refactor 'UniqueKey' to 'NodeId'
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/IntermediateNodeWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/IntermediateNodeWritable.java
index 3f59e32..da9104b 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/IntermediateNodeWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/IntermediateNodeWritable.java
@@ -16,14 +16,14 @@
private KmerListWritable forwardReverseList;
private KmerListWritable reverseForwardList;
private KmerListWritable reverseReverseList;
- private PositionWritable uniqueKey;
+ private PositionWritable nodeId;
public IntermediateNodeWritable(){
forwardForwardList = new KmerListWritable();
forwardReverseList = new KmerListWritable();
reverseForwardList = new KmerListWritable();
reverseReverseList = new KmerListWritable();
- uniqueKey = new PositionWritable();
+ nodeId = new PositionWritable();
}
public IntermediateNodeWritable(KmerListWritable FFList, KmerListWritable FRList,
@@ -34,7 +34,7 @@
public void set(IntermediateNodeWritable node){
set(node.forwardForwardList, node.forwardReverseList, node.reverseForwardList,
- node.reverseReverseList, node.uniqueKey);
+ node.reverseReverseList, node.nodeId);
}
public void set(KmerListWritable FFList, KmerListWritable FRList,
@@ -43,7 +43,7 @@
this.forwardReverseList.set(FRList);
this.reverseForwardList.set(RFList);
this.reverseReverseList.set(RRList);
- this.uniqueKey.set(uniqueKey);
+ this.nodeId.set(uniqueKey);
}
public void reset(int kmerSize) {
@@ -51,7 +51,7 @@
forwardReverseList.reset();
reverseForwardList.reset();
reverseReverseList.reset();
- uniqueKey.reset();
+ nodeId.reset();
}
public KmerListWritable getFFList() {
@@ -86,21 +86,21 @@
this.reverseReverseList.set(reverseReverseList);
}
- public PositionWritable getUniqueKey() {
- return uniqueKey;
- }
+ public PositionWritable getNodeId() {
+ return nodeId;
+ }
- public void setUniqueKey(PositionWritable uniqueKey) {
- this.uniqueKey.set(uniqueKey);
- }
+ public void setNodeId(PositionWritable nodeId) {
+ this.nodeId.set(nodeId);
+ }
- @Override
+ @Override
public void readFields(DataInput in) throws IOException {
this.forwardForwardList.readFields(in);
this.forwardReverseList.readFields(in);
this.reverseForwardList.readFields(in);
this.reverseReverseList.readFields(in);
- this.uniqueKey.readFields(in);
+ this.nodeId.readFields(in);
}
@Override
@@ -109,18 +109,18 @@
this.forwardReverseList.write(out);
this.reverseForwardList.write(out);
this.reverseReverseList.write(out);
- this.uniqueKey.write(out);
+ this.nodeId.write(out);
}
@Override
public int compareTo(IntermediateNodeWritable other) {
// TODO Auto-generated method stub
- return this.uniqueKey.compareTo(other.uniqueKey);
+ return this.nodeId.compareTo(other.nodeId);
}
@Override
public int hashCode() {
- return this.uniqueKey.hashCode();
+ return this.nodeId.hashCode();
}
@Override
@@ -130,7 +130,7 @@
return (this.forwardForwardList.equals(nw.forwardForwardList)
&& this.forwardReverseList.equals(nw.forwardReverseList)
&& this.reverseForwardList.equals(nw.reverseForwardList)
- && this.reverseReverseList.equals(nw.reverseReverseList) && (this.uniqueKey.equals(nw.uniqueKey)));
+ && this.reverseReverseList.equals(nw.reverseReverseList) && (this.nodeId.equals(nw.nodeId)));
}
return false;
}
@@ -143,7 +143,7 @@
sbuilder.append(forwardReverseList.toString()).append('\t');
sbuilder.append(reverseForwardList.toString()).append('\t');
sbuilder.append(reverseReverseList.toString()).append('\t');
- sbuilder.append(uniqueKey.toString()).append(')');
+ sbuilder.append(nodeId.toString()).append(')');
return sbuilder.toString();
}
}
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenCheckReader.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenCheckReader.java
index 8f728cd..c3ec3c7 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenCheckReader.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenCheckReader.java
@@ -18,7 +18,7 @@
import java.io.IOException;
import java.util.Map;
-import edu.uci.ics.genomix.hyracks.newgraph.dataflow.ReadsKeyValueParserFactory;
+import edu.uci.ics.genomix.hyracks.dataflow.ReadsKeyValueParserFactory;
import edu.uci.ics.genomix.oldtype.PositionWritable;
import edu.uci.ics.genomix.type.KmerBytesWritable;
import edu.uci.ics.hyracks.api.client.NodeControllerInfo;
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/ReadsKeyValueParserFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/ReadsKeyValueParserFactory.java
index c929e56..915540a 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/ReadsKeyValueParserFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/ReadsKeyValueParserFactory.java
@@ -44,8 +44,11 @@
private static final Log LOG = LogFactory.getLog(ReadsKeyValueParserFactory.class);
public static final int OutputKmerField = 0;
- public static final int OutputPosition = 1;
- public static final int OutputKmerListField = 2;
+ public static final int OutputNodeId = 1;
+ public static final int OutputForwardForwardField = 2;
+ public static final int OutputForwardReverseField = 3;
+ public static final int OutputReverseForwardField = 4;
+ public static final int OutputReverseReverseField = 5;
private final int readLength;
private final int kmerSize;
@@ -110,7 +113,7 @@
nextKmer.shiftKmerWithNextChar(array[kmerSize]);
kmerList.append(nextKmer);
uniqueKey.set(mateId, readID, 1);
- interMediateNode.setUniqueKey(uniqueKey);
+ interMediateNode.setNodeId(uniqueKey);
interMediateNode.setFFList(kmerList);
InsertToFrame(kmer, interMediateNode, writer);
@@ -121,7 +124,7 @@
nextKmer.shiftKmerWithNextChar(array[i+1]);
kmerList.append(nextKmer);
uniqueKey.set(mateId, readID, i - kmerSize + 2);
- interMediateNode.setUniqueKey(uniqueKey);
+ interMediateNode.setNodeId(uniqueKey);
interMediateNode.setFFList(kmerList);
InsertToFrame(kmer, interMediateNode, writer);
}
@@ -129,17 +132,16 @@
private void InsertToFrame(KmerBytesWritable kmer, IntermediateNodeWritable node, IFrameWriter writer) {
try {
- if (Math.abs(node.getUniqueKey().getPosId()) > 32768) {
- throw new IllegalArgumentException("Position id is beyond 32768 at " + node.getUniqueKey().getReadId());
+ if (Math.abs(node.getNodeId().getPosId()) > 32768) {
+ throw new IllegalArgumentException("Position id is beyond 32768 at " + node.getNodeId().getReadId());
}
tupleBuilder.reset();
tupleBuilder.addField(kmer.getBytes(), kmer.getOffset(), kmer.getLength());
- tupleBuilder.addField(node, instance)
+ tupleBuilder.addField(node.getNodeId().getByteArray(), node.getNodeId().getStartOffset(), node.getNodeId().getLength());
tupleBuilder.addField(node.getFFList().getByteArray(), node.getFFList().getStartOffset(), node.getFFList().getLength());
tupleBuilder.addField(node.getFRList().getByteArray(), node.getFRList().getStartOffset(), node.getFRList().getLength());
tupleBuilder.addField(node.getRFList().getByteArray(), node.getRFList().getStartOffset(), node.getRFList().getLength());
tupleBuilder.addField(node.getRRList().getByteArray(), node.getRRList().getStartOffset(), node.getRRList().getLength());
- tupleBuilder.addField(node.getUniqueKey().getByteArray(), node.getUniqueKey().getStartOffset(), node.getUniqueKey().getLength());
if (!outputAppender.append(tupleBuilder.getFieldEndOffsets(), tupleBuilder.getByteArray(), 0,
tupleBuilder.getSize())) {
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/job/JobGenCheckReader.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/job/JobGenCheckReader.java
index 7c8f10e..2f89cb1 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/job/JobGenCheckReader.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/job/JobGenCheckReader.java
@@ -21,6 +21,7 @@
import edu.uci.ics.genomix.hyracks.dataflow.ReadsKeyValueParserFactory;
import edu.uci.ics.genomix.hyracks.job.GenomixJobConf;
import edu.uci.ics.genomix.oldtype.PositionWritable;
+import edu.uci.ics.genomix.type.IntermediateNodeWritable;
import edu.uci.ics.genomix.type.KmerBytesWritable;
import edu.uci.ics.hyracks.api.client.NodeControllerInfo;
import edu.uci.ics.hyracks.api.context.IHyracksTaskContext;
@@ -75,6 +76,7 @@
private KmerBytesWritable kmer = new KmerBytesWritable(kmerSize);
private PositionWritable pos = new PositionWritable();
+ private IntermediateNodeWritable intermediateNode = new IntermediateNodeWritable();
@Override
public void open(DataOutput output) throws HyracksDataException {