commit 8270c5a390ec0d78d84d5b8c400c3874b49534cc
author Anbang Xu <anbangx@gmail.com> Sun Aug 18 21:47:38 2013 -0700
committer Anbang Xu <anbangx@gmail.com> Sun Aug 18 21:47:38 2013 -0700
tree ad3f520e037b70a0353baa299f53f3fbe1126c56
parent d688b5aaec0a4f26cc669e66ab920103cb2a67d7

Merge cycle to a single node in path merge. P4 test is completed

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genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/BridgePathWithTandemRepeat/txt

diff --git a/genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/BridgePathWithTandemRepeat/txt b/genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/BridgePathWithTandemRepeat/txt
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index 0000000..371a9f3
--- /dev/null
+++ b/genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/BridgePathWithTandemRepeat/txt
@@ -0,0 +1,5 @@
+GAA	{[{AAC:[1]}]	[]	[]	[{CGA:[1]}]	{5':[], ~5':[]}GAA	1.0x}
+CGA	{[{GAA:[1]}]	[{AAT:[1,2]}]	[{CGA:[1]}]	[]	{5':[], ~5':[]}CGA	2.0x}
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+AAC	{[]	[]	[{AGA:[2]}]	[{GAA:[1]}]	{5':[], ~5':[]}AAC	2.0x}
+AAT	{[]	[{CGA:[1]}, {AGA:[2]}]	[]	[]	{5':[(2-0_0),(1-0_0)], ~5':[]}AAATC	2.0x}

genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/ComplexTandemRepeat/.txt.crc

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copy to genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/ComplexTandemRepeat/.txt.crc

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genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/ComplexTandemRepeat/bin/.part-6.crc

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genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/ComplexTandemRepeat/bin/part-3

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genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/ComplexTandemRepeat/bin/part-4

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genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/ComplexTandemRepeat/txt

diff --git a/genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/ComplexTandemRepeat/txt b/genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/ComplexTandemRepeat/txt
new file mode 100755
index 0000000..6b3a9ba
--- /dev/null
+++ b/genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/ComplexTandemRepeat/txt
@@ -0,0 +1,5 @@
+TCA	{[]	[]	[]	[{AAT:[1]}]	{5':[], ~5':[]}TCA	1.0x}
+GAA	{[]	[]	[]	[{GGA:[3]}, {CGA:[1]}]	{5':[], ~5':[]}GAAA	1.5x}
+GGA	{[{GAA:[3]}]	[]	[]	[]	{5':[(3-0_0)], ~5':[]}GGA	1.0x}
+CGA	{[{GAA:[1]}]	[{AAT:[1]}]	[{CGA:[1]}]	[]	{5':[], ~5':[]}CGA	2.0x}
+AAT	{[{TCA:[2]}]	[{CGA:[1]}]	[]	[]	{5':[(1-0_0),(2-1_0)], ~5':[]}AATC	1.5x}

genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/ComplexTreePath/.txt.crc

diff --git a/genomix/genomix-pregelix/data/result/P4ForMergeGraph/2/.txt.crc b/genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/ComplexTreePath/.txt.crc
similarity index 100%
copy from genomix/genomix-pregelix/data/result/P4ForMergeGraph/2/.txt.crc
copy to genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/ComplexTreePath/.txt.crc

genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/ComplexTreePath/bin/.part-0.crc

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new file mode 100644
index 0000000..870dcf4
--- /dev/null
+++ b/genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/ComplexTreePath/bin/.part-0.crc
Binary files differ

genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/ComplexTreePath/bin/.part-1.crc

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new file mode 100644
index 0000000..509025e
--- /dev/null
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Binary files differ

genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/ComplexTreePath/bin/.part-2.crc

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Binary files differ

genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/ComplexTreePath/bin/.part-3.crc

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--- /dev/null
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Binary files differ

genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/ComplexTreePath/bin/.part-4.crc

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new file mode 100644
index 0000000..4faba43
--- /dev/null
+++ b/genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/ComplexTreePath/bin/.part-4.crc
Binary files differ

genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/ComplexTreePath/bin/.part-5.crc

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Binary files differ

genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/ComplexTreePath/bin/.part-6.crc

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new file mode 100644
index 0000000..0bcf341
--- /dev/null
+++ b/genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/ComplexTreePath/bin/.part-6.crc
Binary files differ

genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/ComplexTreePath/bin/.part-7.crc

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Binary files differ

genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/ComplexTreePath/bin/part-0

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new file mode 100755
index 0000000..e58bb49
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genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/ComplexTreePath/txt

diff --git a/genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/ComplexTreePath/txt b/genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/ComplexTreePath/txt
new file mode 100755
index 0000000..43afa19
--- /dev/null
+++ b/genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/ComplexTreePath/txt
@@ -0,0 +1,12 @@
+GAC	{[]	[]	[{CAC:[3]}]	[]	{5':[], ~5':[]}TGAC	1.0x}
+TAA	{[{AGC:[2,3]}, {AAC:[1,2,3]}]	[]	[{TAA:[2,3]}, {CCC:[1]}]	[]	{5':[], ~5':[]}TAA	5.0x}
+ATG	{[]	[{CCC:[1]}]	[{ATG:[1]}]	[]	{5':[], ~5':[]}ATG	2.0x}
+ACT	{[{CTA:[3]}]	[]	[]	[{CAC:[3]}]	{5':[], ~5':[]}ACT	2.0x}
+GCC	{[{CCG:[2]}]	[{AGG:[2]}]	[{GCC:[2]}]	[]	{5':[], ~5':[]}GCC	2.0x}
+CTA	{[]	[{CTA:[3]}]	[]	[{ACT:[3]}]	{5':[], ~5':[]}CTA	2.0x}
+CCC	{[]	[{ATG:[1]}]	[{TAA:[1]}]	[]	{5':[], ~5':[]}TACCCA	1.25x}
+CCG	{[]	[{CAC:[2]}, {AAC:[1,2,3]}]	[]	[{GCC:[2]}]	{5':[(2-1_0),(3-1_0),(1-1_0)], ~5':[]}CCGT	2.5x}
+CAC	{[{ACT:[3]}]	[{CCG:[2]}]	[{GAC:[3]}]	[{AGC:[2,3]}]	{5':[], ~5':[]}CAC	3.0x}
+AAC	{[]	[{CCG:[2]}]	[]	[{TAA:[1,2,3]}]	{5':[], ~5':[]}AAC	3.0x}
+AGC	{[{CAC:[2,3]}]	[]	[]	[{TAA:[2,3]}]	{5':[], ~5':[]}AAGCA	2.0x}
+AGG	{[]	[{GCC:[2]}]	[]	[]	{5':[], ~5':[]}ACAGG	1.0x}

genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/CyclePath/.txt.crc

diff --git a/genomix/genomix-pregelix/data/result/P4ForMergeGraph/2/.txt.crc b/genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/CyclePath/.txt.crc
similarity index 100%
copy from genomix/genomix-pregelix/data/result/P4ForMergeGraph/2/.txt.crc
copy to genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/CyclePath/.txt.crc

genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/CyclePath/bin/.part-0.crc

diff --git a/genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/CyclePath/bin/.part-0.crc b/genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/CyclePath/bin/.part-0.crc
new file mode 100644
index 0000000..b9c5fbb
--- /dev/null
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genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/CyclePath/txt

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genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/LeftAdj/txt

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+AAA	{[{ACC:[1,2,3]}]	[]	[]	[{GAA:[2]}, {CAA:[1]}]	{5':[], ~5':[]}AAA	2.0x}

genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/RF/.txt.crc

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genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/RF/graphviz/result.ps

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genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/RF/txt

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+AGA	{[]	[]	[]	[]	{5':[(1-0_0)], ~5':[]}TAGA	1.0x}

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genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/RightAdj/txt

diff --git a/genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/RightAdj/txt b/genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/RightAdj/txt
new file mode 100755
index 0000000..c382fe3
--- /dev/null
+++ b/genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/RightAdj/txt
@@ -0,0 +1,5 @@
+GAA	{[{AAT:[3]}, {AAC:[1,2]}]	[]	[]	[]	{5':[(2-0_0),(3-0_0),(1-0_0)], ~5':[]}GAAA	3.0x}
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+AAC	{[{ACG:[1]}, {ACC:[2]}]	[]	[]	[{GAA:[1,2,3]}]	{5':[], ~5':[]}AAC	2.0x}
+AAT	{[]	[]	[]	[{GAA:[1,2,3]}]	{5':[], ~5':[]}AAT	1.0x}

genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/RingPath/.txt.crc

diff --git a/genomix/genomix-pregelix/data/result/P4ForMergeGraph/2/.txt.crc b/genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/RingPath/.txt.crc
similarity index 100%
copy from genomix/genomix-pregelix/data/result/P4ForMergeGraph/2/.txt.crc
copy to genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/RingPath/.txt.crc

genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/RingPath/bin/.part-0.crc

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genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/RingPath/bin/.part-3.crc

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genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/RingPath/bin/.part-6.crc

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genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/RingPath/bin/.part-7.crc

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genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/RingPath/bin/part-2

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genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/RingPath/graphviz/result.ps

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genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/SelfTandemRepeat/txt

diff --git a/genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/SelfTandemRepeat/txt b/genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/SelfTandemRepeat/txt
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--- /dev/null
+++ b/genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/SelfTandemRepeat/txt
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copy to genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/SimpleBridgePath/.txt.crc

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genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/SimpleBridgePath/txt

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genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/SimplePath/txt

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genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/SimpleTreePath/txt

diff --git a/genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/SimpleTreePath/txt b/genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/SimpleTreePath/txt
new file mode 100755
index 0000000..fd16e48
--- /dev/null
+++ b/genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/SimpleTreePath/txt
@@ -0,0 +1,5 @@
+GAA	{[{AAT:[3]}]	[{AGG:[1,2]}]	[]	[]	{5':[(2-0_0),(3-0_0),(1-0_0)], ~5':[]}GAAA	3.0x}
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+CAA	{[{AGG:[1]}]	[]	[]	[]	{5':[], ~5':[]}TCAAG	1.0x}
+AGG	{[]	[{GAA:[1,2,3]}]	[]	[{CAA:[1]}, {CCC:[2]}]	{5':[], ~5':[]}AGGTT	2.0x}
+AAT	{[]	[]	[]	[{GAA:[1,2,3]}]	{5':[], ~5':[]}AATCT	1.0x}

genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/TandemRepeatWithMergeEdge/.txt.crc

diff --git a/genomix/genomix-pregelix/data/result/P4ForMergeGraph/2/.txt.crc b/genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/TandemRepeatWithMergeEdge/.txt.crc
similarity index 100%
copy from genomix/genomix-pregelix/data/result/P4ForMergeGraph/2/.txt.crc
copy to genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/TandemRepeatWithMergeEdge/.txt.crc

genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/TandemRepeatWithMergeEdge/bin/.part-0.crc

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new file mode 100644
index 0000000..ec92c92
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+++ b/genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/TandemRepeatWithMergeEdge/bin/.part-0.crc
Binary files differ

genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/TandemRepeatWithMergeEdge/bin/.part-1.crc

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new file mode 100644
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Binary files differ

genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/TandemRepeatWithMergeEdge/bin/.part-2.crc

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genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/TandemRepeatWithMergeEdge/bin/.part-3.crc

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genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/TandemRepeatWithMergeEdge/bin/.part-4.crc

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Binary files differ

genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/TandemRepeatWithMergeEdge/bin/.part-5.crc

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Binary files differ

genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/TandemRepeatWithMergeEdge/bin/.part-6.crc

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genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/TandemRepeatWithMergeEdge/bin/.part-7.crc

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Binary files differ

genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/TandemRepeatWithMergeEdge/bin/part-0

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new file mode 100755
index 0000000..9d42295
--- /dev/null
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genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/head_RF/txt

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genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/twohead_FR/txt

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genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/twohead_RF/txt

diff --git a/genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/twohead_RF/txt b/genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/twohead_RF/txt
new file mode 100755
index 0000000..3ac40a0
--- /dev/null
+++ b/genomix/genomix-pregelix/data/result/PathMerge/P4ForMergeGraph/twohead_RF/txt
@@ -0,0 +1,5 @@
+GAA	{[]	[]	[]	[{AGA:[1]}]	{5':[], ~5':[]}GAA	1.0x}
+GAC	{[]	[]	[]	[{AGA:[2]}]	{5':[], ~5':[]}GAC	1.0x}
+ATA	{[{AGA:[1,2]}]	[]	[]	[]	{5':[(1-0_0)], ~5':[]}ATA	1.0x}
+GTA	{[{AGA:[1,2]}]	[]	[]	[]	{5':[(2-0_0)], ~5':[]}GTA	1.0x}
+AGA	{[{GAA:[1]}, {GAC:[2]}]	[]	[]	[{GTA:[2]}, {ATA:[1]}]	{5':[], ~5':[]}TAGA	2.0x}

genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java

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 496c377..a8ceaf6 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
@@ -54,13 +54,11 @@
     
     private byte state;
     private boolean isFakeVertex;
-    private VKmerBytesWritable startKmer; //use for detect cycle in path merge
 
     public VertexValueWritable() {
         super();
         state = 0;
         isFakeVertex = false;
-        startKmer = new VKmerBytesWritable();
     }
     
     public void setNode(NodeWritable node){
@@ -140,19 +138,10 @@
         this.state = state;
     }
 
-    public VKmerBytesWritable getStartKmer() {
-        return startKmer;
-    }
-
-    public void setStartKmer(VKmerBytesWritable startKmer) {
-        this.startKmer.setAsCopy(startKmer);
-    }
-
     public void reset() {
         super.reset();
         this.state = 0;
         this.isFakeVertex = false;
-        this.startKmer.reset(0);
     }
     
     @Override
@@ -161,7 +150,6 @@
         super.readFields(in);
         this.state = in.readByte();
         this.isFakeVertex = in.readBoolean();
-        this.startKmer.readFields(in);
     }
 
     @Override
@@ -169,7 +157,6 @@
         super.write(out);
         out.writeByte(this.state);
         out.writeBoolean(this.isFakeVertex);
-        this.startKmer.write(out);
     }
     
     public int getDegree(){

genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P4ForPathMergeVertex.java

diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P4ForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P4ForPathMergeVertex.java
index ce4291d..17bd3f9 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P4ForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P4ForPathMergeVertex.java
@@ -13,6 +13,7 @@
 import edu.uci.ics.genomix.pregelix.io.VertexValueWritable.State;
 import edu.uci.ics.genomix.pregelix.type.MessageFlag;
 import edu.uci.ics.genomix.type.VKmerBytesWritable;
+import edu.uci.ics.genomix.type.NodeWritable.DirectionFlag;
 
 /*
  * vertexId: BytesWritable
@@ -215,25 +216,21 @@
             while (msgIterator.hasNext()) {
                 incomingMsg = msgIterator.next();
                 selfFlag = (byte) (State.VERTEX_MASK & getVertexValue().getState());
-                /** record startKmer in merge path **/
-                if(getSuperstep() == 6){
-                    getVertexValue().setStartKmer(getVertexId());
-                }
-                /** check if merge path is a cycle **/
-                if(getVertexValue().getStartKmer() == incomingMsg.getSourceVertexId()){
+                /** process merge **/
+                processMerge();
+                /** if it's a tandem repeat, which means detecting cycle **/
+                if(isTandemRepeat()){
+                    for(byte d : DirectionFlag.values)
+                        getVertexValue().getEdgeList(d).reset();
                     getVertexValue().setState(MessageFlag.IS_HALT);
                     voteToHalt();
-                } else{
-                    /** process merge **/
-                    processMerge();
-                    //head meets head, stop
-                    if(getMsgFlag() == MessageFlag.IS_HEAD && selfFlag == MessageFlag.IS_HEAD){
-                        getVertexValue().setState(MessageFlag.IS_HALT);
-                        voteToHalt();
-                    }
-                    else
-                        this.activate();
+                }/** head meets head, stop **/ 
+                else if((getMsgFlag() == MessageFlag.IS_HEAD && selfFlag == MessageFlag.IS_HEAD)){
+                    getVertexValue().setState(MessageFlag.IS_HALT);
+                    voteToHalt();
                 }
+                else
+                    this.activate();
             }
         }
     }

genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeTestSuite.java

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 0825241..58bbdcc 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
@@ -6,28 +6,15 @@
 
     public static Test suite() throws Exception {
         String pattern ="PathMerge";
-        String testSet[] = //{"2", "3", "4", "5", "6", "7", "8", "9", "head_6", "head_7"};//,
-//            {"LeftAdj",
-            {
-                "CyclePath"
-//                "RightAdj"
-//                "FR",
-//                "RF",
-//                "head_FR",
-//                "head_RF",
-//                "twohead_FR",
-//                "twohead_RF",
-//                "BridgePath2"
-//                "SimplePath",
-//                "ThreeDuplicate",
-//                "RingPath",
-//                "SelfTandemRepeat"
-//                "TandemRepeatWithMergeEdge",
-//                "TandemRepeatWithUnmergeEdge",
-//                "TreePath"
-//                "ComplexTandemRepeat"
-//                "SimpleBridgePath",
-//                "SimpleTreePath"
+        String testSet[] = {"2", "3", "4", "5", "6", "7", "8", "9", "head_6", "head_7",
+                "LeftAdj", "RightAdj",
+                "FR", "RF", "head_FR", "head_RF", "twohead_FR", "twohead_RF",
+                "SelfTandemRepeat", "TandemRepeatWithMergeEdge", 
+                "TandemRepeatWithUnmergeEdge", "ComplexTandemRepeat",
+                "SimplePath", "ThreeDuplicate",
+                "SimpleBridgePath", "BridgePathWithTandemRepeat",
+                "RingPath", "CyclePath",
+                "SimpleTreePath", "ComplexTreePath"
                 };
         init(pattern, testSet);
         BasicGraphCleanTestSuite testSuite = new BasicGraphCleanTestSuite();