fix bug in readFields of KmerListWritable
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/VKmerListWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/VKmerListWritable.java
index 9895406..58e43a2 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/VKmerListWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/VKmerListWritable.java
@@ -260,6 +260,7 @@
in.readFully(storage, curOffset + VKmerBytesWritable.HEADER_SIZE, elemBytes - VKmerBytesWritable.HEADER_SIZE); // write kmer
curOffset += elemBytes;
curLength += elemBytes;
+ valueCount++;
}
valueCount = newValueCount;
Marshal.putInt(valueCount, storage, offset);
diff --git a/genomix/genomix-pregelix/data/PathMergeTestSet/5/part-00000 b/genomix/genomix-pregelix/data/PathMergeTestSet/5/part-00000
index 1887e36..d369b61 100755
--- a/genomix/genomix-pregelix/data/PathMergeTestSet/5/part-00000
+++ b/genomix/genomix-pregelix/data/PathMergeTestSet/5/part-00000
Binary files differ
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/BinaryDataCleanVertexInputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/BinaryDataCleanVertexInputFormat.java
index 396d5ec..e4f0cde 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/BinaryDataCleanVertexInputFormat.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/BinaryDataCleanVertexInputFormat.java
@@ -14,7 +14,7 @@
import edu.uci.ics.pregelix.api.io.VertexInputFormat;
import edu.uci.ics.pregelix.api.io.VertexReader;
import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
public class BinaryDataCleanVertexInputFormat<I extends WritableComparable<?>, V extends Writable, E extends Writable, M extends Writable>
extends VertexInputFormat<I, V, E, M> {
@@ -38,7 +38,7 @@
public static abstract class BinaryDataCleanVertexReader<I extends WritableComparable<?>, V extends Writable, E extends Writable, M extends Writable>
implements VertexReader<I, V, E, M> {
/** Internal line record reader */
- private final RecordReader<KmerBytesWritable, VertexValueWritable> lineRecordReader;
+ private final RecordReader<VKmerBytesWritable, VertexValueWritable> lineRecordReader;
/** Context passed to initialize */
private TaskAttemptContext context;
@@ -48,7 +48,7 @@
* @param recordReader
* Line record reader from SequenceFileInputFormat
*/
- public BinaryDataCleanVertexReader(RecordReader<KmerBytesWritable, VertexValueWritable> recordReader) {
+ public BinaryDataCleanVertexReader(RecordReader<VKmerBytesWritable, VertexValueWritable> recordReader) {
this.lineRecordReader = recordReader;
}
@@ -74,7 +74,7 @@
*
* @return Record reader to be used for reading.
*/
- protected RecordReader<KmerBytesWritable, VertexValueWritable> getRecordReader() {
+ protected RecordReader<VKmerBytesWritable, VertexValueWritable> getRecordReader() {
return lineRecordReader;
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/BinaryDataCleanVertexOutputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/BinaryDataCleanVertexOutputFormat.java
index c07d076..30510a3 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/BinaryDataCleanVertexOutputFormat.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/BinaryDataCleanVertexOutputFormat.java
@@ -11,7 +11,7 @@
import org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat;
import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
import edu.uci.ics.pregelix.api.io.VertexOutputFormat;
import edu.uci.ics.pregelix.api.io.VertexWriter;
@@ -49,7 +49,7 @@
/** Context passed to initialize */
private TaskAttemptContext context;
/** Internal line record writer */
- private final RecordWriter<KmerBytesWritable, VertexValueWritable> lineRecordWriter;
+ private final RecordWriter<VKmerBytesWritable, VertexValueWritable> lineRecordWriter;
/**
* Initialize with the LineRecordWriter.
@@ -57,7 +57,7 @@
* @param lineRecordWriter
* Line record writer from SequenceFileOutputFormat
*/
- public BinaryVertexWriter(RecordWriter<KmerBytesWritable, VertexValueWritable> lineRecordWriter) {
+ public BinaryVertexWriter(RecordWriter<VKmerBytesWritable, VertexValueWritable> lineRecordWriter) {
this.lineRecordWriter = lineRecordWriter;
}
@@ -76,7 +76,7 @@
*
* @return Record writer to be used for writing.
*/
- public RecordWriter<KmerBytesWritable, VertexValueWritable> getRecordWriter() {
+ public RecordWriter<VKmerBytesWritable, VertexValueWritable> getRecordWriter() {
return lineRecordWriter;
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/InitialGraphCleanVertexInputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/InitialGraphCleanVertexInputFormat.java
index d6be23b..4221865 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/InitialGraphCleanVertexInputFormat.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/api/io/binary/InitialGraphCleanVertexInputFormat.java
@@ -14,7 +14,7 @@
import edu.uci.ics.pregelix.api.io.VertexInputFormat;
import edu.uci.ics.pregelix.api.io.VertexReader;
import edu.uci.ics.genomix.type.NodeWritable;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
public class InitialGraphCleanVertexInputFormat<I extends WritableComparable<?>, V extends Writable, E extends Writable, M extends Writable>
extends VertexInputFormat<I, V, E, M> {
@@ -38,7 +38,7 @@
public static abstract class BinaryVertexReader<I extends WritableComparable<?>, V extends Writable, E extends Writable, M extends Writable>
implements VertexReader<I, V, E, M> {
/** Internal line record reader */
- private final RecordReader<KmerBytesWritable, NodeWritable> lineRecordReader;
+ private final RecordReader<VKmerBytesWritable, NodeWritable> lineRecordReader;
/** Context passed to initialize */
private TaskAttemptContext context;
@@ -48,7 +48,7 @@
* @param recordReader
* Line record reader from SequenceFileInputFormat
*/
- public BinaryVertexReader(RecordReader<KmerBytesWritable, NodeWritable> recordReader) {
+ public BinaryVertexReader(RecordReader<VKmerBytesWritable, NodeWritable> recordReader) {
this.lineRecordReader = recordReader;
}
@@ -74,7 +74,7 @@
*
* @return Record reader to be used for reading.
*/
- protected RecordReader<KmerBytesWritable, NodeWritable> getRecordReader() {
+ protected RecordReader<VKmerBytesWritable, NodeWritable> getRecordReader() {
return lineRecordReader;
}
@@ -98,7 +98,6 @@
@Override
public VertexReader<I, V, E, M> createVertexReader(InputSplit split, TaskAttemptContext context) throws IOException {
- // TODO Auto-generated method stub
return null;
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/GraphCleanInputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/GraphCleanInputFormat.java
index 859ddba..e0c8fa5 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/GraphCleanInputFormat.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/GraphCleanInputFormat.java
@@ -14,16 +14,16 @@
import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
import edu.uci.ics.genomix.pregelix.api.io.binary.BinaryDataCleanVertexInputFormat;
import edu.uci.ics.genomix.pregelix.api.io.binary.BinaryDataCleanVertexInputFormat.BinaryDataCleanVertexReader;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
public class GraphCleanInputFormat extends
- BinaryDataCleanVertexInputFormat<KmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> {
+ BinaryDataCleanVertexInputFormat<VKmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> {
/**
* Format INPUT
*/
@SuppressWarnings("unchecked")
@Override
- public VertexReader<KmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> createVertexReader(
+ public VertexReader<VKmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> createVertexReader(
InputSplit split, TaskAttemptContext context) throws IOException {
return new BinaryDataCleanLoadGraphReader(binaryInputFormat.createRecordReader(split, context));
}
@@ -31,12 +31,12 @@
@SuppressWarnings("rawtypes")
class BinaryDataCleanLoadGraphReader extends
- BinaryDataCleanVertexReader<KmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> {
+ BinaryDataCleanVertexReader<VKmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> {
private Vertex vertex;
- private KmerBytesWritable vertexId = new KmerBytesWritable();
+ private VKmerBytesWritable vertexId = new VKmerBytesWritable();
private VertexValueWritable vertexValue = new VertexValueWritable();
- public BinaryDataCleanLoadGraphReader(RecordReader<KmerBytesWritable, VertexValueWritable> recordReader) {
+ public BinaryDataCleanLoadGraphReader(RecordReader<VKmerBytesWritable, VertexValueWritable> recordReader) {
super(recordReader);
}
@@ -47,7 +47,7 @@
@SuppressWarnings("unchecked")
@Override
- public Vertex<KmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> getCurrentVertex()
+ public Vertex<VKmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> getCurrentVertex()
throws IOException, InterruptedException {
if (vertex == null)
vertex = (Vertex) BspUtils.createVertex(getContext().getConfiguration());
@@ -66,7 +66,6 @@
* set the vertex value
*/
vertexValue.set(getRecordReader().getCurrentValue());
- vertexValue.setKmerlength(getRecordReader().getCurrentValue().getKmerlength());
vertex.setVertexValue(vertexValue);
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/GraphCleanOutputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/GraphCleanOutputFormat.java
index 32f71be..77960ba 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/GraphCleanOutputFormat.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/GraphCleanOutputFormat.java
@@ -8,18 +8,18 @@
import edu.uci.ics.genomix.pregelix.api.io.binary.BinaryDataCleanVertexOutputFormat;
import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
import edu.uci.ics.pregelix.api.graph.Vertex;
import edu.uci.ics.pregelix.api.io.VertexWriter;
public class GraphCleanOutputFormat extends
- BinaryDataCleanVertexOutputFormat<KmerBytesWritable, VertexValueWritable, NullWritable> {
+ BinaryDataCleanVertexOutputFormat<VKmerBytesWritable, VertexValueWritable, NullWritable> {
@Override
- public VertexWriter<KmerBytesWritable, VertexValueWritable, NullWritable> createVertexWriter(
+ public VertexWriter<VKmerBytesWritable, VertexValueWritable, NullWritable> createVertexWriter(
TaskAttemptContext context) throws IOException, InterruptedException {
@SuppressWarnings("unchecked")
- RecordWriter<KmerBytesWritable, VertexValueWritable> recordWriter = binaryOutputFormat.getRecordWriter(context);
+ RecordWriter<VKmerBytesWritable, VertexValueWritable> recordWriter = binaryOutputFormat.getRecordWriter(context);
return new BinaryLoadGraphVertexWriter(recordWriter);
}
@@ -27,13 +27,13 @@
* Simple VertexWriter that supports {@link BinaryLoadGraphVertex}
*/
public static class BinaryLoadGraphVertexWriter extends
- BinaryVertexWriter<KmerBytesWritable, VertexValueWritable, NullWritable> {
- public BinaryLoadGraphVertexWriter(RecordWriter<KmerBytesWritable, VertexValueWritable> lineRecordWriter) {
+ BinaryVertexWriter<VKmerBytesWritable, VertexValueWritable, NullWritable> {
+ public BinaryLoadGraphVertexWriter(RecordWriter<VKmerBytesWritable, VertexValueWritable> lineRecordWriter) {
super(lineRecordWriter);
}
@Override
- public void writeVertex(Vertex<KmerBytesWritable, VertexValueWritable, NullWritable, ?> vertex)
+ public void writeVertex(Vertex<VKmerBytesWritable, VertexValueWritable, NullWritable, ?> vertex)
throws IOException, InterruptedException {
getRecordWriter().write(vertex.getVertexId(), vertex.getVertexValue());
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/InitialGraphCleanInputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/InitialGraphCleanInputFormat.java
index 4dfff11..5662da6 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/InitialGraphCleanInputFormat.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/InitialGraphCleanInputFormat.java
@@ -17,16 +17,15 @@
import edu.uci.ics.genomix.pregelix.io.VertexValueWritable.State;
import edu.uci.ics.genomix.pregelix.api.io.binary.InitialGraphCleanVertexInputFormat;
import edu.uci.ics.genomix.pregelix.api.io.binary.InitialGraphCleanVertexInputFormat.BinaryVertexReader;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
public class InitialGraphCleanInputFormat extends
- InitialGraphCleanVertexInputFormat<KmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> {
+ InitialGraphCleanVertexInputFormat<VKmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> {
/**
* Format INPUT
*/
@SuppressWarnings("unchecked")
@Override
- public VertexReader<KmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> createVertexReader(
+ public VertexReader<VKmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> createVertexReader(
InputSplit split, TaskAttemptContext context) throws IOException {
return new BinaryLoadGraphReader(binaryInputFormat.createRecordReader(split, context));
}
@@ -34,14 +33,14 @@
@SuppressWarnings("rawtypes")
class BinaryLoadGraphReader extends
- BinaryVertexReader<KmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> {
+ BinaryVertexReader<VKmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> {
private Vertex vertex;
- private KmerBytesWritable vertexId = new KmerBytesWritable();
+ private VKmerBytesWritable vertexId = new VKmerBytesWritable();
private NodeWritable node = new NodeWritable();
private VertexValueWritable vertexValue = new VertexValueWritable();
- public BinaryLoadGraphReader(RecordReader<KmerBytesWritable, NodeWritable> recordReader) {
+ public BinaryLoadGraphReader(RecordReader<VKmerBytesWritable, NodeWritable> recordReader) {
super(recordReader);
}
@@ -52,7 +51,7 @@
@SuppressWarnings("unchecked")
@Override
- public Vertex<KmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> getCurrentVertex()
+ public Vertex<VKmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> getCurrentVertex()
throws IOException, InterruptedException {
if (vertex == null)
vertex = (Vertex) BspUtils.createVertex(getContext().getConfiguration());
@@ -71,14 +70,13 @@
* set the vertex value
*/
node.set(getRecordReader().getCurrentValue());
- vertexValue.setKmerlength(node.getKmerLength());
vertexValue.setNodeIdList(node.getNodeIdList());
vertexValue.setFFList(node.getFFList());
vertexValue.setFRList(node.getFRList());
vertexValue.setRFList(node.getRFList());
vertexValue.setRRList(node.getRRList());
// TODO make this more efficient (don't use toString)
- vertexValue.setKmer(new VKmerBytesWritable(getRecordReader().getCurrentKey().toString()));
+ vertexValue.setActualKmer(new VKmerBytesWritable(getRecordReader().getCurrentKey().toString()));
vertexValue.setState(State.IS_NON);
vertex.setVertexValue(vertexValue);
}
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 3f8216c..b4c0aee 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
@@ -10,18 +10,18 @@
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.P2ForPathMergeVertex;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
import edu.uci.ics.pregelix.api.graph.Vertex;
import edu.uci.ics.pregelix.api.io.VertexWriter;
public class P2PathMergeOutputFormat extends
- BinaryDataCleanVertexOutputFormat<KmerBytesWritable, VertexValueWritable, NullWritable> {
+ BinaryDataCleanVertexOutputFormat<VKmerBytesWritable, VertexValueWritable, NullWritable> {
@Override
- public VertexWriter<KmerBytesWritable, VertexValueWritable, NullWritable> createVertexWriter(
+ public VertexWriter<VKmerBytesWritable, VertexValueWritable, NullWritable> createVertexWriter(
TaskAttemptContext context) throws IOException, InterruptedException {
@SuppressWarnings("unchecked")
- RecordWriter<KmerBytesWritable, VertexValueWritable> recordWriter = binaryOutputFormat.getRecordWriter(context);
+ RecordWriter<VKmerBytesWritable, VertexValueWritable> recordWriter = binaryOutputFormat.getRecordWriter(context);
return new BinaryLoadGraphVertexWriter(recordWriter);
}
@@ -29,13 +29,13 @@
* Simple VertexWriter that supports {@link BinaryLoadGraphVertex}
*/
public static class BinaryLoadGraphVertexWriter extends
- BinaryVertexWriter<KmerBytesWritable, VertexValueWritable, NullWritable> {
- public BinaryLoadGraphVertexWriter(RecordWriter<KmerBytesWritable, VertexValueWritable> lineRecordWriter) {
+ BinaryVertexWriter<VKmerBytesWritable, VertexValueWritable, NullWritable> {
+ public BinaryLoadGraphVertexWriter(RecordWriter<VKmerBytesWritable, VertexValueWritable> lineRecordWriter) {
super(lineRecordWriter);
}
@Override
- public void writeVertex(Vertex<KmerBytesWritable, VertexValueWritable, NullWritable, ?> vertex)
+ public void writeVertex(Vertex<VKmerBytesWritable, VertexValueWritable, NullWritable, ?> vertex)
throws IOException, InterruptedException {
byte selfFlag = (byte)(vertex.getVertexValue().getState() & State.VERTEX_MASK);
if(selfFlag == State.IS_FINAL)
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/graph/GenerateGraphViz.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/graph/GenerateGraphViz.java
index b65a4a1..bb20797 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/graph/GenerateGraphViz.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/graph/GenerateGraphViz.java
@@ -19,7 +19,7 @@
* Construct a DOT graph in memory, convert it
* to image and store the image in the file system.
*/
- private void convertGraphCleanOutputToGraphViz(String srcDir, String destDir) throws Exception {
+ public static void convertGraphCleanOutputToGraphViz(String srcDir, String destDir) throws Exception {
GraphViz gv = new GraphViz();
gv.addln(gv.start_graph());
@@ -52,11 +52,13 @@
System.out.println(gv.getDotSource());
String type = "ps";
- File out = new File("graphtest/" + "test_out." + type); // Linux
+ File folder = new File(destDir);
+ folder.mkdirs();
+ File out = new File(destDir + "/result." + type); // Linux
gv.writeGraphToFile(gv.getGraph(gv.getDotSource(), type), out);
}
- public String convertEdgeToGraph(String outputNode, VertexValueWritable value){
+ public static String convertEdgeToGraph(String outputNode, VertexValueWritable value){
String outputEdge = "";
Iterator<VKmerBytesWritable> kmerIterator;
kmerIterator = value.getFFList().iterator();
@@ -83,11 +85,6 @@
}
public static void main(String[] args) throws Exception {
- GenerateGraphViz g = new GenerateGraphViz();
- g.convertGraphCleanOutputToGraphViz("data/actual/bubbleadd/BubbleAddGraph/bin/5", "graphtest");
-// g.start("CyclePath_7");
-// g.start("SimplePath_7");
-// g.start("SinglePath_7");
-// g.start("TreePath_7");
+ GenerateGraphViz.convertGraphCleanOutputToGraphViz("data/actual/bubbleadd/BubbleAddGraph/bin/5", "graphtest");
}
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/AdjacencyListWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/AdjacencyListWritable.java
index 44fa444..71d9d01 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/AdjacencyListWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/AdjacencyListWritable.java
@@ -46,7 +46,7 @@
}
public void setForwardList(VKmerListWritable forwardList) {
- this.forwardList = forwardList;
+ this.forwardList.setCopy(forwardList);
}
public VKmerListWritable getReverseList() {
@@ -54,7 +54,7 @@
}
public void setReverseList(VKmerListWritable reverseList) {
- this.reverseList = reverseList;
+ this.reverseList.setCopy(reverseList);
}
@Override
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MergeBubbleMessageWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MergeBubbleMessageWritable.java
index 5702146..3bd423d 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MergeBubbleMessageWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MergeBubbleMessageWritable.java
@@ -117,7 +117,7 @@
}
public int getLengthOfChain() {
- return chainVertexId.getKmerLength();
+ return KmerBytesWritable.getKmerLength();
}
public PositionWritable getStartVertexId() {
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
index e78f090..2d9fdf6 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
@@ -46,9 +46,9 @@
private PositionListWritable nodeIdList;
private AdjacencyListWritable incomingList;
private AdjacencyListWritable outgoingList;
+ private VKmerBytesWritable actualKmer;
+ private float averageCoverage;
private byte state;
- private VKmerBytesWritable kmer;
- private int kmerlength = 0;
private boolean isFakeVertex = false;
public VertexValueWritable() {
@@ -56,38 +56,37 @@
}
public VertexValueWritable(int kmerSize){
- kmerlength = kmerSize;
nodeIdList = new PositionListWritable();
incomingList = new AdjacencyListWritable();
outgoingList = new AdjacencyListWritable();
+ actualKmer = new VKmerBytesWritable();
state = State.IS_NON;
- kmer = new VKmerBytesWritable();
+ averageCoverage = 0;
}
public VertexValueWritable(PositionListWritable nodeIdList, VKmerListWritable forwardForwardList, VKmerListWritable forwardReverseList,
- VKmerListWritable reverseForwardList, VKmerListWritable reverseReverseList,
- byte state, VKmerBytesWritable kmer) {
+ VKmerListWritable reverseForwardList, VKmerListWritable reverseReverseList, VKmerBytesWritable actualKmer,
+ float averageCoverage, byte state) {
set(nodeIdList, forwardForwardList, forwardReverseList,
- reverseForwardList, reverseReverseList,
- state, kmer);
+ reverseForwardList, reverseReverseList, actualKmer,
+ averageCoverage, state);
}
public void set(PositionListWritable nodeIdList, VKmerListWritable forwardForwardList, VKmerListWritable forwardReverseList,
- VKmerListWritable reverseForwardList, VKmerListWritable reverseReverseList,
- byte state, VKmerBytesWritable kmer) {
- this.kmerlength = kmer.getKmerLetterLength();
+ VKmerListWritable reverseForwardList, VKmerListWritable reverseReverseList, VKmerBytesWritable actualKmer,
+ float averageCoverage, byte state) {
this.incomingList.setForwardList(reverseForwardList);
this.incomingList.setReverseList(reverseReverseList);
this.outgoingList.setForwardList(forwardForwardList);
this.outgoingList.setReverseList(forwardReverseList);
+ this.actualKmer.setAsCopy(actualKmer);
+ this.averageCoverage = averageCoverage;
this.state = state;
- this.kmer.setAsCopy(kmer);
}
public void set(VertexValueWritable value) {
- this.kmerlength = value.kmerlength;
- set(value.getNodeIdList(), value.getFFList(),value.getFRList(),value.getRFList(),value.getRRList(),value.getState(),
- value.getKmer());
+ set(value.getNodeIdList(), value.getFFList(),value.getFRList(),value.getRFList(),value.getRRList(),
+ value.getActualKmer(), value.getAverageCoverage(), value.getState());
}
@@ -151,7 +150,22 @@
return state;
}
-
+ public VKmerBytesWritable getActualKmer() {
+ return actualKmer;
+ }
+
+ public void setActualKmer(VKmerBytesWritable kmer) {
+ this.actualKmer.setAsCopy(kmer);
+ }
+
+ public float getAverageCoverage() {
+ return averageCoverage;
+ }
+
+ public void setAverageCoverage(float averageCoverage) {
+ this.averageCoverage = averageCoverage;
+ }
+
public boolean isFakeVertex() {
return isFakeVertex;
}
@@ -165,55 +179,47 @@
}
public int getLengthOfKmer() {
- return kmer.getKmerLetterLength();
+ return actualKmer.getKmerLetterLength();
}
-
- public VKmerBytesWritable getKmer() {
- return kmer;
+
+ public void reset() {
+ this.reset(0);
}
-
- public void setKmer(VKmerBytesWritable kmer) {
- this.kmer.setAsCopy(kmer);
- }
-
- public int getKmerlength() {
- return kmerlength;
- }
-
- public void setKmerlength(int kmerlength) {
- this.kmerlength = kmerlength;
- }
-
+
public void reset(int kmerSize) {
- this.kmerlength = kmerSize;
this.nodeIdList.reset();
this.incomingList.getForwardList().reset();
this.incomingList.getReverseList().reset();
this.outgoingList.getForwardList().reset();
this.outgoingList.getReverseList().reset();
-// this.kmer.reset(0);
+ this.actualKmer.reset(0);
+ averageCoverage = 0;
}
@Override
public void readFields(DataInput in) throws IOException {
- this.kmerlength = in.readInt();
- this.reset(kmerlength);
+ reset();
this.nodeIdList.readFields(in);
- this.incomingList.readFields(in);
- this.outgoingList.readFields(in);
+ this.outgoingList.getForwardList().readFields(in);
+ this.outgoingList.getReverseList().readFields(in);
+ this.incomingList.getForwardList().readFields(in);
+ this.incomingList.getReverseList().readFields(in);
+ this.actualKmer.readFields(in);
+ averageCoverage = in.readFloat();
this.state = in.readByte();
- this.kmer.readFields(in);
this.isFakeVertex = in.readBoolean();
}
@Override
public void write(DataOutput out) throws IOException {
- out.writeInt(this.kmerlength);
this.nodeIdList.write(out);
- this.incomingList.write(out);
- this.outgoingList.write(out);
+ this.outgoingList.getForwardList().write(out);
+ this.outgoingList.getReverseList().write(out);
+ this.incomingList.getForwardList().write(out);
+ this.incomingList.getReverseList().write(out);
+ this.actualKmer.write(out);
+ out.writeFloat(averageCoverage);
out.writeByte(this.state);
- this.kmer.write(out);
out.writeBoolean(this.isFakeVertex);
}
@@ -231,7 +237,7 @@
sbuilder.append(outgoingList.getReverseList().toString()).append('\t');
sbuilder.append(incomingList.getForwardList().toString()).append('\t');
sbuilder.append(incomingList.getReverseList().toString()).append('\t');
- sbuilder.append(kmer.toString()).append('}');
+ sbuilder.append(actualKmer.toString()).append('}');
return sbuilder.toString();
}
@@ -315,19 +321,19 @@
switch (neighborToDeleteDir & MessageFlag.DIR_MASK) {
case MessageFlag.DIR_FF:
this.getFFList().remove(nodeToDelete); //set(null);
- this.getKmer().mergeWithFFKmer(kmerSize, kmer);
+ this.getActualKmer().mergeWithFFKmer(kmerSize, kmer);
break;
case MessageFlag.DIR_FR:
this.getFRList().remove(nodeToDelete);
- this.getKmer().mergeWithFRKmer(kmerSize, kmer);
+ this.getActualKmer().mergeWithFRKmer(kmerSize, kmer);
break;
case MessageFlag.DIR_RF:
this.getRFList().remove(nodeToDelete);
- this.getKmer().mergeWithRFKmer(kmerSize, kmer);
+ this.getActualKmer().mergeWithRFKmer(kmerSize, kmer);
break;
case MessageFlag.DIR_RR:
this.getRRList().remove(nodeToDelete);
- this.getKmer().mergeWithRRKmer(kmerSize, kmer);
+ this.getActualKmer().mergeWithRRKmer(kmerSize, kmer);
break;
}
// TODO: remove switch below and replace with general direction merge
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeAddVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeAddVertex.java
index 3f4e409..0b6a156 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeAddVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeAddVertex.java
@@ -96,7 +96,7 @@
VKmerListWritable kmerRFList = new VKmerListWritable();
kmerRFList.append(otherVertexId);
vertexValue.setRFList(kmerRFList);
- vertexValue.setKmer(vertexId);
+ vertexValue.setActualKmer(vertexId);
vertex.setVertexValue(vertexValue);
addVertex(vertexId, vertex);
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleAddVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleAddVertex.java
index 0c96412..7dd5f32 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleAddVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleAddVertex.java
@@ -64,7 +64,7 @@
initVertex();
if(getSuperstep() == 1){
if(getVertexId().toString().equals("ATA")){
- VKmerBytesWritable vertexId = new VKmerBytesWritable(kmerSize);
+ VKmerBytesWritable vertexId = new VKmerBytesWritable();
vertexId.setByRead(kmerSize, "GTA".getBytes(), 0);
getVertexValue().getFRList().append(vertexId);
@@ -84,18 +84,18 @@
VKmerListWritable kmerFRList = new VKmerListWritable();
kmerFRList.append(getVertexId());
vertexValue.setFRList(kmerFRList);
- VKmerBytesWritable otherVertexId = new VKmerBytesWritable(kmerSize);
+ VKmerBytesWritable otherVertexId = new VKmerBytesWritable();
otherVertexId.setByRead(kmerSize, "AGA".getBytes(), 0);
VKmerListWritable kmerRFList = new VKmerListWritable();
kmerRFList.append(otherVertexId);
vertexValue.setRFList(kmerRFList);
- vertexValue.setKmer(vertexId);
+ vertexValue.setActualKmer(vertexId);
vertex.setVertexValue(vertexValue);
addVertex(vertexId, vertex);
}
else if(getVertexId().toString().equals("AGA")){
- VKmerBytesWritable brdgeVertexId = new VKmerBytesWritable(kmerSize);
+ VKmerBytesWritable brdgeVertexId = new VKmerBytesWritable();
brdgeVertexId.setByRead(kmerSize, "GTA".getBytes(), 0);
getVertexValue().getRFList().append(brdgeVertexId);
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java
index 22b4a73..9b8a03d 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java
@@ -6,20 +6,14 @@
import java.util.Iterator;
import java.util.Map;
-import org.apache.hadoop.io.NullWritable;
-
import edu.uci.ics.genomix.type.VKmerBytesWritable;
-import edu.uci.ics.genomix.type.KmerBytesWritableFactory;
-import edu.uci.ics.pregelix.api.graph.Vertex;
import edu.uci.ics.pregelix.api.job.PregelixJob;
import edu.uci.ics.genomix.pregelix.client.Client;
import edu.uci.ics.genomix.pregelix.format.GraphCleanInputFormat;
import edu.uci.ics.genomix.pregelix.format.GraphCleanOutputFormat;
-import edu.uci.ics.genomix.pregelix.io.MergeBubbleMessageWritable;
import edu.uci.ics.genomix.pregelix.io.MessageWritable;
import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
import edu.uci.ics.genomix.pregelix.operator.pathmerge.BasicGraphCleanVertex;
-import edu.uci.ics.genomix.pregelix.type.AdjMessage;
import edu.uci.ics.genomix.pregelix.type.MessageFlag;
import edu.uci.ics.genomix.pregelix.util.VertexUtil;
@@ -29,8 +23,6 @@
public class BubbleMergeVertex extends
BasicGraphCleanVertex {
- private KmerBytesWritableFactory kmerFactory = new KmerBytesWritableFactory(1);
-
private Map<VKmerBytesWritable, ArrayList<MessageWritable>> receivedMsgMap = new HashMap<VKmerBytesWritable, ArrayList<MessageWritable>>();
private ArrayList<MessageWritable> receivedMsgList = new ArrayList<MessageWritable>();
@@ -54,7 +46,7 @@
if(hasNextDest(getVertexValue())){
outgoingMsg.setStartVertexId(incomingMsg.getSourceVertexId());
outgoingMsg.setSourceVertexId(getVertexId());
- outgoingMsg.setActualKmer(getVertexValue().getKmer());
+ outgoingMsg.setActualKmer(getVertexValue().getActualKmer());
destVertexId.setAsCopy(getNextDestVertexId(getVertexValue()));
sendMsg(destVertexId, outgoingMsg);
}
@@ -64,7 +56,7 @@
if(hasPrevDest(getVertexValue())){
outgoingMsg.setStartVertexId(incomingMsg.getSourceVertexId());
outgoingMsg.setSourceVertexId(getVertexId());
- outgoingMsg.setActualKmer(getVertexValue().getKmer());
+ outgoingMsg.setActualKmer(getVertexValue().getActualKmer());
destVertexId.setAsCopy(getPrevDestVertexId(getVertexValue()));
sendMsg(destVertexId, outgoingMsg);
}
@@ -109,7 +101,7 @@
/** for each startVertex, sort the node by decreasing order of coverage **/
receivedMsgList = receivedMsgMap.get(prevId);
Collections.sort(receivedMsgList, new MessageWritable.SortByCoverage());
-
+ System.out.println("");
/** process similarSet, keep the unchanged set and deleted set & add coverage to unchange node **/
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicGraphCleanVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicGraphCleanVertex.java
index ece573c..080cf35 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicGraphCleanVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicGraphCleanVertex.java
@@ -406,7 +406,7 @@
outgoingMsg.setFlag(outFlag);
outgoingMsg.setNeighberNode(getVertexValue().getIncomingList());
outgoingMsg.setSourceVertexId(getVertexId());
- outgoingMsg.setActualKmer(getVertexValue().getKmer());
+ outgoingMsg.setActualKmer(getVertexValue().getActualKmer());
sendMsg(incomingMsg.getSourceVertexId(), outgoingMsg); //getNextDestVertexId(getVertexValue())
break;
case MessageFlag.DIR_RF:
@@ -419,7 +419,7 @@
outgoingMsg.setFlag(outFlag);
outgoingMsg.setNeighberNode(getVertexValue().getOutgoingList());
outgoingMsg.setSourceVertexId(getVertexId());
- outgoingMsg.setActualKmer(getVertexValue().getKmer());
+ outgoingMsg.setActualKmer(getVertexValue().getActualKmer());
sendMsg(incomingMsg.getSourceVertexId(), outgoingMsg); //getPreDestVertexId(getVertexValue())
break;
}
@@ -444,7 +444,7 @@
outgoingMsg.setFlag(outFlag);
outgoingMsg.setNeighberNode(getVertexValue().getIncomingList());
outgoingMsg.setSourceVertexId(getVertexId());
- outgoingMsg.setActualKmer(getVertexValue().getKmer());
+ outgoingMsg.setActualKmer(getVertexValue().getActualKmer());
sendMsg(incomingMsg.getSourceVertexId(), outgoingMsg); //getNextDestVertexId(getVertexValue())
break;
case MessageFlag.DIR_RF:
@@ -457,7 +457,7 @@
outgoingMsg.setFlag(outFlag);
outgoingMsg.setNeighberNode(getVertexValue().getOutgoingList());
outgoingMsg.setSourceVertexId(getVertexId());
- outgoingMsg.setActualKmer(getVertexValue().getKmer());
+ outgoingMsg.setActualKmer(getVertexValue().getActualKmer());
sendMsg(incomingMsg.getSourceVertexId(), outgoingMsg); //getPreDestVertexId(getVertexValue())
break;
}
@@ -480,7 +480,7 @@
outgoingMsg.setFlag(outFlag);
outgoingMsg.setNeighberNode(getVertexValue().getIncomingList());
outgoingMsg.setSourceVertexId(getVertexId());
- outgoingMsg.setActualKmer(getVertexValue().getKmer());
+ outgoingMsg.setActualKmer(getVertexValue().getActualKmer());
sendMsg(getNextDestVertexId(getVertexValue()), outgoingMsg);
deleteVertex(getVertexId());
break;
@@ -493,7 +493,7 @@
outgoingMsg.setFlag(outFlag);
outgoingMsg.setNeighberNode(getVertexValue().getOutgoingList());
outgoingMsg.setSourceVertexId(getVertexId());
- outgoingMsg.setActualKmer(getVertexValue().getKmer());
+ outgoingMsg.setActualKmer(getVertexValue().getActualKmer());
sendMsg(getPrevDestVertexId(getVertexValue()), outgoingMsg);
deleteVertex(getVertexId());
break;
@@ -649,28 +649,28 @@
int index;
switch(neighborToMeDir){
case MessageFlag.DIR_FF:
- selfString = getVertexValue().getKmer().toString();
+ selfString = getVertexValue().getActualKmer().toString();
match = selfString.substring(selfString.length() - kmerSize + 1,selfString.length());
msgString = msg.getActualKmer().toString();
index = msgString.indexOf(match);
tmpKmer.setByRead(msgString.length() - index, msgString.substring(index).getBytes(), 0);
break;
case MessageFlag.DIR_FR:
- selfString = getVertexValue().getKmer().toString();
+ selfString = getVertexValue().getActualKmer().toString();
match = selfString.substring(selfString.length() - kmerSize + 1,selfString.length());
msgString = GeneCode.reverseComplement(msg.getActualKmer().toString());
index = msgString.indexOf(match);
tmpKmer.setByReadReverse(msgString.length() - index, msgString.substring(index).getBytes(), 0);
break;
case MessageFlag.DIR_RF:
- selfString = getVertexValue().getKmer().toString();
+ selfString = getVertexValue().getActualKmer().toString();
match = selfString.substring(0,kmerSize - 1);
msgString = GeneCode.reverseComplement(msg.getActualKmer().toString());
index = msgString.lastIndexOf(match) + kmerSize - 2;
tmpKmer.setByReadReverse(index + 1, msgString.substring(0, index + 1).getBytes(), 0);
break;
case MessageFlag.DIR_RR:
- selfString = getVertexValue().getKmer().toString();
+ selfString = getVertexValue().getActualKmer().toString();
match = selfString.substring(0,kmerSize - 1);
msgString = msg.getActualKmer().toString();
index = msgString.lastIndexOf(match) + kmerSize - 2;
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/MapReduceVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/MapReduceVertex.java
index 1c981f2..10137da 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/MapReduceVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/MapReduceVertex.java
@@ -96,7 +96,7 @@
public void sendMsgToFakeVertex(){
if(!getVertexValue().isFakeVertex()){
outgoingMsg.setSourceVertexId(getVertexId());
- outgoingMsg.setActualKmer(getVertexValue().getKmer());
+ outgoingMsg.setActualKmer(getVertexValue().getActualKmer());
sendMsg(fakeVertex, outgoingMsg);
voteToHalt();
}
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 f6a005c..f5b0157 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
@@ -185,7 +185,7 @@
//merge chain
lastKmer.setAsCopy(kmerFactory.getLastKmerFromChain(incomingMsg.getLengthOfChain() - kmerSize + 1,
incomingMsg.getActualKmer()));
- getVertexValue().setKmer(kmerFactory.mergeTwoKmer(getVertexValue().getKmer(), lastKmer));
+ getVertexValue().setActualKmer(kmerFactory.mergeTwoKmer(getVertexValue().getActualKmer(), lastKmer));
getVertexValue().setOutgoingList(incomingMsg.getNeighberNode());
}
@@ -221,7 +221,7 @@
public void responseMsgToHeadVertex() {
deleteVertex(getVertexId());
outgoingMsg.setNeighberNode(getVertexValue().getOutgoingList());
- outgoingMsg.setActualKmer(getVertexValue().getKmer());
+ outgoingMsg.setActualKmer(getVertexValue().getActualKmer());
if (getVertexValue().getState() == State.IS_HEAD)//is_tail
outgoingMsg.setFlag(Message.STOP);
destVertexId.setAsCopy(incomingMsg.getSourceVertexId());
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P3ForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P3ForPathMergeVertex.java
index 184a7b2..9a3aed5 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P3ForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P3ForPathMergeVertex.java
@@ -230,8 +230,8 @@
public void mergeChainVertex(){
lastKmer.setAsCopy(kmerFactory.getLastKmerFromChain(incomingMsg.getLengthOfChain() - kmerSize + 1,
incomingMsg.getActualKmer()));
- getVertexValue().setKmer(
- kmerFactory.mergeTwoKmer(getVertexValue().getKmer(),
+ getVertexValue().setActualKmer(
+ kmerFactory.mergeTwoKmer(getVertexValue().getActualKmer(),
lastKmer));
getVertexValue().setOutgoingList(incomingMsg.getNeighberNode());
}
@@ -268,7 +268,7 @@
public void responseMsgToHeadVertexMergePhase() {
deleteVertex(getVertexId());
outgoingMsg.setNeighberNode(getVertexValue().getOutgoingList());
- outgoingMsg.setActualKmer(getVertexValue().getKmer());
+ outgoingMsg.setActualKmer(getVertexValue().getActualKmer());
if (getVertexValue().getState() == State2.END_VERTEX)
outgoingMsg.setFlag(Message.STOP);
sendMsg(incomingMsg.getSourceVertexId(), outgoingMsg);
@@ -322,7 +322,7 @@
else {
deleteVertex(getVertexId());
outgoingMsg.setNeighberNode(getVertexValue().getOutgoingList()); //incomingMsg.getNeighberNode()
- outgoingMsg.setActualKmer(getVertexValue().getKmer());
+ outgoingMsg.setActualKmer(getVertexValue().getActualKmer());
if (getVertexValue().getState() == State2.PSEUDOREAR)
outgoingMsg.setFlag(Message.FROMPSEUDOREAR);
else if (getVertexValue().getState() == State2.END_VERTEX)
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P5ForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P5ForPathMergeVertex.java
index 154fbda..0a43a96 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P5ForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P5ForPathMergeVertex.java
@@ -244,7 +244,7 @@
getVertexValue().setState(MessageFlag.IS_HEAD); //State.START_VERTEX
} else if (incomingMsg.getFlag() == Message.END && getVertexValue().getState() != State.IS_HEAD) {
getVertexValue().setState(MessageFlag.IS_HEAD);
- getVertexValue().setKmer(getVertexValue().getKmer());
+ getVertexValue().setActualKmer(getVertexValue().getActualKmer());
//voteToHalt();
} //else
//voteToHalt();
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipAddVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipAddVertex.java
index cff87c7..0738208 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipAddVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipAddVertex.java
@@ -89,7 +89,7 @@
VKmerListWritable kmerList = new VKmerListWritable();
kmerList.append(getVertexId());
vertexValue.setRFList(kmerList);
- vertexValue.setKmer(vertexId);
+ vertexValue.setActualKmer(vertexId);
vertex.setVertexValue(vertexValue);
addVertex(vertexId, vertex);
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/ConvertNodeToIdValue.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/ConvertNodeToIdValue.java
index 13d9d98..4e728e2 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/ConvertNodeToIdValue.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/ConvertNodeToIdValue.java
@@ -39,7 +39,7 @@
outputValue.setFRList(node.getFRList());
outputValue.setRFList(node.getRFList());
outputValue.setRRList(node.getRRList());
- outputValue.setKmer(node.getKmer());
+ outputValue.setActualKmer(node.getKmer());
outputValue.setState(State.IS_HEAD);
writer.append(outputKey, outputValue);
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/GenerateTextFile.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/GenerateTextFile.java
index 8618237..b3a3d37 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/GenerateTextFile.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/GenerateTextFile.java
@@ -14,12 +14,11 @@
import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
import edu.uci.ics.genomix.pregelix.io.VertexValueWritable.State;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
public class GenerateTextFile {
public static void generateFromPathmergeResult(int kmerSize, String strSrcDir, String outPutDir) throws IOException {
- KmerBytesWritable.setGlobalKmerLength(kmerSize);
Configuration conf = new Configuration();
FileSystem fileSys = FileSystem.getLocal(conf);
@@ -28,7 +27,7 @@
File srcPath = new File(strSrcDir);
for (File f : srcPath.listFiles((FilenameFilter) (new WildcardFileFilter("part*")))) {
SequenceFile.Reader reader = new SequenceFile.Reader(fileSys, new Path(f.getAbsolutePath()), conf);
- KmerBytesWritable key = new KmerBytesWritable();
+ VKmerBytesWritable key = new VKmerBytesWritable();
VertexValueWritable value = new VertexValueWritable();
while (reader.next(key, value)) {
@@ -45,14 +44,13 @@
}
public static void generateSpecificLengthChainFromNaivePathmergeResult(int maxLength) throws IOException {
- KmerBytesWritable.setGlobalKmerLength(55);
BufferedWriter bw = new BufferedWriter(new FileWriter("naive_text_" + maxLength));
Configuration conf = new Configuration();
FileSystem fileSys = FileSystem.get(conf);
for (int i = 0; i < 2; i++) {
Path path = new Path("/home/anbangx/genomix_result/final_naive/part-" + i);
SequenceFile.Reader reader = new SequenceFile.Reader(fileSys, path, conf);
- KmerBytesWritable key = new KmerBytesWritable();
+ VKmerBytesWritable key = new VKmerBytesWritable();
VertexValueWritable value = new VertexValueWritable();
while (reader.next(key, value)) {
@@ -70,14 +68,13 @@
}
public static void generateSpecificLengthChainFromLogPathmergeResult(int maxLength) throws IOException {
- KmerBytesWritable.setGlobalKmerLength(55);
BufferedWriter bw = new BufferedWriter(new FileWriter("log_text_" + maxLength));
Configuration conf = new Configuration();
FileSystem fileSys = FileSystem.get(conf);
for (int i = 0; i < 2; i++) {
Path path = new Path("/home/anbangx/genomix_result/improvelog2/part-" + i);
SequenceFile.Reader reader = new SequenceFile.Reader(fileSys, path, conf);
- KmerBytesWritable key = new KmerBytesWritable();
+ VKmerBytesWritable key = new VKmerBytesWritable();
VertexValueWritable value = new VertexValueWritable();
while (reader.next(key, value)) {
@@ -96,13 +93,12 @@
}
public static void generateFromGraphbuildResult() throws IOException {
- KmerBytesWritable.setGlobalKmerLength(55);
BufferedWriter bw = new BufferedWriter(new FileWriter("textfile"));
Configuration conf = new Configuration();
FileSystem fileSys = FileSystem.get(conf);
Path path = new Path("data/input/part-0-out-3000000");
SequenceFile.Reader reader = new SequenceFile.Reader(fileSys, path, conf);
- KmerBytesWritable key = new KmerBytesWritable();
+ VKmerBytesWritable key = new VKmerBytesWritable();
while (reader.next(key, null)) {
if (key == null) {
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 ff5f404..2ef9958 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
@@ -12,16 +12,14 @@
import edu.uci.ics.genomix.pregelix.operator.bridgeremove.BridgeAddVertex;
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.P2ForPathMergeVertex;
import edu.uci.ics.genomix.pregelix.operator.pathmerge.MapReduceVertex;
-import edu.uci.ics.genomix.pregelix.operator.pathmerge.P1ForPathMergeVertex;
import edu.uci.ics.genomix.pregelix.operator.pathmerge.P3ForPathMergeVertex;
import edu.uci.ics.genomix.pregelix.operator.pathmerge.P4ForPathMergeVertex;
import edu.uci.ics.genomix.pregelix.operator.splitrepeat.SplitRepeatVertex;
import edu.uci.ics.genomix.pregelix.operator.tipremove.TipAddVertex;
import edu.uci.ics.genomix.pregelix.operator.tipremove.TipRemoveVertex;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
import edu.uci.ics.pregelix.api.job.PregelixJob;
public class JobGenerator {
@@ -51,7 +49,7 @@
job.setVertexInputFormatClass(InitialGraphCleanInputFormat.class);
job.setVertexOutputFormatClass(P2PathMergeOutputFormat.class);
job.setDynamicVertexValueSize(true);
- job.setOutputKeyClass(KmerBytesWritable.class);
+ job.setOutputKeyClass(VKmerBytesWritable.class);
job.setOutputValueClass(VertexValueWritable.class);
job.getConfiguration().setInt(P2ForPathMergeVertex.KMER_SIZE, 3);
job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
@@ -103,7 +101,7 @@
job.setVertexInputFormatClass(GraphCleanInputFormat.class);
job.setVertexOutputFormatClass(P2PathMergeOutputFormat.class);
job.setDynamicVertexValueSize(true);
- job.setOutputKeyClass(KmerBytesWritable.class);
+ job.setOutputKeyClass(VKmerBytesWritable.class);
job.setOutputValueClass(VertexValueWritable.class);
job.getConfiguration().setInt(MapReduceVertex.KMER_SIZE, 3);
job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
@@ -119,7 +117,7 @@
job.setVertexInputFormatClass(InitialGraphCleanInputFormat.class);
job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
job.setDynamicVertexValueSize(true);
- job.setOutputKeyClass(KmerBytesWritable.class);
+ job.setOutputKeyClass(VKmerBytesWritable.class);
job.setOutputValueClass(VertexValueWritable.class);
job.getConfiguration().setInt(SplitRepeatVertex.KMER_SIZE, 3);
job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
@@ -134,7 +132,7 @@
job.setVertexInputFormatClass(InitialGraphCleanInputFormat.class);
job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
job.setDynamicVertexValueSize(true);
- job.setOutputKeyClass(KmerBytesWritable.class);
+ job.setOutputKeyClass(VKmerBytesWritable.class);
job.setOutputValueClass(VertexValueWritable.class);
job.getConfiguration().setInt(TipAddVertex.KMER_SIZE, 3);
job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
@@ -151,7 +149,7 @@
job.setVertexInputFormatClass(GraphCleanInputFormat.class);
job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
job.setDynamicVertexValueSize(true);
- job.setOutputKeyClass(KmerBytesWritable.class);
+ job.setOutputKeyClass(VKmerBytesWritable.class);
job.setOutputValueClass(VertexValueWritable.class);
job.getConfiguration().setInt(TipRemoveVertex.KMER_SIZE, 3);
job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
@@ -168,7 +166,7 @@
job.setVertexInputFormatClass(InitialGraphCleanInputFormat.class);
job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
job.setDynamicVertexValueSize(true);
- job.setOutputKeyClass(KmerBytesWritable.class);
+ job.setOutputKeyClass(VKmerBytesWritable.class);
job.setOutputValueClass(VertexValueWritable.class);
job.getConfiguration().setInt(BridgeAddVertex.KMER_SIZE, 3);
job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
@@ -185,7 +183,7 @@
job.setVertexInputFormatClass(GraphCleanInputFormat.class);
job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
job.setDynamicVertexValueSize(true);
- job.setOutputKeyClass(KmerBytesWritable.class);
+ job.setOutputKeyClass(VKmerBytesWritable.class);
job.setOutputValueClass(VertexValueWritable.class);
job.getConfiguration().setInt(TipRemoveVertex.KMER_SIZE, 3);
job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
@@ -202,7 +200,7 @@
job.setVertexInputFormatClass(InitialGraphCleanInputFormat.class);
job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
job.setDynamicVertexValueSize(true);
- job.setOutputKeyClass(KmerBytesWritable.class);
+ job.setOutputKeyClass(VKmerBytesWritable.class);
job.setOutputValueClass(VertexValueWritable.class);
job.getConfiguration().setInt(BubbleAddVertex.KMER_SIZE, 3);
job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BasicSmallTestCase.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BasicSmallTestCase.java
index e138348..70ac94f 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BasicSmallTestCase.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BasicSmallTestCase.java
@@ -23,6 +23,7 @@
import org.apache.hadoop.mapreduce.lib.output.FileOutputFormat;
import org.junit.Test;
+import edu.uci.ics.genomix.pregelix.graph.GenerateGraphViz;
import edu.uci.ics.genomix.pregelix.sequencefile.GenerateTextFile;
import edu.uci.ics.pregelix.api.job.PregelixJob;
import edu.uci.ics.pregelix.core.base.IDriver.Plan;
@@ -33,12 +34,13 @@
private final PregelixJob job;
private final String resultFileDir;
private final String textFileDir;
+ private final String graphvizFileDir;
private final String jobFile;
private final Driver driver = new Driver(this.getClass());
private final FileSystem dfs;
public BasicSmallTestCase(String hadoopConfPath, String jobName, String jobFile, FileSystem dfs,
- String hdfsInput, String resultFile, String textFile) throws Exception {
+ String hdfsInput, String resultFile, String textFile, String graphvizFile) throws Exception {
super("test");
this.jobFile = jobFile;
this.job = new PregelixJob("test");
@@ -46,9 +48,10 @@
this.job.getConfiguration().addResource(new Path(hadoopConfPath));
FileInputFormat.setInputPaths(job, hdfsInput);
FileOutputFormat.setOutputPath(job, new Path(hdfsInput + "_result"));
- this.textFileDir = textFile;
job.setJobName(jobName);
this.resultFileDir = resultFile;
+ this.textFileDir = textFile;
+ this.graphvizFileDir = graphvizFile;
this.dfs = dfs;
}
@@ -75,6 +78,7 @@
private void compareResults() throws Exception {
dfs.copyToLocalFile(FileOutputFormat.getOutputPath(job), new Path(resultFileDir));
GenerateTextFile.generateFromPathmergeResult(3, resultFileDir, textFileDir);
+ GenerateGraphViz.convertGraphCleanOutputToGraphViz(resultFileDir, graphvizFileDir);
}
public String toString() {
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BridgeAddSmallTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BridgeAddSmallTestSuite.java
index c4f0963..c492d1e 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BridgeAddSmallTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BridgeAddSmallTestSuite.java
@@ -143,9 +143,11 @@
+ File.separator + "bin" + File.separator + testDir.getName();
String textFileName = ACTUAL_RESULT_DIR + File.separator + jobExtToResExt(qFile.getName())
+ File.separator + "txt" + File.separator + testDir.getName();
+ String graphvizFileName = ACTUAL_RESULT_DIR + File.separator + jobExtToResExt(qFile.getName())
+ + File.separator + "graphviz" + File.separator + testDir.getName();
testSuite.addTest(new BasicSmallTestCase(HADOOP_CONF_PATH, qFile.getName(), qFile
.getAbsolutePath().toString(), dfs,
- HDFS_INPUTPATH + File.separator + testDir.getName(), resultFileName, textFileName));
+ HDFS_INPUTPATH + File.separator + testDir.getName(), resultFileName, textFileName, graphvizFileName));
}
}
}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BridgeRemoveSmallTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BridgeRemoveSmallTestSuite.java
index 171a6ca..8d22e9a 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BridgeRemoveSmallTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BridgeRemoveSmallTestSuite.java
@@ -143,9 +143,11 @@
+ File.separator + "bin" + File.separator + testDir.getName();
String textFileName = ACTUAL_RESULT_DIR + File.separator + jobExtToResExt(qFile.getName())
+ File.separator + "txt" + File.separator + testDir.getName();
+ String graphvizFileName = ACTUAL_RESULT_DIR + File.separator + jobExtToResExt(qFile.getName())
+ + File.separator + "graphviz" + File.separator + testDir.getName();
testSuite.addTest(new BasicSmallTestCase(HADOOP_CONF_PATH, qFile.getName(), qFile
.getAbsolutePath().toString(), dfs,
- HDFS_INPUTPATH + File.separator + testDir.getName(), resultFileName, textFileName));
+ HDFS_INPUTPATH + File.separator + testDir.getName(), resultFileName, textFileName, graphvizFileName));
}
}
}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleAddSmallTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleAddSmallTestSuite.java
index a9c2774..1e5df13 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleAddSmallTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleAddSmallTestSuite.java
@@ -143,9 +143,11 @@
+ File.separator + "bin" + File.separator + testDir.getName();
String textFileName = ACTUAL_RESULT_DIR + File.separator + jobExtToResExt(qFile.getName())
+ File.separator + "txt" + File.separator + testDir.getName();
+ String graphvizFileName = ACTUAL_RESULT_DIR + File.separator + jobExtToResExt(qFile.getName())
+ + File.separator + "graphviz" + File.separator + testDir.getName();
testSuite.addTest(new BasicSmallTestCase(HADOOP_CONF_PATH, qFile.getName(), qFile
.getAbsolutePath().toString(), dfs,
- HDFS_INPUTPATH + File.separator + testDir.getName(), resultFileName, textFileName));
+ HDFS_INPUTPATH + File.separator + testDir.getName(), resultFileName, textFileName, graphvizFileName));
}
}
}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleMergeSmallTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleMergeSmallTestSuite.java
index a94d31c..57647ab 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleMergeSmallTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/BubbleMergeSmallTestSuite.java
@@ -143,9 +143,11 @@
+ File.separator + "bin" + File.separator + testDir.getName();
String textFileName = ACTUAL_RESULT_DIR + File.separator + jobExtToResExt(qFile.getName())
+ File.separator + "txt" + File.separator + testDir.getName();
+ String graphvizFileName = ACTUAL_RESULT_DIR + File.separator + jobExtToResExt(qFile.getName())
+ + File.separator + "graphviz" + File.separator + testDir.getName();
testSuite.addTest(new BasicSmallTestCase(HADOOP_CONF_PATH, qFile.getName(), qFile
.getAbsolutePath().toString(), dfs,
- HDFS_INPUTPATH + File.separator + testDir.getName(), resultFileName, textFileName));
+ HDFS_INPUTPATH + File.separator + testDir.getName(), resultFileName, textFileName, graphvizFileName));
}
}
}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestSuite.java
index 115f090..7b937c8 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeSmallTestSuite.java
@@ -150,9 +150,11 @@
+ File.separator + "bin" + File.separator + testDir.getName();
String textFileName = ACTUAL_RESULT_DIR + File.separator + jobExtToResExt(qFile.getName())
+ File.separator + "txt" + File.separator + testDir.getName();
+ String graphvizFileName = ACTUAL_RESULT_DIR + File.separator + jobExtToResExt(qFile.getName())
+ + File.separator + "graphviz" + File.separator + testDir.getName();
testSuite.addTest(new BasicSmallTestCase(HADOOP_CONF_PATH, qFile.getName(), qFile
.getAbsolutePath().toString(), dfs,
- HDFS_INPUTPATH + File.separator + testDir.getName(), resultFileName, textFileName));
+ HDFS_INPUTPATH + File.separator + testDir.getName(), resultFileName, textFileName, graphvizFileName));
}
}
}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/SplitRepeatSmallTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/SplitRepeatSmallTestSuite.java
index 1948acd..43f4788 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/SplitRepeatSmallTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/SplitRepeatSmallTestSuite.java
@@ -143,9 +143,11 @@
+ File.separator + "bin" + File.separator + testDir.getName();
String textFileName = ACTUAL_RESULT_DIR + File.separator + jobExtToResExt(qFile.getName())
+ File.separator + "txt" + File.separator + testDir.getName();
+ String graphvizFileName = ACTUAL_RESULT_DIR + File.separator + jobExtToResExt(qFile.getName())
+ + File.separator + "graphviz" + File.separator + testDir.getName();
testSuite.addTest(new BasicSmallTestCase(HADOOP_CONF_PATH, qFile.getName(), qFile
.getAbsolutePath().toString(), dfs,
- HDFS_INPUTPATH + File.separator + testDir.getName(), resultFileName, textFileName));
+ HDFS_INPUTPATH + File.separator + testDir.getName(), resultFileName, textFileName, graphvizFileName));
}
}
}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/TipAddSmallTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/TipAddSmallTestSuite.java
index 57f4ea5..b2d02c8 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/TipAddSmallTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/TipAddSmallTestSuite.java
@@ -143,9 +143,11 @@
+ File.separator + "bin" + File.separator + testDir.getName();
String textFileName = ACTUAL_RESULT_DIR + File.separator + jobExtToResExt(qFile.getName())
+ File.separator + "txt" + File.separator + testDir.getName();
+ String graphvizFileName = ACTUAL_RESULT_DIR + File.separator + jobExtToResExt(qFile.getName())
+ + File.separator + "graphviz" + File.separator + testDir.getName();
testSuite.addTest(new BasicSmallTestCase(HADOOP_CONF_PATH, qFile.getName(), qFile
.getAbsolutePath().toString(), dfs,
- HDFS_INPUTPATH + File.separator + testDir.getName(), resultFileName, textFileName));
+ HDFS_INPUTPATH + File.separator + testDir.getName(), resultFileName, textFileName, graphvizFileName));
}
}
}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/TipRemoveSmallTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/TipRemoveSmallTestSuite.java
index e8ca43f..b4514d6 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/TipRemoveSmallTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/TipRemoveSmallTestSuite.java
@@ -143,9 +143,11 @@
+ File.separator + "bin" + File.separator + testDir.getName();
String textFileName = ACTUAL_RESULT_DIR + File.separator + jobExtToResExt(qFile.getName())
+ File.separator + "txt" + File.separator + testDir.getName();
+ String graphvizFileName = ACTUAL_RESULT_DIR + File.separator + jobExtToResExt(qFile.getName())
+ + File.separator + "graphviz" + File.separator + testDir.getName();
testSuite.addTest(new BasicSmallTestCase(HADOOP_CONF_PATH, qFile.getName(), qFile
.getAbsolutePath().toString(), dfs,
- HDFS_INPUTPATH + File.separator + testDir.getName(), resultFileName, textFileName));
+ HDFS_INPUTPATH + File.separator + testDir.getName(), resultFileName, textFileName, graphvizFileName));
}
}
}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/graphbuilding/JobRunStepByStepTest.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/graphbuilding/JobRunStepByStepTest.java
index 79439a3..0d609bf 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/graphbuilding/JobRunStepByStepTest.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/graphbuilding/JobRunStepByStepTest.java
@@ -41,7 +41,7 @@
import edu.uci.ics.genomix.hyracks.driver.Driver;
import edu.uci.ics.genomix.hyracks.driver.Driver.Plan;
import edu.uci.ics.genomix.hyracks.job.GenomixJobConf;
-import edu.uci.ics.genomix.oldtype.NodeWritable;
+import edu.uci.ics.genomix.type.NodeWritable;
@SuppressWarnings("deprecation")
public class JobRunStepByStepTest {
@@ -175,7 +175,7 @@
}
SequenceFile.Reader reader = new SequenceFile.Reader(dfs, path, conf);
- NodeWritable node = new NodeWritable(conf.getInt(GenomixJobConf.KMER_LENGTH, KmerSize));
+ NodeWritable node = new NodeWritable();
NullWritable value = NullWritable.get();
while (reader.next(node, value)) {
if (node == null) {