add RF/FR with/without head test for pathmerge
diff --git a/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/BridgePath2/bridgepath2 b/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/BridgePath2/bridgepath2
new file mode 100644
index 0000000..f2aeec7
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/BridgePath2/bridgepath2
@@ -0,0 +1,2 @@
+1 AATAGAACTT
+2 AATAGCCCTT
diff --git a/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/FR/FR b/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/FR/FR
new file mode 100644
index 0000000..2891207
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/FR/FR
@@ -0,0 +1 @@
+1 ATAG
diff --git a/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/RF/RF b/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/RF/RF
new file mode 100644
index 0000000..e7dbd0b
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/RF/RF
@@ -0,0 +1 @@
+1 TAGA
diff --git a/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/head_FR/head_FR b/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/head_FR/head_FR
new file mode 100644
index 0000000..aa1c7a9
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/head_FR/head_FR
@@ -0,0 +1,2 @@
+1 AATAG
+2 CATAG
diff --git a/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/head_RF/head_RF b/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/head_RF/head_RF
new file mode 100644
index 0000000..3c622d6
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/head_RF/head_RF
@@ -0,0 +1,2 @@
+1 ATAGA
+2 GTAGA
diff --git a/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/head_RF/head_RF~ b/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/head_RF/head_RF~
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/head_RF/head_RF~
diff --git a/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/twohead_FR/TwoHead_FR b/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/twohead_FR/TwoHead_FR
new file mode 100644
index 0000000..55c3609
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/twohead_FR/TwoHead_FR
@@ -0,0 +1,2 @@
+1 AATAGA
+2 CATAGG
diff --git a/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/twohead_RF/TwoHead_RF b/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/twohead_RF/TwoHead_RF
new file mode 100644
index 0000000..0e4506f
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/twohead_RF/TwoHead_RF
@@ -0,0 +1,2 @@
+1 ATAGAA
+2 GTAGAC
diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTestCase.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTestCase.java
index e1bb49a..5d60c6e 100644
--- a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTestCase.java
+++ b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GraphBuildingTestCase.java
@@ -64,7 +64,7 @@
// Path src = new Path(RESULT_PATH);
// Path dest = new Path(RESULT_PATH);
// dfs.copyToLocalFile(src, dest);
- HadoopMiniClusterTest.copyResultsToLocal(RESULT_PATH, RESULT_PATH + "/test.txt", false, conf, true, dfs);
- GenerateGraphViz.convertGraphBuildingOutputToGraphViz(RESULT_PATH + "/test.txt.bindir", RESULT_PATH + "/graphviz");
+ HadoopMiniClusterTest.copyResultsToLocal(RESULT_PATH, RESULT_PATH + "/", false, conf, true, dfs);
+ GenerateGraphViz.convertGraphBuildingOutputToGraphViz(RESULT_PATH + "/bin", RESULT_PATH + "/graphviz");
}
}
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 52be43a..83e2860 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
@@ -24,7 +24,13 @@
private static int SIZE_KMER = 3;
public static final String PreFix = "data/webmap/PathMerge_TestSet";
public static final String[] TestDir = { PreFix + File.separator
- + "head_7"};
+ + "BridgePath2"};
+// + "FR", PreFix + File.separator
+// + "RF", PreFix + File.separator
+// + "head_FR", PreFix + File.separator
+// + "head_RF", PreFix + File.separator
+// + "twohead_FR", PreFix + File.separator
+// + "twohead_RF"};
// + "2", PreFix + File.separator
// + "3", PreFix + File.separator
// + "4", PreFix + File.separator
diff --git a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/pmcommon/HadoopMiniClusterTest.java b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/pmcommon/HadoopMiniClusterTest.java
index 6db60f3..df4f889 100644
--- a/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/pmcommon/HadoopMiniClusterTest.java
+++ b/genomix/genomix-hadoop/src/test/java/edu/uci/ics/genomix/hadoop/pmcommon/HadoopMiniClusterTest.java
@@ -85,7 +85,7 @@
// file is binary
// save the entire binary output dir
FileUtil.copy(FileSystem.get(conf), new Path(hdfsSrcDir), FileSystem.getLocal(new Configuration()),
- new Path(localDestFile + ".bindir"), false, conf);
+ new Path(localDestFile + "bin"), false, conf); //bindir
// chomp through output files
FileStatus[] files = ArrayUtils.addAll(dfs.globStatus(new Path(hdfsSrcDir + "*")), dfs.globStatus(new Path(hdfsSrcDir + "*/*")));
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/FR/..binmerge.crc b/genomix/genomix-pregelix/data/TestSet/PathMerge/FR/..binmerge.crc
new file mode 100644
index 0000000..eb709bd
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/FR/..binmerge.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/FR/.binmerge b/genomix/genomix-pregelix/data/TestSet/PathMerge/FR/.binmerge
new file mode 100755
index 0000000..f7eefdf
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/FR/.binmerge
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/FR/bin/.part-00000.crc b/genomix/genomix-pregelix/data/TestSet/PathMerge/FR/bin/.part-00000.crc
new file mode 100644
index 0000000..ed34868
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/FR/bin/.part-00000.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/FR/bin/part-00000 b/genomix/genomix-pregelix/data/TestSet/PathMerge/FR/bin/part-00000
new file mode 100755
index 0000000..1ccd2f5
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/FR/bin/part-00000
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/FR/data b/genomix/genomix-pregelix/data/TestSet/PathMerge/FR/data
new file mode 100644
index 0000000..efd4331
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/FR/data
@@ -0,0 +1,2 @@
+ATA {[] [{CTA:[1]}] [] [] {5':[(1-0_0)], ~5':[]} 1.0x}
+CTA {[] [{ATA:[1]}] [] [] {5':[], ~5':[]} 1.0x}
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new file mode 100644
index 0000000..f9fb5b5
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/FR/graphviz/result.ps
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diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/RF/..binmerge.crc b/genomix/genomix-pregelix/data/TestSet/PathMerge/RF/..binmerge.crc
new file mode 100644
index 0000000..f615d7a
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/PathMerge/RF/..binmerge.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/RF/.binmerge b/genomix/genomix-pregelix/data/TestSet/PathMerge/RF/.binmerge
new file mode 100755
index 0000000..e996933
--- /dev/null
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new file mode 100755
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diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicPathMergeVertex.java
index 86c3cf0..2ea5c8c 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicPathMergeVertex.java
@@ -191,7 +191,6 @@
setSuccessorAdjMsg(destVertexId);
outgoingMsg.setFlag(outFlag);
outgoingMsg.setFlip(ifFlipWithPredecessor(destVertexId));
- destVertexId.setAsCopy(kmerIterator.next());
sendMsg(destVertexId, outgoingMsg);
}
}
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 4b0220f..0aa9599 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
@@ -6,8 +6,14 @@
public static Test suite() throws Exception {
String pattern ="PathMerge";
- String testSet[] = {"2", "3", "4", "5", "6", "7", "8", "9", "head_6", "head_7"};
-// {
+ String testSet[] = //{"2", "3", "4", "5", "6", "7", "8", "9", "head_6", "head_7"};
+ {
+ "FR",
+ "RF",
+ "head_FR",
+ "head_RF",
+ "twohead_FR",
+ "twohead_RF"
// "SimplePath",
// "ThreeDuplicate",
// "head_6"
@@ -15,7 +21,7 @@
// "CyclePath",
// "SelfPath"
// "TreePath"
-// };
+ };
init(pattern, testSet);
BasicGraphCleanTestSuite testSuite = new BasicGraphCleanTestSuite();
return makeTestSuite(testSuite);