refactor LogAlgorithm to P2
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/client/Client.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/client/Client.java
index 9d15e8e..43bc73f 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/client/Client.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/client/Client.java
@@ -9,7 +9,7 @@
import org.kohsuke.args4j.CmdLineParser;
import org.kohsuke.args4j.Option;
-import edu.uci.ics.genomix.pregelix.operator.pathmerge.LogAlgorithmForPathMergeVertex;
+import edu.uci.ics.genomix.pregelix.operator.pathmerge.P2ForPathMergeVertex;
import edu.uci.ics.genomix.pregelix.operator.pathmerge.NaiveAlgorithmForPathMergeVertex;
import edu.uci.ics.genomix.pregelix.operator.pathmerge.P3ForPathMergeVertex;
import edu.uci.ics.pregelix.api.job.PregelixJob;
@@ -67,11 +67,11 @@
FileInputFormat.addInputPaths(job, inputs[0]);
FileOutputFormat.setOutputPath(job, new Path(options.outputPath));
job.getConfiguration().setInt(NaiveAlgorithmForPathMergeVertex.KMER_SIZE, options.sizeKmer);
- job.getConfiguration().setInt(LogAlgorithmForPathMergeVertex.KMER_SIZE, options.sizeKmer);
+ job.getConfiguration().setInt(P2ForPathMergeVertex.KMER_SIZE, options.sizeKmer);
job.getConfiguration().setInt(P3ForPathMergeVertex.KMER_SIZE, options.sizeKmer);
if (options.numIteration > 0) {
job.getConfiguration().setInt(NaiveAlgorithmForPathMergeVertex.ITERATIONS, options.numIteration);
- job.getConfiguration().setInt(LogAlgorithmForPathMergeVertex.ITERATIONS, options.numIteration);
+ job.getConfiguration().setInt(P2ForPathMergeVertex.ITERATIONS, options.numIteration);
job.getConfiguration().setInt(P3ForPathMergeVertex.ITERATIONS, options.numIteration);
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/P2PathMergeOutputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/P2PathMergeOutputFormat.java
index 81c6a33..3f8216c 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/P2PathMergeOutputFormat.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/P2PathMergeOutputFormat.java
@@ -9,7 +9,7 @@
import edu.uci.ics.genomix.pregelix.api.io.binary.BinaryDataCleanVertexOutputFormat;
import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
import edu.uci.ics.genomix.pregelix.io.VertexValueWritable.State;
-import edu.uci.ics.genomix.pregelix.operator.pathmerge.LogAlgorithmForPathMergeVertex;
+import edu.uci.ics.genomix.pregelix.operator.pathmerge.P2ForPathMergeVertex;
import edu.uci.ics.genomix.type.KmerBytesWritable;
import edu.uci.ics.pregelix.api.graph.Vertex;
import edu.uci.ics.pregelix.api.io.VertexWriter;
@@ -40,7 +40,7 @@
byte selfFlag = (byte)(vertex.getVertexValue().getState() & State.VERTEX_MASK);
if(selfFlag == State.IS_FINAL)
getRecordWriter().write(vertex.getVertexId(), vertex.getVertexValue());
- LogAlgorithmForPathMergeVertex.fakeVertexExist = false;
+ P2ForPathMergeVertex.fakeVertexExist = false;
}
}
}
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/P2ForPathMergeVertex.java
similarity index 97%
rename from genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java
rename to genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P2ForPathMergeVertex.java
index 4e543ce..b7ab62b 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/P2ForPathMergeVertex.java
@@ -42,7 +42,7 @@
* The succeed node and precursor node will be stored in vertexValue and we don't use edgeValue.
* The details about message are in edu.uci.ics.pregelix.example.io.MessageWritable.
*/
-public class LogAlgorithmForPathMergeVertex extends
+public class P2ForPathMergeVertex extends
MapReduceVertex {
private ArrayList<MessageWritable> receivedMsgList = new ArrayList<MessageWritable>();
@@ -289,8 +289,8 @@
}
public static void main(String[] args) throws Exception {
- PregelixJob job = new PregelixJob(LogAlgorithmForPathMergeVertex.class.getSimpleName());
- job.setVertexClass(LogAlgorithmForPathMergeVertex.class);
+ PregelixJob job = new PregelixJob(P2ForPathMergeVertex.class.getSimpleName());
+ job.setVertexClass(P2ForPathMergeVertex.class);
/**
* BinaryInput and BinaryOutput~/
*/
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java
index b34c9a9..1dae62e 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java
@@ -13,7 +13,7 @@
import edu.uci.ics.genomix.pregelix.operator.bridgeremove.BridgeRemoveVertex;
import edu.uci.ics.genomix.pregelix.operator.bubblemerge.BubbleAddVertex;
import edu.uci.ics.genomix.pregelix.operator.bubblemerge.BubbleMergeVertex;
-import edu.uci.ics.genomix.pregelix.operator.pathmerge.LogAlgorithmForPathMergeVertex;
+import edu.uci.ics.genomix.pregelix.operator.pathmerge.P2ForPathMergeVertex;
import edu.uci.ics.genomix.pregelix.operator.pathmerge.MapReduceVertex;
import edu.uci.ics.genomix.pregelix.operator.pathmerge.NaiveAlgorithmForPathMergeVertex;
import edu.uci.ics.genomix.pregelix.operator.pathmerge.P3ForPathMergeVertex;
@@ -46,13 +46,13 @@
private static void generateLogAlgorithmForMergeGraphJob(String jobName, String outputPath) throws IOException {
PregelixJob job = new PregelixJob(jobName);
- job.setVertexClass(LogAlgorithmForPathMergeVertex.class);
+ job.setVertexClass(P2ForPathMergeVertex.class);
job.setVertexInputFormatClass(InitialGraphCleanInputFormat.class);
job.setVertexOutputFormatClass(P2PathMergeOutputFormat.class);
job.setDynamicVertexValueSize(true);
job.setOutputKeyClass(KmerBytesWritable.class);
job.setOutputValueClass(VertexValueWritable.class);
- job.getConfiguration().setInt(LogAlgorithmForPathMergeVertex.KMER_SIZE, 3);
+ job.getConfiguration().setInt(P2ForPathMergeVertex.KMER_SIZE, 3);
job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
}