change code format in p3
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 e49063b..4014377 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
@@ -68,15 +68,18 @@
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(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(P3ForPathMergeVertex.ITERATIONS, options.numIteration);
}
+
if (options.pseudoRate > 0 && options.pseudoRate <= 1)
job.getConfiguration().setFloat(P3ForPathMergeVertex.PSEUDORATE, options.pseudoRate);
if (options.maxRound > 0)
job.getConfiguration().setInt(P3ForPathMergeVertex.MAXROUND, options.maxRound);
return options;
+
}
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/P3ForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/P3ForPathMergeVertex.java
index e189800..44d47a0 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/P3ForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/P3ForPathMergeVertex.java
@@ -79,7 +79,7 @@
if(pseudoRate < 0)
pseudoRate = getContext().getConfiguration().getFloat(PSEUDORATE, 0.2f);
if (maxRound < 0)
- maxRound = getContext().getConfiguration().getInt(MAXROUND, 4);
+ maxRound = getContext().getConfiguration().getInt(MAXROUND, 2);
outgoingMsg.reset();
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/GenerateSmallFile.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/GenerateSmallFile.java
index 85649b3..bb288ff 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/GenerateSmallFile.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/GenerateSmallFile.java
@@ -2,11 +2,13 @@
import java.io.BufferedReader;
import java.io.BufferedWriter;
+import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
+import org.apache.commons.io.FileUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
@@ -46,15 +48,15 @@
}
public static void main(String[] args) throws IOException {
- /*Path dir = new Path("data/test8m");
- Path outDir = new Path("data/input/test");
- FileUtils.cleanDirectory(new File("data/input/test"));
+ Path dir = new Path("data/split.aa");
+ Path outDir = new Path("data/input");
+ FileUtils.cleanDirectory(new File("data/input"));
Path inFile = new Path(dir, "part-0");
- Path outFile = new Path(outDir, "part-0-out-100");
- generateNumOfLinesFromGraphBuildResuiltBigFile(inFile, outFile, 100);*/
- String inFile = "data/shortjump_1.head8M.fastq";
+ Path outFile = new Path(outDir, "part-0-out-1000");
+ generateNumOfLinesFromGraphBuildResuiltBigFile(inFile, outFile, 1000);
+ /* String inFile = "data/shortjump_1.head8M.fastq";
String outFile = "data/testGeneFile";
- generateNumOfLinesFromGraphBuildResuiltBigFile(inFile, outFile, 100000);
+ generateNumOfLinesFromGraphBuildResuiltBigFile(inFile, outFile, 100000);*/
}
public static String readTextFile(String fileName, int numOfLines) {
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 85ab456..809ea34 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
@@ -61,6 +61,8 @@
job.setOutputKeyClass(KmerBytesWritable.class);
job.setOutputValueClass(ValueStateWritable.class);
job.getConfiguration().setInt(P3ForPathMergeVertex.KMER_SIZE, 5);
+ job.getConfiguration().setFloat(P3ForPathMergeVertex.PSEUDORATE, 0.4f);
+ job.getConfiguration().setInt(P3ForPathMergeVertex.MAXROUND, 1);
job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
}