diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/P1MessageWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/P1MessageWritable.java
deleted file mode 100644
index a86ffe0..0000000
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/P1MessageWritable.java
+++ /dev/null
@@ -1,148 +0,0 @@
-package edu.uci.ics.genomix.pregelix.io;
-
-import java.io.DataInput;
-import java.io.DataOutput;
-import java.io.IOException;
-
-import org.apache.hadoop.io.WritableComparable;
-
-import edu.uci.ics.genomix.pregelix.operator.NaiveAlgorithmForPathMergeVertex;
-import edu.uci.ics.genomix.pregelix.type.CheckMessage;
-import edu.uci.ics.genomix.pregelix.type.Message;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
-import edu.uci.ics.genomix.type.VKmerBytesWritable;
-
-public class P1MessageWritable implements WritableComparable<P1MessageWritable>{
-	/**
-	 * sourceVertexId stores source vertexId when headVertex sends the message
-	 * 				  stores neighber vertexValue when pathVertex sends the message
-	 * file stores the point to the file that stores the chains of connected DNA
-	 */
-	private KmerBytesWritable sourceVertexId;
-	private byte adjMap;
-	private byte lastGeneCode;
-	private byte message;
-	
-	private byte checkMessage;
-	
-	public P1MessageWritable(){
-		sourceVertexId = new VKmerBytesWritable(NaiveAlgorithmForPathMergeVertex.kmerSize);
-		adjMap = (byte)0;
-		lastGeneCode = (byte)0;
-		message = Message.NON;
-		checkMessage = (byte)0;
-	}
-	
-	public void set(KmerBytesWritable sourceVertex, byte adjMap, byte lastGeneCode, byte message){
-		checkMessage = 0;
-		if(sourceVertexId != null){
-			checkMessage |= CheckMessage.SOURCE;
-			this.sourceVertexId.set(sourceVertexId);
-		}
-		if(adjMap != 0){
-			checkMessage |= CheckMessage.ADJMAP;
-			this.adjMap = adjMap;
-		}
-		if(lastGeneCode != 0){
-			checkMessage |= CheckMessage.LASTGENECODE;
-			this.lastGeneCode = lastGeneCode;
-		}
-		this.message = message;
-	}
-	
-	public void reset(){
-		checkMessage = 0;
-		sourceVertexId = new VKmerBytesWritable(NaiveAlgorithmForPathMergeVertex.kmerSize);
-		adjMap = (byte)0;
-		lastGeneCode = (byte)0;
-		message = Message.NON;
-	}
-
-	public KmerBytesWritable getSourceVertexId() {
-		return sourceVertexId;
-	}
-
-	public void setSourceVertexId(KmerBytesWritable sourceVertexId) {
-		if(sourceVertexId != null){
-			checkMessage |= CheckMessage.SOURCE;
-			this.sourceVertexId.set(sourceVertexId);
-		}
-	}
-
-	public byte getAdjMap() {
-		return adjMap;
-	}
-
-	public void setAdjMap(byte adjMap) {
-		if(adjMap != 0){
-			checkMessage |= CheckMessage.ADJMAP;
-			this.adjMap = adjMap;
-		}
-	}
-
-	public byte getLastGeneCode() {
-		return lastGeneCode;
-	}
-
-	public void setLastGeneCode(byte lastGeneCode) {
-		if(lastGeneCode != 0){
-			checkMessage |= CheckMessage.LASTGENECODE;
-			this.lastGeneCode = lastGeneCode;
-		}
-	}
-
-	public byte getMessage() {
-		return message;
-	}
-
-	public void setMessage(byte message) {
-		this.message = message;
-	}
-
-	@Override
-	public void write(DataOutput out) throws IOException {
-		out.writeByte(checkMessage);
-		if((checkMessage & CheckMessage.SOURCE) != 0)
-			sourceVertexId.write(out);
-		if((checkMessage & CheckMessage.ADJMAP) != 0)
-			out.write(adjMap);
-		if((checkMessage & CheckMessage.LASTGENECODE) != 0)
-			out.write(lastGeneCode);
-		out.write(message);
-	}
-
-	@Override
-	public void readFields(DataInput in) throws IOException {
-		this.reset();
-		checkMessage = in.readByte();
-		if((checkMessage & CheckMessage.SOURCE) != 0)
-			sourceVertexId.readFields(in);
-		if((checkMessage & CheckMessage.ADJMAP) != 0)
-			adjMap = in.readByte();
-		if((checkMessage & CheckMessage.LASTGENECODE) != 0)
-			lastGeneCode = in.readByte();
-		message = in.readByte();
-	}
-
-    @Override
-    public int hashCode() {
-        return sourceVertexId.hashCode();
-    }
-    @Override
-    public boolean equals(Object o) {
-        if (o instanceof P1MessageWritable) {
-        	P1MessageWritable tp = (P1MessageWritable) o;
-            return sourceVertexId.equals( tp.sourceVertexId);
-        }
-        return false;
-    }
-    @Override
-    public String toString() {
-        return sourceVertexId.toString();
-    }
-    
-	@Override
-	public int compareTo(P1MessageWritable tp) {
-		return sourceVertexId.compareTo(tp.sourceVertexId);
-	}
-}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/LoadGraphVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/LoadGraphVertex.java
deleted file mode 100644
index 6fef3a6..0000000
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/LoadGraphVertex.java
+++ /dev/null
@@ -1,70 +0,0 @@
-package edu.uci.ics.genomix.pregelix.operator;
-
-import java.util.Iterator;
-
-import org.apache.hadoop.io.NullWritable;
-
-import edu.uci.ics.genomix.pregelix.client.Client;
-import edu.uci.ics.genomix.pregelix.format.NaiveAlgorithmForPathMergeInputFormat;
-import edu.uci.ics.genomix.pregelix.format.NaiveAlgorithmForPathMergeOutputFormat;
-import edu.uci.ics.genomix.pregelix.io.NaiveAlgorithmMessageWritable;
-import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
-import edu.uci.ics.pregelix.api.graph.Vertex;
-import edu.uci.ics.pregelix.api.job.PregelixJob;
-
-/*
- * vertexId: BytesWritable
- * vertexValue: ByteWritable
- * edgeValue: NullWritable
- * message: NaiveAlgorithmMessageWritable
- * 
- * 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<KmerBytesWritable, ValueStateWritable, NullWritable, NaiveAlgorithmMessageWritable>{
-
-	/**
-	 * For test, just output original file
-	 */
-	@Override
-	public void compute(Iterator<NaiveAlgorithmMessageWritable> msgIterator) {
-		voteToHalt();
-	}
-
-	/**
-	 * @param args
-	 */
-	public static void main(String[] args) throws Exception {
-        PregelixJob job = new PregelixJob(LoadGraphVertex.class.getSimpleName());
-        job.setVertexClass(LoadGraphVertex.class);
-        /**
-         * BinaryInput and BinaryOutput
-         */
-        job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class); 
-        job.setVertexOutputFormatClass(NaiveAlgorithmForPathMergeOutputFormat.class); 
-        job.setDynamicVertexValueSize(true);
-        job.setOutputKeyClass(KmerBytesWritable.class);
-        job.setOutputValueClass(ValueStateWritable.class);
-        Client.run(args, job);
-	}
-}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/LogFilterVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/LogFilterVertex.java
deleted file mode 100644
index 62de480..0000000
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/LogFilterVertex.java
+++ /dev/null
@@ -1,347 +0,0 @@
-package edu.uci.ics.genomix.pregelix.operator;
-
-import java.util.Iterator;
-
-import org.apache.hadoop.io.NullWritable;
-
-import edu.uci.ics.pregelix.api.graph.Vertex;
-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.pregelix.util.GraphVertexOperation;
-import edu.uci.ics.genomix.type.GeneCode;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
-import edu.uci.ics.genomix.type.VKmerBytesWritable;
-import edu.uci.ics.genomix.type.VKmerBytesWritableFactory;
-
-/*
- * 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 LogFilterVertex extends Vertex<KmerBytesWritable, ValueStateWritable, NullWritable, LogAlgorithmMessageWritable>{	
-	
-	public static final String KMER_SIZE = "TwoStepLogAlgorithmForPathMergeVertex.kmerSize";
-	public static final String ITERATIONS = "TwoStepLogAlgorithmForPathMergeVertex.iteration";
-	public static int kmerSize = -1;
-	private int maxIteration = -1;
-	
-	private LogAlgorithmMessageWritable msg = new LogAlgorithmMessageWritable();
-	
-	private VKmerBytesWritableFactory kmerFactory = new VKmerBytesWritableFactory(1);
-	private VKmerBytesWritable destVertexId = new VKmerBytesWritable(1); 
-	private VKmerBytesWritable chainVertexId = new VKmerBytesWritable(1);
-	private VKmerBytesWritable lastKmer = new VKmerBytesWritable(1);
-	/**
-	 * initiate kmerSize, maxIteration
-	 */
-	public void initVertex(){
-		if(kmerSize == -1)
-			kmerSize = getContext().getConfiguration().getInt(KMER_SIZE, 5);
-        if (maxIteration < 0) 
-            maxIteration = getContext().getConfiguration().getInt(ITERATIONS, 1000000);
-	}
-	/**
-	 * get destination vertex
-	 */
-	public VKmerBytesWritable getNextDestVertexId(KmerBytesWritable vertexId, byte geneCode){
-		return kmerFactory.shiftKmerWithNextCode(vertexId, geneCode);
-	}
-	
-	public VKmerBytesWritable getPreDestVertexId(KmerBytesWritable vertexId, byte geneCode){
-		return kmerFactory.shiftKmerWithPreCode(vertexId, geneCode);
-	}
-	
-	public VKmerBytesWritable getNextDestVertexIdFromBitmap(KmerBytesWritable chainVertexId, byte adjMap){
-		return getDestVertexIdFromChain(chainVertexId, adjMap);
-	}
-	
-	public VKmerBytesWritable getDestVertexIdFromChain(KmerBytesWritable chainVertexId, byte adjMap){
-		lastKmer.set(kmerFactory.getLastKmerFromChain(kmerSize, chainVertexId));
-		return getNextDestVertexId(lastKmer, GeneCode.getGeneCodeFromBitMap((byte)(adjMap & 0x0F)));
-	}
-	/**
-	 * head send message to all next nodes
-	 */
-	public void sendMsgToAllNextNodes(KmerBytesWritable vertexId, byte adjMap){
-		for(byte x = GeneCode.A; x<= GeneCode.T ; x++){
-			if((adjMap & (1 << x)) != 0){
-				destVertexId.set(getNextDestVertexId(vertexId, x));
-				sendMsg(destVertexId, msg);
-			}
-		}
-	}
-	/**
-	 * head send message to all previous nodes
-	 */
-	public void sendMsgToAllPreviousNodes(KmerBytesWritable vertexId, byte adjMap){
-		for(byte x = GeneCode.A; x<= GeneCode.T ; x++){
-			if(((adjMap >> 4) & (1 << x)) != 0){
-				destVertexId.set(getPreDestVertexId(vertexId, x));
-				sendMsg(destVertexId, msg);
-			}
-		}
-	}
-
-	/**
-	 * set vertex state
-	 */
-	public void setState(){
-		if(msg.getMessage() == Message.START && 
-				(getVertexValue().getState() == State.MID_VERTEX || getVertexValue().getState() == State.END_VERTEX)){
-			getVertexValue().setState(State.START_VERTEX);
-			setVertexValue(getVertexValue());
-		}
-		else if(msg.getMessage() == Message.END && getVertexValue().getState() == State.MID_VERTEX){
-			getVertexValue().setState(State.END_VERTEX);
-			setVertexValue(getVertexValue());
-			voteToHalt();
-		}
-		else
-			voteToHalt();
-	}
-	/**
-	 * send start message to next node
-	 */
-	public void sendStartMsgToNextNode(){
-		msg.reset();
-		msg.setMessage(Message.START);
-		msg.setSourceVertexId(getVertexId());
-		sendMsg(destVertexId, msg);
-		voteToHalt();
-	}
-	/**
-	 * send end message to next node
-	 */
-	public void sendEndMsgToNextNode(){
-		msg.reset();
-		msg.setMessage(Message.END);
-		msg.setSourceVertexId(getVertexId());
-		sendMsg(destVertexId, msg);
-		voteToHalt();
-	}
-	/**
-	 * send non message to next node
-	 */
-	public void sendNonMsgToNextNode(){
-		msg.setMessage(Message.NON);
-		msg.setSourceVertexId(getVertexId());
-		sendMsg(destVertexId, msg);
-	}
-	/**
-	 * head send message to path
-	 */
-	public void sendMsgToPathVertex(KmerBytesWritable chainVertexId, byte adjMap){
-		if(GeneCode.getGeneCodeFromBitMap((byte)(getVertexValue().getAdjMap() & 0x0F)) == -1
-				|| getVertexValue().getState() == State.FINAL_VERTEX) //|| lastKmer == null
-			voteToHalt();
-		else{
-			destVertexId.set(getNextDestVertexIdFromBitmap(chainVertexId, adjMap));
-			if(getVertexValue().getState() == State.START_VERTEX){
-				sendStartMsgToNextNode();
-			}
-			else if(getVertexValue().getState() != State.END_VERTEX){
-				sendEndMsgToNextNode();
-			}
-		}
-	}
-	/**
-	 * path send message to head 
-	 */
-	public void responseMsgToHeadVertex(){
-		if(getVertexValue().getLengthOfMergeChain() == 0){
-			getVertexValue().setMergeChain(getVertexId());
-			setVertexValue(getVertexValue());
-		}
-		destVertexId.set(msg.getSourceVertexId());
-		msg.set(null, getVertexValue().getMergeChain(), getVertexValue().getAdjMap(), msg.getMessage());
-		setMessageType(msg.getMessage());
-		sendMsg(destVertexId,msg);
-	}
-	/**
-	 * set message type
-	 */
-	public void setMessageType(int message){
-		//kill Message because it has been merged by the head
-		if(getVertexValue().getState() == State.END_VERTEX){
-			msg.setMessage(Message.END);
-			getVertexValue().setState(State.END_VERTEX);
-			setVertexValue(getVertexValue());
-		}
-		else
-			msg.setMessage(Message.NON);
-		
-		if(message == Message.START){
-			deleteVertex(getVertexId());
-		}
-	}
-	/**
-	 *  set vertexValue's state chainVertexId, value
-	 */
-	public boolean setVertexValueAttributes(){
-		if(msg.getMessage() == Message.END){
-			if(getVertexValue().getState() != State.START_VERTEX)
-				getVertexValue().setState(State.END_VERTEX);
-			else
-				getVertexValue().setState(State.FINAL_VERTEX);
-		}
-			
-		if(getSuperstep() == 5)
-			chainVertexId.set(getVertexId());
-		else
-			chainVertexId.set(getVertexValue().getMergeChain());
-		lastKmer.set(kmerFactory.getLastKmerFromChain(msg.getLengthOfChain() - kmerSize + 1, msg.getChainVertexId()));
-		chainVertexId.set(kmerFactory.mergeTwoKmer(chainVertexId, lastKmer));
-		if(GraphVertexOperation.isCycle(getVertexId(), chainVertexId)){
-			getVertexValue().setMergeChain(null);
-			getVertexValue().setAdjMap(GraphVertexOperation.reverseAdjMap(getVertexValue().getAdjMap(),
-					chainVertexId.getGeneCodeAtPosition(kmerSize)));
-			getVertexValue().setState(State.CYCLE);
-			return false;
-		}
-		else
-			getVertexValue().setMergeChain(chainVertexId);
-		
-		byte tmpVertexValue = GraphVertexOperation.updateRightNeighber(getVertexValue().getAdjMap(), msg.getAdjMap());
-		getVertexValue().setAdjMap(tmpVertexValue);
-		return true;
-	}
-	/**
-	 *  send message to self
-	 */
-	public void sendMsgToSelf(){
-		if(msg.getMessage() != Message.END){
-			setVertexValue(getVertexValue());
-			msg.reset(); //reset
-			msg.setAdjMap(getVertexValue().getAdjMap());
-			sendMsg(getVertexId(),msg);
-		}
-	}
-	/**
-	 * start sending message 
-	 */
-	public void startSendMsg(){
-		if(GraphVertexOperation.isHeadVertex(getVertexValue().getAdjMap())){
-			msg.set(null, null, (byte)0, Message.START);
-			sendMsgToAllNextNodes(getVertexId(), getVertexValue().getAdjMap());
-			voteToHalt();
-		}
-		if(GraphVertexOperation.isRearVertex(getVertexValue().getAdjMap())){
-			msg.set(null, null, (byte)0, Message.END);
-			sendMsgToAllPreviousNodes(getVertexId(), getVertexValue().getAdjMap());
-			voteToHalt();
-		}
-		if(GraphVertexOperation.isPathVertex(getVertexValue().getAdjMap())){
-			getVertexValue().setState(State.MID_VERTEX);
-			setVertexValue(getVertexValue());
-		}
-	}
-	/**
-	 *  initiate head, rear and path node
-	 */
-	public void initState(Iterator<LogAlgorithmMessageWritable> msgIterator){
-		while(msgIterator.hasNext()){
-			if(!GraphVertexOperation.isPathVertex(getVertexValue().getAdjMap())){
-				msgIterator.next();
-				voteToHalt();
-			}
-			else{
-				msg = msgIterator.next();
-				setState();
-			}
-		}
-	}
-	/**
-	 * head send message to path
-	 */
-	public void sendMsgToPathVertex(Iterator<LogAlgorithmMessageWritable> msgIterator){
-		if(getSuperstep() == 3){
-			sendMsgToPathVertex(getVertexId(), getVertexValue().getAdjMap());
-		}
-		else{
-			if(msgIterator.hasNext()){
-				msg = msgIterator.next();
-				if(mergeChainVertex(msgIterator))
-					sendMsgToPathVertex(getVertexValue().getMergeChain(), getVertexValue().getAdjMap());
-				else
-					voteToHalt();
-			}
-			if(getVertexValue().getState() == State.END_VERTEX){
-				voteToHalt();
-			}
-			if(getVertexValue().getState() == State.FINAL_VERTEX){
-				//String source = getVertexValue().getMergeChain().toString();
-				voteToHalt();
-			}
-		}
-	}
-	/**
-	 * path response message to head
-	 */
-	public void responseMsgToHeadVertex(Iterator<LogAlgorithmMessageWritable> msgIterator){
-		if(msgIterator.hasNext()){		
-			msg = msgIterator.next();
-			responseMsgToHeadVertex();
-		}
-		else{
-			if(getVertexValue().getState() != State.START_VERTEX 
-					&& getVertexValue().getState() != State.END_VERTEX){
-				deleteVertex(getVertexId());//killSelf because it doesn't receive any message
-			}
-		}
-	}
-	/**
-	 * merge chainVertex and store in vertexVal.chainVertexId
-	 */
-	public boolean mergeChainVertex(Iterator<LogAlgorithmMessageWritable> msgIterator){
-		return setVertexValueAttributes();
-	}
-	
-	@Override
-	public void compute(Iterator<LogAlgorithmMessageWritable> msgIterator) {
-		initVertex();
-		if (getSuperstep() == 1){
-			if(getVertexId().toString().equals("AAGAC") 
-					|| getVertexId().toString().equals("AGCAC")){
-				startSendMsg();
-			}
-		}
-		else if(getSuperstep() == 2){
-			initState(msgIterator);
-			if(getVertexValue().getState() == State.NON_VERTEX)
-				voteToHalt();
-		}
-		else if(getSuperstep()%2 == 1 && getSuperstep() <= maxIteration){
-			sendMsgToPathVertex(msgIterator);
-		}
-		else if(getSuperstep()%2 == 0 && getSuperstep() <= maxIteration){
-			responseMsgToHeadVertex(msgIterator);
-		}
-		else
-			voteToHalt();
-	}
-}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/NaiveFilterVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/NaiveFilterVertex.java
deleted file mode 100644
index 12c12af..0000000
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/NaiveFilterVertex.java
+++ /dev/null
@@ -1,221 +0,0 @@
-package edu.uci.ics.genomix.pregelix.operator;
-
-import java.util.Iterator;
-
-import org.apache.hadoop.io.NullWritable;
-
-import edu.uci.ics.genomix.type.GeneCode;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
-import edu.uci.ics.genomix.type.VKmerBytesWritable;
-import edu.uci.ics.genomix.type.VKmerBytesWritableFactory;
-
-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.NaiveAlgorithmForPathMergeInputFormat;
-import edu.uci.ics.genomix.pregelix.format.NaiveAlgorithmForPathMergeOutputFormat;
-import edu.uci.ics.genomix.pregelix.io.NaiveAlgorithmMessageWritable;
-import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
-import edu.uci.ics.genomix.pregelix.type.State;
-import edu.uci.ics.genomix.pregelix.util.GraphVertexOperation;
-
-/*
- * vertexId: BytesWritable
- * vertexValue: ByteWritable
- * edgeValue: NullWritable
- * message: NaiveAlgorithmMessageWritable
- * 
- * 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. 
- */
-/**
- * Naive Algorithm for path merge graph
- */
-public class NaiveFilterVertex extends Vertex<KmerBytesWritable, ValueStateWritable, NullWritable, NaiveAlgorithmMessageWritable>{
-	
-	public static final String KMER_SIZE = "NaiveAlgorithmForPathMergeVertex.kmerSize";
-	public static final String ITERATIONS = "NaiveAlgorithmForPathMergeVertex.iteration";
-	public static final String FILTERKMER = "NaiveFilterVertex.filterKmer";
-	public static int kmerSize = -1;
-	private int maxIteration = -1;
-	private String filterKmer = "";
-
-	private NaiveAlgorithmMessageWritable msg = new NaiveAlgorithmMessageWritable();
-
-	private VKmerBytesWritableFactory kmerFactory = new VKmerBytesWritableFactory(1);
-	private VKmerBytesWritable destVertexId = new VKmerBytesWritable(1); 
-	private VKmerBytesWritable chainVertexId = new VKmerBytesWritable(1);
-	private VKmerBytesWritable lastKmer = new VKmerBytesWritable(1);
-
-	/**
-	 * initiate kmerSize, maxIteration
-	 */
-	public void initVertex(){
-		if(kmerSize == -1)
-			kmerSize = getContext().getConfiguration().getInt(KMER_SIZE, 5);
-        if (maxIteration < 0) 
-            maxIteration = getContext().getConfiguration().getInt(ITERATIONS, 1000000);
-        if(filterKmer.equals(""))
-        	filterKmer = getContext().getConfiguration().get(FILTERKMER, "");
-	}
-	public void findDestination(){
-		destVertexId.set(msg.getSourceVertexId());
-	}
-	/**
-	 * get destination vertex
-	 */
-	public VKmerBytesWritable getDestVertexId(KmerBytesWritable vertexId, byte geneCode){
-		return kmerFactory.shiftKmerWithNextCode(vertexId, geneCode);
-	}
-
-	public VKmerBytesWritable getDestVertexIdFromChain(VKmerBytesWritable chainVertexId, byte adjMap){
-		lastKmer.set(kmerFactory.getLastKmerFromChain(kmerSize, chainVertexId));
-		return getDestVertexId(lastKmer, GeneCode.getGeneCodeFromBitMap((byte)(adjMap & 0x0F)));
-	}
-	/**
-	 * head send message to all next nodes
-	 */
-	public void sendMsgToAllNextNodes(KmerBytesWritable vertexId, byte adjMap){
-		for(byte x = GeneCode.A; x<= GeneCode.T ; x++){
-			if((adjMap & (1 << x)) != 0){
-				destVertexId.set(getDestVertexId(vertexId, x));
-				sendMsg(destVertexId, msg);
-			}
-		}
-	}
-	/**
-	 * initiate chain vertex
-	 */
-	public void initChainVertex(){
-		if(!msg.isRear()){
-			findDestination();
-			if(GraphVertexOperation.isPathVertex(getVertexValue().getAdjMap())){
-				chainVertexId.set(getVertexId());
-				msg.set(getVertexId(), chainVertexId, getVertexId(), getVertexValue().getAdjMap(), false);
-				sendMsg(destVertexId,msg);
-			}else if(GraphVertexOperation.isRearVertex(getVertexValue().getAdjMap()))
-				voteToHalt();
-		}
-	}
-	/**
-	 * head node sends message to path node
-	 */
-	public void sendMsgToPathVertex(){
-		if(!msg.isRear()){
-			destVertexId.set(getDestVertexIdFromChain(msg.getChainVertexId(), msg.getAdjMap()));
-			msg.set(getVertexId(), msg.getChainVertexId(), msg.getHeadVertexId(), (byte)0, msg.isRear());
-		}else{
-			destVertexId.set(msg.getHeadVertexId());
-			msg.set(msg.getSourceVertexId(), msg.getChainVertexId(), msg.getHeadVertexId(), (byte)0, msg.isRear());
-		}
-		sendMsg(destVertexId,msg);
-	}
-	/**
-	 * path node sends message back to head node
-	 */
-	public void responseMsgToHeadVertex(){
-		if(!msg.isRear()){
-			findDestination();
-			if(GraphVertexOperation.isPathVertex(getVertexValue().getAdjMap())){
-				chainVertexId = kmerFactory.mergeKmerWithNextCode(msg.getChainVertexId(),
-						getVertexId().getGeneCodeAtPosition(kmerSize - 1));
-				deleteVertex(getVertexId());
-				msg.set(getVertexId(), chainVertexId, msg.getHeadVertexId(), getVertexValue().getAdjMap(), false);
-				sendMsg(destVertexId,msg);
-			}
-			else if(GraphVertexOperation.isRearVertex(getVertexValue().getAdjMap())){
-				msg.set(getVertexId(), msg.getChainVertexId(), msg.getHeadVertexId(), (byte)0, true);
-				sendMsg(destVertexId,msg);
-			}
-		}else{// is Rear
-			if(msg.getLengthOfChain() > kmerSize){
-				byte tmp = GraphVertexOperation.updateRightNeighberByVertexId(getVertexValue().getAdjMap(), msg.getSourceVertexId(), kmerSize);
-				getVertexValue().set(tmp, State.FINAL_VERTEX, msg.getChainVertexId());
-				setVertexValue(getVertexValue());
-				//String source = msg.getChainVertexId().toString();
-				//System.out.print("");
-			}
-		}
-	}
-	
-	@Override
-	public void compute(Iterator<NaiveAlgorithmMessageWritable> msgIterator) {
-		initVertex();
-		if (getSuperstep() == 1) {
-			if(GraphVertexOperation.isHeadVertex(getVertexValue().getAdjMap())){
-				if(getVertexId().toString().equals(filterKmer)){
-					getVertexValue().setState(State.FILTER);
-					setVertexValue(getVertexValue());
-					msg.set(getVertexId(), chainVertexId, getVertexId(), (byte)0, false);
-					sendMsgToAllNextNodes(getVertexId(), getVertexValue().getAdjMap());
-				}
-				else
-					voteToHalt();
-			}
-		}
-		else if(getSuperstep() == 2){
-			if(msgIterator.hasNext()){
-				getVertexValue().setState(State.FILTER);
-				setVertexValue(getVertexValue());
-				msg = msgIterator.next();
-				initChainVertex();
-				
-			}
-		}
-		//head node sends message to path node
-		else if(getSuperstep()%2 == 1 && getSuperstep() <= maxIteration){
-			while (msgIterator.hasNext()){
-				getVertexValue().setState(State.FILTER);
-				setVertexValue(getVertexValue());
-				msg = msgIterator.next();
-				sendMsgToPathVertex();
-			}
-		}
-		//path node sends message back to head node
-		else if(getSuperstep()%2 == 0 && getSuperstep() > 2 && getSuperstep() <= maxIteration){
-			 while(msgIterator.hasNext()){
-				getVertexValue().setState(State.FILTER);
-				setVertexValue(getVertexValue());
-				msg = msgIterator.next();
-				responseMsgToHeadVertex();
-			}
-		}
-		voteToHalt();
-	}
-	
-	/**
-	 * @param args
-	 */
-	public static void main(String[] args) throws Exception {
-        PregelixJob job = new PregelixJob(NaiveFilterVertex.class.getSimpleName());
-        job.setVertexClass(NaiveFilterVertex.class);
-        /**
-         * BinaryInput and BinaryOutput
-         */
-        job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class); 
-        job.setVertexOutputFormatClass(NaiveAlgorithmForPathMergeOutputFormat.class); 
-        job.setDynamicVertexValueSize(true);
-        job.setOutputKeyClass(KmerBytesWritable.class);
-        job.setOutputValueClass(ValueStateWritable.class);
-        Client.run(args, job);
-	}
-}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/P1ForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/P1ForPathMergeVertex.java
deleted file mode 100644
index ca18c75..0000000
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/P1ForPathMergeVertex.java
+++ /dev/null
@@ -1,232 +0,0 @@
-package edu.uci.ics.genomix.pregelix.operator;
-
-import java.util.Iterator;
-import org.apache.hadoop.io.NullWritable;
-
-import edu.uci.ics.genomix.type.GeneCode;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
-import edu.uci.ics.genomix.type.VKmerBytesWritable;
-import edu.uci.ics.genomix.type.VKmerBytesWritableFactory;
-
-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.NaiveAlgorithmForPathMergeInputFormat;
-import edu.uci.ics.genomix.pregelix.format.NaiveAlgorithmForPathMergeOutputFormat;
-import edu.uci.ics.genomix.pregelix.io.P1MessageWritable;
-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.pregelix.util.GraphVertexOperation;
-
-/*
- * vertexId: BytesWritable
- * vertexValue: ByteWritable
- * edgeValue: NullWritable
- * message: NaiveAlgorithmMessageWritable
- * 
- * 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. 
- */
-/**
- * Naive Algorithm for path merge graph
- */
-public class P1ForPathMergeVertex extends Vertex<KmerBytesWritable, ValueStateWritable, NullWritable, P1MessageWritable>{
-	public static final String KMER_SIZE = "NaiveAlgorithmForPathMergeVertex.kmerSize";
-	public static final String ITERATIONS = "NaiveAlgorithmForPathMergeVertex.iteration";
-	public static int kmerSize = -1;
-	private int maxIteration = -1;
-
-	private P1MessageWritable incomingMsg = new P1MessageWritable();
-	private P1MessageWritable outgoingMsg = new P1MessageWritable();
-
-	private VKmerBytesWritableFactory kmerFactory = new VKmerBytesWritableFactory(1);
-	private VKmerBytesWritable destVertexId = new VKmerBytesWritable(1); 
-	/**
-	 * initiate kmerSize, maxIteration
-	 */
-	public void initVertex(){
-		if(kmerSize == -1)
-			kmerSize = getContext().getConfiguration().getInt(KMER_SIZE, 5);
-        if (maxIteration < 0) 
-            maxIteration = getContext().getConfiguration().getInt(ITERATIONS, 1000000);
-        outgoingMsg.reset();
-	}
-	/**
-	 * get destination vertex
-	 */
-	public VKmerBytesWritable getDestVertexId(KmerBytesWritable vertexId, byte geneCode){
-		return kmerFactory.shiftKmerWithNextCode(vertexId, geneCode);
-	}
-	public VKmerBytesWritable getPreDestVertexId(KmerBytesWritable vertexId, byte geneCode){
-		return kmerFactory.shiftKmerWithPreCode(vertexId, geneCode);
-	}
-	public VKmerBytesWritable getDestVertexIdFromChain(VKmerBytesWritable chainVertexId, byte adjMap){
-		VKmerBytesWritable lastKmer = kmerFactory.getLastKmerFromChain(kmerSize, chainVertexId);
-		return getDestVertexId(lastKmer, GeneCode.getGeneCodeFromBitMap((byte)(adjMap & 0x0F)));
-	}
-	/**
-	 * head send message to all next nodes
-	 */
-	public void sendMsgToAllNextNodes(KmerBytesWritable vertexId, byte adjMap){
-		for(byte x = GeneCode.A; x<= GeneCode.T ; x++){
-			if((adjMap & (1 << x)) != 0){
-				destVertexId.set(getDestVertexId(vertexId, x));
-				sendMsg(destVertexId, outgoingMsg);
-			}
-		}
-	}
-	/**
-	 * head send message to all previous nodes
-	 */
-	public void sendMsgToAllPreviousNodes(KmerBytesWritable vertexId, byte adjMap){
-		for(byte x = GeneCode.A; x<= GeneCode.T ; x++){
-			if(((adjMap >> 4) & (1 << x)) != 0){
-				destVertexId.set(getPreDestVertexId(vertexId, x));
-				sendMsg(destVertexId, outgoingMsg);
-			}
-		}
-	}
-	/**
-	 * start sending message 
-	 */
-	public void startSendMsg(){
-		if(GraphVertexOperation.isHeadVertex(getVertexValue().getAdjMap())){
-			outgoingMsg.setMessage(Message.START);
-			sendMsgToAllNextNodes(getVertexId(), getVertexValue().getAdjMap());
-		}
-		if(GraphVertexOperation.isRearVertex(getVertexValue().getAdjMap())){
-			outgoingMsg.setMessage(Message.END);
-			sendMsgToAllPreviousNodes(getVertexId(), getVertexValue().getAdjMap());
-		}
-	}
-	/**
-	 *  initiate head, rear and path node
-	 */
-	public void initState(Iterator<P1MessageWritable> msgIterator){
-		while(msgIterator.hasNext()){
-			if(!GraphVertexOperation.isPathVertex(getVertexValue().getAdjMap())){
-				msgIterator.next();
-				voteToHalt();
-			}
-			else{
-				incomingMsg = msgIterator.next();
-				setState();
-			}
-		}
-	}
-	/**
-	 * set vertex state
-	 */
-	public void setState(){
-		if(incomingMsg.getMessage() == Message.START){
-			getVertexValue().setState(State.START_VERTEX);
-		}
-		else if(incomingMsg.getMessage() == Message.END 
-				&& getVertexValue().getState() != State.START_VERTEX){
-			getVertexValue().setState(State.END_VERTEX);
-			voteToHalt();
-		}
-		else
-			voteToHalt();
-	}
-	/**
-	 * head node sends message to path node
-	 */
-	public void sendMsgToPathVertex(Iterator<P1MessageWritable> msgIterator){
-		if(getSuperstep() == 3){
-			getVertexValue().setMergeChain(getVertexId());
-			outgoingMsg.setSourceVertexId(getVertexId());
-			destVertexId.set(getDestVertexIdFromChain(getVertexValue().getMergeChain(),
-					getVertexValue().getAdjMap()));
-			sendMsg(destVertexId,outgoingMsg);
-		}else{
-			while (msgIterator.hasNext()){
-				incomingMsg = msgIterator.next();
-				if(incomingMsg.getMessage() != Message.STOP){
-					getVertexValue().setMergeChain(kmerFactory.mergeKmerWithNextCode(getVertexValue().getMergeChain(),
-							incomingMsg.getLastGeneCode()));
-					outgoingMsg.setSourceVertexId(getVertexId());
-					destVertexId.set(getDestVertexIdFromChain(getVertexValue().getMergeChain(),
-							incomingMsg.getAdjMap()));
-					sendMsg(destVertexId,outgoingMsg);
-				}
-				else{
-					getVertexValue().setMergeChain(kmerFactory.mergeKmerWithNextCode(getVertexValue().getMergeChain(),
-							incomingMsg.getLastGeneCode()));
-					byte adjMap = GraphVertexOperation.updateRightNeighber(getVertexValue().getAdjMap(),
-							incomingMsg.getAdjMap());
-					getVertexValue().setAdjMap(adjMap);
-					getVertexValue().setState(State.FINAL_VERTEX);
-					//String source = getVertexValue().getMergeChain().toString();
-					//System.out.println();
-				}
-			}
-		}
-	}
-	/**
-	 * path node sends message back to head node
-	 */
-	public void responseMsgToHeadVertex(){
-		deleteVertex(getVertexId());
-		outgoingMsg.setAdjMap(getVertexValue().getAdjMap());
-		outgoingMsg.setLastGeneCode(getVertexId().getGeneCodeAtPosition(kmerSize - 1));
-		if(getVertexValue().getState() == State.END_VERTEX)
-			outgoingMsg.setMessage(Message.STOP);
-		sendMsg(incomingMsg.getSourceVertexId(),outgoingMsg);
-	}
-	
-	@Override
-	public void compute(Iterator<P1MessageWritable> msgIterator) {
-		initVertex();
-		if (getSuperstep() == 1) {
-			startSendMsg();
-			voteToHalt();
-		}
-		else if(getSuperstep() == 2)
-			initState(msgIterator);
-		else if(getSuperstep()%2 == 1 && getSuperstep() <= maxIteration){
-			sendMsgToPathVertex(msgIterator);
-			voteToHalt();
-		}
-		else if(getSuperstep()%2 == 0 && getSuperstep() > 2 && getSuperstep() <= maxIteration){
-			 while(msgIterator.hasNext()){
-				incomingMsg = msgIterator.next();
-				responseMsgToHeadVertex();
-			}
-			voteToHalt();
-		}
-	}
-	public static void main(String[] args) throws Exception {
-        PregelixJob job = new PregelixJob(NaiveAlgorithmForPathMergeVertex.class.getSimpleName());
-        job.setVertexClass(P1ForPathMergeVertex.class);
-        /**
-         * BinaryInput and BinaryOutput
-         */
-        job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class); 
-        job.setVertexOutputFormatClass(NaiveAlgorithmForPathMergeOutputFormat.class); 
-        job.setDynamicVertexValueSize(true);
-        job.setOutputKeyClass(KmerBytesWritable.class);
-        job.setOutputValueClass(ValueStateWritable.class);
-        Client.run(args, job);
-	}
-}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/P2ForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/P2ForPathMergeVertex.java
deleted file mode 100644
index 7d5263d..0000000
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/P2ForPathMergeVertex.java
+++ /dev/null
@@ -1,274 +0,0 @@
-package edu.uci.ics.genomix.pregelix.operator;
-
-import java.util.Iterator;
-
-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.LogAlgorithmForPathMergeInputFormat;
-import edu.uci.ics.genomix.pregelix.format.LogAlgorithmForPathMergeOutputFormat;
-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.pregelix.util.GraphVertexOperation;
-import edu.uci.ics.genomix.type.GeneCode;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
-import edu.uci.ics.genomix.type.VKmerBytesWritable;
-import edu.uci.ics.genomix.type.VKmerBytesWritableFactory;
-/*
- * 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 P2ForPathMergeVertex extends Vertex<KmerBytesWritable, ValueStateWritable, NullWritable, LogAlgorithmMessageWritable>{	
-	public static final String KMER_SIZE = "TwoStepLogAlgorithmForPathMergeVertex.kmerSize";
-	public static final String ITERATIONS = "TwoStepLogAlgorithmForPathMergeVertex.iteration";
-	public static int kmerSize = -1;
-	private int maxIteration = -1;
-	
-	private LogAlgorithmMessageWritable incomingMsg = new LogAlgorithmMessageWritable();
-	private LogAlgorithmMessageWritable outgoingMsg = new LogAlgorithmMessageWritable();
-	
-	private VKmerBytesWritableFactory kmerFactory = new VKmerBytesWritableFactory(1);
-	private VKmerBytesWritable chainVertexId = new VKmerBytesWritable(1);
-	private VKmerBytesWritable lastKmer = new VKmerBytesWritable(1);
-	/**
-	 * initiate kmerSize, maxIteration
-	 */
-	public void initVertex(){
-		if(kmerSize == -1)
-			kmerSize = getContext().getConfiguration().getInt(KMER_SIZE, 5);
-        if (maxIteration < 0) 
-            maxIteration = getContext().getConfiguration().getInt(ITERATIONS, 1000000);
-        outgoingMsg.reset();
-	}
-	/**
-	 * get destination vertex
-	 */
-	public VKmerBytesWritable getNextDestVertexId(KmerBytesWritable vertexId, byte geneCode){
-		return kmerFactory.shiftKmerWithNextCode(vertexId, geneCode);
-	}
-	
-	public VKmerBytesWritable getPreDestVertexId(KmerBytesWritable vertexId, byte geneCode){
-		return kmerFactory.shiftKmerWithPreCode(vertexId, geneCode);
-	}
-	
-	public VKmerBytesWritable getNextDestVertexIdFromBitmap(KmerBytesWritable chainVertexId, byte adjMap){
-		return getDestVertexIdFromChain(chainVertexId, adjMap);
-	}
-	
-	public VKmerBytesWritable getDestVertexIdFromChain(KmerBytesWritable chainVertexId, byte adjMap){
-		VKmerBytesWritable lastKmer = kmerFactory.getLastKmerFromChain(kmerSize, chainVertexId);
-		return getNextDestVertexId(lastKmer, GeneCode.getGeneCodeFromBitMap((byte)(adjMap & 0x0F)));
-	}
-	/**
-	 * head send message to all next nodes
-	 */
-	public void sendMsgToAllNextNodes(KmerBytesWritable vertexId, byte adjMap){
-		for(byte x = GeneCode.A; x<= GeneCode.T ; x++){
-			if((adjMap & (1 << x)) != 0){
-				sendMsg(getNextDestVertexId(vertexId, x), outgoingMsg);
-			}
-		}
-	}
-	/**
-	 * head send message to all previous nodes
-	 */
-	public void sendMsgToAllPreviousNodes(KmerBytesWritable vertexId, byte adjMap){
-		for(byte x = GeneCode.A; x<= GeneCode.T ; x++){
-			if(((adjMap >> 4) & (1 << x)) != 0){
-				sendMsg(getPreDestVertexId(vertexId, x), outgoingMsg);
-			}
-		}
-	}
-	/**
-	 * start sending message 
-	 */
-	public void startSendMsg(){
-		if(GraphVertexOperation.isHeadVertex(getVertexValue().getAdjMap())){
-			outgoingMsg.setMessage(Message.START);
-			sendMsgToAllNextNodes(getVertexId(), getVertexValue().getAdjMap());
-			voteToHalt();
-		}
-		if(GraphVertexOperation.isRearVertex(getVertexValue().getAdjMap())){
-			outgoingMsg.setMessage(Message.END);
-			sendMsgToAllPreviousNodes(getVertexId(), getVertexValue().getAdjMap());
-			voteToHalt();
-		}
-	}
-	/**
-	 *  initiate head, rear and path node
-	 */
-	public void initState(Iterator<LogAlgorithmMessageWritable> msgIterator){
-		while(msgIterator.hasNext()){
-			if(!GraphVertexOperation.isPathVertex(getVertexValue().getAdjMap())){
-				msgIterator.next();
-				voteToHalt();
-			}
-			else{
-				incomingMsg = msgIterator.next();
-				setState();
-			}
-		}
-	}
-	/**
-	 * set vertex state
-	 */
-	public void setState(){
-		if(incomingMsg.getMessage() == Message.START){
-			getVertexValue().setState(State.START_VERTEX);
-			getVertexValue().setMergeChain(null);
-		}
-		else if(incomingMsg.getMessage() == Message.END && getVertexValue().getState() != State.START_VERTEX){
-			getVertexValue().setState(State.END_VERTEX);
-			getVertexValue().setMergeChain(getVertexId());
-			voteToHalt();
-		}
-		else
-			voteToHalt();
-	}
-	/**
-	 * head send message to path
-	 */
-	public void sendOutMsg(KmerBytesWritable chainVertexId, byte adjMap){
-		if(getVertexValue().getState() == State.START_VERTEX){
-			outgoingMsg.setMessage(Message.START);
-			outgoingMsg.setSourceVertexId(getVertexId());
-			sendMsg(getNextDestVertexIdFromBitmap(chainVertexId, adjMap), outgoingMsg);
-		}
-		else if(getVertexValue().getState() != State.END_VERTEX){
-			outgoingMsg.setMessage(Message.NON);
-			outgoingMsg.setSourceVertexId(getVertexId());
-			sendMsg(getNextDestVertexIdFromBitmap(chainVertexId, adjMap), outgoingMsg);
-		}
-	}
-	/**
-	 * head send message to path
-	 */
-	public void sendMsgToPathVertex(Iterator<LogAlgorithmMessageWritable> msgIterator){
-		if(getSuperstep() == 3){
-			getVertexValue().setMergeChain(getVertexId());
-			sendOutMsg(getVertexId(), getVertexValue().getAdjMap());
-		}
-		else{
-			if(msgIterator.hasNext()){
-				incomingMsg = msgIterator.next();
-				if(mergeChainVertex(msgIterator)){
-					if(incomingMsg.getMessage() == Message.END){
-						if(getVertexValue().getState() == State.START_VERTEX){
-							getVertexValue().setState(State.FINAL_VERTEX);
-							//String source = getVertexValue().getMergeChain().toString();
-							//System.out.println();
-						}
-						else
-							getVertexValue().setState(State.END_VERTEX);
-					}
-					else
-						sendOutMsg(getVertexValue().getMergeChain(), getVertexValue().getAdjMap());
-				}
-			}
-		}
-	}
-	/**
-	 * path response message to head
-	 */
-	public void responseMsgToHeadVertex(Iterator<LogAlgorithmMessageWritable> msgIterator){
-		if(msgIterator.hasNext()){		
-			incomingMsg = msgIterator.next();
-			outgoingMsg.setChainVertexId(getVertexValue().getMergeChain());
-			outgoingMsg.setAdjMap(getVertexValue().getAdjMap());
-			if(getVertexValue().getState() == State.END_VERTEX)
-				outgoingMsg.setMessage(Message.END);
-			sendMsg(incomingMsg.getSourceVertexId(),outgoingMsg);
-			
-			if(incomingMsg.getMessage() == Message.START)
-				deleteVertex(getVertexId());
-		}
-		else{
-			if(getVertexValue().getState() != State.START_VERTEX 
-					&& getVertexValue().getState() != State.END_VERTEX)
-				deleteVertex(getVertexId());//killSelf because it doesn't receive any message
-		}
-	}
-	/**
-	 * merge chainVertex and store in vertexVal.chainVertexId
-	 */
-	public boolean mergeChainVertex(Iterator<LogAlgorithmMessageWritable> msgIterator){
-		//merge chain
-		lastKmer.set(kmerFactory.getLastKmerFromChain(incomingMsg.getLengthOfChain() - kmerSize + 1, 
-				incomingMsg.getChainVertexId()));
-		chainVertexId.set(kmerFactory.mergeTwoKmer(getVertexValue().getMergeChain(), 
-				lastKmer));
-		if(GraphVertexOperation.isCycle(getVertexId(), chainVertexId)){
-			getVertexValue().setMergeChain(null);
-			getVertexValue().setAdjMap(GraphVertexOperation.reverseAdjMap(getVertexValue().getAdjMap(),
-					chainVertexId.getGeneCodeAtPosition(kmerSize)));
-			getVertexValue().setState(State.CYCLE);
-			return false;
-		}
-		else
-			getVertexValue().setMergeChain(chainVertexId);
-		
-		byte tmpVertexValue = GraphVertexOperation.updateRightNeighber(getVertexValue().getAdjMap(),
-				incomingMsg.getAdjMap());
-		getVertexValue().setAdjMap(tmpVertexValue);
-		return true;
-	}
-	@Override
-	public void compute(Iterator<LogAlgorithmMessageWritable> msgIterator) {
-		initVertex();
-		if (getSuperstep() == 1) 
-			startSendMsg();
-		else if(getSuperstep() == 2)
-			initState(msgIterator);
-		else if(getSuperstep()%2 == 1 && getSuperstep() <= maxIteration){
-			sendMsgToPathVertex(msgIterator);
-			voteToHalt();
-		}
-		else if(getSuperstep()%2 == 0 && getSuperstep() <= maxIteration){
-			responseMsgToHeadVertex(msgIterator);
-			voteToHalt();
-		}
-		else
-			voteToHalt();
-	}
-	public static void main(String[] args) throws Exception {
-        PregelixJob job = new PregelixJob(TwoStepLogAlgorithmForPathMergeVertex.class.getSimpleName());
-        job.setVertexClass(P2ForPathMergeVertex.class);
-        /**
-         * BinaryInput and BinaryOutput~/
-         */
-        job.setVertexInputFormatClass(LogAlgorithmForPathMergeInputFormat.class); 
-        job.setVertexOutputFormatClass(LogAlgorithmForPathMergeOutputFormat.class); 
-        job.setOutputKeyClass(KmerBytesWritable.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/operator/ThreeStepLogAlgorithmForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/ThreeStepLogAlgorithmForPathMergeVertex.java
deleted file mode 100644
index 7946460..0000000
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/ThreeStepLogAlgorithmForPathMergeVertex.java
+++ /dev/null
@@ -1,362 +0,0 @@
-package edu.uci.ics.genomix.pregelix.operator;
-
-import java.util.Iterator;
-
-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.LogAlgorithmForPathMergeInputFormat;
-import edu.uci.ics.genomix.pregelix.format.LogAlgorithmForPathMergeOutputFormat;
-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.pregelix.util.GraphVertexOperation;
-import edu.uci.ics.genomix.type.GeneCode;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
-import edu.uci.ics.genomix.type.VKmerBytesWritable;
-import edu.uci.ics.genomix.type.VKmerBytesWritableFactory;
-
-/*
- * 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 ThreeStepLogAlgorithmForPathMergeVertex extends Vertex<KmerBytesWritable, ValueStateWritable, NullWritable, LogAlgorithmMessageWritable>{	
-	
-	public static final String KMER_SIZE = "ThreeStepLogAlgorithmForPathMergeVertex.kmerSize";
-	public static final String ITERATIONS = "ThreeStepLogAlgorithmForPathMergeVertex.iteration";
-	public static int kmerSize = -1;
-	private int maxIteration = -1;
-	
-	private LogAlgorithmMessageWritable msg = new LogAlgorithmMessageWritable();
-	
-	private VKmerBytesWritableFactory kmerFactory = new VKmerBytesWritableFactory(1);
-	private VKmerBytesWritable destVertexId = new VKmerBytesWritable(1); 
-	private VKmerBytesWritable chainVertexId = new VKmerBytesWritable(1);
-	private VKmerBytesWritable lastKmer = new VKmerBytesWritable(1);
-	/**
-	 * initiate kmerSize, maxIteration
-	 */
-	public void initVertex(){
-		if(kmerSize == -1)
-			kmerSize = getContext().getConfiguration().getInt(KMER_SIZE, 5);
-        if (maxIteration < 0) 
-            maxIteration = getContext().getConfiguration().getInt(ITERATIONS, 20);
-	}
-	/**
-	 * get destination vertex
-	 */
-	public VKmerBytesWritable getNextDestVertexId(KmerBytesWritable vertexId, byte geneCode){
-		return kmerFactory.shiftKmerWithNextCode(vertexId, geneCode);
-	}
-	
-	public VKmerBytesWritable getPreDestVertexId(KmerBytesWritable vertexId, byte geneCode){
-		return kmerFactory.shiftKmerWithPreCode(vertexId, geneCode);
-	}
-	
-	public VKmerBytesWritable getNextDestVertexIdFromBitmap(KmerBytesWritable chainVertexId, byte adjMap){
-		return getDestVertexIdFromChain(chainVertexId, adjMap);//GeneCode.getGeneCodeFromBitMap((byte)(adjMap & 0x0F)
-	}
-	
-	public VKmerBytesWritable getDestVertexIdFromChain(KmerBytesWritable chainVertexId, byte adjMap){
-		lastKmer.set(kmerFactory.getLastKmerFromChain(kmerSize, chainVertexId));
-		return getNextDestVertexId(lastKmer, GeneCode.getGeneCodeFromBitMap((byte)(adjMap & 0x0F)));
-	}
-	/**
-	 * head send message to all next nodes
-	 */
-	public void sendMsgToAllNextNodes(KmerBytesWritable vertexId, byte adjMap){
-		for(byte x = GeneCode.A; x<= GeneCode.T ; x++){
-			if((adjMap & (1 << x)) != 0){
-				destVertexId.set(getNextDestVertexId(vertexId, x));
-				sendMsg(destVertexId, msg);
-			}
-		}
-	}
-	/**
-	 * head send message to all previous nodes
-	 */
-	public void sendMsgToAllPreviousNodes(KmerBytesWritable vertexId, byte adjMap){
-		for(byte x = GeneCode.A; x<= GeneCode.T ; x++){
-			if(((adjMap >> 4) & (1 << x)) != 0){
-				destVertexId.set(getPreDestVertexId(vertexId, x));
-				sendMsg(destVertexId, msg);
-			}
-		}
-	}
-
-	/**
-	 * set vertex state
-	 */
-	public void setState(){
-		if(msg.getMessage() == Message.START && 
-				(getVertexValue().getState() == State.MID_VERTEX || getVertexValue().getState() == State.END_VERTEX)){
-			getVertexValue().setState(State.START_VERTEX);
-			setVertexValue(getVertexValue());
-		}
-		else if(msg.getMessage() == Message.END && getVertexValue().getState() == State.MID_VERTEX){
-			getVertexValue().setState(State.END_VERTEX);
-			setVertexValue(getVertexValue());
-			voteToHalt();
-		}
-		else
-			voteToHalt();
-	}
-	/**
-	 * send start message to next node
-	 */
-	public void sendStartMsgToNextNode(){
-		msg.setMessage(Message.START);
-		msg.setSourceVertexId(getVertexId());
-		sendMsg(destVertexId, msg);
-		voteToHalt();
-	}
-	/**
-	 * send end message to next node
-	 */
-	public void sendEndMsgToNextNode(){
-		msg.setMessage(Message.END);
-		msg.setSourceVertexId(getVertexId());
-		sendMsg(destVertexId, msg);
-		voteToHalt();
-	}
-	/**
-	 * send non message to next node
-	 */
-	public void sendNonMsgToNextNode(){
-		msg.setMessage(Message.NON);
-		msg.setSourceVertexId(getVertexId());
-		sendMsg(destVertexId, msg);
-	}
-	/**
-	 * head send message to path
-	 */
-	public void sendMsgToPathVertex(KmerBytesWritable chainVertexId, byte adjMap){
-		if(GeneCode.getGeneCodeFromBitMap((byte)(getVertexValue().getAdjMap() & 0x0F)) == -1) //|| lastKmer == null
-			voteToHalt();
-		else{
-			destVertexId.set(getNextDestVertexIdFromBitmap(chainVertexId, adjMap));
-			if(getVertexValue().getState() == State.START_VERTEX){
-				sendStartMsgToNextNode();
-			}
-			else if(getVertexValue().getState() != State.END_VERTEX){
-				sendEndMsgToNextNode();
-			}
-		}
-	}
-	/**
-	 * path send message to head 
-	 */
-	public void responseMsgToHeadVertex(){
-		if(getVertexValue().getLengthOfMergeChain() == -1){
-			getVertexValue().setMergeChain(getVertexId());
-			setVertexValue(getVertexValue());
-		}
-		msg.set(null, getVertexValue().getMergeChain(), getVertexValue().getAdjMap(), msg.getMessage());
-		//msg.set(msg.getSourceVertexId(), getVertexValue().getMergeChain(), getVertexValue().getAdjMap(), msg.getMessage(), getVertexValue().getState());
-		setMessageType(msg.getMessage());
-		destVertexId.set(msg.getSourceVertexId());
-		sendMsg(destVertexId,msg);
-	}
-	/**
-	 * set message type
-	 */
-	public void setMessageType(int message){
-		//kill Message because it has been merged by the head
-		if(getVertexValue().getState() == State.END_VERTEX){
-			msg.setMessage(Message.END);
-			getVertexValue().setState(State.END_VERTEX);
-			setVertexValue(getVertexValue());
-			//deleteVertex(getVertexId());
-		}
-		else
-			msg.setMessage(Message.NON);
-		
-		if(message == Message.START){
-			getVertexValue().setState(State.TODELETE);
-			setVertexValue(getVertexValue());
-		}
-	}
-	/**
-	 *  set vertexValue's state chainVertexId, value
-	 */
-	public void setVertexValueAttributes(){
-		if(msg.getMessage() == Message.END){
-			if(getVertexValue().getState() != State.START_VERTEX)
-				getVertexValue().setState(State.END_VERTEX);
-			else
-				getVertexValue().setState(State.FINAL_VERTEX);
-		}
-			
-		if(getSuperstep() == 5)
-			chainVertexId.set(getVertexId());
-		else
-			chainVertexId.set(getVertexValue().getMergeChain());
-		lastKmer.set(kmerFactory.getLastKmerFromChain(msg.getLengthOfChain() - kmerSize + 1, msg.getChainVertexId()));
-		chainVertexId.set(kmerFactory.mergeTwoKmer(chainVertexId, lastKmer));
-		getVertexValue().setMergeChain(chainVertexId);
-		
-		byte tmpVertexValue = GraphVertexOperation.updateRightNeighber(getVertexValue().getAdjMap(), msg.getAdjMap());
-		getVertexValue().setAdjMap(tmpVertexValue);
-	}
-	/**
-	 *  send message to self
-	 */
-	public void sendMsgToSelf(){
-		if(msg.getMessage() != Message.END){
-			setVertexValue(getVertexValue());
-			msg.reset(); //reset
-			msg.setAdjMap(getVertexValue().getAdjMap());
-			sendMsg(getVertexId(),msg);
-		}
-	}
-	/**
-	 * start sending message
-	 */
-	public void startSendMsg(){
-		if(GraphVertexOperation.isHeadVertex(getVertexValue().getAdjMap())){
-			msg.set(null, null, (byte)0, Message.START);
-			//msg.set(getVertexId(), chainVertexId, (byte)0, Message.START, State.NON_VERTEX); //msg.set(null, (byte)0, chainVertexId, Message.START, State.NON_VERTEX);
-			sendMsgToAllNextNodes(getVertexId(), getVertexValue().getAdjMap());
-			voteToHalt();
-		}
-		if(GraphVertexOperation.isRearVertex(getVertexValue().getAdjMap())){
-			msg.set(null, null, (byte)0, Message.END);
-			//msg.set(getVertexId(), chainVertexId, (byte)0, Message.END, State.NON_VERTEX);
-			sendMsgToAllPreviousNodes(getVertexId(), getVertexValue().getAdjMap());
-			voteToHalt();
-		}
-		if(GraphVertexOperation.isPathVertex(getVertexValue().getAdjMap())){
-			getVertexValue().setState(State.MID_VERTEX);
-			setVertexValue(getVertexValue());
-		}
-	}
-	/**
-	 *  initiate head, rear and path node
-	 */
-	public void initState(Iterator<LogAlgorithmMessageWritable> msgIterator){
-		while(msgIterator.hasNext()){
-			if(!GraphVertexOperation.isPathVertex(getVertexValue().getAdjMap())){
-				msgIterator.next();
-				voteToHalt();
-			}
-			else{
-				msg = msgIterator.next();
-				setState();
-			}
-		}
-	}
-	/**
-	 * head send message to path
-	 */
-	public void sendMsgToPathVertex(Iterator<LogAlgorithmMessageWritable> msgIterator){
-		if(getSuperstep() == 3){
-			msg.reset();
-			sendMsgToPathVertex(getVertexId(), getVertexValue().getAdjMap());
-		}
-		else{
-			if(msgIterator.hasNext()){
-				msg = msgIterator.next();
-				sendMsgToPathVertex(getVertexValue().getMergeChain(), msg.getAdjMap());
-			}
-		}
-	}
-	/**
-	 * path response message to head
-	 */
-	public void responseMsgToHeadVertex(Iterator<LogAlgorithmMessageWritable> msgIterator){
-		if(msgIterator.hasNext()){
-			msg = msgIterator.next();
-			responseMsgToHeadVertex();
-		}
-		else{
-			if(getVertexValue().getState() != State.START_VERTEX 
-					&& getVertexValue().getState() != State.END_VERTEX){
-				deleteVertex(getVertexId());//killSelf because it doesn't receive any message
-			}
-		}
-	}
-	/**
-	 * merge chainVertex and store in vertexVal.chainVertexId
-	 */
-	public void mergeChainVertex(Iterator<LogAlgorithmMessageWritable> msgIterator){
-		if(msgIterator.hasNext()){
-			msg = msgIterator.next();
-			setVertexValueAttributes();
-			sendMsgToSelf();
-		}
-		if(getVertexValue().getState() == State.END_VERTEX){
-			voteToHalt();
-		}
-		if(getVertexValue().getState() == State.FINAL_VERTEX){
-			//String source = getVertexValue().getMergeChain().toString();
-			voteToHalt();
-		}
-	}
-	@Override
-	public void compute(Iterator<LogAlgorithmMessageWritable> msgIterator) {
-		initVertex();
-		if (getSuperstep() == 1) 
-			startSendMsg();
-		else if(getSuperstep() == 2)
-			initState(msgIterator);
-		else if(getSuperstep()%3 == 0 && getSuperstep() <= maxIteration){
-			sendMsgToPathVertex(msgIterator);
-		}
-		else if(getSuperstep()%3 == 1 && getSuperstep() <= maxIteration){
-			responseMsgToHeadVertex(msgIterator);
-		}
-		else if(getSuperstep()%3 == 2 && getSuperstep() <= maxIteration){
-			if(getVertexValue().getState() == State.TODELETE){ 
-				deleteVertex(getVertexId()); //killSelf
-			}
-			else{
-				mergeChainVertex(msgIterator);
-			}
-		}
-		else
-			voteToHalt();
-	}
-	/**
-	 * @param args
-	 */
-	public static void main(String[] args) throws Exception {
-        PregelixJob job = new PregelixJob(ThreeStepLogAlgorithmForPathMergeVertex.class.getSimpleName());
-        job.setVertexClass(ThreeStepLogAlgorithmForPathMergeVertex.class);
-        /**
-         * BinaryInput and BinaryOutput~/
-         */
-        job.setVertexInputFormatClass(LogAlgorithmForPathMergeInputFormat.class); 
-        job.setVertexOutputFormatClass(LogAlgorithmForPathMergeOutputFormat.class); 
-        job.setOutputKeyClass(KmerBytesWritable.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/operator/TwoStepLogAlgorithmForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/TwoStepLogAlgorithmForPathMergeVertex.java
deleted file mode 100644
index 6b67333..0000000
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/TwoStepLogAlgorithmForPathMergeVertex.java
+++ /dev/null
@@ -1,367 +0,0 @@
-package edu.uci.ics.genomix.pregelix.operator;
-
-import java.util.Iterator;
-import java.util.logging.Logger;
-
-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.LogAlgorithmForPathMergeInputFormat;
-import edu.uci.ics.genomix.pregelix.format.LogAlgorithmForPathMergeOutputFormat;
-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.pregelix.util.GraphVertexOperation;
-import edu.uci.ics.genomix.type.GeneCode;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
-import edu.uci.ics.genomix.type.VKmerBytesWritable;
-import edu.uci.ics.genomix.type.VKmerBytesWritableFactory;
-/*
- * 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 TwoStepLogAlgorithmForPathMergeVertex extends Vertex<KmerBytesWritable, ValueStateWritable, NullWritable, LogAlgorithmMessageWritable>{	
-	public static Logger logger = Logger.getLogger(TwoStepLogAlgorithmForPathMergeVertex.class.getName()); 
-	
-	public static final String KMER_SIZE = "TwoStepLogAlgorithmForPathMergeVertex.kmerSize";
-	public static final String ITERATIONS = "TwoStepLogAlgorithmForPathMergeVertex.iteration";
-	public static int kmerSize = -1;
-	private int maxIteration = -1;
-	
-	private LogAlgorithmMessageWritable msg = new LogAlgorithmMessageWritable();
-	
-	private VKmerBytesWritableFactory kmerFactory = new VKmerBytesWritableFactory(1);
-	private VKmerBytesWritable destVertexId = new VKmerBytesWritable(1); 
-	private VKmerBytesWritable chainVertexId = new VKmerBytesWritable(1);
-	private VKmerBytesWritable lastKmer = new VKmerBytesWritable(1);
-	/**
-	 * initiate kmerSize, maxIteration
-	 */
-	public void initVertex(){
-		if(kmerSize == -1)
-			kmerSize = getContext().getConfiguration().getInt(KMER_SIZE, 5);
-        if (maxIteration < 0) 
-            maxIteration = getContext().getConfiguration().getInt(ITERATIONS, 1000000);
-	}
-	/**
-	 * get destination vertex
-	 */
-	public VKmerBytesWritable getNextDestVertexId(KmerBytesWritable vertexId, byte geneCode){
-		return kmerFactory.shiftKmerWithNextCode(vertexId, geneCode);
-	}
-	
-	public VKmerBytesWritable getPreDestVertexId(KmerBytesWritable vertexId, byte geneCode){
-		return kmerFactory.shiftKmerWithPreCode(vertexId, geneCode);
-	}
-	
-	public VKmerBytesWritable getNextDestVertexIdFromBitmap(KmerBytesWritable chainVertexId, byte adjMap){
-		return getDestVertexIdFromChain(chainVertexId, adjMap);
-	}
-	
-	public VKmerBytesWritable getDestVertexIdFromChain(KmerBytesWritable chainVertexId, byte adjMap){
-		lastKmer.set(kmerFactory.getLastKmerFromChain(kmerSize, chainVertexId));
-		return getNextDestVertexId(lastKmer, GeneCode.getGeneCodeFromBitMap((byte)(adjMap & 0x0F)));
-	}
-	/**
-	 * head send message to all next nodes
-	 */
-	public void sendMsgToAllNextNodes(KmerBytesWritable vertexId, byte adjMap){
-		for(byte x = GeneCode.A; x<= GeneCode.T ; x++){
-			if((adjMap & (1 << x)) != 0){
-				destVertexId.set(getNextDestVertexId(vertexId, x));
-				sendMsg(destVertexId, msg);
-			}
-		}
-	}
-	/**
-	 * head send message to all previous nodes
-	 */
-	public void sendMsgToAllPreviousNodes(KmerBytesWritable vertexId, byte adjMap){
-		for(byte x = GeneCode.A; x<= GeneCode.T ; x++){
-			if(((adjMap >> 4) & (1 << x)) != 0){
-				destVertexId.set(getPreDestVertexId(vertexId, x));
-				sendMsg(destVertexId, msg);
-			}
-		}
-	}
-	/**
-	 * set vertex state
-	 */
-	public void setState(){
-		if(msg.getMessage() == Message.START && 
-				(getVertexValue().getState() == State.MID_VERTEX || getVertexValue().getState() == State.END_VERTEX)){
-			getVertexValue().setState(State.START_VERTEX);
-			setVertexValue(getVertexValue());
-		}
-		else if(msg.getMessage() == Message.END && getVertexValue().getState() == State.MID_VERTEX){
-			getVertexValue().setState(State.END_VERTEX);
-			setVertexValue(getVertexValue());
-			voteToHalt();
-		}
-		else
-			voteToHalt();
-	}
-	/**
-	 * send start message to next node
-	 */
-	public void sendStartMsgToNextNode(){
-		msg.reset();
-		msg.setMessage(Message.START);
-		msg.setSourceVertexId(getVertexId());
-		sendMsg(destVertexId, msg);
-		voteToHalt();
-	}
-	/**
-	 * send end message to next node
-	 */
-	public void sendEndMsgToNextNode(){
-		msg.reset();
-		msg.setMessage(Message.END);
-		msg.setSourceVertexId(getVertexId());
-		sendMsg(destVertexId, msg);
-		voteToHalt();
-	}
-	/**
-	 * send non message to next node
-	 */
-	public void sendNonMsgToNextNode(){
-		msg.reset();
-		msg.setMessage(Message.NON);
-		msg.setSourceVertexId(getVertexId());
-		sendMsg(destVertexId, msg);
-		voteToHalt();
-	}
-	/**
-	 * head send message to path
-	 */
-	public void sendMsgToPathVertex(KmerBytesWritable chainVertexId, byte adjMap){
-		//if(GeneCode.getGeneCodeFromBitMap((byte)(getVertexValue().getAdjMap() & 0x0F)) == -1
-		//		|| getVertexValue().getState() == State.FINAL_VERTEX) //|| lastKmer == null
-		//	voteToHalt();
-		//else{
-			destVertexId.set(getNextDestVertexIdFromBitmap(chainVertexId, adjMap));
-			if(getVertexValue().getState() == State.START_VERTEX){
-				sendStartMsgToNextNode();
-			}
-			else if(getVertexValue().getState() != State.END_VERTEX){ //FINAL_DELETE
-				sendNonMsgToNextNode();//sendEndMsgToNextNode();
-			}
-		//}
-	}
-	/**
-	 * path send message to head 
-	 */
-	public void responseMsgToHeadVertex(){
-		if(getVertexValue().getLengthOfMergeChain() == 0){
-			getVertexValue().setMergeChain(getVertexId());
-			setVertexValue(getVertexValue());
-		}
-		destVertexId.set(msg.getSourceVertexId());
-		msg.set(null, getVertexValue().getMergeChain(), getVertexValue().getAdjMap(), msg.getMessage());
-		setMessageType(msg.getMessage());
-		sendMsg(destVertexId,msg);
-	}
-	/**
-	 * set message type
-	 */
-	public void setMessageType(int message){
-		//kill Message because it has been merged by the head
-		if(getVertexValue().getState() == State.END_VERTEX){ //FINAL_DELETE
-			msg.setMessage(Message.END);
-			getVertexValue().setState(State.END_VERTEX); //FINAL_DELETE
-			setVertexValue(getVertexValue());
-		}
-		else
-			msg.setMessage(Message.NON);
-		
-		if(message == Message.START){
-			deleteVertex(getVertexId());
-		}
-	}
-	/**
-	 *  set vertexValue's state chainVertexId, value
-	 */
-	public boolean setVertexValueAttributes(){
-		if(msg.getMessage() == Message.END){
-			if(getVertexValue().getState() != State.START_VERTEX)
-				getVertexValue().setState(State.END_VERTEX);
-			else
-				getVertexValue().setState(State.FINAL_VERTEX);
-		}
-			
-		if(getSuperstep() == 5)
-			chainVertexId.set(getVertexId());
-		else
-			chainVertexId.set(getVertexValue().getMergeChain());
-		lastKmer.set(kmerFactory.getLastKmerFromChain(msg.getLengthOfChain() - kmerSize + 1, msg.getChainVertexId()));
-		chainVertexId.set(kmerFactory.mergeTwoKmer(chainVertexId, lastKmer));
-		if(GraphVertexOperation.isCycle(getVertexId(), chainVertexId)){
-			getVertexValue().setMergeChain(null);
-			getVertexValue().setAdjMap(GraphVertexOperation.reverseAdjMap(getVertexValue().getAdjMap(),
-					chainVertexId.getGeneCodeAtPosition(kmerSize)));
-			getVertexValue().setState(State.CYCLE);
-			return false;
-		}
-		else
-			getVertexValue().setMergeChain(chainVertexId);
-		
-		byte tmpVertexValue = GraphVertexOperation.updateRightNeighber(getVertexValue().getAdjMap(), msg.getAdjMap());
-		getVertexValue().setAdjMap(tmpVertexValue);
-		return true;
-	}
-	/**
-	 *  send message to self
-	 */
-	public void sendMsgToSelf(){
-		if(msg.getMessage() != Message.END){
-			setVertexValue(getVertexValue());
-			msg.reset(); //reset
-			msg.setAdjMap(getVertexValue().getAdjMap());
-			sendMsg(getVertexId(),msg);
-		}
-	}
-	/**
-	 * start sending message 
-	 */
-	public void startSendMsg(){
-		if(GraphVertexOperation.isHeadVertex(getVertexValue().getAdjMap())){
-			msg.set(null, null, (byte)0, Message.START);
-			sendMsgToAllNextNodes(getVertexId(), getVertexValue().getAdjMap());
-			//voteToHalt();
-		}
-		if(GraphVertexOperation.isRearVertex(getVertexValue().getAdjMap())){
-			msg.set(null, null, (byte)0, Message.END);
-			sendMsgToAllPreviousNodes(getVertexId(), getVertexValue().getAdjMap());
-			//voteToHalt();
-		}
-		if(GraphVertexOperation.isPathVertex(getVertexValue().getAdjMap())){
-			getVertexValue().setState(State.MID_VERTEX);
-			setVertexValue(getVertexValue());
-		}
-		else 
-			voteToHalt();
-	}
-	/**
-	 *  initiate head, rear and path node
-	 */
-	public void initState(Iterator<LogAlgorithmMessageWritable> msgIterator){
-		while(msgIterator.hasNext()){
-			if(!GraphVertexOperation.isPathVertex(getVertexValue().getAdjMap())){
-				msgIterator.next();
-				voteToHalt();
-			}
-			else{
-				msg = msgIterator.next();
-				setState();
-			}
-		}
-	}
-	/**
-	 * head send message to path
-	 */
-	public void sendMsgToPathVertex(Iterator<LogAlgorithmMessageWritable> msgIterator){
-		if(getSuperstep() == 3){
-			sendMsgToPathVertex(getVertexId(), getVertexValue().getAdjMap());
-		}
-		else{
-			if(msgIterator.hasNext()){
-				msg = msgIterator.next();
-				if(mergeChainVertex(msgIterator))
-					sendMsgToPathVertex(getVertexValue().getMergeChain(), getVertexValue().getAdjMap());
-				else
-					voteToHalt();
-			}
-			if(getVertexValue().getState() == State.END_VERTEX){ //FINAL_DELETE
-				voteToHalt();
-			}
-			if(getVertexValue().getState() == State.FINAL_VERTEX){
-				//String source = getVertexValue().getMergeChain().toString();
-				voteToHalt();
-			}
-		}
-	}
-	/**
-	 * path response message to head
-	 */
-	public void responseMsgToHeadVertex(Iterator<LogAlgorithmMessageWritable> msgIterator){
-		if(msgIterator.hasNext()){		
-			msg = msgIterator.next();
-			responseMsgToHeadVertex();
-		}
-		else{
-			if(getVertexValue().getState() != State.START_VERTEX 
-					&& getVertexValue().getState() != State.END_VERTEX){ //FINAL_DELETE
-				deleteVertex(getVertexId());//killSelf because it doesn't receive any message
-			}
-		}
-	}
-	/**
-	 * merge chainVertex and store in vertexVal.chainVertexId
-	 */
-	public boolean mergeChainVertex(Iterator<LogAlgorithmMessageWritable> msgIterator){
-		return setVertexValueAttributes();
-	}
-	@Override
-	public void compute(Iterator<LogAlgorithmMessageWritable> msgIterator) {
-		initVertex();
-		if(getVertexValue().getState() == State.FINAL_VERTEX)
-			voteToHalt();
-		else{
-			if (getSuperstep() == 1) 
-				startSendMsg();
-			else if(getSuperstep() == 2)
-				initState(msgIterator);
-			else if(getSuperstep()%2 == 1 && getSuperstep() <= maxIteration){
-				sendMsgToPathVertex(msgIterator);
-			}
-			else if(getSuperstep()%2 == 0 && getSuperstep() <= maxIteration){
-				responseMsgToHeadVertex(msgIterator);
-			}
-			else
-				voteToHalt();
-		}
-	}
-	/**
-	 * @param args
-	 */
-	public static void main(String[] args) throws Exception {
-        PregelixJob job = new PregelixJob(TwoStepLogAlgorithmForPathMergeVertex.class.getSimpleName());
-        job.setVertexClass(TwoStepLogAlgorithmForPathMergeVertex.class);
-        /**
-         * BinaryInput and BinaryOutput~/
-         */
-        job.setVertexInputFormatClass(LogAlgorithmForPathMergeInputFormat.class); 
-        job.setVertexOutputFormatClass(LogAlgorithmForPathMergeOutputFormat.class); 
-        job.setOutputKeyClass(KmerBytesWritable.class);
-        job.setOutputValueClass(ValueStateWritable.class);
-        job.setDynamicVertexValueSize(true);
-        Client.run(args, job);
-	}
-}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/FilterJobGenerator.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/FilterJobGenerator.java
deleted file mode 100644
index bead712..0000000
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/FilterJobGenerator.java
+++ /dev/null
@@ -1,65 +0,0 @@
-package edu.uci.ics.genomix.pregelix.JobGen;
-
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.IOException;
-
-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.operator.LogFilterVertex;
-import edu.uci.ics.genomix.pregelix.operator.NaiveAlgorithmForPathMergeVertex;
-import edu.uci.ics.genomix.pregelix.operator.NaiveFilterVertex;
-import edu.uci.ics.genomix.pregelix.operator.TwoStepLogAlgorithmForPathMergeVertex;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
-import edu.uci.ics.pregelix.api.job.PregelixJob;
-
-
-public class FilterJobGenerator {
-
-    public static String outputBase = "src/test/resources/jobs/";
-    
-    private static void generateNaiveFilterJob(String jobName, String outputPath) throws IOException {
-    	PregelixJob job = new PregelixJob(jobName);
-    	job.setVertexClass(NaiveFilterVertex.class);
-    	job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class);
-        job.setVertexOutputFormatClass(NaiveAlgorithmForPathMergeOutputFormat.class);
-        job.setDynamicVertexValueSize(true);
-        job.setOutputKeyClass(KmerBytesWritable.class);
-        job.setOutputValueClass(ValueStateWritable.class);
-        job.getConfiguration().setInt(NaiveAlgorithmForPathMergeVertex.KMER_SIZE, 55);
-        job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
-    }
-    
-    private static void genNaiveFilter() throws IOException {
-    	generateNaiveFilterJob("NaiveFilterVertex", outputBase + "NaiveFilterVertex.xml");
-    }
-    
-    private static void generateLogFilterJob(String jobName, String outputPath) throws IOException {
-    	PregelixJob job = new PregelixJob(jobName);
-    	job.setVertexClass(LogFilterVertex.class);
-        job.setVertexInputFormatClass(LogAlgorithmForPathMergeInputFormat.class); 
-        job.setVertexOutputFormatClass(LogAlgorithmForPathMergeOutputFormat.class);
-        job.setDynamicVertexValueSize(true);
-        job.setOutputKeyClass(KmerBytesWritable.class);
-        job.setOutputValueClass(ValueStateWritable.class);
-        job.getConfiguration().setInt(TwoStepLogAlgorithmForPathMergeVertex.KMER_SIZE, 5);
-        job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
-    }
-    
-    private static void genLogFilter() throws IOException {
-    	generateLogFilterJob("LogFilterVertex", outputBase + "LogFilterVertex.xml");
-    }
-    
-	/**
-	 * @param args
-	 * @throws IOException 
-	 */
-	public static void main(String[] args) throws IOException {
-		genNaiveFilter();
-		//genLogFilter();
-	}
-
-}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/RunJobTestCase.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/RunJobTestCase.java
deleted file mode 100644
index a5ddce3..0000000
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/RunJobTestCase.java
+++ /dev/null
@@ -1,168 +0,0 @@
-package edu.uci.ics.genomix.pregelix.JobRun;
-
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileWriter;
-
-import junit.framework.TestCase;
-
-import org.apache.hadoop.conf.Configuration;
-import org.apache.hadoop.fs.FileSystem;
-import org.apache.hadoop.fs.FileUtil;
-import org.apache.hadoop.fs.Path;
-import org.apache.hadoop.mapred.JobConf;
-import org.apache.hadoop.mapreduce.lib.input.FileInputFormat;
-import org.apache.hadoop.mapreduce.lib.output.FileOutputFormat;
-import org.junit.Test;
-
-import edu.uci.ics.genomix.pregelix.example.util.TestUtils;
-import edu.uci.ics.hyracks.api.job.JobSpecification;
-import edu.uci.ics.pregelix.api.job.PregelixJob;
-import edu.uci.ics.pregelix.core.jobgen.JobGen;
-import edu.uci.ics.pregelix.core.jobgen.JobGenInnerJoin;
-import edu.uci.ics.pregelix.core.jobgen.JobGenOuterJoin;
-import edu.uci.ics.pregelix.core.jobgen.JobGenOuterJoinSingleSort;
-import edu.uci.ics.pregelix.core.jobgen.JobGenOuterJoinSort;
-import edu.uci.ics.pregelix.core.util.PregelixHyracksIntegrationUtil;
-import edu.uci.ics.pregelix.dataflow.util.IterationUtils;
-
-public class RunJobTestCase extends TestCase{
-	
-	private static final String NC1 = "nc1";
-    private static final String HYRACKS_APP_NAME = "pregelix";
-    private static String HDFS_INPUTPATH = "/webmap";
-    private static String HDFS_OUTPUTPAH = "/result";
-    
-    private final PregelixJob job;
-    private JobGen[] giraphJobGens;
-    private final String resultFileName;
-    private final String expectedFileName;
-    private final String jobFile;
-    
-
-
-    public RunJobTestCase(String hadoopConfPath, String jobName, String jobFile, String resultFile, String expectedFile)
-            throws Exception {
-        super("test");
-        this.jobFile = jobFile;
-        this.job = new PregelixJob("test");
-        this.job.getConfiguration().addResource(new Path(jobFile));
-        this.job.getConfiguration().addResource(new Path(hadoopConfPath));
-        Path[] inputPaths = FileInputFormat.getInputPaths(job);
-        if (inputPaths[0].toString().endsWith(HDFS_INPUTPATH)) {
-            FileInputFormat.setInputPaths(job, HDFS_INPUTPATH);
-            FileOutputFormat.setOutputPath(job, new Path(HDFS_OUTPUTPAH));
-        } 
-        
-        job.setJobName(jobName);
-        this.resultFileName = resultFile;
-        this.expectedFileName = expectedFile;
-        giraphJobGens = new JobGen[1];
-        giraphJobGens[0] = new JobGenOuterJoin(job);
-        /*waitawhile();
-        giraphJobGens[1] = new JobGenInnerJoin(job);
-        waitawhile();
-        giraphJobGens[2] = new JobGenOuterJoinSort(job);
-        waitawhile();
-        giraphJobGens[3] = new JobGenOuterJoinSingleSort(job);*/
-    }
-    
-    private void waitawhile() throws InterruptedException {
-        synchronized (this) {
-            this.wait(20);
-        }
-    }
-	@Test
-	public void test() throws Exception {
-		setUp();
-		
-        for (JobGen jobGen : giraphJobGens) {
-            FileSystem dfs = FileSystem.get(job.getConfiguration());
-            dfs.delete(new Path(HDFS_OUTPUTPAH), true);
-            runCreate(jobGen);
-            runDataLoad(jobGen);
-            int i = 1;
-            boolean terminate = false;
-            do {
-                runLoopBodyIteration(jobGen, i);
-                terminate = IterationUtils.readTerminationState(job.getConfiguration(), jobGen.getJobId());
-                i++;
-            } while (!terminate);
-            runIndexScan(jobGen);
-            runHDFSWRite(jobGen);
-            runCleanup(jobGen);
-            compareResults();
-        }
-        tearDown();
-        waitawhile();
-	}
-	
-	private void runCreate(JobGen jobGen) throws Exception {
-        try {
-            JobSpecification treeCreateJobSpec = jobGen.generateCreatingJob();
-            PregelixHyracksIntegrationUtil.runJob(treeCreateJobSpec, HYRACKS_APP_NAME);
-        } catch (Exception e) {
-            throw e;
-        }
-    }
-
-    private void runDataLoad(JobGen jobGen) throws Exception {
-        try {
-            JobSpecification bulkLoadJobSpec = jobGen.generateLoadingJob();
-            PregelixHyracksIntegrationUtil.runJob(bulkLoadJobSpec, HYRACKS_APP_NAME);
-        } catch (Exception e) {
-            throw e;
-        }
-    }
-
-    private void runLoopBodyIteration(JobGen jobGen, int iteration) throws Exception {
-        try {
-            JobSpecification loopBody = jobGen.generateJob(iteration);
-            PregelixHyracksIntegrationUtil.runJob(loopBody, HYRACKS_APP_NAME);
-        } catch (Exception e) {
-            throw e;
-        }
-    }
-
-    private void runIndexScan(JobGen jobGen) throws Exception {
-        try {
-            JobSpecification scanSortPrintJobSpec = jobGen.scanIndexPrintGraph(NC1, resultFileName);
-            PregelixHyracksIntegrationUtil.runJob(scanSortPrintJobSpec, HYRACKS_APP_NAME);
-        } catch (Exception e) {
-            throw e;
-        }
-    }
-
-    private void runHDFSWRite(JobGen jobGen) throws Exception {
-        try {
-            JobSpecification scanSortPrintJobSpec = jobGen.scanIndexWriteGraph();
-            PregelixHyracksIntegrationUtil.runJob(scanSortPrintJobSpec, HYRACKS_APP_NAME);
-        } catch (Exception e) {
-            throw e;
-        }
-    }
-
-    private void runCleanup(JobGen jobGen) throws Exception {
-        try {
-            JobSpecification[] cleanups = jobGen.generateCleanup();
-            runJobArray(cleanups);
-        } catch (Exception e) {
-            throw e;
-        }
-    }
-
-    private void runJobArray(JobSpecification[] jobs) throws Exception {
-        for (JobSpecification job : jobs) {
-            PregelixHyracksIntegrationUtil.runJob(job, HYRACKS_APP_NAME);
-        }
-    }
-
-    private void compareResults() throws Exception {
-        TestUtils.compareWithResult(new File(resultFileName), new File(expectedFileName));
-    }
-
-    public String toString() {
-        return jobFile;
-    }
-
-}
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
deleted file mode 100644
index 1af0d6e..0000000
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/RunJobTestSuite.java
+++ /dev/null
@@ -1,194 +0,0 @@
-package edu.uci.ics.genomix.pregelix.JobRun;
-
-import java.io.BufferedReader;
-import java.io.DataOutputStream;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.FileReader;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.logging.Logger;
-
-import junit.framework.Test;
-import junit.framework.TestResult;
-import junit.framework.TestSuite;
-
-import org.apache.commons.io.FileUtils;
-import org.apache.hadoop.conf.Configuration;
-import org.apache.hadoop.fs.FileSystem;
-import org.apache.hadoop.fs.Path;
-import org.apache.hadoop.hdfs.MiniDFSCluster;
-import org.apache.hadoop.mapred.JobConf;
-
-import edu.uci.ics.pregelix.core.jobgen.clusterconfig.ClusterConfig;
-import edu.uci.ics.pregelix.core.util.PregelixHyracksIntegrationUtil;
-
-public class RunJobTestSuite extends TestSuite {
-
-	private static final Logger LOGGER = Logger.getLogger(RunJobTestSuite.class
-			.getName());
-
-	private static final String ACTUAL_RESULT_DIR = "actual";
-	private static final String EXPECTED_RESULT_DIR = "src/test/resources/expected";
-	private static final String PATH_TO_HADOOP_CONF = "src/test/resources/hadoop/conf";
-	private static final String PATH_TO_CLUSTER_STORE = "src/test/resources/cluster/stores.properties";
-	private static final String PATH_TO_CLUSTER_PROPERTIES = "src/test/resources/cluster/cluster.properties";
-	private static final String PATH_TO_JOBS = "src/test/resources/jobs/";
-	private static final String PATH_TO_IGNORE = "src/test/resources/ignore.txt";
-	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/sequencefile/Path";
-	private static final String HDFS_PATH = "/webmap/";
-
-	private static final String HYRACKS_APP_NAME = "pregelix";
-	private static final String HADOOP_CONF_PATH = ACTUAL_RESULT_DIR
-			+ File.separator + "conf.xml";
-	private MiniDFSCluster dfsCluster;
-
-	private JobConf conf = new JobConf();
-	private int numberOfNC = 2;
-
-	public void setUp() throws Exception {
-		ClusterConfig.setStorePath(PATH_TO_CLUSTER_STORE);
-		ClusterConfig.setClusterPropertiesPath(PATH_TO_CLUSTER_PROPERTIES);
-		cleanupStores();
-		PregelixHyracksIntegrationUtil.init("src/test/resources/topology.xml");
-		LOGGER.info("Hyracks mini-cluster started");
-		FileUtils.forceMkdir(new File(ACTUAL_RESULT_DIR));
-		FileUtils.cleanDirectory(new File(ACTUAL_RESULT_DIR));
-		startHDFS();
-	}
-
-	private void cleanupStores() throws IOException {
-		FileUtils.forceMkdir(new File("teststore"));
-		FileUtils.forceMkdir(new File("build"));
-		FileUtils.cleanDirectory(new File("teststore"));
-		FileUtils.cleanDirectory(new File("build"));
-	}
-
-	private void startHDFS() throws IOException {
-		conf.addResource(new Path(PATH_TO_HADOOP_CONF + "/core-site.xml"));
-		conf.addResource(new Path(PATH_TO_HADOOP_CONF + "/mapred-site.xml"));
-		conf.addResource(new Path(PATH_TO_HADOOP_CONF + "/hdfs-site.xml"));
-		FileSystem lfs = FileSystem.getLocal(new Configuration());
-		lfs.delete(new Path("build"), true);
-		System.setProperty("hadoop.log.dir", "logs");
-		dfsCluster = new MiniDFSCluster(conf, numberOfNC, true, null);
-		FileSystem dfs = FileSystem.get(conf);
-		Path src = new Path(DATA_PATH);
-		Path dest = new Path(HDFS_PATH);
-		dfs.mkdirs(dest);
-		dfs.copyFromLocalFile(src, dest);
-
-		DataOutputStream confOutput = new DataOutputStream(
-				new FileOutputStream(new File(HADOOP_CONF_PATH)));
-		conf.writeXml(confOutput);
-		confOutput.flush();
-		confOutput.close();
-	}
-
-	/**
-	 * cleanup hdfs cluster
-	 */
-	private void cleanupHDFS() throws Exception {
-		dfsCluster.shutdown();
-	}
-
-	public void tearDown() throws Exception {
-		PregelixHyracksIntegrationUtil.deinit();
-		LOGGER.info("Hyracks mini-cluster shut down");
-		cleanupHDFS();
-	}
-
-	public static Test suite() throws Exception {
-		List<String> ignores = getFileList(PATH_TO_IGNORE);
-		List<String> onlys = getFileList(PATH_TO_ONLY);
-		File testData = new File(PATH_TO_JOBS);
-		File[] queries = testData.listFiles();
-		RunJobTestSuite testSuite = new RunJobTestSuite();
-		testSuite.setUp();
-		boolean onlyEnabled = false;
-
-		if (onlys.size() > 0) {
-			onlyEnabled = true;
-		}
-		for (File qFile : queries) {
-			if (isInList(ignores, qFile.getName()))
-				continue;
-
-			if (qFile.isFile()) {
-				if (onlyEnabled && !isInList(onlys, qFile.getName())) {
-					continue;
-				} else {
-					String resultFileName = ACTUAL_RESULT_DIR + File.separator
-							+ jobExtToResExt(qFile.getName());
-					String expectedFileName = EXPECTED_RESULT_DIR
-							+ File.separator + jobExtToResExt(qFile.getName());
-					testSuite.addTest(new RunJobTestCase(HADOOP_CONF_PATH,
-							qFile.getName(),
-							qFile.getAbsolutePath().toString(), resultFileName,
-							expectedFileName));
-				}
-			}
-		}
-		return testSuite;
-	}
-
-	/**
-	 * Runs the tests and collects their result in a TestResult.
-	 */
-	@Override
-	public void run(TestResult result) {
-		try {
-			int testCount = countTestCases();
-			for (int i = 0; i < testCount; i++) {
-				// cleanupStores();
-				Test each = this.testAt(i);
-				if (result.shouldStop())
-					break;
-				runTest(each, result);
-			}
-
-			tearDown();
-		} catch (Exception e) {
-			throw new IllegalStateException(e);
-		}
-
-	}
-
-	protected static List<String> getFileList(String ignorePath)
-			throws FileNotFoundException, IOException {
-		BufferedReader reader = new BufferedReader(new FileReader(ignorePath));
-		String s = null;
-		List<String> ignores = new ArrayList<String>();
-		while ((s = reader.readLine()) != null) {
-			ignores.add(s);
-		}
-		reader.close();
-		return ignores;
-	}
-
-	private static String jobExtToResExt(String fname) {
-		int dot = fname.lastIndexOf('.');
-		return fname.substring(0, dot + 1) + FILE_EXTENSION_OF_RESULTS;
-	}
-
-	private static boolean isInList(List<String> onlys, String name) {
-		for (String only : onlys)
-			if (name.indexOf(only) >= 0)
-				return true;
-		return false;
-	}
-
-	public JobConf getConf() {
-		return conf;
-	}
-
-	public void setConf(JobConf conf) {
-		this.conf = conf;
-	}
-
-}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/PathMergeSmallTestCase.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/PathMergeSmallTestCase.java
deleted file mode 100644
index 4b6d367..0000000
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/PathMergeSmallTestCase.java
+++ /dev/null
@@ -1,89 +0,0 @@
-/*
- * Copyright 2009-2010 by The Regents of the University of California
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * you may obtain a copy of the License from
- * 
- *     http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package edu.uci.ics.genomix.pregelix.pathmerge;
-
-import junit.framework.TestCase;
-
-import org.apache.hadoop.fs.FileSystem;
-import org.apache.hadoop.fs.Path;
-import org.apache.hadoop.mapreduce.lib.input.FileInputFormat;
-import org.apache.hadoop.mapreduce.lib.output.FileOutputFormat;
-import org.junit.Test;
-
-import edu.uci.ics.genomix.pregelix.sequencefile.GenerateTextFile;
-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;
-import edu.uci.ics.pregelix.core.util.PregelixHyracksIntegrationUtil;
-
-public class PathMergeSmallTestCase extends TestCase {
-	private final PregelixJob job;
-	private final String resultFileDir;
-	private final String textFileDir;
-	private final String jobFile;
-	private final Driver driver = new Driver(this.getClass());
-	private final FileSystem dfs;
-
-	public PathMergeSmallTestCase(String hadoopConfPath, String jobName,
-			String jobFile, FileSystem dfs, String hdfsInput, String resultFile, String textFile)
-			throws Exception {
-		super("test");
-		this.jobFile = jobFile;
-		this.job = new PregelixJob("test");
-		this.job.getConfiguration().addResource(new Path(jobFile));
-		this.job.getConfiguration().addResource(new Path(hadoopConfPath));
-		FileInputFormat.setInputPaths(job, hdfsInput);
-		FileOutputFormat.setOutputPath(job, new Path(hdfsInput + "_result"));
-		this.textFileDir = textFile;
-		job.setJobName(jobName);
-		this.resultFileDir = resultFile;
-		
-		this.dfs = dfs;
-	}
-
-	private void waitawhile() throws InterruptedException {
-		synchronized (this) {
-			this.wait(20);
-		}
-	}
-
-	@Test
-	public void test() throws Exception {
-		setUp();
-		Plan[] plans = new Plan[] { Plan.OUTER_JOIN };
-		for (Plan plan : plans) {
-			driver.runJob(job, plan, PregelixHyracksIntegrationUtil.CC_HOST,
-					PregelixHyracksIntegrationUtil.TEST_HYRACKS_CC_CLIENT_PORT,
-					false);
-		}
-		compareResults();
-		tearDown();
-		waitawhile();
-	}
-
-	private void compareResults() throws Exception {
-		dfs.copyToLocalFile(FileOutputFormat.getOutputPath(job), new Path(
-				resultFileDir));
-		GenerateTextFile.generateFromPathmergeResult(55, resultFileDir, textFileDir);
-		// TestUtils.compareWithResultDir(new File(expectedFileDir), new
-		// File(resultFileDir));
-	}
-
-	public String toString() {
-		return jobFile;
-	}
-
-}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/PathMergeSmallTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/PathMergeSmallTestSuite.java
deleted file mode 100644
index 898d059..0000000
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/PathMergeSmallTestSuite.java
+++ /dev/null
@@ -1,236 +0,0 @@
-/*
- * Copyright 2009-2010 by The Regents of the University of California
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * you may obtain a copy of the License from
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package edu.uci.ics.genomix.pregelix.pathmerge;
-
-import java.io.BufferedReader;
-import java.io.DataOutputStream;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.FileReader;
-import java.io.FilenameFilter;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.logging.Logger;
-
-import junit.framework.Test;
-import junit.framework.TestResult;
-import junit.framework.TestSuite;
-
-import org.apache.commons.io.FileUtils;
-import org.apache.commons.io.filefilter.WildcardFileFilter;
-import org.apache.hadoop.conf.Configuration;
-import org.apache.hadoop.fs.FileSystem;
-import org.apache.hadoop.fs.Path;
-import org.apache.hadoop.hdfs.MiniDFSCluster;
-import org.apache.hadoop.mapred.JobConf;
-
-import edu.uci.ics.pregelix.core.jobgen.clusterconfig.ClusterConfig;
-import edu.uci.ics.pregelix.core.util.PregelixHyracksIntegrationUtil;
-
-@SuppressWarnings("deprecation")
-public class PathMergeSmallTestSuite extends TestSuite {
-	private static final Logger LOGGER = Logger
-			.getLogger(PathMergeSmallTestSuite.class.getName());
-
-	public static final String PreFix = "graphbuildresult"; //"graphbuildresult";
-	public static final String[] TestDir = { PreFix + File.separator
-		+  "result"};
-		/*+ "BridgePath", PreFix + File.separator
-		+ "CyclePath", PreFix + File.separator
-		+ "SimplePath", PreFix + File.separator
-		+ "SinglePath", PreFix + File.separator
-		+ "TreePath"};
-		+ "2"}, PreFix + File.separator
-		+ "3", PreFix + File.separator
-		+ "4", PreFix + File.separator
-		+ "5", PreFix + File.separator
-		+ "6", PreFix + File.separator
-		+ "7", PreFix + File.separator
-		+ "8", PreFix + File.separator
-		+ "9", PreFix + File.separator
-		+ "TwoKmer", PreFix + File.separator
-		+ "ThreeKmer", PreFix + File.separator
-		+ "SinglePath", PreFix + File.separator
-		+ "SimplePath", PreFix + File.separator
-		+ "Path", PreFix + File.separator
-		+ "BridgePath", PreFix + File.separator
-		+ "CyclePath", PreFix + File.separator
-		+ "RingPath", PreFix + File.separator
-		+ "LongPath", PreFix + File.separator
-		+ "TreePath"};*/
-	private static final String ACTUAL_RESULT_DIR = "actual";
-	private static final String PATH_TO_HADOOP_CONF = "src/test/resources/hadoop/conf";
-	private static final String PATH_TO_CLUSTER_STORE = "src/test/resources/cluster/stores.properties";
-	private static final String PATH_TO_CLUSTER_PROPERTIES = "src/test/resources/cluster/cluster.properties";
-	private static final String PATH_TO_JOBS = "src/test/resources/jobs/";
-	private static final String PATH_TO_ONLY = "src/test/resources/only.txt";
-
-	public static final String HDFS_INPUTPATH = "/PathTestSet";
-
-	private static final String HADOOP_CONF_PATH = ACTUAL_RESULT_DIR
-			+ File.separator + "conf.xml";
-	private MiniDFSCluster dfsCluster;
-
-	private JobConf conf = new JobConf();
-	private int numberOfNC = 2;
-
-	public void setUp() throws Exception {
-		ClusterConfig.setStorePath(PATH_TO_CLUSTER_STORE);
-		ClusterConfig.setClusterPropertiesPath(PATH_TO_CLUSTER_PROPERTIES);
-		cleanupStores();
-		PregelixHyracksIntegrationUtil.init("src/test/resources/topology.xml");
-		LOGGER.info("Hyracks mini-cluster started");
-		FileUtils.forceMkdir(new File(ACTUAL_RESULT_DIR));
-		FileUtils.cleanDirectory(new File(ACTUAL_RESULT_DIR));
-		startHDFS();
-	}
-
-	private void startHDFS() throws IOException {
-		conf.addResource(new Path(PATH_TO_HADOOP_CONF + "/core-site.xml"));
-		conf.addResource(new Path(PATH_TO_HADOOP_CONF + "/mapred-site.xml"));
-		conf.addResource(new Path(PATH_TO_HADOOP_CONF + "/hdfs-site.xml"));
-		FileSystem lfs = FileSystem.getLocal(new Configuration());
-		lfs.delete(new Path("build"), true);
-		System.setProperty("hadoop.log.dir", "logs");
-		dfsCluster = new MiniDFSCluster(conf, numberOfNC, true, null);
-		FileSystem dfs = FileSystem.get(conf);
-
-		for (String testDir : TestDir) {
-			File src = new File(testDir);
-			Path dest = new Path(HDFS_INPUTPATH + File.separator + src.getName());
-			dfs.mkdirs(dest);
-			//src.listFiles()
-			//src.listFiles((FilenameFilter)(new WildcardFileFilter("part*")))
-			for (File f : src.listFiles()){
-				dfs.copyFromLocalFile(new Path(f.getAbsolutePath()), dest);
-			}
-		}
-
-		DataOutputStream confOutput = new DataOutputStream(
-				new FileOutputStream(new File(HADOOP_CONF_PATH)));
-		conf.writeXml(confOutput);
-		confOutput.flush();
-		confOutput.close();
-	}
-	
-	private void cleanupStores() throws IOException {
-		FileUtils.forceMkdir(new File("teststore"));
-		FileUtils.forceMkdir(new File("build"));
-		FileUtils.cleanDirectory(new File("teststore"));
-		FileUtils.cleanDirectory(new File("build"));
-	}
-
-	/**
-	 * cleanup hdfs cluster
-	 */
-	private void cleanupHDFS() throws Exception {
-		dfsCluster.shutdown();
-	}
-
-	public void tearDown() throws Exception {
-		PregelixHyracksIntegrationUtil.deinit();
-		LOGGER.info("Hyracks mini-cluster shut down");
-		cleanupHDFS();
-	}
-
-	public static Test suite() throws Exception {
-		List<String> onlys = getFileList(PATH_TO_ONLY);
-		File testData = new File(PATH_TO_JOBS);
-		File[] queries = testData.listFiles();
-		PathMergeSmallTestSuite testSuite = new PathMergeSmallTestSuite();
-		testSuite.setUp();
-		boolean onlyEnabled = false;
-		FileSystem dfs = FileSystem.get(testSuite.conf);
-
-		if (onlys.size() > 0) {
-			onlyEnabled = true;
-		}
-
-		for (File qFile : queries) {
-			if (qFile.isFile()) {
-				if (onlyEnabled && !isInList(onlys, qFile.getName())) {
-					continue;
-				} else {
-					for (String testPathStr : TestDir) {
-						File testDir = new File(testPathStr);
-						String resultFileName = ACTUAL_RESULT_DIR
-								+ File.separator
-								+ jobExtToResExt(qFile.getName())
-								+ File.separator + "BinaryOutput"
-								+ File.separator + testDir.getName();
-						String textFileName = ACTUAL_RESULT_DIR
-								+ File.separator
-								+ jobExtToResExt(qFile.getName())
-								+ File.separator + "TextOutput"
-								+ File.separator + testDir.getName();
-						testSuite.addTest(new PathMergeSmallTestCase(
-								HADOOP_CONF_PATH, qFile.getName(), qFile
-										.getAbsolutePath().toString(),
-								 dfs, HDFS_INPUTPATH + File.separator + testDir.getName(),
-								 resultFileName, textFileName));
-					}
-				}
-			}
-		}
-		return testSuite;
-	}
-
-	/**
-	 * Runs the tests and collects their result in a TestResult.
-	 */
-	@Override
-	public void run(TestResult result) {
-		try {
-			int testCount = countTestCases();
-			for (int i = 0; i < testCount; i++) {
-				// cleanupStores();
-				Test each = this.testAt(i);
-				if (result.shouldStop())
-					break;
-				runTest(each, result);
-			}
-			tearDown();
-		} catch (Exception e) {
-			throw new IllegalStateException(e);
-		}
-	}
-
-	protected static List<String> getFileList(String ignorePath)
-			throws FileNotFoundException, IOException {
-		BufferedReader reader = new BufferedReader(new FileReader(ignorePath));
-		String s = null;
-		List<String> ignores = new ArrayList<String>();
-		while ((s = reader.readLine()) != null) {
-			ignores.add(s);
-		}
-		reader.close();
-		return ignores;
-	}
-
-	private static String jobExtToResExt(String fname) {
-		int dot = fname.lastIndexOf('.');
-		return fname.substring(0, dot);
-	}
-
-	private static boolean isInList(List<String> onlys, String name) {
-		for (String only : onlys)
-			if (name.indexOf(only) >= 0)
-				return true;
-		return false;
-	}
-
-}