reachToSet);
+        // reachToSet = removeTransitivelyReachToSet(reachToSet);
+
+        Set<HNode> curReachToSet = new HashSet<HNode>();
+        for (Iterator iterator2 = reachToSet.iterator(); iterator2.hasNext();) {
+          HNode reachSkeletonNode = (HNode) iterator2.next();
+          curReachToSet.add(getCurrentHNode(reachSkeletonNode));
+        }
+
+        // System.out.println("-curReachToSett=" + curReachToSet + "  reachToSet=" + reachToSet);
+
+        reachToSet = curReachToSet;
+        // System.out.println("$node=" + node + "   reachToNodeSet=" + reachToSet + " tempSet="
+        // + tempSet);
         if (reachToSet.size() > 1) {
           // if (countSkeletonNodes(reachToSet) > 1) {
-          System.out.println("-node=" + node + "  reachToSet=" + reachToSet);
+          System.out.println("\n-node=" + node + "  reachToSet=" + reachToSet);
           System.out.println("-set combinationnode=" + node);
           node.setCombinationNode(true);
           mapCombinationNodeToCombineNodeSet.put(node, reachToSet);
+
+          // check if this node is the first node of the chain
+          // boolean isFirstNodeOfChain = false;
+          // Set<HNode> inNodeSet = getIncomingNodeSet(node);
+          // for (Iterator iterator2 = inNodeSet.iterator(); iterator2.hasNext();) {
+          // HNode inNode = (HNode) iterator2.next();
+          // if (inNode.isSkeleton()) {
+          // isFirstNodeOfChain = true;
+          // } else if (inNode.isCombinationNode()) {
+          // Set<HNode> inNodeReachToSet = getSkeleteNodeSetReachTo(inNode);
+          // if (!reachToSet.equals(inNodeReachToSet)) {
+          // isFirstNodeOfChain = true;
+          // }
+          // }
+          // }
+          //
+          // if (isFirstNodeOfChain) {
+          // node.setDirectCombinationNode(true);
+          // addFirstNodeOfChain(reachToSet, node);
+          // }
+
         }
       }
     }
@@ -893,6 +1081,52 @@ public class HierarchyGraph {
 
   }
 
+  public void addFirstNodeOfChain(Set<HNode> combineSet, HNode firstNode) {
+
+    if (!mapCombineNodeSetToFirstNodeOfChainSet.containsKey(combineSet)) {
+      mapCombineNodeSetToFirstNodeOfChainSet.put(combineSet, new HashSet<HNode>());
+    }
+
+    mapCombineNodeSetToFirstNodeOfChainSet.get(combineSet).add(firstNode);
+
+  }
+
+  public Set<HNode> getFirstNodeOfCombinationNodeChainSet(Set<HNode> combineNodeSet) {
+    return mapCombineNodeSetToFirstNodeOfChainSet.get(combineNodeSet);
+  }
+
+  private Set<HNode> removeTransitivelyReachToSet(Set<HNode> reachToSet) {
+
+    Set<HNode> toberemoved = new HashSet<HNode>();
+    Set<HNode> visited = new HashSet<HNode>();
+    for (Iterator iterator = reachToSet.iterator(); iterator.hasNext();) {
+      HNode node = (HNode) iterator.next();
+      visited.add(node);
+      recurIsReachingTo(node, reachToSet, toberemoved, visited);
+    }
+
+    Set<HNode> rSet = new HashSet<HNode>();
+    rSet.addAll(reachToSet);
+    rSet.removeAll(toberemoved);
+    return rSet;
+  }
+
+  private void recurIsReachingTo(HNode curNode, Set<HNode> reachToSet, Set<HNode> toberemoved,
+      Set<HNode> visited) {
+    Set<HNode> inNodeSet = getIncomingNodeSet(curNode);
+
+    for (Iterator iterator = inNodeSet.iterator(); iterator.hasNext();) {
+      HNode inNode = (HNode) iterator.next();
+      if (reachToSet.contains(inNode)) {
+        toberemoved.add(inNode);
+      } else if (!visited.contains(inNode)) {
+        visited.add(inNode);
+        recurIsReachingTo(inNode, reachToSet, toberemoved, visited);
+      }
+    }
+
+  }
+
   public Map<HNode, Set<HNode>> getMapCombinationNodeToCombineNodeSet() {
     return mapCombinationNodeToCombineNodeSet;
   }
@@ -978,7 +1212,7 @@ public class HierarchyGraph {
 
   public void assignUniqueIndexToNode() {
     int idx = 1;
-    System.out.println("nodeSet=" + nodeSet);
+    // System.out.println("nodeSet=" + nodeSet);
     for (Iterator iterator = nodeSet.iterator(); iterator.hasNext();) {
       HNode node = (HNode) iterator.next();
       mapHNodeToUniqueIndex.put(node, idx);
@@ -991,7 +1225,7 @@ public class HierarchyGraph {
     }
   }
 
-  public BasisSet computeBasisSet() {
+  public BasisSet computeBasisSet(Set<HNode> notGenerateSet) {
 
     // assign a unique index to a node
     assignUniqueIndexToNode();
@@ -1000,21 +1234,25 @@ public class HierarchyGraph {
     for (Iterator iterator = nodeSet.iterator(); iterator.hasNext();) {
       HNode node = (HNode) iterator.next();
 
+      if (notGenerateSet.contains(node)) {
+        System.out.println("%%%SKIP =" + node);
+        continue;
+      }
       Set<Integer> basis = new HashSet<Integer>();
       basis.addAll(BASISTOPELEMENT);
 
       Set<HNode> reachableNodeSet = getReachableNodeSetFrom(node);
-      System.out.println("node=" + node + "    reachableNodeSet=" + reachableNodeSet);
-      System.out.println("mapHNodeToUniqueIndex.get(node)=" + mapHNodeToUniqueIndex.get(node));
+      // System.out.println("node=" + node + "    reachableNodeSet=" + reachableNodeSet);
+      // System.out.println("mapHNodeToUniqueIndex.get(node)=" + mapHNodeToUniqueIndex.get(node));
       // if a node is reachable from the current node
       // need to remove the index of the reachable node from the basis
 
       basis.remove(getHNodeIndex(node));
       for (Iterator iterator2 = reachableNodeSet.iterator(); iterator2.hasNext();) {
         HNode reachableNode = (HNode) iterator2.next();
-        System.out.println("reachableNode=" + reachableNode);
-        System.out.println("getHNodeIndex(reachableNode))="
-            + mapHNodeToUniqueIndex.get(reachableNode));
+        // System.out.println("reachableNode=" + reachableNode);
+        // System.out.println("getHNodeIndex(reachableNode))="
+        // + mapHNodeToUniqueIndex.get(reachableNode));
         int idx = getHNodeIndex(reachableNode);
         basis.remove(idx);
       }
@@ -1065,10 +1303,20 @@ public class HierarchyGraph {
   }
 
   public void writeGraph() {
+    writeGraph(false);
+  }
+
+  public void writeGraph(boolean isSimple) {
 
     String graphName = "hierarchy" + name;
     graphName = graphName.replaceAll("[\\W]", "");
 
+    if (isSimple) {
+      graphName += "_PAPER";
+    }
+
+    // System.out.println("***graphName=" + graphName + "   node siz=" + nodeSet.size());
+
     try {
       BufferedWriter bw = new BufferedWriter(new FileWriter(graphName + ".dot"));
 
@@ -1085,18 +1333,30 @@ public class HierarchyGraph {
 
         if (outSet.size() == 0) {
           if (!addedNodeSet.contains(u)) {
-            drawNode(bw, u);
+            if (!isSimple) {
+              drawNode(bw, u);
+            } else {
+              drawNodeName(bw, u);
+            }
             addedNodeSet.add(u);
           }
         } else {
           for (Iterator iterator = outSet.iterator(); iterator.hasNext();) {
             HNode v = (HNode) iterator.next();
             if (!addedNodeSet.contains(u)) {
-              drawNode(bw, u);
+              if (!isSimple) {
+                drawNode(bw, u);
+              } else {
+                drawNodeName(bw, u);
+              }
               addedNodeSet.add(u);
             }
             if (!addedNodeSet.contains(v)) {
-              drawNode(bw, v);
+              if (!isSimple) {
+                drawNode(bw, v);
+              } else {
+                drawNodeName(bw, v);
+              }
               addedNodeSet.add(v);
             }
             bw.write("" + u.getName() + " -> " + v.getName() + ";\n");
@@ -1134,11 +1394,17 @@ public class HierarchyGraph {
     return str;
   }
 
+  private void drawNodeName(BufferedWriter bw, HNode node) throws IOException {
+    String nodeName = node.getNamePropertyString();
+    bw.write(node.getName() + " [label=\"" + nodeName + "\"]" + ";\n");
+  }
+
   private void drawNode(BufferedWriter bw, HNode node) throws IOException {
     String nodeName;
     if (node.isMergeNode()) {
       nodeName = node.getNamePropertyString();
       Set<HNode> mergeSet = mapMergeNodetoMergingSet.get(node);
+      // System.out.println("node=" + node + "   mergeSet=" + mergeSet);
       nodeName += ":" + convertMergeSetToString(mergeSet);
     } else {
       nodeName = node.getNamePropertyString();
@@ -1173,4 +1439,205 @@ public class HierarchyGraph {
     return max;
   }
 
+  public Stack<String> computeDistance2(HNode startNode, Set<HNode> endNodeSet,
+      HierarchyGraph scGraph, Set<HNode> combineSet) {
+    System.out
+        .println("#####computeDistanceance startNode=" + startNode + " endNode=" + endNodeSet);
+    Stack<String> trace = new Stack<String>();
+    return recur_computeDistance2(startNode, endNodeSet, scGraph, 0, combineSet, trace);
+  }
+
+  public Stack<String> computeDistance(HNode startNode, Set<HNode> endNodeSet,
+      HierarchyGraph scGraph, Set<HNode> combineSet) {
+    System.out
+        .println("#####computeDistanceance startNode=" + startNode + " endNode=" + endNodeSet);
+    Stack<String> trace = new Stack<String>();
+    return recur_computeDistance(startNode, endNodeSet, 0, combineSet, trace);
+  }
+
+  private Stack<String> recur_computeDistance(HNode curNode, Set<HNode> endNodeSet, int count,
+      Set<HNode> combineSet, Stack<String> trace) {
+
+    if (!curNode.isSkeleton()) {
+      if (curNode.isSharedNode()) {
+        trace.add("S");
+      } else {
+        trace.add("N");
+      }
+    }
+
+    if (endNodeSet.contains(curNode)) {
+      // it reaches to one of endNodeSet
+      return trace;
+    }
+
+    Set<HNode> inNodeSet = getIncomingNodeSet(curNode);
+
+    int curMaxDistance = 0;
+    Stack<String> curMaxTrace = (Stack<String>) trace.clone();
+    ;
+    for (Iterator iterator = inNodeSet.iterator(); iterator.hasNext();) {
+      HNode inNode = (HNode) iterator.next();
+      // traverse more...
+
+      if (inNode.isCombinationNode() && combineSet != null) {
+        // check if inNode have the same combination set of the starting node
+        Set<HNode> inNodeCombineSet = getCombineSetByCombinationNode(inNode);
+        if (!inNodeCombineSet.equals(combineSet)) {
+          continue;
+        }
+      }
+
+      // System.out.println("    traverse more to" + inNode + "  before-trace=" + trace);
+      Stack<String> newTrace = (Stack<String>) trace.clone();
+      Stack<String> curTrace =
+          recur_computeDistance(inNode, endNodeSet, count, combineSet, newTrace);
+      // System.out.println("curTracerTrace=" + curTrace);
+
+      if (curTrace != null && curTrace.size() > curMaxDistance) {
+        curMaxTrace = curTrace;
+        curMaxDistance = curTrace.size();
+      }
+    }
+    return curMaxTrace;
+
+  }
+
+  private Stack<String> recur_computeDistance2(HNode curNode, Set<HNode> endNodeSet,
+      HierarchyGraph scGraph, int count, Set<HNode> combineSet, Stack<String> trace) {
+
+    if (!curNode.isSkeleton()) {
+      if (curNode.isSharedNode()) {
+        trace.add("S");
+      } else {
+        trace.add("N");
+      }
+    }
+
+    System.out.println("   curNode=" + curNode + "  curTrace=" + trace);
+    // System.out.println("     curNode=" + curNode + "  curSCNode="
+    // + scGraph.getCurrentHNode(curNode) + " contains="
+    // + endNodeSet.contains(scGraph.getCurrentHNode(curNode)));
+    if (endNodeSet.contains(scGraph.getCurrentHNode(curNode))) {
+      // it reaches to one of endNodeSet
+      return trace;
+    }
+
+    Set<HNode> inNodeSet = getIncomingNodeSet(curNode);
+
+    int curMaxDistance = 0;
+    Stack<String> curMaxTrace = (Stack<String>) trace.clone();
+    ;
+    for (Iterator iterator = inNodeSet.iterator(); iterator.hasNext();) {
+      HNode inNode = (HNode) iterator.next();
+      // traverse more...
+
+      if (inNode.isCombinationNode() && combineSet != null) {
+        // check if inNode have the same combination set of the starting node
+        Set<HNode> inNodeCombineSet = getCombineSetByCombinationNode(inNode);
+        if (!inNodeCombineSet.equals(combineSet)) {
+          continue;
+        }
+      }
+
+      // Stack<String> newTrace = (Stack<String>) trace.clone();
+      // Stack<String> curTrace =
+      // recur_computeDistance(inNode, endNodeSet, scGraph, count, combineSet, newTrace);
+      // if (curTrace != null) {
+      // return curTrace;
+      // }
+
+      Set<HNode> inReachToNodeSet = getSkeleteNodeSetReachToNoTransitive(inNode);
+      Set<HNode> inCurReachToNodeSet = new HashSet<HNode>();
+      for (Iterator iterator2 = inReachToNodeSet.iterator(); iterator2.hasNext();) {
+        HNode aboveNode = (HNode) iterator2.next();
+        inCurReachToNodeSet.add(getCurrentHNode(aboveNode));
+      }
+
+      if (combineSet != null || inCurReachToNodeSet.equals(endNodeSet)) {
+        System.out
+            .println("        traverse to incomingNode=" + inNode + "  before-trace=" + trace);
+
+        Stack<String> newTrace = (Stack<String>) trace.clone();
+        Stack<String> curTrace =
+            recur_computeDistance2(inNode, endNodeSet, scGraph, count, combineSet, newTrace);
+
+        if (curTrace != null && curTrace.size() > curMaxDistance) {
+          curMaxTrace = curTrace;
+          curMaxDistance = curTrace.size();
+        }
+      } else {
+        System.out.println("NOT TRAVERSE a new inNode=" + inNode + " inReachToNodeSet="
+            + inCurReachToNodeSet);
+      }
+
+    }
+    return curMaxTrace;
+  }
+
+  public int countNonSharedNode(HNode startNode, Set<HNode> endNodeSet) {
+    System.out.println("countNonSharedNode startNode=" + startNode + " endNode=" + endNodeSet);
+    return recur_countNonSharedNode(startNode, endNodeSet, 0);
+  }
+
+  private int recur_countNonSharedNode(HNode startNode, Set<HNode> endNodeSet, int count) {
+
+    Set<HNode> inNodeSet = getIncomingNodeSet(startNode);
+
+    for (Iterator iterator = inNodeSet.iterator(); iterator.hasNext();) {
+      HNode inNode = (HNode) iterator.next();
+      if (endNodeSet.contains(inNode)) {
+        count++;
+        return count;
+      } else {
+        if (!inNode.isSharedNode()) {
+          count++;
+        }
+        return recur_countNonSharedNode2(inNode, endNodeSet, count);
+      }
+    }
+
+    return 0;
+  }
+
+  public int countNonSharedNode2(HNode startNode, Set<HNode> endNodeSet) {
+    System.out.println("countNonSharedNode startNode=" + startNode + " endNode=" + endNodeSet);
+    return recur_countNonSharedNode2(startNode, endNodeSet, 0);
+  }
+
+  private int recur_countNonSharedNode2(HNode startNode, Set<HNode> endNodeSet, int count) {
+
+    Set<HNode> inNodeSet = getIncomingNodeSet(startNode);
+
+    if (inNodeSet.size() == 0) {
+      // it is directly connected to the TOP node
+    }
+
+    for (Iterator iterator = inNodeSet.iterator(); iterator.hasNext();) {
+      HNode inNode = (HNode) iterator.next();
+      if (endNodeSet.contains(inNode)) {
+        return count;
+      } else {
+        if (!inNode.isSharedNode()) {
+          count++;
+        }
+        return recur_countNonSharedNode2(inNode, endNodeSet, count);
+      }
+    }
+
+    // System.out.println("startNode=" + startNode + " inNodeSet=" + inNodeSet);
+    // HNode inNode = inNodeSet.iterator().next();
+    return -1;
+  }
+
+  public void removeIsolatedNodes() {
+    Set<HNode> toberemoved = new HashSet<HNode>();
+    for (Iterator iterator = nodeSet.iterator(); iterator.hasNext();) {
+      HNode node = (HNode) iterator.next();
+      if (getIncomingNodeSet(node).isEmpty() && getOutgoingNodeSet(node).isEmpty()) {
+        toberemoved.add(node);
+      }
+    }
+    nodeSet.removeAll(toberemoved);
+  }
 }