add SymmetryChecker
diff --git a/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/sameWithEdge/okay b/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/sameWithEdge/okay
new file mode 100644
index 0000000..7fb459e
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/sameWithEdge/okay
@@ -0,0 +1 @@
+1 GTAAAAAAAAAACC
diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTestSuite.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTestSuite.java
index 63e875a..b2bafef 100644
--- a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTestSuite.java
+++ b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTestSuite.java
@@ -30,7 +30,7 @@
// + "P2_5", PreFix + File.separator
// + "P2_7", PreFix + File.separator
// + "P2_8"
- + "same"
+ + "sameWithEdge"
};
// + "SimpleRectangle", PreFix + File.separator
// + "MediumRectangle", PreFix + File.separator
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/sameWithEdge/..binmerge.crc b/genomix/genomix-pregelix/data/TestSet/PathMerge/sameWithEdge/..binmerge.crc
new file mode 100644
index 0000000..7936d21
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/sameWithEdge/..binmerge.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/sameWithEdge/.binmerge b/genomix/genomix-pregelix/data/TestSet/PathMerge/sameWithEdge/.binmerge
new file mode 100755
index 0000000..ac38fae
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/sameWithEdge/.binmerge
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/sameWithEdge/bin/.part-00000.crc b/genomix/genomix-pregelix/data/TestSet/PathMerge/sameWithEdge/bin/.part-00000.crc
new file mode 100644
index 0000000..0bfaa03
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/sameWithEdge/bin/.part-00000.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/sameWithEdge/bin/part-00000 b/genomix/genomix-pregelix/data/TestSet/PathMerge/sameWithEdge/bin/part-00000
new file mode 100755
index 0000000..abba88d
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/sameWithEdge/bin/part-00000
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/sameWithEdge/data b/genomix/genomix-pregelix/data/TestSet/PathMerge/sameWithEdge/data
new file mode 100644
index 0000000..bd2f057
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/sameWithEdge/data
@@ -0,0 +1,5 @@
+AAA {[{AAA:[1]},{AAC:[1]}] [] [] [{AAA:[1]},{TAA:[1]}] {5':[], ~5':[]} 8.0x}
+TAA {[{AAA:[1]}] [] [] [{GTA:[1]}] {5':[], ~5':[]} 1.0x}
+GTA {[{TAA:[1]}] [] [] [] {5':[(1-0_0)], ~5':[]} 1.0x}
+AAC {[{ACC:[1]}] [] [] [{AAA:[1]}] {5':[], ~5':[]} 1.0x}
+ACC {[] [] [] [{AAC:[1]}] {5':[], ~5':[]} 1.0x}
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/sameWithEdge/graphviz/result.svg b/genomix/genomix-pregelix/data/TestSet/PathMerge/sameWithEdge/graphviz/result.svg
new file mode 100644
index 0000000..fe1ec66
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/sameWithEdge/graphviz/result.svg
@@ -0,0 +1,128 @@
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diff --git a/genomix/genomix-pregelix/data/TestSet/SymmetryChecker/2/bin/part-00000 b/genomix/genomix-pregelix/data/TestSet/SymmetryChecker/2/bin/part-00000
new file mode 100755
index 0000000..d3766af
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/SymmetryChecker/2/bin/part-00000
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/SymmetryChecker/2/graphviz/result.ps b/genomix/genomix-pregelix/data/TestSet/SymmetryChecker/2/graphviz/result.ps
new file mode 100644
index 0000000..3afc04f
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+++ b/genomix/genomix-pregelix/data/TestSet/SymmetryChecker/2/graphviz/result.ps
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+0 1 1 edgecolor
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+0 0 0 edgecolor
+14 /Times-Roman set_font
+74 57.4 moveto 48 (RR: [1]) alignedtext
+grestore
+% AAT->ATA
+gsave
+1 setlinewidth
+0 0 0 edgecolor
+newpath 139.51 35.99 moveto
+133.87 33.51 127.87 31.33 122 30 curveto
+101.2 25.28 94.8 25.28 74 30 curveto
+71.34 30.6 68.65 31.38 65.99 32.28 curveto
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+0 0 0 edgecolor
+newpath 64.53 29.09 moveto
+56.49 35.99 lineto
+67.08 35.61 lineto
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+1 setlinewidth
+solid
+0 0 0 edgecolor
+newpath 64.53 29.09 moveto
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+0 0 0 edgecolor
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+75.5 35.4 moveto 45 (FF: [1]) alignedtext
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+%%PageTrailer
+%%EndPage: 1
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+%%Pages: 1
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+end
+restore
+%%EOF
diff --git a/genomix/genomix-pregelix/data/TestSet/SymmetryChecker/2/test.txt b/genomix/genomix-pregelix/data/TestSet/SymmetryChecker/2/test.txt
new file mode 100644
index 0000000..51e1252
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/SymmetryChecker/2/test.txt
@@ -0,0 +1,2 @@
+ATA {[] [] [] [{AAT:[1]}] {5':[], ~5':[]} 1.0x}
+AAT {[{ATA:[1]}] [] [] [] {5':[(1-0_0)], ~5':[]} 1.0x}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/checker/SymmetryCheckerVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/checker/SymmetryCheckerVertex.java
new file mode 100644
index 0000000..1d86859
--- /dev/null
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/checker/SymmetryCheckerVertex.java
@@ -0,0 +1,57 @@
+package edu.uci.ics.genomix.pregelix.checker;
+
+import java.util.Iterator;
+
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable.State;
+import edu.uci.ics.genomix.pregelix.io.message.MessageWritable;
+import edu.uci.ics.genomix.pregelix.operator.BasicGraphCleanVertex;
+import edu.uci.ics.genomix.pregelix.operator.aggregator.StatisticsAggregator;
+import edu.uci.ics.genomix.pregelix.type.MessageFlag;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
+
+public class SymmetryCheckerVertex extends
+ BasicGraphCleanVertex<VertexValueWritable, MessageWritable> {
+
+ @Override
+ public void initVertex() {
+ super.initVertex();
+ if(incomingMsg == null)
+ incomingMsg = new MessageWritable();
+ if(outgoingMsg == null)
+ outgoingMsg = new MessageWritable();
+ else
+ outgoingMsg.reset();
+ if(destVertexId == null)
+ destVertexId = new VKmerBytesWritable();
+ if(getSuperstep() == 1)
+ StatisticsAggregator.preGlobalCounters.clear();
+// else
+// StatisticsAggregator.preGlobalCounters = BasicGraphCleanVertex.readStatisticsCounterResult(getContext().getConfiguration());
+ counters.clear();
+ getVertexValue().getCounters().clear();
+ outFlag = 0;
+ }
+
+ @Override
+ public void compute(Iterator<MessageWritable> msgIterator) throws Exception {
+ initVertex();
+ if(getSuperstep() == 1){
+ sendSettledMsgToAllNeighborNodes(getVertexValue());
+ voteToHalt();
+ } else if(getSuperstep() == 2){
+ //check if the corresponding edge exists
+ while(msgIterator.hasNext()){
+ incomingMsg = msgIterator.next();
+ byte meToNeighborDir = (byte) (incomingMsg.getFlag() & MessageFlag.DIR_MASK);
+ byte neighborToMeDir = mirrorDirection(meToNeighborDir);
+ boolean exist = getVertexValue().getEdgeList(neighborToMeDir).contains(incomingMsg.getSourceVertexId());
+ if(!exist){
+ getVertexValue().setState(State.IS_ERROR);
+ }
+ }
+ voteToHalt();
+ }
+ }
+
+}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/CheckerOutputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/CheckerOutputFormat.java
new file mode 100644
index 0000000..e562559
--- /dev/null
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/CheckerOutputFormat.java
@@ -0,0 +1,44 @@
+package edu.uci.ics.genomix.pregelix.format;
+
+import java.io.IOException;
+
+import org.apache.hadoop.io.NullWritable;
+import org.apache.hadoop.mapreduce.RecordWriter;
+import org.apache.hadoop.mapreduce.TaskAttemptContext;
+
+import edu.uci.ics.genomix.pregelix.api.io.binary.GraphCleanVertexOutputFormat;
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable.State;
+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 CheckerOutputFormat extends
+ GraphCleanVertexOutputFormat<VKmerBytesWritable, VertexValueWritable, NullWritable> {
+
+ @Override
+ public VertexWriter<VKmerBytesWritable, VertexValueWritable, NullWritable> createVertexWriter(
+ TaskAttemptContext context) throws IOException, InterruptedException {
+ @SuppressWarnings("unchecked")
+ RecordWriter<VKmerBytesWritable, VertexValueWritable> recordWriter = binaryOutputFormat.getRecordWriter(context);
+ return new BinaryLoadGraphVertexWriter(recordWriter);
+ }
+
+ /**
+ * Simple VertexWriter that supports {@link BinaryLoadGraphVertex}
+ */
+ public static class BinaryLoadGraphVertexWriter extends
+ BinaryVertexWriter<VKmerBytesWritable, VertexValueWritable, NullWritable> {
+ public BinaryLoadGraphVertexWriter(RecordWriter<VKmerBytesWritable, VertexValueWritable> lineRecordWriter) {
+ super(lineRecordWriter);
+ }
+
+ @Override
+ public void writeVertex(Vertex<VKmerBytesWritable, VertexValueWritable, NullWritable, ?> vertex)
+ throws IOException, InterruptedException {
+ byte state = (byte)(vertex.getVertexValue().getState() & State.VERTEX_MASK);
+ if(state == State.IS_ERROR)
+ getRecordWriter().write(vertex.getVertexId(), vertex.getVertexValue());
+ }
+ }
+}
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 303d9b7..b8f768d 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
@@ -66,6 +66,7 @@
public static final byte IS_HALT = 0b100 << 3;
public static final byte IS_DEAD = 0b101 << 3;
+ public static final byte IS_ERROR = 0b110 << 3;
public static final byte VERTEX_MASK = 0b111 << 3;
public static final byte VERTEX_CLEAR = (byte)1000111;
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 d8c6bb0..08a7dab 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
@@ -5,6 +5,8 @@
import java.io.IOException;
import edu.uci.ics.genomix.config.GenomixJobConf;
+import edu.uci.ics.genomix.pregelix.checker.SymmetryCheckerVertex;
+import edu.uci.ics.genomix.pregelix.format.CheckerOutputFormat;
import edu.uci.ics.genomix.pregelix.format.GraphCleanInputFormat;
import edu.uci.ics.genomix.pregelix.format.GraphCleanOutputFormat;
import edu.uci.ics.genomix.pregelix.format.InitialGraphCleanInputFormat;
@@ -302,6 +304,23 @@
+ "ScaffoldingGraph.xml");
}
+ private static void generateSymmetryCheckerGraphJob(String jobName, String outputPath) throws IOException {
+ PregelixJob job = new PregelixJob(new GenomixJobConf(3), jobName);
+ job.setVertexClass(SymmetryCheckerVertex.class);
+ job.setGlobalAggregatorClass(StatisticsAggregator.class);
+ job.setVertexInputFormatClass(InitialGraphCleanInputFormat.class);
+ job.setVertexOutputFormatClass(CheckerOutputFormat.class);
+ job.setDynamicVertexValueSize(true);
+ job.setOutputKeyClass(VKmerBytesWritable.class);
+ job.setOutputValueClass(VertexValueWritable.class);
+ job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
+ }
+
+ private static void genSymmetryCheckerGraph() throws IOException {
+ generateSymmetryCheckerGraphJob("SymmetryCheckerGraph", outputBase
+ + "SymmetryCheckerGraph.xml");
+ }
+
public static void main(String[] args) throws IOException {
genUnrollTandemRepeatGraph();
genMapReduceGraph();
@@ -318,6 +337,7 @@
genSplitRepeatGraph();
getBFSTraverseGraph();
genScaffoldingGraph();
+ genSymmetryCheckerGraph();
}
}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeTestSuite.java
index ff6bb69..6ff2e26 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeTestSuite.java
@@ -6,7 +6,7 @@
public static Test suite() throws Exception {
String pattern ="PathMerge";
- String testSet[] = {"same"
+ String testSet[] = {"sameWithEdge"
// "2", "3", "4", "5", "6", "7", "8", "9", "head_6", "head_7",
// "P2_3", "P2_4", "P2_5", "P2_6", "P2_7", "P2_8",
// "LeftAdj", "RightAdj",
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/SymmetryCheckerTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/SymmetryCheckerTestSuite.java
new file mode 100644
index 0000000..00c0414
--- /dev/null
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/SymmetryCheckerTestSuite.java
@@ -0,0 +1,14 @@
+package edu.uci.ics.genomix.pregelix.JobRun;
+
+import junit.framework.Test;
+
+public class SymmetryCheckerTestSuite extends BasicGraphCleanTestSuite{
+
+ public static Test suite() throws Exception {
+ String pattern ="SymmetryChecker";
+ String testSet[] = {"2"};
+ init(pattern, testSet);
+ BasicGraphCleanTestSuite testSuite = new BasicGraphCleanTestSuite();
+ return makeTestSuite(testSuite);
+ }
+}
diff --git a/genomix/genomix-pregelix/src/test/resources/only_SymmetryChecker.txt b/genomix/genomix-pregelix/src/test/resources/only_SymmetryChecker.txt
new file mode 100644
index 0000000..e19a09b
--- /dev/null
+++ b/genomix/genomix-pregelix/src/test/resources/only_SymmetryChecker.txt
@@ -0,0 +1 @@
+SymmetryCheckerGraph.xml
