change code format of LoadVertex, MessageWritable
git-svn-id: https://hyracks.googlecode.com/svn/branches/fullstack_genomix@3308 123451ca-8445-de46-9d55-352943316053
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/BinaryLoadGraphInputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/BinaryLoadGraphInputFormat.java
index deac3c8..2bbc1c2 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/BinaryLoadGraphInputFormat.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/BinaryLoadGraphInputFormat.java
@@ -1,8 +1,6 @@
package edu.uci.ics.pregelix;
import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
import org.apache.hadoop.io.ByteWritable;
import org.apache.hadoop.io.BytesWritable;
@@ -16,25 +14,23 @@
import edu.uci.ics.pregelix.api.io.binary.BinaryVertexInputFormat;
import edu.uci.ics.pregelix.api.io.binary.BinaryVertexInputFormat.BinaryVertexReader;
import edu.uci.ics.pregelix.api.util.BspUtils;
-import edu.uci.ics.pregelix.bitwise.BitwiseOperation;
import edu.uci.ics.pregelix.example.io.MessageWritable;
-import edu.uci.ics.pregelix.example.io.VLongWritable;
import edu.uci.ics.genomix.type.KmerCountValue;
public class BinaryLoadGraphInputFormat extends
BinaryVertexInputFormat<BytesWritable, ByteWritable, NullWritable, MessageWritable>{
- //static int number = 0;
+ static int number = 0;
/**
* Format INPUT
*/
@Override
public VertexReader<BytesWritable, ByteWritable, NullWritable, MessageWritable> createVertexReader(
InputSplit split, TaskAttemptContext context) throws IOException {
- /*try{
+ try{
System.out.println("split: " + number++ + " length:"+ split.getLength());
}catch (Exception ex){
- }*/
+ }
return new BinaryLoadGraphReader(binaryInputFormat.createRecordReader(split, context));
}
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/GraphVertexOperation.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/GraphVertexOperation.java
index 8197ea8..8fa34c3 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/GraphVertexOperation.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/GraphVertexOperation.java
@@ -24,7 +24,7 @@
import edu.uci.ics.pregelix.type.KmerCountValue;
public class GraphVertexOperation {
- public static final int k = 3; //kmer, k: the length of kmer
+ public static final int k = 55; //kmer, k: the length of kmer
static private final Path TMP_DIR = new Path(
GenerateSequenceFile.class.getSimpleName() + "_INTERIM");
/**
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/LogAlgorithmForMergeGraphInputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/LogAlgorithmForMergeGraphInputFormat.java
index 4044a06..5aad613 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/LogAlgorithmForMergeGraphInputFormat.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/LogAlgorithmForMergeGraphInputFormat.java
@@ -15,8 +15,8 @@
import edu.uci.ics.pregelix.bitwise.BitwiseOperation;
import edu.uci.ics.pregelix.example.io.LogAlgorithmMessageWritable;
import edu.uci.ics.pregelix.example.io.ValueStateWritable;
-import edu.uci.ics.genomix.type.KmerCountValue;
import edu.uci.ics.pregelix.type.State;
+import edu.uci.ics.genomix.type.KmerCountValue;
public class LogAlgorithmForMergeGraphInputFormat extends
BinaryVertexInputFormat<BytesWritable, ValueStateWritable, NullWritable, LogAlgorithmMessageWritable>{
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/SequenceFile/GenerateSequenceFile.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/SequenceFile/GenerateSequenceFile.java
index aedd1c9..b8fc24d 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/SequenceFile/GenerateSequenceFile.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/SequenceFile/GenerateSequenceFile.java
@@ -11,8 +11,8 @@
import org.apache.hadoop.io.SequenceFile;
import org.apache.hadoop.io.SequenceFile.CompressionType;
-import edu.uci.ics.genomix.pregelix.GraphVertexOperation;
import edu.uci.ics.genomix.type.KmerCountValue;
+import edu.uci.ics.pregelix.GraphVertexOperation;
import edu.uci.ics.pregelix.bitwise.BitwiseOperation;
public class GenerateSequenceFile {
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/TestLoadGraphVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/TestLoadGraphVertex.java
index 085d3be..3992a56 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/TestLoadGraphVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/TestLoadGraphVertex.java
@@ -10,7 +10,6 @@
import edu.uci.ics.pregelix.api.graph.Vertex;
import edu.uci.ics.pregelix.api.job.PregelixJob;
import edu.uci.ics.pregelix.bitwise.BitwiseOperation;
-import edu.uci.ics.pregelix.example.GraphMutationVertex;
import edu.uci.ics.pregelix.example.client.Client;
import edu.uci.ics.pregelix.example.io.MessageWritable;
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/example/io/LogAlgorithmMessageWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/example/io/LogAlgorithmMessageWritable.java
index 9b53fe6..262ce7f 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/example/io/LogAlgorithmMessageWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/example/io/LogAlgorithmMessageWritable.java
@@ -7,7 +7,7 @@
import org.apache.hadoop.io.WritableComparable;
-import edu.uci.ics.genomix.pregelix.GraphVertexOperation;
+import edu.uci.ics.pregelix.GraphVertexOperation;
public class LogAlgorithmMessageWritable implements WritableComparable<LogAlgorithmMessageWritable>{
/**
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/example/io/MessageWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/example/io/MessageWritable.java
index ba3053b..e18a062 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/example/io/MessageWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/pregelix/example/io/MessageWritable.java
@@ -7,8 +7,7 @@
import org.apache.hadoop.io.WritableComparable;
-import edu.uci.ics.genomix.pregelix.GraphVertexOperation;
-import edu.uci.ics.pregelix.api.graph.Vertex;
+import edu.uci.ics.pregelix.GraphVertexOperation;
public class MessageWritable implements WritableComparable<MessageWritable>{
/**
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/pregelix/JobGen/JobGenerator.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/pregelix/JobGen/JobGenerator.java
index 62624a8..625c1d4 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/pregelix/JobGen/JobGenerator.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/pregelix/JobGen/JobGenerator.java
@@ -10,17 +10,17 @@
import org.apache.hadoop.mapreduce.lib.input.FileInputFormat;
import org.apache.hadoop.mapreduce.lib.output.FileOutputFormat;
-import edu.uci.ics.genomix.pregelix.BinaryLoadGraphInputFormat;
-import edu.uci.ics.genomix.pregelix.BinaryLoadGraphOutputFormat;
-import edu.uci.ics.genomix.pregelix.LoadGraphVertex;
-import edu.uci.ics.genomix.pregelix.LogAlgorithmForMergeGraphInputFormat;
-import edu.uci.ics.genomix.pregelix.LogAlgorithmForMergeGraphOutputFormat;
-import edu.uci.ics.genomix.pregelix.LogAlgorithmForMergeGraphVertex;
-import edu.uci.ics.genomix.pregelix.MergeGraphVertex;
-import edu.uci.ics.genomix.pregelix.TestLoadGraphVertex;
-import edu.uci.ics.genomix.pregelix.TextLoadGraphInputFormat;
-import edu.uci.ics.genomix.pregelix.testDeleteVertexId;
-import edu.uci.ics.genomix.pregelix.LoadGraphVertex.SimpleLoadGraphVertexOutputFormat;
+import edu.uci.ics.pregelix.BinaryLoadGraphInputFormat;
+import edu.uci.ics.pregelix.BinaryLoadGraphOutputFormat;
+import edu.uci.ics.pregelix.LoadGraphVertex;
+import edu.uci.ics.pregelix.LogAlgorithmForMergeGraphInputFormat;
+import edu.uci.ics.pregelix.LogAlgorithmForMergeGraphOutputFormat;
+import edu.uci.ics.pregelix.LogAlgorithmForMergeGraphVertex;
+import edu.uci.ics.pregelix.MergeGraphVertex;
+import edu.uci.ics.pregelix.TestLoadGraphVertex;
+import edu.uci.ics.pregelix.TextLoadGraphInputFormat;
+import edu.uci.ics.pregelix.testDeleteVertexId;
+import edu.uci.ics.pregelix.LoadGraphVertex.SimpleLoadGraphVertexOutputFormat;
import edu.uci.ics.pregelix.api.job.PregelixJob;
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/pregelix/LoadGraphVertexTest.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/pregelix/LoadGraphVertexTest.java
index d75e2c2..e88098d 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/pregelix/LoadGraphVertexTest.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/pregelix/LoadGraphVertexTest.java
@@ -14,7 +14,7 @@
import org.junit.Test;
-import edu.uci.ics.genomix.pregelix.LoadGraphVertex.SimpleLoadGraphVertexOutputFormat;
+import edu.uci.ics.pregelix.LoadGraphVertex.SimpleLoadGraphVertexOutputFormat;
import edu.uci.ics.pregelix.api.job.PregelixJob;
import edu.uci.ics.pregelix.example.client.Client;