Refactor tipremove
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/NodeWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/NodeWritable.java
index 4263242..e7b0509 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/NodeWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/NodeWritable.java
@@ -369,8 +369,16 @@
return internalKmer.getKmerLetterLength();
}
+ //This function works on only this case: in this DIR, vertex has and only has one EDGETYPE
public EDGETYPE getEdgetypeFromDir(DIR direction){
- EnumSet<EDGETYPE> ets = DIR.
+ if(getDegree(direction) != 1)
+ throw new IllegalArgumentException("getEdgetypeFromDir is used on the case, in which the vertex has and only has one EDGETYPE!");
+ EnumSet<EDGETYPE> ets = direction.edgeType();
+ for(EDGETYPE et : ets){
+ if(getEdgeList(et).getCountOfPosition() > 0)
+ return et;
+ }
+ return null;
}
public EdgeListWritable getEdgeList(EDGETYPE edgeType) {
diff --git a/genomix/genomix-pregelix/data/TestSet/TipRemove/SmallGenome/.txt.crc b/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/.statistics.crc
similarity index 100%
rename from genomix/genomix-pregelix/data/TestSet/TipRemove/SmallGenome/.txt.crc
rename to genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/.statistics.crc
diff --git a/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/bin/.part-0.crc b/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/bin/.part-0.crc
index bf60a71..de75c33 100644
--- a/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/bin/.part-0.crc
+++ b/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/bin/.part-0.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/bin/.part-1.crc b/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/bin/.part-1.crc
index 744fbef..7120be2 100644
--- a/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/bin/.part-1.crc
+++ b/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/bin/.part-1.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/bin/part-0 b/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/bin/part-0
index 7934715..89795c2 100755
--- a/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/bin/part-0
+++ b/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/bin/part-0
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/bin/part-1 b/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/bin/part-1
index fc82ad0..0ca2113 100755
--- a/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/bin/part-1
+++ b/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/bin/part-1
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/graphviz.svg b/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/graphviz.svg
new file mode 100644
index 0000000..a9f1169
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+++ b/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/graphviz.svg
@@ -0,0 +1,151 @@
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diff --git a/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/graphviz/result.ps b/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/graphviz/result.ps
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index bc35149..0000000
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diff --git a/genomix/genomix-pregelix/data/TestSet/TipRemove/SmallGenome/.txt.crc b/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/statistics
old mode 100644
new mode 100755
similarity index 100%
copy from genomix/genomix-pregelix/data/TestSet/TipRemove/SmallGenome/.txt.crc
copy to genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/statistics
diff --git a/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/txt b/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/txt
index 2b549e1..16d0f51 100755
--- a/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/txt
+++ b/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/txt
@@ -1,6 +1,6 @@
-GAA {[] [] [] [{AGA:[1]}] {5':[], ~5':[]} GAA 1.0x}
-AGA {[{GAA:[1]}] [] [{CTA:[1]}] [] {5':[], ~5':[]} AGA 1.0x}
-ATA {[] [{CTA:[1]}] [] [{AAT:[1]}] {5':[], ~5':[]} ATA 1.0x}
-AGC {[] [{CTA:[0]}] [] [] {5':[], ~5':[]} 0.0x}
-AAT {[{ATA:[1]}] [] [] [] {5':[(1-0_0)], ~5':[]} AAT 1.0x}
-CTA {[] [{ATA:[1]},{AGC:[0]}] [{AGA:[1]}] [] {5':[], ~5':[]} CTA 1.0x}
+GAA {[] [] [] [{AGA:[1]}] {5':[], ~5':[]} GAA 1.0x} IS_NON
+AGA {[{GAA:[1]}] [] [{CTA:[1]}] [] {5':[], ~5':[]} AGA 1.0x} IS_NON
+ATA {[] [{CTA:[1]}] [] [{AAT:[1]}] {5':[], ~5':[]} ATA 1.0x} IS_NON
+AGC {[] [{CTA:[0]}] [] [] {5':[], ~5':[]} 0.0x} IS_NON
+AAT {[{ATA:[1]}] [] [] [] {5':[(1-0_0)], ~5':[]} AAT 1.0x} IS_NON
+CTA {[] [{ATA:[1]},{AGC:[0]}] [{AGA:[1]}] [] {5':[], ~5':[]} CTA 1.0x} IS_NON
diff --git a/genomix/genomix-pregelix/data/TestSet/TipRemove/SmallGenome/.txt.crc b/genomix/genomix-pregelix/data/TestSet/TipRemove/RF_Tip/.statistics.crc
similarity index 100%
copy from genomix/genomix-pregelix/data/TestSet/TipRemove/SmallGenome/.txt.crc
copy to genomix/genomix-pregelix/data/TestSet/TipRemove/RF_Tip/.statistics.crc
diff --git a/genomix/genomix-pregelix/data/TestSet/TipRemove/RF_Tip/bin/.part-0.crc b/genomix/genomix-pregelix/data/TestSet/TipRemove/RF_Tip/bin/.part-0.crc
index dbb171a..9a96e5d 100644
--- a/genomix/genomix-pregelix/data/TestSet/TipRemove/RF_Tip/bin/.part-0.crc
+++ b/genomix/genomix-pregelix/data/TestSet/TipRemove/RF_Tip/bin/.part-0.crc
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diff --git a/genomix/genomix-pregelix/data/TestSet/TipRemove/RF_Tip/bin/.part-1.crc b/genomix/genomix-pregelix/data/TestSet/TipRemove/RF_Tip/bin/.part-1.crc
index 5973fb2..c78e320 100644
--- a/genomix/genomix-pregelix/data/TestSet/TipRemove/RF_Tip/bin/.part-1.crc
+++ b/genomix/genomix-pregelix/data/TestSet/TipRemove/RF_Tip/bin/.part-1.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/TipRemove/RF_Tip/bin/part-0 b/genomix/genomix-pregelix/data/TestSet/TipRemove/RF_Tip/bin/part-0
index 8bf8a00..d561373 100755
--- a/genomix/genomix-pregelix/data/TestSet/TipRemove/RF_Tip/bin/part-0
+++ b/genomix/genomix-pregelix/data/TestSet/TipRemove/RF_Tip/bin/part-0
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/TipRemove/RF_Tip/bin/part-1 b/genomix/genomix-pregelix/data/TestSet/TipRemove/RF_Tip/bin/part-1
index 88d597c..82ca566 100755
--- a/genomix/genomix-pregelix/data/TestSet/TipRemove/RF_Tip/bin/part-1
+++ b/genomix/genomix-pregelix/data/TestSet/TipRemove/RF_Tip/bin/part-1
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/TipRemove/RF_Tip/graphviz.svg b/genomix/genomix-pregelix/data/TestSet/TipRemove/RF_Tip/graphviz.svg
new file mode 100644
index 0000000..724495a
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/TipRemove/RF_Tip/graphviz.svg
@@ -0,0 +1,151 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
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+ "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
+<!-- Generated by graphviz version 2.26.3 (20100126.1600)
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+<!-- AGA -->
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+<!-- GAA->AGA -->
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+</g>
+<!-- AGA->GAA -->
+<g id="edge4" class="edge"><title>AGA->GAA</title>
+<path fill="none" stroke="black" d="M139.511,-123.987C133.868,-121.508 127.871,-119.332 122,-118 101.195,-113.281 94.8048,-113.281 74,-118 71.3399,-118.603 68.6538,-119.38 65.9864,-120.28"/>
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+<!-- CTA -->
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+<text text-anchor="middle" x="306" y="-84.4" font-family="Times Roman,serif" font-size="14.00">CTA</text>
+</g>
+<!-- AGA->CTA -->
+<g id="edge6" class="edge"><title>AGA->CTA</title>
+<path fill="none" stroke="green" d="M196.259,-140C216.818,-140 244.894,-140 267.501,-140"/>
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+<text text-anchor="middle" x="237" y="-145.4" font-family="Times Roman,serif" font-size="14.00">RF: [1]</text>
+</g>
+<!-- CTA->AGA -->
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deleted file mode 100644
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old mode 100644
new mode 100755
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copy from genomix/genomix-pregelix/data/TestSet/TipRemove/SmallGenome/.txt.crc
copy to genomix/genomix-pregelix/data/TestSet/TipRemove/RF_Tip/statistics
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diff --git a/genomix/genomix-pregelix/data/TestSet/TipRemove/SmallGenome/txt b/genomix/genomix-pregelix/data/TestSet/TipRemove/SmallGenome/txt
deleted file mode 100755
index 334f3e9..0000000
--- a/genomix/genomix-pregelix/data/TestSet/TipRemove/SmallGenome/txt
+++ /dev/null
@@ -1,27 +0,0 @@
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-ACC {[{CCG:[5,7,15,21,23,37,40,48,56]}] [] [{TAA:[7,11,37,40,56]}] [] {5':[(5-0_0),(15-1_0),(23-1_0),(48-1_0)], ~5':[]} TACC 8.5x}
-GCC {[{CCA:[19,26,31,50,69,90,92]},{CCC:[6,36,53,70,76,87]},{CCG:[5,7,15,21,23,40,48,96]}] [{AGG:[12,24,39,58,61,88]}] [] [{AGC:[6,12,19,24,25,26,31,36,46,50,53,58,60,61,69,70,72,76,80,87,88,90,92,99]},{ATG:[5,13,15,17,21,23,48,59,96,98]}] {5':[(39-0_0),(40-0_0)], ~5':[]} GCC 34.0x}
-AGC {[{GCC:[6,12,19,24,25,26,31,36,46,50,53,58,60,61,69,70,72,76,80,87,88,90,92,99]}] [{AGC:[10,24,43,58,63,65,99,100]},{CGC:[16,32,38,39,47,52,62,71,82,84,85,91,93]}] [{CTA:[12,16,24,43,58,61,65,82,85,88,93,99,100]},{CTC:[6,10,25,36,43,46,53,54,58,63,65,66,70,76,80,87,99,100]}] [{AAG:[32,38,39,47,52,62,71,84,88,91]},{CAG:[19,26,31,50,60,69,72,90,92]}] {5':[(10-0_0),(24-0_0)], ~5':[(61-0_0),(66-0_0),(88-0_0)]} AGC 59.0x}
-ATC {[{TCA:[19,26,60,72,90,92]}] [{CGA:[9,18,22,28,30,34,35,44,55,57,64,68,73,74,95]},{GGA:[11,16,37,56,82,85]}] [{ATA:[22,28,29,34,35,44,55,57,68,73,95]},{ATC:[19,60,72,90,92]}] [{AAT:[7,9,11,16,18,27,30,37,40,41,56,64,74,82,85]}] {5':[], ~5':[(7-0_0),(19-0_0)]} ATC 37.0x}
-AAG {[{AGA:[79,83,89]},{AGC:[32,38,39,47,52,62,71,84,88,91]},{AGG:[6,32,36,47,52,53,62,76,84,87]}] [{ACT:[8,31,42,50,66,69,78,86]}] [] [{AAA:[81,83,89,93,94,97]},{GAA:[8,25,32,36,42,46,47,52,53,62,66,71,76,78,80,84,86,87]},{TAA:[38,39,47,52,71,88,91]}] {5':[(6-0_0),(50-0_0),(62-0_0)], ~5':[(25-0_0),(46-0_0),(71-0_0),(80-0_0),(94-0_0),(97-0_0)]} AAG 39.0x}
-ACG {[{CGA:[13,17,18,33,45,59,74,77,98]}] [] [] [{GAC:[13,17,18,33,45,59,74,77,98]}] {5':[], ~5':[]} ACG 9.0x}
-AGG {[] [{CCC:[6,32,36,53,62,76,84,87]},{GCC:[12,24,39,58,61,88]}] [{CTA:[12,24,38,39,61,88,91]}] [{AAG:[6,32,36,47,52,53,62,76,84,87]}] {5':[], ~5':[(52-0_0)]} AGG 18.0x}
-ATG {[{GCC:[5,15,21,23,48,59,96]}] [] [] [{AAT:[5,13,15,17,21,23,45,48,59,77,96,98]}] {5':[], ~5':[(13-1_0),(45-0_0),(77-0_0),(98-1_0)]} ATGC 11.0x}
-AAT {[{ATA:[2,14,22,28,29,34,49,55,57,68,73,75,79,81,83,89,94,95,97]},{ATC:[7,9,11,16,18,27,30,37,40,41,56,64,74,82,85]},{ATG:[5,13,15,17,21,23,45,48,59,77,96,98]}] [] [] [{AAA:[2,4,9,14,27,30,41,49,64,75,81,83,94,97]},{CAA:[22,29,34,55,57,68,73,79]},{GAA:[13,15,17,23,33,45,48,59,77,96,98]},{TAA:[7,11,37,40,56,85]}] {5':[(16-0_0),(18-0_0),(21-0_0),(74-0_0),(82-0_0),(89-0_0),(95-0_0)], ~5':[(33-0_0)]} AAT 48.0x}
-ACT {[{CTC:[1,3,4,20,27,35,41,44,51,67]}] [{AAG:[8,31,42,50,66,69,78,86]}] [] [{CCA:[8,19,26,31,42,50,69,78,86,92]},{TCA:[1,3,4,20,27,41,51,67]}] {5':[], ~5':[(26-1_0),(92-0_0)]} CACT 18.5x}
-CAA {[{AAT:[22,29,34,55,57,68,73,79]}] [] [] [{GAC:[29,55,79,89]}] {5':[(22-0_0),(34-0_0),(57-0_0)], ~5':[]} ACAA 8.0x}
-TAA {[{AAA:[49,81,83,89,93,94,97]},{AAG:[38,39,47,52,71,88,91]},{AAT:[7,11,37,40,56,85]}] [] [{ACC:[5,7,11,21,37,40,56]}] [{ATA:[49,75,81,83,89,94,97]},{CTA:[12,16,38,39,61,71,82,88,91,93]}] {5':[(47-0_0)], ~5':[(12-0_0),(75-0_0)]} TAA 25.0x}
-CCA {[{CAG:[2,10,14,43,54,63,75,100]},{ACT:[1,3,4,8,20,26,27,31,41,42,50,51,67,69,78,86]}] [] [{GGA:[2,10,14,43,49,54,63,75]}] [{GCC:[19,26,31,50,69,90,92]}] {5':[(78-0_0),(86-0_0)], ~5':[]} CCA 20.0x}
-TCA {[{CAG:[6,8,19,25,26,31,42,46,50,60,66,69,70,72,78,80,86,90,92]},{ACT:[1,3,4,8,20,26,27,31,41,42,50,51,67,69,78,86]}] [] [{GAA:[1,4,20,27,30,41,64,67]}] [{ATC:[19,26,60,72,90,92]},{CTC:[6,25,36,46,53,66,70,80,87]}] {5':[(8-0_0),(31-0_0),(42-0_0),(69-0_0)], ~5':[(87-0_0),(90-0_0)]} TCA 35.0x}
-CGA {[{GAA:[13,17,32,33,38,45,47,52,59,62,71,76,77,84,91,96,98]}] [{ATC:[9,18,22,28,30,34,35,44,55,57,64,68,73,74,95]}] [{CGC:[32,38,39,47,52,62,71,84,91]}] [{ACG:[13,17,18,33,45,59,74,77,98]},{CCG:[3,9,18,22,28,30,33,34,35,44,51,57,64,68,73,74,95]}] {5':[(55-0_0),(76-0_0)], ~5':[(3-0_0),(51-0_0)]} CGA 38.0x}
-CTA {[{TAA:[12,16,38,39,61,71,82,88,91,93]}] [{CTA:[12,24,58,61,65,99,100]}] [{AGC:[12,16,24,43,58,61,65,82,85,88,93,99,100]},{AGG:[12,24,38,39,61,88,91]}] [] {5':[(100-0_0)], ~5':[(43-0_0),(85-0_0)]} CTA 28.0x}
-CCC {[{CCG:[3,20,28,35,44,51,73,95]}] [{AGG:[6,32,36,53,62,76,84,87]}] [{GGA:[1,3,20,28,35,44,51,67,95]}] [{GCC:[6,36,53,70,76,87]}] {5':[(32-0_0),(73-0_0),(84-0_0)], ~5':[]} CCC 19.0x}
-CGC {[] [{AGC:[16,32,38,39,47,52,62,71,82,84,85,91,93]}] [{CGA:[32,38,39,47,52,62,71,84,91]}] [{CCG:[11,16,82,85,93]}] {5':[], ~5':[(11-0_0)]} CGC 14.0x}
-CTC {[{TCA:[6,25,36,46,53,66,70,80,87]}] [{AGA:[10,43,54,63,65,99,100]},{GGA:[1,3,4,20,35,44,51,67]}] [{AGC:[6,10,25,36,43,46,53,54,58,63,65,66,70,76,80,87,99,100]}] [{ACT:[1,3,4,20,27,35,41,44,51,67]}] {5':[], ~5':[(27-0_0),(41-0_0),(58-0_0)]} CTC 28.0x}
-CAG {[{AGA:[2,8,10,14,25,42,43,46,54,63,65,66,70,78,80,86,100]},{AGC:[19,26,31,50,60,69,72,90,92]}] [] [] [{CCA:[2,10,14,43,54,63,75,100]},{TCA:[6,8,19,25,26,31,42,46,50,60,66,69,70,72,78,80,86,90,92]}] {5':[(65-0_0)], ~5':[(60-0_0),(72-0_0)]} CAG 30.0x}
-CCG {[{CGA:[3,9,18,22,28,30,33,34,35,44,51,57,64,68,73,74,95]},{CGC:[11,16,82,85,93]}] [{CCG:[5,7,15,21,23,37,40,48,96]}] [{GGA:[9,11,16,18,30,33,45,56,64,74,77,82,85]}] [{ACC:[5,7,15,21,23,37,40,48,56]},{CCC:[3,20,28,35,44,51,73,95]},{GCC:[5,7,15,21,23,40,48,96]}] {5':[(68-0_0),(93-0_0),(96-0_0)], ~5':[(20-0_0),(56-0_0)]} CCG 45.0x}
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 6ac20cb..8c64cea 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
@@ -194,24 +194,6 @@
/**
* get destination vertex
*/
- public VKmerBytesWritable getDestVertexId(DIR direction){
- int degree = getVertexValue().getDegree(direction);
- if(degree > 1)
- throw new IllegalArgumentException("getDestVertexId(DIR direction) only can use for degree == 1 + \n" + getVertexValue().toString());
-
- if(degree == 1){
- EnumSet<EDGETYPE> edgeTypes = (direction == DIR.PREVIOUS ? EDGETYPE.INCOMING : EDGETYPE.OUTGOING);
- for(EDGETYPE e : edgeTypes){
- if(getVertexValue().getEdgeList(e).getCountOfPosition() > 0)
- return getVertexValue().getEdgeList(e).get(0).getKey();
- }
- }
- return null;
- }
-
- /**
- * get destination vertex
- */
public VKmerBytesWritable getPrevDestVertexIdAndSetFlag() {
if (!getVertexValue().getRFList().isEmpty()){ // #RFList() > 0
kmerIterator = getVertexValue().getRFList().getKeyIterator();
@@ -705,4 +687,23 @@
outgoingEdgeType = connectedTable[i][1];
}
+//2013.9.21 ------------------------------------------------------------------//
+ /**
+ * get destination vertex
+ */
+ public VKmerBytesWritable getDestVertexId(DIR direction){
+ int degree = getVertexValue().getDegree(direction);
+ if(degree > 1)
+ throw new IllegalArgumentException("degree > 1, getDestVertexId(DIR direction) only can use for degree == 1 + \n" + getVertexValue().toString());
+
+ if(degree == 1){
+ EnumSet<EDGETYPE> edgeTypes = direction.edgeType();
+ for(EDGETYPE et : edgeTypes){
+ if(getVertexValue().getEdgeList(et).getCountOfPosition() > 0)
+ return getVertexValue().getEdgeList(et).get(0).getKey();
+ }
+ }
+ //degree in this direction == 0
+ throw new IllegalArgumentException("degree > 0, getDestVertexId(DIR direction) only can use for degree == 1 + \n" + getVertexValue().toString());
+ }
}
\ No newline at end of file
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 a4a792e..d344ad2 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
@@ -4,6 +4,7 @@
import java.util.Iterator;
import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
+import edu.uci.ics.genomix.pregelix.io.VertexValueWritable.P4State;
import edu.uci.ics.genomix.pregelix.io.VertexValueWritable.State;
import edu.uci.ics.genomix.pregelix.io.message.MessageWritable;
import edu.uci.ics.genomix.pregelix.io.message.PathMergeMessageWritable;
@@ -11,6 +12,7 @@
import edu.uci.ics.genomix.pregelix.operator.BasicGraphCleanVertex;
import edu.uci.ics.genomix.pregelix.type.MessageFlag;
import edu.uci.ics.genomix.type.EdgeWritable;
+import edu.uci.ics.genomix.type.NodeWritable;
import edu.uci.ics.genomix.type.NodeWritable.DIR;
import edu.uci.ics.genomix.type.NodeWritable.EDGETYPE;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
@@ -407,7 +409,7 @@
getVertexValue().setState(state);
}
-//--------------------------------------------------------------------------------------------------//
+// 2013.9.21 --------------------------------------------------------------------------------------------------//
/**
* Send merge restrictions to my neighbor nodes
*/
@@ -477,4 +479,123 @@
activate();
}
}
+
+ public void updateNeighbors() {
+ VertexValueWritable vertex = getVertexValue();
+ short state = vertex.getState();
+ EDGETYPE edgeType = EDGETYPE.fromByte(state);
+ if ((state & P4State.MERGE) == 0) {
+ return; // no merge requested; don't have to update neighbors
+ }
+
+ DIR mergeDir = edgeType.dir();
+ EnumSet<EDGETYPE> mergeEdges = mergeDir.edgeType();
+
+ DIR updateDir = mergeDir.mirror();
+ EnumSet<EDGETYPE> updateEdges = updateDir.edgeType();
+
+ // prepare the update message s.t. the receiver can do a simple unionupdate
+ // that means we figure out any hops and place our merge-dir edges in the appropriate list of the outgoing msg
+ for (EDGETYPE updateEdge : updateEdges) {
+ outgoingMsg.reset();
+ outgoingMsg.setSourceVertexId(getVertexId());
+ outgoingMsg.setFlag(updateEdge.mirror().get()); // neighbor's edge to me (so he can remove me)
+ for (EDGETYPE mergeEdge : mergeEdges) {
+ EDGETYPE newEdgetype = EDGETYPE.resolveLinkThroughMiddleNode(updateEdge, mergeEdge);
+ outgoingMsg.getNode().setEdgeList(newEdgetype, getVertexValue().getEdgeList(mergeEdge)); // copy into outgoingMsg
+ }
+
+ // send the update to all kmers in this list // TODO perhaps we could skip all this if there are no neighbors here
+ for (VKmerBytesWritable dest : vertex.getEdgeList(updateEdge).getKeys()) {
+// LOG.info("send update message from " + getVertexId() + " to " + dest + ": " + outgoingMsg);
+ sendMsg(dest, outgoingMsg);
+ }
+ }
+ }
+
+ public void receiveUpdates(Iterator<M> msgIterator){
+ VertexValueWritable vertex = getVertexValue();
+ NodeWritable node = vertex.getNode();
+ boolean updated = false;
+ while (msgIterator.hasNext()) {
+// LOG.info("before update from neighbor: " + getVertexValue());
+ incomingMsg = msgIterator.next();
+ // remove the edge to the node that will merge elsewhere
+ node.getEdgeList(EDGETYPE.fromByte(incomingMsg.getFlag())).remove(incomingMsg.getSourceVertexId());
+ // add the node this neighbor will merge into
+ for (EDGETYPE edgeType : EnumSet.allOf(EDGETYPE.class)) {
+ node.getEdgeList(edgeType).unionUpdate(incomingMsg.getEdgeList(edgeType));
+ }
+ updated = true;
+// LOG.info("after update from neighbor: " + getVertexValue());
+ }
+ if (updated) {
+ if (DIR.enumSetFromByte(vertex.getState()).containsAll(EnumSet.allOf(DIR.class)))
+ voteToHalt();
+ else
+ activate();
+ }
+ }
+
+ public void sendMergeMsg() {
+ VertexValueWritable vertex = getVertexValue();
+ short state = vertex.getState();
+ if ((state & P4State.MERGE) != 0) {
+ outgoingMsg.reset();
+ // tell neighbor where this is coming from (so they can merge kmers and delete)
+ EDGETYPE mergeEdgetype = EDGETYPE.fromByte(vertex.getState());
+ byte neighborRestrictions = DIR.fromSet(mergeEdgetype.causesFlip() ? DIR.flipSetFromByte(state) : DIR.enumSetFromByte(state));
+
+ outgoingMsg.setFlag((short) (mergeEdgetype.mirror().get() | neighborRestrictions));
+ outgoingMsg.setSourceVertexId(getVertexId());
+ outgoingMsg.setNode(vertex.getNode());
+ if (vertex.getDegree(mergeEdgetype.dir()) != 1)
+ throw new IllegalStateException("Merge attempted in node with degree in " + mergeEdgetype + " direction != 1!\n" + vertex);
+ VKmerBytesWritable dest = vertex.getEdgeList(mergeEdgetype).get(0).getKey();
+// LOG.info("send merge mesage from " + getVertexId() + " to " + dest + ": " + outgoingMsg + "; my restrictions are: " + DIR.enumSetFromByte(vertex.getState()) + ", their restrictions are: " + DIR.enumSetFromByte(outgoingMsg.getFlag()));
+ sendMsg(dest, outgoingMsg);
+
+// LOG.info("killing self: " + getVertexId());
+ deleteVertex(getVertexId());
+ }
+ }
+
+ /**
+ * step4: receive and process Merges
+ */
+ public void receiveMerges(Iterator<M> msgIterator) {
+ VertexValueWritable vertex = getVertexValue();
+ NodeWritable node = vertex.getNode();
+ short state = vertex.getState();
+ boolean updated = false;
+ EDGETYPE senderEdgetype;
+ @SuppressWarnings("unused")
+ int numMerged = 0;
+ while (msgIterator.hasNext()) {
+// LOG.info("before merge: " + getVertexValue() + " restrictions: " + DIR.enumSetFromByte(state));
+ incomingMsg = msgIterator.next();
+ senderEdgetype = EDGETYPE.fromByte(incomingMsg.getFlag());
+ node.mergeWithNode(senderEdgetype, incomingMsg.getNode());
+ state |= (byte) (incomingMsg.getFlag() & DIR.MASK); // update incoming restricted directions
+ numMerged++;
+ updated = true;
+// LOG.info("after merge: " + getVertexValue() + " restrictions: " + DIR.enumSetFromByte(state));
+ }
+ if(isTandemRepeat(getVertexValue())) {
+ // tandem repeats can't merge anymore; restrict all future merges
+ state |= DIR.NEXT.get();
+ state |= DIR.PREVIOUS.get();
+ updated = true;
+// updateStatisticsCounter(StatisticsCounter.Num_Cycles);
+ }
+// updateStatisticsCounter(StatisticsCounter.Num_MergedNodes);
+// getVertexValue().setCounters(counters);
+ if (updated) {
+ vertex.setState(state);
+ if (DIR.enumSetFromByte(state).containsAll(EnumSet.allOf(DIR.class)))
+ voteToHalt();
+ else
+ activate();
+ }
+ }
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P0ForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P0ForPathMergeVertex.java
index 9a9fe9d..ae67a57 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P0ForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P0ForPathMergeVertex.java
@@ -7,12 +7,13 @@
import edu.uci.ics.genomix.pregelix.io.VertexValueWritable.P4State;
import edu.uci.ics.genomix.pregelix.io.message.PathMergeMessageWritable;
import edu.uci.ics.genomix.pregelix.operator.aggregator.StatisticsAggregator;
+import edu.uci.ics.genomix.type.NodeWritable.EDGETYPE;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
import edu.uci.ics.genomix.type.NodeWritable.DIR;
public class P0ForPathMergeVertex extends
BasicPathMergeVertex<VertexValueWritable, PathMergeMessageWritable> {
-
+
/**
* initiate kmerSize, maxIteration
*/
@@ -41,13 +42,25 @@
VertexValueWritable vertex = getVertexValue();
short state = vertex.getState();
EnumSet<DIR> restrictedDirs = DIR.enumSetFromByte(state);
+ boolean updated = false;
//initiate merge dir
+ state &= P4State.MERGE_CLEAR;
state |= P4State.NO_MERGE; //setMerge(P4State.NO_MERGE);
- //choose merge dir
+ //choose merge dir -- principle: only merge with nextDir
+ if(restrictedDirs.size() == 1){
+ EDGETYPE edgeType = restrictedDirs.contains(DIR.PREVIOUS) ? vertex.getEdgetypeFromDir(DIR.NEXT) : vertex.getEdgetypeFromDir(DIR.PREVIOUS);
+ state |= P4State.MERGE | edgeType.get();
+ updated = true;
+ }
-
+ getVertexValue().setState(state);
+ if (updated)
+ activate();
+ else
+ voteToHalt();
}
+
@Override
public void compute(Iterator<PathMergeMessageWritable> msgIterator) throws Exception {
initVertex();
@@ -57,8 +70,14 @@
} else if (getSuperstep() % 2 == 0) {
if (getSuperstep() == 2)
recieveRestrictions(msgIterator);
-
- }
+ else
+ receiveMerges(msgIterator);
+ chooseMergeDir();
+ updateNeighbors();
+ } else if (getSuperstep() % 2 == 1) {
+ receiveUpdates(msgIterator);
+ sendMergeMsg();
+ }
}
}
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 f940c2d..dba03fe 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
@@ -10,7 +10,6 @@
import edu.uci.ics.genomix.pregelix.io.VertexValueWritable.P4State;
import edu.uci.ics.genomix.pregelix.io.message.PathMergeMessageWritable;
import edu.uci.ics.genomix.pregelix.operator.aggregator.StatisticsAggregator;
-import edu.uci.ics.genomix.type.NodeWritable;
import edu.uci.ics.genomix.type.NodeWritable.DIR;
import edu.uci.ics.genomix.type.NodeWritable.EDGETYPE;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
@@ -99,7 +98,7 @@
hasNext = false;
} else {
hasNext = true;
- nextEdgetype = vertex.getEdgeList(EDGETYPE.FF).getCountOfPosition() > 0 ? EDGETYPE.FF : EDGETYPE.FR;
+ nextEdgetype = vertex.getEdgetypeFromDir(DIR.NEXT); //getEdgeList(EDGETYPE.FF).getCountOfPosition() > 0 ? EDGETYPE.FF : EDGETYPE.FR;
nextKmer = vertex.getEdgeList(nextEdgetype).get(0).getKey();
nextHead = isNodeRandomHead(nextKmer);
}
@@ -109,7 +108,7 @@
hasPrev = false;
} else {
hasPrev = true;
- prevEdgetype = vertex.getEdgeList(EDGETYPE.RF).getCountOfPosition() > 0 ? EDGETYPE.RF : EDGETYPE.RR;
+ prevEdgetype = vertex.getEdgetypeFromDir(DIR.PREVIOUS); //vertex.getEdgeList(EDGETYPE.RF).getCountOfPosition() > 0 ? EDGETYPE.RF : EDGETYPE.RR;
prevKmer = vertex.getEdgeList(prevEdgetype).get(0).getKey();
prevHead = isNodeRandomHead(prevKmer);
}
@@ -165,125 +164,6 @@
// }
}
- public void updateNeighbors() {
- VertexValueWritable vertex = getVertexValue();
- short state = vertex.getState();
- EDGETYPE edgeType = EDGETYPE.fromByte(state);
- if ((state & P4State.MERGE) == 0) {
- return; // no merge requested; don't have to update neighbors
- }
-
- DIR mergeDir = edgeType.dir();
- EnumSet<EDGETYPE> mergeEdges = mergeDir.edgeType();
-
- DIR updateDir = mergeDir.mirror();
- EnumSet<EDGETYPE> updateEdges = updateDir.edgeType();
-
- // prepare the update message s.t. the receiver can do a simple unionupdate
- // that means we figure out any hops and place our merge-dir edges in the appropriate list of the outgoing msg
- for (EDGETYPE updateEdge : updateEdges) {
- outgoingMsg.reset();
- outgoingMsg.setSourceVertexId(getVertexId());
- outgoingMsg.setFlag(updateEdge.mirror().get()); // neighbor's edge to me (so he can remove me)
- for (EDGETYPE mergeEdge : mergeEdges) {
- EDGETYPE newEdgetype = EDGETYPE.resolveLinkThroughMiddleNode(updateEdge, mergeEdge);
- outgoingMsg.getNode().setEdgeList(newEdgetype, getVertexValue().getEdgeList(mergeEdge)); // copy into outgoingMsg
- }
-
- // send the update to all kmers in this list // TODO perhaps we could skip all this if there are no neighbors here
- for (VKmerBytesWritable dest : vertex.getEdgeList(updateEdge).getKeys()) {
-// LOG.info("send update message from " + getVertexId() + " to " + dest + ": " + outgoingMsg);
- sendMsg(dest, outgoingMsg);
- }
- }
- }
-
- public void receiveUpdates(Iterator<PathMergeMessageWritable> msgIterator){
- VertexValueWritable vertex = getVertexValue();
- NodeWritable node = vertex.getNode();
- boolean updated = false;
- while (msgIterator.hasNext()) {
-// LOG.info("before update from neighbor: " + getVertexValue());
- incomingMsg = msgIterator.next();
- // remove the edge to the node that will merge elsewhere
- node.getEdgeList(EDGETYPE.fromByte(incomingMsg.getFlag())).remove(incomingMsg.getSourceVertexId());
- // add the node this neighbor will merge into
- for (EDGETYPE edgeType : EnumSet.allOf(EDGETYPE.class)) {
- node.getEdgeList(edgeType).unionUpdate(incomingMsg.getEdgeList(edgeType));
- }
- updated = true;
-// LOG.info("after update from neighbor: " + getVertexValue());
- }
- if (updated) {
- if (DIR.enumSetFromByte(vertex.getState()).containsAll(EnumSet.allOf(DIR.class)))
- voteToHalt();
- else
- activate();
- }
- }
-
- public void sendMergeMsg() {
- VertexValueWritable vertex = getVertexValue();
- short state = vertex.getState();
- if ((state & P4State.MERGE) != 0) {
- outgoingMsg.reset();
- // tell neighbor where this is coming from (so they can merge kmers and delete)
- EDGETYPE mergeEdgetype = EDGETYPE.fromByte(vertex.getState());
- byte neighborRestrictions = DIR.fromSet(mergeEdgetype.causesFlip() ? DIR.flipSetFromByte(state) : DIR.enumSetFromByte(state));
-
- outgoingMsg.setFlag((short) (mergeEdgetype.mirror().get() | neighborRestrictions));
- outgoingMsg.setSourceVertexId(getVertexId());
- outgoingMsg.setNode(vertex.getNode());
- if (vertex.getDegree(mergeEdgetype.dir()) != 1)
- throw new IllegalStateException("Merge attempted in node with degree in " + mergeEdgetype + " direction != 1!\n" + vertex);
- VKmerBytesWritable dest = vertex.getEdgeList(mergeEdgetype).get(0).getKey();
-// LOG.info("send merge mesage from " + getVertexId() + " to " + dest + ": " + outgoingMsg + "; my restrictions are: " + DIR.enumSetFromByte(vertex.getState()) + ", their restrictions are: " + DIR.enumSetFromByte(outgoingMsg.getFlag()));
- sendMsg(dest, outgoingMsg);
-
-// LOG.info("killing self: " + getVertexId());
- deleteVertex(getVertexId());
- }
- }
-
- /**
- * step4: processMerges
- */
- public void receiveMerges(Iterator<PathMergeMessageWritable> msgIterator) {
- VertexValueWritable vertex = getVertexValue();
- NodeWritable node = vertex.getNode();
- short state = vertex.getState();
- boolean updated = false;
- EDGETYPE senderEdgetype;
- @SuppressWarnings("unused")
- int numMerged = 0;
- while (msgIterator.hasNext()) {
-// LOG.info("before merge: " + getVertexValue() + " restrictions: " + DIR.enumSetFromByte(state));
- incomingMsg = msgIterator.next();
- senderEdgetype = EDGETYPE.fromByte(incomingMsg.getFlag());
- node.mergeWithNode(senderEdgetype, incomingMsg.getNode());
- state |= (byte) (incomingMsg.getFlag() & DIR.MASK); // update incoming restricted directions
- numMerged++;
- updated = true;
-// LOG.info("after merge: " + getVertexValue() + " restrictions: " + DIR.enumSetFromByte(state));
- }
- if(isTandemRepeat(getVertexValue())) {
- // tandem repeats can't merge anymore; restrict all future merges
- state |= DIR.NEXT.get();
- state |= DIR.PREVIOUS.get();
- updated = true;
-// updateStatisticsCounter(StatisticsCounter.Num_Cycles);
- }
-// updateStatisticsCounter(StatisticsCounter.Num_MergedNodes);
-// getVertexValue().setCounters(counters);
- if (updated) {
- vertex.setState(state);
- if (DIR.enumSetFromByte(state).containsAll(EnumSet.allOf(DIR.class)))
- voteToHalt();
- else
- activate();
- }
- }
-
@Override
public void compute(Iterator<PathMergeMessageWritable> msgIterator) {
initVertex();
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipAddVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipAddVertex.java
index 170947a..09be8e5 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipAddVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipAddVertex.java
@@ -17,38 +17,10 @@
import edu.uci.ics.genomix.pregelix.format.GraphCleanOutputFormat;
import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
import edu.uci.ics.genomix.pregelix.io.message.MessageWritable;
-import edu.uci.ics.genomix.pregelix.type.MessageFlag;
-/*
- * vertexId: BytesWritable
- * vertexValue: ByteWritable
- * edgeValue: NullWritable
- * message: MessageWritable
- *
- * DNA:
- * A: 00
- * C: 01
- * G: 10
- * T: 11
- *
- * succeed node
- * A 00000001 1
- * G 00000010 2
- * C 00000100 4
- * T 00001000 8
- * precursor node
- * A 00010000 16
- * G 00100000 32
- * C 01000000 64
- * T 10000000 128
- *
- * For example, ONE LINE in input file: 00,01,10 0001,0010,
- * That means that vertexId is ACG, its succeed node is A and its precursor node is C.
- * The succeed node and precursor node will be stored in vertexValue and we don't use edgeValue.
- * The details about message are in edu.uci.ics.pregelix.example.io.MessageWritable.
- */
/**
- * Remove tip or single node when l > constant
+ * @author anbangx
+ * Add tip
*/
public class TipAddVertex extends
Vertex<VKmerBytesWritable, VertexValueWritable, NullWritable, MessageWritable> {
@@ -56,7 +28,7 @@
private VKmerBytesWritable splitNode = new VKmerBytesWritable("CTA");
private VKmerBytesWritable insertedTip = new VKmerBytesWritable("AGC");
- private EDGETYPE tipToSplitDir = EDGETYPE.RF;
+ private EDGETYPE tipToSplitDir = EDGETYPE.FR;
/**
* initiate kmerSize, length
*/
@@ -103,24 +75,6 @@
}
/**
- * Returns the edge dir for B->A when the A->B edge is type @dir
- */
- public byte mirrorDirection(byte dir) {
- switch (dir) {
- case MessageFlag.DIR_FF:
- return MessageFlag.DIR_RR;
- case MessageFlag.DIR_FR:
- return MessageFlag.DIR_FR;
- case MessageFlag.DIR_RF:
- return MessageFlag.DIR_RF;
- case MessageFlag.DIR_RR:
- return MessageFlag.DIR_FF;
- default:
- throw new RuntimeException("Unrecognized direction in flipDirection: " + dir);
- }
- }
-
- /**
* create a new vertex point to split node
*/
@Override
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipRemoveVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipRemoveVertex.java
index d0c3a51..576d0da 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipRemoveVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipRemoveVertex.java
@@ -8,8 +8,9 @@
import edu.uci.ics.genomix.pregelix.operator.BasicGraphCleanVertex;
import edu.uci.ics.genomix.pregelix.operator.aggregator.StatisticsAggregator;
import edu.uci.ics.genomix.pregelix.type.StatisticsCounter;
-import edu.uci.ics.genomix.pregelix.util.VertexUtil;
+import edu.uci.ics.genomix.type.NodeWritable.EDGETYPE;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
+import edu.uci.ics.genomix.type.NodeWritable.DIR;
/**
* Remove tip or single node when l > constant
@@ -41,45 +42,82 @@
counters.clear();
getVertexValue().getCounters().clear();
}
-
+
+ /**
+ * detect the tip and figure out what edgeType neighborToTip is
+ */
+ public EDGETYPE getTipEdgetype(){
+ VertexValueWritable vertex = getVertexValue();
+ if(vertex.getDegree(DIR.PREVIOUS) == 0 && vertex.getDegree(DIR.NEXT) == 1){ //INCOMING TIP
+ return vertex.getEdgetypeFromDir(DIR.NEXT);
+ } else if(vertex.getDegree(DIR.PREVIOUS) == 1 && vertex.getDegree(DIR.NEXT) == 0){ //OUTGOING TIP
+ return vertex.getEdgetypeFromDir(DIR.PREVIOUS);
+ } else
+ return null;
+ }
+
@Override
public void compute(Iterator<MessageWritable> msgIterator) {
initVertex();
if(getSuperstep() == 1){
- if(VertexUtil.isIncomingTipVertex(getVertexValue())){
- if(getVertexValue().getKmerLength() <= length){
- sendSettledMsgToNextNode();
- deleteVertex(getVertexId());
- //set statistics counter: Num_RemovedTips
- updateStatisticsCounter(StatisticsCounter.Num_RemovedTips);
- getVertexValue().setCounters(counters);
- }
+ EDGETYPE neighborToTipEdgetype = getTipEdgetype();
+ //I'm tip and my length is less than the minimum
+ if(neighborToTipEdgetype != null && getVertexValue().getKmerLength() <= length){
+ EDGETYPE tipToNeighborEdgetype = neighborToTipEdgetype.mirror();
+ outgoingMsg.setFlag(tipToNeighborEdgetype.get());
+ outgoingMsg.setSourceVertexId(getVertexId());
+ destVertexId = getDestVertexId(neighborToTipEdgetype.dir());
+ sendMsg(destVertexId, outgoingMsg);
+ deleteVertex(getVertexId());
+
+ //set statistics counter: Num_RemovedTips
+ updateStatisticsCounter(StatisticsCounter.Num_RemovedTips);
+ getVertexValue().setCounters(counters);
}
- else if(VertexUtil.isOutgoingTipVertex(getVertexValue())){
- if(getVertexValue().getKmerLength() <= length){
- sendSettledMsgToPrevNode();
- deleteVertex(getVertexId());
- //set statistics counter: Num_RemovedTips
- updateStatisticsCounter(StatisticsCounter.Num_RemovedTips);
- getVertexValue().setCounters(counters);
- }
+ } else if(getSuperstep() == 2){
+ while(msgIterator.hasNext()){
+ incomingMsg = msgIterator.next();
+ EDGETYPE tipToMeEdgetype = EDGETYPE.fromByte(incomingMsg.getFlag());
+ getVertexValue().getEdgeList(tipToMeEdgetype).remove(incomingMsg.getSourceVertexId());
}
- else if(VertexUtil.isSingleVertex(getVertexValue())){
- if(getVertexValue().getKmerLength() <= length){
- deleteVertex(getVertexId());
- //set statistics counter: Num_RemovedTips
- updateStatisticsCounter(StatisticsCounter.Num_RemovedTips);
- getVertexValue().setCounters(counters);
- }
- }
- }
- else if(getSuperstep() == 2){
- while(msgIterator.hasNext()){
- incomingMsg = msgIterator.next();
- responseToDeadVertex();
- }
}
voteToHalt();
+
+// if(getSuperstep() == 1){
+// if(VertexUtil.isIncomingTipVertex(getVertexValue())){
+// if(getVertexValue().getKmerLength() <= length){
+// sendSettledMsgToNextNode();
+// deleteVertex(getVertexId());
+// //set statistics counter: Num_RemovedTips
+// updateStatisticsCounter(StatisticsCounter.Num_RemovedTips);
+// getVertexValue().setCounters(counters);
+// }
+// }
+// else if(VertexUtil.isOutgoingTipVertex(getVertexValue())){
+// if(getVertexValue().getKmerLength() <= length){
+// sendSettledMsgToPrevNode();
+// deleteVertex(getVertexId());
+// //set statistics counter: Num_RemovedTips
+// updateStatisticsCounter(StatisticsCounter.Num_RemovedTips);
+// getVertexValue().setCounters(counters);
+// }
+// }
+// else if(VertexUtil.isSingleVertex(getVertexValue())){
+// if(getVertexValue().getKmerLength() <= length){
+// deleteVertex(getVertexId());
+// //set statistics counter: Num_RemovedTips
+// updateStatisticsCounter(StatisticsCounter.Num_RemovedTips);
+// getVertexValue().setCounters(counters);
+// }
+// }
+// }
+// else if(getSuperstep() == 2){
+// while(msgIterator.hasNext()){
+// incomingMsg = msgIterator.next();
+// responseToDeadVertex();
+// }
+// }
+// voteToHalt();
}
public static void main(String[] args) throws Exception {
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 a40e52b..e50cbc6 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
@@ -21,6 +21,7 @@
import edu.uci.ics.genomix.pregelix.operator.bridgeremove.BridgeRemoveVertex;
import edu.uci.ics.genomix.pregelix.operator.bubblemerge.BubbleAddVertex;
import edu.uci.ics.genomix.pregelix.operator.bubblemerge.BubbleMergeVertex;
+import edu.uci.ics.genomix.pregelix.operator.pathmerge.P0ForPathMergeVertex;
import edu.uci.ics.genomix.pregelix.operator.pathmerge.P1ForPathMergeVertex;
import edu.uci.ics.genomix.pregelix.operator.pathmerge.P2ForPathMergeVertex;
import edu.uci.ics.genomix.pregelix.operator.pathmerge.MapReduceVertex;
@@ -71,6 +72,23 @@
generateMapReduceGraphJob("MapReduceGraph", outputBase + "MapReduceGraph.xml");
}
+ private static void generateP0ForMergeGraphJob(String jobName, String outputPath) throws IOException {
+ PregelixJob job = new PregelixJob(new GenomixJobConf(3), jobName);
+ job.setVertexClass(P0ForPathMergeVertex.class);
+ job.setGlobalAggregatorClass(StatisticsAggregator.class);
+ job.setVertexInputFormatClass(InitialGraphCleanInputFormat.class);
+ job.setVertexOutputFormatClass(GraphCleanOutputFormat.class);
+ job.setDynamicVertexValueSize(true);
+ job.setOutputKeyClass(VKmerBytesWritable.class);
+ job.setOutputValueClass(VertexValueWritable.class);
+ job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
+ }
+
+ private static void genP0ForMergeGraph() throws IOException {
+ generateP0ForMergeGraphJob("P0ForMergeGraph", outputBase
+ + "P0ForMergeGraph.xml");
+ }
+
private static void generateP1ForMergeGraphJob(String jobName, String outputPath) throws IOException {
PregelixJob job = new PregelixJob(new GenomixJobConf(3), jobName);
job.setVertexClass(P1ForPathMergeVertex.class);
@@ -329,6 +347,7 @@
FileUtils.forceMkdir(new File(outputBase));
genUnrollTandemRepeatGraph();
genMapReduceGraph();
+ genP0ForMergeGraph();
genP1ForMergeGraph();
genP2ForMergeGraph();
genP4ForMergeGraph();
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 84635a0..e52e0c2 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[] = {"9", "SimpleTreePath", "RingPath", "ThreeNodesCycle", "CyclePath", "P2_8", "ComplexTandemRepeat", "SimpleTreePath"
+ String testSet[] = {"4"//"9", "SimpleTreePath", "RingPath", "ThreeNodesCycle", "CyclePath", "P2_8", "ComplexTandemRepeat", "SimpleTreePath"
// "2", "3", "4", "5", "6", "7", "8",
// "9", "head_6", "head_7",
// "P2_3", "P2_4", "P2_5", "P2_6", "P2_7", "P2_8",
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/TipRemoveTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/TipRemoveTestSuite.java
index 81dc9ba..eb4a099 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/TipRemoveTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/TipRemoveTestSuite.java
@@ -6,7 +6,7 @@
public static Test suite() throws Exception {
String pattern ="TipRemove";
- String testSet[] = {"SmallGenome", "FR_Tip", "RF_Tip"};
+ String testSet[] = {"FR_Tip", "RF_Tip"};
init(pattern, testSet);
BasicGraphCleanTestSuite testSuite = new BasicGraphCleanTestSuite();
return makeTestSuite(testSuite);
diff --git a/genomix/genomix-pregelix/src/test/resources/only_PathMerge.txt b/genomix/genomix-pregelix/src/test/resources/only_PathMerge.txt
index 3d007d2..437ae6e 100644
--- a/genomix/genomix-pregelix/src/test/resources/only_PathMerge.txt
+++ b/genomix/genomix-pregelix/src/test/resources/only_PathMerge.txt
@@ -1 +1 @@
-P4ForMergeGraph.xml
+P0ForMergeGraph.xml
