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+14 /Times-Roman set_font
+569.5 265.4 moveto 29 (AAT) alignedtext
+1 setlinewidth
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+0 0 0 nodecolor
+newpath 556 256 moveto
+612 256 lineto
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+14 /Times-Roman set_font
+565.5 239.4 moveto 37 (5':[1]) alignedtext
+1 setlinewidth
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+0 0 0 nodecolor
+newpath 556 230 moveto
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+0 0 0 nodecolor
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+564 213.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
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+0 0 0 nodecolor
+newpath 556 204 moveto
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+1 setlinewidth
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+0 0 0 nodecolor
+newpath 556 178 moveto
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+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+569.5 161.4 moveto 29 (AAT) alignedtext
+grestore
+% ATA->AAT
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+1 setlinewidth
+0 1 1 edgecolor
+newpath 472.23 187.46 moveto
+477.9 191.06 483.97 194.44 490 197 curveto
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+0 1 1 edgecolor
+newpath 545.16 215.71 moveto
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+1 setlinewidth
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+0 1 1 edgecolor
+newpath 545.16 215.71 moveto
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+0 0 0 edgecolor
+14 /Times-Roman set_font
+490 215.4 moveto 48 (RR: [1]) alignedtext
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+% CTA->AGA
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+newpath 555.99 54.5 moveto
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+457.32 27.61 435.11 15.24 352 23 curveto
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diff --git a/genomix/genomix-pregelix/data/TestSet/MapReduce/TwoBubbles/txt b/genomix/genomix-pregelix/data/TestSet/MapReduce/TwoBubbles/txt
new file mode 100755
index 0000000..789a22b
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/MapReduce/TwoBubbles/txt
@@ -0,0 +1,6 @@
+GAA {[] [] [] [{AGA:[1]}] {5':[], ~5':[]}GAA 1.0x}
+ATA {[] [{CTA:[1]}, {GTA:[0]}] [] [{AAT:[1]}] {5':[], ~5':[]}ATA 1.0x}
+GTA {[] [{ATA:[1]}] [{AGA:[1]}] [] {5':[], ~5':[]}CTA 0.0x}
+CTA {[] [{ATA:[1]}] [{AGA:[1]}] [] {5':[], ~5':[]}CTA 1.0x}
+AGA {[{GAA:[1]}] [{GTA:[0]}] [{CTA:[1]}] [] {5':[], ~5':[]}AGA 1.0x}
+AAT {[{ATA:[1]}] [] [] [] {5':[(1-0_0)], ~5':[]}AAT 1.0x}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/InitialGraphCleanInputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/InitialGraphCleanInputFormat.java
index 8a02388..e120c82 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/InitialGraphCleanInputFormat.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/InitialGraphCleanInputFormat.java
@@ -12,7 +12,6 @@
import edu.uci.ics.pregelix.api.util.BspUtils;
import edu.uci.ics.genomix.type.NodeWritable;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
-import edu.uci.ics.genomix.type.NodeWritable.DirectionFlag;
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;
@@ -72,6 +71,7 @@
*/
node.setAsCopy(getRecordReader().getCurrentValue());
vertexValue.setNode(node);
+ vertexValue.setInternalKmer(vertexId);
vertexValue.setState(State.IS_NON);
vertex.setVertexValue(vertexValue);
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/BasicGraphCleanVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/BasicGraphCleanVertex.java
index 9e97aa1..79640ec 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/BasicGraphCleanVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/BasicGraphCleanVertex.java
@@ -12,7 +12,7 @@
import edu.uci.ics.genomix.pregelix.util.VertexUtil;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
-public abstract class BasicGraphCleanVertex<I extends VKmerBytesWritable, V extends VertexValueWritable, E extends NullWritable, M extends MessageWritable> extends
+public abstract class BasicGraphCleanVertex<M extends MessageWritable> extends
Vertex<VKmerBytesWritable, VertexValueWritable, NullWritable, M> {
public static final String KMER_SIZE = "BasicGraphCleanVertex.kmerSize";
public static final String ITERATIONS = "BasicGraphCleanVertex.iteration";
@@ -451,6 +451,6 @@
@Override
public void compute(Iterator<M> msgIterator) {
+
}
-
}
\ No newline at end of file
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicPathMergeVertex.java
index e8d6a58..0a017d4 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicPathMergeVertex.java
@@ -1,27 +1,21 @@
package edu.uci.ics.genomix.pregelix.operator.pathmerge;
import java.io.IOException;
-import java.util.Iterator;
-
-import org.apache.hadoop.io.NullWritable;
-
import edu.uci.ics.genomix.pregelix.io.MessageWritable;
import edu.uci.ics.genomix.pregelix.io.PathMergeMessageWritable;
-import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
import edu.uci.ics.genomix.pregelix.io.VertexValueWritable.State;
import edu.uci.ics.genomix.pregelix.operator.BasicGraphCleanVertex;
import edu.uci.ics.genomix.pregelix.type.MessageFlag;
import edu.uci.ics.genomix.type.GeneCode;
-import edu.uci.ics.genomix.type.VKmerBytesWritable;
import edu.uci.ics.genomix.type.NodeWritable.OutgoingListFlag;
import edu.uci.ics.genomix.type.NodeWritable.IncomingListFlag;
-public class BasicPathMergeVertex extends
- BasicGraphCleanVertex<VKmerBytesWritable, VertexValueWritable, NullWritable, PathMergeMessageWritable>{
+public abstract class BasicPathMergeVertex<M extends PathMergeMessageWritable> extends
+ BasicGraphCleanVertex<M>{
- protected PathMergeMessageWritable incomingMsg = null;
- protected PathMergeMessageWritable outgoingMsg = null;
+ protected M incomingMsg = null;
+ protected M outgoingMsg = null;
public void setStateAsMergeWithPrev(){
byte state = getVertexValue().getState();
@@ -363,9 +357,4 @@
break;
}
}
-
- @Override
- public void compute(Iterator<PathMergeMessageWritable> msgIterator) {
-
- }
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/MapReduceVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/MapReduceVertex.java
index 671a98f..3a28a38 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/MapReduceVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/MapReduceVertex.java
@@ -19,7 +19,7 @@
import edu.uci.ics.pregelix.api.util.BspUtils;
public class MapReduceVertex extends
- BasicPathMergeVertex{
+ BasicPathMergeVertex<PathMergeMessageWritable>{
public static boolean fakeVertexExist = false;
protected static VKmerBytesWritable fakeVertex = null;
@@ -55,6 +55,8 @@
}
if(destVertexId == null)
destVertexId = new VKmerBytesWritable();
+ if(tmpKmer == null)
+ tmpKmer = new VKmerBytesWritable();
}
/**
@@ -106,20 +108,23 @@
while(msgIterator.hasNext()){
incomingMsg = msgIterator.next();
String kmerString = incomingMsg.getInternalKmer().toString();
- tmpKmer.reset(kmerString.length());
tmpKmer.setByRead(kmerString.length(), kmerString.getBytes(), 0);
reverseKmer.setByReadReverse(kmerString.length(), kmerString.getBytes(), 0);
- if(reverseKmer.compareTo(tmpKmer) < 0)
- tmpKmer.setAsCopy(reverseKmer);
+ VKmerBytesWritable kmer = new VKmerBytesWritable();
+ kmerList = new VKmerListWritable();
+ if(reverseKmer.compareTo(tmpKmer) > 0)
+ kmer.setAsCopy(tmpKmer);
+ else
+ kmer.setAsCopy(reverseKmer);
if(!kmerMapper.containsKey(tmpKmer)){
- kmerList.reset();
+ //kmerList.reset();
kmerList.append(incomingMsg.getSourceVertexId());
- kmerMapper.put(tmpKmer, kmerList);
+ kmerMapper.put(kmer, kmerList);
} else{
kmerList.setCopy(kmerMapper.get(tmpKmer));
kmerList.append(incomingMsg.getSourceVertexId());
- kmerMapper.put(tmpKmer, kmerList);
+ kmerMapper.put(kmer, kmerList);
}
}
}
@@ -190,4 +195,5 @@
job.setOutputValueClass(VertexValueWritable.class);
Client.run(args, job);
}
+
}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BasicGraphCleanTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BasicGraphCleanTestSuite.java
index feae27e..796eb9d 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BasicGraphCleanTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BasicGraphCleanTestSuite.java
@@ -119,7 +119,19 @@
LOGGER.info("Hyracks mini-cluster shut down");
cleanupHDFS();
}
-
+
+ public static void init(String pattern, String[] testSet){
+ PreFix = "data/TestSet/" + pattern;
+ SufFix = "bin";
+ PATH_TO_ONLY = "src/test/resources/only_" + pattern + ".txt";
+ ACTUAL_RESULT_DIR = "data/actual/" + pattern;
+ HADOOP_CONF_PATH = ACTUAL_RESULT_DIR + File.separator + "conf.xml";
+ /** Multiple Tests **/
+ TestDir.clear();
+ for(String testcase : testSet)
+ TestDir.add(PreFix + File.separator + testcase + File.separator + SufFix);
+ }
+
public static Test makeTestSuite(BasicGraphCleanTestSuite testSuite) throws Exception{
testSuite.setUp();
List<String> onlys = getFileList(PATH_TO_ONLY);
@@ -159,7 +171,7 @@
// BasicGraphCleanTestSuite testSuite = new BasicGraphCleanTestSuite();
// return makeTestSuite(testSuite);
// }
-
+
/**
* Runs the tests and collects their result in a TestResult.
*/
@@ -210,52 +222,4 @@
return false;
}
- public static String getPreFix() {
- return PreFix;
- }
-
- public static void setPreFix(String preFix) {
- PreFix = preFix;
- }
-
- public static String getSufFix() {
- return SufFix;
- }
-
- public static void setSufFix(String sufFix) {
- SufFix = sufFix;
- }
-
- public static ArrayList<String> getTestDir() {
- return TestDir;
- }
-
- public static void setTestDir(ArrayList<String> testDir) {
- TestDir = testDir;
- }
-
- public static String getPATH_TO_ONLY() {
- return PATH_TO_ONLY;
- }
-
- public static void setPATH_TO_ONLY(String pATH_TO_ONLY) {
- PATH_TO_ONLY = pATH_TO_ONLY;
- }
-
- public static String getACTUAL_RESULT_DIR() {
- return ACTUAL_RESULT_DIR;
- }
-
- public static void setACTUAL_RESULT_DIR(String aCTUAL_RESULT_DIR) {
- ACTUAL_RESULT_DIR = aCTUAL_RESULT_DIR;
- }
-
- public static String getHADOOP_CONF_PATH() {
- return HADOOP_CONF_PATH;
- }
-
- public static void setHADOOP_CONF_PATH(String hADOOP_CONF_PATH) {
- HADOOP_CONF_PATH = hADOOP_CONF_PATH;
- }
-
}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleAddSmallTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleAddSmallTestSuite.java
deleted file mode 100644
index 5ff4729..0000000
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleAddSmallTestSuite.java
+++ /dev/null
@@ -1,209 +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.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;
-
-@SuppressWarnings("deprecation")
-public class BubbleAddSmallTestSuite extends TestSuite {
- private static final Logger LOGGER = Logger.getLogger(BubbleAddSmallTestSuite.class.getName());
-
- public static final String PreFix = "data/PathMergeTestSet";
- public static final String SufFix = "bin";
- public static final String[] TestDir = { PreFix + File.separator
- + "5" + File.separator + SufFix};
- private static final String ACTUAL_RESULT_DIR = "data/actual/bubbleadd";
- 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_bubbleadd.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();
- 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();
- BubbleAddSmallTestSuite testSuite = new BubbleAddSmallTestSuite();
- 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 + getTestCaseName(testPathStr) + File.separator + "bin";
- String textFileName = ACTUAL_RESULT_DIR + File.separator + jobExtToResExt(qFile.getName())
- + File.separator + getTestCaseName(testPathStr) + File.separator + "txt" ;
- String graphvizFileName = ACTUAL_RESULT_DIR + File.separator + jobExtToResExt(qFile.getName())
- + File.separator + getTestCaseName(testPathStr) + File.separator + "graphviz";
- testSuite.addTest(new BasicSmallTestCase(HADOOP_CONF_PATH, qFile.getName(), qFile
- .getAbsolutePath().toString(), dfs,
- HDFS_INPUTPATH + File.separator + testDir.getName(), resultFileName, textFileName, graphvizFileName));
- }
- }
- }
- }
- 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);
- }
- }
-
- public static String getTestCaseName(String path) {
- char separatorChar = '/';
- int index = path.lastIndexOf(separatorChar);
- int secindex = path.substring(0, index).lastIndexOf(separatorChar);
- return path.substring(0, index).substring(secindex + 1);
- }
-
- 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;
- }
-
-}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleAddTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleAddTestSuite.java
new file mode 100644
index 0000000..9f062af
--- /dev/null
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleAddTestSuite.java
@@ -0,0 +1,14 @@
+package edu.uci.ics.genomix.pregelix.JobRun;
+
+import junit.framework.Test;
+
+public class BubbleAddTestSuite extends BasicGraphCleanTestSuite{
+
+ public static Test suite() throws Exception {
+ String pattern ="BubbleAdd";
+ String testSet[] = {"5"};
+ init(pattern, testSet);
+ BasicGraphCleanTestSuite testSuite = new BasicGraphCleanTestSuite();
+ return makeTestSuite(testSuite);
+ }
+}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/MapReduceTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/MapReduceTestSuite.java
new file mode 100644
index 0000000..307aa69
--- /dev/null
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/MapReduceTestSuite.java
@@ -0,0 +1,14 @@
+package edu.uci.ics.genomix.pregelix.JobRun;
+
+import junit.framework.Test;
+
+public class MapReduceTestSuite extends BasicGraphCleanTestSuite{
+
+ public static Test suite() throws Exception {
+ String pattern ="MapReduce";
+ String testSet[] = {"TwoBubbles"};
+ init(pattern, testSet);
+ BasicGraphCleanTestSuite testSuite = new BasicGraphCleanTestSuite();
+ return makeTestSuite(testSuite);
+ }
+}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/TestBubbleAddSmallTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/TestBubbleAddSmallTestSuite.java
deleted file mode 100644
index 8636339..0000000
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/TestBubbleAddSmallTestSuite.java
+++ /dev/null
@@ -1,39 +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.JobRun;
-
-import java.io.File;
-
-import junit.framework.Test;
-
-public class TestBubbleAddSmallTestSuite extends BasicGraphCleanTestSuite {
-
- public static void init(){
- PreFix = "data/AddBubbleTestSet";
- SufFix = "bin";
- PATH_TO_ONLY = "src/test/resources/only_bubbleadd.txt";
- ACTUAL_RESULT_DIR = "data/actual/bubbleadd";
- HADOOP_CONF_PATH = ACTUAL_RESULT_DIR + File.separator + "conf.xml";
- /** Multiple Tests **/
- TestDir.clear();
- TestDir.add(PreFix + File.separator + "5" + File.separator + SufFix);
- }
-
- public static Test suite() throws Exception {
- init();
- BasicGraphCleanTestSuite testSuite_bubbleadd = new BasicGraphCleanTestSuite();
- return makeTestSuite(testSuite_bubbleadd);
- }
-}
diff --git a/genomix/genomix-pregelix/src/test/resources/only_bridgeadd.txt b/genomix/genomix-pregelix/src/test/resources/only_BridgeAdd.txt
similarity index 100%
rename from genomix/genomix-pregelix/src/test/resources/only_bridgeadd.txt
rename to genomix/genomix-pregelix/src/test/resources/only_BridgeAdd.txt
diff --git a/genomix/genomix-pregelix/src/test/resources/only_bridgeremove.txt b/genomix/genomix-pregelix/src/test/resources/only_BridgeRemove.txt
similarity index 100%
rename from genomix/genomix-pregelix/src/test/resources/only_bridgeremove.txt
rename to genomix/genomix-pregelix/src/test/resources/only_BridgeRemove.txt
diff --git a/genomix/genomix-pregelix/src/test/resources/only_bubbleadd.txt b/genomix/genomix-pregelix/src/test/resources/only_BubbleAdd.txt
similarity index 100%
rename from genomix/genomix-pregelix/src/test/resources/only_bubbleadd.txt
rename to genomix/genomix-pregelix/src/test/resources/only_BubbleAdd.txt
diff --git a/genomix/genomix-pregelix/src/test/resources/only_bubblemerge.txt b/genomix/genomix-pregelix/src/test/resources/only_BubbleMerge.txt
similarity index 100%
rename from genomix/genomix-pregelix/src/test/resources/only_bubblemerge.txt
rename to genomix/genomix-pregelix/src/test/resources/only_BubbleMerge.txt
diff --git a/genomix/genomix-pregelix/src/test/resources/only_MapReduce.txt b/genomix/genomix-pregelix/src/test/resources/only_MapReduce.txt
new file mode 100644
index 0000000..710a096
--- /dev/null
+++ b/genomix/genomix-pregelix/src/test/resources/only_MapReduce.txt
@@ -0,0 +1 @@
+MapReduceGraph.xml
diff --git a/genomix/genomix-pregelix/src/test/resources/only_pathmerge.txt b/genomix/genomix-pregelix/src/test/resources/only_PathMerge.txt
similarity index 100%
rename from genomix/genomix-pregelix/src/test/resources/only_pathmerge.txt
rename to genomix/genomix-pregelix/src/test/resources/only_PathMerge.txt
diff --git a/genomix/genomix-pregelix/src/test/resources/only_removelowcoverage.txt b/genomix/genomix-pregelix/src/test/resources/only_RemovelowCoverage.txt
similarity index 100%
rename from genomix/genomix-pregelix/src/test/resources/only_removelowcoverage.txt
rename to genomix/genomix-pregelix/src/test/resources/only_RemovelowCoverage.txt
diff --git a/genomix/genomix-pregelix/src/test/resources/only_scaffolding.txt b/genomix/genomix-pregelix/src/test/resources/only_Scaffolding.txt
similarity index 100%
rename from genomix/genomix-pregelix/src/test/resources/only_scaffolding.txt
rename to genomix/genomix-pregelix/src/test/resources/only_Scaffolding.txt
diff --git a/genomix/genomix-pregelix/src/test/resources/only_tipadd.txt b/genomix/genomix-pregelix/src/test/resources/only_TipAdd.txt
similarity index 100%
rename from genomix/genomix-pregelix/src/test/resources/only_tipadd.txt
rename to genomix/genomix-pregelix/src/test/resources/only_TipAdd.txt
diff --git a/genomix/genomix-pregelix/src/test/resources/only_tipremove.txt b/genomix/genomix-pregelix/src/test/resources/only_TipRemove.txt
similarity index 100%
rename from genomix/genomix-pregelix/src/test/resources/only_tipremove.txt
rename to genomix/genomix-pregelix/src/test/resources/only_TipRemove.txt