diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/GraphVertexOperation.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/GraphVertexOperation.java
deleted file mode 100644
index 553de45..0000000
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/GraphVertexOperation.java
+++ /dev/null
@@ -1,64 +0,0 @@
-package edu.uci.ics.genomix.pregelix;
-
-import org.apache.hadoop.io.BytesWritable;
-
-import edu.uci.ics.genomix.type.old.Kmer;
-import edu.uci.ics.genomix.type.old.KmerUtil;
-
-public class GraphVertexOperation {
-	
-	/**
-	 *  generate the valid data(byte[]) from BytesWritable
-	 */
-	public static byte[] generateValidDataFromBytesWritable(BytesWritable bw){
-		byte[] wholeBytes = bw.getBytes();
-		int validNum = bw.getLength();
-		byte[] validBytes = new byte[validNum];
-		for(int i = 0; i < validNum; i++)
-			validBytes[i] = wholeBytes[i];
-		return validBytes;
-	}
-	/**
-	 * Single Vertex: in-degree = out-degree = 1
-	 * @param vertexValue 
-	 */
-	public static boolean isPathVertex(byte value){
-		if(KmerUtil.inDegree(value) == 1 && KmerUtil.outDegree(value) == 1)
-			return true;
-		return false;
-	}
-	/** 
-	 * Head Vertex:  out-degree > 0, 
-	 * @param vertexValue 
-	 */
-	public static boolean isHeadVertex(byte value){
-		if(KmerUtil.outDegree(value) > 0 && !isPathVertex(value))
-			return true;
-		return false;
-	}
-	/**
-	 * Rear Vertex:  in-degree > 0, 
-	 * @param vertexValue 
-	 */
-	public static boolean isRearVertex(byte value){
-		if(KmerUtil.inDegree(value) > 0 && !isPathVertex(value))
-			return true;
-		return false;
-	}
-	/**
-	 * update right neighber based on next vertexId
-	 */
-	public static byte updateRightNeighberByVertexId(byte oldVertexValue, byte[] neighberVertexId, int k){
-		
-		String neighberVertex = Kmer.recoverKmerFrom(k, neighberVertexId, 0, neighberVertexId.length);
-		
-		byte newBit = Kmer.GENE_CODE.getAdjBit((byte)neighberVertex.charAt(neighberVertex.length() - 1));
-		return (byte) ((byte)(oldVertexValue & 0xF0) | (byte) (newBit & 0x0F));
-	}
-	/**
-	 * update right neighber
-	 */
-	public static byte updateRightNeighber(byte oldVertexValue, byte newVertexValue){
-		return (byte) ((byte)(oldVertexValue & 0xF0) | (byte) (newVertexValue & 0x0F));
-	}
-}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/LoadGraphVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/LoadGraphVertex.java
deleted file mode 100644
index 580e1fe..0000000
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/LoadGraphVertex.java
+++ /dev/null
@@ -1,72 +0,0 @@
-package edu.uci.ics.genomix.pregelix;
-
-import java.util.Iterator;
-
-import org.apache.hadoop.io.ByteWritable;
-import org.apache.hadoop.io.BytesWritable;
-import org.apache.hadoop.io.NullWritable;
-
-import edu.uci.ics.genomix.pregelix.client.Client;
-import edu.uci.ics.genomix.pregelix.format.BinaryLoadGraphInputFormat;
-import edu.uci.ics.genomix.pregelix.format.BinaryLoadGraphOutputFormat;
-import edu.uci.ics.genomix.pregelix.io.MessageWritable;
-import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
-import edu.uci.ics.pregelix.api.graph.Vertex;
-import edu.uci.ics.pregelix.api.job.PregelixJob;
-
-/*
- * vertexId: BytesWritable
- * vertexValue: ByteWritable
- * edgeValue: NullWritable
- * message: MessageWritable
- * 
- * DNA:
- * A: 00
- * C: 01
- * G: 10
- * T: 11
- * 
- * succeed node
- *  A 00000001 1
- *  G 00000010 2
- *  C 00000100 4
- *  T 00001000 8
- * precursor node
- *  A 00010000 16
- *  G 00100000 32
- *  C 01000000 64
- *  T 10000000 128
- *  
- * For example, ONE LINE in input file: 00,01,10	0001,0010,
- * That means that vertexId is ACG, its succeed node is A and its precursor node is C.
- * The succeed node and precursor node will be stored in vertexValue and we don't use edgeValue.
- * The details about message are in edu.uci.ics.pregelix.example.io.MessageWritable. 
- */
-public class LoadGraphVertex extends Vertex<BytesWritable, ByteWritable, NullWritable, MessageWritable>{
-
-	/**
-	 * For test, just output original file
-	 */
-	@Override
-	public void compute(Iterator<MessageWritable> msgIterator) {
-		deleteVertex(getVertexId());
-		voteToHalt();
-	}
-
-	/**
-	 * @param args
-	 */
-	public static void main(String[] args) throws Exception {
-		//final int k = Integer.parseInt(args[0]);
-        PregelixJob job = new PregelixJob(LoadGraphVertex.class.getSimpleName());
-        job.setVertexClass(LoadGraphVertex.class);
-        /**
-         * BinaryInput and BinaryOutput
-         */
-        job.setVertexInputFormatClass(BinaryLoadGraphInputFormat.class); 
-        job.setVertexOutputFormatClass(BinaryLoadGraphOutputFormat.class); 
-        job.setOutputKeyClass(BytesWritable.class);
-        job.setOutputValueClass(ValueStateWritable.class);
-        Client.run(args, job);
-	}
-}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/LogAlgorithmForMergeGraphVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/LogAlgorithmForMergeGraphVertex.java
deleted file mode 100644
index 88c5c35..0000000
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/LogAlgorithmForMergeGraphVertex.java
+++ /dev/null
@@ -1,309 +0,0 @@
-package edu.uci.ics.genomix.pregelix;
-
-import java.util.Iterator;
-
-import org.apache.hadoop.io.BytesWritable;
-import org.apache.hadoop.io.NullWritable;
-
-import edu.uci.ics.pregelix.api.graph.Vertex;
-import edu.uci.ics.pregelix.api.job.PregelixJob;
-import edu.uci.ics.genomix.pregelix.client.Client;
-import edu.uci.ics.genomix.pregelix.format.LogAlgorithmForMergeGraphInputFormat;
-import edu.uci.ics.genomix.pregelix.format.LogAlgorithmForMergeGraphOutputFormat;
-import edu.uci.ics.genomix.pregelix.io.LogAlgorithmMessageWritable;
-import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
-import edu.uci.ics.genomix.pregelix.type.Message;
-import edu.uci.ics.genomix.pregelix.type.State;
-import edu.uci.ics.genomix.type.old.Kmer;
-import edu.uci.ics.genomix.type.old.KmerUtil;
-
-/*
- * vertexId: BytesWritable
- * vertexValue: ValueStateWritable
- * edgeValue: NullWritable
- * message: LogAlgorithmMessageWritable
- * 
- * DNA:
- * A: 00
- * C: 01
- * G: 10
- * T: 11
- * 
- * succeed node
- *  A 00000001 1
- *  G 00000010 2
- *  C 00000100 4
- *  T 00001000 8
- * precursor node
- *  A 00010000 16
- *  G 00100000 32
- *  C 01000000 64
- *  T 10000000 128
- *  
- * For example, ONE LINE in input file: 00,01,10	0001,0010,
- * That means that vertexId is ACG, its succeed node is A and its precursor node is C.
- * The succeed node and precursor node will be stored in vertexValue and we don't use edgeValue.
- * The details about message are in edu.uci.ics.pregelix.example.io.MessageWritable. 
- */
-public class LogAlgorithmForMergeGraphVertex extends Vertex<BytesWritable, ValueStateWritable, NullWritable, LogAlgorithmMessageWritable>{	
-	public static final String KMER_SIZE = "LogAlgorithmForMergeGraphVertex.kmerSize";
-	public static final String ITERATIONS = "MergeGraphVertex.iteration";
-	public static int kmerSize = -1;
-	private int maxIteration = -1;
-	
-	private byte[] tmpVertexId;
-	private byte[] tmpDestVertexId;
-	private BytesWritable destVertexId = new BytesWritable();
-	private byte[] mergeChainVertexId;
-	private int lengthOfMergeChainVertex;
-	private byte tmpVertexValue;
-	private ValueStateWritable tmpVal = new ValueStateWritable();
-	private LogAlgorithmMessageWritable tmpMsg = new LogAlgorithmMessageWritable();
-	/**
-	 * Log Algorithm for path merge graph
-	 */
-	/**
-     *	Load KmerSize, MaxIteration
-     */
-	@Override
-	public void compute(Iterator<LogAlgorithmMessageWritable> msgIterator) {
-		if(kmerSize == -1)
-			kmerSize = getContext().getConfiguration().getInt(KMER_SIZE, 5);
-        if (maxIteration < 0)
-            maxIteration = getContext().getConfiguration().getInt(ITERATIONS, 100);
-		tmpVertexId = GraphVertexOperation.generateValidDataFromBytesWritable(getVertexId());
-		tmpVal = getVertexValue();
-		if (getSuperstep() == 1) {
-			tmpMsg.setChainVertexId(new byte[0]);
-			if(GraphVertexOperation.isHeadVertex(tmpVal.getValue())){
-				tmpMsg.setMessage(Message.START);
-				for(byte x = Kmer.GENE_CODE.A; x<= Kmer.GENE_CODE.T ; x++){
-					if((tmpVal.getValue() & (1 << x)) != 0){
-						tmpDestVertexId = KmerUtil.shiftKmerWithNextCode(kmerSize, tmpVertexId, 0, tmpVertexId.length, x);
-						destVertexId.set(tmpDestVertexId, 0, tmpDestVertexId.length);
-						sendMsg(destVertexId,tmpMsg);
-					}
-				}
-				voteToHalt();
-			}
-			if(GraphVertexOperation.isRearVertex(tmpVal.getValue())){
-				tmpMsg.setMessage(Message.END);
-				
-				for(byte x = Kmer.GENE_CODE.A; x<= Kmer.GENE_CODE.T ; x++){
-					if(((tmpVal.getValue()>> 4) & (1 << x)) != 0){
-						tmpDestVertexId = KmerUtil.shiftKmerWithPreCode(kmerSize, tmpVertexId, 0, tmpVertexId.length, x);
-						destVertexId.set(tmpDestVertexId, 0, tmpDestVertexId.length);
-						sendMsg(destVertexId,tmpMsg);
-					}
-				}
-				voteToHalt();
-			}
-			if(GraphVertexOperation.isPathVertex(tmpVal.getValue())){
-				tmpVal.setState(State.MID_VERTEX);
-				setVertexValue(tmpVal);
-			}
-			/*if(!GraphVertexOperation.isHeadVertex(tmpVal.getValue())
-					&& !GraphVertexOperation.isRearVertex(tmpVal.getValue())
-					&& !GraphVertexOperation.isRearVertex(tmpVal.getValue()))
-				voteToHalt();*/
-		}
-		else if(getSuperstep() == 2 && getSuperstep() <= maxIteration){
-			while(msgIterator.hasNext()){
-				if(!GraphVertexOperation.isPathVertex(tmpVal.getValue())){
-					msgIterator.next();
-					voteToHalt();
-				}
-				else{
-					tmpMsg = msgIterator.next();
-					if(tmpMsg.getMessage() == Message.START && 
-							(tmpVal.getState() == State.MID_VERTEX || tmpVal.getState() == State.END_VERTEX)){
-						tmpVal.setState(State.START_VERTEX);
-						setVertexValue(tmpVal);
-					}
-					else if(tmpMsg.getMessage() == Message.END && tmpVal.getState() == State.MID_VERTEX){
-						tmpVal.setState(State.END_VERTEX);
-						setVertexValue(tmpVal);
-						voteToHalt();
-					}
-					else
-						voteToHalt();
-				}
-			}
-		}
-		//head node sends message to path node
-		else if(getSuperstep()%3 == 0 && getSuperstep() <= maxIteration){
-			if(tmpVal.getState() == State.TODELETE || tmpVal.getState() == State.KILL_SELF)
-				voteToHalt();
-			else{
-				if(getSuperstep() == 3){
-					tmpMsg = new LogAlgorithmMessageWritable();
-					if(Kmer.GENE_CODE.getGeneCodeFromBitMap((byte)(tmpVal.getValue() & 0x0F)) == -1)
-						voteToHalt();
-					else{
-						tmpDestVertexId = KmerUtil.shiftKmerWithNextCode(kmerSize, tmpVertexId, 
-								0, tmpVertexId.length, 
-								Kmer.GENE_CODE.getGeneCodeFromBitMap((byte)(tmpVal.getValue() & 0x0F)));
-						destVertexId.set(tmpDestVertexId, 0, tmpDestVertexId.length);
-						if(tmpVal.getState() == State.START_VERTEX){
-							tmpMsg.setMessage(Message.START);
-							tmpMsg.setSourceVertexId(getVertexId().getBytes());
-							sendMsg(destVertexId, tmpMsg);
-							voteToHalt();
-						}
-						else if(tmpVal.getState() != State.END_VERTEX && tmpVal.getState() != State.FINAL_DELETE){
-							tmpMsg.setMessage(Message.NON);
-							tmpMsg.setSourceVertexId(getVertexId().getBytes());
-							sendMsg(destVertexId,tmpMsg);
-							voteToHalt();
-						}
-					}
-				}
-				else{
-					if(msgIterator.hasNext()){
-						tmpMsg = msgIterator.next();
-						byte[] lastKmer = KmerUtil.getLastKmerFromChain(kmerSize,
-								tmpVal.getLengthOfMergeChain(),
-								tmpVal.getMergeChain(),
-								0, tmpVal.getMergeChain().length);
-						if(Kmer.GENE_CODE.getGeneCodeFromBitMap((byte)(tmpVal.getValue() & 0x0F)) == -1 || lastKmer == null)
-							voteToHalt();
-						else{
-							tmpDestVertexId = KmerUtil.shiftKmerWithNextCode(kmerSize, lastKmer, 
-									0, lastKmer.length,
-									Kmer.GENE_CODE.getGeneCodeFromBitMap((byte)(tmpVal.getValue() & 0x0F))); 
-							destVertexId.set(tmpDestVertexId, 0, tmpDestVertexId.length);
-							if(tmpVal.getState() == State.START_VERTEX){
-								tmpMsg.setMessage(Message.START);
-								tmpMsg.setSourceVertexId(getVertexId().getBytes());
-								sendMsg(destVertexId, tmpMsg);
-								voteToHalt();
-							}
-							else if(tmpVal.getState() != State.END_VERTEX && tmpVal.getState() != State.FINAL_DELETE){
-								tmpMsg.setMessage(Message.NON);
-								tmpMsg.setSourceVertexId(getVertexId().getBytes());
-								sendMsg(destVertexId,tmpMsg);
-							}
-						}
-					}
-				}
-			}
-		}
-		
-		//path node sends message back to head node
-		else if(getSuperstep()%3 == 1 && getSuperstep() <= maxIteration){
-			if(tmpVal.getState() == State.TODELETE || tmpVal.getState() == State.KILL_SELF)
-				voteToHalt();
-			else{
-				if(msgIterator.hasNext()){
-					tmpMsg = msgIterator.next();
-					int message = tmpMsg.getMessage();
-					if(tmpVal.getLengthOfMergeChain() == 0){
-						tmpVal.setLengthOfMergeChain(kmerSize);
-						tmpVal.setMergeChain(tmpVertexId);
-						setVertexValue(tmpVal);
-					}
-					tmpMsg.setLengthOfChain(tmpVal.getLengthOfMergeChain());
-					tmpMsg.setChainVertexId(tmpVal.getMergeChain());
-					
-					tmpMsg.setNeighberInfo(tmpVal.getValue()); //set neighber
-					tmpMsg.setSourceVertexState(tmpVal.getState());
-					
-					//kill Message because it has been merged by the head
-					if(tmpVal.getState() == State.END_VERTEX || tmpVal.getState() == State.FINAL_DELETE){
-						tmpMsg.setMessage(Message.END);
-						tmpVal.setState(State.FINAL_DELETE);
-						setVertexValue(tmpVal);
-						//deleteVertex(getVertexId());
-					}
-					else
-						tmpMsg.setMessage(Message.NON);
-					
-					if(message == Message.START){
-						tmpVal.setState(State.TODELETE);
-						setVertexValue(tmpVal);
-					}
-					destVertexId.set(tmpMsg.getSourceVertexId(), 0, tmpMsg.getSourceVertexId().length);
-					sendMsg(destVertexId,tmpMsg);
-					//voteToHalt();
-				}
-				else{
-					if(getVertexValue().getState() != State.START_VERTEX //&& getVertexValue().getState() != State.NON_EXIST
-							&& getVertexValue().getState() != State.END_VERTEX && getVertexValue().getState() != State.FINAL_DELETE){
-						tmpVal.setState(State.KILL_SELF);
-						setVertexValue(tmpVal);
-						voteToHalt();
-						//deleteVertex(getVertexId()); //killSelf because it doesn't receive any message
-					}
-				}
-			}
-		}
-		else if(getSuperstep()%3 == 2 && getSuperstep() <= maxIteration){
-			if(tmpVal.getState() == State.TODELETE || tmpVal.getState() == State.KILL_SELF)
-				voteToHalt(); //deleteVertex(getVertexId()); //killSelf
-			else{
-				if(msgIterator.hasNext()){
-					tmpMsg = msgIterator.next();
-
-					if(tmpMsg.getMessage() == Message.END){
-						if(tmpVal.getState() != State.START_VERTEX)
-							tmpVal.setState(State.END_VERTEX);
-						else
-							tmpVal.setState(State.FINAL_VERTEX);
-					}
-						
-					if(getSuperstep() == 5){
-						lengthOfMergeChainVertex = kmerSize;
-						mergeChainVertexId = tmpVertexId;
-					}
-					else{
-						lengthOfMergeChainVertex = tmpVal.getLengthOfMergeChain(); 
-						mergeChainVertexId = tmpVal.getMergeChain(); 
-					}
-					byte[] tmplastKmer = KmerUtil.getLastKmerFromChain(tmpMsg.getLengthOfChain() - kmerSize + 1,
-							tmpMsg.getLengthOfChain(), tmpMsg.getChainVertexId(),0, tmpMsg.getChainVertexId().length);
-					mergeChainVertexId = KmerUtil.mergeTwoKmer(lengthOfMergeChainVertex, 
-							mergeChainVertexId, 
-							0, mergeChainVertexId.length,
-							tmpMsg.getLengthOfChain() - kmerSize + 1, 
-							tmplastKmer, 0, tmplastKmer.length);
-					lengthOfMergeChainVertex = lengthOfMergeChainVertex + tmpMsg.getLengthOfChain()
-							- kmerSize + 1;
-					tmpVal.setLengthOfMergeChain(lengthOfMergeChainVertex);
-					tmpVal.setMergeChain(mergeChainVertexId);
-
-					tmpVertexValue = GraphVertexOperation.updateRightNeighber(getVertexValue().getValue(),tmpMsg.getNeighberInfo());
-					tmpVal.setValue(tmpVertexValue);
-					if(tmpMsg.getMessage() != Message.END){
-						setVertexValue(tmpVal);
-						tmpMsg = new LogAlgorithmMessageWritable(); //reset
-						tmpMsg.setNeighberInfo(tmpVertexValue);
-						sendMsg(getVertexId(),tmpMsg);
-					}
-				}
-				if(tmpVal.getState() == State.END_VERTEX || tmpVal.getState() == State.FINAL_DELETE)
-					voteToHalt();
-				if(tmpVal.getState() == State.FINAL_VERTEX){
-					//String source = Kmer.recoverKmerFrom(tmpVal.getLengthOfMergeChain(), tmpVal.getMergeChain(), 0, tmpVal.getMergeChain().length);
-					voteToHalt();
-				}
-			}
-		}
-	}
-
-	/**
-	 * @param args
-	 */
-	public static void main(String[] args) throws Exception {
-        PregelixJob job = new PregelixJob(LogAlgorithmForMergeGraphVertex.class.getSimpleName());
-        job.setVertexClass(LogAlgorithmForMergeGraphVertex.class);
-        /**
-         * BinaryInput and BinaryOutput~/
-         */
-        job.setVertexInputFormatClass(LogAlgorithmForMergeGraphInputFormat.class); 
-        job.setVertexOutputFormatClass(LogAlgorithmForMergeGraphOutputFormat.class); 
-        job.setOutputKeyClass(BytesWritable.class);
-        job.setOutputValueClass(ValueStateWritable.class);
-        job.setDynamicVertexValueSize(true);
-        Client.run(args, job);
-	}
-}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/MergeGraphVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/MergeGraphVertex.java
deleted file mode 100644
index ec45019..0000000
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/MergeGraphVertex.java
+++ /dev/null
@@ -1,191 +0,0 @@
-package edu.uci.ics.genomix.pregelix;
-
-import java.util.Iterator;
-
-import org.apache.hadoop.io.BytesWritable;
-import org.apache.hadoop.io.NullWritable;
-
-import edu.uci.ics.genomix.type.old.Kmer;
-import edu.uci.ics.genomix.type.old.KmerUtil;
-import edu.uci.ics.pregelix.api.graph.Vertex;
-import edu.uci.ics.pregelix.api.job.PregelixJob;
-import edu.uci.ics.genomix.pregelix.client.Client;
-import edu.uci.ics.genomix.pregelix.format.BinaryLoadGraphInputFormat;
-import edu.uci.ics.genomix.pregelix.format.BinaryLoadGraphOutputFormat;
-import edu.uci.ics.genomix.pregelix.io.MessageWritable;
-import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
-import edu.uci.ics.genomix.pregelix.type.State;
-
-/*
- * vertexId: BytesWritable
- * vertexValue: ByteWritable
- * edgeValue: NullWritable
- * message: MessageWritable
- * 
- * DNA:
- * A: 00
- * C: 01
- * G: 10
- * T: 11
- * 
- * succeed node
- *  A 00000001 1
- *  G 00000010 2
- *  C 00000100 4
- *  T 00001000 8
- * precursor node
- *  A 00010000 16
- *  G 00100000 32
- *  C 01000000 64
- *  T 10000000 128
- *  
- * For example, ONE LINE in input file: 00,01,10	0001,0010,
- * That means that vertexId is ACG, its succeed node is A and its precursor node is C.
- * The succeed node and precursor node will be stored in vertexValue and we don't use edgeValue.
- * The details about message are in edu.uci.ics.pregelix.example.io.MessageWritable. 
- */
-public class MergeGraphVertex extends Vertex<BytesWritable, ValueStateWritable, NullWritable, MessageWritable>{
-	
-	public static final String KMER_SIZE = "MergeGraphVertex.kmerSize";
-	public static final String ITERATIONS = "MergeGraphVertex.iteration";
-	public static int kmerSize = -1;
-	private int maxIteration = -1;
-	
-    private byte[] tmpVertexId;
-    private byte[] tmpDestVertexId;
-	private BytesWritable destVertexId = new BytesWritable();
-	private BytesWritable tmpChainVertexId = new BytesWritable();
-	private ValueStateWritable tmpVertexValue = new ValueStateWritable();
-	private MessageWritable tmpMsg = new MessageWritable();
-	/**
-	 * Naive Algorithm for path merge graph
-	 * @throws Exception 
-	 * @throws  
-	 */
-	/**
-     *	Load KmerSize, MaxIteration
-     */
-	@Override
-	public void compute(Iterator<MessageWritable> msgIterator) {
-		if(kmerSize == -1)
-			kmerSize = getContext().getConfiguration().getInt(KMER_SIZE, 5);
-        if (maxIteration < 0) 
-            maxIteration = getContext().getConfiguration().getInt(ITERATIONS, 100);
-		tmpVertexId = GraphVertexOperation.generateValidDataFromBytesWritable(getVertexId());
-		if (getSuperstep() == 1) {
-			if(GraphVertexOperation.isHeadVertex(getVertexValue().getValue())){ 
-				tmpMsg.setSourceVertexId(tmpVertexId);
-				tmpMsg.setHead(tmpVertexId);
-				tmpMsg.setLengthOfChain(0);
-				tmpMsg.setChainVertexId(tmpChainVertexId.getBytes());
-				for(byte x = Kmer.GENE_CODE.A; x<= Kmer.GENE_CODE.T ; x++){
-					if((getVertexValue().getValue() & (1 << x)) != 0){
-						tmpDestVertexId = KmerUtil.shiftKmerWithNextCode(kmerSize, tmpVertexId, 0, tmpVertexId.length, x);
-						destVertexId.set(tmpDestVertexId, 0, tmpDestVertexId.length);
-						sendMsg(destVertexId,tmpMsg);
-					}
-				}
-			}
-		}
-		
-		//path node sends message back to head node
-		else if(getSuperstep()%2 == 0 && getSuperstep() <= maxIteration){
-			 if(msgIterator.hasNext()){
-				tmpMsg = msgIterator.next();
-					
-				if(!tmpMsg.isRear()){
-					if(getSuperstep() == 2)
-						tmpMsg.setHead(tmpVertexId);
-					if(GraphVertexOperation.isPathVertex(getVertexValue().getValue())){
-						tmpDestVertexId = tmpMsg.getSourceVertexId();
-						tmpMsg.setNeighberInfo(getVertexValue().getValue()); //set neighber
-						if(tmpMsg.getLengthOfChain() == 0){
-							tmpMsg.setLengthOfChain(kmerSize);
-							tmpMsg.setChainVertexId(tmpVertexId);
-						}
-						else{
-							String source = Kmer.recoverKmerFrom(kmerSize, tmpVertexId, 0, tmpVertexId.length);
-							tmpMsg.setChainVertexId(KmerUtil.mergeKmerWithNextCode(
-									tmpMsg.getLengthOfChain(),
-									tmpMsg.getChainVertexId(), 
-									0, tmpMsg.getChainVertexId().length,
-									Kmer.GENE_CODE.getCodeFromSymbol((byte)source.charAt(source.length() - 1))));
-							tmpMsg.incrementLength();
-							deleteVertex(getVertexId());
-						}
-						destVertexId.set(tmpDestVertexId, 0, tmpDestVertexId.length);
-						sendMsg(destVertexId,tmpMsg);
-					}
-					else if(GraphVertexOperation.isRearVertex(getVertexValue().getValue())){
-						if(getSuperstep() == 2)
-							voteToHalt();
-						else{
-							tmpDestVertexId = tmpMsg.getSourceVertexId();
-							tmpMsg.setSourceVertexId(tmpVertexId);
-							tmpMsg.setRear(true);
-							destVertexId.set(tmpDestVertexId, 0, tmpDestVertexId.length);
-							sendMsg(destVertexId,tmpMsg);
-						}
-					}
-				}
-				else{
-					tmpVertexValue.setState(State.START_VERTEX);
-					tmpVertexValue.setValue(GraphVertexOperation.updateRightNeighberByVertexId(getVertexValue().getValue(),
-							tmpMsg.getSourceVertexId(), kmerSize));
-					tmpVertexValue.setLengthOfMergeChain(tmpMsg.getLengthOfChain());
-					tmpVertexValue.setMergeChain(tmpMsg.getChainVertexId());
-					setVertexValue(tmpVertexValue);
-					//String source = Kmer.recoverKmerFrom(tmpMsg.getLengthOfChain(), tmpMsg.getChainVertexId(), 0, tmpMsg.getChainVertexId().length);
-					//System.out.print("");
-					/*try {
-						
-						GraphVertexOperation.flushChainToFile(tmpMsg.getChainVertexId(), 
-								tmpMsg.getLengthOfChain(),tmpVertexId);
-					} catch (IOException e) { e.printStackTrace(); }*/
-				}
-			}
-		}
-		//head node sends message to path node
-		else if(getSuperstep()%2 == 1 && getSuperstep() <= maxIteration){
-			while (msgIterator.hasNext()){
-				tmpMsg = msgIterator.next();
-				if(!tmpMsg.isRear()){
-					byte[] lastKmer = KmerUtil.getLastKmerFromChain(kmerSize,
-							tmpMsg.getLengthOfChain(),
-							tmpMsg.getChainVertexId(),
-							0, tmpMsg.getChainVertexId().length);
-					tmpDestVertexId = KmerUtil.shiftKmerWithNextCode(kmerSize, lastKmer, 
-							0, lastKmer.length,
-							Kmer.GENE_CODE.getGeneCodeFromBitMap((byte)(tmpMsg.getNeighberInfo() & 0x0F)));
-
-					tmpMsg.setSourceVertexId(tmpVertexId);
-					destVertexId.set(tmpDestVertexId, 0, tmpDestVertexId.length);
-					sendMsg(destVertexId,tmpMsg);
-				}
-				else{	
-					tmpDestVertexId = tmpMsg.getHead();
-					destVertexId.set(tmpDestVertexId, 0, tmpDestVertexId.length);
-					sendMsg(destVertexId,tmpMsg);
-				}
-			}
-		}
-		voteToHalt();
-	}
-
-	/**
-	 * @param args
-	 */
-	public static void main(String[] args) throws Exception {
-        PregelixJob job = new PregelixJob(MergeGraphVertex.class.getSimpleName());
-        job.setVertexClass(MergeGraphVertex.class);
-        /**
-         * BinaryInput and BinaryOutput
-         */
-        job.setVertexInputFormatClass(BinaryLoadGraphInputFormat.class); 
-        job.setVertexOutputFormatClass(BinaryLoadGraphOutputFormat.class); 
-        job.setDynamicVertexValueSize(true);
-        job.setOutputKeyClass(BytesWritable.class);
-        job.setOutputValueClass(ValueStateWritable.class);
-        Client.run(args, job);
-	}
-}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/BinaryVertexInputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/BinaryVertexInputFormat.java
index 823a984..e1868b1 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/BinaryVertexInputFormat.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/BinaryVertexInputFormat.java
@@ -3,7 +3,6 @@
 import java.io.IOException;
 import java.util.List;
 
-import org.apache.hadoop.io.BytesWritable;
 import org.apache.hadoop.io.Writable;
 import org.apache.hadoop.io.WritableComparable;
 import org.apache.hadoop.mapreduce.InputSplit;
@@ -14,12 +13,14 @@
 
 import edu.uci.ics.pregelix.api.io.VertexInputFormat;
 import edu.uci.ics.pregelix.api.io.VertexReader;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
 import edu.uci.ics.genomix.type.KmerCountValue;
 
 public class BinaryVertexInputFormat <I extends WritableComparable<?>, V extends Writable, E extends Writable, M extends Writable>
 	extends VertexInputFormat<I, V, E, M>{
 	
     /** Uses the SequenceFileInputFormat to do everything */
+	@SuppressWarnings("rawtypes")
 	protected SequenceFileInputFormat binaryInputFormat = new SequenceFileInputFormat();
     
     /**
@@ -37,7 +38,7 @@
     public static abstract class BinaryVertexReader<I extends WritableComparable<?>, V extends Writable, E extends Writable, M extends Writable>
             implements VertexReader<I, V, E, M> {
         /** Internal line record reader */
-        private final RecordReader<BytesWritable,KmerCountValue> lineRecordReader;
+        private final RecordReader<KmerBytesWritable,KmerCountValue> lineRecordReader;
         /** Context passed to initialize */
         private TaskAttemptContext context;
 
@@ -47,7 +48,7 @@
          * @param recordReader
          *            Line record reader from SequenceFileInputFormat
          */
-        public BinaryVertexReader(RecordReader<BytesWritable, KmerCountValue> recordReader) {
+        public BinaryVertexReader(RecordReader<KmerBytesWritable, KmerCountValue> recordReader) {
             this.lineRecordReader = recordReader;
         }
 
@@ -73,7 +74,7 @@
          * 
          * @return Record reader to be used for reading.
          */
-        protected RecordReader<BytesWritable,KmerCountValue> getRecordReader() {
+        protected RecordReader<KmerBytesWritable,KmerCountValue> getRecordReader() {
             return lineRecordReader;
         }
 
@@ -87,7 +88,8 @@
         }
     }
 
-    @Override
+    @SuppressWarnings("unchecked")
+	@Override
     public List<InputSplit> getSplits(JobContext context, int numWorkers) throws IOException, InterruptedException {
         // Ignore the hint of numWorkers here since we are using SequenceFileInputFormat
         // to do this for us
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/BinaryVertexOutputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/BinaryVertexOutputFormat.java
index f497f21..1435770 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/BinaryVertexOutputFormat.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/BinaryVertexOutputFormat.java
@@ -2,7 +2,6 @@
 
 import java.io.IOException;
 
-import org.apache.hadoop.io.BytesWritable;
 import org.apache.hadoop.io.Writable;
 import org.apache.hadoop.io.WritableComparable;
 import org.apache.hadoop.mapreduce.JobContext;
@@ -12,6 +11,7 @@
 import org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat;
 
 import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
 import edu.uci.ics.pregelix.api.io.VertexOutputFormat;
 import edu.uci.ics.pregelix.api.io.VertexWriter;
 
@@ -49,7 +49,7 @@
         /** Context passed to initialize */
         private TaskAttemptContext context;
         /** Internal line record writer */
-        private final RecordWriter<BytesWritable, ValueStateWritable> lineRecordWriter;
+        private final RecordWriter<KmerBytesWritable, ValueStateWritable> lineRecordWriter;
 
         /**
          * Initialize with the LineRecordWriter.
@@ -57,7 +57,7 @@
          * @param lineRecordWriter
          *            Line record writer from SequenceFileOutputFormat
          */
-        public BinaryVertexWriter(RecordWriter<BytesWritable, ValueStateWritable> lineRecordWriter) {
+        public BinaryVertexWriter(RecordWriter<KmerBytesWritable, ValueStateWritable> lineRecordWriter) {
             this.lineRecordWriter = lineRecordWriter;
         }
 
@@ -76,7 +76,7 @@
          * 
          * @return Record writer to be used for writing.
          */
-        public RecordWriter<BytesWritable, ValueStateWritable> getRecordWriter() {
+        public RecordWriter<KmerBytesWritable, ValueStateWritable> getRecordWriter() {
             return lineRecordWriter;
         }
 
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/client/Client.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/client/Client.java
index 2d70fdf..60342a7 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/client/Client.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/client/Client.java
@@ -10,8 +10,8 @@
 import org.kohsuke.args4j.CmdLineParser;
 import org.kohsuke.args4j.Option;
 
-import edu.uci.ics.genomix.pregelix.LogAlgorithmForMergeGraphVertex;
-import edu.uci.ics.genomix.pregelix.MergeGraphVertex;
+import edu.uci.ics.genomix.pregelix.operator.LogAlgorithmForPathMergeVertex;
+import edu.uci.ics.genomix.pregelix.operator.NaiveAlgorithmForPathMergeVertex;
 import edu.uci.ics.pregelix.api.job.PregelixJob;
 import edu.uci.ics.pregelix.core.base.IDriver.Plan;
 import edu.uci.ics.pregelix.core.driver.Driver;
@@ -60,11 +60,11 @@
         for (int i = 1; i < inputs.length; i++)
             FileInputFormat.addInputPaths(job, inputs[0]);
         FileOutputFormat.setOutputPath(job, new Path(options.outputPath));
-        job.getConfiguration().setInt(MergeGraphVertex.KMER_SIZE, options.sizeKmer);
-        job.getConfiguration().setInt(LogAlgorithmForMergeGraphVertex.KMER_SIZE, options.sizeKmer);
+        job.getConfiguration().setInt(NaiveAlgorithmForPathMergeVertex.KMER_SIZE, options.sizeKmer);
+        job.getConfiguration().setInt(LogAlgorithmForPathMergeVertex.KMER_SIZE, options.sizeKmer);
         if (options.numIteration > 0){
-            job.getConfiguration().setLong(MergeGraphVertex.ITERATIONS, options.numIteration);
-            //job.getConfiguration().setLong(LogAlgorithmForMergeGraphVertex.ITERATIONS, options.numIteration);
+            job.getConfiguration().setLong(NaiveAlgorithmForPathMergeVertex.ITERATIONS, options.numIteration);
+            job.getConfiguration().setLong(LogAlgorithmForPathMergeVertex.ITERATIONS, options.numIteration);
         }
         return options;
     }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/BinaryLoadGraphInputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/BinaryLoadGraphInputFormat.java
deleted file mode 100644
index 4cd22ac..0000000
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/BinaryLoadGraphInputFormat.java
+++ /dev/null
@@ -1,81 +0,0 @@
-package edu.uci.ics.genomix.pregelix.format;
-
-import java.io.IOException;
-import java.util.logging.FileHandler;
-import java.util.logging.Logger;
-
-import org.apache.hadoop.io.ByteWritable;
-import org.apache.hadoop.io.BytesWritable;
-import org.apache.hadoop.io.NullWritable;
-import org.apache.hadoop.mapreduce.InputSplit;
-import org.apache.hadoop.mapreduce.RecordReader;
-import org.apache.hadoop.mapreduce.TaskAttemptContext;
-
-import edu.uci.ics.genomix.type.KmerCountValue;
-import edu.uci.ics.pregelix.api.graph.Vertex;
-import edu.uci.ics.pregelix.api.io.VertexReader;
-import edu.uci.ics.pregelix.api.util.BspUtils;
-import edu.uci.ics.genomix.pregelix.GraphVertexOperation;
-import edu.uci.ics.genomix.pregelix.io.MessageWritable;
-import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
-import edu.uci.ics.genomix.pregelix.io.ValueWritable;
-import edu.uci.ics.genomix.pregelix.log.DataLoadLogFormatter;
-import edu.uci.ics.genomix.pregelix.api.io.binary.BinaryVertexInputFormat;
-import edu.uci.ics.genomix.pregelix.api.io.binary.BinaryVertexInputFormat.BinaryVertexReader;
-
-public class BinaryLoadGraphInputFormat extends
-	BinaryVertexInputFormat<BytesWritable, ValueStateWritable, NullWritable, MessageWritable>{
-	/**
-	 * Format INPUT
-	 */
-    @Override
-    public VertexReader<BytesWritable, ValueStateWritable, NullWritable, MessageWritable> createVertexReader(
-            InputSplit split, TaskAttemptContext context) throws IOException {
-        return new BinaryLoadGraphReader(binaryInputFormat.createRecordReader(split, context));
-    }	
-}
-
-@SuppressWarnings("rawtypes")
-class BinaryLoadGraphReader extends
-        BinaryVertexReader<BytesWritable, ValueStateWritable, NullWritable, MessageWritable> {
-    private Vertex vertex;
-    private BytesWritable vertexId = new BytesWritable();
-    private ValueStateWritable vertexValue = new ValueStateWritable();
-
-    public BinaryLoadGraphReader(RecordReader<BytesWritable,KmerCountValue> recordReader) {
-        super(recordReader);
-    }
-
-    @Override
-    public boolean nextVertex() throws IOException, InterruptedException {
-        return getRecordReader().nextKeyValue();
-    }
-
-    @SuppressWarnings("unchecked")
-    @Override
-    public Vertex<BytesWritable, ValueStateWritable, NullWritable, MessageWritable> getCurrentVertex() throws IOException,
-            InterruptedException {
-        if (vertex == null)
-            vertex = (Vertex) BspUtils.createVertex(getContext().getConfiguration());
-
-        vertex.getMsgList().clear();
-        vertex.getEdges().clear();
-        
-        vertex.reset();
-        if(getRecordReader() != null){
-            /**
-             * set the src vertex id
-             */
-    		vertexId.set(getRecordReader().getCurrentKey());
-    		vertex.setVertexId(vertexId);
-            /**
-             * set the vertex value
-             */
-            KmerCountValue kmerCountValue = getRecordReader().getCurrentValue();
-            vertexValue.setValue(kmerCountValue.getAdjBitMap()); 
-            vertex.setVertexValue(vertexValue);
-        }
-        
-        return vertex;
-    }
-}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/BinaryLoadGraphOutputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/BinaryLoadGraphOutputFormat.java
deleted file mode 100644
index 2b87379..0000000
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/BinaryLoadGraphOutputFormat.java
+++ /dev/null
@@ -1,40 +0,0 @@
-package edu.uci.ics.genomix.pregelix.format;
-
-import java.io.IOException;
-
-import org.apache.hadoop.io.BytesWritable;
-import org.apache.hadoop.io.NullWritable;
-import org.apache.hadoop.mapreduce.RecordWriter;
-import org.apache.hadoop.mapreduce.TaskAttemptContext;
-
-import edu.uci.ics.genomix.pregelix.api.io.binary.BinaryVertexOutputFormat;
-import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
-import edu.uci.ics.pregelix.api.graph.Vertex;
-import edu.uci.ics.pregelix.api.io.VertexWriter;
-
-public class BinaryLoadGraphOutputFormat extends 
-	BinaryVertexOutputFormat<BytesWritable, ValueStateWritable, NullWritable> {
-
-        @Override
-        public VertexWriter<BytesWritable, ValueStateWritable, NullWritable> createVertexWriter(TaskAttemptContext context)
-                throws IOException, InterruptedException {
-            RecordWriter<BytesWritable, ValueStateWritable> recordWriter = binaryOutputFormat.getRecordWriter(context);
-            return new BinaryLoadGraphVertexWriter(recordWriter);
-        }
-        
-        /**
-         * Simple VertexWriter that supports {@link BinaryLoadGraphVertex}
-         */
-        public static class BinaryLoadGraphVertexWriter extends
-                BinaryVertexWriter<BytesWritable, ValueStateWritable, NullWritable> {
-            public BinaryLoadGraphVertexWriter(RecordWriter<BytesWritable, ValueStateWritable> lineRecordWriter) {
-                super(lineRecordWriter);
-            }
-
-            @Override
-            public void writeVertex(Vertex<BytesWritable, ValueStateWritable, NullWritable, ?> vertex) throws IOException,
-                    InterruptedException {
-                getRecordWriter().write(vertex.getVertexId(),vertex.getVertexValue());
-            }
-        }
-}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/LogAlgorithmForMergeGraphInputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/LogAlgorithmForMergeGraphInputFormat.java
deleted file mode 100644
index 0e74c2d..0000000
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/LogAlgorithmForMergeGraphInputFormat.java
+++ /dev/null
@@ -1,79 +0,0 @@
-package edu.uci.ics.genomix.pregelix.format;
-
-import java.io.IOException;
-
-import org.apache.hadoop.io.BytesWritable;
-import org.apache.hadoop.io.NullWritable;
-import org.apache.hadoop.mapreduce.InputSplit;
-import org.apache.hadoop.mapreduce.RecordReader;
-import org.apache.hadoop.mapreduce.TaskAttemptContext;
-
-import edu.uci.ics.genomix.pregelix.api.io.binary.BinaryVertexInputFormat;
-import edu.uci.ics.genomix.pregelix.io.LogAlgorithmMessageWritable;
-import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
-import edu.uci.ics.genomix.pregelix.type.State;
-import edu.uci.ics.genomix.type.KmerCountValue;
-import edu.uci.ics.pregelix.api.graph.Vertex;
-import edu.uci.ics.pregelix.api.io.VertexReader;
-import edu.uci.ics.pregelix.api.util.BspUtils;
-
-public class LogAlgorithmForMergeGraphInputFormat extends
-	BinaryVertexInputFormat<BytesWritable, ValueStateWritable, NullWritable, LogAlgorithmMessageWritable>{
-
-	/**
-	 * Format INPUT
-	 */
-    @Override
-    public VertexReader<BytesWritable, ValueStateWritable, NullWritable, LogAlgorithmMessageWritable> createVertexReader(
-            InputSplit split, TaskAttemptContext context) throws IOException {
-        return new BinaryLoadGraphReader(binaryInputFormat.createRecordReader(split, context));
-    }
-    
-    @SuppressWarnings("rawtypes")
-    class BinaryLoadGraphReader extends
-            BinaryVertexReader<BytesWritable, ValueStateWritable, NullWritable, LogAlgorithmMessageWritable> {
-        private Vertex vertex;
-        private BytesWritable vertexId = new BytesWritable();
-        private ValueStateWritable vertexValue = new ValueStateWritable();
-
-        public BinaryLoadGraphReader(RecordReader<BytesWritable,KmerCountValue> recordReader) {
-            super(recordReader);
-        }
-
-        @Override
-        public boolean nextVertex() throws IOException, InterruptedException {
-            return getRecordReader().nextKeyValue();
-        }
-
-        @SuppressWarnings("unchecked")
-        @Override
-        public Vertex<BytesWritable, ValueStateWritable, NullWritable, LogAlgorithmMessageWritable> getCurrentVertex() throws IOException,
-                InterruptedException {
-            if (vertex == null)
-                vertex = (Vertex) BspUtils.createVertex(getContext().getConfiguration());
-
-            vertex.getMsgList().clear();
-            vertex.getEdges().clear();
-            
-            
-            if(getRecordReader() != null){
-	            /**
-	             * set the src vertex id
-	             */
-	            
-        		vertexId = getRecordReader().getCurrentKey();
-        		vertex.setVertexId(vertexId);
-	            /**
-	             * set the vertex value
-	             */
-	            KmerCountValue kmerCountValue = getRecordReader().getCurrentValue();
-	            vertexValue.setValue(kmerCountValue.getAdjBitMap()); 
-	            vertexValue.setState(State.NON_VERTEX);
-	            vertex.setVertexValue(vertexValue);
-            }
-            
-            return vertex;
-        }
-    }
-	
-}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/LogAlgorithmForMergeGraphOutputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/LogAlgorithmForMergeGraphOutputFormat.java
deleted file mode 100644
index 865a787..0000000
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/LogAlgorithmForMergeGraphOutputFormat.java
+++ /dev/null
@@ -1,49 +0,0 @@
-package edu.uci.ics.genomix.pregelix.format;
-
-import java.io.IOException;
-
-import org.apache.hadoop.io.BytesWritable;
-import org.apache.hadoop.io.NullWritable;
-import org.apache.hadoop.mapreduce.RecordWriter;
-import org.apache.hadoop.mapreduce.TaskAttemptContext;
-
-import edu.uci.ics.genomix.pregelix.GraphVertexOperation;
-import edu.uci.ics.genomix.pregelix.api.io.binary.BinaryVertexOutputFormat;
-import edu.uci.ics.pregelix.api.graph.Vertex;
-import edu.uci.ics.pregelix.api.io.VertexWriter;
-import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
-import edu.uci.ics.genomix.pregelix.type.State;
-import edu.uci.ics.genomix.type.old.Kmer;
-
-public class LogAlgorithmForMergeGraphOutputFormat extends 
-	BinaryVertexOutputFormat<BytesWritable, ValueStateWritable, NullWritable> {
-
-		
-        @Override
-        public VertexWriter<BytesWritable, ValueStateWritable, NullWritable> createVertexWriter(TaskAttemptContext context)
-                throws IOException, InterruptedException {
-            RecordWriter<BytesWritable, ValueStateWritable> recordWriter = binaryOutputFormat.getRecordWriter(context);
-            return new BinaryLoadGraphVertexWriter(recordWriter);
-        }
-        
-        /**
-         * Simple VertexWriter that supports {@link BinaryLoadGraphVertex}
-         */
-        public static class BinaryLoadGraphVertexWriter extends
-                BinaryVertexWriter<BytesWritable, ValueStateWritable, NullWritable> {
-        	
-            public BinaryLoadGraphVertexWriter(RecordWriter<BytesWritable, ValueStateWritable> lineRecordWriter) {
-                super(lineRecordWriter);
-            }
-
-            @Override
-            public void writeVertex(Vertex<BytesWritable, ValueStateWritable, NullWritable, ?> vertex) throws IOException,
-                    InterruptedException {
-            	if(vertex.getVertexValue().getState() != State.FINAL_DELETE
-            			&& vertex.getVertexValue().getState() != State.END_VERTEX
-            			&& vertex.getVertexValue().getState() != State.TODELETE
-            			&& vertex.getVertexValue().getState() != State.KILL_SELF)
-                    getRecordWriter().write(vertex.getVertexId(),vertex.getVertexValue());
-            }
-        }
-}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/LogAlgorithmMessageWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/LogAlgorithmMessageWritable.java
index 3d07c5b..ac84d8e 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/LogAlgorithmMessageWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/LogAlgorithmMessageWritable.java
@@ -2,11 +2,12 @@
 
 import java.io.DataInput;
 import java.io.DataOutput;
-import java.io.File;
 import java.io.IOException;
 
 import org.apache.hadoop.io.WritableComparable;
-import edu.uci.ics.genomix.pregelix.LogAlgorithmForMergeGraphVertex;
+
+import edu.uci.ics.genomix.pregelix.operator.LogAlgorithmForPathMergeVertex;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
 
 public class LogAlgorithmMessageWritable implements WritableComparable<LogAlgorithmMessageWritable>{
 	/**
@@ -15,65 +16,55 @@
 	 * chainVertexId stores the chains of connected DNA
 	 * file stores the point to the file that stores the chains of connected DNA
 	 */
-	private byte[] sourceVertexId;
-	private byte neighberInfo;
-	private int lengthOfChain;
-	private byte[] chainVertexId;
-	private File file;
+	private VKmerBytesWritable sourceVertexId;
+	private VKmerBytesWritable chainVertexId;
+	private byte adjMap;
 	private int message;
 	private int sourceVertexState;
 	
 	public LogAlgorithmMessageWritable(){
-		sourceVertexId = new byte[(LogAlgorithmForMergeGraphVertex.kmerSize-1)/4 + 1];
+		sourceVertexId = new VKmerBytesWritable(LogAlgorithmForPathMergeVertex.kmerSize);
+		chainVertexId = new VKmerBytesWritable(LogAlgorithmForPathMergeVertex.kmerSize);
 	}
 	
-	public void set(byte[] sourceVertexId,byte neighberInfo, byte[] chainVertexId, File file){
-		this.sourceVertexId = sourceVertexId;
-		this.chainVertexId = chainVertexId;
-		this.file = file;
-		this.message = 0;
-		this.lengthOfChain = 0;
+	public void set(VKmerBytesWritable sourceVertexId, VKmerBytesWritable chainVertexId, byte adjMap, int message, int sourceVertexState){
+		this.sourceVertexId.set(sourceVertexId);
+		this.chainVertexId.set(chainVertexId);
+		this.adjMap = adjMap;
+		this.message = message;
+		this.sourceVertexState = sourceVertexState;
 	}
 	
 	public void reset(){
-		sourceVertexId = new byte[(LogAlgorithmForMergeGraphVertex.kmerSize-1)/4 + 1];
-		neighberInfo = (Byte) null;
-		lengthOfChain = 0;
-		chainVertexId = null;
+		//sourceVertexId.reset(LogAlgorithmForPathMergeVertex.kmerSize);
+		chainVertexId.reset(LogAlgorithmForPathMergeVertex.kmerSize);
+		adjMap = (byte)0;
 		message = 0;
 		sourceVertexState = 0;
 	}
 
-	public byte[] getSourceVertexId() {
+	public VKmerBytesWritable getSourceVertexId() {
 		return sourceVertexId;
 	}
 
-	public void setSourceVertexId(byte[] sourceVertexId) {
-		this.sourceVertexId = sourceVertexId;
+	public void setSourceVertexId(VKmerBytesWritable sourceVertexId) {
+		this.sourceVertexId.set(sourceVertexId);
 	}
 
-	public byte getNeighberInfo() {
-		return neighberInfo;
+	public byte getAdjMap() {
+		return adjMap;
 	}
 
-	public void setNeighberInfo(byte neighberInfo) {
-		this.neighberInfo = neighberInfo;
+	public void setAdjMap(byte adjMap) {
+		this.adjMap = adjMap;
 	}
 
-	public byte[] getChainVertexId() {
+	public VKmerBytesWritable getChainVertexId() {
 		return chainVertexId;
 	}
 
-	public void setChainVertexId(byte[] chainVertexId) {
-		this.chainVertexId = chainVertexId;
-	}
-
-	public File getFile() {
-		return file;
-	}
-
-	public void setFile(File file) {
-		this.file = file;
+	public void setChainVertexId(VKmerBytesWritable chainVertexId) {
+		this.chainVertexId.set(chainVertexId);
 	}
 
 	public int getMessage() {
@@ -93,84 +84,48 @@
 	}
 
 	public int getLengthOfChain() {
-		return lengthOfChain;
-	}
-
-	public void setLengthOfChain(int lengthOfChain) {
-		this.lengthOfChain = lengthOfChain;
-	}
-
-	public void incrementLength(){
-		this.lengthOfChain++;
+		return chainVertexId.getKmerLength();
 	}
 	
 	@Override
 	public void write(DataOutput out) throws IOException {
-		// TODO Auto-generated method stub
-		out.writeInt(lengthOfChain);
-		if(lengthOfChain != 0)
-			out.write(chainVertexId);
-
+		sourceVertexId.write(out);
+		chainVertexId.write(out);
+		out.write(adjMap);
 		out.writeInt(message);
 		out.writeInt(sourceVertexState);
-		
-		out.write(sourceVertexId); 
-		out.write(neighberInfo);
 	}
 
 	@Override
 	public void readFields(DataInput in) throws IOException {
-		// TODO Auto-generated method stub
-		lengthOfChain = in.readInt();
-		if(lengthOfChain > 0){
-			chainVertexId = new byte[(lengthOfChain-1)/4 + 1];
-			in.readFully(chainVertexId);
-		}
-		else
-			chainVertexId = new byte[0];
-
+		sourceVertexId.readFields(in);
+		chainVertexId.readFields(in);
+		adjMap = in.readByte();
 		message = in.readInt();
 		sourceVertexState = in.readInt();
-		
-		sourceVertexId = new byte[(LogAlgorithmForMergeGraphVertex.kmerSize-1)/4 + 1];
-		in.readFully(sourceVertexId);
-		neighberInfo = in.readByte();
 	}
 
-    @Override
+	 @Override
     public int hashCode() {
-    	int hashCode = 0;
-    	for(int i = 0; i < chainVertexId.length; i++)
-    		hashCode = (int)chainVertexId[i];
-        return hashCode;
+        return chainVertexId.hashCode();
     }
+	 
     @Override
     public boolean equals(Object o) {
-        if (o instanceof LogAlgorithmMessageWritable) {
+        if (o instanceof NaiveAlgorithmMessageWritable) {
         	LogAlgorithmMessageWritable tp = (LogAlgorithmMessageWritable) o;
-            return chainVertexId == tp.chainVertexId && file == tp.file;
+            return chainVertexId.equals(tp.chainVertexId);
         }
         return false;
     }
+    
     @Override
     public String toString() {
-        return chainVertexId.toString() + "\t" + file.getAbsolutePath();
+        return chainVertexId.toString();
     }
-    @Override
+    
+	@Override
 	public int compareTo(LogAlgorithmMessageWritable tp) {
-		// TODO Auto-generated method stub
-        int cmp;
-        if (chainVertexId == tp.chainVertexId)
-            cmp = 0;
-        else
-            cmp = 1;
-        if (cmp != 0)
-            return cmp;
-        if (file == tp.file)
-            return 0;
-        else
-            return 1;
+		return chainVertexId.compareTo(tp.chainVertexId);
 	}
-
-
 }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MessageWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MessageWritable.java
deleted file mode 100644
index 3872514..0000000
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MessageWritable.java
+++ /dev/null
@@ -1,167 +0,0 @@
-package edu.uci.ics.genomix.pregelix.io;
-
-import java.io.DataInput;
-import java.io.DataOutput;
-import java.io.File;
-import java.io.IOException;
-
-import org.apache.hadoop.io.WritableComparable;
-import edu.uci.ics.genomix.pregelix.MergeGraphVertex;
-
-public class MessageWritable implements WritableComparable<MessageWritable>{
-	/**
-	 * sourceVertexId stores source vertexId when headVertex sends the message
-	 * 				  stores neighber vertexValue when pathVertex sends the message
-	 * chainVertexId stores the chains of connected DNA
-	 * file stores the point to the file that stores the chains of connected DNA
-	 */
-	private byte[] sourceVertexId;
-	private byte neighberInfo;
-	private byte[] chainVertexId;
-	private File file;
-	private boolean isRear;
-	private int lengthOfChain;
-	private byte[] head;
-	
-	public MessageWritable(){		
-	}
-	
-	public void set(byte[] sourceVertexId, byte neighberInfo, byte[] chainVertexId, File file, byte[] head){
-		this.sourceVertexId = sourceVertexId;
-		this.neighberInfo = neighberInfo;
-		this.chainVertexId = chainVertexId;
-		this.file = file;
-		this.isRear = false;
-		this.lengthOfChain = 0;
-		this.head = head;
-	}
-
-	public byte[] getSourceVertexId() {
-		return sourceVertexId;
-	}
-
-	public void setSourceVertexId(byte[] sourceVertexId) {
-		this.sourceVertexId = sourceVertexId;
-	}
-
-	public byte getNeighberInfo() {
-		return neighberInfo;
-	}
-
-	public void setNeighberInfo(byte neighberInfo) {
-		this.neighberInfo = neighberInfo;
-	}
-
-	public byte[] getChainVertexId() {
-		return chainVertexId;
-	}
-
-	public void setChainVertexId(byte[] chainVertexId) {
-		this.chainVertexId = chainVertexId;
-	}
-
-	public File getFile() {
-		return file;
-	}
-
-	public void setFile(File file) {
-		this.file = file;
-	}
-
-	public boolean isRear() {
-		return isRear;
-	}
-
-	public void setRear(boolean isRear) {
-		this.isRear = isRear;
-	}
-
-	public int getLengthOfChain() {
-		return lengthOfChain;
-	}
-
-	public void setLengthOfChain(int lengthOfChain) {
-		this.lengthOfChain = lengthOfChain;
-	}
-	
-
-	public byte[] getHead() {
-		return head;
-	}
-
-	public void setHead(byte[] head) {
-		this.head = head;
-	}
-
-	public void incrementLength(){
-		this.lengthOfChain++;
-	}
-	
-	@Override
-	public void write(DataOutput out) throws IOException {
-		// TODO Auto-generated method stub
-		out.writeInt(lengthOfChain);
-		if(lengthOfChain != 0)
-			out.write(chainVertexId);
-		out.write(sourceVertexId);
-		out.write(head);
-		out.write(neighberInfo);
-		out.writeBoolean(isRear);
-	}
-
-	@Override
-	public void readFields(DataInput in) throws IOException {
-		// TODO Auto-generated method stub
-		lengthOfChain = in.readInt();
-		if(lengthOfChain > 0){
-			chainVertexId = new byte[(lengthOfChain-1)/4 + 1];
-			in.readFully(chainVertexId);
-		}
-		else
-			chainVertexId = new byte[0];
-		sourceVertexId = new byte[(MergeGraphVertex.kmerSize-1)/4 + 1];
-		in.readFully(sourceVertexId);
-		head = new byte[(MergeGraphVertex.kmerSize-1)/4 + 1];
-		in.readFully(head);
-		neighberInfo = in.readByte();
-		isRear = in.readBoolean();
-
-	}
-
-    @Override
-    public int hashCode() {
-    	int hashCode = 0;
-    	for(int i = 0; i < chainVertexId.length; i++)
-    		hashCode = (int)chainVertexId[i];
-        return hashCode;
-    }
-    @Override
-    public boolean equals(Object o) {
-        if (o instanceof MessageWritable) {
-        	MessageWritable tp = (MessageWritable) o;
-            return chainVertexId == tp.chainVertexId && file == tp.file;
-        }
-        return false;
-    }
-    @Override
-    public String toString() {
-        return chainVertexId.toString() + "\t" + file.getAbsolutePath();
-    }
-    
-	@Override
-	public int compareTo(MessageWritable tp) {
-		// TODO Auto-generated method stub
-        int cmp;
-        if (chainVertexId == tp.chainVertexId)
-            cmp = 0;
-        else
-            cmp = 1;
-        if (cmp != 0)
-            return cmp;
-        if (file == tp.file)
-            return 0;
-        else
-            return 1;
-	}
-
-}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/ValueStateWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/ValueStateWritable.java
index ffc1d38..769277c 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/ValueStateWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/ValueStateWritable.java
@@ -4,35 +4,42 @@
 
 import org.apache.hadoop.io.WritableComparable;
 
+import edu.uci.ics.genomix.pregelix.operator.NaiveAlgorithmForPathMergeVertex;
 import edu.uci.ics.genomix.pregelix.type.State;
-import edu.uci.ics.genomix.type.old.Kmer;
+import edu.uci.ics.genomix.type.GeneCode;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
 
 
 public class ValueStateWritable implements WritableComparable<ValueStateWritable> {
 
-	private byte value;
+	private byte adjMap;
 	private int state;
-	private int lengthOfMergeChain;
-	private byte[] mergeChain;
+	private VKmerBytesWritable mergeChain;
 
 	public ValueStateWritable() {
 		state = State.NON_VERTEX;
-		lengthOfMergeChain = 0;
+		mergeChain = new VKmerBytesWritable(NaiveAlgorithmForPathMergeVertex.kmerSize);
 	}
 
-	public ValueStateWritable(byte value, int state, int lengthOfMergeChain, byte[] mergeChain) {
-		this.value = value;
+	public ValueStateWritable(byte adjMap, int state, VKmerBytesWritable mergeChain) {
+		this.adjMap = adjMap;
 		this.state = state;
-		this.lengthOfMergeChain = lengthOfMergeChain;
-		this.mergeChain = mergeChain;
+		this.mergeChain.set(mergeChain);
+	}
+	
+	public void set(byte adjMap, int state, VKmerBytesWritable mergeChain){
+		this.adjMap = adjMap;
+		this.state = state;
+		this.mergeChain.set(mergeChain);
 	}
 
-	public byte getValue() {
-		return value;
+	public byte getAdjMap() {
+		return adjMap;
 	}
 
-	public void setValue(byte value) {
-		this.value = value;
+	public void setAdjMap(byte adjMap) {
+		this.adjMap = adjMap;
 	}
 
 	public int getState() {
@@ -44,43 +51,33 @@
 	}
 
 	public int getLengthOfMergeChain() {
-		return lengthOfMergeChain;
+		return mergeChain.getKmerLength();
 	}
 
-	public void setLengthOfMergeChain(int lengthOfMergeChain) {
-		this.lengthOfMergeChain = lengthOfMergeChain;
-	}
-
-	public byte[] getMergeChain() {
+	public VKmerBytesWritable getMergeChain() {
 		return mergeChain;
 	}
 
-	public void setMergeChain(byte[] mergeChain) {
-		this.mergeChain = mergeChain;
+	public void setMergeChain(KmerBytesWritable mergeChain) {
+		this.mergeChain.set(mergeChain);
+	}
+	
+	public void setMergeChain(VKmerBytesWritable mergeChain) {
+		this.mergeChain.set(mergeChain);
 	}
 
 	@Override
 	public void readFields(DataInput in) throws IOException {
-		value = in.readByte();
+		adjMap = in.readByte();
 		state = in.readInt();
-		lengthOfMergeChain = in.readInt();
-		if(lengthOfMergeChain < 0)
-			System.out.println();
-		if(lengthOfMergeChain != 0){
-			mergeChain = new byte[(lengthOfMergeChain-1)/4 + 1];
-			in.readFully(mergeChain);
-		}
-		else
-			mergeChain = new byte[0];
+		mergeChain.readFields(in);
 	}
 
 	@Override
 	public void write(DataOutput out) throws IOException {
-		out.writeByte(value);
+		out.writeByte(adjMap);
 		out.writeInt(state);
-		out.writeInt(lengthOfMergeChain);
-		if(lengthOfMergeChain != 0)
-			out.write(mergeChain);
+		mergeChain.write(out);
 	}
 
 	@Override
@@ -91,11 +88,11 @@
 	
 	@Override
 	public String toString() {
-		if(lengthOfMergeChain == 0)
-			return Kmer.GENE_CODE.getSymbolFromBitMap(value);
-		return 	Kmer.GENE_CODE.getSymbolFromBitMap(value) + "\t" +
-				lengthOfMergeChain + "\t" +
-				Kmer.recoverKmerFrom(lengthOfMergeChain, mergeChain, 0, mergeChain.length) + "\t" +
+		if(mergeChain.getKmerLength() == 0)
+			return GeneCode.getSymbolFromBitMap(adjMap);
+		return 	GeneCode.getSymbolFromBitMap(adjMap) + "\t" +
+				getLengthOfMergeChain() + "\t" +
+				mergeChain.toString() + "\t" +
 				state;
 	}
 	
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/ValueWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/ValueWritable.java
deleted file mode 100644
index a3f0b9f..0000000
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/ValueWritable.java
+++ /dev/null
@@ -1,73 +0,0 @@
-package edu.uci.ics.genomix.pregelix.io;
-
-import java.io.*;
-
-import org.apache.hadoop.io.WritableComparable;
-
-public class ValueWritable implements WritableComparable<ValueWritable> {
-
-	private byte value;
-	private int lengthOfMergeChain;
-	private byte[] mergeChain;
-
-	public ValueWritable() {
-		lengthOfMergeChain = 0;
-	}
-
-	public ValueWritable(byte value, int lengthOfMergeChain, byte[] mergeChain) {
-		this.value = value;
-		this.lengthOfMergeChain = lengthOfMergeChain;
-		this.mergeChain = mergeChain;
-	}
-
-	public byte getValue() {
-		return value;
-	}
-
-	public void setValue(byte value) {
-		this.value = value;
-	}
-
-	public int getLengthOfMergeChain() {
-		return lengthOfMergeChain;
-	}
-
-	public void setLengthOfMergeChain(int lengthOfMergeChain) {
-		this.lengthOfMergeChain = lengthOfMergeChain;
-	}
-
-	public byte[] getMergeChain() {
-		return mergeChain;
-	}
-
-	public void setMergeChain(byte[] mergeChain) {
-		this.mergeChain = mergeChain;
-	}
-
-	@Override
-	public void readFields(DataInput in) throws IOException {
-		value = in.readByte();
-		lengthOfMergeChain = in.readInt();
-		if(lengthOfMergeChain != 0){
-			mergeChain = new byte[(lengthOfMergeChain-1)/4 + 1];
-			in.readFully(mergeChain);
-		}
-		else
-			mergeChain = new byte[0];
-	}
-
-	@Override
-	public void write(DataOutput out) throws IOException {
-		out.writeByte(value);
-		out.writeInt(lengthOfMergeChain);
-		if(lengthOfMergeChain != 0)
-			out.write(mergeChain);
-	}
-
-	@Override
-	public int compareTo(ValueWritable o) {
-		// TODO Auto-generated method stub
-		return 0;
-	}
-	
-}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/DataLoadLogFormatter.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/DataLoadLogFormatter.java
index 7e56a66..6105f18 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/DataLoadLogFormatter.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/DataLoadLogFormatter.java
@@ -4,27 +4,22 @@
 import java.util.logging.Handler;
 import java.util.logging.LogRecord;
 
-import org.apache.hadoop.io.BytesWritable;
-
-import edu.uci.ics.genomix.type.old.Kmer;
 import edu.uci.ics.genomix.type.KmerCountValue;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
 
 public class DataLoadLogFormatter extends Formatter{
-    private BytesWritable key;
+    private VKmerBytesWritable key;
     private KmerCountValue value;
-    private int k;
 
-    public void set(BytesWritable key, 
-    		KmerCountValue value, int k){
-    	this.key = key;
+    public void set(VKmerBytesWritable key, 
+    		KmerCountValue value){
+    	this.key.set(key);
     	this.value = value;
-    	this.k = k;
     }
     public String format(LogRecord record) {
-        StringBuilder builder = new StringBuilder(1000);
+        StringBuilder builder = new StringBuilder(1000); 
         
-        builder.append(Kmer.recoverKmerFrom(k, key.getBytes(), 0,
-							key.getLength())
+        builder.append(key.toString()
 							+ "\t" + value.toString() + "\r\n");
 
         if(!formatMessage(record).equals(""))
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/LogAlgorithmLogFormatter.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/LogAlgorithmLogFormatter.java
index 3af9b6f..d4f03ee 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/LogAlgorithmLogFormatter.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/LogAlgorithmLogFormatter.java
@@ -5,7 +5,7 @@
 import edu.uci.ics.genomix.pregelix.io.LogAlgorithmMessageWritable;
 import edu.uci.ics.genomix.pregelix.type.Message;
 import edu.uci.ics.genomix.pregelix.type.State;
-import edu.uci.ics.genomix.type.old.Kmer;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
 
 public class LogAlgorithmLogFormatter extends Formatter {
 	//
@@ -13,13 +13,11 @@
     //
     //private static final DateFormat df = new SimpleDateFormat("dd/MM/yyyy hh:mm:ss.SSS");
     private long step;
-    private byte[] sourceVertexId;
-    private byte[] destVertexId;
-    private LogAlgorithmMessageWritable msg;
+    private VKmerBytesWritable sourceVertexId = new VKmerBytesWritable(1);
+    private VKmerBytesWritable destVertexId = new VKmerBytesWritable(1);
+    private LogAlgorithmMessageWritable msg = new LogAlgorithmMessageWritable();
     private int state;
-    private int k;
-    private byte[] mergeChain;
-    private int lengthOfMergeChain;
+    private VKmerBytesWritable mergeChain = new VKmerBytesWritable(1);;
     //private boolean testDelete = false;
     /** 0: general operation 
      *  1: testDelete 
@@ -27,60 +25,57 @@
      *  3: testVoteToHalt
      */ 
     private int operation; 
+    
+    public LogAlgorithmLogFormatter(){
+    }
 
-    public void set(long step, byte[] sourceVertexId, 
-    		byte[] destVertexId, LogAlgorithmMessageWritable msg, int state, int k){
+    public void set(long step, VKmerBytesWritable sourceVertexId, 
+    		VKmerBytesWritable destVertexId, LogAlgorithmMessageWritable msg, int state){
     	this.step = step;
-    	this.sourceVertexId = sourceVertexId;
-    	this.destVertexId = destVertexId;
+    	this.sourceVertexId.set(sourceVertexId);
+    	this.destVertexId.set(destVertexId);
     	this.msg = msg;
     	this.state = state;
-    	this.k = k;
     	this.operation = 0;
     }
-    public void setMergeChain(long step, byte[] sourceVertexId, 
-    		int lengthOfMergeChain, byte[] mergeChain, int k){
+    public void setMergeChain(long step, VKmerBytesWritable sourceVertexId, 
+    		VKmerBytesWritable mergeChain){
     	this.reset();
     	this.step = step;
-    	this.sourceVertexId = sourceVertexId;
-    	this.lengthOfMergeChain = lengthOfMergeChain;
-    	this.mergeChain = mergeChain;
-    	this.k = k;
+    	this.sourceVertexId.set(sourceVertexId);
+    	this.mergeChain.set(mergeChain);
     	this.operation = 2;
     }
-    public void setVotoToHalt(long step, byte[] sourceVertexId, int k){
+    public void setVotoToHalt(long step, VKmerBytesWritable sourceVertexId){
     	this.reset();
     	this.step = step;
-    	this.sourceVertexId = sourceVertexId;
-    	this.k = k;
+    	this.sourceVertexId.set(sourceVertexId);
     	this.operation = 3;
     }
     public void reset(){
-    	this.sourceVertexId = null;
-    	this.destVertexId = null;
-    	this.msg = null;
+    	this.sourceVertexId = new VKmerBytesWritable(1);
+    	this.destVertexId = new VKmerBytesWritable(1);
+    	this.msg = new LogAlgorithmMessageWritable();
     	this.state = 0;
-    	this.k = 0;
-    	this.mergeChain = null;
-    	this.lengthOfMergeChain = 0;
+    	this.mergeChain = new VKmerBytesWritable(1);
     }
     public String format(LogRecord record) {
         StringBuilder builder = new StringBuilder(1000);
-        String source = Kmer.recoverKmerFrom(k, sourceVertexId, 0, sourceVertexId.length);
+        String source = sourceVertexId.toString();
         String chain = "";
         
         builder.append("Step: " + step + "\r\n");
         builder.append("Source Code: " + source + "\r\n");
         if(operation == 0){
-	        if(destVertexId != null){
-	        	String dest = Kmer.recoverKmerFrom(k, destVertexId, 0, destVertexId.length);
+	        if(destVertexId.getKmerLength() != -1){
+	        	String dest = destVertexId.toString();
 		        builder.append("Send message to " + "\r\n");
 		        builder.append("Destination Code: " + dest + "\r\n");
 	        }
 	        builder.append("Message is: " + Message.MESSAGE_CONTENT.getContentFromCode(msg.getMessage()) + "\r\n");
 	        	
-	        if(msg.getLengthOfChain() != 0){
-	        	chain = Kmer.recoverKmerFrom(msg.getLengthOfChain(), msg.getChainVertexId(), 0, msg.getChainVertexId().length);
+	        if(msg.getLengthOfChain() != -1){
+	        	chain = msg.getChainVertexId().toString();
 	        	builder.append("Chain Message: " + chain + "\r\n");
 	        	builder.append("Chain Length: " + msg.getLengthOfChain() + "\r\n");
 	        }
@@ -88,9 +83,9 @@
 	        builder.append("State is: " + State.STATE_CONTENT.getContentFromCode(state) + "\r\n");
         }
         if(operation == 2){
-        	chain = Kmer.recoverKmerFrom(lengthOfMergeChain, mergeChain, 0, mergeChain.length);
+        	chain = mergeChain.toString();
         	builder.append("Merge Chain: " + chain + "\r\n");
-        	builder.append("Merge Chain Length: " + lengthOfMergeChain + "\r\n");
+        	builder.append("Merge Chain Length: " + mergeChain.getKmerLength() + "\r\n");
         }
         if(operation == 3)
         	builder.append("Vote to halt!");
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/NaiveAlgorithmLogFormatter.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/NaiveAlgorithmLogFormatter.java
index c337a16..332d6d0 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/NaiveAlgorithmLogFormatter.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/NaiveAlgorithmLogFormatter.java
@@ -2,8 +2,8 @@
 
 import java.util.logging.*;
 
-import edu.uci.ics.genomix.pregelix.io.MessageWritable;
-import edu.uci.ics.genomix.type.old.Kmer;
+import edu.uci.ics.genomix.pregelix.io.NaiveAlgorithmMessageWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
 
 public class NaiveAlgorithmLogFormatter extends Formatter {
 	//
@@ -11,22 +11,20 @@
     //
     //private static final DateFormat df = new SimpleDateFormat("dd/MM/yyyy hh:mm:ss.SSS");
     private long step;
-    private byte[] sourceVertexId;
-    private byte[] destVertexId;
-    private MessageWritable msg;
-    private int k;
+    private VKmerBytesWritable sourceVertexId;
+    private VKmerBytesWritable destVertexId;
+    private NaiveAlgorithmMessageWritable msg;
 
-    public void set(long step, byte[] sourceVertexId, 
-    		byte[] destVertexId, MessageWritable msg, int k){
+    public void set(long step, VKmerBytesWritable sourceVertexId, 
+    		VKmerBytesWritable destVertexId, NaiveAlgorithmMessageWritable msg){
     	this.step = step;
-    	this.sourceVertexId = sourceVertexId;
-    	this.destVertexId = destVertexId;
+    	this.sourceVertexId.set(sourceVertexId);
+    	this.destVertexId.set(destVertexId);
     	this.msg = msg;
-    	this.k = k;
     }
     public String format(LogRecord record) {
         StringBuilder builder = new StringBuilder(1000);
-        String source = Kmer.recoverKmerFrom(k, sourceVertexId, 0, sourceVertexId.length);
+        String source = sourceVertexId.toString();
         
         String chain = "";
         
@@ -35,11 +33,11 @@
         
         if(destVertexId != null){
         	builder.append("Send message to " + "\r\n");
-        	String dest = Kmer.recoverKmerFrom(k, destVertexId, 0, destVertexId.length);
+        	String dest = destVertexId.toString();
         	builder.append("Destination Code: " + dest + "\r\n");
         }
         if(msg.getLengthOfChain() != 0){
-        	chain = Kmer.recoverKmerFrom(msg.getLengthOfChain(), msg.getChainVertexId(), 0, msg.getChainVertexId().length);
+        	chain = msg.getChainVertexId().toString();
         	builder.append("Chain Message: " + chain + "\r\n");
         	builder.append("Chain Length: " + msg.getLengthOfChain() + "\r\n");
         }
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/CombineSequenceFile.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/CombineSequenceFile.java
index d9f0efe..c7349dd 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/CombineSequenceFile.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/CombineSequenceFile.java
@@ -5,14 +5,12 @@
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.fs.FileSystem;
 import org.apache.hadoop.fs.Path;
-import org.apache.hadoop.io.BytesWritable;
 import org.apache.hadoop.io.SequenceFile;
 import org.apache.hadoop.io.SequenceFile.CompressionType;
 
-import edu.uci.ics.genomix.type.old.Kmer;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
 import edu.uci.ics.genomix.type.KmerCountValue;
 
-
 public class CombineSequenceFile {
 
 	/**
@@ -25,24 +23,23 @@
 		Configuration conf = new Configuration();
 		FileSystem fileSys = FileSystem.get(conf);
 		
-		Path p = new Path("data/SinglePath_55");
-		Path p2 = new Path("data/result");
-		Path outFile = new Path(p2, "output"); 
+		Path p = new Path("output");
+		//Path p2 = new Path("data/result");
+		Path outFile = new Path("output"); 
 		SequenceFile.Reader reader;
 	    SequenceFile.Writer writer = SequenceFile.createWriter(fileSys, conf,
-	         outFile, BytesWritable.class, KmerCountValue.class, 
+	         outFile, KmerBytesWritable.class, KmerCountValue.class, 
 	         CompressionType.NONE);
-	    BytesWritable key = new BytesWritable();
+	    KmerBytesWritable key = new KmerBytesWritable(kmerSize);
 	    KmerCountValue value = new KmerCountValue();
 	    
-	    File dir = new File("data/SinglePath_55");
+	    File dir = new File("output");
 		for(File child : dir.listFiles()){
 			String name = child.getAbsolutePath();
 			Path inFile = new Path(p, name);
 			reader = new SequenceFile.Reader(fileSys, inFile, conf);
 			while (reader.next(key, value)) {
-				System.out.println(Kmer.recoverKmerFrom(kmerSize, key.getBytes(), 0,
-						key.getLength())
+				System.out.println(key.toString()
 						+ "\t" + value.toString());
 				writer.append(key, value);
 			}
@@ -53,8 +50,7 @@
 		
 		reader = new SequenceFile.Reader(fileSys, outFile, conf);
 		while (reader.next(key, value)) {
-			System.err.println(Kmer.recoverKmerFrom(kmerSize, key.getBytes(), 0,
-					key.getLength())
+			System.err.println(key.toString()
 					+ "\t" + value.toString());
 		}
 		reader.close();
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/GenerateTextFile.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/GenerateTextFile.java
index 18214a8..c759261 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/GenerateTextFile.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/GenerateTextFile.java
@@ -7,30 +7,28 @@
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.fs.FileSystem;
 import org.apache.hadoop.fs.Path;
-import org.apache.hadoop.io.BytesWritable;
 import org.apache.hadoop.io.SequenceFile;
 
 import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
-import edu.uci.ics.genomix.type.old.Kmer;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
 
 public class GenerateTextFile {
 
 	public static void generate() throws IOException{
-		BufferedWriter bw = new BufferedWriter(new FileWriter("text/new_SimplePath"));
+		BufferedWriter bw = new BufferedWriter(new FileWriter("text/log_TreePath"));
 		Configuration conf = new Configuration();
 		FileSystem fileSys = FileSystem.get(conf);
 		for(int i = 0; i < 2; i++){
 			Path path = new Path("output/part-" + i);
 			SequenceFile.Reader reader = new SequenceFile.Reader(fileSys, path, conf);
-		    BytesWritable key = new BytesWritable();
+			KmerBytesWritable key = new KmerBytesWritable(5);
 		    ValueStateWritable value = new ValueStateWritable();
 		    
 		    while(reader.next(key, value)){
 				if (key == null || value == null){
 					break;
 				}
-				bw.write(Kmer.recoverKmerFrom(5, key.getBytes(), 0,
-						key.getLength())
+				bw.write(key.toString()
 						+ "\t" + value.toString());
 				bw.newLine();
 		    }
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java
index 763d46e..f03a4ab 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java
@@ -5,19 +5,18 @@
 import java.io.IOException;
 
 import org.apache.hadoop.fs.Path;
-import org.apache.hadoop.io.ByteWritable;
-import org.apache.hadoop.io.BytesWritable;
 import org.apache.hadoop.mapreduce.lib.input.FileInputFormat;
 import org.apache.hadoop.mapreduce.lib.output.FileOutputFormat;
 
-import edu.uci.ics.genomix.pregelix.LoadGraphVertex;
-import edu.uci.ics.genomix.pregelix.format.BinaryLoadGraphInputFormat;
-import edu.uci.ics.genomix.pregelix.format.BinaryLoadGraphOutputFormat;
-import edu.uci.ics.genomix.pregelix.format.LogAlgorithmForMergeGraphInputFormat;
-import edu.uci.ics.genomix.pregelix.format.LogAlgorithmForMergeGraphOutputFormat;
+import edu.uci.ics.genomix.pregelix.format.LogAlgorithmForPathMergeOutputFormat;
+import edu.uci.ics.genomix.pregelix.format.NaiveAlgorithmForPathMergeInputFormat;
+import edu.uci.ics.genomix.pregelix.format.NaiveAlgorithmForPathMergeOutputFormat;
+import edu.uci.ics.genomix.pregelix.format.LogAlgorithmForPathMergeInputFormat;
 import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
-import edu.uci.ics.genomix.pregelix.LogAlgorithmForMergeGraphVertex;
-import edu.uci.ics.genomix.pregelix.MergeGraphVertex;
+import edu.uci.ics.genomix.pregelix.operator.LoadGraphVertex;
+import edu.uci.ics.genomix.pregelix.operator.LogAlgorithmForPathMergeVertex;
+import edu.uci.ics.genomix.pregelix.operator.NaiveAlgorithmForPathMergeVertex;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
 import edu.uci.ics.pregelix.api.job.PregelixJob;
 
 
@@ -30,10 +29,11 @@
     private static void generateLoadGraphJob(String jobName, String outputPath) throws IOException {
     	PregelixJob job = new PregelixJob(jobName);
     	job.setVertexClass(LoadGraphVertex.class);
-    	job.setVertexInputFormatClass(BinaryLoadGraphInputFormat.class);
-        job.setVertexOutputFormatClass(BinaryLoadGraphOutputFormat.class);
-        job.setOutputKeyClass(BytesWritable.class);
-        job.setOutputValueClass(ByteWritable.class);
+    	job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class);
+        job.setVertexOutputFormatClass(NaiveAlgorithmForPathMergeOutputFormat.class);
+        job.setDynamicVertexValueSize(true);
+        job.setOutputKeyClass(KmerBytesWritable.class);
+        job.setOutputValueClass(ValueStateWritable.class);
         FileInputFormat.setInputPaths(job, HDFS_INPUTPATH);
         FileOutputFormat.setOutputPath(job, new Path(HDFS_OUTPUTPAH));
         job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
@@ -45,15 +45,15 @@
     
     private static void generateMergeGraphJob(String jobName, String outputPath) throws IOException {
     	PregelixJob job = new PregelixJob(jobName);
-    	job.setVertexClass(MergeGraphVertex.class);
-    	job.setVertexInputFormatClass(BinaryLoadGraphInputFormat.class);
-        job.setVertexOutputFormatClass(BinaryLoadGraphOutputFormat.class);
+    	job.setVertexClass(NaiveAlgorithmForPathMergeVertex.class);
+    	job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class);
+        job.setVertexOutputFormatClass(NaiveAlgorithmForPathMergeOutputFormat.class);
         job.setDynamicVertexValueSize(true);
-        job.setOutputKeyClass(BytesWritable.class);
+        job.setOutputKeyClass(KmerBytesWritable.class);
         job.setOutputValueClass(ValueStateWritable.class);
         FileInputFormat.setInputPaths(job, HDFS_INPUTPATH);
         FileOutputFormat.setOutputPath(job, new Path(HDFS_OUTPUTPAH));
-        job.getConfiguration().setInt(MergeGraphVertex.KMER_SIZE, 55);
+        job.getConfiguration().setInt(NaiveAlgorithmForPathMergeVertex.KMER_SIZE, 5);
         job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
     }
     
@@ -63,15 +63,15 @@
     
     private static void generateLogAlgorithmForMergeGraphJob(String jobName, String outputPath) throws IOException {
     	PregelixJob job = new PregelixJob(jobName);
-    	job.setVertexClass(LogAlgorithmForMergeGraphVertex.class);
-        job.setVertexInputFormatClass(LogAlgorithmForMergeGraphInputFormat.class); 
-        job.setVertexOutputFormatClass(LogAlgorithmForMergeGraphOutputFormat.class);
+    	job.setVertexClass(LogAlgorithmForPathMergeVertex.class);
+        job.setVertexInputFormatClass(LogAlgorithmForPathMergeInputFormat.class); 
+        job.setVertexOutputFormatClass(LogAlgorithmForPathMergeOutputFormat.class);
         job.setDynamicVertexValueSize(true);
-        job.setOutputKeyClass(BytesWritable.class);
+        job.setOutputKeyClass(KmerBytesWritable.class);
         job.setOutputValueClass(ValueStateWritable.class);
         FileInputFormat.setInputPaths(job, HDFS_INPUTPATH);
         FileOutputFormat.setOutputPath(job, new Path(HDFS_OUTPUTPAH));
-        job.getConfiguration().setInt(LogAlgorithmForMergeGraphVertex.KMER_SIZE, 5);
+        job.getConfiguration().setInt(LogAlgorithmForPathMergeVertex.KMER_SIZE, 5);
         job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
     }
     
@@ -88,8 +88,6 @@
 		//genLoadGraph();
 		//genMergeGraph();
 		genLogAlgorithmForMergeGraph();
-		//genSequenceLoadGraph();
-		//genBasicBinaryLoadGraph();
 	}
 
 }
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/RunJobTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/RunJobTestSuite.java
index ffc1a25..45d8185 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/RunJobTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/RunJobTestSuite.java
@@ -40,7 +40,7 @@
 	private static final String PATH_TO_ONLY = "src/test/resources/only.txt";
 	private static final String FILE_EXTENSION_OF_RESULTS = "result";
 
-	private static final String DATA_PATH = "data/result/TreePath";// sequenceShortFileMergeTest
+	private static final String DATA_PATH = "data/sequencefile/TreePath";
 	private static final String HDFS_PATH = "/webmap/";
 
 	private static final String HYRACKS_APP_NAME = "pregelix";
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/example/util/TestUtils.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/example/util/TestUtils.java
index 4ea3c1d..8ac1b09 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/example/util/TestUtils.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/example/util/TestUtils.java
@@ -20,6 +20,13 @@
 
 public class TestUtils {
 
+    public static void compareWithResultDir(File expectedFileDir, File actualFileDir) throws Exception {
+        String[] fileNames = expectedFileDir.list();
+        for (String fileName : fileNames) {
+            compareWithResult(new File(expectedFileDir, fileName), new File(actualFileDir, fileName));
+        }
+    }
+
     public static void compareWithResult(File expectedFile, File actualFile) throws Exception {
         BufferedReader readerExpected = new BufferedReader(new FileReader(expectedFile));
         BufferedReader readerActual = new BufferedReader(new FileReader(actualFile));
@@ -28,7 +35,6 @@
         try {
             while ((lineExpected = readerExpected.readLine()) != null) {
                 lineActual = readerActual.readLine();
-                // Assert.assertEquals(lineExpected, lineActual);
                 if (lineActual == null) {
                     throw new Exception("Actual result changed at line " + num + ":\n< " + lineExpected + "\n> ");
                 }
@@ -62,8 +68,10 @@
             if (row1.equals(row2))
                 continue;
 
-            String[] fields1 = row1.split(" ");
-            String[] fields2 = row2.split(" ");
+            boolean spaceOrTab = false;
+            spaceOrTab = row1.contains(" ");
+            String[] fields1 = spaceOrTab ? row1.split(" ") : row1.split("\t");
+            String[] fields2 = spaceOrTab ? row2.split(" ") : row2.split("\t");
 
             for (int j = 0; j < fields1.length; j++) {
                 if (fields1[j].equals(fields2[j])) {
@@ -76,7 +84,7 @@
                     float float1 = (float) double1.doubleValue();
                     float float2 = (float) double2.doubleValue();
 
-                    if (Math.abs(float1 - float2) == 0)
+                    if (Math.abs(float1 - float2) < 1.0e-7)
                         continue;
                     else {
                         return false;