diff --git a/genomix/genomix-hadoop/pom.xml b/genomix/genomix-hadoop/pom.xml
index 8ca2fa3..f305c49 100755
--- a/genomix/genomix-hadoop/pom.xml
+++ b/genomix/genomix-hadoop/pom.xml
@@ -160,6 +160,8 @@
 			<groupId>edu.uci.ics.hyracks</groupId>
 			<artifactId>genomix-hyracks</artifactId>
 			<version>0.2.6-SNAPSHOT</version>
+			<type>test-jar</type>
+			<scope>test</scope>
 		</dependency>
 		<dependency>
 			<groupId>edu.uci.ics.hyracks</groupId>
diff --git a/genomix/genomix-pregelix/pom.xml b/genomix/genomix-pregelix/pom.xml
index f609d3b..95227c5 100644
--- a/genomix/genomix-pregelix/pom.xml
+++ b/genomix/genomix-pregelix/pom.xml
@@ -1,60 +1,61 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
-  <modelVersion>4.0.0</modelVersion>
-  <groupId>edu.uci.ics.pregelix</groupId>
-  <artifactId>genomix-pregelix</artifactId>
-  <packaging>jar</packaging>
-  <version>0.2.6-SNAPSHOT</version>
-  <name>genomix-pregelix</name>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<groupId>edu.uci.ics.pregelix</groupId>
+	<artifactId>genomix-pregelix</artifactId>
+	<packaging>jar</packaging>
+	<version>0.2.6-SNAPSHOT</version>
+	<name>genomix-pregelix</name>
 
 	<properties>
 		<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
 	</properties>
 
-  <profiles>
-    <profile>
-      <id>macosx</id>
-      <activation>
-        <os>
-          <name>mac os x</name>
-        </os>
-        <jdk>1.7</jdk>
-      </activation>
-      <properties>
-        <jvm.extraargs>-Djava.nio.channels.spi.SelectorProvider=sun.nio.ch.KQueueSelectorProvider</jvm.extraargs>
-      </properties>
-    </profile>
-  </profiles>
+	<profiles>
+		<profile>
+			<id>macosx</id>
+			<activation>
+				<os>
+					<name>mac os x</name>
+				</os>
+				<jdk>1.7</jdk>
+			</activation>
+			<properties>
+				<jvm.extraargs>-Djava.nio.channels.spi.SelectorProvider=sun.nio.ch.KQueueSelectorProvider</jvm.extraargs>
+			</properties>
+		</profile>
+	</profiles>
 
-  <build>
-        <plugins>
-            <plugin>
-                                <groupId>org.apache.maven.plugins</groupId>
-                                <artifactId>maven-compiler-plugin</artifactId>
-                                <version>2.0.2</version>
-                                <configuration>
-                                        <source>1.7</source>
-                                        <target>1.7</target>
-                                        <fork>true</fork>
-                                </configuration>
-                        </plugin>
-                        <plugin>
-                                <artifactId>maven-assembly-plugin</artifactId>
-                                <configuration>
-                                        <descriptorRefs>
-                                                <descriptorRef>jar-with-dependencies</descriptorRef>
-                                        </descriptorRefs>
-                                </configuration>
-                                <executions>
-                                        <execution>
-                                                <id>make-my-jar-with-dependencies</id>
-                                                <phase>package</phase>
-                                                <goals>
-                                                        <goal>single</goal>
-                                                </goals>
-                                        </execution>
-                                </executions>
-                        </plugin>
+	<build>
+		<plugins>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-compiler-plugin</artifactId>
+				<version>2.0.2</version>
+				<configuration>
+					<source>1.7</source>
+					<target>1.7</target>
+					<fork>true</fork>
+				</configuration>
+			</plugin>
+			<plugin>
+				<artifactId>maven-assembly-plugin</artifactId>
+				<configuration>
+					<descriptorRefs>
+						<descriptorRef>jar-with-dependencies</descriptorRef>
+					</descriptorRefs>
+				</configuration>
+				<executions>
+					<execution>
+						<id>make-my-jar-with-dependencies</id>
+						<phase>package</phase>
+						<goals>
+							<goal>single</goal>
+						</goals>
+					</execution>
+				</executions>
+			</plugin>
 			<plugin>
 				<groupId>org.codehaus.mojo</groupId>
 				<artifactId>appassembler-maven-plugin</artifactId>
@@ -78,207 +79,207 @@
 					</execution>
 				</executions>
 			</plugin>
-                        <plugin>
-                                <groupId>org.apache.maven.plugins</groupId>
-                                <artifactId>maven-surefire-plugin</artifactId>
-                                <version>2.7.2</version>
-                                <configuration>
-                                        <forkMode>pertest</forkMode>
-                                        <argLine>-enableassertions -Xmx2047m -Dfile.encoding=UTF-8
-                                                -Djava.util.logging.config.file=src/test/resources/logging.properties</argLine>
-                                        <includes>
-                                                <include>**/*TestSuite.java</include>
-                                                <include>**/*Test.java</include>
-                                        </includes>
-                                </configuration>
-                        </plugin>
-                        <plugin>
-                                <artifactId>maven-clean-plugin</artifactId>
-                                <configuration>
-                                        <filesets>
-                                                <fileset>
-                                                        <directory>.</directory>
-                                                        <includes>
-                                                                <include>teststore*</include>
-                                                                <include>edu*</include>
-                                                                <include>actual*</include>
-                                                                <include>build*</include>
-                                                                <include>expect*</include>
-                                                                <include>ClusterController*</include>
-                                                                <include>edu.uci.*</include>
-                                                        </includes>
-                                                </fileset>
-                                        </filesets>
-                                </configuration>
-                        </plugin>
-                </plugins>
-        </build>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-surefire-plugin</artifactId>
+				<version>2.7.2</version>
+				<configuration>
+					<forkMode>pertest</forkMode>
+					<argLine>-enableassertions -Xmx2047m -Dfile.encoding=UTF-8
+						-Djava.util.logging.config.file=src/test/resources/logging.properties</argLine>
+					<includes>
+						<include>**/*TestSuite.java</include>
+						<include>**/*Test.java</include>
+					</includes>
+				</configuration>
+			</plugin>
+			<plugin>
+				<artifactId>maven-clean-plugin</artifactId>
+				<configuration>
+					<filesets>
+						<fileset>
+							<directory>.</directory>
+							<includes>
+								<include>teststore*</include>
+								<include>edu*</include>
+								<include>actual*</include>
+								<include>build*</include>
+								<include>expect*</include>
+								<include>ClusterController*</include>
+								<include>edu.uci.*</include>
+							</includes>
+						</fileset>
+					</filesets>
+				</configuration>
+			</plugin>
+		</plugins>
+	</build>
 
-        <dependencies>
-                <dependency>
-                        <groupId>junit</groupId>
-                        <artifactId>junit</artifactId>
-                        <version>4.8.1</version>
-                        <scope>test</scope>
-                </dependency>
-                <dependency>
-                	<groupId>edu.uci.ics.hyracks</groupId>
-                	<artifactId>pregelix-core</artifactId>
-                	<version>0.2.6-SNAPSHOT</version>
-                	<type>jar</type>
-                	<scope>compile</scope>
-                </dependency>
-                 <dependency>
-                	<groupId>edu.uci.ics.hyracks</groupId>
-                	<artifactId>genomix-data</artifactId>
-                	<version>0.2.6-SNAPSHOT</version>
-                	<type>jar</type>
-                	<scope>compile</scope>
-                </dependency>
-                <dependency>
-					<groupId>edu.uci.ics.hyracks</groupId>
-					<artifactId>hyracks-dataflow-std</artifactId>
-					<version>0.2.6-SNAPSHOT</version>
-					<type>jar</type>
-					<scope>compile</scope>
-				</dependency>
-				<dependency>
-					<groupId>edu.uci.ics.hyracks</groupId>
-					<artifactId>hyracks-api</artifactId>
-					<version>0.2.6-SNAPSHOT</version>
-					<type>jar</type>
-					<scope>compile</scope>
-				</dependency>
-				<dependency>
-					<groupId>edu.uci.ics.hyracks</groupId>
-					<artifactId>hyracks-dataflow-common</artifactId>
-					<version>0.2.6-SNAPSHOT</version>
-					<type>jar</type>
-					<scope>compile</scope>
-				</dependency>
-				<dependency>
-					<groupId>edu.uci.ics.hyracks</groupId>
-					<artifactId>hyracks-data-std</artifactId>
-					<version>0.2.6-SNAPSHOT</version>
-				</dependency>
-				<dependency>
-					<groupId>edu.uci.ics.hyracks</groupId>
-					<artifactId>hyracks-control-cc</artifactId>
-					<version>0.2.6-SNAPSHOT</version>
-					<type>jar</type>
-					<scope>compile</scope>
-				</dependency>
-				<dependency>
-					<groupId>edu.uci.ics.hyracks</groupId>
-					<artifactId>hyracks-control-nc</artifactId>
-					<version>0.2.6-SNAPSHOT</version>
-					<type>jar</type>
-					<scope>compile</scope>
-				</dependency>
-				<dependency>
-					<groupId>com.kenai.nbpwr</groupId>
-					<artifactId>org-apache-commons-io</artifactId>
-					<version>1.3.1-201002241208</version>
-					<type>nbm</type>
-					<scope>test</scope>
-				</dependency>
-				<dependency>
-					<groupId>edu.uci.ics.hyracks.examples</groupId>
-					<artifactId>hyracks-integration-tests</artifactId>
-					<version>0.2.6-SNAPSHOT</version>
-					<scope>test</scope>
-				</dependency>
-				<dependency>
-					<groupId>edu.uci.ics.hyracks</groupId>
-					<artifactId>hyracks-ipc</artifactId>
-					<version>0.2.6-SNAPSHOT</version>
-					<type>jar</type>
-					<scope>compile</scope>
-				</dependency>
-				<dependency>
-					<groupId>org.apache.hadoop</groupId>
-					<artifactId>hadoop-core</artifactId>
-					<version>0.20.2</version>
-				</dependency>
-				<dependency>
-					<groupId>org.apache.hadoop</groupId>
-					<artifactId>hadoop-test</artifactId>
-					<version>0.20.2</version>
-				</dependency>
-				<dependency>
-					<groupId>edu.uci.ics.hyracks</groupId>
-					<artifactId>hyracks-hdfs-core</artifactId>
-					<version>0.2.6-SNAPSHOT</version>
-				</dependency>
-				<dependency>
-					<groupId>edu.uci.ics.hyracks</groupId>
-					<artifactId>hyracks-hdfs-core</artifactId>
-					<version>0.2.6-SNAPSHOT</version>
-					<type>test-jar</type>
-					<scope>test</scope>
-				</dependency>
-                <dependency>
-                	<groupId>edu.uci.ics.hyracks</groupId>
-                	<artifactId>genomix-hyracks</artifactId>
-                	<version>0.2.6-SNAPSHOT</version>
-                	<type>jar</type>
-                	<scope>compile</scope>
-                </dependency>
-                <dependency>
-                	<groupId>edu.uci.ics.hyracks</groupId>
-                	<artifactId>genomix-hadoop</artifactId>
-                	<version>0.2.6-SNAPSHOT</version>
-                	<type>jar</type>
-                	<scope>compile</scope>
-                </dependency>
-        </dependencies>
+	<dependencies>
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+			<version>4.8.1</version>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>edu.uci.ics.hyracks</groupId>
+			<artifactId>pregelix-core</artifactId>
+			<version>0.2.6-SNAPSHOT</version>
+			<type>jar</type>
+			<scope>compile</scope>
+		</dependency>
+		<dependency>
+			<groupId>edu.uci.ics.hyracks</groupId>
+			<artifactId>genomix-data</artifactId>
+			<version>0.2.6-SNAPSHOT</version>
+			<type>jar</type>
+			<scope>compile</scope>
+		</dependency>
+		<dependency>
+			<groupId>edu.uci.ics.hyracks</groupId>
+			<artifactId>hyracks-dataflow-std</artifactId>
+			<version>0.2.6-SNAPSHOT</version>
+			<type>jar</type>
+			<scope>compile</scope>
+		</dependency>
+		<dependency>
+			<groupId>edu.uci.ics.hyracks</groupId>
+			<artifactId>hyracks-api</artifactId>
+			<version>0.2.6-SNAPSHOT</version>
+			<type>jar</type>
+			<scope>compile</scope>
+		</dependency>
+		<dependency>
+			<groupId>edu.uci.ics.hyracks</groupId>
+			<artifactId>hyracks-dataflow-common</artifactId>
+			<version>0.2.6-SNAPSHOT</version>
+			<type>jar</type>
+			<scope>compile</scope>
+		</dependency>
+		<dependency>
+			<groupId>edu.uci.ics.hyracks</groupId>
+			<artifactId>hyracks-data-std</artifactId>
+			<version>0.2.6-SNAPSHOT</version>
+		</dependency>
+		<dependency>
+			<groupId>edu.uci.ics.hyracks</groupId>
+			<artifactId>hyracks-control-cc</artifactId>
+			<version>0.2.6-SNAPSHOT</version>
+			<type>jar</type>
+			<scope>compile</scope>
+		</dependency>
+		<dependency>
+			<groupId>edu.uci.ics.hyracks</groupId>
+			<artifactId>hyracks-control-nc</artifactId>
+			<version>0.2.6-SNAPSHOT</version>
+			<type>jar</type>
+			<scope>compile</scope>
+		</dependency>
+		<dependency>
+			<groupId>com.kenai.nbpwr</groupId>
+			<artifactId>org-apache-commons-io</artifactId>
+			<version>1.3.1-201002241208</version>
+			<type>nbm</type>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>edu.uci.ics.hyracks.examples</groupId>
+			<artifactId>hyracks-integration-tests</artifactId>
+			<version>0.2.6-SNAPSHOT</version>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>edu.uci.ics.hyracks</groupId>
+			<artifactId>hyracks-ipc</artifactId>
+			<version>0.2.6-SNAPSHOT</version>
+			<type>jar</type>
+			<scope>compile</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.hadoop</groupId>
+			<artifactId>hadoop-core</artifactId>
+			<version>0.20.2</version>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.hadoop</groupId>
+			<artifactId>hadoop-test</artifactId>
+			<version>0.20.2</version>
+		</dependency>
+		<dependency>
+			<groupId>edu.uci.ics.hyracks</groupId>
+			<artifactId>hyracks-hdfs-core</artifactId>
+			<version>0.2.6-SNAPSHOT</version>
+		</dependency>
+		<dependency>
+			<groupId>edu.uci.ics.hyracks</groupId>
+			<artifactId>hyracks-hdfs-core</artifactId>
+			<version>0.2.6-SNAPSHOT</version>
+			<type>test-jar</type>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>edu.uci.ics.hyracks</groupId>
+			<artifactId>genomix-hyracks</artifactId>
+			<version>0.2.6-SNAPSHOT</version>
+			<type>jar</type>
+			<scope>compile</scope>
+		</dependency>
+		<dependency>
+			<groupId>edu.uci.ics.hyracks</groupId>
+			<artifactId>genomix-hadoop</artifactId>
+			<version>0.2.6-SNAPSHOT</version>
+			<type>jar</type>
+			<scope>compile</scope>
+		</dependency>
+	</dependencies>
 
-  <scm>
-    <connection>scm:svn:https://hyracks.googlecode.com/svn/trunk/fullstack/pregelix</connection>
-    <developerConnection>scm:svn:https://hyracks.googlecode.com/svn/trunk/fullstack/pregelix</developerConnection>
-    <url>http://code.google.com/p/hyracks/source/browse/#svn/trunk/fullstack/pregelix</url>
-  </scm>
+	<scm>
+		<connection>scm:svn:https://hyracks.googlecode.com/svn/trunk/fullstack/pregelix</connection>
+		<developerConnection>scm:svn:https://hyracks.googlecode.com/svn/trunk/fullstack/pregelix</developerConnection>
+		<url>http://code.google.com/p/hyracks/source/browse/#svn/trunk/fullstack/pregelix</url>
+	</scm>
 
-  <distributionManagement>
-    <repository>
-      <id>hyracks-releases</id>
-      <url>http://obelix.ics.uci.edu/nexus/content/repositories/hyracks-releases/</url>
-    </repository>
-    <snapshotRepository>
-      <id>hyracks-snapshots</id>
-      <url>http://obelix.ics.uci.edu/nexus/content/repositories/hyracks-snapshots/</url>
-    </snapshotRepository>
-  </distributionManagement>
+	<distributionManagement>
+		<repository>
+			<id>hyracks-releases</id>
+			<url>http://obelix.ics.uci.edu/nexus/content/repositories/hyracks-releases/</url>
+		</repository>
+		<snapshotRepository>
+			<id>hyracks-snapshots</id>
+			<url>http://obelix.ics.uci.edu/nexus/content/repositories/hyracks-snapshots/</url>
+		</snapshotRepository>
+	</distributionManagement>
 
-  <reporting>
-    <plugins>
-      <plugin>
-        <groupId>org.apache.maven.plugins</groupId>
-        <artifactId>maven-changelog-plugin</artifactId>
-      </plugin>
-    </plugins>
-  </reporting>
+	<reporting>
+		<plugins>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-changelog-plugin</artifactId>
+			</plugin>
+		</plugins>
+	</reporting>
 
-  <repositories>
-    <repository>
-      <id>hyracks-public</id>
-      <url>http://obelix.ics.uci.edu/nexus/content/groups/hyracks-public/</url>
-    </repository>
-    <repository>
-      <id>jboss-public</id>
-      <url>https://repository.jboss.org/nexus/content/groups/public/</url>
-    </repository>
-  </repositories>
+	<repositories>
+		<repository>
+			<id>hyracks-public</id>
+			<url>http://obelix.ics.uci.edu/nexus/content/groups/hyracks-public/</url>
+		</repository>
+		<repository>
+			<id>jboss-public</id>
+			<url>https://repository.jboss.org/nexus/content/groups/public/</url>
+		</repository>
+	</repositories>
 
-  <pluginRepositories>
-    <pluginRepository>
-      <id>hyracks-public</id>
-      <url>http://obelix.ics.uci.edu/nexus/content/groups/hyracks-public/</url>
-      <releases>
-        <updatePolicy>always</updatePolicy>
-      </releases>
-    </pluginRepository>
-  </pluginRepositories>
+	<pluginRepositories>
+		<pluginRepository>
+			<id>hyracks-public</id>
+			<url>http://obelix.ics.uci.edu/nexus/content/groups/hyracks-public/</url>
+			<releases>
+				<updatePolicy>always</updatePolicy>
+			</releases>
+		</pluginRepository>
+	</pluginRepositories>
 </project>
 
 
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P1ForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P1ForPathMergeVertex.java
deleted file mode 100644
index f5b0157..0000000
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P1ForPathMergeVertex.java
+++ /dev/null
@@ -1,265 +0,0 @@
-package edu.uci.ics.genomix.pregelix.operator.pathmerge;
-
-import java.util.Iterator;
-import org.apache.hadoop.io.NullWritable;
-
-import edu.uci.ics.genomix.type.KmerBytesWritableFactory;
-
-import edu.uci.ics.pregelix.api.graph.Vertex;
-import edu.uci.ics.pregelix.api.job.PregelixJob;
-import edu.uci.ics.genomix.type.VKmerBytesWritable;
-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.MessageWritable;
-import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
-import edu.uci.ics.genomix.pregelix.io.VertexValueWritable.State;
-import edu.uci.ics.genomix.pregelix.type.Message;
-import edu.uci.ics.genomix.pregelix.util.VertexUtil;
-
-/*
- * vertexId: BytesWritable
- * vertexValue: ByteWritable
- * edgeValue: NullWritable
- * message: MessageWritable
- * 
- * DNA:
- * A: 00
- * C: 01
- * G: 10
- * T: 11
- * 
- * succeed node
- *  A 00000001 1
- *  G 00000010 2
- *  C 00000100 4
- *  T 00001000 8
- * precursor node
- *  A 00010000 16
- *  G 00100000 32
- *  C 01000000 64
- *  T 10000000 128
- *  
- * For example, ONE LINE in input file: 00,01,10	0001,0010,
- * That means that vertexId is ACG, its succeed node is A and its precursor node is C.
- * The succeed node and precursor node will be stored in vertexValue and we don't use edgeValue.
- * The details about message are in edu.uci.ics.pregelix.example.io.MessageWritable. 
- */
-/**
- * Naive Algorithm for path merge graph
- */
-public class P1ForPathMergeVertex extends
-        Vertex<VKmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> {
-    public static final String KMER_SIZE = "P1ForPathMergeVertex.kmerSize";
-    public static final String ITERATIONS = "P1ForPathMergeVertex.iteration";
-    public static int kmerSize = -1;
-    private int maxIteration = -1;
-
-    private MessageWritable incomingMsg = new MessageWritable();
-    private MessageWritable outgoingMsg = new MessageWritable();
-  
-    private KmerBytesWritableFactory kmerFactory = new KmerBytesWritableFactory(1);
-    private VKmerBytesWritable lastKmer = new VKmerBytesWritable();
-    
-    private VKmerBytesWritable destVertexId = new VKmerBytesWritable();
-    private Iterator<VKmerBytesWritable> posIterator;
-    
-    /**
-     * 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(VertexValueWritable value) {
-        if(value.getFFList().getCountOfPosition() > 0) // #FFList() > 0
-            posIterator = value.getFFList().iterator();
-        else // #FRList() > 0
-            posIterator = value.getFRList().iterator();
-        return posIterator.next();
-    }
-
-    public VKmerBytesWritable getPreDestVertexId(VertexValueWritable value) {
-        if(value.getRFList().getCountOfPosition() > 0) // #RFList() > 0
-            posIterator = value.getRFList().iterator();
-        else // #RRList() > 0
-            posIterator = value.getRRList().iterator();
-        return posIterator.next();
-    }
-
-    /**
-     * head send message to all next nodes
-     */
-    public void sendMsgToAllNextNodes(VertexValueWritable value) {
-        posIterator = value.getFFList().iterator(); // FFList
-        while(posIterator.hasNext()){
-            destVertexId.setAsCopy(posIterator.next());
-            sendMsg(destVertexId, outgoingMsg);
-        }
-        posIterator = value.getFRList().iterator(); // FRList
-        while(posIterator.hasNext()){
-            destVertexId.setAsCopy(posIterator.next());
-            sendMsg(destVertexId, outgoingMsg);
-        }
-    }
-
-    /**
-     * head send message to all previous nodes
-     */
-    public void sendMsgToAllPreviousNodes(VertexValueWritable value) {
-        posIterator = value.getRFList().iterator(); // RFList
-        while(posIterator.hasNext()){
-            destVertexId.setAsCopy(posIterator.next());
-            sendMsg(destVertexId, outgoingMsg);
-        }
-        posIterator = value.getRRList().iterator(); // RRList
-        while(posIterator.hasNext()){
-            destVertexId.setAsCopy(posIterator.next());
-            sendMsg(destVertexId, outgoingMsg);
-        }
-    }
-
-    /**
-     * start sending message
-     */
-    public void startSendMsg() {
-        if (VertexUtil.isHeadVertexWithIndegree(getVertexValue())) {
-            outgoingMsg.setFlag(Message.START);
-            sendMsgToAllNextNodes(getVertexValue());
-        }
-        if (VertexUtil.isRearVertexWithOutdegree(getVertexValue())) {
-            outgoingMsg.setFlag(Message.END);
-            sendMsgToAllPreviousNodes(getVertexValue());
-        }
-        if (VertexUtil.isHeadWithoutIndegree(getVertexValue())){
-            outgoingMsg.setFlag(Message.START);
-            sendMsg(getVertexId(), outgoingMsg); //send to itself
-        }
-        if (VertexUtil.isRearWithoutOutdegree(getVertexValue())){
-            outgoingMsg.setFlag(Message.END);
-            sendMsg(getVertexId(), outgoingMsg); //send to itself
-        }
-    }
-
-    /**
-     * initiate head, rear and path node
-     */
-    public void initState(Iterator<MessageWritable> msgIterator) {
-        while (msgIterator.hasNext()) {
-            if (!VertexUtil.isPathVertex(getVertexValue()) 
-                    && !VertexUtil.isHeadWithoutIndegree(getVertexValue())
-                    && !VertexUtil.isRearWithoutOutdegree(getVertexValue())) {
-                msgIterator.next();
-                voteToHalt();
-            } else {
-                incomingMsg = msgIterator.next();
-                setState();
-            }
-        }
-    }
-
-    /**
-     * set vertex state
-     */
-    public void setState() {
-        if (incomingMsg.getFlag() == Message.START) {
-            getVertexValue().setState(State.IS_HEAD);
-        } else if (incomingMsg.getFlag() == Message.END && getVertexValue().getState() != State.IS_HEAD) {
-            getVertexValue().setState(State.IS_HEAD);//is tail
-            voteToHalt();
-        } else
-            voteToHalt();
-    }
-    
-    /**
-     * merge chainVertex and store in vertexVal.chainVertexId
-     */
-    public void mergeChainVertex() {
-        //merge chain
-        lastKmer.setAsCopy(kmerFactory.getLastKmerFromChain(incomingMsg.getLengthOfChain() - kmerSize + 1,
-                incomingMsg.getActualKmer()));
-        getVertexValue().setActualKmer(kmerFactory.mergeTwoKmer(getVertexValue().getActualKmer(), lastKmer));
-        getVertexValue().setOutgoingList(incomingMsg.getNeighberNode());
-    }
-
-    /**
-     * head node sends message to path node
-     */
-    public void sendMsgToPathVertex(Iterator<MessageWritable> msgIterator) {
-        if (getSuperstep() == 3) {
-            outgoingMsg.setSourceVertexId(getVertexId());
-            destVertexId.setAsCopy(getNextDestVertexId(getVertexValue()));
-            sendMsg(destVertexId, outgoingMsg);
-        } else {
-            while (msgIterator.hasNext()) {
-                incomingMsg = msgIterator.next();
-                if (incomingMsg.getFlag() != Message.STOP) {
-                    mergeChainVertex();
-                    outgoingMsg.setSourceVertexId(getVertexId());
-                    destVertexId.setAsCopy(getNextDestVertexId(getVertexValue()));
-                    sendMsg(destVertexId, outgoingMsg);
-                } else {
-                    mergeChainVertex();
-                    getVertexValue().setState(State.IS_FINAL);
-                    //String source = getVertexValue().getKmer().toString();
-                    //System.out.println();
-                }
-            }
-        }
-    }
-
-    /**
-     * path node sends message back to head node
-     */
-    public void responseMsgToHeadVertex() {
-        deleteVertex(getVertexId());
-        outgoingMsg.setNeighberNode(getVertexValue().getOutgoingList());
-        outgoingMsg.setActualKmer(getVertexValue().getActualKmer());
-        if (getVertexValue().getState() == State.IS_HEAD)//is_tail
-            outgoingMsg.setFlag(Message.STOP);
-        destVertexId.setAsCopy(incomingMsg.getSourceVertexId());
-        sendMsg(destVertexId, outgoingMsg);
-    }
-
-    @Override
-    public void compute(Iterator<MessageWritable> 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();
-        } else
-            voteToHalt();
-    }
-
-    public static void main(String[] args) throws Exception {
-        PregelixJob job = new PregelixJob(P1ForPathMergeVertex.class.getSimpleName());
-        job.setVertexClass(P1ForPathMergeVertex.class);
-        /**
-         * BinaryInput and BinaryOutput
-         */
-        job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class);
-        job.setVertexOutputFormatClass(NaiveAlgorithmForPathMergeOutputFormat.class);
-        job.setDynamicVertexValueSize(true);
-        job.setOutputKeyClass(VKmerBytesWritable.class);
-        job.setOutputValueClass(VertexValueWritable.class);
-        Client.run(args, job);
-    }
-}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P3ForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P3ForPathMergeVertex.java
deleted file mode 100644
index 9a3aed5..0000000
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P3ForPathMergeVertex.java
+++ /dev/null
@@ -1,414 +0,0 @@
-package edu.uci.ics.genomix.pregelix.operator.pathmerge;
-
-import java.util.Iterator;
-import org.apache.hadoop.io.NullWritable;
-
-import edu.uci.ics.genomix.type.KmerBytesWritableFactory;
-import edu.uci.ics.genomix.type.VKmerBytesWritable;
-
-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.MessageWritable;
-import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
-import edu.uci.ics.genomix.pregelix.type.Message;
-import edu.uci.ics.genomix.pregelix.type.State2;
-import edu.uci.ics.genomix.pregelix.util.VertexUtil;
-
-/*
- * vertexId: BytesWritable
- * vertexValue: ByteWritable
- * edgeValue: NullWritable
- * message: MessageWritable
- * 
- * DNA:
- * A: 00
- * C: 01
- * G: 10
- * T: 11
- * 
- * succeed node
- *  A 00000001 1
- *  G 00000010 2
- *  C 00000100 4
- *  T 00001000 8
- * precursor node
- *  A 00010000 16
- *  G 00100000 32
- *  C 01000000 64
- *  T 10000000 128
- *  
- * For example, ONE LINE in input file: 00,01,10	0001,0010,
- * That means that vertexId is ACG, its succeed node is A and its precursor node is C.
- * The succeed node and precursor node will be stored in vertexValue and we don't use edgeValue.
- * The details about message are in edu.uci.ics.pregelix.example.io.MessageWritable. 
- */
-/**
- * Naive Algorithm for path merge graph
- */
-public class P3ForPathMergeVertex extends
-        Vertex<VKmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> {
-    public static final String KMER_SIZE = "P3ForPathMergeVertex.kmerSize";
-    public static final String ITERATIONS = "P3ForPathMergeVertex.iteration";
-    public static final String PSEUDORATE = "P3ForPathMergeVertex.pseudoRate";
-    public static final String MAXROUND = "P3ForPathMergeVertex.maxRound";
-    public static int kmerSize = -1;
-    private int maxIteration = -1;
-    public static float pseudoRate = -1;
-    public static int maxRound = -1;
-
-    private MessageWritable incomingMsg = new MessageWritable();
-    private MessageWritable outgoingMsg = new MessageWritable();
-
-    private KmerBytesWritableFactory kmerFactory = new KmerBytesWritableFactory(1);
-    private VKmerBytesWritable lastKmer = new VKmerBytesWritable(1);
-
-    private VKmerBytesWritable destVertexId = new VKmerBytesWritable();
-    private Iterator<VKmerBytesWritable> posIterator;
-    /**
-     * 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(pseudoRate < 0)
-            pseudoRate = getContext().getConfiguration().getFloat(PSEUDORATE, 0.2f);
-        if (maxRound < 0)
-            maxRound = getContext().getConfiguration().getInt(MAXROUND, 2);
-        outgoingMsg.reset();
-    }
-
-    /**
-     * get destination vertex
-     */
-    public VKmerBytesWritable getNextDestVertexId(VertexValueWritable value) {
-        if(value.getFFList().getCountOfPosition() > 0) // #FFList() > 0
-            posIterator = value.getFFList().iterator();
-        else // #FRList() > 0
-            posIterator = value.getFRList().iterator();
-        return posIterator.next();
-    }
-
-    public VKmerBytesWritable getPreDestVertexId(VertexValueWritable value) {
-        if(value.getRFList().getCountOfPosition() > 0) // #RFList() > 0
-            posIterator = value.getRFList().iterator();
-        else // #RRList() > 0
-            posIterator = value.getRRList().iterator();
-        return posIterator.next();
-    }
-
-    /**
-     * head send message to all next nodes
-     */
-    public void sendMsgToAllNextNodes(VertexValueWritable value) {
-        posIterator = value.getFFList().iterator(); // FFList
-        while(posIterator.hasNext()){
-            destVertexId.setAsCopy(posIterator.next());
-            sendMsg(destVertexId, outgoingMsg);
-        }
-        posIterator = value.getFRList().iterator(); // FRList
-        while(posIterator.hasNext()){
-            destVertexId.setAsCopy(posIterator.next());
-            sendMsg(destVertexId, outgoingMsg);
-        }
-    }
-
-    /**
-     * head send message to all previous nodes
-     */
-    public void sendMsgToAllPreviousNodes(VertexValueWritable value) {
-        posIterator = value.getRFList().iterator(); // RFList
-        while(posIterator.hasNext()){
-            destVertexId.setAsCopy(posIterator.next());
-            sendMsg(destVertexId, outgoingMsg);
-        }
-        posIterator = value.getRRList().iterator(); // RRList
-        while(posIterator.hasNext()){
-            destVertexId.setAsCopy(posIterator.next());
-            sendMsg(destVertexId, outgoingMsg);
-        }
-    }
-
-    /**
-     * start sending message
-     */
-    public void startSendMsg() {
-        if (VertexUtil.isHeadVertexWithIndegree(getVertexValue())) {
-            outgoingMsg.setFlag(Message.START);
-            sendMsgToAllNextNodes(getVertexValue());
-        }
-        if (VertexUtil.isRearVertexWithOutdegree(getVertexValue())) {
-            outgoingMsg.setFlag(Message.END);
-            sendMsgToAllPreviousNodes(getVertexValue());
-        }
-        if (VertexUtil.isHeadWithoutIndegree(getVertexValue())){
-            outgoingMsg.setFlag(Message.START);
-            sendMsg(getVertexId(), outgoingMsg); //send to itself
-        }
-        if (VertexUtil.isRearWithoutOutdegree(getVertexValue())){
-            outgoingMsg.setFlag(Message.END);
-            sendMsg(getVertexId(), outgoingMsg); //send to itself
-        }
-    }
-    
-    /**
-     * initiate head, rear and path node
-     */
-    public void initState(Iterator<MessageWritable> msgIterator) {
-        if (msgIterator.hasNext()) {
-            do {
-                if (!VertexUtil.isPathVertex(getVertexValue())
-                        && !VertexUtil.isHeadWithoutIndegree(getVertexValue())
-                        && !VertexUtil.isRearWithoutOutdegree(getVertexValue())) {
-                    msgIterator.next();
-                    voteToHalt();
-                } else {
-                    incomingMsg = msgIterator.next();
-                    setState();
-                }
-            } while (msgIterator.hasNext());
-        } else {
-            float random = (float) Math.random();
-            if (random < pseudoRate)
-                markPseudoHead();
-            else{
-                getVertexValue().setState(State2.NON_VERTEX);
-                voteToHalt();
-            }
-            /*if (getVertexId().toString().equals("CCTCA") || getVertexId().toString().equals("CTCAG")) //AGTAC CCTCA CTCAG CGCCC ACGCC
-                markPseudoHead();
-            else
-                voteToHalt();*/
-        }
-    }
-    
-    /**
-     * set vertex state
-     */
-    public void setState() {
-        if (incomingMsg.getFlag() == Message.START) {
-            getVertexValue().setState(State2.START_VERTEX);
-        } else if (incomingMsg.getFlag() == Message.END && getVertexValue().getState() != State2.START_VERTEX) {
-            getVertexValue().setState(State2.END_VERTEX);
-            voteToHalt();
-        } else
-            voteToHalt();
-    }
-   
-    /**
-     * mark the pseudoHead
-     */
-    public void markPseudoHead() {
-        getVertexValue().setState(State2.PSEUDOHEAD);
-        outgoingMsg.setFlag(Message.FROMPSEUDOHEAD);
-        destVertexId.setAsCopy(getPreDestVertexId(getVertexValue()));
-        sendMsg(destVertexId, outgoingMsg);
-    }
-
-    /**
-     * mark the pseudoRear
-     */
-    public void markPseudoRear() {
-        if (incomingMsg.getFlag() == Message.FROMPSEUDOHEAD 
-                && getVertexValue().getState() != State2.START_VERTEX) {
-            getVertexValue().setState(State2.PSEUDOREAR);
-            voteToHalt();
-        }
-        else if(incomingMsg.getFlag() == Message.FROMPSEUDOHEAD 
-                && getVertexValue().getState() == State2.START_VERTEX){
-            getVertexValue().setState(State2.START_HALT);
-        }
-    }
- 
-    /**
-     * merge chain vertex
-     */
-    public void mergeChainVertex(){
-        lastKmer.setAsCopy(kmerFactory.getLastKmerFromChain(incomingMsg.getLengthOfChain() - kmerSize + 1,
-                incomingMsg.getActualKmer()));
-        getVertexValue().setActualKmer(
-                kmerFactory.mergeTwoKmer(getVertexValue().getActualKmer(), 
-                        lastKmer));
-        getVertexValue().setOutgoingList(incomingMsg.getNeighberNode());
-    }
-    
-    /**
-     * head node sends message to path node
-     */
-    public void sendMsgToPathVertexMergePhase(Iterator<MessageWritable> msgIterator) {
-        if (getSuperstep() == 3 + 2 * maxRound + 2) {
-            outgoingMsg.setSourceVertexId(getVertexId());
-            destVertexId.setAsCopy(getNextDestVertexId(getVertexValue()));
-            sendMsg(destVertexId, outgoingMsg);
-        } else {
-            while (msgIterator.hasNext()) {
-                incomingMsg = msgIterator.next();
-                if (incomingMsg.getFlag() != Message.STOP) {
-                    mergeChainVertex();
-                    outgoingMsg.setSourceVertexId(getVertexId());
-                    destVertexId.setAsCopy(getNextDestVertexId(getVertexValue()));
-                    sendMsg(destVertexId, outgoingMsg);
-                } else {
-                    mergeChainVertex();
-                    getVertexValue().setState(State2.FINAL_VERTEX);
-                    //String source = getVertexValue().getKmer().toString();
-                    //System.out.println();
-                }
-            }
-        }
-    }
-
-    /**
-     * path node sends message back to head node
-     */
-    public void responseMsgToHeadVertexMergePhase() {
-        deleteVertex(getVertexId());
-        outgoingMsg.setNeighberNode(getVertexValue().getOutgoingList());
-        outgoingMsg.setActualKmer(getVertexValue().getActualKmer());
-        if (getVertexValue().getState() == State2.END_VERTEX)
-            outgoingMsg.setFlag(Message.STOP);
-        sendMsg(incomingMsg.getSourceVertexId(), outgoingMsg);
-    }
-    
-    /**
-     * head node sends message to path node in partition phase
-     */
-    public void sendMsgToPathVertexPartitionPhase(Iterator<MessageWritable> msgIterator) {
-        if (getSuperstep() == 4) {
-            if(getVertexValue().getState() != State2.START_HALT){
-                outgoingMsg.setSourceVertexId(getVertexId());
-                destVertexId.setAsCopy(getNextDestVertexId(getVertexValue()));
-                sendMsg(destVertexId, outgoingMsg);
-                voteToHalt();
-            }
-        } else {
-            while (msgIterator.hasNext()) {
-                incomingMsg = msgIterator.next();
-                //if from pseudoHead, voteToHalt(), otherwise ...
-                if (incomingMsg.getFlag() != Message.FROMPSEUDOHEAD){
-                    mergeChainVertex();
-                    if (incomingMsg.getFlag() != Message.STOP 
-                            && incomingMsg.getFlag() != Message.FROMPSEUDOREAR) {
-                        outgoingMsg.setSourceVertexId(getVertexId());
-                        destVertexId.setAsCopy(getNextDestVertexId(getVertexValue()));
-                        sendMsg(destVertexId, outgoingMsg);
-                        voteToHalt();
-                    } else {
-                        //check head or pseudoHead
-                        if (getVertexValue().getState() == State2.START_VERTEX
-                                && incomingMsg.getFlag() == Message.STOP) {
-                            getVertexValue().setState(State2.FINAL_VERTEX);
-                            //String source = getVertexValue().getKmer().toString();
-                            //System.out.println();
-                        } else if(getVertexValue().getState() == State2.PSEUDOHEAD
-                                && incomingMsg.getFlag() == Message.STOP)
-                            getVertexValue().setState(State2.END_VERTEX);
-                    }
-                }
-            }
-        }
-    }
-
-    /**
-     * path node sends message back to head node in partition phase
-     */
-    public void responseMsgToHeadVertexPartitionPhase() {
-        if (getVertexValue().getState() == State2.PSEUDOHEAD)
-            outgoingMsg.setFlag(Message.FROMPSEUDOHEAD);
-        else {
-            deleteVertex(getVertexId());
-            outgoingMsg.setNeighberNode(getVertexValue().getOutgoingList()); //incomingMsg.getNeighberNode()
-            outgoingMsg.setActualKmer(getVertexValue().getActualKmer());
-            if (getVertexValue().getState() == State2.PSEUDOREAR)
-                outgoingMsg.setFlag(Message.FROMPSEUDOREAR);
-            else if (getVertexValue().getState() == State2.END_VERTEX)
-                outgoingMsg.setFlag(Message.STOP);
-        }
-        sendMsg(incomingMsg.getSourceVertexId(), outgoingMsg);
-        voteToHalt();
-    }
-    
-    /**
-     * final process the result of partition phase
-     */
-    public void finalProcessPartitionPhase(Iterator<MessageWritable> msgIterator){
-        while (msgIterator.hasNext()) {
-            incomingMsg = msgIterator.next();
-            mergeChainVertex();
-            getVertexValue().setOutgoingList(incomingMsg.getNeighberNode());
-            //check head or pseudoHead
-            if (getVertexValue().getState() == State2.START_VERTEX
-                    && incomingMsg.getFlag() == Message.STOP) {
-                getVertexValue().setState(State2.FINAL_VERTEX);
-                //String source = getVertexValue().getKmer().toString();
-                //System.out.println();
-            } else if(getVertexValue().getState() == State2.PSEUDOHEAD
-                    && incomingMsg.getFlag() == Message.STOP)
-                getVertexValue().setState(State2.END_VERTEX);
-        }
-    }
-    /**
-     * After partition phase, reset state: ex. psudoHead and psudoRear -> null
-     */
-    public void resetState() {
-        if (getVertexValue().getState() == State2.PSEUDOHEAD || getVertexValue().getState() == State2.PSEUDOREAR) {
-            getVertexValue().setState(State2.NON_VERTEX);
-        }
-        if(getVertexValue().getState() == State2.START_HALT)
-            getVertexValue().setState(State2.START_VERTEX);
-    }
-
-    @Override
-    public void compute(Iterator<MessageWritable> msgIterator) {
-        initVertex();
-        if (getSuperstep() == 1)
-            startSendMsg();
-        else if (getSuperstep() == 2)
-            initState(msgIterator);
-        else if (getSuperstep() == 3) {
-            if (msgIterator.hasNext()) {
-                incomingMsg = msgIterator.next();
-                markPseudoRear();
-            }
-        } else if (getSuperstep() % 2 == 0 && getSuperstep() <= 3 + 2 * maxRound && getSuperstep() <= maxIteration) {
-            sendMsgToPathVertexPartitionPhase(msgIterator);
-        } else if (getSuperstep() % 2 == 1 && getSuperstep() <= 3 + 2 * maxRound && getSuperstep() <= maxIteration) {
-            while (msgIterator.hasNext()) {
-                incomingMsg = msgIterator.next();
-                responseMsgToHeadVertexPartitionPhase();
-            }
-        } else if(getSuperstep() == 3 + 2 * maxRound + 1 && getSuperstep() <= maxIteration){
-            finalProcessPartitionPhase(msgIterator);
-        } else if (getSuperstep() % 2 == 1 && getSuperstep() <= maxIteration) {
-            resetState();
-            if(getVertexValue().getState() == State2.START_VERTEX)
-                sendMsgToPathVertexMergePhase(msgIterator);
-            voteToHalt();
-        } else if (getSuperstep() % 2 == 0 && getSuperstep() <= maxIteration) {
-            while (msgIterator.hasNext()) {
-                incomingMsg = msgIterator.next();
-                responseMsgToHeadVertexMergePhase();
-            }
-            voteToHalt();
-        } else
-            voteToHalt();
-    }
-
-    public static void main(String[] args) throws Exception {
-        PregelixJob job = new PregelixJob(P3ForPathMergeVertex.class.getSimpleName());
-        job.setVertexClass(P3ForPathMergeVertex.class);
-        /**
-         * BinaryInput and BinaryOutput
-         */
-        job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class);
-        job.setVertexOutputFormatClass(NaiveAlgorithmForPathMergeOutputFormat.class);
-        job.setDynamicVertexValueSize(true);
-        job.setOutputKeyClass(VKmerBytesWritable.class);
-        job.setOutputValueClass(VertexValueWritable.class);
-        Client.run(args, job);
-    }
-}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P5ForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P5ForPathMergeVertex.java
deleted file mode 100644
index 0a43a96..0000000
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P5ForPathMergeVertex.java
+++ /dev/null
@@ -1,501 +0,0 @@
-package edu.uci.ics.genomix.pregelix.operator.pathmerge;
-
-import java.io.IOException;
-import java.util.Iterator;
-import java.util.Random;
-
-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.type.VKmerBytesWritable;
-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.MessageWritable;
-import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
-import edu.uci.ics.genomix.pregelix.io.VertexValueWritable.State;
-import edu.uci.ics.genomix.pregelix.type.Message;
-import edu.uci.ics.genomix.pregelix.type.MessageFlag;
-import edu.uci.ics.genomix.pregelix.util.VertexUtil;
-
-/*
- * vertexId: BytesWritable
- * vertexValue: ByteWritable
- * edgeValue: NullWritable
- * message: MessageWritable
- * 
- * DNA:
- * A: 00
- * C: 01
- * G: 10
- * T: 11
- * 
- * succeed node
- *  A 00000001 1
- *  G 00000010 2
- *  C 00000100 4
- *  T 00001000 8
- * precursor node
- *  A 00010000 16
- *  G 00100000 32
- *  C 01000000 64
- *  T 10000000 128
- *  
- * For example, ONE LINE in input file: 00,01,10    0001,0010,
- * That means that vertexId is ACG, its succeed node is A and its precursor node is C.
- * The succeed node and precursor node will be stored in vertexValue and we don't use edgeValue.
- * The details about message are in edu.uci.ics.pregelix.example.io.MessageWritable. 
- */
-/**
- * Naive Algorithm for path merge graph
- */
-public class P5ForPathMergeVertex extends
-        Vertex<VKmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> {
-    public static final String KMER_SIZE = "P5ForPathMergeVertex.kmerSize";
-    public static final String ITERATIONS = "P5ForPathMergeVertex.iteration";
-    public static final String RANDSEED = "P5ForPathMergeVertex.randSeed";
-    public static final String PROBBEINGRANDOMHEAD = "P4ForPathMergeVertex.probBeingRandomHead";
-    public static int kmerSize = -1;
-    private int maxIteration = -1;
-
-    private static long randSeed = -1;
-    private float probBeingRandomHead = -1;
-    private Random randGenerator;
-    
-    private VKmerBytesWritable curID = new VKmerBytesWritable();
-    private VKmerBytesWritable nextID = new VKmerBytesWritable();
-    private VKmerBytesWritable prevID = new VKmerBytesWritable();
-    private boolean hasNext;
-    private boolean hasPrev;
-    private boolean curHead;
-    private boolean nextHead;
-    private boolean prevHead;
-    private byte headFlag;
-    private byte tailFlag;
-    private byte outFlag;
-    
-    private MessageWritable incomingMsg = new MessageWritable();
-    private MessageWritable outgoingMsg = new MessageWritable();
-    private VKmerBytesWritable destVertexId = new VKmerBytesWritable();
-    private Iterator<VKmerBytesWritable> posIterator;
-    
-    /**
-     * 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 (randSeed < 0)
-            randSeed = getContext().getConfiguration().getLong("randomSeed", 0);
-        randGenerator = new Random(randSeed);
-        if (probBeingRandomHead < 0)
-            probBeingRandomHead = getContext().getConfiguration().getFloat("probBeingRandomHead", 0.5f);
-        hasNext = false;
-        hasPrev = false;
-        curHead = false;
-        nextHead = false;
-        prevHead = false;
-        outgoingMsg.reset();
-    }
-
-    protected boolean isNodeRandomHead(VKmerBytesWritable nodeID) {
-        // "deterministically random", based on node id
-        randGenerator.setSeed(randSeed ^ nodeID.hashCode());
-        return randGenerator.nextFloat() < probBeingRandomHead;
-    }
-
-    /**
-     * set nextID to the element that's next (in the node's FF or FR list), returning true when there is a next neighbor
-     */
-    protected boolean setNextInfo(VertexValueWritable value) {
-        if (value.getFFList().getCountOfPosition() > 0) {
-            nextID.setAsCopy(value.getFFList().getPosition(0));
-            nextHead = isNodeRandomHead(nextID);
-            return true;
-        }
-        if (value.getFRList().getCountOfPosition() > 0) {
-            nextID.setAsCopy(value.getFRList().getPosition(0));
-            nextHead = isNodeRandomHead(nextID);
-            return true;
-        }
-        return false;
-    }
-
-    /**
-     * set prevID to the element that's previous (in the node's RR or RF list), returning true when there is a previous neighbor
-     */
-    protected boolean setPrevInfo(VertexValueWritable value) {
-        if (value.getRRList().getCountOfPosition() > 0) {
-            prevID.setAsCopy(value.getRRList().getPosition(0));
-            prevHead = isNodeRandomHead(prevID);
-            return true;
-        }
-        if (value.getRFList().getCountOfPosition() > 0) {
-            prevID.setAsCopy(value.getRFList().getPosition(0));
-            prevHead = isNodeRandomHead(prevID);
-            return true;
-        }
-        return false;
-    }
-    
-    /**
-     * get destination vertex
-     */
-    public VKmerBytesWritable getNextDestVertexId(VertexValueWritable value) {
-        if(value.getFFList().getCountOfPosition() > 0) // #FFList() > 0
-            posIterator = value.getFFList().iterator();
-        else // #FRList() > 0
-            posIterator = value.getFRList().iterator();
-        return posIterator.next();
-    }
-
-    public VKmerBytesWritable getPreDestVertexId(VertexValueWritable value) {
-        if(value.getRFList().getCountOfPosition() > 0) // #RFList() > 0
-            posIterator = value.getRFList().iterator();
-        else // #RRList() > 0
-            posIterator = value.getRRList().iterator();
-        return posIterator.next();
-    }
-
-    /**
-     * head send message to all next nodes
-     */
-    public void sendMsgToAllNextNodes(VertexValueWritable value) {
-        posIterator = value.getFFList().iterator(); // FFList
-        while(posIterator.hasNext()){
-            destVertexId.setAsCopy(posIterator.next());
-            sendMsg(destVertexId, outgoingMsg);
-        }
-        posIterator = value.getFRList().iterator(); // FRList
-        while(posIterator.hasNext()){
-            destVertexId.setAsCopy(posIterator.next());
-            sendMsg(destVertexId, outgoingMsg);
-        }
-    }
-
-    /**
-     * head send message to all previous nodes
-     */
-    public void sendMsgToAllPreviousNodes(VertexValueWritable value) {
-        posIterator = value.getRFList().iterator(); // RFList
-        while(posIterator.hasNext()){
-            destVertexId.setAsCopy(posIterator.next());
-            sendMsg(destVertexId, outgoingMsg);
-        }
-        posIterator = value.getRRList().iterator(); // RRList
-        while(posIterator.hasNext()){
-            destVertexId.setAsCopy(posIterator.next());
-            sendMsg(destVertexId, outgoingMsg);
-        }
-    }
-
-    /**
-     * start sending message
-     */
-    public void startSendMsg() {
-        if (VertexUtil.isHeadVertexWithIndegree(getVertexValue())) {
-            outgoingMsg.setFlag(Message.START);
-            sendMsgToAllNextNodes(getVertexValue());
-            voteToHalt();
-        }
-        if (VertexUtil.isRearVertexWithOutdegree(getVertexValue())) {
-            outgoingMsg.setFlag(Message.END);
-            sendMsgToAllPreviousNodes(getVertexValue());
-            voteToHalt();
-        }
-        if (VertexUtil.isHeadWithoutIndegree(getVertexValue())){
-            outgoingMsg.setFlag(Message.START);
-            sendMsg(getVertexId(), outgoingMsg); //send to itself
-            voteToHalt();
-        }
-        if (VertexUtil.isRearWithoutOutdegree(getVertexValue())){
-            outgoingMsg.setFlag(Message.END);
-            sendMsg(getVertexId(), outgoingMsg); //send to itself
-            voteToHalt();
-        }
-    }
-
-    /**
-     * initiate head, rear and path node
-     */
-    public void initState(Iterator<MessageWritable> msgIterator) {
-        while (msgIterator.hasNext()) {
-            if (!VertexUtil.isPathVertex(getVertexValue())
-                    && !VertexUtil.isHeadWithoutIndegree(getVertexValue())
-                    && !VertexUtil.isRearWithoutOutdegree(getVertexValue())) {
-                msgIterator.next();
-                voteToHalt();
-            } else {
-                incomingMsg = msgIterator.next();
-                setState();
-            }
-        }
-    }
-
-    /**
-     * set vertex state
-     */
-    public void setState() {
-        if (incomingMsg.getFlag() == Message.START) {
-            getVertexValue().setState(MessageFlag.IS_HEAD); //State.START_VERTEX
-        } else if (incomingMsg.getFlag() == Message.END && getVertexValue().getState() != State.IS_HEAD) {
-            getVertexValue().setState(MessageFlag.IS_HEAD);
-            getVertexValue().setActualKmer(getVertexValue().getActualKmer());
-            //voteToHalt();
-        } //else
-            //voteToHalt();
-    }
-    
-    /**
-     * check if A need to be flipped with successor
-     */
-    public boolean ifFilpWithSuccessor(){
-        if(getVertexValue().getFRList().getLength() > 0)
-            return true;
-        else
-            return false;
-    }
-    
-    /**
-     * check if A need to be filpped with predecessor
-     */
-    public boolean ifFlipWithPredecessor(){
-        if(getVertexValue().getRFList().getLength() > 0)
-            return true;
-        else
-            return false;
-    }
-    
-    /**
-     * set adjMessage to successor(from predecessor)
-     */
-    public void setSuccessorAdjMsg(){
-        if(getVertexValue().getFFList().getLength() > 0)
-            outFlag |= MessageFlag.DIR_FF;
-        else
-            outFlag |= MessageFlag.DIR_FR;
-    }
-    
-    /**
-     * set adjMessage to predecessor(from successor)
-     */
-    public void setPredecessorAdjMsg(){
-        if(getVertexValue().getRFList().getLength() > 0)
-            outFlag |= MessageFlag.DIR_RF;
-        else
-            outFlag |= MessageFlag.DIR_RF;
-    }
-    
-    /**
-     * send update message to neighber
-     * @throws IOException 
-     */
-    public void broadcastUpdateMsg(){
-       /* switch(getVertexValue().getState() & 0b0001){
-            case MessageFlag.SHOULD_MERGEWITHPREV:
-                setSuccessorAdjMsg();
-                if(ifFlipWithPredecessor())
-                    outFlag |= MessageFlag.FLIP;
-                outgoingMsg.setFlag(outFlag);
-                outgoingMsg.setNeighberNode(getVertexValue().getIncomingList());
-                outgoingMsg.setSourceVertexId(getVertexId());
-                sendMsg(getNextDestVertexId(getVertexValue()), outgoingMsg);
-                break;
-            case MessageFlag.SHOULD_MERGEWITHNEXT:
-                setPredecessorAdjMsg();
-                if(ifFilpWithSuccessor())
-                    outFlag |= MessageFlag.FLIP;
-                outgoingMsg.setFlag(outFlag);
-                outgoingMsg.setNeighberNode(getVertexValue().getOutgoingList());
-                outgoingMsg.setSourceVertexId(getVertexId());
-                sendMsg(getPreDestVertexId(getVertexValue()), outgoingMsg);
-                break; 
-        }*/
-    }
-    
-    /**
-     * This vertex tries to merge with next vertex and send update msg to neighber
-     * @throws IOException 
-     */
-    public void sendUpMsgFromPredecessor(){
-        byte state = getVertexValue().getState();
-        state |= MessageFlag.SHOULD_MERGEWITHNEXT;
-        getVertexValue().setState(state);
-        if(getVertexValue().getFFList().getLength() > 0)
-            getVertexValue().setMergeDest(getVertexValue().getFFList().getPosition(0));
-        else
-            getVertexValue().setMergeDest(getVertexValue().getFRList().getPosition(0));
-        broadcastUpdateMsg();
-    }
-    
-    /**
-     * This vertex tries to merge with next vertex and send update msg to neighber
-     * @throws IOException 
-     */
-    public void sendUpMsgFromSuccessor(){
-        byte state = getVertexValue().getState();
-        state |= MessageFlag.SHOULD_MERGEWITHPREV;
-        getVertexValue().setState(state);
-        if(getVertexValue().getRFList().getLength() > 0)
-            getVertexValue().setMergeDest(getVertexValue().getRFList().getPosition(0));
-        else
-            getVertexValue().setMergeDest(getVertexValue().getRRList().getPosition(0));
-        broadcastUpdateMsg();
-    }
-    
-    /**
-     * Returns the edge dir for B->A when the A->B edge is type @dir
-     */
-    public byte mirrorDirection(byte dir) {
-        switch (dir) {
-            case MessageFlag.DIR_FF:
-                return MessageFlag.DIR_RR;
-            case MessageFlag.DIR_FR:
-                return MessageFlag.DIR_FR;
-            case MessageFlag.DIR_RF:
-                return MessageFlag.DIR_RF;
-            case MessageFlag.DIR_RR:
-                return MessageFlag.DIR_FF;
-            default:
-                throw new RuntimeException("Unrecognized direction in flipDirection: " + dir);
-        }
-    }
-    
-    /**
-     * check if need filp
-     */
-    public byte flipDirection(byte neighborDir, boolean flip){
-        if(flip){
-            switch (neighborDir) {
-                case MessageFlag.DIR_FF:
-                    return MessageFlag.DIR_FR;
-                case MessageFlag.DIR_FR:
-                    return MessageFlag.DIR_FF;
-                case MessageFlag.DIR_RF:
-                    return MessageFlag.DIR_RR;
-                case MessageFlag.DIR_RR:
-                    return MessageFlag.DIR_RF;
-                default:
-                    throw new RuntimeException("Unrecognized direction for neighborDir: " + neighborDir);
-            }
-        } else 
-            return neighborDir;
-    }
-    
-    /**
-     * updateAdjList
-     */
-    public void processUpdate(){
-        /*byte meToNeighborDir = (byte) (incomingMsg.getFlag() & MessageFlag.DIR_MASK);
-        byte neighborToMeDir = mirrorDirection(meToNeighborDir);
-        
-        boolean flip;
-        if((outFlag & MessageFlag.FLIP) > 0)
-            flip = true;
-        else
-            flip = false;
-        byte neighborToMergeDir = flipDirection(neighborToMeDir, flip);
-        
-        getVertexValue().processUpdates(neighborToMeDir, incomingMsg.getSourceVertexId(), 
-                neighborToMergeDir, VertexUtil.getNodeIdFromAdjacencyList(incomingMsg.getNeighberNode()));*/
-    }
-    
-    /**
-     * merge and updateAdjList
-     */
-    public void processMerge(){
-        /*byte meToNeighborDir = (byte) (incomingMsg.getFlag() & MessageFlag.DIR_MASK);
-        byte neighborToMeDir = mirrorDirection(meToNeighborDir);
-        
-        boolean flip;
-        if((outFlag & MessageFlag.FLIP) > 0)
-            flip = true;
-        else
-            flip = false;
-        byte neighborToMergeDir = flipDirection(neighborToMeDir, flip);
-        
-        getVertexValue().processMerges(neighborToMeDir, incomingMsg.getSourceVertexId(), 
-                neighborToMergeDir, VertexUtil.getNodeIdFromAdjacencyList(incomingMsg.getNeighberNode()),
-                kmerSize, incomingMsg.getKmer());*/
-    }
-    
-    @Override
-    public void compute(Iterator<MessageWritable> msgIterator) {
-        initVertex();
-        if (getSuperstep() == 1)
-            startSendMsg();
-        else if (getSuperstep() == 2)
-            initState(msgIterator);
-        else if (getSuperstep() % 4 == 3){
-            // Node may be marked as head b/c it's a real head or a real tail
-            headFlag = (byte) (State.IS_HEAD & getVertexValue().getState());
-            tailFlag = (byte) (State.IS_HEAD & getVertexValue().getState()); //is_tail
-            outFlag = (byte) (headFlag | tailFlag);
-            
-            // only PATH vertices are present. Find the ID's for my neighbors
-            curID.setAsCopy(getVertexId());
-            
-            curHead = isNodeRandomHead(curID);
-            
-            // the headFlag and tailFlag's indicate if the node is at the beginning or end of a simple path. 
-            // We prevent merging towards non-path nodes
-            hasNext = setNextInfo(getVertexValue()) && tailFlag == 0;
-            hasPrev = setPrevInfo(getVertexValue()) && headFlag == 0;
-            if ((outFlag & MessageFlag.IS_HEAD) > 0 && (outFlag & MessageFlag.IS_HEAD) > 0) {
-                getVertexValue().setState(outFlag);
-                voteToHalt();
-            }
-            if (hasNext || hasPrev) {
-                if (curHead) {
-                    if (hasNext && !nextHead) {
-                        // compress this head to the forward tail
-                        sendUpMsgFromPredecessor();
-                    } else if (hasPrev && !prevHead) {
-                        // compress this head to the reverse tail
-                        sendUpMsgFromSuccessor();
-                    }
-                } else {
-                    // I'm a tail
-                    if (hasNext && hasPrev) {
-                        if ((!nextHead && !prevHead) && (curID.compareTo(nextID) < 0 && curID.compareTo(prevID) < 0)) {
-                            // tails on both sides, and I'm the "local minimum"
-                            // compress me towards the tail in forward dir
-                            sendUpMsgFromPredecessor();
-                        }
-                    } else if (!hasPrev) {
-                        // no previous node
-                        if (!nextHead && curID.compareTo(nextID) < 0) {
-                            // merge towards tail in forward dir
-                            sendUpMsgFromPredecessor();
-                        }
-                    } else if (!hasNext) {
-                        // no next node
-                        if (!prevHead && curID.compareTo(prevID) < 0) {
-                            // merge towards tail in reverse dir
-                            sendUpMsgFromSuccessor();
-                        }
-                    }
-                }
-            }
-        }
-      
-    }
-
-    public static void main(String[] args) throws Exception {
-        PregelixJob job = new PregelixJob(P5ForPathMergeVertex.class.getSimpleName());
-        job.setVertexClass(P5ForPathMergeVertex.class);
-        /**
-         * BinaryInput and BinaryOutput
-         */
-        job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class);
-        job.setVertexOutputFormatClass(NaiveAlgorithmForPathMergeOutputFormat.class);
-        job.setDynamicVertexValueSize(true);
-        job.setOutputKeyClass(VKmerBytesWritable.class);
-        job.setOutputValueClass(VertexValueWritable.class);
-        Client.run(args, job);
-    }
-}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java
index 2ef9958..e810623 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java
@@ -14,8 +14,6 @@
 import edu.uci.ics.genomix.pregelix.operator.bubblemerge.BubbleAddVertex;
 import edu.uci.ics.genomix.pregelix.operator.pathmerge.P2ForPathMergeVertex;
 import edu.uci.ics.genomix.pregelix.operator.pathmerge.MapReduceVertex;
-import edu.uci.ics.genomix.pregelix.operator.pathmerge.P3ForPathMergeVertex;
-import edu.uci.ics.genomix.pregelix.operator.pathmerge.P4ForPathMergeVertex;
 import edu.uci.ics.genomix.pregelix.operator.splitrepeat.SplitRepeatVertex;
 import edu.uci.ics.genomix.pregelix.operator.tipremove.TipAddVertex;
 import edu.uci.ics.genomix.pregelix.operator.tipremove.TipRemoveVertex;
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/graphbuilding/JobRunStepByStepTest.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/graphbuilding/JobRunStepByStepTest.java
deleted file mode 100644
index 0d609bf..0000000
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/graphbuilding/JobRunStepByStepTest.java
+++ /dev/null
@@ -1,211 +0,0 @@
-/*
- * Copyright 2009-2013 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.graphbuilding;
-
-import java.io.BufferedWriter;
-import java.io.DataOutputStream;
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.FileWriter;
-import java.io.IOException;
-
-import junit.framework.Assert;
-
-import org.apache.commons.io.FileUtils;
-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.hdfs.MiniDFSCluster;
-import org.apache.hadoop.io.NullWritable;
-import org.apache.hadoop.io.SequenceFile;
-import org.apache.hadoop.mapred.FileInputFormat;
-import org.apache.hadoop.mapred.FileOutputFormat;
-import org.apache.hadoop.mapred.JobConf;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
-import edu.uci.ics.genomix.hyracks.driver.Driver;
-import edu.uci.ics.genomix.hyracks.driver.Driver.Plan;
-import edu.uci.ics.genomix.hyracks.job.GenomixJobConf;
-import edu.uci.ics.genomix.type.NodeWritable;
-
-@SuppressWarnings("deprecation")
-public class JobRunStepByStepTest {
-    private static final int KmerSize = 3;
-    private static final int ReadLength = 8;
-    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 DATA_INPUT_PATH = "data/graphbuild.test/tworead3.txt";
-    private static final String HDFS_INPUT_PATH = "/webmap";
-    private static final String HDFS_OUTPUT_PATH = "/webmap_result";
-
-    private static final String EXPECTED_DIR = "src/test/resources/expected/";
-    private static final String EXPECTED_OUPUT_NODE = EXPECTED_DIR + "result_after_generateNode";
-    private static final String EXPECTED_UNMERGED = EXPECTED_DIR + "result_unmerged";
-
-    private static final String DUMPED_RESULT = ACTUAL_RESULT_DIR + HDFS_OUTPUT_PATH + "/merged.txt";
-    private static final String CONVERT_RESULT = DUMPED_RESULT + ".txt";
-    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;
-    private int numPartitionPerMachine = 2;
-
-    private Driver driver;
-
-    @Test
-    public void TestAll() throws Exception {
-        //TestEndToEnd();
-        TestUnMergedNode();
-    }
-
-    public void TestEndToEnd() throws Exception {
-        //conf.set(GenomixJobConf.OUTPUT_FORMAT, GenomixJobConf.OUTPUT_FORMAT_TEXT);
-        conf.set(GenomixJobConf.OUTPUT_FORMAT, GenomixJobConf.OUTPUT_FORMAT_BINARY);
-        cleanUpReEntry();
-        conf.set(GenomixJobConf.GROUPBY_TYPE, GenomixJobConf.GROUPBY_TYPE_PRECLUSTER);
-        driver.runJob(new GenomixJobConf(conf), Plan.BUILD_DEBRUJIN_GRAPH, true);
-        Assert.assertEquals(true, checkResults(EXPECTED_OUPUT_NODE, new int[] { 1, 2, 3, 4 }));
-    }
-    
-    public void TestUnMergedNode() throws Exception {
-        conf.set(GenomixJobConf.OUTPUT_FORMAT, GenomixJobConf.OUTPUT_FORMAT_BINARY);
-        cleanUpReEntry();
-        conf.set(GenomixJobConf.GROUPBY_TYPE, GenomixJobConf.GROUPBY_TYPE_PRECLUSTER);
-        driver.runJob(new GenomixJobConf(conf), Plan.BUILD_UNMERGED_GRAPH, true);
-        Assert.assertEquals(true, checkResults(EXPECTED_UNMERGED, new int[] { 1, 2, 3, 4 }));
-    }
-
-    @Before
-    public void setUp() throws Exception {
-        cleanupStores();
-        edu.uci.ics.hyracks.hdfs.utils.HyracksUtils.init();
-        FileUtils.forceMkdir(new File(ACTUAL_RESULT_DIR));
-        FileUtils.cleanDirectory(new File(ACTUAL_RESULT_DIR));
-        startHDFS();
-
-        FileInputFormat.setInputPaths(conf, HDFS_INPUT_PATH);
-        FileOutputFormat.setOutputPath(conf, new Path(HDFS_OUTPUT_PATH));
-
-        conf.setInt(GenomixJobConf.KMER_LENGTH, KmerSize);
-        conf.setInt(GenomixJobConf.READ_LENGTH, ReadLength);
-        driver = new Driver(edu.uci.ics.hyracks.hdfs.utils.HyracksUtils.CC_HOST,
-                edu.uci.ics.hyracks.hdfs.utils.HyracksUtils.TEST_HYRACKS_CC_CLIENT_PORT, numPartitionPerMachine);
-    }
-
-    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_INPUT_PATH);
-        Path dest = new Path(HDFS_INPUT_PATH);
-        dfs.mkdirs(dest);
-        // dfs.mkdirs(result);
-        dfs.copyFromLocalFile(src, dest);
-
-        DataOutputStream confOutput = new DataOutputStream(new FileOutputStream(new File(HADOOP_CONF_PATH)));
-        conf.writeXml(confOutput);
-        confOutput.flush();
-        confOutput.close();
-    }
-
-    private void cleanUpReEntry() throws IOException {
-        FileSystem lfs = FileSystem.getLocal(new Configuration());
-        if (lfs.exists(new Path(DUMPED_RESULT))) {
-            lfs.delete(new Path(DUMPED_RESULT), true);
-        }
-        FileSystem dfs = FileSystem.get(conf);
-        if (dfs.exists(new Path(HDFS_OUTPUT_PATH))) {
-            dfs.delete(new Path(HDFS_OUTPUT_PATH), true);
-        }
-    }
-
-    private boolean checkResults(String expectedPath, int[] poslistField) throws Exception {
-        File dumped = null;
-        String format = conf.get(GenomixJobConf.OUTPUT_FORMAT);
-        if (GenomixJobConf.OUTPUT_FORMAT_TEXT.equalsIgnoreCase(format)) {
-            FileUtil.copyMerge(FileSystem.get(conf), new Path(HDFS_OUTPUT_PATH),
-                    FileSystem.getLocal(new Configuration()), new Path(DUMPED_RESULT), false, conf, null);
-            dumped = new File(DUMPED_RESULT);
-        } else {
-
-            FileSystem.getLocal(new Configuration()).mkdirs(new Path(ACTUAL_RESULT_DIR + HDFS_OUTPUT_PATH));
-            File filePathTo = new File(CONVERT_RESULT);
-            BufferedWriter bw = new BufferedWriter(new FileWriter(filePathTo));
-            for (int i = 0; i < numPartitionPerMachine * numberOfNC; i++) {
-                String partname = "/part-" + i;
-                 FileUtil.copy(FileSystem.get(conf), new Path(HDFS_OUTPUT_PATH
-                 + partname), FileSystem.getLocal(new Configuration()),
-                 new Path(ACTUAL_RESULT_DIR + HDFS_OUTPUT_PATH + partname),
-                 false, conf);
-
-                Path path = new Path(HDFS_OUTPUT_PATH + partname);
-                FileSystem dfs = FileSystem.get(conf);
-                if (dfs.getFileStatus(path).getLen() == 0) {
-                    continue;
-                }
-                SequenceFile.Reader reader = new SequenceFile.Reader(dfs, path, conf);
-
-                NodeWritable node = new NodeWritable();
-                NullWritable value = NullWritable.get();
-                while (reader.next(node, value)) {
-                    if (node == null) {
-                        break;
-                    }
-                    bw.write(node.toString());
-                    System.out.println(node.toString());
-                    bw.newLine();
-                }
-                reader.close();
-            }
-            bw.close();
-            dumped = new File(CONVERT_RESULT);
-        }
-
-        if (poslistField != null) {
-            TestUtils.compareWithUnSortedPosition(new File(expectedPath), dumped, poslistField);
-        } else {
-            TestUtils.compareWithSortedResult(new File(expectedPath), dumped);
-        }
-        return true;
-    }
-
-    @After
-    public void tearDown() throws Exception {
-        edu.uci.ics.hyracks.hdfs.utils.HyracksUtils.deinit();
-        cleanupHDFS();
-    }
-
-    private void cleanupHDFS() throws Exception {
-        dfsCluster.shutdown();
-    }
-}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/graphbuilding/TestUtils.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/graphbuilding/TestUtils.java
deleted file mode 100644
index ca7755e..0000000
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/graphbuilding/TestUtils.java
+++ /dev/null
@@ -1,235 +0,0 @@
-/*
- * Copyright 2009-2013 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.graphbuilding;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileReader;
-import java.util.ArrayList;
-import java.util.Collections;
-
-public class TestUtils {
-    /**
-     * Compare with the sorted expected file.
-     * The actual file may not be sorted;
-     * 
-     * @param expectedFile
-     * @param actualFile
-     */
-    public static void compareWithSortedResult(File expectedFile, File actualFile) throws Exception {
-        BufferedReader readerActual = new BufferedReader(new FileReader(actualFile));
-        BufferedReader readerExpected = new BufferedReader(new FileReader(expectedFile));
-        ArrayList<String> actualLines = new ArrayList<String>();
-        String lineExpected, lineActual;
-        try {
-            while ((lineActual = readerActual.readLine()) != null) {
-                actualLines.add(lineActual);
-            }
-            Collections.sort(actualLines);
-            int num = 1;
-            for (String actualLine : actualLines) {
-                lineExpected = readerExpected.readLine();
-                if (lineExpected == null) {
-                    throw new Exception("Actual result changed at line " + num + ":\n< " + actualLine + "\n> ");
-                }
-                if (!equalStrings(lineExpected, actualLine)) {
-                    throw new Exception("Result for changed at line " + num + ":\n< " + lineExpected + "\n> "
-                            + actualLine);
-                }
-                ++num;
-            }
-            lineExpected = readerExpected.readLine();
-            if (lineExpected != null) {
-                throw new Exception("Actual result changed at line " + num + ":\n< \n> " + lineExpected);
-            }
-        } finally {
-            readerActual.close();
-            readerExpected.close();
-        }
-    }
-
-    public static void compareWithUnSortedPosition(File expectedFile, File actualFile, int[] poslistField)
-            throws Exception {
-        BufferedReader readerActual = new BufferedReader(new FileReader(actualFile));
-        BufferedReader readerExpected = new BufferedReader(new FileReader(expectedFile));
-        ArrayList<String> actualLines = new ArrayList<String>();
-        String lineExpected, lineActual;
-        try {
-            while ((lineActual = readerActual.readLine()) != null) {
-                actualLines.add(lineActual);
-            }
-            Collections.sort(actualLines);
-            int num = 1;
-            for (String actualLine : actualLines) {
-                lineExpected = readerExpected.readLine();
-                if (lineExpected == null) {
-                    throw new Exception("Actual result changed at line " + num + ":\n< " + actualLine + "\n> ");
-                }
-                if (!containStrings(lineExpected, actualLine, poslistField)) {
-                    throw new Exception("Result for changed at line " + num + ":\n< " + lineExpected + "\n> "
-                            + actualLine);
-                }
-                ++num;
-            }
-            lineExpected = readerExpected.readLine();
-            if (lineExpected != null) {
-                throw new Exception("Actual result changed at line " + num + ":\n< \n> " + lineExpected);
-            }
-        } finally {
-            readerActual.close();
-            readerExpected.close();
-        }
-    }
-
-    public static void compareWithResult(File expectedFile, File actualFile) throws Exception {
-        BufferedReader readerExpected = new BufferedReader(new FileReader(expectedFile));
-        BufferedReader readerActual = new BufferedReader(new FileReader(actualFile));
-        String lineExpected, lineActual;
-        int num = 1;
-        try {
-            while ((lineExpected = readerExpected.readLine()) != null) {
-                lineActual = readerActual.readLine();
-                // Assert.assertEquals(lineExpected, lineActual);
-                if (lineActual == null) {
-                    throw new Exception("Actual result changed at line " + num + ":\n< " + lineExpected + "\n> ");
-                }
-                if (!equalStrings(lineExpected, lineActual)) {
-                    throw new Exception("Result for changed at line " + num + ":\n< " + lineExpected + "\n> "
-                            + lineActual);
-                }
-                ++num;
-            }
-            lineActual = readerActual.readLine();
-            if (lineActual != null) {
-                throw new Exception("Actual result changed at line " + num + ":\n< \n> " + lineActual);
-            }
-        } finally {
-            readerExpected.close();
-            readerActual.close();
-        }
-    }
-
-    private static boolean equalStrings(String s1, String s2) {
-        String[] rowsOne = s1.split("\n");
-        String[] rowsTwo = s2.split("\n");
-
-        if (rowsOne.length != rowsTwo.length)
-            return false;
-
-        for (int i = 0; i < rowsOne.length; i++) {
-            String row1 = rowsOne[i];
-            String row2 = rowsTwo[i];
-
-            if (row1.equals(row2))
-                continue;
-
-            String[] fields1 = row1.split(",");
-            String[] fields2 = row2.split(",");
-
-            for (int j = 0; j < fields1.length; j++) {
-                if (fields1[j].equals(fields2[j])) {
-                    continue;
-                } else if (fields1[j].indexOf('.') < 0) {
-                    return false;
-                } else {
-                    fields1[j] = fields1[j].split("=")[1];
-                    fields2[j] = fields2[j].split("=")[1];
-                    Double double1 = Double.parseDouble(fields1[j]);
-                    Double double2 = Double.parseDouble(fields2[j]);
-                    float float1 = (float) double1.doubleValue();
-                    float float2 = (float) double2.doubleValue();
-
-                    if (Math.abs(float1 - float2) == 0)
-                        continue;
-                    else {
-                        return false;
-                    }
-                }
-            }
-        }
-        return true;
-    }
-
-    private static boolean containStrings(String lineExpected, String actualLine, int[] poslistField) {
-        if (lineExpected.equals(actualLine)) {
-            return true;
-        }
-        String[] fieldsExp = lineExpected.split("\\\t");
-        String[] fieldsAct = actualLine.split("\\\t");
-        if (fieldsAct.length != fieldsExp.length) {
-            return false;
-        }
-        for (int i = 0; i < fieldsAct.length; i++) {
-            boolean cont = false;
-            for (int x : poslistField) {
-                if (i == x) {
-                    cont = true;
-                    break;
-                }
-            }
-            if (cont) {
-                continue;
-            }
-            if (!fieldsAct[i].equals(fieldsExp[i])) {
-                return false;
-            }
-        }
-
-        ArrayList<String> posExp = new ArrayList<String>();
-        ArrayList<String> posAct = new ArrayList<String>();
-
-        for (int x : poslistField) {
-            String valueExp = lineExpected.split("\\\t")[x];
-            for (int i = 1; i < valueExp.length() - 1;) {
-                if (valueExp.charAt(i) == '(') {
-                    String str = "";
-                    i++;
-                    while (i < valueExp.length() - 1 && valueExp.charAt(i) != ')') {
-                        str += valueExp.charAt(i);
-                        i++;
-                    }
-                    posExp.add(str);
-                }
-                i++;
-            }
-            String valueAct = actualLine.split("\\\t")[x];
-            for (int i = 1; i < valueAct.length() - 1;) {
-                if (valueAct.charAt(i) == '(') {
-                    String str = "";
-                    i++;
-                    while (i < valueAct.length() - 1 && valueAct.charAt(i) != ')') {
-                        str += valueAct.charAt(i);
-                        i++;
-                    }
-                    posAct.add(str);
-                }
-                i++;
-            }
-
-            if (posExp.size() != posAct.size()) {
-                return false;
-            }
-            Collections.sort(posExp);
-            Collections.sort(posAct);
-            for (int i = 0; i < posExp.size(); i++) {
-                if (!posExp.get(i).equals(posAct.get(i))) {
-                    return false;
-                }
-            }
-        }
-        return true;
-    }
-}