delete unuse variable
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 8a70bd5..6941865 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
@@ -62,7 +62,6 @@
private NaiveAlgorithmMessageWritable msg = new NaiveAlgorithmMessageWritable();
private VKmerBytesWritableFactory kmerFactory = new VKmerBytesWritableFactory(1);
- private VKmerBytesWritable vertexId = new VKmerBytesWritable(1);
private VKmerBytesWritable destVertexId = new VKmerBytesWritable(1);
private VKmerBytesWritable chainVertexId = new VKmerBytesWritable(1);
private VKmerBytesWritable lastKmer = new VKmerBytesWritable(1);
@@ -75,7 +74,6 @@
kmerSize = getContext().getConfiguration().getInt(KMER_SIZE, 5);
if (maxIteration < 0)
maxIteration = getContext().getConfiguration().getInt(ITERATIONS, 100);
- vertexId.set(getVertexId());
vertexVal = getVertexValue();
}
public void findDestination(){
@@ -84,7 +82,7 @@
/**
* get destination vertex
*/
- public VKmerBytesWritable getDestVertexId(VKmerBytesWritable vertexId, byte geneCode){
+ public VKmerBytesWritable getDestVertexId(KmerBytesWritable vertexId, byte geneCode){
return kmerFactory.shiftKmerWithNextCode(vertexId, geneCode);
}
@@ -95,7 +93,7 @@
/**
* head send message to all next nodes
*/
- public void sendMsgToAllNextNodes(VKmerBytesWritable vertexId, byte adjMap){
+ public void sendMsgToAllNextNodes(KmerBytesWritable vertexId, byte adjMap){
for(byte x = GeneCode.A; x<= GeneCode.T ; x++){
if((adjMap & (1 << x)) != 0){
destVertexId.set(getDestVertexId(vertexId, x));
@@ -110,8 +108,8 @@
if(!msg.isRear()){
findDestination();
if(GraphVertexOperation.isPathVertex(vertexVal.getAdjMap())){
- chainVertexId.set(vertexId);
- msg.set(vertexId, chainVertexId, vertexId, vertexVal.getAdjMap(), false);
+ chainVertexId.set(getVertexId());
+ msg.set(getVertexId(), chainVertexId, getVertexId(), vertexVal.getAdjMap(), false);
sendMsg(destVertexId,msg);
}else if(GraphVertexOperation.isRearVertex(vertexVal.getAdjMap()))
voteToHalt();
@@ -126,7 +124,7 @@
}else{
destVertexId.set(msg.getHeadVertexId());
}
- msg.set(vertexId, msg.getChainVertexId(), msg.getHeadVertexId(), (byte)0, msg.isRear());
+ msg.set(getVertexId(), msg.getChainVertexId(), msg.getHeadVertexId(), (byte)0, msg.isRear());
sendMsg(destVertexId,msg);
}
/**
@@ -137,15 +135,13 @@
findDestination();
if(GraphVertexOperation.isPathVertex(vertexVal.getAdjMap())){
chainVertexId = kmerFactory.mergeKmerWithNextCode(msg.getChainVertexId(),
- vertexId.getGeneCodeAtPosition(kmerSize - 1));
+ getVertexId().getGeneCodeAtPosition(kmerSize - 1));
deleteVertex(getVertexId());
- //vertexVal.setState(State.NON_EXIST);
- //setVertexValue(vertexVal);
- msg.set(vertexId, chainVertexId, msg.getHeadVertexId(), vertexVal.getAdjMap(), false);
+ msg.set(getVertexId(), chainVertexId, msg.getHeadVertexId(), vertexVal.getAdjMap(), false);
sendMsg(destVertexId,msg);
}
else if(GraphVertexOperation.isRearVertex(vertexVal.getAdjMap())){
- msg.set(vertexId, msg.getChainVertexId(), msg.getHeadVertexId(), (byte)0, true);
+ msg.set(getVertexId(), msg.getChainVertexId(), msg.getHeadVertexId(), (byte)0, true);
sendMsg(destVertexId,msg);
}
}else{// is Rear
@@ -161,32 +157,30 @@
@Override
public void compute(Iterator<NaiveAlgorithmMessageWritable> msgIterator) {
initVertex();
- if(vertexVal.getState() != State.NON_EXIST){
- if (getSuperstep() == 1) {
- if(GraphVertexOperation.isHeadVertex(vertexVal.getAdjMap())){
- msg.set(vertexId, chainVertexId, vertexId, (byte)0, false);
- sendMsgToAllNextNodes(vertexId, vertexVal.getAdjMap());
- }
+ if (getSuperstep() == 1) {
+ if(GraphVertexOperation.isHeadVertex(vertexVal.getAdjMap())){
+ msg.set(getVertexId(), chainVertexId, getVertexId(), (byte)0, false);
+ sendMsgToAllNextNodes(getVertexId(), vertexVal.getAdjMap());
}
- else if(getSuperstep() == 2){
- if(msgIterator.hasNext()){
- msg = msgIterator.next();
- initChainVertex();
- }
+ }
+ else if(getSuperstep() == 2){
+ if(msgIterator.hasNext()){
+ msg = msgIterator.next();
+ initChainVertex();
}
- //head node sends message to path node
- else if(getSuperstep()%2 == 1 && getSuperstep() <= maxIteration){
- while (msgIterator.hasNext()){
- msg = msgIterator.next();
- sendMsgToPathVertex();
- }
+ }
+ //head node sends message to path node
+ else if(getSuperstep()%2 == 1 && getSuperstep() <= maxIteration){
+ while (msgIterator.hasNext()){
+ msg = msgIterator.next();
+ sendMsgToPathVertex();
}
- //path node sends message back to head node
- else if(getSuperstep()%2 == 0 && getSuperstep() > 2 && getSuperstep() <= maxIteration){
- while(msgIterator.hasNext()){
- msg = msgIterator.next();
- responseMsgToHeadVertex();
- }
+ }
+ //path node sends message back to head node
+ else if(getSuperstep()%2 == 0 && getSuperstep() > 2 && getSuperstep() <= maxIteration){
+ while(msgIterator.hasNext()){
+ msg = msgIterator.next();
+ responseMsgToHeadVertex();
}
}
voteToHalt();