Add skip tandem repeat to pathmerge. TODO: detect cycle in pathmerge
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 84816f4..4856657 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
@@ -96,7 +96,7 @@
Marshal.putInt(valueCount, storage, offset);
}
}
-
+
/**
* Save the union of my list and otherList. Uses a temporary HashSet for
* uniquefication
@@ -230,6 +230,15 @@
return it;
}
+ public boolean contains(VKmerListWritable kmer){
+ Iterator<VKmerBytesWritable> posIterator = this.iterator();
+ while (posIterator.hasNext()) {
+ if (kmer.equals(posIterator.next()))
+ return true;
+ }
+ return false;
+ }
+
/*
* remove the first instance of `toRemove`. Uses a linear scan. Throws an
* exception if not in this list.
diff --git a/genomix/genomix-hadoop/data/webmap/MergeBubble.txt b/genomix/genomix-hadoop/data/webmap/MergeBubble.txt
deleted file mode 100644
index 087f43e..0000000
--- a/genomix/genomix-hadoop/data/webmap/MergeBubble.txt
+++ /dev/null
@@ -1,2 +0,0 @@
-1 AATAGAA
-2 AATACAA
diff --git a/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/BridgePath/BridgePath b/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/BridgePathWithTandemRepeat/BridgePath
similarity index 100%
rename from genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/BridgePath/BridgePath
rename to genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/BridgePathWithTandemRepeat/BridgePath
diff --git a/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/ComplexTandemRepeat/Complex b/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/ComplexTandemRepeat/Complex
new file mode 100644
index 0000000..8f321a1
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/ComplexTandemRepeat/Complex
@@ -0,0 +1,3 @@
+1 AATCGAA
+2 ATCA
+3 GGAAA
diff --git a/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/TreePath/TreePath b/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/ComplexTreePath/TreePath
similarity index 100%
rename from genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/TreePath/TreePath
rename to genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/ComplexTreePath/TreePath
diff --git a/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/LeftAdj/leftAdj b/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/LeftAdj/leftAdj
new file mode 100644
index 0000000..cb2d036
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/LeftAdj/leftAdj
@@ -0,0 +1,3 @@
+1 CAAACC
+2 GAAACC
+3 TAACC
diff --git a/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/RightAdj/rightAdj b/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/RightAdj/rightAdj
new file mode 100644
index 0000000..21c66ff
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/RightAdj/rightAdj
@@ -0,0 +1,3 @@
+1 GAAACG
+2 GAAACC
+3 GAAAT
diff --git a/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/SelfPath/SelfPath.txt b/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/SelfTandemRepeat/SelfPath.txt
similarity index 100%
rename from genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/SelfPath/SelfPath.txt
rename to genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/SelfTandemRepeat/SelfPath.txt
diff --git a/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/BridgePath2/bridgepath2 b/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/SimpleBridgePath/bridgepath2
similarity index 100%
rename from genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/BridgePath2/bridgepath2
rename to genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/SimpleBridgePath/bridgepath2
diff --git a/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/SimpleTreePath/tree b/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/SimpleTreePath/tree
new file mode 100644
index 0000000..9f52537
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/SimpleTreePath/tree
@@ -0,0 +1,3 @@
+1 GAAACCTTGA
+2 GAAACCTGGG
+3 GAAATCT
diff --git a/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/TandemRepeatWithMergeEdge/MergeEdge b/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/TandemRepeatWithMergeEdge/MergeEdge
new file mode 100644
index 0000000..f6da661
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/TandemRepeatWithMergeEdge/MergeEdge
@@ -0,0 +1 @@
+1 AAGGCCCA
diff --git a/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/TandemRepeatWithUnmergeEdge/UnmergeEdge b/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/TandemRepeatWithUnmergeEdge/UnmergeEdge
new file mode 100644
index 0000000..ada0dab
--- /dev/null
+++ b/genomix/genomix-hadoop/data/webmap/PathMerge_TestSet/TandemRepeatWithUnmergeEdge/UnmergeEdge
@@ -0,0 +1 @@
+1 AGGCCC
diff --git a/genomix/genomix-hadoop/data/webmap/test.txt b/genomix/genomix-hadoop/data/webmap/test.txt
deleted file mode 100644
index 990dbd1..0000000
--- a/genomix/genomix-hadoop/data/webmap/test.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-1 AATAGAAG
-2 TATAGACC
-3 CATAGATT
diff --git a/genomix/genomix-hadoop/data/webmap/text.txt b/genomix/genomix-hadoop/data/webmap/text.txt
deleted file mode 100755
index 01c49e5..0000000
--- a/genomix/genomix-hadoop/data/webmap/text.txt
+++ /dev/null
@@ -1,6 +0,0 @@
-1 AATAGAAG
-2 AATAGCTT
-3 AATAGAAG
-4 AATAGCTT
-5 AATAGAAG
-6 AGAAGAAG
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 83e2860..b49dc4f 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 +24,10 @@
private static int SIZE_KMER = 3;
public static final String PreFix = "data/webmap/PathMerge_TestSet";
public static final String[] TestDir = { PreFix + File.separator
- + "BridgePath2"};
+// + "LeftAdj", PreFix + File.separator
+ + "RingPath"};
+// + "TandemRepeatWithMergeEdge", PreFix + File.separator
+// + "TandemRepeatWithUnmergeEdge"};
// + "FR", PreFix + File.separator
// + "RF", PreFix + File.separator
// + "head_FR", PreFix + File.separator
diff --git a/genomix/genomix-pregelix/data/AddBridge/SimpleTest/part-00000 b/genomix/genomix-pregelix/data/AddBridge/SimpleTest/part-00000
deleted file mode 100755
index 22508c2..0000000
--- a/genomix/genomix-pregelix/data/AddBridge/SimpleTest/part-00000
+++ /dev/null
Binary files differ
diff --git a/genomix/genomix-pregelix/data/PathMergeTestSet/2/bin/part-00000 b/genomix/genomix-pregelix/data/PathMergeTestSet/2/bin/part-00000
deleted file mode 100755
index d3766af..0000000
--- a/genomix/genomix-pregelix/data/PathMergeTestSet/2/bin/part-00000
+++ /dev/null
Binary files differ
diff --git a/genomix/genomix-pregelix/data/PathMergeTestSet/2/test.txt b/genomix/genomix-pregelix/data/PathMergeTestSet/2/test.txt
deleted file mode 100644
index 51e1252..0000000
--- a/genomix/genomix-pregelix/data/PathMergeTestSet/2/test.txt
+++ /dev/null
@@ -1,2 +0,0 @@
-ATA {[] [] [] [{AAT:[1]}] {5':[], ~5':[]} 1.0x}
-AAT {[{ATA:[1]}] [] [] [] {5':[(1-0_0)], ~5':[]} 1.0x}
diff --git a/genomix/genomix-pregelix/data/PathMergeTestSet/3/bin/part-00000 b/genomix/genomix-pregelix/data/PathMergeTestSet/3/bin/part-00000
deleted file mode 100755
index 7a31cd9..0000000
--- a/genomix/genomix-pregelix/data/PathMergeTestSet/3/bin/part-00000
+++ /dev/null
Binary files differ
diff --git a/genomix/genomix-pregelix/data/PathMergeTestSet/3/graphviz/result.ps b/genomix/genomix-pregelix/data/PathMergeTestSet/3/graphviz/result.ps
deleted file mode 100644
index e720671..0000000
--- a/genomix/genomix-pregelix/data/PathMergeTestSet/3/graphviz/result.ps
+++ /dev/null
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diff --git a/genomix/genomix-pregelix/data/PathMergeTestSet/3/test.txt b/genomix/genomix-pregelix/data/PathMergeTestSet/3/test.txt
deleted file mode 100644
index d661685..0000000
--- a/genomix/genomix-pregelix/data/PathMergeTestSet/3/test.txt
+++ /dev/null
@@ -1,3 +0,0 @@
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diff --git a/genomix/genomix-pregelix/data/PathMergeTestSet/4/.test.txt.binmerge.crc b/genomix/genomix-pregelix/data/PathMergeTestSet/4/.test.txt.binmerge.crc
deleted file mode 100644
index fd1d21d..0000000
--- a/genomix/genomix-pregelix/data/PathMergeTestSet/4/.test.txt.binmerge.crc
+++ /dev/null
Binary files differ
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deleted file mode 100755
index 23817bd..0000000
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Binary files differ
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deleted file mode 100644
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diff --git a/genomix/genomix-pregelix/data/PathMergeTestSet/ThreeDuplicate/test.txt b/genomix/genomix-pregelix/data/PathMergeTestSet/ThreeDuplicate/test.txt
deleted file mode 100644
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diff --git a/genomix/genomix-pregelix/data/PathMergeTestSet/TreePath/test.txt b/genomix/genomix-pregelix/data/PathMergeTestSet/TreePath/test.txt
deleted file mode 100644
index a4992ef..0000000
--- a/genomix/genomix-pregelix/data/PathMergeTestSet/TreePath/test.txt
+++ /dev/null
@@ -1,21 +0,0 @@
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diff --git a/genomix/genomix-pregelix/data/SplitRepeat/AdjSplitRepeat/part-00000 b/genomix/genomix-pregelix/data/SplitRepeat/AdjSplitRepeat/part-00000
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index 665db46..0000000
--- a/genomix/genomix-pregelix/data/SplitRepeat/AdjSplitRepeat/part-00000
+++ /dev/null
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diff --git a/genomix/genomix-pregelix/data/SplitRepeat/SplitOnce/part-00000 b/genomix/genomix-pregelix/data/SplitRepeat/SplitOnce/part-00000
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diff --git a/genomix/genomix-pregelix/data/SplitRepeat/SplitTwice/part-00000 b/genomix/genomix-pregelix/data/SplitRepeat/SplitTwice/part-00000
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--- a/genomix/genomix-pregelix/data/SplitRepeat/SplitTwice/part-00000
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diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BridgePath/bin/part-00000 b/genomix/genomix-pregelix/data/TestSet/PathMerge/BridgePathWithTandemRepeat/bin/part-00000
similarity index 100%
rename from genomix/genomix-pregelix/data/TestSet/PathMerge/BridgePath/bin/part-00000
rename to genomix/genomix-pregelix/data/TestSet/PathMerge/BridgePathWithTandemRepeat/bin/part-00000
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diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BridgePath/graphviz/result.ps b/genomix/genomix-pregelix/data/TestSet/PathMerge/BridgePathWithTandemRepeat/graphviz/result.ps
similarity index 100%
rename from genomix/genomix-pregelix/data/TestSet/PathMerge/BridgePath/graphviz/result.ps
rename to genomix/genomix-pregelix/data/TestSet/PathMerge/BridgePathWithTandemRepeat/graphviz/result.ps
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BridgePath/test.txt b/genomix/genomix-pregelix/data/TestSet/PathMerge/BridgePathWithTandemRepeat/test.txt
similarity index 100%
rename from genomix/genomix-pregelix/data/TestSet/PathMerge/BridgePath/test.txt
rename to genomix/genomix-pregelix/data/TestSet/PathMerge/BridgePathWithTandemRepeat/test.txt
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BridgePath_AfterUnroll/.txt.crc b/genomix/genomix-pregelix/data/TestSet/PathMerge/BridgePath_AfterUnroll/.txt.crc
deleted file mode 100644
index e69de29..0000000
--- a/genomix/genomix-pregelix/data/TestSet/PathMerge/BridgePath_AfterUnroll/.txt.crc
+++ /dev/null
diff --git a/genomix/genomix-pregelix/data/TestSet/PathMerge/BridgePath_AfterUnroll/bin/.part-0.crc b/genomix/genomix-pregelix/data/TestSet/PathMerge/BridgePath_AfterUnroll/bin/.part-0.crc
deleted file mode 100644
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+++ /dev/null
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deleted file mode 100644
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deleted file mode 100644
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deleted file mode 100644
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deleted file mode 100644
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+1 setlinewidth
+solid
+0.33333 1 1 edgecolor
+newpath 181.12 114.76 moveto
+180.22 104.2 lineto
+174.34 113.02 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+145 127.4 moveto 46 (RF: [1]) alignedtext
+grestore
+% AGG
+gsave
+0 0 0.75294 nodecolor
+newpath 278 0 moveto
+278 104 lineto
+334 104 lineto
+334 0 lineto
+closepath fill
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 278 0 moveto
+278 104 lineto
+334 104 lineto
+334 0 lineto
+closepath stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+289.5 87.4 moveto 33 (AGG) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 278 78 moveto
+334 78 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+287.5 61.4 moveto 37 (5':[1]) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 278 52 moveto
+334 52 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+286 35.4 moveto 40 (~5':[]) alignedtext
+1 setlinewidth
+filled
+0 0 0 nodecolor
+newpath 278 26 moveto
+334 26 lineto
+stroke
+0 0 0 nodecolor
+14 /Times-Roman set_font
+294.5 9.4 moveto 23 (1.0) alignedtext
+grestore
+% GCC->AGG
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 196.26 52 moveto
+216.82 52 244.89 52 267.5 52 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 267.78 55.5 moveto
+277.78 52 lineto
+267.78 48.5 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 267.78 55.5 moveto
+277.78 52 lineto
+267.78 48.5 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+214 57.4 moveto 46 (FR: [1]) alignedtext
+grestore
+% AGG->GCC
+gsave
+1 setlinewidth
+0.66667 1 1 edgecolor
+newpath 277.51 35.99 moveto
+271.87 33.51 265.87 31.33 260 30 curveto
+240.06 25.48 233.94 25.48 214 30 curveto
+211.34 30.6 208.65 31.38 205.99 32.28 curveto
+stroke
+0.66667 1 1 edgecolor
+newpath 204.53 29.09 moveto
+196.49 35.99 lineto
+207.08 35.61 lineto
+closepath fill
+1 setlinewidth
+solid
+0.66667 1 1 edgecolor
+newpath 204.53 29.09 moveto
+196.49 35.99 lineto
+207.08 35.61 lineto
+closepath stroke
+0 0 0 edgecolor
+14 /Times-Roman set_font
+214 35.4 moveto 46 (FR: [1]) alignedtext
+grestore
endpage
showpage
grestore
@@ -323,7 +432,7 @@
%%EndPage: 1
%%Trailer
%%Pages: 1
-%%BoundingBox: 36 36 240 148
+%%BoundingBox: 36 36 378 184
end
restore
%%EOF
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 696755d..496c377 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
@@ -8,7 +8,6 @@
import edu.uci.ics.genomix.type.KmerBytesWritable;
import edu.uci.ics.genomix.type.NodeWritable;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
-import edu.uci.ics.genomix.type.VKmerListWritable;
public class VertexValueWritable
extends NodeWritable{
@@ -55,23 +54,15 @@
private byte state;
private boolean isFakeVertex;
-
- private HashMapWritable<VKmerBytesWritable, VKmerListWritable> traverseMap;
+ private VKmerBytesWritable startKmer; //use for detect cycle in path merge
public VertexValueWritable() {
super();
state = 0;
isFakeVertex = false;
- traverseMap = new HashMapWritable<VKmerBytesWritable, VKmerListWritable>();
+ startKmer = new VKmerBytesWritable();
}
-// public NodeWritable getNode(){
-// NodeWritable node = new NodeWritable();
-// node.setAsCopy(this.getEdges(), this.getStartReads(), this.getEndReads(),
-// this.getInternalKmer(), this.getAverageCoverage());
-// return super();
-// }
-
public void setNode(NodeWritable node){
super.setAsCopy(node.getEdges(), node.getStartReads(), node.getEndReads(),
node.getInternalKmer(), node.getAverageCoverage());
@@ -148,20 +139,20 @@
public void setState(byte state) {
this.state = state;
}
-
- public HashMapWritable<VKmerBytesWritable, VKmerListWritable> getTraverseMap() {
- return traverseMap;
+
+ public VKmerBytesWritable getStartKmer() {
+ return startKmer;
}
- public void setTraverseMap(HashMapWritable<VKmerBytesWritable, VKmerListWritable> traverseMap) {
- this.traverseMap = traverseMap;
+ public void setStartKmer(VKmerBytesWritable startKmer) {
+ this.startKmer.setAsCopy(startKmer);
}
public void reset() {
super.reset();
this.state = 0;
this.isFakeVertex = false;
- this.traverseMap.clear();
+ this.startKmer.reset(0);
}
@Override
@@ -170,7 +161,7 @@
super.readFields(in);
this.state = in.readByte();
this.isFakeVertex = in.readBoolean();
- this.traverseMap.readFields(in);
+ this.startKmer.readFields(in);
}
@Override
@@ -178,7 +169,7 @@
super.write(out);
out.writeByte(this.state);
out.writeBoolean(this.isFakeVertex);
- this.traverseMap.write(out);
+ this.startKmer.write(out);
}
public int getDegree(){
@@ -207,46 +198,17 @@
/**
* Process any changes to value. This is for edge updates. nodeToAdd should be only edge
*/
-// public void processUpdates(byte neighborToDeleteDir, VKmerBytesWritable nodeToDelete,
-// byte neighborToMergeDir, NodeWritable node){
-// byte deleteDir = (byte)(neighborToDeleteDir & MessageFlag.DIR_MASK);
-// this.getEdgeList(deleteDir).remove(nodeToDelete);
-//
-// byte mergeDir = (byte)(neighborToMergeDir & MessageFlag.DIR_MASK);
-//// this.getEdgeList(mergeDir).add(nodeToAdd);
-//
-// this.getNode().mergeEdges(mergeDir, node);
-// }
public void processUpdates(byte deleteDir, VKmerBytesWritable toDelete, byte updateDir, NodeWritable other){
this.getNode().updateEdges(deleteDir, toDelete, updateDir, other);
}
- public void processMerges(byte mergeDir, NodeWritable node, int kmerSize){
- KmerBytesWritable.setGlobalKmerLength(kmerSize);
- mergeDir = (byte)(mergeDir & MessageFlag.DIR_MASK);
- super.getNode().mergeWithNode(mergeDir, node);
- }
-
/**
* Process any changes to value. This is for merging. nodeToAdd should be only edge
*/
- public void processMerges(byte neighborToDeleteDir, VKmerBytesWritable nodeToDelete,
- byte neighborToMergeDir, EdgeWritable nodeToAdd,
- int kmerSize, NodeWritable node){
+ public void processMerges(byte mergeDir, NodeWritable node, int kmerSize){
KmerBytesWritable.setGlobalKmerLength(kmerSize);
- byte deleteDir = (byte)(neighborToDeleteDir & MessageFlag.DIR_MASK);
-// this.getEdgeList(deleteDir).remove(nodeToDelete);
- super.getNode().mergeWithNode(deleteDir, node);
-// this.getInternalKmer().mergeWithKmerInDir(deleteDir, kmerSize, kmer);
-
-// if(nodeToAdd != null){
-// byte mergeDir = (byte)(neighborToMergeDir & MessageFlag.DIR_MASK);
-// this.getEdgeList(mergeDir).add(nodeToAdd);
-// }
- }
-
- public boolean hasPathTo(VKmerBytesWritable nodeToSeek){
- return traverseMap.containsKey(nodeToSeek);
+ mergeDir = (byte)(mergeDir & MessageFlag.DIR_MASK);
+ super.getNode().mergeWithNode(mergeDir, node);
}
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/BasicGraphCleanVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/BasicGraphCleanVertex.java
index c2d29d2..7a1dec5 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/BasicGraphCleanVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/BasicGraphCleanVertex.java
@@ -28,7 +28,7 @@
protected VKmerBytesWritable destVertexId = null;
protected Iterator<VKmerBytesWritable> kmerIterator;
protected VKmerListWritable kmerList = null;
- protected VKmerBytesWritable curKmer = null; //for detect tandemRepeat
+ protected VKmerBytesWritable repeatKmer = null; //for detect tandemRepeat
protected byte repeatDir; //for detect tandemRepeat
protected VKmerBytesWritable tmpKmer = null;
protected byte headFlag;
@@ -39,6 +39,7 @@
public static boolean fakeVertexExist = false;
protected static VKmerBytesWritable fakeVertex = null;
+ protected VertexValueWritable tmpValue = new VertexValueWritable();
/**
* initiate kmerSize, maxIteration
@@ -61,7 +62,7 @@
* reset selfFlag
*/
public void resetSelfFlag(){
- selfFlag =(byte)(getVertexValue().getState() & MessageFlag.VERTEX_MASK);
+ selfFlag = (byte)(getVertexValue().getState() & MessageFlag.VERTEX_MASK);
}
/**
@@ -75,6 +76,29 @@
return (byte) (getVertexValue().getState() & State.HEAD_SHOULD_MERGE_MASK);
}
+ public byte getHeadFlagAndMergeDir(){
+ byte flagAndMergeDir = (byte)(getVertexValue().getState() & State.IS_HEAD);
+ flagAndMergeDir |= (byte)(getVertexValue().getState() & State.HEAD_SHOULD_MERGE_MASK);
+ return flagAndMergeDir;
+ }
+
+ public byte getMsgFlagAndMergeDir(){
+ byte flagAndMergeDir = (byte)(getVertexValue().getState() & State.IS_HEAD);
+ byte meToNeighborDir = (byte) (incomingMsg.getFlag() & MessageFlag.DIR_MASK);
+ byte neighborToMeDir = mirrorDirection(meToNeighborDir);
+ switch(neighborToMeDir){
+ case MessageFlag.DIR_FF:
+ case MessageFlag.DIR_FR:
+ flagAndMergeDir |= MessageFlag.HEAD_SHOULD_MERGEWITHPREV;
+ break;
+ case MessageFlag.DIR_RF:
+ case MessageFlag.DIR_RR:
+ flagAndMergeDir |= MessageFlag.HEAD_SHOULD_MERGEWITHNEXT;
+ break;
+ }
+ return flagAndMergeDir;
+ }
+
/**
* set head state
*/
@@ -271,8 +295,8 @@
/**
* head send message to all previous nodes
*/
- public void sendSettledMsgToAllPrevNodes() {
- kmerIterator = getVertexValue().getRFList().getKeys(); // RFList
+ public void sendSettledMsgToAllPrevNodes(VertexValueWritable value) {
+ kmerIterator = value.getRFList().getKeys(); // RFList
while(kmerIterator.hasNext()){
outFlag &= MessageFlag.DIR_CLEAR;
outFlag |= MessageFlag.DIR_RF;
@@ -281,7 +305,7 @@
destVertexId.setAsCopy(kmerIterator.next());
sendMsg(destVertexId, outgoingMsg);
}
- kmerIterator = getVertexValue().getRRList().getKeys(); // RRList
+ kmerIterator = value.getRRList().getKeys(); // RRList
while(kmerIterator.hasNext()){
outFlag &= MessageFlag.DIR_CLEAR;
outFlag |= MessageFlag.DIR_RR;
@@ -295,8 +319,8 @@
/**
* head send message to all next nodes
*/
- public void sendSettledMsgToAllNextNodes() {
- kmerIterator = getVertexValue().getFFList().getKeys(); // FFList
+ public void sendSettledMsgToAllNextNodes(VertexValueWritable value) {
+ kmerIterator = value.getFFList().getKeys(); // FFList
while(kmerIterator.hasNext()){
outFlag &= MessageFlag.DIR_CLEAR;
outFlag |= MessageFlag.DIR_FF;
@@ -305,7 +329,7 @@
destVertexId.setAsCopy(kmerIterator.next());
sendMsg(destVertexId, outgoingMsg);
}
- kmerIterator = getVertexValue().getFRList().getKeys(); // FRList
+ kmerIterator = value.getFRList().getKeys(); // FRList
while(kmerIterator.hasNext()){
outFlag &= MessageFlag.DIR_CLEAR;
outFlag |= MessageFlag.DIR_FR;
@@ -316,42 +340,49 @@
}
}
- public void sendSettledMsgToAllNeighborNodes() {
- sendSettledMsgToAllPrevNodes();
- sendSettledMsgToAllNextNodes();
+ public void sendSettledMsgToAllNeighborNodes(VertexValueWritable value) {
+ sendSettledMsgToAllPrevNodes(value);
+ sendSettledMsgToAllNextNodes(value);
}
/**
* start sending message
*/
public void startSendMsg() {
-// if(isTandemRepeat())
-
- if (VertexUtil.isVertexWithOnlyOneIncoming(getVertexValue())){
+ if(isTandemRepeat()){
+ tmpValue.setAsCopy(getVertexValue());
+ tmpValue.getEdgeList(repeatDir).remove(repeatKmer);
outFlag = 0;
outFlag |= MessageFlag.IS_HEAD;
- outFlag |= MessageFlag.HEAD_SHOULD_MERGEWITHPREV;
- getVertexValue().setState(outFlag);
- activate();
+ sendSettledMsgToAllNeighborNodes(tmpValue);
+ } else{
+ if (VertexUtil.isVertexWithOnlyOneIncoming(getVertexValue())){
+ outFlag = 0;
+ outFlag |= MessageFlag.IS_HEAD;
+ outFlag |= MessageFlag.HEAD_SHOULD_MERGEWITHPREV;
+ getVertexValue().setState(outFlag);
+ activate();
+ }
+ if (VertexUtil.isVertexWithOnlyOneOutgoing(getVertexValue())){
+ outFlag = 0;
+ outFlag |= MessageFlag.IS_HEAD;
+ outFlag |= MessageFlag.HEAD_SHOULD_MERGEWITHNEXT;
+ getVertexValue().setState(outFlag);
+ activate();
+ }
+ if (VertexUtil.isVertexWithManyIncoming(getVertexValue())) {
+ outFlag = 0;
+ outFlag |= MessageFlag.IS_HEAD;
+ sendSettledMsgToAllPrevNodes(getVertexValue());
+ }
+ if (VertexUtil.isVertexWithManyOutgoing(getVertexValue())) {
+ outFlag = 0;
+ outFlag |= MessageFlag.IS_HEAD;
+ sendSettledMsgToAllNextNodes(getVertexValue());
+ }
}
- if (VertexUtil.isVertexWithOnlyOneOutgoing(getVertexValue())){
- outFlag = 0;
- outFlag |= MessageFlag.IS_HEAD;
- outFlag |= MessageFlag.HEAD_SHOULD_MERGEWITHNEXT;
- getVertexValue().setState(outFlag);
- activate();
- }
- if (VertexUtil.isVertexWithManyIncoming(getVertexValue())) {
- outFlag = 0;
- outFlag |= MessageFlag.IS_HEAD;
- sendSettledMsgToAllPrevNodes();
- }
- if (VertexUtil.isVertexWithManyOutgoing(getVertexValue())) {
- outFlag = 0;
- outFlag |= MessageFlag.IS_HEAD;
- sendSettledMsgToAllNextNodes();
- }
- if(!VertexUtil.isActiveVertex(getVertexValue())){
+ if(!VertexUtil.isActiveVertex(getVertexValue())
+ || isTandemRepeat()){
getVertexValue().setState(MessageFlag.IS_HALT);
voteToHalt();
}
@@ -379,54 +410,17 @@
public void initState(Iterator<M> msgIterator) {
while (msgIterator.hasNext()) {
incomingMsg = msgIterator.next();
- if(getHeadFlag() != MessageFlag.IS_HEAD){
+ if(getHeadFlag() != MessageFlag.IS_HEAD && !isTandemRepeat()){
setHeadMergeDir();
activate();
+ } else if(getHeadFlagAndMergeDir() == getMsgFlagAndMergeDir()){
+ activate();
} else{ /** already set up **/
/** if headMergeDir are not the same **/
getVertexValue().setState(MessageFlag.IS_HALT);
voteToHalt();
}
}
-// byte headMergeDir = (byte) (incomingMsg.getFlag() & MessageFlag.HEAD_SHOULD_MERGE_MASK);
-// switch(headMergeDir){
-// case MessageFlag.HEAD_SHOULD_MERGEWITHPREV:
-// /** not set up yet **/
-// if(getHeadFlag() != MessageFlag.IS_HEAD){
-// getVertexValue().setState(incomingMsg.getFlag());
-// } else{ /** already set up **/
-// /** if headMergeDir are not the same **/
-// if(getHeadMergeDir() != headMergeDir){
-// getVertexValue().setState(MessageFlag.IS_HALT);
-// voteToHalt();
-// }
-// }
-// break;
-// case MessageFlag.HEAD_SHOULD_MERGEWITHNEXT:
-// /** not set up yet **/
-// if(getHeadFlag() != MessageFlag.IS_HEAD){
-// getVertexValue().setState(incomingMsg.getFlag());
-// } else{ /** already set up **/
-// /** if headMergeDir are not the same **/
-// if(getHeadMergeDir() != headMergeDir){
-// getVertexValue().setState(MessageFlag.IS_HALT);
-// voteToHalt();
-// }
-// }
-// break;
-// }
-// if (!VertexUtil.isPathVertex(getVertexValue())
-// && !VertexUtil.isHeadWithoutIndegree(getVertexValue())
-// && !VertexUtil.isRearWithoutOutdegree(getVertexValue())) {
-// msgIterator.next();
-// voteToHalt();
-// } else {
-// incomingMsg = msgIterator.next();
-// if(getHeadFlag() > 0)
-// voteToHalt();
-// else
-// getVertexValue().setState(incomingMsg.getFlag());
-// }
}
/**
@@ -558,7 +552,7 @@
outFlag |= MessageFlag.KILL;
outFlag |= MessageFlag.DIR_FROM_DEADVERTEX;
- sendSettledMsgToAllNeighborNodes();
+ sendSettledMsgToAllNeighborNodes(getVertexValue());
deleteVertex(getVertexId());
}
@@ -615,8 +609,8 @@
for(byte d : DirectionFlag.values){
Iterator<VKmerBytesWritable> it = getVertexValue().getEdgeList(d).getKeys();
while(it.hasNext()){
- curKmer.setAsCopy(it.next());
- if(curKmer.equals(getVertexId())){
+ repeatKmer.setAsCopy(it.next());
+ if(repeatKmer.equals(getVertexId())){
repeatDir = d;
return true;
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeRemoveVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeRemoveVertex.java
index 37547c5..55facb7 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeRemoveVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeRemoveVertex.java
@@ -76,10 +76,10 @@
initVertex();
if (getSuperstep() == 1) {
if(VertexUtil.isUpBridgeVertex(getVertexValue())){
- sendSettledMsgToAllNextNodes();
+ sendSettledMsgToAllNextNodes(getVertexValue());
}
else if(VertexUtil.isDownBridgeVertex(getVertexValue())){
- sendSettledMsgToAllPrevNodes();
+ sendSettledMsgToAllPrevNodes(getVertexValue());
}
}
else if (getSuperstep() == 2){
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 4a34106..938600f 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
@@ -91,7 +91,7 @@
if (getSuperstep() == 3) {
if(getVertexValue().getState() == State.IS_HEAD)
outFlag |= MessageFlag.IS_HEAD;
- sendSettledMsgToAllNextNodes();
+ sendSettledMsgToAllNextNodes(getVertexValue());
} else {
while (msgIterator.hasNext()) {
incomingMsg = msgIterator.next();
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P2ForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P2ForPathMergeVertex.java
index 489a059..19779f5 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P2ForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P2ForPathMergeVertex.java
@@ -212,7 +212,7 @@
/** processing general case **/
else{
if(isPathNode())
- sendSettledMsgToAllNeighborNodes();
+ sendSettledMsgToAllNeighborNodes(getVertexValue());
if(!isHeadNode())
voteToHalt();
}
@@ -227,7 +227,7 @@
/** head doesn't receive msg and send out final msg **/
if(!msgIterator.hasNext() && isHeadNode()){
outFlag |= MessageFlag.IS_FINAL;
- sendSettledMsgToAllNeighborNodes();
+ sendSettledMsgToAllNeighborNodes(getVertexValue());
voteToHalt();
} else{
while (msgIterator.hasNext()) {
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 8663320..ce4291d 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
@@ -93,6 +93,9 @@
// Node may be marked as head b/c it's a real head or a real tail
headFlag = getHeadFlag();
headMergeDir = getHeadMergeDir();
+ if(repeatKmer == null)
+ repeatKmer = new VKmerBytesWritable();
+ tmpValue.reset();
}
protected boolean isNodeRandomHead(VKmerBytesWritable nodeKmer) {
@@ -212,14 +215,25 @@
while (msgIterator.hasNext()) {
incomingMsg = msgIterator.next();
selfFlag = (byte) (State.VERTEX_MASK & getVertexValue().getState());
- processMerge();
- //head meets head, stop
- if(getMsgFlag() == MessageFlag.IS_HEAD && selfFlag == MessageFlag.IS_HEAD){
+ /** record startKmer in merge path **/
+ if(getSuperstep() == 6){
+ getVertexValue().setStartKmer(getVertexId());
+ }
+ /** check if merge path is a cycle **/
+ if(getVertexValue().getStartKmer() == incomingMsg.getSourceVertexId()){
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();
}
- else
- this.activate();
}
}
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/scaffolding/BFSTraverseVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/scaffolding/BFSTraverseVertex.java
index 0f82bda..c155e9e 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/scaffolding/BFSTraverseVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/scaffolding/BFSTraverseVertex.java
@@ -75,9 +75,9 @@
outgoingMsg.setPathList(kmerList);
outgoingMsg.setReadId(incomingMsg.getReadId()); //only one readId
if(incomingMsg.isSrcFlip())
- sendSettledMsgToAllPrevNodes();
+ sendSettledMsgToAllPrevNodes(getVertexValue());
else
- sendSettledMsgToAllNextNodes();
+ sendSettledMsgToAllNextNodes(getVertexValue());
}
public void broadcaseBFSTraverse(){
@@ -97,11 +97,11 @@
switch(neighborToMeDir){
case MessageFlag.DIR_FF:
case MessageFlag.DIR_FR:
- sendSettledMsgToAllPrevNodes();
+ sendSettledMsgToAllPrevNodes(getVertexValue());
break;
case MessageFlag.DIR_RF:
case MessageFlag.DIR_RR:
- sendSettledMsgToAllNextNodes();
+ sendSettledMsgToAllNextNodes(getVertexValue());
break;
}
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/unrolltandemrepeat/UnrollTandemRepeat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/unrolltandemrepeat/UnrollTandemRepeat.java
index c2569d2..ffd53a9 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/unrolltandemrepeat/UnrollTandemRepeat.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/unrolltandemrepeat/UnrollTandemRepeat.java
@@ -19,7 +19,6 @@
public static final String KMER_SIZE = "BasicGraphCleanVertex.kmerSize";
public static int kmerSize = -1;
- private VertexValueWritable tmpValue = new VertexValueWritable();
private EdgeWritable tmpEdge = new EdgeWritable();
/**
@@ -36,7 +35,7 @@
*/
public boolean repeatCanBeMerged(){
tmpValue.setAsCopy(getVertexValue());
- tmpValue.getEdgeList(repeatDir).remove(curKmer);
+ tmpValue.getEdgeList(repeatDir).remove(repeatKmer);
boolean hasFlip = false;
/** pick one edge and flip **/
for(byte d : DirectionFlag.values){
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 60a6a1b..0825241 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
@@ -6,21 +6,28 @@
public static Test suite() throws Exception {
String pattern ="PathMerge";
- String testSet[] = {"2", "3", "4", "5", "6", "7", "8", "9", "head_6", "head_7",
- "FR",
- "RF",
- "head_FR",
- "head_RF",
- "twohead_FR",
- "twohead_RF",
- "BridgePath2"
+ 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",
-// "head_6"
-// "head_7"
-// "CyclePath",
-// "SelfPath"
+// "RingPath",
+// "SelfTandemRepeat"
+// "TandemRepeatWithMergeEdge",
+// "TandemRepeatWithUnmergeEdge",
// "TreePath"
+// "ComplexTandemRepeat"
+// "SimpleBridgePath",
+// "SimpleTreePath"
};
init(pattern, testSet);
BasicGraphCleanTestSuite testSuite = new BasicGraphCleanTestSuite();