Merge branch 'genomix/fullstack_genomix' of https://code.google.com/p/hyracks into genomix/fullstack_genomix
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/VKmerBytesWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/VKmerBytesWritable.java
index 71efb5f..f6061fd 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/VKmerBytesWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/VKmerBytesWritable.java
@@ -675,7 +675,12 @@
}
return new KmerBytesWritable(bytes, kmerStartOffset);
}
-
+
+ /**
+ * return the edit distance required to transform kemr1 into kmer2 using substitutions, insertions, and deletions.
+ *
+ * This uses the classic dynamic programming algorithm and takes O(length_1 * length_2) time and space.
+ */
public static int editDistance(VKmerBytesWritable kmer1, VKmerBytesWritable kmer2) {
int rows = kmer1.getKmerLetterLength() + 1, columns = kmer2.getKmerLetterLength() + 1, r=0, c=0, match=0;
int[][] distMat = new int[rows][columns];
@@ -703,9 +708,25 @@
private static int min(int a, int b, int c) {
return a <= b ? (a <= c ? a : c) : (b <= c ? b : c);
}
+ private static int min(int a, int b) {
+ return a <= b ? a : b;
+ }
public int editDistance(VKmerBytesWritable other) {
return editDistance(this, other);
}
+
+ /**
+ * return the fractional difference between the given kmers. This is the edit distance divided by the smaller length.
+ *
+ * Note: the fraction may be larger than 1 (when the edit distance is larger than the kmer)
+ */
+ public static float fracDissimilar(VKmerBytesWritable kmer1, VKmerBytesWritable kmer2) {
+ return editDistance(kmer1, kmer2) / (float) min(kmer1.getKmerLetterLength(), kmer2.getKmerLetterLength());
+ }
+
+ public float fracDissimilar(VKmerBytesWritable other) {
+ return fracDissimilar(this, other);
+ }
}
diff --git a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/VKmerBytesWritableTest.java b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/VKmerBytesWritableTest.java
index 7460776..9bf728d 100644
--- a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/VKmerBytesWritableTest.java
+++ b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/VKmerBytesWritableTest.java
@@ -564,6 +564,7 @@
Assert.assertEquals(kmer1.editDistance(kmer2), 3);
Assert.assertEquals(kmer1.editDistance(kmer2), kmer2.editDistance(kmer1));
+ Assert.assertEquals(kmer1.fracDissimilar(kmer2), .75f);
kmer1.setAsCopy("");
Assert.assertEquals(kmer1.editDistance(kmer2), kmer2.getKmerLetterLength());
@@ -572,6 +573,8 @@
kmer2.setAsCopy("");
Assert.assertEquals(kmer1.editDistance(kmer2), kmer2.getKmerLetterLength());
Assert.assertEquals(kmer1.editDistance(kmer2), kmer2.editDistance(kmer1));
+
+
}
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/client/Client.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/client/Client.java
index 0da4a77..73a8648 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/client/Client.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/client/Client.java
@@ -9,9 +9,7 @@
import org.kohsuke.args4j.CmdLineParser;
import org.kohsuke.args4j.Option;
-import edu.uci.ics.genomix.pregelix.operator.pathmerge.P2ForPathMergeVertex;
-import edu.uci.ics.genomix.pregelix.operator.pathmerge.P1ForPathMergeVertex;
-import edu.uci.ics.genomix.pregelix.operator.pathmerge.P3ForPathMergeVertex;
+import edu.uci.ics.genomix.pregelix.operator.pathmerge.BasicGraphCleanVertex;
import edu.uci.ics.pregelix.api.job.PregelixJob;
import edu.uci.ics.pregelix.core.base.IDriver.Plan;
import edu.uci.ics.pregelix.core.driver.Driver;
@@ -43,11 +41,11 @@
@Option(name = "-runtime-profiling", usage = "whether to do runtime profifling", required = false)
public String profiling = "false";
- @Option(name = "-pseudo-rate", usage = "the rate of pseduHead", required = false)
- public float pseudoRate = -1;
-
- @Option(name = "-max-patitionround", usage = "max rounds in partition phase", required = false)
- public int maxRound = -1;
+// @Option(name = "-pseudo-rate", usage = "the rate of pseduHead", required = false)
+// public float pseudoRate = -1;
+//
+// @Option(name = "-max-patitionround", usage = "max rounds in partition phase", required = false)
+// public int maxRound = -1;
}
public static void run(String[] args, PregelixJob job) throws Exception {
@@ -66,19 +64,15 @@
for (int i = 1; i < inputs.length; i++)
FileInputFormat.addInputPaths(job, inputs[0]);
FileOutputFormat.setOutputPath(job, new Path(options.outputPath));
- job.getConfiguration().setInt(P1ForPathMergeVertex.KMER_SIZE, options.sizeKmer);
- job.getConfiguration().setInt(P2ForPathMergeVertex.KMER_SIZE, options.sizeKmer);
- job.getConfiguration().setInt(P3ForPathMergeVertex.KMER_SIZE, options.sizeKmer);
+ job.getConfiguration().setInt(BasicGraphCleanVertex.KMER_SIZE, options.sizeKmer);
if (options.numIteration > 0) {
- job.getConfiguration().setInt(P1ForPathMergeVertex.ITERATIONS, options.numIteration);
- job.getConfiguration().setInt(P2ForPathMergeVertex.ITERATIONS, options.numIteration);
- job.getConfiguration().setInt(P3ForPathMergeVertex.ITERATIONS, options.numIteration);
+ job.getConfiguration().setInt(BasicGraphCleanVertex.ITERATIONS, options.numIteration);
}
- if (options.pseudoRate > 0 && options.pseudoRate <= 1)
- job.getConfiguration().setFloat(P3ForPathMergeVertex.PSEUDORATE, options.pseudoRate);
- if (options.maxRound > 0)
- job.getConfiguration().setInt(P3ForPathMergeVertex.MAXROUND, options.maxRound);
+// if (options.pseudoRate > 0 && options.pseudoRate <= 1)
+// job.getConfiguration().setFloat(P3ForPathMergeVertex.PSEUDORATE, options.pseudoRate);
+// if (options.maxRound > 0)
+// job.getConfiguration().setInt(P3ForPathMergeVertex.MAXROUND, options.maxRound);
return options;
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
index 70ef13f..245fe85 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
@@ -9,7 +9,9 @@
import edu.uci.ics.genomix.type.VKmerBytesWritable;
import edu.uci.ics.genomix.type.VKmerListWritable;
-public class VertexValueWritable implements WritableComparable<VertexValueWritable> {
+public class VertexValueWritable implements WritableComparable<VertexValueWritable>, Serializable {
+
+ private static final long serialVersionUID = 1L;
public static class State extends VertexStateFlag{
public static final byte NO_MERGE = 0b00 << 3;
@@ -18,10 +20,12 @@
public static final byte SHOULD_MERGE_MASK = 0b11 << 3;
public static final byte SHOULD_MERGE_CLEAR = 0b1100111;
+ public static final byte UNCHANGE = 0b0 << 3;
public static final byte KILL = 0b1 << 3;
public static final byte KILL_MASK = 0b1 << 3;
public static final byte DIR_FROM_DEADVERTEX = 0b10 << 3;
+ public static final byte DEAD_MASK = 0b10 << 3;
}
public static class VertexStateFlag extends FakeFlag {
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java
index 9b8a03d..c92148f 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java
@@ -3,8 +3,10 @@
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
+import java.util.HashSet;
import java.util.Iterator;
import java.util.Map;
+import java.util.Set;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
import edu.uci.ics.pregelix.api.job.PregelixJob;
@@ -22,10 +24,12 @@
*/
public class BubbleMergeVertex extends
BasicGraphCleanVertex {
-
+ public static final String DISSIMILARITY_THRESHOLD = "BubbleMergeVertex.dissimilarThreshold";
+ private float dissimilarThreshold = -1;
+
private Map<VKmerBytesWritable, ArrayList<MessageWritable>> receivedMsgMap = new HashMap<VKmerBytesWritable, ArrayList<MessageWritable>>();
private ArrayList<MessageWritable> receivedMsgList = new ArrayList<MessageWritable>();
-
+
/**
* initiate kmerSize, maxIteration
*/
@@ -34,7 +38,17 @@
kmerSize = getContext().getConfiguration().getInt(KMER_SIZE, 5);
if (maxIteration < 0)
maxIteration = getContext().getConfiguration().getInt(ITERATIONS, 1000000);
- outgoingMsg.reset();
+ if(dissimilarThreshold == -1)
+ dissimilarThreshold = getContext().getConfiguration().getFloat(DISSIMILARITY_THRESHOLD, (float) 0.05);
+ if(incomingMsg == null)
+ incomingMsg = new MessageWritable();
+ if(outgoingMsg == null)
+ outgoingMsg = new MessageWritable();
+ else
+ outgoingMsg.reset(kmerSize);
+ if(destVertexId == null)
+ destVertexId = new VKmerBytesWritable();
+ outFlag = 0;
}
public void sendBubbleAndMajorVertexMsgToMinorVertex(){
@@ -64,7 +78,24 @@
}
}
- @SuppressWarnings("unchecked")
+ @SuppressWarnings({ "unchecked" })
+ public void aggregateBubbleNodesByMajorNode(Iterator<MessageWritable> msgIterator){
+ while (msgIterator.hasNext()) {
+ incomingMsg = msgIterator.next();
+ if(!receivedMsgMap.containsKey(incomingMsg.getStartVertexId())){
+ receivedMsgList.clear();
+ receivedMsgList.add(incomingMsg);
+ receivedMsgMap.put(incomingMsg.getStartVertexId(), (ArrayList<MessageWritable>)receivedMsgList.clone());
+ }
+ else{
+ receivedMsgList.clear();
+ receivedMsgList.addAll(receivedMsgMap.get(incomingMsg.getStartVertexId()));
+ receivedMsgList.add(incomingMsg);
+ receivedMsgMap.put(incomingMsg.getStartVertexId(), (ArrayList<MessageWritable>)receivedMsgList.clone());
+ }
+ }
+ }
+
@Override
public void compute(Iterator<MessageWritable> msgIterator) {
initVertex();
@@ -82,32 +113,50 @@
}
}
} else if (getSuperstep() == 3){
- while (msgIterator.hasNext()) {
- incomingMsg = msgIterator.next();
- if(!receivedMsgMap.containsKey(incomingMsg.getStartVertexId())){
- receivedMsgList.clear();
- receivedMsgList.add(incomingMsg);
- receivedMsgMap.put(incomingMsg.getStartVertexId(), (ArrayList<MessageWritable>)receivedMsgList.clone());
- }
- else{
- receivedMsgList.clear();
- receivedMsgList.addAll(receivedMsgMap.get(incomingMsg.getStartVertexId()));
- receivedMsgList.add(incomingMsg);
- receivedMsgMap.put(incomingMsg.getStartVertexId(), (ArrayList<MessageWritable>)receivedMsgList.clone());
- }
- }
+ /** aggregate bubble nodes and grouped by major vertex **/
+ aggregateBubbleNodesByMajorNode(msgIterator);
+
+ Set<MessageWritable> unchangedSet = new HashSet<MessageWritable>();
+ Set<MessageWritable> deletedSet = new HashSet<MessageWritable>();
for(VKmerBytesWritable prevId : receivedMsgMap.keySet()){
if(receivedMsgList.size() > 1){ // filter bubble
/** for each startVertex, sort the node by decreasing order of coverage **/
receivedMsgList = receivedMsgMap.get(prevId);
Collections.sort(receivedMsgList, new MessageWritable.SortByCoverage());
- System.out.println("");
-
/** process similarSet, keep the unchanged set and deleted set & add coverage to unchange node **/
+ MessageWritable topCoverageMessage = new MessageWritable();
+ MessageWritable tmpMessage = new MessageWritable();
+ Iterator<MessageWritable> it;
+ while(!receivedMsgList.isEmpty()){
+ it = receivedMsgList.iterator();
+ topCoverageMessage.set(it.next());
+ it.remove(); //delete topCoverage node
+ while(it.hasNext()){
+ tmpMessage.set(it.next());
+ //compute the similarity
+ float fracDissimilar = (float) 0.02;
+ if(fracDissimilar < dissimilarThreshold){ //If similar with top node, delete this node and put it in deletedSet
+ //TODO add coverage to top node
+ deletedSet.add(tmpMessage);
+ it.remove();
+ }
+ }
+ unchangedSet.add(topCoverageMessage);
+ }
/** send message to the unchanged set for updating coverage & send kill message to the deleted set **/
-
+ for(MessageWritable msg : unchangedSet){
+ outFlag = MessageFlag.UNCHANGE;
+ outgoingMsg.setFlag(outFlag);
+ outgoingMsg.setAverageCoverage(msg.getAverageCoverage());
+ sendMsg(msg.getSourceVertexId(), outgoingMsg);
+ }
+ for(MessageWritable msg : deletedSet){
+ outFlag = MessageFlag.KILL;
+ outgoingMsg.setFlag(outFlag);
+ sendMsg(msg.getSourceVertexId(), outgoingMsg);
+ }
}
}
} else if (getSuperstep() == 4){
@@ -115,12 +164,14 @@
incomingMsg = msgIterator.next();
if(incomingMsg.getFlag() == MessageFlag.KILL){
broadcaseKillself();
- }
+ } else if(incomingMsg.getFlag() == MessageFlag.UNCHANGE){
+ getVertexValue().setAverageCoverage(incomingMsg.getAverageCoverage());
+ }
}
} else if(getSuperstep() == 5){
if(msgIterator.hasNext()) {
incomingMsg = msgIterator.next();
- if(incomingMsg.getFlag() == MessageFlag.KILL){
+ if(isResponseKillMsg()){
responseToDeadVertex();
}
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicGraphCleanVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicGraphCleanVertex.java
index 080cf35..58ef4d6 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicGraphCleanVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicGraphCleanVertex.java
@@ -22,14 +22,14 @@
public static final String KMER_SIZE = "BasicGraphCleanVertex.kmerSize";
public static final String ITERATIONS = "BasicGraphCleanVertex.iteration";
public static int kmerSize = -1;
- protected int maxIteration = -1;
+ public static int maxIteration = -1;
protected MessageWritable incomingMsg = null;
protected MessageWritable outgoingMsg = null;
protected VKmerBytesWritable destVertexId = null;
protected Iterator<VKmerBytesWritable> kmerIterator;
- protected VKmerBytesWritable tmpKmer = new VKmerBytesWritable(kmerSize);
- byte headFlag;
+ protected VKmerBytesWritable tmpKmer = null;
+ protected byte headFlag;
protected byte outFlag;
protected byte inFlag;
protected byte selfFlag;
@@ -814,9 +814,16 @@
}
}
- public boolean isKillMsg(){
+ public boolean isReceiveKillMsg(){
byte killFlag = (byte) (incomingMsg.getFlag() & MessageFlag.KILL_MASK);
- return killFlag == MessageFlag.KILL;
+ byte deadFlag = (byte) (incomingMsg.getFlag() & MessageFlag.DEAD_MASK);
+ return killFlag == MessageFlag.KILL & deadFlag != MessageFlag.DIR_FROM_DEADVERTEX;
+ }
+
+ public boolean isResponseKillMsg(){
+ byte killFlag = (byte) (incomingMsg.getFlag() & MessageFlag.KILL_MASK);
+ byte deadFlag = (byte) (incomingMsg.getFlag() & MessageFlag.DEAD_MASK);
+ return killFlag == MessageFlag.KILL & deadFlag == MessageFlag.DIR_FROM_DEADVERTEX;
}
@Override
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 10137da..5baf492 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
@@ -171,7 +171,7 @@
} else if(getSuperstep() == 5){
while (msgIterator.hasNext()) {
incomingMsg = msgIterator.next();
- if(isKillMsg())
+ if(isReceiveKillMsg())
responseToDeadVertex();
}
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P2ForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P2ForPathMergeVertex.java
index 6b7ad1f..c042f49 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P2ForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P2ForPathMergeVertex.java
@@ -249,7 +249,7 @@
processFinalMerge(incomingMsg);
/** NON-FAKE and Final vertice send msg to FAKE vertex **/
sendMsgToFakeVertex();
- } else if(isKillMsg()){
+ } else if(isReceiveKillMsg()){
responseToDeadVertex();
}
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/MessageFlag.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/MessageFlag.java
index 9468681..3ce6c5a 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/MessageFlag.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/MessageFlag.java
@@ -2,11 +2,6 @@
public class MessageFlag extends DirectionFlag {
- //public static final byte FLIP = 1 << 6;
- public static final byte HEAD_SHOULD_MERGEWITHPREV = 0b101 << 0;
- public static final byte HEAD_SHOULD_MERGEWITHNEXT = 0b111 << 0;
-
-
public static String getFlagAsString(byte code) {
// TODO: allow multiple flags to be set
return "ERROR_BAD_MESSAGE";
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 e810623..de2fcd3 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
@@ -12,6 +12,7 @@
import edu.uci.ics.genomix.pregelix.operator.bridgeremove.BridgeAddVertex;
import edu.uci.ics.genomix.pregelix.operator.bridgeremove.BridgeRemoveVertex;
import edu.uci.ics.genomix.pregelix.operator.bubblemerge.BubbleAddVertex;
+import edu.uci.ics.genomix.pregelix.operator.bubblemerge.BubbleMergeVertex;
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.splitrepeat.SplitRepeatVertex;
@@ -208,42 +209,32 @@
generateBubbleAddGraphJob("BubbleAddGraph", outputBase
+ "BubbleAddGraph.xml");
}
-//
-// private static void generateBubbleMergeGraphJob(String jobName, String outputPath) throws IOException {
-// PregelixJob job = new PregelixJob(jobName);
-// job.setVertexClass(BubbleMergeVertex.class);
-// job.setVertexInputFormatClass(NaiveAlgorithmForPathMergeInputFormat.class);
-// job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
-// job.setDynamicVertexValueSize(true);
-// job.setOutputKeyClass(PositionWritable.class);
-// job.setOutputValueClass(VertexValueWritable.class);
-// job.getConfiguration().setInt(BubbleMergeVertex.KMER_SIZE, 5);
-// job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
-// }
-//
-// private static void genBubbleMergeGraph() throws IOException {
-// generateBubbleMergeGraphJob("BubbleMergeGraph", outputBase
-// + "BubbleMergeGraph.xml");
-// }
+
+ private static void generateBubbleMergeGraphJob(String jobName, String outputPath) throws IOException {
+ PregelixJob job = new PregelixJob(jobName);
+ job.setVertexClass(BubbleMergeVertex.class);
+ job.setVertexInputFormatClass(GraphCleanInputFormat.class);
+ job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
+ job.setDynamicVertexValueSize(true);
+ job.setOutputKeyClass(VKmerBytesWritable.class);
+ job.setOutputValueClass(VertexValueWritable.class);
+ job.getConfiguration().setInt(BubbleMergeVertex.KMER_SIZE, 3);
+ job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
+ }
+
+ private static void genBubbleMergeGraph() throws IOException {
+ generateBubbleMergeGraphJob("BubbleMergeGraph", outputBase
+ + "BubbleMergeGraph.xml");
+ }
public static void main(String[] args) throws IOException {
- //genNaiveAlgorithmForMergeGraph();
-// genLogAlgorithmForMergeGraph();
- //genP3ForMergeGraph();
- //genTipAddGraph();
-// genTipRemoveGraph();
-// genBridgeAddGraph();
-// genBridgeRemoveGraph();
-// genBubbleAddGraph();
-// genBubbleMergeGraph();
-// genP4ForMergeGraph();
-// genMapReduceGraph();
genSplitRepeatGraph();
genTipAddGraph();
genBridgeAddGraph();
genTipRemoveGraph();
genBridgeRemoveGraph();
genBubbleAddGraph();
+ genBubbleMergeGraph();
}
}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleMergeSmallTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleMergeSmallTestSuite.java
index 57647ab..21020ce 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleMergeSmallTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleMergeSmallTestSuite.java
@@ -43,9 +43,9 @@
public class BubbleMergeSmallTestSuite extends TestSuite {
private static final Logger LOGGER = Logger.getLogger(BubbleMergeSmallTestSuite.class.getName());
- public static final String PreFix = "data/input"; //"graphbuildresult";
+ public static final String PreFix = "data/actual/bubbleadd/BubbleAddGraph/bin";
public static final String[] TestDir = { PreFix + File.separator
- + "graphs/bubblemerge/fr_bubble"};
+ + "5"};
private static final String ACTUAL_RESULT_DIR = "data/actual/bubblemerge";
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";