delete some log
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/NaiveAlgorithmForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/NaiveAlgorithmForPathMergeVertex.java
index ac52e0d..0df5e6b 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/NaiveAlgorithmForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/NaiveAlgorithmForPathMergeVertex.java
@@ -1,8 +1,6 @@
package edu.uci.ics.genomix.pregelix.operator;
import java.util.Iterator;
-import java.util.logging.Logger;
-
import org.apache.hadoop.io.NullWritable;
import edu.uci.ics.genomix.type.GeneCode;
@@ -52,9 +50,6 @@
* Naive Algorithm for path merge graph
*/
public class NaiveAlgorithmForPathMergeVertex extends Vertex<KmerBytesWritable, ValueStateWritable, NullWritable, NaiveAlgorithmMessageWritable>{
- //public static Logger logger = Logger.getLogger(NaiveAlgorithmForPathMergeVertex.class.getName());
-
-
public static final String KMER_SIZE = "NaiveAlgorithmForPathMergeVertex.kmerSize";
public static final String ITERATIONS = "NaiveAlgorithmForPathMergeVertex.iteration";
public static int kmerSize = -1;
@@ -186,12 +181,6 @@
responseMsgToHeadVertex();
}
}
- /*String log = "Iterator:" + getSuperstep();
- log += getVertexId().toString() + "\t";
- log += getVertexValue().getMergeChain().toString() + "\t";
- log += GeneCode.getSymbolFromBitMap(getVertexValue().getAdjMap()) + "\t";
- log += getVertexValue().getState();
- logger.info(log);*/
voteToHalt();
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/TwoStepLogAlgorithmForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/TwoStepLogAlgorithmForPathMergeVertex.java
index 2fe0227..11a2447 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/TwoStepLogAlgorithmForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/TwoStepLogAlgorithmForPathMergeVertex.java
@@ -98,13 +98,14 @@
if((adjMap & (1 << x)) != 0){
destVertexId.set(getNextDestVertexId(vertexId, x));
sendMsg(destVertexId, msg);
- String log = "Iterator:" + getSuperstep();
+ /*String log = "Iterator:" + getSuperstep() + "\t";
log += getVertexId().toString() + "\t";
log += getVertexValue().getMergeChain().toString() + "\t";
log += GeneCode.getSymbolFromBitMap(getVertexValue().getAdjMap()) + "\t";
log += getVertexValue().getState() + "\t";
log += "Dest: " + destVertexId.toString();
logger.info(log);
+ System.out.println(log);*/
}
}
}
@@ -144,7 +145,7 @@
msg.reset();
msg.setMessage(Message.START);
msg.setSourceVertexId(getVertexId());
- if(getVertexId().toString().equals("CGGAACGATGGGCAGGCAGAGTGTTCTACCTTTTCTCTGTATTTTACGATGAAGG")){
+ /*if(getVertexId().toString().equals("GGAACGATGGGCAGGCAGAGTGTTCTACCTTTTCTCTGTATTTTACGATGAAGGC")){
String log = "Iterator:" + getSuperstep();
log += getVertexId().toString() + "\t";
log += getVertexValue().getMergeChain().toString() + "\t";
@@ -152,7 +153,8 @@
log += getVertexValue().getState() + "\t";
log += "Dest: " + destVertexId.toString();
logger.info(log);
- }
+ System.out.println(log);
+ }*/
sendMsg(destVertexId, msg);
voteToHalt();
}
@@ -163,7 +165,7 @@
msg.reset();
msg.setMessage(Message.END);
msg.setSourceVertexId(getVertexId());
- if(getVertexId().toString().equals("CGGAACGATGGGCAGGCAGAGTGTTCTACCTTTTCTCTGTATTTTACGATGAAGG")){
+ /*if(getVertexId().toString().equals("GGAACGATGGGCAGGCAGAGTGTTCTACCTTTTCTCTGTATTTTACGATGAAGGC")){
String log = "Iterator:" + getSuperstep();
log += getVertexId().toString() + "\t";
log += getVertexValue().getMergeChain().toString() + "\t";
@@ -171,7 +173,8 @@
log += getVertexValue().getState() + "\t";
log += "Dest: " + destVertexId.toString();
logger.info(log);
- }
+ System.out.println(log);
+ }*/
sendMsg(destVertexId, msg);
voteToHalt();
}
@@ -278,9 +281,9 @@
public void startSendMsg(){
if(GraphVertexOperation.isHeadVertex(getVertexValue().getAdjMap())){
msg.set(null, null, (byte)0, Message.START);
- if(getVertexId().toString().equals("CGGAACGATGGGCAGGCAGAGTGTTCTACCTTTTCTCTGTATTTTACGATGAAGG")){
- sendMsgToAllNextNodes(getVertexId(), getVertexValue().getAdjMap());
- }
+ sendMsgToAllNextNodes(getVertexId(), getVertexValue().getAdjMap());
+ //if(getVertexId().toString().equals("CGGAACGATGGGCAGGCAGAGTGTTCTACCTTTTCTCTGTATTTTACGATGAAGG")){
+ //}
voteToHalt();
}
if(GraphVertexOperation.isRearVertex(getVertexValue().getAdjMap())){
@@ -298,12 +301,15 @@
*/
public void initState(Iterator<LogAlgorithmMessageWritable> msgIterator){
while(msgIterator.hasNext()){
+ /*if(getVertexId().toString().equals("GGAACGATGGGCAGGCAGAGTGTTCTACCTTTTCTCTGTATTTTACGATGAAGGC")){
String log = "Iterator:" + getSuperstep();
log += getVertexId().toString() + "\t";
log += getVertexValue().getMergeChain().toString() + "\t";
log += GeneCode.getSymbolFromBitMap(getVertexValue().getAdjMap()) + "\t";
log += getVertexValue().getState();
logger.info(log);
+ System.out.println(log);
+ }*/
if(!GraphVertexOperation.isPathVertex(getVertexValue().getAdjMap())){
msgIterator.next();
voteToHalt();
@@ -362,6 +368,10 @@
@Override
public void compute(Iterator<LogAlgorithmMessageWritable> msgIterator) {
initVertex();
+ /*if(getVertexId().toString().equals("GGAACGATGGGCAGGCAGAGTGTTCTACCTTTTCTCTGTATTTTACGATGAAGGC")){
+ System.out.println("found");
+ //sendMsgToAllNextNodes(getVertexId(), getVertexValue().getAdjMap());
+ }*/
if (getSuperstep() == 1)
startSendMsg();
else if(getSuperstep() == 2)