add first small test case
diff --git a/genomix/genomix-pregelix/data/input/.out.crc b/genomix/genomix-pregelix/data/input/.out.crc
new file mode 100644
index 0000000..422fddb
--- /dev/null
+++ b/genomix/genomix-pregelix/data/input/.out.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/input/test/result.graphbuild.txt.bin b/genomix/genomix-pregelix/data/input/test/result.graphbuild.txt.bin
new file mode 100644
index 0000000..4865aeb
--- /dev/null
+++ b/genomix/genomix-pregelix/data/input/test/result.graphbuild.txt.bin
Binary files differ
diff --git a/genomix/genomix-pregelix/data/test/result.graphbuild.bidirectional.txt b/genomix/genomix-pregelix/data/test/result.graphbuild.bidirectional.txt
new file mode 100644
index 0000000..a41ce56
--- /dev/null
+++ b/genomix/genomix-pregelix/data/test/result.graphbuild.bidirectional.txt
@@ -0,0 +1,18 @@
+((2,1) [(2,3)] [] [] [] AATAGA) (null)
+((2,3) [(6,1),(2,4)] [] [] [(2,1)] TAGAA) (null)
+((2,4) [(6,2)] [] [] [(2,3)] AGAAG) (null)
+((4,1) [(4,3)] [] [] [] AATAGA) (null)
+((4,3) [(6,1),(4,4)] [] [] [(4,1)] TAGAA) (null)
+((4,4) [(6,2)] [] [] [(4,3)] AGAAG) (null)
+((6,1) [(6,2)] [] [] [(2,3),(1,3),(3,3),(4,3),(5,3)] AGAAG) (null)
+((6,2) [(6,3)] [] [] [(2,4),(3,4),(1,4),(4,4),(5,4),(6,1)] GAAGA) (null)
+((6,3) [] [] [] [(6,2)] AAGAAG) (null)
+((1,1) [(1,3)] [] [] [] AATAGA) (null)
+((1,3) [(6,1),(1,4)] [] [] [(1,1)] TAGAA) (null)
+((1,4) [(6,2)] [] [] [(1,3)] AGAAG) (null)
+((3,1) [(3,3)] [] [] [] AATAGA) (null)
+((3,3) [(6,1),(3,4)] [] [] [(3,1)] TAGAA) (null)
+((3,4) [(6,2)] [] [] [(3,3)] AGAAG) (null)
+((5,1) [(5,3)] [] [] [] AATAGA) (null)
+((5,3) [(6,1),(5,4)] [] [] [(5,1)] TAGAA) (null)
+((5,4) [(6,2)] [] [] [(5,3)] AGAAG) (null)
diff --git a/genomix/genomix-pregelix/data/test/result.graphbuild.txt.bin b/genomix/genomix-pregelix/data/test/result.graphbuild.txt.bin
new file mode 100644
index 0000000..4865aeb
--- /dev/null
+++ b/genomix/genomix-pregelix/data/test/result.graphbuild.txt.bin
Binary files differ
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
new file mode 100644
index 0000000..b81491b
--- /dev/null
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/ConvertNodeToIdValue.java
@@ -0,0 +1,58 @@
+package edu.uci.ics.genomix.pregelix.sequencefile;
+
+import java.io.File;
+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;
+import org.apache.hadoop.io.NullWritable;
+import org.apache.hadoop.io.SequenceFile;
+import org.apache.hadoop.io.SequenceFile.CompressionType;
+
+import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
+import edu.uci.ics.genomix.pregelix.type.State;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.NodeWritable;
+import edu.uci.ics.genomix.type.PositionWritable;
+
+public class ConvertNodeToIdValue {
+
+ public static void convert(Path inFile, Path outFile)
+ throws IOException {
+ Configuration conf = new Configuration();
+ FileSystem fileSys = FileSystem.get(conf);
+
+ SequenceFile.Reader reader = new SequenceFile.Reader(fileSys, inFile, conf);
+ SequenceFile.Writer writer = SequenceFile.createWriter(fileSys, conf, outFile, PositionWritable.class,
+ ValueStateWritable.class, CompressionType.NONE);
+ NodeWritable node = new NodeWritable();
+ NullWritable value = NullWritable.get();
+ PositionWritable outputKey = new PositionWritable();
+ ValueStateWritable outputValue = new ValueStateWritable();
+
+ while(reader.next(node, value)) {
+ System.out.println(node.getNodeID().toString());
+ outputKey.set(node.getNodeID());
+ outputValue.setFFList(node.getFFList());
+ outputValue.setFRList(node.getFRList());
+ outputValue.setRFList(node.getRFList());
+ outputValue.setRRList(node.getRRList());
+ outputValue.setMergeChain(node.getKmer());
+ outputValue.setState(State.NON_VERTEX);
+ writer.append(outputKey, outputValue);
+ }
+ writer.close();
+ reader.close();
+ }
+
+ public static void main(String[] args) throws IOException {
+ Path dir = new Path("data/test");
+ Path outDir = new Path("data/input");
+ FileUtils.cleanDirectory(new File("data/input"));
+ Path inFile = new Path(dir, "result.graphbuild.txt.bin");
+ Path outFile = new Path(outDir, "out");
+ convert(inFile,outFile);
+ }
+}
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 f1fcdac..cdc97c1 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
@@ -73,8 +73,8 @@
public static void main(String[] args) throws IOException {
genNaiveAlgorithmForMergeGraph();
- genLogAlgorithmForMergeGraph();
- genP3ForMergeGraph();
+ //genLogAlgorithmForMergeGraph();
+ //genP3ForMergeGraph();
}
}
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 c8aaa84..a8f5a81 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
@@ -43,9 +43,9 @@
public class PathMergeSmallTestSuite extends TestSuite {
private static final Logger LOGGER = Logger.getLogger(PathMergeSmallTestSuite.class.getName());
- public static final String PreFix = "data/PathTestSet"; //"graphbuildresult";
+ public static final String PreFix = "data/input"; //"graphbuildresult";
public static final String[] TestDir = { PreFix + File.separator
- + "LongPath"};/*, PreFix + File.separator
+ + "test"};/*, PreFix + File.separator
/*+ "CyclePath"};, PreFix + File.separator
+ "SimplePath", PreFix + File.separator
+ "SinglePath", PreFix + File.separator