diff --git a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/PositionWritableTest.java b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/PositionWritableTest.java
index fc67245..003406d 100644
--- a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/PositionWritableTest.java
+++ b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/PositionWritableTest.java
@@ -42,7 +42,6 @@
             Assert.assertEquals(pos.getPosId(), posId);
             
             Assert.assertEquals(pos1.toString(), pos.toString());
-            String out = pos.toString();
         }
     }
 }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeRemoveVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeRemoveVertex.java
index 9db9418..7f85fc7 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeRemoveVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeRemoveVertex.java
@@ -10,7 +10,7 @@
 import edu.uci.ics.genomix.pregelix.format.GraphCleanOutputFormat;
 import edu.uci.ics.genomix.pregelix.io.MessageWritable;
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
-import edu.uci.ics.genomix.pregelix.operator.pathmerge.BasicPathMergeVertex;
+import edu.uci.ics.genomix.pregelix.operator.pathmerge.BasicGraphCleanVertex;
 import edu.uci.ics.genomix.pregelix.type.AdjMessage;
 import edu.uci.ics.genomix.pregelix.util.VertexUtil;
 
@@ -46,7 +46,7 @@
  * Naive Algorithm for path merge graph
  */
 public class BridgeRemoveVertex extends
-    BasicPathMergeVertex {
+    BasicGraphCleanVertex {
     public static final String LENGTH = "BridgeRemoveVertex.length";
     private int length = -1;
 
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicGraphCleanVertex.java
similarity index 99%
rename from genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicPathMergeVertex.java
rename to genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicGraphCleanVertex.java
index 3039bc1..8cb8382 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicGraphCleanVertex.java
@@ -19,10 +19,10 @@
 /**
  * Naive Algorithm for path merge graph
  */
-public class BasicPathMergeVertex extends
+public class BasicGraphCleanVertex extends
         Vertex<KmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> {
-    public static final String KMER_SIZE = "BasicPathMergeVertex.kmerSize";
-    public static final String ITERATIONS = "BasicPathMergeVertex.iteration";
+    public static final String KMER_SIZE = "BasicGraphCleanVertex.kmerSize";
+    public static final String ITERATIONS = "BasicGraphCleanVertex.iteration";
     public static int kmerSize = -1;
     protected int maxIteration = -1;
     
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java
index 1309fba..d9cfc8c 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java
@@ -42,7 +42,7 @@
  * The details about message are in edu.uci.ics.pregelix.example.io.MessageWritable. 
  */
 public class LogAlgorithmForPathMergeVertex extends
-    BasicPathMergeVertex {
+    BasicGraphCleanVertex {
 
     private ArrayList<MessageWritable> receivedMsgList = new ArrayList<MessageWritable>();
     KmerBytesWritable tmpKmer = new KmerBytesWritable();
@@ -156,6 +156,7 @@
       //process merge when receiving msg
         while (msgIterator.hasNext()) {
             incomingMsg = msgIterator.next();
+            /** for final processing **/
             if(getMsgFlag() == MessageFlag.IS_FINAL){
                 sendFinalMergeMsg();
                 break;
@@ -199,13 +200,15 @@
         else if (getSuperstep() == 2)
             initState(msgIterator);
         else if (getSuperstep() % 3 == 0 && getSuperstep() <= maxIteration) {
-            if(msgIterator.hasNext()){ //for processing final merge
+            /** for processing final merge **/
+            if(msgIterator.hasNext()){
                 incomingMsg = msgIterator.next();
                 if(getMsgFlag() == MessageFlag.IS_FINAL){
                     setFinalState();
                     processFinalMerge(incomingMsg);
                 }
             }
+            /** processing general case **/
             else{
                 sendMsgToPathVertex(msgIterator);
                 if(selfFlag != State.IS_HEAD)
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/MapReduceVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/MapReduceVertex.java
index 5f70772..9d0bb13 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/MapReduceVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/MapReduceVertex.java
@@ -19,7 +19,7 @@
 import edu.uci.ics.pregelix.api.util.BspUtils;
 
 public class MapReduceVertex extends
-    BasicPathMergeVertex {
+    BasicGraphCleanVertex {
     
     private static boolean fakeVertexExist = false;
     private static KmerBytesWritable fakeVertex = null;
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P4ForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P4ForPathMergeVertex.java
index a14be92..8f97c5a 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P4ForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P4ForPathMergeVertex.java
@@ -48,7 +48,7 @@
  * Naive Algorithm for path merge graph
  */
 public class P4ForPathMergeVertex extends
-    BasicPathMergeVertex {
+    BasicGraphCleanVertex {
     public static final String RANDSEED = "P4ForPathMergeVertex.randSeed";
     public static final String PROBBEINGRANDOMHEAD = "P4ForPathMergeVertex.probBeingRandomHead";
 
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipRemoveVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipRemoveVertex.java
index 7141ae7..c1138de 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipRemoveVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipRemoveVertex.java
@@ -9,7 +9,7 @@
 import edu.uci.ics.genomix.pregelix.format.GraphCleanOutputFormat;
 import edu.uci.ics.genomix.pregelix.io.MessageWritable;
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
-import edu.uci.ics.genomix.pregelix.operator.pathmerge.BasicPathMergeVertex;
+import edu.uci.ics.genomix.pregelix.operator.pathmerge.BasicGraphCleanVertex;
 import edu.uci.ics.genomix.pregelix.type.AdjMessage;
 import edu.uci.ics.genomix.pregelix.util.VertexUtil;
 
@@ -45,7 +45,7 @@
  *  Remove tip or single node when l > constant
  */
 public class TipRemoveVertex extends
-        BasicPathMergeVertex {
+        BasicGraphCleanVertex {
     public static final String LENGTH = "TipRemoveVertex.length";
     private int length = -1;