Make getCopyWithoutTandemRepeats() function
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 de60f19..104c290 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
@@ -80,10 +80,10 @@
}
//TODO make it correct
- public byte getHeadFlag(){
-// return (byte)(getVertexValue().getState() & State.VERTEX_MASK);
- return (byte)(getVertexValue().getState() & State.IS_HEAD);
- }
+// public byte getHeadFlag(){
+//// return (byte)(getVertexValue().getState() & State.VERTEX_MASK);
+// return (byte)(getVertexValue().getState() & State.IS_HEAD);
+// }
public boolean isHeadNode(){
byte state = (byte)(getVertexValue().getState() & State.VERTEX_MASK);
@@ -399,7 +399,6 @@
*/
public void startSendMsg() {
if(isTandemRepeat()){
- //TODO make a function
getCopyWithoutTandemRepeats(getVertexValue());
outFlag = 0;
outFlag |= MessageFlag.IS_HEAD;
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P1ForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P1ForPathMergeVertex.java
index e7340d9..4bc92c2 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P1ForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P1ForPathMergeVertex.java
@@ -41,8 +41,6 @@
destVertexId = new VKmerBytesWritable();
inFlag = 0;
outFlag = 0;
- headFlag = getHeadFlag();
- headMergeDir = getHeadMergeDir();
if(repeatKmer == null)
repeatKmer = new VKmerBytesWritable();
tmpValue.reset();
@@ -55,7 +53,6 @@
}
if(tmpKmer == null)
tmpKmer = new VKmerBytesWritable();
- headMergeDir = getHeadMergeDir();
if(reverseKmer == null)
reverseKmer = new VKmerBytesWritable();
if(kmerList == null)
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 d99d0f4..dc6cadc 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
@@ -45,7 +45,6 @@
if (maxIteration < 0)
maxIteration = Integer.parseInt(getContext().getConfiguration().get(GenomixJobConf.GRAPH_CLEAN_MAX_ITERATIONS));
GenomixJobConf.setGlobalStaticConstants(getContext().getConfiguration());
- headFlag = (byte)(getVertexValue().getState() & State.IS_HEAD);
selfFlag = (byte)(getVertexValue().getState() & State.VERTEX_MASK);
outFlag = 0;
if(incomingMsg == null)
@@ -72,7 +71,6 @@
destVertexId = new VKmerBytesWritable();
if(tmpKmer == null)
tmpKmer = new VKmerBytesWritable();
- headMergeDir = getHeadMergeDir();
if(repeatKmer == null)
repeatKmer = new VKmerBytesWritable();
tmpValue.reset();
@@ -430,7 +428,7 @@
incomingMsg = msgIterator.next();
if(isHaltNode())
voteToHalt();
- else if(getHeadFlag() != MessageFlag.IS_HEAD && !isTandemRepeat()){
+ else if(isHeadNode() && !isTandemRepeat()){
if(isValidPath()){
setHeadMergeDir();
//set deleteKmer and deleteDir
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 2b9eda9..c0367fc 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
@@ -120,7 +120,6 @@
@Override
public void compute(Iterator<PathMergeMessageWritable> msgIterator) {
initVertex();
-
if (getSuperstep() == 1)
startSendMsg();
else if (getSuperstep() == 2)