refactor 'BasicPathMergeVertex' to 'BasicGraphCleanVertex', make it more general
diff --git a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/PositionWritableTest.java b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/PositionWritableTest.java
index fc67245..003406d 100644
--- a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/PositionWritableTest.java
+++ b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/PositionWritableTest.java
@@ -42,7 +42,6 @@
Assert.assertEquals(pos.getPosId(), posId);
Assert.assertEquals(pos1.toString(), pos.toString());
- String out = pos.toString();
}
}
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeRemoveVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeRemoveVertex.java
index 9db9418..7f85fc7 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeRemoveVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeRemoveVertex.java
@@ -10,7 +10,7 @@
import edu.uci.ics.genomix.pregelix.format.GraphCleanOutputFormat;
import edu.uci.ics.genomix.pregelix.io.MessageWritable;
import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
-import edu.uci.ics.genomix.pregelix.operator.pathmerge.BasicPathMergeVertex;
+import edu.uci.ics.genomix.pregelix.operator.pathmerge.BasicGraphCleanVertex;
import edu.uci.ics.genomix.pregelix.type.AdjMessage;
import edu.uci.ics.genomix.pregelix.util.VertexUtil;
@@ -46,7 +46,7 @@
* Naive Algorithm for path merge graph
*/
public class BridgeRemoveVertex extends
- BasicPathMergeVertex {
+ BasicGraphCleanVertex {
public static final String LENGTH = "BridgeRemoveVertex.length";
private int length = -1;
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/BasicGraphCleanVertex.java
similarity index 99%
rename from genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicPathMergeVertex.java
rename to genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicGraphCleanVertex.java
index 3039bc1..8cb8382 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/BasicGraphCleanVertex.java
@@ -19,10 +19,10 @@
/**
* Naive Algorithm for path merge graph
*/
-public class BasicPathMergeVertex extends
+public class BasicGraphCleanVertex extends
Vertex<KmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> {
- public static final String KMER_SIZE = "BasicPathMergeVertex.kmerSize";
- public static final String ITERATIONS = "BasicPathMergeVertex.iteration";
+ public static final String KMER_SIZE = "BasicGraphCleanVertex.kmerSize";
+ public static final String ITERATIONS = "BasicGraphCleanVertex.iteration";
public static int kmerSize = -1;
protected int maxIteration = -1;
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java
index 1309fba..d9cfc8c 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java
@@ -42,7 +42,7 @@
* The details about message are in edu.uci.ics.pregelix.example.io.MessageWritable.
*/
public class LogAlgorithmForPathMergeVertex extends
- BasicPathMergeVertex {
+ BasicGraphCleanVertex {
private ArrayList<MessageWritable> receivedMsgList = new ArrayList<MessageWritable>();
KmerBytesWritable tmpKmer = new KmerBytesWritable();
@@ -156,6 +156,7 @@
//process merge when receiving msg
while (msgIterator.hasNext()) {
incomingMsg = msgIterator.next();
+ /** for final processing **/
if(getMsgFlag() == MessageFlag.IS_FINAL){
sendFinalMergeMsg();
break;
@@ -199,13 +200,15 @@
else if (getSuperstep() == 2)
initState(msgIterator);
else if (getSuperstep() % 3 == 0 && getSuperstep() <= maxIteration) {
- if(msgIterator.hasNext()){ //for processing final merge
+ /** for processing final merge **/
+ if(msgIterator.hasNext()){
incomingMsg = msgIterator.next();
if(getMsgFlag() == MessageFlag.IS_FINAL){
setFinalState();
processFinalMerge(incomingMsg);
}
}
+ /** processing general case **/
else{
sendMsgToPathVertex(msgIterator);
if(selfFlag != State.IS_HEAD)
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 5f70772..9d0bb13 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 {
+ BasicGraphCleanVertex {
private static boolean fakeVertexExist = false;
private static KmerBytesWritable fakeVertex = null;
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P4ForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P4ForPathMergeVertex.java
index a14be92..8f97c5a 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P4ForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P4ForPathMergeVertex.java
@@ -48,7 +48,7 @@
* Naive Algorithm for path merge graph
*/
public class P4ForPathMergeVertex extends
- BasicPathMergeVertex {
+ BasicGraphCleanVertex {
public static final String RANDSEED = "P4ForPathMergeVertex.randSeed";
public static final String PROBBEINGRANDOMHEAD = "P4ForPathMergeVertex.probBeingRandomHead";
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipRemoveVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipRemoveVertex.java
index 7141ae7..c1138de 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipRemoveVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipRemoveVertex.java
@@ -9,7 +9,7 @@
import edu.uci.ics.genomix.pregelix.format.GraphCleanOutputFormat;
import edu.uci.ics.genomix.pregelix.io.MessageWritable;
import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
-import edu.uci.ics.genomix.pregelix.operator.pathmerge.BasicPathMergeVertex;
+import edu.uci.ics.genomix.pregelix.operator.pathmerge.BasicGraphCleanVertex;
import edu.uci.ics.genomix.pregelix.type.AdjMessage;
import edu.uci.ics.genomix.pregelix.util.VertexUtil;
@@ -45,7 +45,7 @@
* Remove tip or single node when l > constant
*/
public class TipRemoveVertex extends
- BasicPathMergeVertex {
+ BasicGraphCleanVertex {
public static final String LENGTH = "TipRemoveVertex.length";
private int length = -1;