Merge with main branch after some refactor
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/EdgeListWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/EdgeListWritable.java
index 8010694..ba5fb53 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/EdgeListWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/EdgeListWritable.java
@@ -36,15 +36,15 @@
private static final long serialVersionUID = 1L;
private static final int SIZE_INT = 4;
-
+
protected EdgeWritable edgeIter = new EdgeWritable();
-
+
private ArrayList<EdgeWritable> edges;
public EdgeListWritable() {
edges = new ArrayList<EdgeWritable>(1);
}
-
+
/**
* Set the internal readIDs when the given positionList has readid, position, and mateid set
*/
@@ -52,14 +52,14 @@
this();
setAsCopy(other);
}
-
+
public EdgeListWritable(List<EdgeWritable> otherList) {
this();
for (EdgeWritable e : otherList) {
add(e);
}
}
-
+
public void setAsCopy(EdgeListWritable otherEdge){
reset();
for (EdgeWritable e : otherEdge.edges) {
@@ -70,33 +70,33 @@
public void reset() {
edges.clear();
}
-
+
public EdgeWritable get(int i) {
return edges.get(i);
}
-
+
public boolean add(EdgeWritable element) {
return edges.add(new EdgeWritable(element));
}
-
+
public boolean add(VKmerBytesWritable kmer) {
EdgeWritable edge = new EdgeWritable();
edge.setKey(kmer);
return edges.add(edge);
}
-
+
public EdgeWritable set(int i, EdgeWritable element) {
return edges.set(i, element);
}
-
+
public boolean isEmpty(){
return getCountOfPosition() == 0;
}
-
+
public int getCountOfPosition() {
return edges.size();
}
-
+
public int getLength() {
int total = SIZE_INT;
for (EdgeWritable e : edges) {
@@ -104,7 +104,7 @@
}
return total;
}
-
+
public EdgeWritable getEdge(VKmerBytesWritable key){
for(EdgeWritable edge : edges){
if(edge.getKey().equals(key)){
@@ -114,7 +114,7 @@
return null;
}
/**
- * Return this Edge's representation as a new byte array
+ * Return this Edge's representation as a new byte array
*/
public byte[] marshalToByteArray() throws IOException {
ByteArrayOutputStream baos = new ByteArrayOutputStream(getLength());
@@ -122,7 +122,7 @@
write(out);
return baos.toByteArray();
}
-
+
public void setAsCopy(byte[] data, int offset) {
int curOffset = offset;
int count = Marshal.getInt(data, offset);
@@ -135,7 +135,7 @@
curOffset += e.getLength();
}
}
-
+
public void setAsReference(byte[] data, int offset) {
int curOffset = offset;
int count = Marshal.getInt(data, offset);
@@ -146,7 +146,7 @@
curOffset += edges.get(i).getLength();
}
}
-
+
@Override
public void write(DataOutput out) throws IOException {
out.writeInt(edges.size());
@@ -171,7 +171,7 @@
*/
@Override
public int compareTo(EdgeListWritable other) {
- int result = Integer.compare(edges.size(), other.edges.size());
+ int result = Integer.compare(edges.size(), other.edges.size());
if (result != 0) {
return result;
}
@@ -183,21 +183,21 @@
}
return 0;
}
-
+
@Override
public int hashCode() {
return edges.hashCode();
}
-
+
@Override
public boolean equals(Object o) {
if (! (o instanceof EdgeListWritable))
return false;
-
+
EdgeListWritable ew = (EdgeListWritable) o;
return compareTo(ew) == 0;
}
-
+
/**
* this version of toString sorts the readIds so they're a little easier to see
*/
@@ -220,9 +220,9 @@
public Iterator<EdgeWritable> iterator() {
return edges.iterator();
}
-
+
/**
- * return an iterator over the keys of this edgeList. Using the iterator.remove() function will remove the entire edge (not just the keys you're iterating over!)
+ * return an iterator over the keys of this edgeList. Using the iterator.remove() function will remove the entire edge (not just the keys you're iterating over!)
*/
public Iterator<VKmerBytesWritable> getKeyIterator() {
Iterator<VKmerBytesWritable> it = new Iterator<VKmerBytesWritable>() {
@@ -263,8 +263,8 @@
}
throw new IllegalArgumentException("Cannot get readIDs for VKmer \""+ key +"\". They key was not in the edgeList!");
}
-
-
+
+
public boolean contains(VKmerBytesWritable toFind){
Iterator<VKmerBytesWritable> posIterator = this.getKeyIterator();
while (posIterator.hasNext()) {
@@ -273,7 +273,7 @@
}
return false;
}
-
+
/*
* remove the first instance of `toRemove`. Uses a linear scan. Throws an
* exception if not in this list.
@@ -283,7 +283,7 @@
while (posIterator.hasNext()) {
if (toRemove.equals(posIterator.next())) {
posIterator.remove();
- return; // break as soon as the element is found
+ return; // break as soon as the element is found
}
}
// element was not found
@@ -305,7 +305,7 @@
while (edgeIterator.hasNext()) {
if (toRemove.equals(edgeIterator.next())) {
edgeIterator.remove();
- return; // found it. return early.
+ return; // found it. return early.
}
}
// element not found.
@@ -318,7 +318,7 @@
public void remove(EdgeWritable toRemove) {
remove(toRemove, false);
}
-
+
public void removeSubEdge(EdgeWritable toRemove){
Iterator<Long> it = toRemove.readIDIter();
while(it.hasNext()){
@@ -334,11 +334,11 @@
// this.edges.addAll(other.edges.clone());
// }
// }
-
-
+
+
/**
* Adds all edges in edgeList to me. If I have the same edge as `other`, that entry will be the union of both sets of readIDs.
- *
+ *
* NOTE: This function may change the order of the original list!
*/
public void unionUpdate(EdgeListWritable other) {
@@ -355,7 +355,7 @@
unionEdges.put(key, new PositionListWritable(e.getReadIDs())); // make a new copy of their list
}
}
-
+
for (EdgeWritable e : other.edges) {
VKmerBytesWritable key = e.getKey();
if (unionEdges.containsKey(key)) {
@@ -388,7 +388,7 @@
// didn't find the edge; add a copy of it now
edges.add(new EdgeWritable(otherEdge));
}
-
+
public void unionAdd(EdgeListWritable otherEdgeList){
for(EdgeWritable otherEdge : otherEdgeList)
unionAdd(otherEdge);
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritable.java
index 4ba12c0..951e45e 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritable.java
@@ -1,5 +1,5 @@
/*
- * Copyright 2009-2013 by The Regents of the University of California
+* Copyright 2009-2013 by The Regents of the University of California
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* you may obtain a copy of the License from
@@ -32,7 +32,7 @@
* NodeWritable. Kmer length should be set once during configuration and should
* never change.
*/
-public class KmerBytesWritable extends BinaryComparable implements Serializable, WritableComparable<BinaryComparable> {
+public class KmerBytesWritable extends BinaryComparable implements Serializable, WritableComparable<BinaryComparable> { // TODO make consistent with NodeWritable
private static final long serialVersionUID = 1L;
protected static final byte[] EMPTY_BYTES = {};
@@ -220,7 +220,7 @@
* @param start
*/
@SuppressWarnings("static-access")
- public void setByRead(byte[] stringBytes, int start) {
+ public void setByRead(byte[] stringBytes, int start) { // TODO "setFromStringBytes"
byte l = 0;
int bytecount = 0;
int bcount = this.getBytesUsed() - 1;
@@ -248,7 +248,7 @@
* @param start
* position
*/
- public void setByReadReverse(byte[] array, int start) {
+ public void setByReadReverse(byte[] array, int start) { // TODO "setReversedFromStringBytes"
byte l = 0;
int bytecount = 0;
int bcount = getBytesUsed() - 1;
@@ -307,7 +307,7 @@
* Input new gene character
* @return the shiftout gene, in gene code format
*/
- public byte shiftKmerWithPreChar(byte c) {
+ public byte shiftKmerWithPreChar(byte c) { // TODO remove
return shiftKmerWithPreCode(GeneCode.getCodeFromSymbol(c));
}
@@ -318,7 +318,7 @@
* Input new gene code
* @return the shiftout gene, in gene code format
*/
- public byte shiftKmerWithPreCode(byte c) {
+ public byte shiftKmerWithPreCode(byte c) { // TODO remove
int pos = ((lettersInKmer - 1) % 4) << 1;
byte output = (byte) ((bytes[offset] >> pos) & 0x03);
for (int i = 0; i < getBytesUsed() - 1; i++) {
@@ -406,7 +406,7 @@
KmerBytesWritable.bytesUsed = bytesUsed;
}
- public static class Comparator extends WritableComparator {
+ public static class Comparator extends WritableComparator { // TODO do we need this?
public Comparator() {
super(KmerBytesWritable.class);
}
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 11e684c..ffcb449 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
@@ -28,74 +28,259 @@
import edu.uci.ics.genomix.data.Marshal;
-public class NodeWritable implements WritableComparable<NodeWritable>, Serializable {
+public class NodeWritable implements WritableComparable<NodeWritable>, Serializable { // TODO is it more efficient to just use binaryComparable with Comparator?
public enum DIR {
+
PREVIOUS((byte) (0b01 << 2)),
- NEXT((byte) (0b10 << 2));
-
- public static final byte MASK = (byte)(0b11 << 2);
-
- private final byte val;
- private DIR(byte val) {
- this.val = val;
+ NEXT((byte) (0b10 << 2));
+
+ public static final byte MASK = (byte)(0b11 << 2);
+
+ private final byte val;
+ private DIR(byte val) {
+ this.val = val;
+ }
+ public final byte get() {
+ return val;
+ }
+ public static DIR mirror(DIR direction) {
+ switch (direction) {
+ case PREVIOUS:
+ return NEXT;
+ case NEXT:
+ return PREVIOUS;
+ default:
+ throw new IllegalArgumentException("Invalid direction given: " + direction);
+ }
+ }
+ public DIR mirror() {
+ return mirror(this);
+ }
+
+ public static DIR fromByte(short b) { // TODO remove this function
+ //TODO change shorts to byte? (anbangx)
+ b &= MASK;
+ if (b == PREVIOUS.val)
+ return PREVIOUS;
+ if (b == NEXT.val)
+ return NEXT;
+ return null;
+ }
+
+ public static byte fromSet(EnumSet<DIR> set) {
+ byte b = 0;
+ if (set.contains(PREVIOUS))
+ b |= PREVIOUS.val;
+ if (set.contains(NEXT))
+ b |= NEXT.val;
+ return b;
}
- public final byte get() {
- return val;
- }
- public static DIR mirror(DIR direction) {
- switch (direction) {
- case PREVIOUS:
- return NEXT;
- case NEXT:
- return PREVIOUS;
- default:
- throw new IllegalArgumentException("test");
- }
- }
- public DIR mirror() {
- return mirror(this);
- }
-
- public static DIR mirror(byte dir){
- switch(dir){
- case DirectionFlag.DIR_FF:
- case DirectionFlag.DIR_RF:
- return PREVIOUS;
- case DirectionFlag.DIR_FR:
- case DirectionFlag.DIR_RR:
- return NEXT;
- }
- return null;
- }
-
- public static byte mirrorFromByte(short b){
- b &= MASK;
- if(b != 0)
- return mirror(fromByte(b)).get();
- else
- return 0;
- }
-
- public static DIR fromByte(short b) {
- b &= MASK;
- if (b == PREVIOUS.val)
- return PREVIOUS;
- if (b == NEXT.val)
- return NEXT;
- return null;
- }
-
- public static EnumSet<DIR> enumSetFromByte(short s) {
+ public final EnumSet<EDGETYPE> edgeType(){
+ return edgeTypesInDir(this);
+ }
+
+ public static final EnumSet<EDGETYPE> edgeTypesInDir(DIR direction) {
+ return direction == DIR.PREVIOUS ? EDGETYPE.INCOMING : EDGETYPE.OUTGOING;
+ }
+
+ public static EnumSet<DIR> enumSetFromByte(short s) {
+ EnumSet<DIR> retSet = EnumSet.noneOf(DIR.class);
+ if ((s & PREVIOUS.get()) != 0)
+ retSet.add(DIR.PREVIOUS);
+ if ((s & NEXT.get()) != 0)
+ retSet.add(DIR.NEXT);
+ return retSet;
+ }
+
+ /**
+ * Given a byte representing NEXT, PREVIOUS, or both, return an enumset representing PREVIOUS, NEXT, or both, respectively.
+ */
+ public static EnumSet<DIR> flipSetFromByte(short s) {
EnumSet<DIR> retSet = EnumSet.noneOf(DIR.class);
if ((s & PREVIOUS.get()) != 0)
- retSet.add(DIR.PREVIOUS);
- if ((s & NEXT.get()) != 0)
retSet.add(DIR.NEXT);
+ if ((s & NEXT.get()) != 0)
+ retSet.add(DIR.PREVIOUS);
return retSet;
}
}
-
+
+ public enum EDGETYPE {
+
+ FF((byte)(0b00 << 0)),
+ FR((byte)(0b01 << 0)),
+ RF((byte)(0b10 << 0)),
+ RR((byte)(0b11 << 0));
+
+ public static final byte MASK = (byte)(0b11 << 0);
+ public static final byte CLEAR = (byte)(0b1111100 << 0);
+ private final byte val;
+
+ private EDGETYPE(byte val){
+ this.val = val;
+ }
+
+ public final byte get(){
+ return val;
+ }
+
+ public static final EnumSet<EDGETYPE> INCOMING = EnumSet.of(RF, RR);
+ public static final EnumSet<EDGETYPE> OUTGOING = EnumSet.of(FF, FR);
+
+ public static EDGETYPE fromByte(short b) {
+ b &= MASK;
+ if(b == FF.val)
+ return FF;
+ if(b == FR.val)
+ return FR;
+ if(b == RF.val)
+ return RF;
+ if(b == RR.val)
+ return RR;
+ return null;
+
+ }
+ /**
+ * Returns the edge dir for B->A when the A->B edge is type @dir
+ */
+ public EDGETYPE mirror(){
+ return mirror(this);
+ }
+
+ public static EDGETYPE mirror(EDGETYPE edgeType){
+ switch (edgeType) {
+ case FF:
+ return RR;
+ case FR:
+ return FR;
+ case RF:
+ return RF;
+ case RR:
+ return FF;
+ default:
+ throw new RuntimeException("Unrecognized direction in mirrorDirection: " + edgeType);
+ }
+ }
+
+ public DIR dir() {
+ return dir(this);
+ }
+
+ public static DIR dir(EDGETYPE edgeType){ // .dir static / non-static
+ switch(edgeType){
+ case FF:
+ case FR:
+ return DIR.NEXT;
+ case RF:
+ case RR:
+ return DIR.PREVIOUS;
+ default:
+ throw new RuntimeException("Unrecognized direction in dirFromEdgeType: " + edgeType);
+ }
+ }
+
+ /**
+ * return the edgetype corresponding to moving across edge1 and edge2.
+ *
+ * So if A <-e1- B -e2-> C, we will return the relationship from A -> C
+ *
+ * If the relationship isn't a valid path (e.g., e1,e2 are both FF), an exception is raised.
+ */
+ public static EDGETYPE resolveLinkThroughMiddleNode(EDGETYPE BtoA, EDGETYPE BtoC) {
+ EDGETYPE AtoB = mirror(BtoA);
+ // a valid path must exist from A to C
+ // specifically, two rules apply for AtoB and BtoC
+ // 1) the internal letters must be the same (so FF, RF will be an error)
+ // 2) the final direction is the 1st letter of AtoB + 2nd letter of BtoC
+ // TODO? maybe we could use the string version to resolve this following above rules
+ switch(AtoB) {
+ case FF:
+ switch (BtoC) {
+ case FF:
+ case FR:
+ return BtoC;
+ case RF:
+ case RR:
+ throw new IllegalArgumentException("Tried to resolve an invalid link type: A --" + AtoB + "--> B --" + BtoC + "--> C");
+ }
+ break;
+ case FR:
+ switch (BtoC) {
+ case FF:
+ case FR:
+ throw new IllegalArgumentException("Tried to resolve an invalid link type: A --" + AtoB + "--> B --" + BtoC + "--> C");
+ case RF:
+ return FF;
+ case RR:
+ return FR;
+ }
+ break;
+ case RF:
+ switch (BtoC) {
+ case FF:
+ return RF;
+ case FR:
+ return RR;
+ case RF:
+ case RR:
+ throw new IllegalArgumentException("Tried to resolve an invalid link type: A --" + AtoB + "--> B --" + BtoC + "--> C");
+ }
+ break;
+ case RR:
+ switch (BtoC) {
+ case FF:
+ case FR:
+ throw new IllegalArgumentException("Tried to resolve an invalid link type: A --" + AtoB + "--> B --" + BtoC + "--> C");
+ case RF:
+ return RF;
+ case RR:
+ return RR;
+ }
+ break;
+ }
+ throw new IllegalStateException("Logic Error or unrecognized direction... original values were: " + BtoA + " and " + BtoC);
+ }
+
+ public boolean causesFlip(){
+ return causesFlip(this);
+ }
+ public static boolean causesFlip(EDGETYPE edgeType) {
+ switch (edgeType) {
+ case FF:
+ case RR:
+ return false;
+ case FR:
+ case RF:
+ return true;
+ default:
+ throw new IllegalArgumentException("unrecognized direction: " + edgeType);
+ }
+ }
+
+ /**
+ * check if need filp
+ */
+ public EDGETYPE flip(){
+ return flip(this);
+ }
+
+ public static EDGETYPE flip(EDGETYPE neighborToMe){ // TODO use NodeWritable
+ switch (neighborToMe) {
+ case FF:
+ return FR;
+ case FR:
+ return FF;
+ case RF:
+ return RR;
+ case RR:
+ return RF;
+ default:
+ throw new RuntimeException("Unrecognized direction for neighborDir: " + neighborToMe);
+ }
+ }
+ }
+
private static final long serialVersionUID = 1L;
public static final NodeWritable EMPTY_NODE = new NodeWritable();
@@ -115,38 +300,12 @@
// public String previous;
// public int stepCount;
// merge/update directions
- public static class DirectionFlag {
- public static final byte DIR_FF = 0b00 << 0;
- public static final byte DIR_FR = 0b01 << 0;
- public static final byte DIR_RF = 0b10 << 0;
- public static final byte DIR_RR = 0b11 << 0;
- public static final byte DIR_MASK = 0b11 << 0;
- public static final byte DIR_CLEAR = 0b1111100 << 0;
-
- public static final byte[] values = { DIR_FF, DIR_FR, DIR_RF, DIR_RR };
- }
- public static class IncomingListFlag { // TODO refactor as a function using DIR
- public static final byte DIR_RF = 0b10 << 0;
- public static final byte DIR_RR = 0b11 << 0;
-
- public static final byte[] values = {DIR_RF, DIR_RR };
- }
-
- public static class OutgoingListFlag {
- public static final byte DIR_FF = 0b00 << 0;
- public static final byte DIR_FR = 0b01 << 0;
-
- public static final byte[] values = {DIR_FF, DIR_FR };
- }
-
- public static final byte[] edgeTypesInDir(DIR direction) {
- return direction == DIR.PREVIOUS ? IncomingListFlag.values : OutgoingListFlag.values;
- }
public NodeWritable() {
- for (byte d : DirectionFlag.values) {
- edges[d] = new EdgeListWritable();
+
+ for (EDGETYPE e : EnumSet.allOf(EDGETYPE.class)) {
+ edges[e.get()] = new EdgeListWritable();
}
startReads = new PositionListWritable();
endReads = new PositionListWritable();
@@ -180,8 +339,8 @@
public void setAsCopy(EdgeListWritable[] edges, PositionListWritable startReads, PositionListWritable endReads,
VKmerBytesWritable kmer2, float coverage) {
- for (byte d : DirectionFlag.values) {
- this.edges[d].setAsCopy(edges[d]);
+ for (EDGETYPE e : EnumSet.allOf(EDGETYPE.class)) {
+ this.edges[e.get()].setAsCopy(edges[e.get()]);
}
this.startReads.set(startReads);
this.endReads.set(endReads);
@@ -190,8 +349,8 @@
}
public void reset() {
- for (byte d : DirectionFlag.values) {
- edges[d].reset();
+ for (EDGETYPE e : EnumSet.allOf(EDGETYPE.class)) {
+ edges[e.get()].reset();
}
startReads.reset();
endReads.reset();
@@ -210,13 +369,25 @@
public int getKmerLength() {
return internalKmer.getKmerLetterLength();
}
-
- public EdgeListWritable getEdgeList(byte dir) {
- return edges[dir & DirectionFlag.DIR_MASK];
+
+ //This function works on only this case: in this DIR, vertex has and only has one EDGETYPE
+ public EDGETYPE getEdgetypeFromDir(DIR direction){
+ 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) {
+ return edges[edgeType.get() & EDGETYPE.MASK];
}
- public void setEdgeList(byte dir, EdgeListWritable edgeList) {
- this.edges[dir & DirectionFlag.DIR_MASK].setAsCopy(edgeList);
+ public void setEdgeList(EDGETYPE edgeType, EdgeListWritable edgeList) {
+ this.edges[edgeType.get() & EDGETYPE.MASK].setAsCopy(edgeList);
}
public EdgeListWritable[] getEdges() {
@@ -288,8 +459,8 @@
*/
public int getSerializedLength() {
int length = 0;
- for (byte d : DirectionFlag.values) {
- length += edges[d].getLength();
+ for (EDGETYPE e : EnumSet.allOf(EDGETYPE.class)) {
+ length += edges[e.get()].getLength();
}
length += startReads.getLength();
length += endReads.getLength();
@@ -310,9 +481,9 @@
public void setAsCopy(byte[] data, int offset) {
int curOffset = offset;
- for (byte d : DirectionFlag.values) {
- edges[d].setAsCopy(data, curOffset);
- curOffset += edges[d].getLength();
+ for (EDGETYPE e : EnumSet.allOf(EDGETYPE.class)) {
+ edges[e.get()].setAsCopy(data, curOffset);
+ curOffset += edges[e.get()].getLength();
}
startReads.set(data, curOffset);
curOffset += startReads.getLength();
@@ -325,9 +496,9 @@
public void setAsReference(byte[] data, int offset) {
int curOffset = offset;
- for (byte d : DirectionFlag.values) {
- edges[d].setAsReference(data, curOffset);
- curOffset += edges[d].getLength();
+ for (EDGETYPE e : EnumSet.allOf(EDGETYPE.class)) {
+ edges[e.get()].setAsReference(data, curOffset);
+ curOffset += edges[e.get()].getLength();
}
startReads.setNewReference(data, curOffset);
curOffset += startReads.getLength();
@@ -341,8 +512,8 @@
@Override
public void write(DataOutput out) throws IOException {
- for (byte d : DirectionFlag.values) {
- edges[d].write(out);
+ for (EDGETYPE e : EnumSet.allOf(EDGETYPE.class)) {
+ edges[e.get()].write(out);
}
startReads.write(out);
endReads.write(out);
@@ -353,8 +524,8 @@
@Override
public void readFields(DataInput in) throws IOException {
reset();
- for (byte d : DirectionFlag.values) {
- edges[d].readFields(in);
+ for (EDGETYPE e : EnumSet.allOf(EDGETYPE.class)) {
+ edges[e.get()].readFields(in);
}
startReads.readFields(in);
endReads.readFields(in);
@@ -385,8 +556,8 @@
return false;
NodeWritable nw = (NodeWritable) o;
- for (byte d : DirectionFlag.values) {
- if (!edges[d].equals(nw.edges[d]))
+ for (EDGETYPE e : EnumSet.allOf(EDGETYPE.class)) {
+ if (!edges[e.get()].equals(nw.edges[e.get()]))
return false;
}
@@ -398,8 +569,8 @@
public String toString() {
StringBuilder sbuilder = new StringBuilder();
sbuilder.append('{');
- for (byte d : DirectionFlag.values) {
- sbuilder.append(edges[d].toString()).append('\t');
+ for (EDGETYPE e : EnumSet.allOf(EDGETYPE.class)) {
+ sbuilder.append(edges[e.get()].toString()).append('\t');
}
sbuilder.append("{5':" + startReads.toString() + ", ~5':" + endReads.toString() + "}").append('\t');
sbuilder.append(internalKmer.toString()).append('\t');
@@ -424,23 +595,23 @@
* @param other
* : the node to merge with. I should have a `dir` edge towards `other`
*/
- public void mergeWithNode(byte dir, final NodeWritable other) {
- mergeEdges(dir, other);
- mergeStartAndEndReadIDs(dir, other);
+ public void mergeWithNode(EDGETYPE edgeType, final NodeWritable other) {
+ mergeEdges(edgeType, other);
+ mergeStartAndEndReadIDs(edgeType, other);
mergeCoverage(other);
- internalKmer.mergeWithKmerInDir(dir, KmerBytesWritable.lettersInKmer, other.internalKmer);
+ internalKmer.mergeWithKmerInDir(edgeType, KmerBytesWritable.lettersInKmer, other.internalKmer);
}
- public void mergeWithNodeWithoutKmer(byte dir, final NodeWritable other) {
- mergeEdges(dir, other);
- mergeStartAndEndReadIDs(dir, other);
+ public void mergeWithNodeWithoutKmer(EDGETYPE edgeType, final NodeWritable other) {
+ mergeEdges(edgeType, other);
+ mergeStartAndEndReadIDs(edgeType, other);
mergeCoverage(other);
}
public void mergeWithNodeWithoutKmer(final NodeWritable other) {
- byte dir = DirectionFlag.DIR_FF;
- mergeEdges(dir, other);
- mergeStartAndEndReadIDs(dir, other);
+ EDGETYPE edgeType = EDGETYPE.FF;
+ mergeEdges(edgeType, other);
+ mergeStartAndEndReadIDs(edgeType, other);
mergeCoverage(other);
}
@@ -482,92 +653,76 @@
}
}
}
-
+//
/**
* update my edge list
*/
- public void updateEdges(byte deleteDir, VKmerBytesWritable toDelete, byte updateDir, byte replaceDir, NodeWritable other, boolean applyDelete){
+ public void updateEdges(EDGETYPE deleteDir, VKmerBytesWritable toDelete, EDGETYPE updateDir, EDGETYPE replaceDir, NodeWritable other, boolean applyDelete){
if(applyDelete)
- edges[deleteDir].remove(toDelete);
- edges[updateDir].unionUpdate(other.edges[replaceDir]);
-// switch (replaceDir) {
-// case DirectionFlag.DIR_FF:
-// case DirectionFlag.DIR_FR:
-// if (other.inDegree() != 1)
-// throw new IllegalStateException("In update, expected other node's indegree to be 1!" + this + other);
-// edges[updateDir].unionUpdate(other.edges[DirectionFlag.DIR_RF]);
-// edges[updateDir].unionUpdate(other.edges[DirectionFlag.DIR_RR]);
-// break;
-// case DirectionFlag.DIR_RF:
-// case DirectionFlag.DIR_RR:
-// if (other.outDegree() != 1)
-// throw new IllegalStateException("In update, expected other node's outdegree to be 1!" + this + other);
-// edges[updateDir].unionUpdate(other.edges[DirectionFlag.DIR_FF]);
-// edges[updateDir].unionUpdate(other.edges[DirectionFlag.DIR_FR]);
-// break;
-// }
+ edges[deleteDir.get()].remove(toDelete);
+ edges[updateDir.get()].unionUpdate(other.edges[replaceDir.get()]);
}
/**
* merge my edge list (both kmers and readIDs) with those of `other`. Assumes that `other` is doing the flipping, if any.
*/
- public void mergeEdges(byte dir, NodeWritable other) {
- switch (dir & DirectionFlag.DIR_MASK) {
- case DirectionFlag.DIR_FF:
+ public void mergeEdges(EDGETYPE edgeType, NodeWritable other) {
+ switch (edgeType) {
+ case FF:
if (outDegree() > 1)
throw new IllegalArgumentException("Illegal FF merge attempted! My outgoing degree is " + outDegree() + " in " + toString());
if (other.inDegree() > 1)
throw new IllegalArgumentException("Illegal FF merge attempted! Other incoming degree is " + other.inDegree() + " in " + other.toString());
- edges[DirectionFlag.DIR_FF].setAsCopy(other.edges[DirectionFlag.DIR_FF]);
- edges[DirectionFlag.DIR_FR].setAsCopy(other.edges[DirectionFlag.DIR_FR]);
+ edges[EDGETYPE.FF.get()].setAsCopy(other.edges[EDGETYPE.FF.get()]);
+ edges[EDGETYPE.FR.get()].setAsCopy(other.edges[EDGETYPE.FR.get()]);
break;
- case DirectionFlag.DIR_FR:
+ case FR:
if (outDegree() > 1)
throw new IllegalArgumentException("Illegal FR merge attempted! My outgoing degree is " + outDegree() + " in " + toString());
if (other.outDegree() > 1)
throw new IllegalArgumentException("Illegal FR merge attempted! Other outgoing degree is " + other.outDegree() + " in " + other.toString());
- edges[DirectionFlag.DIR_FF].setAsCopy(other.edges[DirectionFlag.DIR_RF]);
- edges[DirectionFlag.DIR_FR].setAsCopy(other.edges[DirectionFlag.DIR_RR]);
+ edges[EDGETYPE.FF.get()].setAsCopy(other.edges[EDGETYPE.RF.get()]);
+ edges[EDGETYPE.FR.get()].setAsCopy(other.edges[EDGETYPE.RR.get()]);
break;
- case DirectionFlag.DIR_RF:
+ case RF:
if (inDegree() > 1)
throw new IllegalArgumentException("Illegal RF merge attempted! My incoming degree is " + inDegree() + " in " + toString());
if (other.inDegree() > 1)
throw new IllegalArgumentException("Illegal RF merge attempted! Other incoming degree is " + other.inDegree() + " in " + other.toString());
- edges[DirectionFlag.DIR_RF].setAsCopy(other.edges[DirectionFlag.DIR_FF]);
- edges[DirectionFlag.DIR_RR].setAsCopy(other.edges[DirectionFlag.DIR_FR]);
+ edges[EDGETYPE.RF.get()].setAsCopy(other.edges[EDGETYPE.FF.get()]);
+ edges[EDGETYPE.RR.get()].setAsCopy(other.edges[EDGETYPE.FR.get()]);
break;
- case DirectionFlag.DIR_RR:
+ case RR:
if (inDegree() > 1)
throw new IllegalArgumentException("Illegal RR merge attempted! My incoming degree is " + inDegree() + " in " + toString());
if (other.outDegree() > 1)
throw new IllegalArgumentException("Illegal RR merge attempted! Other outgoing degree is " + other.outDegree() + " in " + other.toString());
- edges[DirectionFlag.DIR_RF].setAsCopy(other.edges[DirectionFlag.DIR_RF]);
- edges[DirectionFlag.DIR_RR].setAsCopy(other.edges[DirectionFlag.DIR_RR]);
+ edges[EDGETYPE.RF.get()].setAsCopy(other.edges[EDGETYPE.RF.get()]);
+ edges[EDGETYPE.RR.get()].setAsCopy(other.edges[EDGETYPE.RR.get()]);
break;
}
}
private void addEdges(boolean flip, NodeWritable other) {
if (!flip) {
- for (byte d : DirectionFlag.values) {
- edges[d].unionUpdate(other.edges[d]);
+ for (EDGETYPE e : EnumSet.allOf(EDGETYPE.class)) {
+ edges[e.get()].unionUpdate(other.edges[e.get()]);
}
} else {
- edges[DirectionFlag.DIR_FF].unionUpdate(other.edges[DirectionFlag.DIR_RF]);
- edges[DirectionFlag.DIR_FR].unionUpdate(other.edges[DirectionFlag.DIR_RR]);
- edges[DirectionFlag.DIR_RF].unionUpdate(other.edges[DirectionFlag.DIR_FF]);
- edges[DirectionFlag.DIR_RR].unionUpdate(other.edges[DirectionFlag.DIR_FR]);
+ edges[EDGETYPE.FF.get()].unionUpdate(other.edges[EDGETYPE.RF.get()]);
+ edges[EDGETYPE.FR.get()].unionUpdate(other.edges[EDGETYPE.RR.get()]);
+ edges[EDGETYPE.RF.get()].unionUpdate(other.edges[EDGETYPE.FF.get()]);
+ edges[EDGETYPE.RR.get()].unionUpdate(other.edges[EDGETYPE.FR.get()]);
}
}
- private void mergeStartAndEndReadIDs(byte dir, NodeWritable other) {
+ private void mergeStartAndEndReadIDs(EDGETYPE edgeType, NodeWritable other) {
int K = KmerBytesWritable.lettersInKmer;
int otherLength = other.internalKmer.lettersInKmer;
int thisLength = internalKmer.lettersInKmer;
int newOtherOffset, newThisOffset;
- switch (dir & DirectionFlag.DIR_MASK) {
- case DirectionFlag.DIR_FF:
+ switch (edgeType) {
+ case FF:
newOtherOffset = thisLength - K + 1;
// stream theirs in with my offset
for (PositionWritable p : other.startReads) {
@@ -577,7 +732,7 @@
endReads.append(p.getMateId(), p.getReadId(), newOtherOffset + p.getPosId());
}
break;
- case DirectionFlag.DIR_FR:
+ case FR:
newOtherOffset = thisLength - K + 1 + otherLength - K;
// stream theirs in, offset and flipped
for (PositionWritable p : other.startReads) {
@@ -587,7 +742,7 @@
startReads.append(p.getMateId(), p.getReadId(), newOtherOffset + p.getPosId());
}
break;
- case DirectionFlag.DIR_RF:
+ case RF:
newThisOffset = otherLength - K + 1;
newOtherOffset = otherLength - K;
// shift my offsets (other is prepended)
@@ -605,7 +760,7 @@
startReads.append(p.getMateId(), p.getReadId(), newOtherOffset + p.getPosId());
}
break;
- case DirectionFlag.DIR_RR:
+ case RR:
newThisOffset = otherLength - K + 1;
// shift my offsets (other is prepended)
for (PositionWritable p : startReads) {
@@ -625,11 +780,11 @@
}
public int inDegree() {
- return edges[DirectionFlag.DIR_RR].getCountOfPosition() + edges[DirectionFlag.DIR_RF].getCountOfPosition();
+ return edges[EDGETYPE.RR.get()].getCountOfPosition() + edges[EDGETYPE.RF.get()].getCountOfPosition();
}
public int outDegree() {
- return edges[DirectionFlag.DIR_FF].getCountOfPosition() + edges[DirectionFlag.DIR_FR].getCountOfPosition();
+ return edges[EDGETYPE.FF.get()].getCountOfPosition() + edges[EDGETYPE.FR.get()].getCountOfPosition();
}
public int getDegree(DIR direction){
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/VKmerBytesWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/VKmerBytesWritable.java
index 5105388..74bbaa0 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/VKmerBytesWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/VKmerBytesWritable.java
@@ -27,7 +27,7 @@
import edu.uci.ics.genomix.data.KmerUtil;
import edu.uci.ics.genomix.data.Marshal;
-import edu.uci.ics.genomix.type.NodeWritable.DirectionFlag;
+import edu.uci.ics.genomix.type.NodeWritable.EDGETYPE;
/**
@@ -35,7 +35,7 @@
* Note: `offset` as used in this class is the offset at which the *kmer*
* begins. There is a {@value HEADER_SIZE}-byte header preceding the kmer
*/
-public class VKmerBytesWritable extends BinaryComparable implements Serializable, WritableComparable<BinaryComparable> {
+public class VKmerBytesWritable extends BinaryComparable implements Serializable, WritableComparable<BinaryComparable> { // TODO should be Writable<VKmer>
private static final long serialVersionUID = 1L;
protected static final byte[] EMPTY_BYTES = { 0, 0, 0, 0 }; // int indicating 0 length
protected static final int HEADER_SIZE = 4; // number of bytes for header info
@@ -653,27 +653,27 @@
mergeWithRRKmer(kmerSize, new VKmerBytesWritable(kmer.toString()));
}
- public void mergeWithKmerInDir(byte dir, int initialKmerSize, VKmerBytesWritable kmer) {
- switch (dir & DirectionFlag.DIR_MASK) {
- case DirectionFlag.DIR_FF:
+ public void mergeWithKmerInDir(EDGETYPE edgeType, int initialKmerSize, VKmerBytesWritable kmer) {
+ switch (edgeType) {
+ case FF:
mergeWithFFKmer(initialKmerSize, kmer);
break;
- case DirectionFlag.DIR_FR:
+ case FR:
mergeWithFRKmer(initialKmerSize, kmer);
break;
- case DirectionFlag.DIR_RF:
+ case RF:
mergeWithRFKmer(initialKmerSize, kmer);
break;
- case DirectionFlag.DIR_RR:
+ case RR:
mergeWithRRKmer(initialKmerSize, kmer);
break;
default:
- throw new RuntimeException("Direction not recognized: " + dir);
+ throw new RuntimeException("Direction not recognized: " + edgeType);
}
}
- public void mergeWithKmerInDir(byte dir, int initialKmerSize, KmerBytesWritable kmer) {
+ public void mergeWithKmerInDir(EDGETYPE edgeType, int initialKmerSize, KmerBytesWritable kmer) {
// TODO make this more efficient
- mergeWithKmerInDir(dir, initialKmerSize, new VKmerBytesWritable(kmer.toString()));
+ mergeWithKmerInDir(edgeType, initialKmerSize, new VKmerBytesWritable(kmer.toString()));
}
public KmerBytesWritable asFixedLengthKmer() {
diff --git a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/EdgeListWritableTest.java b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/EdgeListWritableTest.java
index 43740a4..318e58e 100644
--- a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/EdgeListWritableTest.java
+++ b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/EdgeListWritableTest.java
@@ -15,15 +15,14 @@
import org.junit.Test;
-import edu.uci.ics.genomix.data.KmerUtil;
import edu.uci.ics.genomix.type.EdgeListWritable;
import edu.uci.ics.genomix.type.EdgeWritable;
import edu.uci.ics.genomix.type.KmerBytesWritable;
import edu.uci.ics.genomix.type.NodeWritable;
-import edu.uci.ics.genomix.type.NodeWritable.DirectionFlag;
import edu.uci.ics.genomix.type.PositionListWritable;
import edu.uci.ics.genomix.type.PositionWritable;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
+import edu.uci.ics.genomix.type.NodeWritable.EDGETYPE;
public class EdgeListWritableTest {
@@ -52,18 +51,18 @@
for (long i = numelements * 2 / 3; i < numelements; i++) {
plist3.appendReadId(i);
}
- n1.getEdgeList(DirectionFlag.DIR_RF).add(new EdgeWritable(k2, plist1));
- Assert.assertEquals(numelements / 3, n1.getEdgeList(DirectionFlag.DIR_RF).get(0).getReadIDs()
+ n1.getEdgeList(EDGETYPE.FF).add(new EdgeWritable(k2, plist1));
+ Assert.assertEquals(numelements / 3, n1.getEdgeList(EDGETYPE.RF).get(0).getReadIDs()
.getCountOfPosition());
- n1.getEdgeList(DirectionFlag.DIR_RF).unionUpdate(
+ n1.getEdgeList(EDGETYPE.RF).unionUpdate(
new EdgeListWritable(Arrays.asList(new EdgeWritable(k2, plist2))));
- Assert.assertEquals(numelements * 2 / 3 + numoverlap, n1.getEdgeList(DirectionFlag.DIR_RF).get(0).getReadIDs()
+ Assert.assertEquals(numelements * 2 / 3 + numoverlap, n1.getEdgeList(EDGETYPE.RF).get(0).getReadIDs()
.getCountOfPosition());
- n1.getEdgeList(DirectionFlag.DIR_RF).unionUpdate(
+ n1.getEdgeList(EDGETYPE.RF).unionUpdate(
new EdgeListWritable(Arrays.asList(new EdgeWritable(k2, plist3))));
- Assert.assertEquals(numelements, n1.getEdgeList(DirectionFlag.DIR_RF).get(0).getReadIDs().getCountOfPosition());
+ Assert.assertEquals(numelements, n1.getEdgeList(EDGETYPE.RF).get(0).getReadIDs().getCountOfPosition());
- long[] allReadIDs = n1.getEdgeList(DirectionFlag.DIR_RF).get(0).readIDArray();
+ long[] allReadIDs = n1.getEdgeList(EDGETYPE.RF).get(0).readIDArray();
// make sure all readids are accounted for...
for (long i = 0; i < numelements; i++) {
boolean found = false;
diff --git a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/EdgeWritableTest.java b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/EdgeWritableTest.java
index 32d5338..03b54cc 100644
--- a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/EdgeWritableTest.java
+++ b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/EdgeWritableTest.java
@@ -114,8 +114,7 @@
VKmerBytesWritable kmer2 = new VKmerBytesWritable("ATAGCTGAC");
elist.add(new EdgeWritable(kmer2, plist1));
- Iterator<VKmerBytesWritable> keyIter = elist.getKeys().iterator();//TODO
-
+ Iterator<VKmerBytesWritable> keyIter = elist.getKeyIterator();
Assert.assertTrue(keyIter.hasNext());
Assert.assertEquals(kmer1, keyIter.next());
Assert.assertEquals(kmer2, keyIter.next());
diff --git a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/NodeWritableTest.java b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/NodeWritableTest.java
index 538a1fe..97f7fbd 100644
--- a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/NodeWritableTest.java
+++ b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/NodeWritableTest.java
@@ -8,15 +8,13 @@
import org.junit.Test;
-import edu.uci.ics.genomix.data.KmerUtil;
-import edu.uci.ics.genomix.type.EdgeListWritable;
import edu.uci.ics.genomix.type.EdgeWritable;
import edu.uci.ics.genomix.type.KmerBytesWritable;
import edu.uci.ics.genomix.type.NodeWritable;
-import edu.uci.ics.genomix.type.NodeWritable.DirectionFlag;
import edu.uci.ics.genomix.type.PositionListWritable;
import edu.uci.ics.genomix.type.PositionWritable;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
+import edu.uci.ics.genomix.type.NodeWritable.EDGETYPE;
public class NodeWritableTest {
@@ -50,8 +48,8 @@
n1.setInternalKmer(k1);
n1.setAvgCoverage(10);
n1.getStartReads().append(read1);
- n1.getEdgeList(DirectionFlag.DIR_RF).add(new EdgeWritable(k2, plist1));
- Assert.assertEquals("(50-0_0)", n1.getEdgeList(DirectionFlag.DIR_RF).get(0).getReadIDs().getPosition(0)
+ n1.getEdgeList(EDGETYPE.RF).add(new EdgeWritable(k2, plist1));
+ Assert.assertEquals("(50-0_0)", n1.getEdgeList(EDGETYPE.RF).get(0).getReadIDs().getPosition(0)
.toString());
Assert.assertEquals(10f, n1.getAvgCoverage());
@@ -60,16 +58,16 @@
n2.setAvgCoverage(20);
n2.getStartReads().append(read2);
Assert.assertEquals(1, n2.getStartReads().getCountOfPosition());
- n2.getEdgeList(DirectionFlag.DIR_RF).add(new EdgeWritable(k1, plist1));
- n2.getEdgeList(DirectionFlag.DIR_FF).add(new EdgeWritable(k3, plist3));
+ n2.getEdgeList(EDGETYPE.RF).add(new EdgeWritable(k1, plist1));
+ n2.getEdgeList(EDGETYPE.FF).add(new EdgeWritable(k3, plist3));
Assert.assertEquals(20f, n2.getAvgCoverage());
NodeWritable n3 = new NodeWritable();
n3.setInternalKmer(k3);
n3.setAvgCoverage(30);
n3.getEndReads().append(read3);
- n3.getEdgeList(DirectionFlag.DIR_RR).add(new EdgeWritable(k2, plist3));
- Assert.assertEquals("(100-0_0)", n3.getEdgeList(DirectionFlag.DIR_RR).get(0).getReadIDs().getPosition(0)
+ n3.getEdgeList(EDGETYPE.RR).add(new EdgeWritable(k2, plist3));
+ Assert.assertEquals("(100-0_0)", n3.getEdgeList(EDGETYPE.RR).get(0).getReadIDs().getPosition(0)
.toString());
Assert.assertEquals(30f, n3.getAvgCoverage());
@@ -96,7 +94,7 @@
// Assert.assertEquals("ATCTAG", k2.toString());
// k2.mergeWithFFKmer(5, k3);
// Assert.assertEquals("ATCTAGC", k2.toString());
- n2.mergeWithNode(DirectionFlag.DIR_RF, n1);
+ n2.mergeWithNode(EDGETYPE.RF, n1);
Assert.assertEquals("ATCTAG", n2.getInternalKmer().toString());
Assert.assertEquals(15f, n2.getAvgCoverage());
Assert.assertEquals(1, n2.getEndReads().getCountOfPosition());
@@ -105,9 +103,9 @@
Assert.assertEquals("(75-1_1)", n2.getStartReads().getPosition(0).toString());
Assert.assertEquals(0, n2.inDegree());
Assert.assertEquals(1, n2.outDegree());
- Assert.assertEquals(k3, n2.getEdgeList(DirectionFlag.DIR_FF).get(0).getKey());
+ Assert.assertEquals(k3, n2.getEdgeList(EDGETYPE.FF).get(0).getKey());
- n2.mergeWithNode(DirectionFlag.DIR_FF, n3);
+ n2.mergeWithNode(EDGETYPE.FF, n3);
Assert.assertEquals("ATCTAGC", n2.getInternalKmer().toString());
Assert.assertEquals(20f, n2.getAvgCoverage());
Assert.assertEquals(2, n2.getEndReads().getCountOfPosition());
@@ -150,21 +148,21 @@
n1.setInternalKmer(k1);
n1.setAvgCoverage(10);
n1.getStartReads().append(read1);
- n1.getEdgeList(DirectionFlag.DIR_RF).add(new EdgeWritable(k2, plist1));
+ n1.getEdgeList(EDGETYPE.RF).add(new EdgeWritable(k2, plist1));
NodeWritable n1_2 = new NodeWritable(); // duplicate node which should end up union'ed in
n1_2.setInternalKmer(k1);
n1_2.setAvgCoverage(10);
n1_2.getStartReads().append(read1);
- n1_2.getEdgeList(DirectionFlag.DIR_RF).add(new EdgeWritable(k3, plist3));
- n1_2.getEdgeList(DirectionFlag.DIR_RF).add(new EdgeWritable(k2, plist2));
+ n1_2.getEdgeList(EDGETYPE.RF).add(new EdgeWritable(k3, plist3));
+ n1_2.getEdgeList(EDGETYPE.RF).add(new EdgeWritable(k2, plist2));
// take the union of the edges (a la graphbuilding)
- n1.getEdgeList(DirectionFlag.DIR_RF).unionUpdate(n1_2.getEdgeList(DirectionFlag.DIR_RF));
+ n1.getEdgeList(EDGETYPE.RF).unionUpdate(n1_2.getEdgeList(EDGETYPE.RF));
// the union-update may change the ordering of the original list (what a pain!)
- Iterator<EdgeWritable> rf_edges = n1.getEdgeList(DirectionFlag.DIR_RF).iterator();
+ Iterator<EdgeWritable> rf_edges = n1.getEdgeList(EDGETYPE.RF).iterator();
int k2_index = 0, k3_index = 0;
- for (int i=0; i < n1.getEdgeList(DirectionFlag.DIR_RF).getCountOfPosition(); i++) {
+ for (int i=0; i < n1.getEdgeList(EDGETYPE.RF).getCountOfPosition(); i++) {
VKmerBytesWritable curKmer = rf_edges.next().getKey();
if (curKmer.equals(k2))
k2_index = i;
@@ -172,15 +170,15 @@
k3_index = i;
}
- Assert.assertEquals(2, n1.getEdgeList(DirectionFlag.DIR_RF).getCountOfPosition()); // only k2 and k3 in list
- Assert.assertEquals(k2, n1.getEdgeList(DirectionFlag.DIR_RF).get(k2_index).getKey());
- Assert.assertEquals(k3, n1.getEdgeList(DirectionFlag.DIR_RF).get(k3_index).getKey());
- Assert.assertEquals(3, n1.getEdgeList(DirectionFlag.DIR_RF).get(k2_index).getReadIDs().getCountOfPosition()); // k2 has r1,r2,r3
- Assert.assertEquals(1, n1.getEdgeList(DirectionFlag.DIR_RF).get(k3_index).getReadIDs().getCountOfPosition()); // k3 has r3
+ Assert.assertEquals(2, n1.getEdgeList(EDGETYPE.RF).getCountOfPosition()); // only k2 and k3 in list
+ Assert.assertEquals(k2, n1.getEdgeList(EDGETYPE.RF).get(k2_index).getKey());
+ Assert.assertEquals(k3, n1.getEdgeList(EDGETYPE.RF).get(k3_index).getKey());
+ Assert.assertEquals(3, n1.getEdgeList(EDGETYPE.RF).get(k2_index).getReadIDs().getCountOfPosition()); // k2 has r1,r2,r3
+ Assert.assertEquals(1, n1.getEdgeList(EDGETYPE.RF).get(k3_index).getReadIDs().getCountOfPosition()); // k3 has r3
- long[] k2_readids = n1.getEdgeList(DirectionFlag.DIR_RF).get(k2_index).readIDArray();
+ long[] k2_readids = n1.getEdgeList(EDGETYPE.RF).get(k2_index).readIDArray();
Assert.assertEquals(3, k2_readids.length);
- long[] k3_readids = n1.getEdgeList(DirectionFlag.DIR_RF).get(k3_index).readIDArray();
+ long[] k3_readids = n1.getEdgeList(EDGETYPE.RF).get(k3_index).readIDArray();
Assert.assertEquals(1, k3_readids.length);
boolean[] found = {false, false, false};
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixDriver.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixDriver.java
index c928c84..7733999 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixDriver.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixDriver.java
@@ -11,7 +11,6 @@
import org.apache.hadoop.mapred.SequenceFileOutputFormat;
import org.apache.hadoop.mapred.TextInputFormat;
import org.apache.hadoop.mapred.TextOutputFormat;
-import org.apache.hadoop.mapred.lib.NLineInputFormat;
import org.kohsuke.args4j.CmdLineParser;
import org.kohsuke.args4j.Option;
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixMapper.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixMapper.java
index 849f8cf..759419a 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixMapper.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixMapper.java
@@ -7,7 +7,6 @@
import org.apache.hadoop.io.LongWritable;
import org.apache.hadoop.io.Text;
-import org.apache.hadoop.mapred.InputFormat;
import org.apache.hadoop.mapred.JobConf;
import org.apache.hadoop.mapred.MapReduceBase;
import org.apache.hadoop.mapred.Mapper;
@@ -18,11 +17,11 @@
import edu.uci.ics.genomix.type.EdgeListWritable;
import edu.uci.ics.genomix.type.EdgeWritable;
import edu.uci.ics.genomix.type.KmerBytesWritable;
-import edu.uci.ics.genomix.type.NodeWritable.DirectionFlag;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
import edu.uci.ics.genomix.type.NodeWritable;
import edu.uci.ics.genomix.type.PositionListWritable;
import edu.uci.ics.genomix.type.PositionWritable;
+import edu.uci.ics.genomix.type.NodeWritable.EDGETYPE;
@SuppressWarnings("deprecation")
public class GenomixMapper extends MapReduceBase implements
@@ -202,14 +201,14 @@
edgeForPreKmer.setKey(preForwardKmer);
edgeForPreKmer.setReadIDs(nodeIdList);
edgeListForPreKmer.add(edgeForPreKmer);
- outputNode.setEdgeList(DirectionFlag.DIR_RR, edgeListForPreKmer);
+ outputNode.setEdgeList(EDGETYPE.RR, edgeListForPreKmer);
break;
case REVERSE:
edgeListForPreKmer.reset();
edgeForPreKmer.setKey(preReverseKmer);
edgeForPreKmer.setReadIDs(nodeIdList);
edgeListForPreKmer.add(edgeForPreKmer);
- outputNode.setEdgeList(DirectionFlag.DIR_RF, edgeListForPreKmer);
+ outputNode.setEdgeList(EDGETYPE.RF, edgeListForPreKmer);
break;
}
break;
@@ -220,14 +219,14 @@
edgeForPreKmer.setKey(preForwardKmer);
edgeForPreKmer.setReadIDs(nodeIdList);
edgeListForPreKmer.add(edgeForPreKmer);
- outputNode.setEdgeList(DirectionFlag.DIR_FR, edgeListForPreKmer);
+ outputNode.setEdgeList(EDGETYPE.FR, edgeListForPreKmer);
break;
case REVERSE:
edgeListForPreKmer.reset();
edgeForPreKmer.setKey(preReverseKmer);
edgeForPreKmer.setReadIDs(nodeIdList);
edgeListForPreKmer.add(edgeForPreKmer);
- outputNode.setEdgeList(DirectionFlag.DIR_FF, edgeListForPreKmer);
+ outputNode.setEdgeList(EDGETYPE.FF, edgeListForPreKmer);
break;
}
break;
@@ -243,14 +242,14 @@
edgeForNextKmer.setKey(nextForwardKmer);
edgeForNextKmer.setReadIDs(nodeIdList);
edgeListForNextKmer.add(edgeForNextKmer);
- outputNode.setEdgeList(DirectionFlag.DIR_FF, edgeListForNextKmer);
+ outputNode.setEdgeList(EDGETYPE.FF, edgeListForNextKmer);
break;
case REVERSE:
edgeListForNextKmer.reset();
edgeForNextKmer.setKey(nextReverseKmer);
edgeForNextKmer.setReadIDs(nodeIdList);
edgeListForNextKmer.add(edgeForNextKmer);
- outputNode.setEdgeList(DirectionFlag.DIR_FR, edgeListForNextKmer);
+ outputNode.setEdgeList(EDGETYPE.FR, edgeListForNextKmer);
break;
}
break;
@@ -262,14 +261,14 @@
edgeForNextKmer.setReadIDs(nodeIdList);
edgeListForNextKmer.add(edgeForNextKmer);
new EdgeListWritable(Arrays.asList(new EdgeWritable(nextForwardKmer, nodeIdList)));
- outputNode.setEdgeList(DirectionFlag.DIR_RF, edgeListForNextKmer);
+ outputNode.setEdgeList(EDGETYPE.RF, edgeListForNextKmer);
break;
case REVERSE:
edgeListForNextKmer.reset();
edgeForNextKmer.setKey(nextReverseKmer);
edgeForNextKmer.setReadIDs(nodeIdList);
edgeListForNextKmer.add(edgeForNextKmer);
- outputNode.setEdgeList(DirectionFlag.DIR_RR, edgeListForNextKmer);
+ outputNode.setEdgeList(EDGETYPE.RR, edgeListForNextKmer);
break;
}
break;
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixReducer.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixReducer.java
index 6bc4549..a1c21ee 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixReducer.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixReducer.java
@@ -1,6 +1,7 @@
package edu.uci.ics.genomix.hadoop.contrailgraphbuilding;
import java.io.IOException;
+import java.util.EnumSet;
import java.util.Iterator;
import org.apache.hadoop.mapred.JobConf;
@@ -10,7 +11,7 @@
import org.apache.hadoop.mapred.Reporter;
import edu.uci.ics.genomix.type.NodeWritable;
-import edu.uci.ics.genomix.type.NodeWritable.DirectionFlag;
+import edu.uci.ics.genomix.type.NodeWritable.EDGETYPE;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
@SuppressWarnings("deprecation")
@@ -38,8 +39,8 @@
while (values.hasNext()) {
tmpNode.setAsCopy(values.next());
- for (byte d: DirectionFlag.values) {
- outputNode.getEdgeList(d).unionUpdate(tmpNode.getEdgeList(d));
+ for (EDGETYPE e: EnumSet.allOf(EDGETYPE.class)) {
+ outputNode.getEdgeList(e).unionUpdate(tmpNode.getEdgeList(e));
}
outputNode.getStartReads().unionUpdate(tmpNode.getStartReads());
outputNode.getEndReads().unionUpdate(tmpNode.getEndReads());
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graph/GenerateGraphViz.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graph/GenerateGraphViz.java
index 84a5361..90b66ee 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graph/GenerateGraphViz.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graph/GenerateGraphViz.java
@@ -12,8 +12,8 @@
import edu.uci.ics.genomix.type.EdgeWritable;
import edu.uci.ics.genomix.type.NodeWritable;
+import edu.uci.ics.genomix.type.NodeWritable.EDGETYPE;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
-import edu.uci.ics.genomix.type.NodeWritable.DirectionFlag;
public class GenerateGraphViz {
@@ -74,25 +74,25 @@
public static String convertEdgeToGraph(String outputNode, NodeWritable value) {
String outputEdge = "";
Iterator<EdgeWritable> edgeIterator;
- edgeIterator = value.getEdgeList(DirectionFlag.DIR_FF).iterator();
+ edgeIterator = value.getEdgeList(EDGETYPE.FF).iterator();
while(edgeIterator.hasNext()){
EdgeWritable edge = edgeIterator.next();
outputEdge += outputNode + " -> " + edge.getKey().toString() + "[color = \"black\" label =\"FF: " +
edge.printReadIdSet() + "\"]\n";
}
- edgeIterator = value.getEdgeList(DirectionFlag.DIR_FR).iterator();
+ edgeIterator = value.getEdgeList(EDGETYPE.FR).iterator();
while(edgeIterator.hasNext()){
EdgeWritable edge = edgeIterator.next();
outputEdge += outputNode + " -> " + edge.getKey().toString() + "[color = \"blue\" label =\"FR: " +
edge.printReadIdSet() + "\"]\n";
}
- edgeIterator = value.getEdgeList(DirectionFlag.DIR_RF).iterator();
+ edgeIterator = value.getEdgeList(EDGETYPE.RF).iterator();
while(edgeIterator.hasNext()){
EdgeWritable edge = edgeIterator.next();
outputEdge += outputNode + " -> " + edge.getKey().toString() + "[color = \"green\" label =\"RF: " +
edge.printReadIdSet() + "\"]\n";
}
- edgeIterator = value.getEdgeList(DirectionFlag.DIR_RR).iterator();
+ edgeIterator = value.getEdgeList(EDGETYPE.RR).iterator();
while(edgeIterator.hasNext()){
EdgeWritable edge = edgeIterator.next();
outputEdge += outputNode + " -> " + edge.getKey().toString() + "[color = \"red\" label =\"RR: " +
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphbuilding/checkingtool/ResultsCheckingMapper.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphbuilding/checkingtool/ResultsCheckingMapper.java
index 3b5738f..e4a00fd 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphbuilding/checkingtool/ResultsCheckingMapper.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphbuilding/checkingtool/ResultsCheckingMapper.java
@@ -25,7 +25,6 @@
import org.apache.hadoop.mapred.Reporter;
import edu.uci.ics.genomix.type.NodeWritable;
-import edu.uci.ics.genomix.type.NodeWritable.DirectionFlag;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
@SuppressWarnings("deprecation")
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/graph/dataflow/ReadsKeyValueParserFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/graph/dataflow/ReadsKeyValueParserFactory.java
index 0b22295..10d18ac 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/graph/dataflow/ReadsKeyValueParserFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/graph/dataflow/ReadsKeyValueParserFactory.java
@@ -31,9 +31,9 @@
import edu.uci.ics.genomix.type.EdgeWritable;
import edu.uci.ics.genomix.type.KmerBytesWritable;
import edu.uci.ics.genomix.type.NodeWritable;
+import edu.uci.ics.genomix.type.NodeWritable.EDGETYPE;
import edu.uci.ics.genomix.type.PositionListWritable;
import edu.uci.ics.genomix.type.PositionWritable;
-import edu.uci.ics.genomix.type.NodeWritable.DirectionFlag;
import edu.uci.ics.hyracks.api.comm.IFrameWriter;
import edu.uci.ics.hyracks.api.context.IHyracksTaskContext;
import edu.uci.ics.hyracks.api.dataflow.value.ISerializerDeserializer;
@@ -251,27 +251,27 @@
NodeWritable nextNode, PositionListWritable readIdList, EdgeWritable tempEdge) {
if (curKmerDir == KmerDir.FORWARD && nextKmerDir == KmerDir.FORWARD) {
tempEdge.setAsCopy(nextForwardKmer, readIdList);
- curNode.getEdgeList(DirectionFlag.DIR_FF).add(tempEdge);
+ curNode.getEdgeList(EDGETYPE.FF).add(tempEdge);
tempEdge.setAsCopy(curForwardKmer, readIdList);
- nextNode.getEdgeList(DirectionFlag.DIR_RR).add(tempEdge);
+ nextNode.getEdgeList(EDGETYPE.RR).add(tempEdge);
}
if (curKmerDir == KmerDir.FORWARD && nextKmerDir == KmerDir.REVERSE) {
tempEdge.setAsCopy(nextReverseKmer, readIdList);
- curNode.getEdgeList(DirectionFlag.DIR_FR).add(tempEdge);
+ curNode.getEdgeList(EDGETYPE.FR).add(tempEdge);
tempEdge.setAsCopy(curForwardKmer, readIdList);
- nextNode.getEdgeList(DirectionFlag.DIR_FR).add(tempEdge);
+ nextNode.getEdgeList(EDGETYPE.FR).add(tempEdge);
}
if (curKmerDir == KmerDir.REVERSE && nextKmerDir == KmerDir.FORWARD) {
tempEdge.setAsCopy(nextForwardKmer, readIdList);
- curNode.getEdgeList(DirectionFlag.DIR_RF).add(tempEdge);
+ curNode.getEdgeList(EDGETYPE.RF).add(tempEdge);
tempEdge.setAsCopy(curReverseKmer, readIdList);
- nextNode.getEdgeList(DirectionFlag.DIR_RF).add(tempEdge);
+ nextNode.getEdgeList(EDGETYPE.RF).add(tempEdge);
}
if (curKmerDir == KmerDir.REVERSE && nextKmerDir == KmerDir.REVERSE) {
tempEdge.setAsCopy(nextReverseKmer, readIdList);
- curNode.getEdgeList(DirectionFlag.DIR_RR).add(tempEdge);
+ curNode.getEdgeList(EDGETYPE.RR).add(tempEdge);
tempEdge.setAsCopy(curReverseKmer, readIdList);
- nextNode.getEdgeList(DirectionFlag.DIR_FF).add(tempEdge);
+ nextNode.getEdgeList(EDGETYPE.FF).add(tempEdge);
}
}
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/graph/dataflow/aggregators/AggregateKmerAggregateFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/graph/dataflow/aggregators/AggregateKmerAggregateFactory.java
index a74f3b8..3825d48 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/graph/dataflow/aggregators/AggregateKmerAggregateFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/graph/dataflow/aggregators/AggregateKmerAggregateFactory.java
@@ -17,12 +17,13 @@
import java.io.DataOutput;
import java.io.IOException;
+import java.util.EnumSet;
import java.util.Iterator;
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.NodeWritable.DirectionFlag;
+import edu.uci.ics.genomix.type.NodeWritable.EDGETYPE;
import edu.uci.ics.hyracks.api.comm.IFrameTupleAccessor;
import edu.uci.ics.hyracks.api.context.IHyracksTaskContext;
import edu.uci.ics.hyracks.api.dataflow.value.RecordDescriptor;
@@ -98,8 +99,8 @@
// localUniNode.foundMe = true;
// }
// }
- for (byte d: DirectionFlag.values) {
- localUniNode.getEdgeList(d).unionUpdate((readNode.getEdgeList(d)));
+ for (EDGETYPE e : EnumSet.allOf(EDGETYPE.class)) {
+ localUniNode.getEdgeList(e).unionUpdate((readNode.getEdgeList(e)));
}
localUniNode.getStartReads().appendList(readNode.getStartReads());
localUniNode.getEndReads().appendList(readNode.getEndReads());
@@ -115,8 +116,8 @@
// readKmer.setAsCopy(accessor.getBuffer().array(), getOffSet(accessor, tIndex, 0));
readNode.setAsReference(accessor.getBuffer().array(), getOffSet(accessor, tIndex, 1));
- for (byte d: DirectionFlag.values) {
- localUniNode.getEdgeList(d).unionUpdate(readNode.getEdgeList(d));
+ for (EDGETYPE e : EnumSet.allOf(EDGETYPE.class)) {
+ localUniNode.getEdgeList(e).unionUpdate(readNode.getEdgeList(e));
}
localUniNode.getStartReads().appendList(readNode.getStartReads());
localUniNode.getEndReads().appendList(readNode.getEndReads());
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/graph/dataflow/aggregators/MergeKmerAggregateFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/graph/dataflow/aggregators/MergeKmerAggregateFactory.java
index a3a7e1a..8abe8d8 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/graph/dataflow/aggregators/MergeKmerAggregateFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/graph/dataflow/aggregators/MergeKmerAggregateFactory.java
@@ -17,6 +17,7 @@
import java.io.DataOutput;
import java.io.IOException;
+import java.util.EnumSet;
import java.util.logging.Logger;
import org.apache.commons.logging.Log;
@@ -24,7 +25,7 @@
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.NodeWritable.DirectionFlag;
+import edu.uci.ics.genomix.type.NodeWritable.EDGETYPE;
import edu.uci.ics.hyracks.api.comm.IFrameTupleAccessor;
import edu.uci.ics.hyracks.api.context.IHyracksTaskContext;
import edu.uci.ics.hyracks.api.dataflow.value.RecordDescriptor;
@@ -85,8 +86,8 @@
// }
// }
- for (byte d : DirectionFlag.values) {
- localUniNode.getEdgeList(d).unionUpdate(readNode.getEdgeList(d));
+ for (EDGETYPE e : EnumSet.allOf(EDGETYPE.class)) {
+ localUniNode.getEdgeList(e).unionUpdate(readNode.getEdgeList(e));
}
localUniNode.getStartReads().unionUpdate(readNode.getStartReads());
localUniNode.getEndReads().unionUpdate(readNode.getEndReads());
@@ -124,8 +125,8 @@
// }
// }
- for (byte d : DirectionFlag.values) {
- localUniNode.getEdgeList(d).unionUpdate(readNode.getEdgeList(d));
+ for (EDGETYPE e : EnumSet.allOf(EDGETYPE.class)) {
+ localUniNode.getEdgeList(e).unionUpdate(readNode.getEdgeList(e));
}
localUniNode.getStartReads().unionUpdate(readNode.getStartReads());
localUniNode.getEndReads().unionUpdate(readNode.getEndReads());
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/graph/util/GenerateGraphViz.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/graph/util/GenerateGraphViz.java
index b90e30f..ff7f7fa 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/graph/util/GenerateGraphViz.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/graph/util/GenerateGraphViz.java
@@ -12,8 +12,8 @@
import edu.uci.ics.genomix.type.EdgeWritable;
import edu.uci.ics.genomix.type.NodeWritable;
+import edu.uci.ics.genomix.type.NodeWritable.EDGETYPE;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
-import edu.uci.ics.genomix.type.NodeWritable.DirectionFlag;
public class GenerateGraphViz {
@@ -74,25 +74,25 @@
public static String convertEdgeToGraph(String outputNode, NodeWritable value) {
String outputEdge = "";
Iterator<EdgeWritable> edgeIterator;
- edgeIterator = value.getEdgeList(DirectionFlag.DIR_FF).iterator();
+ edgeIterator = value.getEdgeList(EDGETYPE.FF).iterator();
while(edgeIterator.hasNext()){
EdgeWritable edge = edgeIterator.next();
outputEdge += outputNode + " -> " + edge.getKey().toString() + "[color = \"black\" label =\"FF: " +
edge.printReadIdSet() + "\"]\n";
}
- edgeIterator = value.getEdgeList(DirectionFlag.DIR_FR).iterator();
+ edgeIterator = value.getEdgeList(EDGETYPE.FR).iterator();
while(edgeIterator.hasNext()){
EdgeWritable edge = edgeIterator.next();
outputEdge += outputNode + " -> " + edge.getKey().toString() + "[color = \"blue\" label =\"FR: " +
edge.printReadIdSet() + "\"]\n";
}
- edgeIterator = value.getEdgeList(DirectionFlag.DIR_RF).iterator();
+ edgeIterator = value.getEdgeList(EDGETYPE.RF).iterator();
while(edgeIterator.hasNext()){
EdgeWritable edge = edgeIterator.next();
outputEdge += outputNode + " -> " + edge.getKey().toString() + "[color = \"green\" label =\"RF: " +
edge.printReadIdSet() + "\"]\n";
}
- edgeIterator = value.getEdgeList(DirectionFlag.DIR_RR).iterator();
+ edgeIterator = value.getEdgeList(EDGETYPE.RR).iterator();
while(edgeIterator.hasNext()){
EdgeWritable edge = edgeIterator.next();
outputEdge += outputNode + " -> " + edge.getKey().toString() + "[color = \"red\" label =\"RR: " +
diff --git a/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hadoop/graph/test/GenerateGraphViz.java b/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hadoop/graph/test/GenerateGraphViz.java
index 43bb8ff..85c0ec6 100644
--- a/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hadoop/graph/test/GenerateGraphViz.java
+++ b/genomix/genomix-hyracks/src/test/java/edu/uci/ics/genomix/hadoop/graph/test/GenerateGraphViz.java
@@ -13,7 +13,7 @@
import edu.uci.ics.genomix.type.EdgeWritable;
import edu.uci.ics.genomix.type.NodeWritable;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
-import edu.uci.ics.genomix.type.NodeWritable.DirectionFlag;
+import edu.uci.ics.genomix.type.NodeWritable.EDGETYPE;
public class GenerateGraphViz {
@@ -74,25 +74,25 @@
public static String convertEdgeToGraph(String outputNode, NodeWritable value) {
String outputEdge = "";
Iterator<EdgeWritable> edgeIterator;
- edgeIterator = value.getEdgeList(DirectionFlag.DIR_FF).iterator();
+ edgeIterator = value.getEdgeList(EDGETYPE.FF).iterator();
while(edgeIterator.hasNext()){
EdgeWritable edge = edgeIterator.next();
outputEdge += outputNode + " -> " + edge.getKey().toString() + "[color = \"black\" label =\"FF: " +
edge.printReadIdSet() + "\"]\n";
}
- edgeIterator = value.getEdgeList(DirectionFlag.DIR_FR).iterator();
+ edgeIterator = value.getEdgeList(EDGETYPE.FR).iterator();
while(edgeIterator.hasNext()){
EdgeWritable edge = edgeIterator.next();
outputEdge += outputNode + " -> " + edge.getKey().toString() + "[color = \"blue\" label =\"FR: " +
edge.printReadIdSet() + "\"]\n";
}
- edgeIterator = value.getEdgeList(DirectionFlag.DIR_RF).iterator();
+ edgeIterator = value.getEdgeList(EDGETYPE.RF).iterator();
while(edgeIterator.hasNext()){
EdgeWritable edge = edgeIterator.next();
outputEdge += outputNode + " -> " + edge.getKey().toString() + "[color = \"green\" label =\"RF: " +
edge.printReadIdSet() + "\"]\n";
}
- edgeIterator = value.getEdgeList(DirectionFlag.DIR_RR).iterator();
+ edgeIterator = value.getEdgeList(EDGETYPE.RR).iterator();
while(edgeIterator.hasNext()){
EdgeWritable edge = edgeIterator.next();
outputEdge += outputNode + " -> " + edge.getKey().toString() + "[color = \"red\" label =\"RR: " +
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%
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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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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
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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 @@
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+ "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
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+</g>
+<!-- AGA->GAA -->
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+</g>
+<!-- AGA->CTA -->
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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
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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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-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/checker/SymmetryCheckerVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/checker/SymmetryCheckerVertex.java
index 1d86859..5b3f9c4 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/checker/SymmetryCheckerVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/checker/SymmetryCheckerVertex.java
@@ -7,8 +7,8 @@
import edu.uci.ics.genomix.pregelix.io.message.MessageWritable;
import edu.uci.ics.genomix.pregelix.operator.BasicGraphCleanVertex;
import edu.uci.ics.genomix.pregelix.operator.aggregator.StatisticsAggregator;
-import edu.uci.ics.genomix.pregelix.type.MessageFlag;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
+import edu.uci.ics.genomix.type.NodeWritable.EDGETYPE;
public class SymmetryCheckerVertex extends
BasicGraphCleanVertex<VertexValueWritable, MessageWritable> {
@@ -43,8 +43,8 @@
//check if the corresponding edge exists
while(msgIterator.hasNext()){
incomingMsg = msgIterator.next();
- byte meToNeighborDir = (byte) (incomingMsg.getFlag() & MessageFlag.DIR_MASK);
- byte neighborToMeDir = mirrorDirection(meToNeighborDir);
+ EDGETYPE meToNeighborDir = EDGETYPE.fromByte(incomingMsg.getFlag());
+ EDGETYPE neighborToMeDir = meToNeighborDir.mirror();
boolean exist = getVertexValue().getEdgeList(neighborToMeDir).contains(incomingMsg.getSourceVertexId());
if(!exist){
getVertexValue().setState(State.IS_ERROR);
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/graph/GenerateGraphViz.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/graph/GenerateGraphViz.java
index 2593c34..b440dc4 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/graph/GenerateGraphViz.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/graph/GenerateGraphViz.java
@@ -13,8 +13,8 @@
import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
import edu.uci.ics.genomix.type.EdgeWritable;
import edu.uci.ics.genomix.type.NodeWritable;
+import edu.uci.ics.genomix.type.NodeWritable.EDGETYPE;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
-import edu.uci.ics.genomix.type.NodeWritable.DirectionFlag;
public class GenerateGraphViz {
@@ -132,25 +132,25 @@
public static String convertEdgeToGraph(String outputNode, NodeWritable value){
String outputEdge = "";
Iterator<EdgeWritable> edgeIterator;
- edgeIterator = value.getEdgeList(DirectionFlag.DIR_FF).iterator();
+ edgeIterator = value.getEdgeList(EDGETYPE.FF).iterator();
while(edgeIterator.hasNext()){
EdgeWritable edge = edgeIterator.next();
outputEdge += outputNode + " -> " + edge.getKey().toString() + "[color = \"black\" label =\"FF: " +
edge.printReadIdSet() + "\"]\n";
}
- edgeIterator = value.getEdgeList(DirectionFlag.DIR_FR).iterator();
+ edgeIterator = value.getEdgeList(EDGETYPE.FR).iterator();
while(edgeIterator.hasNext()){
EdgeWritable edge = edgeIterator.next();
outputEdge += outputNode + " -> " + edge.getKey().toString() + "[color = \"blue\" label =\"FR: " +
edge.printReadIdSet() + "\"]\n";
}
- edgeIterator = value.getEdgeList(DirectionFlag.DIR_RF).iterator();
+ edgeIterator = value.getEdgeList(EDGETYPE.RF).iterator();
while(edgeIterator.hasNext()){
EdgeWritable edge = edgeIterator.next();
outputEdge += outputNode + " -> " + edge.getKey().toString() + "[color = \"green\" label =\"RF: " +
edge.printReadIdSet() + "\"]\n";
}
- edgeIterator = value.getEdgeList(DirectionFlag.DIR_RR).iterator();
+ edgeIterator = value.getEdgeList(EDGETYPE.RR).iterator();
while(edgeIterator.hasNext()){
EdgeWritable edge = edgeIterator.next();
outputEdge += outputNode + " -> " + edge.getKey().toString() + "[color = \"red\" label =\"RR: " +
@@ -171,25 +171,25 @@
public static String convertEdgeToGraph(String outputNode, VertexValueWritable value){
String outputEdge = "";
Iterator<EdgeWritable> edgeIterator;
- edgeIterator = value.getEdgeList(DirectionFlag.DIR_FF).iterator();
+ edgeIterator = value.getEdgeList(EDGETYPE.FF).iterator();
while(edgeIterator.hasNext()){
EdgeWritable edge = edgeIterator.next();
outputEdge += outputNode + " -> " + edge.getKey().toString() + "[color = \"black\" label =\"FF: " +
edge.printReadIdSet() + "\"]\n";
}
- edgeIterator = value.getEdgeList(DirectionFlag.DIR_FR).iterator();
+ edgeIterator = value.getEdgeList(EDGETYPE.FR).iterator();
while(edgeIterator.hasNext()){
EdgeWritable edge = edgeIterator.next();
outputEdge += outputNode + " -> " + edge.getKey().toString() + "[color = \"blue\" label =\"FR: " +
edge.printReadIdSet() + "\"]\n";
}
- edgeIterator = value.getEdgeList(DirectionFlag.DIR_RF).iterator();
+ edgeIterator = value.getEdgeList(EDGETYPE.RF).iterator();
while(edgeIterator.hasNext()){
EdgeWritable edge = edgeIterator.next();
outputEdge += outputNode + " -> " + edge.getKey().toString() + "[color = \"green\" label =\"RF: " +
edge.printReadIdSet() + "\"]\n";
}
- edgeIterator = value.getEdgeList(DirectionFlag.DIR_RR).iterator();
+ edgeIterator = value.getEdgeList(EDGETYPE.RR).iterator();
while(edgeIterator.hasNext()){
EdgeWritable edge = edgeIterator.next();
outputEdge += outputNode + " -> " + edge.getKey().toString() + "[color = \"red\" label =\"RR: " +
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 c9de567..3c7b409 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
@@ -6,7 +6,6 @@
import edu.uci.ics.genomix.pregelix.io.common.ByteWritable;
import edu.uci.ics.genomix.pregelix.io.common.HashMapWritable;
import edu.uci.ics.genomix.pregelix.io.common.VLongWritable;
-import edu.uci.ics.genomix.pregelix.type.MessageFlag;
import edu.uci.ics.genomix.type.EdgeListWritable;
import edu.uci.ics.genomix.type.EdgeWritable;
import edu.uci.ics.genomix.type.KmerBytesWritable;
@@ -75,6 +74,15 @@
public static final short FAKEFLAG_MASK = 1 << 7;
}
+ public static class P4State {
+ // 2 bits for DirectionFlag, then 2 bits for set of DIR's
+ // each merge has an edge-type direction (e.g., FF)
+ public static final byte NO_MERGE = 0b0 << 4;
+ public static final byte MERGE = 0b1 << 4;
+ public static final byte MERGE_CLEAR = 0b1101100; // clear the MERGE/NO_MERGE and the MERGE_DIRECTION
+ public static final byte MERGE_MASK = 0b0010011;
+ }
+
private short state;
private boolean isFakeVertex;
private HashMapWritable<ByteWritable, VLongWritable> counters;
@@ -104,35 +112,35 @@
}
public EdgeListWritable getFFList() {
- return getEdgeList(DirectionFlag.DIR_FF);
+ return getEdgeList(EDGETYPE.FF);
}
public EdgeListWritable getFRList() {
- return getEdgeList(DirectionFlag.DIR_FR);
+ return getEdgeList(EDGETYPE.FR);
}
public EdgeListWritable getRFList() {
- return getEdgeList(DirectionFlag.DIR_RF);
+ return getEdgeList(EDGETYPE.RF);
}
public EdgeListWritable getRRList() {
- return getEdgeList(DirectionFlag.DIR_RR);
+ return getEdgeList(EDGETYPE.RR);
}
public void setFFList(EdgeListWritable forwardForwardList){
- setEdgeList(DirectionFlag.DIR_FF, forwardForwardList);
+ setEdgeList(EDGETYPE.FF, forwardForwardList);
}
public void setFRList(EdgeListWritable forwardReverseList){
- setEdgeList(DirectionFlag.DIR_FR, forwardReverseList);
+ setEdgeList(EDGETYPE.FR, forwardReverseList);
}
public void setRFList(EdgeListWritable reverseForwardList){
- setEdgeList(DirectionFlag.DIR_RF, reverseForwardList);
+ setEdgeList(EDGETYPE.RF, reverseForwardList);
}
public void setRRList(EdgeListWritable reverseReverseList){
- setEdgeList(DirectionFlag.DIR_RR, reverseReverseList);
+ setEdgeList(EDGETYPE.RR, reverseReverseList);
}
public AdjacencyListWritable getIncomingList() {
@@ -238,42 +246,23 @@
/**
* Delete the corresponding edge
*/
- public void processDelete(byte neighborToDeleteDir, EdgeWritable nodeToDelete){
- byte dir = (byte)(neighborToDeleteDir & MessageFlag.DIR_MASK);
- this.getEdgeList(dir).remove(nodeToDelete);
+ public void processDelete(EDGETYPE neighborToDeleteEdgetype, EdgeWritable nodeToDelete){
+ this.getEdgeList(neighborToDeleteEdgetype).remove(nodeToDelete);
}
- public void processFinalUpdates(byte deleteDir, byte updateDir, NodeWritable other){
- byte replaceDir = mirrorDirection(deleteDir);
+ public void processFinalUpdates(EDGETYPE deleteDir, EDGETYPE updateDir, NodeWritable other){
+ EDGETYPE replaceDir = deleteDir.mirror();
this.getNode().updateEdges(deleteDir, null, updateDir, replaceDir, other, false);
}
/**
* Process any changes to value. This is for merging. nodeToAdd should be only edge
*/
- public void processMerges(byte mergeDir, NodeWritable node, int kmerSize){
+ public void processMerges(EDGETYPE mergeDir, NodeWritable node, int kmerSize){
KmerBytesWritable.setGlobalKmerLength(kmerSize); // TODO Do this once at the init of your function, then you don't need it as a parameter here
super.getNode().mergeWithNode(mergeDir, node);
}
- /**
- * 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);
- }
- }
-
@Override
public String toString() {
return super.toString() + "\t" + State.getContent(state);
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/message/BubbleMergeMessageWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/message/BubbleMergeMessageWritable.java
index fef5c15..59108d4 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/message/BubbleMergeMessageWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/message/BubbleMergeMessageWritable.java
@@ -8,6 +8,7 @@
import edu.uci.ics.genomix.pregelix.type.MessageFlag;
import edu.uci.ics.genomix.type.NodeWritable;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
+import edu.uci.ics.genomix.type.NodeWritable.EDGETYPE;
public class BubbleMergeMessageWritable extends MessageWritable{
@@ -19,8 +20,8 @@
private VKmerBytesWritable majorVertexId; //use for MergeBubble
private VKmerBytesWritable minorVertexId;
private NodeWritable node; //except kmer, other field should be updated when MergeBubble
- private byte meToMajorDir;
- private byte meToMinorDir;
+ private byte meToMajorEdgetype;
+ private byte meToMinorEdgetype;
private VKmerBytesWritable topCoverageVertexId;
private boolean isFlip;
@@ -29,8 +30,8 @@
majorVertexId = new VKmerBytesWritable();
minorVertexId = new VKmerBytesWritable();
node = new NodeWritable();
- meToMajorDir = 0;
- meToMinorDir = 0;
+ meToMajorEdgetype = 0;
+ meToMinorEdgetype = 0;
topCoverageVertexId = new VKmerBytesWritable();
isFlip = false;
}
@@ -45,8 +46,8 @@
this.setMajorVertexId(msg.getMajorVertexId());
this.setMinorVertexId(msg.getMinorVertexId());
this.setNode(msg.node);
- this.setMeToMajorDir(msg.meToMajorDir);
- this.setMeToMinorDir(msg.meToMinorDir);
+ this.setMeToMajorEdgetype(msg.meToMajorEdgetype);
+ this.setMeToMinorEdgetype(msg.meToMinorEdgetype);
this.setTopCoverageVertexId(msg.topCoverageVertexId);
this.setFlip(msg.isFlip());
}
@@ -56,19 +57,20 @@
majorVertexId.reset(0);
minorVertexId.reset(0);
node.reset();
- meToMajorDir = 0;
- meToMinorDir = 0;
+ meToMajorEdgetype = 0;
+ meToMinorEdgetype = 0;
topCoverageVertexId.reset(0);
isFlip = false;
}
public byte getRelativeDirToMajor(){
- switch(meToMajorDir){
- case MessageFlag.DIR_FF:
- case MessageFlag.DIR_RR:
+ EDGETYPE et = EDGETYPE.fromByte(meToMajorEdgetype);
+ switch(et){
+ case FF:
+ case RR:
return DirToMajor.FORWARD;
- case MessageFlag.DIR_FR:
- case MessageFlag.DIR_RF:
+ case FR:
+ case RF:
return DirToMajor.REVERSE;
}
return 0;
@@ -115,22 +117,22 @@
this.node.setAsCopy(node);
}
- public byte getMeToMajorDir() {
- return meToMajorDir;
+ public byte getMeToMajorEdgetype() {
+ return meToMajorEdgetype;
}
- public void setMeToMajorDir(byte meToMajorDir) {
- this.meToMajorDir = meToMajorDir;
+ public void setMeToMajorEdgetype(byte meToMajorEdgetype) {
+ this.meToMajorEdgetype = meToMajorEdgetype;
}
- public byte getMeToMinorDir() {
- return meToMinorDir;
+ public byte getMeToMinorEdgetype() {
+ return meToMinorEdgetype;
}
- public void setMeToMinorDir(byte meToMinorDir) {
- this.meToMinorDir = meToMinorDir;
+ public void setMeToMinorEdgetype(byte meToMinorEdgetype) {
+ this.meToMinorEdgetype = meToMinorEdgetype;
}
-
+
public boolean isFlip() {
return isFlip;
}
@@ -146,8 +148,8 @@
majorVertexId.readFields(in);
minorVertexId.readFields(in);
node.readFields(in);
- meToMajorDir = in.readByte();
- meToMinorDir = in.readByte();
+ meToMajorEdgetype = in.readByte();
+ meToMinorEdgetype = in.readByte();
topCoverageVertexId.readFields(in);
isFlip = in.readBoolean();
}
@@ -158,8 +160,8 @@
majorVertexId.write(out);
minorVertexId.write(out);
node.write(out);
- out.writeByte(meToMajorDir);
- out.write(meToMinorDir);
+ out.writeByte(meToMajorEdgetype);
+ out.write(meToMinorEdgetype);
topCoverageVertexId.write(out);
out.writeBoolean(isFlip);
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/message/PathMergeMessageWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/message/PathMergeMessageWritable.java
index 07ededf..a1a2e1f 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/message/PathMergeMessageWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/message/PathMergeMessageWritable.java
@@ -3,13 +3,14 @@
import java.io.DataInput;
import java.io.DataOutput;
import java.io.IOException;
+import java.util.EnumSet;
import edu.uci.ics.genomix.type.EdgeListWritable;
import edu.uci.ics.genomix.type.EdgeWritable;
import edu.uci.ics.genomix.type.NodeWritable;
+import edu.uci.ics.genomix.type.NodeWritable.EDGETYPE;
import edu.uci.ics.genomix.type.PositionListWritable;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
-import edu.uci.ics.genomix.type.NodeWritable.DirectionFlag;
public class PathMergeMessageWritable extends MessageWritable{
@@ -46,20 +47,20 @@
this.node.setInternalKmer(internalKmer);
}
- public EdgeListWritable getEdgeList(byte dir) {
- return node.getEdgeList((byte) (dir & DirectionFlag.DIR_MASK));
+ public EdgeListWritable getEdgeList(EDGETYPE edgeType) {
+ return node.getEdgeList(edgeType);
}
public EdgeWritable getNeighborEdge(){
- for(byte d : DirectionFlag.values){
- if(!getEdgeList(d).isEmpty())
- return getEdgeList(d).get(0);
+ for(EDGETYPE e : EnumSet.allOf(EDGETYPE.class)){
+ if(!getEdgeList(e).isEmpty())
+ return getEdgeList(e).get(0);
}
return null;
}
- public void setEdgeList(byte dir, EdgeListWritable edgeList) {
- this.node.setEdgeList((byte) (dir & DirectionFlag.DIR_MASK), edgeList);
+ public void setEdgeList(EDGETYPE edgeType, EdgeListWritable edgeList) {
+ this.node.setEdgeList(edgeType, edgeList);
}
public PositionListWritable getStartReads() {
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 17cf4bc..373fdde 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
@@ -1,6 +1,7 @@
package edu.uci.ics.genomix.pregelix.operator;
import java.io.IOException;
+import java.util.EnumSet;
import java.util.Iterator;
import java.util.Random;
import java.util.logging.Logger;
@@ -16,6 +17,7 @@
import edu.uci.ics.genomix.pregelix.format.GraphCleanOutputFormat;
import edu.uci.ics.genomix.config.GenomixJobConf;
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.common.ByteWritable;
import edu.uci.ics.genomix.pregelix.io.common.HashMapWritable;
@@ -25,12 +27,10 @@
import edu.uci.ics.genomix.pregelix.type.MessageFlag;
import edu.uci.ics.genomix.pregelix.util.VertexUtil;
import edu.uci.ics.genomix.type.NodeWritable.DIR;
-import edu.uci.ics.genomix.type.NodeWritable.OutgoingListFlag;
+import edu.uci.ics.genomix.type.NodeWritable.EDGETYPE;
import edu.uci.ics.genomix.type.EdgeListWritable;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
import edu.uci.ics.genomix.type.VKmerListWritable;
-import edu.uci.ics.genomix.type.NodeWritable.DirectionFlag;
-import edu.uci.ics.genomix.type.NodeWritable.IncomingListFlag;
public abstract class BasicGraphCleanVertex<V extends VertexValueWritable, M extends MessageWritable> extends
Vertex<VKmerBytesWritable, V, NullWritable, M> {
@@ -45,11 +45,11 @@
public static boolean fakeVertexExist = false;
public static VKmerBytesWritable fakeVertex = null;
- public byte[][] connectedTable = new byte[][]{
- {MessageFlag.DIR_RF, MessageFlag.DIR_FF},
- {MessageFlag.DIR_RF, MessageFlag.DIR_FR},
- {MessageFlag.DIR_RR, MessageFlag.DIR_FF},
- {MessageFlag.DIR_RR, MessageFlag.DIR_FR}
+ public EDGETYPE[][] connectedTable = new EDGETYPE[][]{
+ {EDGETYPE.RF, EDGETYPE.FF},
+ {EDGETYPE.RF, EDGETYPE.FR},
+ {EDGETYPE.RR, EDGETYPE.FF},
+ {EDGETYPE.RR, EDGETYPE.FR}
};
protected M incomingMsg = null;
@@ -60,7 +60,7 @@
protected Iterator<VKmerBytesWritable> kmerIterator;
protected VKmerListWritable kmerList = null;
protected VKmerBytesWritable repeatKmer = null; //for detect tandemRepeat
- protected byte repeatDir; //for detect tandemRepeat
+ protected EDGETYPE repeatEdgetype; //for detect tandemRepeat
protected VKmerBytesWritable tmpKmer = null;
protected short outFlag;
protected short inFlag;
@@ -68,8 +68,8 @@
protected EdgeListWritable incomingEdgeList = null; //SplitRepeat and BubbleMerge
protected EdgeListWritable outgoingEdgeList = null; //SplitRepeat and BubbleMerge
- protected byte incomingEdgeDir = 0; //SplitRepeat and BubbleMerge
- protected byte outgoingEdgeDir = 0; //SplitRepeat and BubbleMerge
+ protected EDGETYPE incomingEdgeType; //SplitRepeat and BubbleMerge
+ protected EDGETYPE outgoingEdgeType; //SplitRepeat and BubbleMerge
protected HashMapWritable<ByteWritable, VLongWritable> counters = new HashMapWritable<ByteWritable, VLongWritable>();
/**
@@ -118,22 +118,22 @@
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_CAN_MERGEWITHPREV;
- break;
- case MessageFlag.DIR_RF:
- case MessageFlag.DIR_RR:
- flagAndMergeDir |= MessageFlag.HEAD_CAN_MERGEWITHNEXT;
- break;
- }
- 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_CAN_MERGEWITHPREV;
+// break;
+// case MessageFlag.DIR_RF:
+// case MessageFlag.DIR_RR:
+// flagAndMergeDir |= MessageFlag.HEAD_CAN_MERGEWITHNEXT;
+// break;
+// }
+// return flagAndMergeDir;
+// }
/**
* set head state
@@ -191,35 +191,6 @@
return selfFlag != State.IS_HEAD && selfFlag != State.IS_OLDHEAD;
}
- public byte[] getDirList(DIR direction){
- byte[] values = new byte[2];
- if(direction == DIR.PREVIOUS)
- values = IncomingListFlag.values;
- else if(direction == DIR.NEXT)
- values = OutgoingListFlag.values;
- else
- throw new IllegalArgumentException("DIR should only have two options: PREVIOUS or NEXT!");
- return values;
- }
-
- /**
- * 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){
- byte[] dirs = (direction == DIR.PREVIOUS ? IncomingListFlag.values : OutgoingListFlag.values);
- for(byte dir : dirs){
- if(getVertexValue().getEdgeList(dir).getCountOfPosition() > 0)
- return getVertexValue().getEdgeList(dir).get(0).getKey();
- }
- }
- return null;
- }
-
/**
* get destination vertex
*/
@@ -293,12 +264,12 @@
*/
public void sendSettledMsgs(DIR direction, VertexValueWritable value){
//TODO THE less context you send, the better (send simple messages)
- byte dirs[] = direction == DIR.PREVIOUS ? IncomingListFlag.values : OutgoingListFlag.values;
- for(byte dir : dirs){
- kmerIterator = value.getEdgeList(dir).getKeyIterator();
+ EnumSet<EDGETYPE> edgeTypes = (direction == DIR.PREVIOUS ? EDGETYPE.INCOMING : EDGETYPE.OUTGOING);
+ for(EDGETYPE e : edgeTypes){
+ kmerIterator = value.getEdgeList(e).getKeyIterator();
while(kmerIterator.hasNext()){
outFlag &= MessageFlag.DIR_CLEAR;
- outFlag |= dir;
+ outFlag |= e.get();
outgoingMsg.setFlag(outFlag);
outgoingMsg.setSourceVertexId(getVertexId());
destVertexId.setAsCopy(kmerIterator.next());
@@ -317,19 +288,19 @@
*/
public void headSendSettledMsgs(DIR direction, VertexValueWritable value){
//TODO THE less context you send, the better (send simple messages)
- byte dirs[] = direction == DIR.PREVIOUS ? IncomingListFlag.values : OutgoingListFlag.values;
- for(byte dir : dirs){
- kmerIterator = value.getEdgeList(dir).getKeyIterator();
+ EnumSet<EDGETYPE> edgeTypes = (direction == DIR.PREVIOUS ? EDGETYPE.INCOMING : EDGETYPE.OUTGOING);
+ for(EDGETYPE e : edgeTypes){
+ kmerIterator = value.getEdgeList(e).getKeyIterator();
while(kmerIterator.hasNext()){
outFlag &= MessageFlag.HEAD_CAN_MERGE_CLEAR;
- byte meToNeighborDir = mirrorDirection(dir);
- switch(meToNeighborDir){
- case MessageFlag.DIR_FF:
- case MessageFlag.DIR_FR:
+ EDGETYPE meToNeighborEdgeType = e.mirror();
+ switch(meToNeighborEdgeType){
+ case FF:
+ case FR:
outFlag |= MessageFlag.HEAD_CAN_MERGEWITHPREV;
break;
- case MessageFlag.DIR_RF:
- case MessageFlag.DIR_RR:
+ case RF:
+ case RR:
outFlag |= MessageFlag.HEAD_CAN_MERGEWITHNEXT;
break;
}
@@ -348,30 +319,31 @@
/**
* get a copy of the original Kmer without TandemRepeat
+ * @param destVertex
*/
- public void getCopyWithoutTandemRepeats(V vertexValue){
- tmpValue.setAsCopy(vertexValue);
- tmpValue.getEdgeList(repeatDir).remove(repeatKmer);
- while(isTandemRepeat(tmpValue))
- tmpValue.getEdgeList(repeatDir).remove(repeatKmer);
+ public void copyWithoutTandemRepeats(V srcVertex, VertexValueWritable destVertex){
+ destVertex.setAsCopy(srcVertex);
+ destVertex.getEdgeList(repeatEdgetype).remove(repeatKmer);
+ while(isTandemRepeat(destVertex))
+ destVertex.getEdgeList(repeatEdgetype).remove(repeatKmer);
}
- /**
- * check if it is valid path
- */
- public boolean isValidPath(){
- byte meToNeighborDir = (byte) (incomingMsg.getFlag() & MessageFlag.DIR_MASK);
- byte neighborToMeDir = mirrorDirection(meToNeighborDir);
- switch(neighborToMeDir){
- case MessageFlag.DIR_FF:
- case MessageFlag.DIR_FR:
- return getVertexValue().inDegree() == 1;
- case MessageFlag.DIR_RF:
- case MessageFlag.DIR_RR:
- return getVertexValue().outDegree() == 1;
- }
- return true;
- }
+// /**
+// * check if it is valid path
+// */
+// public boolean isValidPath(){
+// byte meToNeighborDir = (byte) (incomingMsg.getFlag() & MessageFlag.DIR_MASK);
+// byte neighborToMeDir = mirrorDirection(meToNeighborDir);
+// switch(neighborToMeDir){
+// case MessageFlag.DIR_FF:
+// case MessageFlag.DIR_FR:
+// return getVertexValue().inDegree() == 1;
+// case MessageFlag.DIR_RF:
+// case MessageFlag.DIR_RR:
+// return getVertexValue().outDegree() == 1;
+// }
+// return true;
+// }
/**
* check if A need to be filpped with neighbor
@@ -430,14 +402,11 @@
public void setNeighborToMeDir(DIR direction){
if(getVertexValue().getDegree(direction) != 1)
throw new IllegalArgumentException("In merge dir, the degree is not 1");
- byte[] dirs = direction == DIR.PREVIOUS ? IncomingListFlag.values : OutgoingListFlag.values;
+ EnumSet<EDGETYPE> edgeTypes = direction == DIR.PREVIOUS ? EDGETYPE.INCOMING : EDGETYPE.OUTGOING;
outFlag &= MessageFlag.DIR_CLEAR;
- if(getVertexValue().getEdgeList(dirs[0]).getCountOfPosition() == 1){
- outFlag |= dirs[0];
- } else if(getVertexValue().getEdgeList(dirs[1]).getCountOfPosition() == 1){
- outFlag |= dirs[1];
- }
+ for (EDGETYPE et : edgeTypes)
+ outFlag |= et.get();
}
/**
@@ -452,9 +421,20 @@
}
/**
+ * set state as no_merge
+ */
+ public void setMerge(byte mergeState){
+ short state = getVertexValue().getState();
+ state &= P4State.MERGE_CLEAR;
+ state |= (mergeState & P4State.MERGE_MASK);
+ getVertexValue().setState(state);
+ activate();
+ }
+
+ /**
* Returns the edge dir for B->A when the A->B edge is type @dir
*/
- public byte mirrorDirection(byte dir) {
+ public byte meToNeighborDir(byte dir) {
switch (dir) {
case MessageFlag.DIR_FF:
return MessageFlag.DIR_RR;
@@ -518,8 +498,8 @@
* do some remove operations on adjMap after receiving the info about dead Vertex
*/
public void responseToDeadVertex(){
- byte meToNeighborDir = (byte) (incomingMsg.getFlag() & MessageFlag.DIR_MASK);
- byte neighborToMeDir = mirrorDirection(meToNeighborDir);
+ EDGETYPE meToNeighborDir = EDGETYPE.fromByte(incomingMsg.getFlag());
+ EDGETYPE neighborToMeDir = meToNeighborDir.mirror();
getVertexValue().getEdgeList(neighborToMeDir).remove(incomingMsg.getSourceVertexId());
}
@@ -566,35 +546,18 @@
return ((byte)getVertexValue().getState() & State.FAKEFLAG_MASK) > 0;
}
- public boolean isTandemRepeat(VertexValueWritable value){
- VKmerBytesWritable kmerToCheck;
- for(byte d : DirectionFlag.values){
- Iterator<VKmerBytesWritable> it = value.getEdgeList(d).getKeyIterator();
- while(it.hasNext()){
- kmerToCheck = it.next();
- if(kmerToCheck.equals(getVertexId())){
- repeatDir = d;
- repeatKmer.setAsCopy(kmerToCheck);
- return true;
- }
+ /**
+ * Look inside of vertex for the given edge, returning the direction we found it in (or null)
+ */
+ public static EDGETYPE findEdge(VKmerBytesWritable id, VertexValueWritable vertex){
+ // TODO move into Node?
+ for(EDGETYPE e : EnumSet.allOf(EDGETYPE.class)){
+ for (VKmerBytesWritable curKey : vertex.getEdgeList(e).getKeys()) {
+ if(curKey.equals(id)) // points to self
+ return e;
}
}
- return false;
- }
-
- public byte flipDir(byte dir){
- switch(dir){
- case DirectionFlag.DIR_FF:
- return DirectionFlag.DIR_RF;
- case DirectionFlag.DIR_FR:
- return DirectionFlag.DIR_RR;
- case DirectionFlag.DIR_RF:
- return DirectionFlag.DIR_FF;
- case DirectionFlag.DIR_RR:
- return DirectionFlag.DIR_FR;
- default:
- throw new RuntimeException("Unrecognized direction in flipDirection: " + dir);
- }
+ return null;
}
/**
@@ -646,9 +609,9 @@
public void startSendMsgForP2() {
if(isTandemRepeat(getVertexValue())){
tmpValue.setAsCopy(getVertexValue());
- tmpValue.getEdgeList(repeatDir).remove(repeatKmer);
+ tmpValue.getEdgeList(repeatEdgetype).remove(repeatKmer);
while(isTandemRepeat(tmpValue))
- tmpValue.getEdgeList(repeatDir).remove(repeatKmer);
+ tmpValue.getEdgeList(repeatEdgetype).remove(repeatKmer);
outFlag = 0;
outFlag |= MessageFlag.IS_HEAD;
sendSettledMsgToAllNeighborNodes(tmpValue);
@@ -700,12 +663,67 @@
* use for SplitRepeatVertex and BubbleMerge
* @param i
*/
- public void setEdgeListAndEdgeDir(int i){
+ public void setEdgeListAndEdgeType(int i){
incomingEdgeList.setAsCopy(getVertexValue().getEdgeList(connectedTable[i][0]));
- incomingEdgeDir = connectedTable[i][0];
+ incomingEdgeType = connectedTable[i][0];
outgoingEdgeList.setAsCopy(getVertexValue().getEdgeList(connectedTable[i][1]));
- outgoingEdgeDir = connectedTable[i][1];
+ outgoingEdgeType = connectedTable[i][1];
}
+//2013.9.21 ------------------------------------------------------------------//
+ /**
+ * get destination vertex ex. RemoveTip
+ */
+ 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());
+ }
+
+ /**
+ * check if I am a tandemRepeat
+ */
+ public boolean isTandemRepeat(VertexValueWritable value){
+ VKmerBytesWritable kmerToCheck;
+ for(EDGETYPE et : EnumSet.allOf(EDGETYPE.class)){
+ Iterator<VKmerBytesWritable> it = value.getEdgeList(et).getKeyIterator();
+ while(it.hasNext()){
+ kmerToCheck = it.next();
+ if(kmerToCheck.equals(getVertexId())){
+ repeatEdgetype = et;
+ repeatKmer.setAsCopy(kmerToCheck);
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+
+ /**
+ * broadcastKillself ex. RemoveLow
+ */
+ public void broadcastKillself(){
+ VertexValueWritable vertex = getVertexValue();
+ for(EDGETYPE et : EnumSet.allOf(EDGETYPE.class)){
+ for(VKmerBytesWritable kmer : vertex.getEdgeList(et).getKeys()){
+ outFlag &= EDGETYPE.CLEAR;
+ outFlag |= et.mirror().get();
+ outgoingMsg.setFlag(outFlag);
+ outgoingMsg.setSourceVertexId(getVertexId());
+ destVertexId = kmer;
+ sendMsg(destVertexId, outgoingMsg);
+ }
+ }
+ }
}
\ No newline at end of file
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeAddVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeAddVertex.java
index adbc526..c740bae 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeAddVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bridgeremove/BridgeAddVertex.java
@@ -7,6 +7,7 @@
import edu.uci.ics.genomix.type.EdgeListWritable;
import edu.uci.ics.genomix.type.EdgeWritable;
import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.NodeWritable.EDGETYPE;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
import edu.uci.ics.pregelix.api.graph.Vertex;
import edu.uci.ics.pregelix.api.job.PregelixJob;
@@ -33,8 +34,8 @@
private VKmerBytesWritable upBridge = new VKmerBytesWritable("ATA");
private VKmerBytesWritable downBridge = new VKmerBytesWritable("ACG");
private VKmerBytesWritable insertedBridge = new VKmerBytesWritable("GTA");
- private byte bridgeToUpDir = MessageFlag.DIR_FR;
- private byte bridgeToDownDir = MessageFlag.DIR_RF;
+ private EDGETYPE bridgeToUpDir = EDGETYPE.FR;
+ private EDGETYPE bridgeToDownDir = EDGETYPE.RF;
/**
* initiate kmerSize, maxIteration
@@ -49,7 +50,7 @@
}
@SuppressWarnings({ "unchecked", "rawtypes" })
- public void insertBridge(byte dirToUp, EdgeListWritable edgeListToUp, byte dirToDown,
+ public void insertBridge(EDGETYPE dirToUp, EdgeListWritable edgeListToUp, EDGETYPE dirToDown,
EdgeListWritable edgeListToDown, VKmerBytesWritable insertedBridge){
Vertex vertex = (Vertex) BspUtils.createVertex(getContext().getConfiguration());
vertex.getMsgList().clear();
@@ -79,7 +80,7 @@
return edgeList;
}
- public void addEdgeToInsertedBridge(byte dir, VKmerBytesWritable insertedBridge){
+ public void addEdgeToInsertedBridge(EDGETYPE dir, VKmerBytesWritable insertedBridge){
EdgeWritable newEdge = new EdgeWritable();
newEdge.setKey(insertedBridge);
newEdge.appendReadID(0);
@@ -110,7 +111,7 @@
if(getSuperstep() == 1){
if(getVertexId().toString().equals("ATA")){
/** add edge pointing to inserted bridge **/
- byte upToBridgeDir = mirrorDirection(bridgeToUpDir);
+ EDGETYPE upToBridgeDir = bridgeToUpDir.mirror();
addEdgeToInsertedBridge(upToBridgeDir, insertedBridge);
/** insert bridge **/
@@ -120,7 +121,7 @@
}
else if(getVertexId().toString().equals("ACG")){
/** add edge pointing to new bridge **/
- byte downToBridgeDir = mirrorDirection(bridgeToDownDir);
+ EDGETYPE downToBridgeDir = bridgeToDownDir.mirror();
addEdgeToInsertedBridge(downToBridgeDir, insertedBridge);
}
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleAddVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleAddVertex.java
index e446129..074fb4e 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleAddVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleAddVertex.java
@@ -1,5 +1,6 @@
package edu.uci.ics.genomix.pregelix.operator.bubblemerge;
+import java.util.EnumSet;
import java.util.Iterator;
import org.apache.hadoop.io.NullWritable;
@@ -7,7 +8,7 @@
import edu.uci.ics.genomix.type.EdgeListWritable;
import edu.uci.ics.genomix.type.EdgeWritable;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
-import edu.uci.ics.genomix.type.NodeWritable.DirectionFlag;
+import edu.uci.ics.genomix.type.NodeWritable.EDGETYPE;
import edu.uci.ics.pregelix.api.graph.Vertex;
import edu.uci.ics.pregelix.api.job.PregelixJob;
import edu.uci.ics.pregelix.api.util.BspUtils;
@@ -35,8 +36,8 @@
private VKmerBytesWritable insertedBubble = new VKmerBytesWritable("ATA"); //reverse
private VKmerBytesWritable internalKmerInNewBubble = new VKmerBytesWritable("ATG");
private float coverageOfInsertedBubble = 1;
- private byte majorToNewBubbleDir = MessageFlag.DIR_FR;
- private byte minorToNewBubbleDir = MessageFlag.DIR_FR;
+ private EDGETYPE majorToNewBubbleDir = EDGETYPE.FR;
+ private EDGETYPE minorToNewBubbleDir = EDGETYPE.FR;
private EdgeListWritable[] edges = new EdgeListWritable[4];
@@ -95,20 +96,20 @@
addVertex(insertedBubble, vertex);
}
- public void addEdgeToInsertedBubble(byte meToNewBubbleDir, VKmerBytesWritable insertedBubble){
+ public void addEdgeToInsertedBubble(EDGETYPE meToNewBubbleDir, VKmerBytesWritable insertedBubble){
EdgeWritable newEdge = new EdgeWritable();
newEdge.setKey(insertedBubble);
newEdge.appendReadID(0);
- byte newBubbleToMeDir = mirrorDirection(meToNewBubbleDir);
+ EDGETYPE newBubbleToMeDir = meToNewBubbleDir.mirror();
getVertexValue().getEdgeList(newBubbleToMeDir).add(newEdge);
}
public void setupEdgeForInsertedBubble(){
- for (byte d : DirectionFlag.values) {
- edges[d] = new EdgeListWritable();
+ for (EDGETYPE et : EnumSet.allOf(EDGETYPE.class)) {
+ edges[et.get()] = new EdgeListWritable();
}
- edges[majorToNewBubbleDir].add(majorVertexId);
- edges[minorToNewBubbleDir].add(minorVertexId);
+ edges[majorToNewBubbleDir.get()].add(majorVertexId);
+ edges[minorToNewBubbleDir.get()].add(minorVertexId);
}
@Override
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java
index 9bb5746..8c84000 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/bubblemerge/BubbleMergeVertex.java
@@ -10,6 +10,8 @@
import edu.uci.ics.genomix.type.EdgeListWritable;
import edu.uci.ics.genomix.type.EdgeWritable;
+import edu.uci.ics.genomix.type.NodeWritable;
+import edu.uci.ics.genomix.type.NodeWritable.EDGETYPE;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
import edu.uci.ics.genomix.config.GenomixJobConf;
import edu.uci.ics.genomix.pregelix.client.Client;
@@ -18,7 +20,6 @@
import edu.uci.ics.genomix.pregelix.operator.BasicGraphCleanVertex;
import edu.uci.ics.genomix.pregelix.operator.aggregator.StatisticsAggregator;
import edu.uci.ics.genomix.pregelix.type.MessageFlag;
-import edu.uci.ics.genomix.pregelix.type.StatisticsCounter;
import edu.uci.ics.genomix.pregelix.util.VertexUtil;
/**
@@ -37,18 +38,19 @@
private Map<VKmerBytesWritable, ArrayList<BubbleMergeMessageWritable>> receivedMsgMap = new HashMap<VKmerBytesWritable, ArrayList<BubbleMergeMessageWritable>>();
private ArrayList<BubbleMergeMessageWritable> receivedMsgList = new ArrayList<BubbleMergeMessageWritable>();
- private BubbleMergeMessageWritable topCoverageMessage = new BubbleMergeMessageWritable();
- private BubbleMergeMessageWritable curMessage = new BubbleMergeMessageWritable();
- private Set<BubbleMergeMessageWritable> unchangedSet = new HashSet<BubbleMergeMessageWritable>();
- private Set<BubbleMergeMessageWritable> deletedSet = new HashSet<BubbleMergeMessageWritable>();
+ private BubbleMergeMessageWritable topMsg = new BubbleMergeMessageWritable();
+ private BubbleMergeMessageWritable curMsg = new BubbleMergeMessageWritable();
+// private Set<BubbleMergeMessageWritable> unchangedSet = new HashSet<BubbleMergeMessageWritable>();
+// private Set<BubbleMergeMessageWritable> deletedSet = new HashSet<BubbleMergeMessageWritable>();
private EdgeWritable tmpEdge = new EdgeWritable();
- private static Set<BubbleMergeMessageWritable> allDeletedSet = Collections.synchronizedSet(new HashSet<BubbleMergeMessageWritable>());
+// private static Set<BubbleMergeMessageWritable> allDeletedSet = Collections.synchronizedSet(new HashSet<BubbleMergeMessageWritable>());
+ private static Set<VKmerBytesWritable> allDeletedSet = Collections.synchronizedSet(new HashSet<VKmerBytesWritable>());
- private VKmerBytesWritable incomingKmer = new VKmerBytesWritable();
- private VKmerBytesWritable outgoingKmer = new VKmerBytesWritable();
- private VKmerBytesWritable majorVertexId = new VKmerBytesWritable();
- private VKmerBytesWritable minorVertexId = new VKmerBytesWritable();
+// private VKmerBytesWritable incomingKmer = new VKmerBytesWritable();
+// private VKmerBytesWritable outgoingKmer = new VKmerBytesWritable();
+// private VKmerBytesWritable majorVertexId = new VKmerBytesWritable();
+// private VKmerBytesWritable minorVertexId = new VKmerBytesWritable();
/**
* initiate kmerSize, maxIteration
@@ -86,27 +88,40 @@
public void sendBubbleAndMajorVertexMsgToMinorVertex(){
for(int i = 0; i < 4; i++){
- /** set edgeList and edgeDir based on connectedTable **/
- setEdgeListAndEdgeDir(i);
+ // set edgeList and edgeDir based on connectedTable
+ setEdgeListAndEdgeType(i);
for(EdgeWritable incomingEdge : incomingEdgeList){
for(EdgeWritable outgoingEdge : outgoingEdgeList){
- /** get majorVertex and minorVertex and meToMajorDir and meToMinorDir **/
- incomingKmer.setAsCopy(incomingEdge.getKey());
- outgoingKmer.setAsCopy(outgoingEdge.getKey());
- majorVertexId.setAsCopy(incomingKmer.compareTo(outgoingKmer) >= 0 ? incomingKmer : outgoingKmer);
- minorVertexId.setAsCopy(incomingKmer.compareTo(outgoingKmer) < 0 ? incomingKmer : outgoingKmer);
- byte majorToMeDir = (incomingKmer.compareTo(outgoingKmer) >= 0 ? incomingEdgeDir : outgoingEdgeDir);
- byte meToMajorDir = mirrorDirection(majorToMeDir);
- byte minorToMeDir = (incomingKmer.compareTo(outgoingKmer) < 0 ? incomingEdgeDir : outgoingEdgeDir);
- byte meToMinorDir = mirrorDirection(minorToMeDir);
-
- /** setup outgoingMsg **/
+ // get majorVertex and minorVertex and meToMajorDir and meToMinorDir
+ VKmerBytesWritable incomingKmer = incomingEdge.getKey();
+ VKmerBytesWritable outgoingKmer = outgoingEdge.getKey();
+ VKmerBytesWritable majorVertexId = null;
+ EDGETYPE majorToMeEdgetype = null;
+ EDGETYPE minorToMeEdgetype = null;
+ VKmerBytesWritable minorVertexId = null;
+ if(incomingKmer.compareTo(outgoingKmer) >= 0){
+ majorVertexId = incomingKmer;
+ majorToMeEdgetype = incomingEdgeType;
+ minorVertexId = outgoingKmer;
+ minorToMeEdgetype = outgoingEdgeType;
+ } else{
+ majorVertexId = outgoingKmer;
+ majorToMeEdgetype = outgoingEdgeType;
+ minorVertexId = incomingKmer;
+ minorToMeEdgetype = incomingEdgeType;
+ }
+ if(majorVertexId == minorVertexId)
+ throw new IllegalArgumentException("majorVertexId is equal to minorVertexId, this is not allowd!");
+ EDGETYPE meToMajorEdgetype = majorToMeEdgetype.mirror();
+ EDGETYPE meToMinorEdgetype = minorToMeEdgetype.mirror();
+
+ // setup outgoingMsg
outgoingMsg.setMajorVertexId(majorVertexId);
outgoingMsg.setSourceVertexId(getVertexId());
outgoingMsg.setNode(getVertexValue().getNode());
- outgoingMsg.setMeToMajorDir(meToMajorDir);
- outgoingMsg.setMeToMinorDir(meToMinorDir);
+ outgoingMsg.setMeToMajorEdgetype(meToMajorEdgetype.get());
+ outgoingMsg.setMeToMinorEdgetype(meToMinorEdgetype.get());
sendMsg(minorVertexId, outgoingMsg);
}
}
@@ -131,28 +146,12 @@
}
}
- public byte getEdgeTypeFromDir(byte dir){
- switch(dir){
- case MessageFlag.DIR_FF:
- case MessageFlag.DIR_FR:
- return EdgeType.OUTGOINGEDGE;
- case MessageFlag.DIR_RF:
- case MessageFlag.DIR_RR:
- return EdgeType.INCOMINGEDGE;
- }
- return 0;
- }
-
- public boolean isSameEdgeType(byte edgeDir1, byte edgeDir2){
- return getEdgeTypeFromDir(edgeDir1) == getEdgeTypeFromDir(edgeDir2);
- }
-
public boolean isValidMajorAndMinor(){
- byte topBubbleToMajorDir = topCoverageMessage.getMeToMajorDir();
- byte curBubbleToMajorDir = curMessage.getMeToMajorDir();
- byte topBubbleToMinorDir = topCoverageMessage.getMeToMinorDir();
- byte curBubbleToMinorDir = curMessage.getMeToMinorDir();
- return isSameEdgeType(topBubbleToMajorDir, curBubbleToMajorDir) && isSameEdgeType(topBubbleToMinorDir, curBubbleToMinorDir);
+ EDGETYPE topBubbleToMajorEdgetype = EDGETYPE.fromByte(topMsg.getMeToMajorEdgetype());
+ EDGETYPE curBubbleToMajorEdgetype = EDGETYPE.fromByte(curMsg.getMeToMajorEdgetype());
+ EDGETYPE topBubbleToMinorEdgetype = EDGETYPE.fromByte(topMsg.getMeToMinorEdgetype());
+ EDGETYPE curBubbleToMinorEdgetype = EDGETYPE.fromByte(curMsg.getMeToMinorEdgetype());
+ return (topBubbleToMajorEdgetype.dir() == curBubbleToMajorEdgetype.dir()) && topBubbleToMinorEdgetype.dir() == curBubbleToMinorEdgetype.dir();
}
public boolean isFlipRelativeToMajor(BubbleMergeMessageWritable msg1, BubbleMergeMessageWritable msg2){
@@ -160,75 +159,101 @@
}
public void processSimilarSetToUnchangeSetAndDeletedSet(){
- unchangedSet.clear();
- deletedSet.clear();
- topCoverageMessage.reset();
- curMessage.reset();
- Iterator<BubbleMergeMessageWritable> it;
+// unchangedSet.clear();
+// deletedSet.clear();
+ topMsg.reset();
+ curMsg.reset();
while(!receivedMsgList.isEmpty()){
- it = receivedMsgList.iterator();
- topCoverageMessage.set(it.next());
+ Iterator<BubbleMergeMessageWritable> it = receivedMsgList.iterator();
+ topMsg.set(it.next());
it.remove(); //delete topCoverage node
+ NodeWritable topNode = topMsg.getNode();
while(it.hasNext()){
- curMessage.set(it.next());
+ curMsg.set(it.next());
//check if the vertex is valid minor and if it comes from valid major
if(!isValidMajorAndMinor())
continue;
+
//compute the similarity
- float fracDissimilar = topCoverageMessage.computeDissimilar(curMessage);
- if(fracDissimilar < dissimilarThreshold){ //if similar with top node, delete this node and put it in deletedSet
- //add coverage to top node
- topCoverageMessage.getNode().addFromNode(isFlipRelativeToMajor(topCoverageMessage, curMessage),
- curMessage.getNode());
- boolean flip = curMessage.isFlip(topCoverageMessage);
- curMessage.setFlip(flip);
- curMessage.setTopCoverageVertexId(topCoverageMessage.getSourceVertexId());
- curMessage.setMinorVertexId(getVertexId());
- deletedSet.add(new BubbleMergeMessageWritable(curMessage));
- allDeletedSet.add(new BubbleMergeMessageWritable(curMessage));
+ float fracDissimilar = topMsg.computeDissimilar(curMsg);
+
+ if(fracDissimilar < dissimilarThreshold){ //if similar with top node, delete this node and put it in deletedSet
+ // 1. update my own(minor's) edges
+ EDGETYPE bubbleToMinor = EDGETYPE.fromByte(curMsg.getMeToMinorEdgetype());
+ getVertexValue().getEdgeList(bubbleToMinor).remove(curMsg.getSourceVertexId());
+ activate();
+
+ // 2. add coverage to top node -- for unchangedSet
+ topNode.addFromNode(isFlipRelativeToMajor(topMsg, curMsg),
+ curMsg.getNode());
+
+ // 3. treat msg as a bubble vertex, broadcast kill self message to major vertex to update their edges
+ EDGETYPE bubbleToMajor = EDGETYPE.fromByte(curMsg.getMeToMajorEdgetype());
+ EDGETYPE majorToBubble = bubbleToMajor.mirror();
+ outgoingMsg.reset();
+ outFlag = 0;
+ outFlag |= majorToBubble.get() | MessageFlag.UPDATE;
+ outgoingMsg.setFlag(outFlag);
+ sendMsg(curMsg.getMajorVertexId(), outgoingMsg);
+// boolean flip = curMsg.isFlip(topCoverageVertexMsg);
+// curMsg.setFlip(flip);
+// curMsg.setTopCoverageVertexId(topCoverageVertexMsg.getSourceVertexId());
+// curMsg.setMinorVertexId(getVertexId());
+// deletedSet.add(new BubbleMergeMessageWritable(curMsg));
+
+ // 4. store deleted vertices -- for deletedSet
+ allDeletedSet.add(new VKmerBytesWritable(curMsg.getSourceVertexId()));
it.remove();
}
}
- unchangedSet.add(new BubbleMergeMessageWritable(topCoverageMessage));
- }
- }
-
- public void processUnchangedSet(){
- for(BubbleMergeMessageWritable msg : unchangedSet){
- outFlag = MessageFlag.UNCHANGE;
+
+ //process unchangedSet -- send message to topVertex to update their coverage
+ outgoingMsg.reset();
+ outFlag = 0;
+ outFlag |= MessageFlag.UNCHANGE;
+ outgoingMsg.setNode(topNode);
outgoingMsg.setFlag(outFlag);
- outgoingMsg.setNode(msg.getNode());
- sendMsg(msg.getSourceVertexId(), outgoingMsg);
+ sendMsg(topMsg.getSourceVertexId(), outgoingMsg);
+// unchangedSet.add(new BubbleMergeMessageWritable(topCoverageVertexMsg));
}
}
- public void processDeletedSet(){
- for(BubbleMergeMessageWritable msg : deletedSet){
- outgoingMsg.set(msg);
- outFlag = MessageFlag.KILL;
- outgoingMsg.setFlag(outFlag);
- outgoingMsg.setSourceVertexId(msg.getMinorVertexId());
- sendMsg(msg.getSourceVertexId(), outgoingMsg);
- }
- }
+// public void processUnchangedSet(){
+// for(BubbleMergeMessageWritable msg : unchangedSet){
+// outFlag = MessageFlag.UNCHANGE;
+// outgoingMsg.setFlag(outFlag);
+// outgoingMsg.setNode(msg.getNode());
+// sendMsg(msg.getSourceVertexId(), outgoingMsg);
+// }
+// }
+//
+// public void processDeletedSet(){
+// for(BubbleMergeMessageWritable msg : deletedSet){
+// outgoingMsg.set(msg);
+// outFlag = MessageFlag.KILL;
+// outgoingMsg.setFlag(outFlag);
+// outgoingMsg.setSourceVertexId(msg.getMinorVertexId());
+// sendMsg(msg.getSourceVertexId(), outgoingMsg);
+// }
+// }
- public void processAllDeletedSet(){
- synchronized(allDeletedSet){
- for(BubbleMergeMessageWritable msg : allDeletedSet){
- outgoingMsg.set(msg);
- outFlag = MessageFlag.KILL;
- outgoingMsg.setFlag(outFlag);
- outgoingMsg.setSourceVertexId(msg.getMinorVertexId());
- sendMsg(msg.getSourceVertexId(), outgoingMsg);
- }
- }
- }
+// public void processAllDeletedSet(){
+// synchronized(allDeletedSet){
+// for(BubbleMergeMessageWritable msg : allDeletedSet){
+// outgoingMsg.set(msg);
+// outFlag = MessageFlag.KILL;
+// outgoingMsg.setFlag(outFlag);
+// outgoingMsg.setSourceVertexId(msg.getMinorVertexId());
+// sendMsg(msg.getSourceVertexId(), outgoingMsg);
+// }
+// }
+// }
public void removeEdgesToMajorAndMinor(){
- byte meToMajorDir = incomingMsg.getMeToMajorDir();
- byte majorToMeDir = mirrorDirection(meToMajorDir);
- byte meToMinorDir = incomingMsg.getMeToMinorDir();
- byte minorToMeDir = mirrorDirection(meToMinorDir);
+ EDGETYPE meToMajorDir = EDGETYPE.fromByte(incomingMsg.getMeToMajorEdgetype());
+ EDGETYPE majorToMeDir = meToMajorDir.mirror();
+ EDGETYPE meToMinorDir = EDGETYPE.fromByte(incomingMsg.getMeToMinorEdgetype());
+ EDGETYPE minorToMeDir = meToMinorDir.mirror();
getVertexValue().getEdgeList(majorToMeDir).remove(incomingMsg.getMajorVertexId());
getVertexValue().getEdgeList(minorToMeDir).remove(incomingMsg.getSourceVertexId());
}
@@ -262,8 +287,8 @@
* do some remove operations on adjMap after receiving the info about dead Vertex
*/
public void responseToDeadVertexAndUpdateEdges(){
- byte meToNeighborDir = (byte) (incomingMsg.getFlag() & MessageFlag.DIR_MASK);
- byte neighborToMeDir = mirrorDirection(meToNeighborDir);
+ EDGETYPE meToNeighborDir = EDGETYPE.fromByte(incomingMsg.getFlag());
+ EDGETYPE neighborToMeDir = meToNeighborDir.mirror();
if(getVertexValue().getEdgeList(neighborToMeDir).getEdge(incomingMsg.getSourceVertexId()) != null){
tmpEdge.setAsCopy(getVertexValue().getEdgeList(neighborToMeDir).getEdge(incomingMsg.getSourceVertexId()));
@@ -271,7 +296,7 @@
getVertexValue().getEdgeList(neighborToMeDir).remove(incomingMsg.getSourceVertexId());
}
tmpEdge.setKey(incomingMsg.getTopCoverageVertexId());
- byte updateDir = flipDirection(neighborToMeDir, incomingMsg.isFlip());
+ EDGETYPE updateDir = incomingMsg.isFlip() ? neighborToMeDir.flip() : neighborToMeDir;
getVertexValue().getEdgeList(updateDir).unionAdd(tmpEdge);
}
@@ -280,80 +305,96 @@
initVertex();
if (getSuperstep() == 1) {
if(VertexUtil.isBubbleVertex(getVertexValue())){
- /** clean allDeleteSet **/
+ // clean allDeleteSet
allDeletedSet.clear();
- /** add a fake node **/
- addFakeVertex();
- /** send bubble and major vertex msg to minor vertex **/
+// // add a fake node
+// addFakeVertex();
+ // send bubble and major vertex msg to minor vertex
sendBubbleAndMajorVertexMsgToMinorVertex();
}
} else if (getSuperstep() == 2){
if(!isFakeVertex()){
- /** aggregate bubble nodes and grouped by major vertex **/
+ // aggregate bubble nodes and grouped by major vertex
aggregateBubbleNodesByMajorNode(msgIterator);
- for(VKmerBytesWritable prevId : receivedMsgMap.keySet()){
+ for(VKmerBytesWritable majorVertexId : receivedMsgMap.keySet()){
receivedMsgList.clear();
- receivedMsgList.addAll(receivedMsgMap.get(prevId));
+ receivedMsgList = receivedMsgMap.get(majorVertexId);
+// receivedMsgList.addAll(receivedMsgMap.get(majorVertexId));
if(receivedMsgList.size() > 1){ // filter bubble
- /** for each majorVertex, sort the node by decreasing order of coverage **/
- receivedMsgList = receivedMsgMap.get(prevId);
+ // for each majorVertex, sort the node by decreasing order of coverage
Collections.sort(receivedMsgList, new BubbleMergeMessageWritable.SortByCoverage());
- /** process similarSet, keep the unchanged set and deleted set & add coverage to unchange node **/
+ // process similarSet, keep the unchanged set and deleted set & add coverage to unchange node
processSimilarSetToUnchangeSetAndDeletedSet();
- /** send message to the unchanged set for updating coverage & send kill message to the deleted set **/
- processUnchangedSet();
- processDeletedSet();
+// // send message to the unchanged set for updating coverage & send kill message to the deleted set
+// processUnchangedSet();
+// processDeletedSet();
}
}
}
} else if (getSuperstep() == 3){
- if(!isFakeVertex()){
- while(msgIterator.hasNext()) {
- incomingMsg = msgIterator.next();
- if(incomingMsg.getFlag() == MessageFlag.KILL){
- broadcaseUpdateEdges();
- } else
- if(incomingMsg.getFlag() == MessageFlag.UNCHANGE){
- /** update Node including average coverage **/
- getVertexValue().setNode(incomingMsg.getNode());
- }
- }
- }
- } else if(getSuperstep() == 4){
- if(!isFakeVertex()){
- while(msgIterator.hasNext()) {
- incomingMsg = msgIterator.next();
- if(isResponseKillMsg()){
- responseToDeadVertexAndUpdateEdges();
- }
- }
- }else{
- processAllDeletedSet();
+ if(allDeletedSet.contains(getVertexId()))
deleteVertex(getVertexId());
+ else{
+ while(msgIterator.hasNext()){
+ incomingMsg = msgIterator.next();
+ short msgType = (short) (incomingMsg.getFlag() & MessageFlag.MSG_TYPE_MASK);
+ switch(msgType){
+ case MessageFlag.UPDATE:
+ break;
+ case MessageFlag.UNCHANGE:
+ break;
+ }
+ }
}
- } else if(getSuperstep() == 5){
- while(msgIterator.hasNext()) {
- incomingMsg = msgIterator.next();
- if(incomingMsg.getFlag() == MessageFlag.KILL){
+
+// if(!isFakeVertex()){
+// while(msgIterator.hasNext()) {
+// incomingMsg = msgIterator.next();
+// if(incomingMsg.getFlag() == MessageFlag.KILL){
+// broadcaseUpdateEdges();
+// } else
+// if(incomingMsg.getFlag() == MessageFlag.UNCHANGE){
+// // update Node including average coverage
+// getVertexValue().setNode(incomingMsg.getNode());
+// }
+// }
+// }
+ }
+// else if(getSuperstep() == 4){
+// if(!isFakeVertex()){
+// while(msgIterator.hasNext()) {
+// incomingMsg = msgIterator.next();
+// if(isResponseKillMsg()){
+// responseToDeadVertexAndUpdateEdges();
+// }
+// }
+// }else{
+// processAllDeletedSet();
+// deleteVertex(getVertexId());
+// }
+// } else if(getSuperstep() == 5){
+// while(msgIterator.hasNext()) {
+// incomingMsg = msgIterator.next();
+// if(incomingMsg.getFlag() == MessageFlag.KILL){
broadcaseKillselfAndNoticeToUpdateEdges();
- //set statistics counter: Num_RemovedBubbles
- updateStatisticsCounter(StatisticsCounter.Num_RemovedBubbles);
- getVertexValue().setCounters(counters);
- }
- }
- } else if(getSuperstep() == 6){
- while(msgIterator.hasNext()) {
- incomingMsg = msgIterator.next();
- if(isResponseKillMsg()){
+// //set statistics counter: Num_RemovedBubbles
+// updateStatisticsCounter(StatisticsCounter.Num_RemovedBubbles);
+// getVertexValue().setCounters(counters);
+// }
+// }
+// } else if(getSuperstep() == 6){
+// while(msgIterator.hasNext()) {
+// incomingMsg = msgIterator.next();
+// if(isResponseKillMsg()){
responseToDeadVertexAndUpdateEdges();
- }
- }
- }
- if(!isFakeVertex())
- voteToHalt();
+// }
+// }
+// }
+// if(!isFakeVertex())
+// voteToHalt();
}
public static void main(String[] args) throws Exception {
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 70c3c33..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
@@ -4,18 +4,17 @@
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;
import edu.uci.ics.genomix.pregelix.log.LogUtil;
import edu.uci.ics.genomix.pregelix.operator.BasicGraphCleanVertex;
import edu.uci.ics.genomix.pregelix.type.MessageFlag;
-import edu.uci.ics.genomix.pregelix.util.VertexUtil;
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.OutgoingListFlag;
-import edu.uci.ics.genomix.type.NodeWritable.IncomingListFlag;
+import edu.uci.ics.genomix.type.NodeWritable.EDGETYPE;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
public abstract class BasicPathMergeVertex<V extends VertexValueWritable, M extends PathMergeMessageWritable> extends
@@ -44,72 +43,6 @@
public DIR revert(DIR direction){
return direction == DIR.PREVIOUS ? DIR.NEXT : DIR.PREVIOUS;
}
- /**
- * start sending message
- */
- public void startSendMsg() {
- if(isTandemRepeat(getVertexValue())){
- getCopyWithoutTandemRepeats(getVertexValue());
- outFlag = 0;
- headSendSettledMsgToAllNeighborNodes(tmpValue);
- voteToHalt();
- } else{
- /** check incoming **/
- // update internal state
- if (VertexUtil.isVertexWithOnlyOneIncoming(getVertexValue())){
- byte state = 0;
- state |= State.HEAD_CAN_MERGEWITHPREV;
- getVertexValue().setState(state);
- activate();
- }
- // send to neighbors
- else if (VertexUtil.isVertexWithManyIncoming(getVertexValue())){
- outFlag = 0;
- headSendSettledMsgs(DIR.PREVIOUS, getVertexValue());
- }
-
- /** check outgoing **/
- // update internal state
- if (VertexUtil.isVertexWithOnlyOneOutgoing(getVertexValue())){
- byte state = 0;
- state |= State.HEAD_CAN_MERGEWITHNEXT;
- getVertexValue().setState(state);
- activate();
- }
- // send to neighbors
- else if (VertexUtil.isVertexWithManyOutgoing(getVertexValue())){
- outFlag = 0;
- headSendSettledMsgs(DIR.NEXT, getVertexValue());
- }
-
- if(VertexUtil.isUnMergeVertex(getVertexValue()))
- voteToHalt();
- }
- }
-
- /**
- * initiate head, rear and path node
- */
- public void initState(Iterator<M> msgIterator) {
- if(isInactiveNode())
- voteToHalt();
- else{
- if(msgIterator.hasNext()){
- // aggregate all the incomingMsgs first
- aggregateMsg(msgIterator);
- // update state based on aggregateMsg
- updateState();
- }
- }
- }
-
- public void setStateAsMergeDir(DIR direction){
- short state = getVertexValue().getState();
- state &= State.CAN_MERGE_CLEAR;
- state |= direction == DIR.PREVIOUS ? State.CAN_MERGEWITHPREV : State.CAN_MERGEWITHNEXT;
- getVertexValue().setState(state);
- activate();
- }
/**
* send UPDATE msg boolean: true == P4, false == P2
@@ -122,8 +55,8 @@
// outgoingMsg.setFlip(ifFilpWithSuccessor(incomingMsg.getSourceVertexId()));
DIR revertDirection = revert(direction);
- byte[] mergeDirs = direction == DIR.PREVIOUS ? OutgoingListFlag.values : IncomingListFlag.values;
- byte[] updateDirs = direction == DIR.PREVIOUS ? IncomingListFlag.values : OutgoingListFlag.values;
+ EnumSet<EDGETYPE> mergeDirs = direction == DIR.PREVIOUS ? EDGETYPE.OUTGOING : EDGETYPE.INCOMING;
+ EnumSet<EDGETYPE> updateDirs = direction == DIR.PREVIOUS ? EDGETYPE.INCOMING : EDGETYPE.OUTGOING;
//set deleteKmer
outgoingMsg.setSourceVertexId(getVertexId());
@@ -131,11 +64,11 @@
//set replaceDir
setReplaceDir(mergeDirs);
- for(byte dir : updateDirs){
+ for(EDGETYPE dir : updateDirs){
kmerIterator = getVertexValue().getEdgeList(dir).getKeyIterator();
while(kmerIterator.hasNext()){
//set deleteDir
- byte deleteDir = setDeleteDir(dir);
+ EDGETYPE deleteDir = setDeleteDir(dir);
//set mergeDir, so it won't need flip
setMergeDir(deleteDir, revertDirection);
outgoingMsg.setFlag(outFlag);
@@ -151,9 +84,9 @@
public void processUpdate(M msg){
// A -> B -> C with B merging with C
inFlag = msg.getFlag();
- byte deleteDir = (byte) ((inFlag & MessageFlag.DELETE_DIR_MASK) >> 11); // B -> A dir
- byte mergeDir = (byte) ((inFlag & MessageFlag.MERGE_DIR_MASK) >> 9); // C -> A dir
- byte replaceDir = (byte) ((inFlag & MessageFlag.REPLACE_DIR_MASK)); // C -> B dir
+ EDGETYPE deleteDir = EDGETYPE.fromByte((short) ((inFlag & MessageFlag.DELETE_DIR_MASK) >> 11)); // B -> A dir
+ EDGETYPE mergeDir = EDGETYPE.fromByte((short) ((inFlag & MessageFlag.MERGE_DIR_MASK) >> 9)); // C -> A dir
+ EDGETYPE replaceDir = EDGETYPE.fromByte((short)(inFlag & MessageFlag.REPLACE_DIR_MASK)); // C -> B dir
getVertexValue().getNode().updateEdges(deleteDir, msg.getSourceVertexId(),
mergeDir, replaceDir, msg.getNode(), true);
@@ -177,7 +110,7 @@
outgoingMsg.setFlag(outFlag);
outgoingMsg.setSourceVertexId(getVertexId());
outgoingMsg.setNode(getVertexValue().getNode()); //half of edges are enough
- destVertexId = getDestVertexId(direction); //(direction == DIR.PREVIOUS ? getPrevDestVertexId() : getNextDestVertexId()); //getDestVertexId(direction)
+ destVertexId = getDestVertexId(direction);
sendMsg(destVertexId, outgoingMsg);
if(isP4)
@@ -228,9 +161,9 @@
}
}
- public void setReplaceDir(byte[] mergeDirs){
- byte replaceDir = 0;
- for(byte dir : mergeDirs){
+ public void setReplaceDir(EnumSet<EDGETYPE> mergeDirs){
+ EDGETYPE replaceDir = null;
+ for(EDGETYPE dir : mergeDirs){
int num = getVertexValue().getEdgeList(dir).getCountOfPosition();
if(num > 0){
if(num != 1)
@@ -241,89 +174,31 @@
}
}
outFlag &= MessageFlag.REPLACE_DIR_CLEAR;
- outFlag |= replaceDir;
+ outFlag |= replaceDir.get();
}
- public byte setDeleteDir(byte dir){
- byte deleteDir = mirrorDirection(dir);
+ public EDGETYPE setDeleteDir(EDGETYPE dir){
+ EDGETYPE deleteDir = dir.mirror();
outFlag &= MessageFlag.DELETE_DIR_CLEAR;
- outFlag |= (deleteDir << 11);
+ outFlag |= deleteDir.get();
return deleteDir;
}
- public void setMergeDir(byte deleteDir, DIR revertDirection){
- byte mergeDir = flipDirection(deleteDir, ifFlipWithNeighbor(revertDirection));
+ public void setMergeDir(EDGETYPE deleteDir, DIR revertDirection){
+ EDGETYPE mergeDir = ifFlipWithNeighbor(revertDirection) ? deleteDir.flip() : deleteDir;
outFlag &= MessageFlag.MERGE_DIR_CLEAR;
- outFlag |= (mergeDir << 9);
- }
-//------------------------------------
- /**
- * Send merge restrictions to my neighbor nodes
- */
- public void restrictNeighbors() {
- EnumSet<DIR> dirsToRestrict;
- V vertex = getVertexValue();
- if(isTandemRepeat(vertex)) {
- // tandem repeats are not allowed to merge at all
- dirsToRestrict = EnumSet.of(DIR.NEXT, DIR.PREVIOUS);
- }
- else {
- // degree > 1 can't merge in that direction
- dirsToRestrict = EnumSet.noneOf(DIR.class);
- for (DIR dir : DIR.values()) {
- if (vertex.getDegree(dir) == 0 || vertex.getDegree(dir) > 1){
- short restrictedDirs = getVertexValue().getState();
- restrictedDirs |= dir.get();
- getVertexValue().setState(restrictedDirs);
- activate();
- }
- if (vertex.getDegree(dir) > 1)
- dirsToRestrict.add(dir);
- }
- }
-
- // send a message to each neighbor indicating they can't merge towards me
- for (DIR dir : dirsToRestrict) {
- for (byte d : NodeWritable.edgeTypesInDir(dir)) {
- for (VKmerBytesWritable destId : vertex.getEdgeList(d).getKeys()) {
- outgoingMsg.reset();
- outgoingMsg.setFlag(DIR.mirror(d).get());
- sendMsg(destId, outgoingMsg);
- }
- }
- }
+ outFlag |= mergeDir.get();
}
/**
- * initiate head, rear and path node
- */
- public void recieveRestrictions(Iterator<M> msgIterator) {
- short restrictedDirs = 0;
- while (msgIterator.hasNext()) {
- incomingMsg = msgIterator.next();
- restrictedDirs |= incomingMsg.getFlag();
- }
- // special case: tandem repeats cannot merge at all
- if (isTandemRepeat(getVertexValue())) {
- restrictedDirs |= DIR.PREVIOUS.get();
- restrictedDirs |= DIR.NEXT.get();
- }
-
- short selfRestrictedDirs = (short) (getVertexValue().getState() & DIR.MASK);
- selfRestrictedDirs |= restrictedDirs;
- getVertexValue().setState(selfRestrictedDirs);
- activate();
- }
-//------------------------------------
- /**
* final updateAdjList
*/
public void processFinalUpdate(){
inFlag = incomingMsg.getFlag();
- byte meToNeighborDir = (byte) (inFlag & MessageFlag.DIR_MASK);
- byte neighborToMeDir = mirrorDirection(meToNeighborDir);
+ EDGETYPE meToNeighborDir = EDGETYPE.fromByte(incomingMsg.getFlag());
+ EDGETYPE neighborToMeDir = meToNeighborDir.mirror();
- byte neighborToMergeDir = flipDirection(neighborToMeDir, incomingMsg.isFlip());
+ EDGETYPE neighborToMergeDir = incomingMsg.isFlip() ? neighborToMeDir.flip() : neighborToMeDir;
getVertexValue().processFinalUpdates(neighborToMeDir, neighborToMergeDir, incomingMsg.getNode());
}
@@ -332,8 +207,8 @@
*/
public void processFinalUpdate2(){
inFlag = incomingMsg.getFlag();
- byte meToNeighborDir = (byte) (inFlag & MessageFlag.DIR_MASK);
- byte neighborToMeDir = mirrorDirection(meToNeighborDir);
+ EDGETYPE meToNeighborDir = EDGETYPE.fromByte(inFlag);
+ EDGETYPE neighborToMeDir = meToNeighborDir.mirror();
EdgeWritable edge = new EdgeWritable();
edge.setKey(incomingMsg.getSourceVertexId());
@@ -341,13 +216,6 @@
getVertexValue().getEdgeList(neighborToMeDir).unionAdd(edge);
}
- public byte flipHeadMergeDir(byte d, boolean isFlip){
- if(isFlip){
- return DIR.mirrorFromByte((byte)(d & DIR.MASK));
- } else
- return d;
- }
-
public boolean isDifferentDirWithMergeKmer(byte neighborToMeDir){
return neighborToMeDir == MessageFlag.DIR_FR || neighborToMeDir == MessageFlag.DIR_RF;
}
@@ -373,18 +241,11 @@
*/
public void processMerge(PathMergeMessageWritable msg){
inFlag = msg.getFlag();
- byte meToNeighborDir = (byte) (inFlag & MessageFlag.DIR_MASK);
- byte neighborToMeDir = mirrorDirection(meToNeighborDir);
+ EDGETYPE meToNeighborDir = EDGETYPE.fromByte(inFlag);
+ EDGETYPE neighborToMeDir = meToNeighborDir.mirror();
-// if(isNonHeadReceivedFromHead()){ // TODO? why sepcial-case the path vs heads? just aggregate your state flags
-// short state = getVertexValue().getState();
-// state &= State.HEAD_CAN_MERGE_CLEAR;
-// byte headMergeDir = flipHeadMergeDir((byte)(inFlag & MessageFlag.HEAD_CAN_MERGE_MASK), isDifferentDirWithMergeKmer(neighborToMeDir));
-// state |= headMergeDir;
-// getVertexValue().setState(state);
-// }
short state = getVertexValue().getState();
- state |= flipHeadMergeDir((byte)(inFlag & DIR.MASK), isDifferentDirWithMergeKmer(neighborToMeDir));
+// state |= flipHeadMergeDir((byte)(inFlag & DIR.MASK), isDifferentDirWithMergeKmer(neighborToMeDir));
getVertexValue().setState(state);
getVertexValue().processMerges(neighborToMeDir, msg.getNode(), kmerSize);
@@ -408,15 +269,15 @@
public void sendUpdateMsgForP2(MessageWritable msg){
outgoingMsg.reset();
outgoingMsg.setUpdateMsg(true);
- byte meToNeighborDir = (byte) (msg.getFlag() & MessageFlag.DIR_MASK);
- byte neighborToMeDir = mirrorDirection(meToNeighborDir);
+ EDGETYPE meToNeighborDir = EDGETYPE.fromByte(incomingMsg.getFlag());
+ EDGETYPE neighborToMeDir = meToNeighborDir.mirror();
switch(neighborToMeDir){
- case MessageFlag.DIR_FF:
- case MessageFlag.DIR_FR:
+ case FF:
+ case FR:
sendUpdateMsg(isP2, DIR.PREVIOUS);
break;
- case MessageFlag.DIR_RF:
- case MessageFlag.DIR_RR:
+ case RF:
+ case RR:
sendUpdateMsg(isP2, DIR.NEXT);
break;
}
@@ -442,8 +303,7 @@
else
outgoingMsg.setFlip(false);
outgoingMsg.setFlag(outFlag);
-// outgoingMsg.setNeighberNode(getVertexValue().getIncomingList());
- for(byte d: IncomingListFlag.values)
+ for(EDGETYPE d: EDGETYPE.INCOMING)
outgoingMsg.setEdgeList(d, getVertexValue().getEdgeList(d));
outgoingMsg.setSourceVertexId(getVertexId());
outgoingMsg.setInternalKmer(getVertexValue().getInternalKmer());
@@ -451,29 +311,29 @@
}
public boolean canMergeWithHead(MessageWritable msg){
- byte meToNeighborDir = (byte) (msg.getFlag() & MessageFlag.DIR_MASK);
- byte neighborToMeDir = mirrorDirection(meToNeighborDir);
+ EDGETYPE meToNeighborDir = EDGETYPE.fromByte(msg.getFlag());
+ EDGETYPE neighborToMeDir = meToNeighborDir.mirror();
switch(neighborToMeDir){
- case MessageFlag.DIR_FF:
- case MessageFlag.DIR_FR:
+ case FF:
+ case FR:
return getVertexValue().outDegree() == 1;
- case MessageFlag.DIR_RF:
- case MessageFlag.DIR_RR:
+ case RF:
+ case RR:
return getVertexValue().inDegree() == 1;
}
return false;
}
public void sendMergeMsgByIncomingMsgDir(){
- byte meToNeighborDir = (byte) (incomingMsg.getFlag() & MessageFlag.DIR_MASK);
- byte neighborToMeDir = mirrorDirection(meToNeighborDir);
+ EDGETYPE meToNeighborDir = EDGETYPE.fromByte(incomingMsg.getFlag());
+ EDGETYPE neighborToMeDir = meToNeighborDir.mirror();
switch(neighborToMeDir){
- case MessageFlag.DIR_FF:
- case MessageFlag.DIR_FR:
+ case FF:
+ case FR:
configureMergeMsgForSuccessor(incomingMsg.getSourceVertexId());
break;
- case MessageFlag.DIR_RF:
- case MessageFlag.DIR_RR:
+ case RF:
+ case RR:
configureMergeMsgForPredecessor(incomingMsg.getSourceVertexId());
break;
}
@@ -534,18 +394,208 @@
*/
public void setHeadMergeDir(){
byte state = 0;
- byte meToNeighborDir = (byte) (incomingMsg.getFlag() & MessageFlag.DIR_MASK);
- byte neighborToMeDir = mirrorDirection(meToNeighborDir);
+ EDGETYPE meToNeighborDir = EDGETYPE.fromByte(incomingMsg.getFlag());
+ EDGETYPE neighborToMeDir = meToNeighborDir.mirror();
switch(neighborToMeDir){
- case MessageFlag.DIR_FF:
- case MessageFlag.DIR_FR:
+ case FF:
+ case FR:
state |= State.HEAD_CAN_MERGEWITHPREV;
break;
- case MessageFlag.DIR_RF:
- case MessageFlag.DIR_RR:
+ case RF:
+ case RR:
state |= State.HEAD_CAN_MERGEWITHNEXT;
break;
}
getVertexValue().setState(state);
}
+
+// 2013.9.21 --------------------------------------------------------------------------------------------------//
+ /**
+ * Send merge restrictions to my neighbor nodes
+ */
+ public void restrictNeighbors() {
+ EnumSet<DIR> dirsToRestrict;
+ VertexValueWritable vertex = getVertexValue();
+ short state = vertex.getState();
+ boolean updated = false;
+ if(isTandemRepeat(vertex)) {
+ // tandem repeats are not allowed to merge at all
+ dirsToRestrict = EnumSet.of(DIR.NEXT, DIR.PREVIOUS);
+ state |= DIR.NEXT.get();
+ state |= DIR.PREVIOUS.get();
+ updated = true;
+ }
+ else {
+ // degree > 1 can't merge in that direction; == 0 means we are a tip
+ dirsToRestrict = EnumSet.noneOf(DIR.class);
+ for (DIR dir : DIR.values()) {
+ if (vertex.getDegree(dir) > 1 || vertex.getDegree(dir) == 0) {
+ dirsToRestrict.add(dir);
+ state |= dir.get();
+ updated = true;
+ }
+ }
+ }
+ if (updated) {
+ vertex.setState(state);
+ if (DIR.enumSetFromByte(state).containsAll(EnumSet.allOf(DIR.class)))
+ voteToHalt();
+ else
+ activate();
+ }
+
+ // send a message to each neighbor indicating they can't merge towards me
+ for (DIR dir : dirsToRestrict) {
+ for (EDGETYPE et : dir.edgeType()) {
+ for (VKmerBytesWritable destId : vertex.getEdgeList(et).getKeys()) {
+ outgoingMsg.reset();
+ outgoingMsg.setFlag(et.mirror().dir().get());
+
+// LOG.info("send restriction from " + getVertexId() + " to " + destId + " in my " + d + " and their " + DirectionFlag.mirrorEdge(d) + " (" + DirectionFlag.dirFromEdgeType(DirectionFlag.mirrorEdge(d)) + "); I am " + getVertexValue());
+ sendMsg(destId, outgoingMsg);
+ }
+ }
+ }
+ }
+
+ /**
+ * initiate head, rear and path node
+ */
+ public void recieveRestrictions(Iterator<M> msgIterator) {
+ short restrictedDirs = 0; // the directions (NEXT/PREVIOUS) that I'm not allowed to merge in
+ boolean updated = false;
+ while (msgIterator.hasNext()) {
+// LOG.info("before restriction " + getVertexId() + ": " + DIR.fromByte(restrictedDirs));
+ incomingMsg = msgIterator.next();
+ restrictedDirs |= incomingMsg.getFlag();
+// LOG.info("after restriction " + getVertexId() + ": " + DIR.fromByte(restrictedDirs));
+ updated = true;
+ }
+ if (updated) {
+ getVertexValue().setState(restrictedDirs);
+ if (DIR.enumSetFromByte(restrictedDirs).containsAll(EnumSet.allOf(DIR.class)))
+ voteToHalt();
+ else
+ 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
new file mode 100644
index 0000000..ae67a57
--- /dev/null
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P0ForPathMergeVertex.java
@@ -0,0 +1,83 @@
+package edu.uci.ics.genomix.pregelix.operator.pathmerge;
+
+import java.util.EnumSet;
+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.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
+ */
+ @Override
+ public void initVertex() {
+ super.initVertex();
+ if(incomingMsg == null)
+ incomingMsg = new PathMergeMessageWritable();
+ if(outgoingMsg == null)
+ outgoingMsg = new PathMergeMessageWritable();
+ else
+ outgoingMsg.reset();
+ if(destVertexId == null)
+ destVertexId = new VKmerBytesWritable();
+ if(repeatKmer == null)
+ repeatKmer = new VKmerBytesWritable();
+ if(getSuperstep() == 1)
+ StatisticsAggregator.preGlobalCounters.clear();
+// else
+// StatisticsAggregator.preGlobalCounters = BasicGraphCleanVertex.readStatisticsCounterResult(getContext().getConfiguration());
+ counters.clear();
+ getVertexValue().getCounters().clear();
+ }
+
+ public void chooseMergeDir() {
+ 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 -- 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();
+
+ if (getSuperstep() == 1) {
+ restrictNeighbors();
+ } 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/P1ForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P1ForPathMergeVertex.java
index 6e42280..d78a7cd 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
@@ -5,6 +5,7 @@
import java.util.Iterator;
import edu.uci.ics.genomix.type.EdgeWritable;
+import edu.uci.ics.genomix.type.NodeWritable.EDGETYPE;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
import edu.uci.ics.genomix.type.VKmerListWritable;
import edu.uci.ics.genomix.type.NodeWritable.DIR;
@@ -14,6 +15,7 @@
import edu.uci.ics.genomix.pregelix.io.message.PathMergeMessageWritable;
import edu.uci.ics.genomix.pregelix.operator.aggregator.StatisticsAggregator;
import edu.uci.ics.genomix.pregelix.type.MessageFlag;
+import edu.uci.ics.genomix.pregelix.util.VertexUtil;
/**
* Graph clean pattern: P1(Naive-algorithm) for path merge
@@ -150,8 +152,8 @@
* do some remove operations on adjMap after receiving the info about dead Vertex
*/
public void responseToDeadVertexAndUpdateEdges(){
- byte meToNeighborDir = (byte) (incomingMsg.getFlag() & MessageFlag.DIR_MASK);
- byte neighborToMeDir = mirrorDirection(meToNeighborDir);
+ EDGETYPE meToNeighborDir = EDGETYPE.fromByte(incomingMsg.getFlag());
+ EDGETYPE neighborToMeDir = meToNeighborDir.mirror();
if(getVertexValue().getEdgeList(neighborToMeDir).getEdge(incomingMsg.getSourceVertexId()) != null){
tmpEdge.setAsCopy(getVertexValue().getEdgeList(neighborToMeDir).getEdge(incomingMsg.getSourceVertexId()));
@@ -159,7 +161,7 @@
getVertexValue().getEdgeList(neighborToMeDir).remove(incomingMsg.getSourceVertexId());
}
tmpEdge.setKey(incomingMsg.getNode().getInternalKmer());
- byte updateDir = flipDirection(neighborToMeDir, incomingMsg.isFlip());
+ EDGETYPE updateDir = incomingMsg.isFlip() ? neighborToMeDir.flip() : neighborToMeDir;
getVertexValue().getEdgeList(updateDir).unionAdd(tmpEdge);
}
@@ -262,6 +264,76 @@
voteToHalt();
}
+ /**
+ * start sending message
+ */
+ public void startSendMsg() {
+ if(isTandemRepeat(getVertexValue())){
+ copyWithoutTandemRepeats(getVertexValue(), tmpValue);
+ outFlag = 0;
+ sendSettledMsgToAllNeighborNodes(tmpValue);
+ voteToHalt();
+ } else{
+ /** check incoming **/
+ // update internal state
+ if (VertexUtil.isVertexWithOnlyOneIncoming(getVertexValue())){
+ byte state = 0;
+ state |= State.HEAD_CAN_MERGEWITHPREV;
+ getVertexValue().setState(state);
+ activate();
+ }
+ // send to neighbors
+ else if (VertexUtil.isVertexWithManyIncoming(getVertexValue())){
+ outFlag = 0;
+ sendSettledMsgs(DIR.PREVIOUS, getVertexValue());
+ }
+
+ /** check outgoing **/
+ // update internal state
+ if (VertexUtil.isVertexWithOnlyOneOutgoing(getVertexValue())){
+ byte state = 0;
+ state |= State.HEAD_CAN_MERGEWITHNEXT;
+ getVertexValue().setState(state);
+ activate();
+ }
+ // send to neighbors
+ else if (VertexUtil.isVertexWithManyOutgoing(getVertexValue())){
+ outFlag = 0;
+ sendSettledMsgs(DIR.NEXT, getVertexValue());
+ }
+
+ if(VertexUtil.isUnMergeVertex(getVertexValue()))
+ voteToHalt();
+ }
+ }
+
+ public void initState(Iterator<PathMergeMessageWritable> msgIterator) {
+ if(isInactiveNode())
+ voteToHalt();
+ else{
+ while (msgIterator.hasNext()) {
+ incomingMsg = msgIterator.next();
+ switch(getHeadMergeDir()){
+ case State.PATH_NON_HEAD: // TODO Change name to Path
+ setHeadMergeDir();
+ activate();
+ break;
+ case State.HEAD_CAN_MERGEWITHPREV: // TODO aggregate all the incomingMsgs first, then make a decision about halting
+ case State.HEAD_CAN_MERGEWITHNEXT:
+ if(true){ //if (getHeadFlagAndMergeDir() != getMsgFlagAndMergeDir()){
+ getVertexValue().setState(State.HEAD_CANNOT_MERGE);
+ voteToHalt();
+ }
+ break;
+ case State.HEAD_CANNOT_MERGE:
+ voteToHalt();
+ break;
+ }
+ }
+ }
+ }
+
+
@Override
public void compute(Iterator<PathMergeMessageWritable> msgIterator) {
initVertex();
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 7b97260..4a168af 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
@@ -21,6 +21,7 @@
import edu.uci.ics.genomix.pregelix.type.MessageFlag;
import edu.uci.ics.genomix.pregelix.type.MessageType;
import edu.uci.ics.genomix.type.NodeWritable.DIR;
+import edu.uci.ics.genomix.type.NodeWritable.EDGETYPE;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
import edu.uci.ics.genomix.type.VKmerListWritable;
import edu.uci.ics.pregelix.api.graph.Vertex;
@@ -227,25 +228,25 @@
}
public void sendP2MergeMsgByIncomingMsgDir(){
- byte meToNeighborDir = (byte) (incomingMsg.getFlag() & MessageFlag.DIR_MASK);
+ EDGETYPE meToNeighborDir = EDGETYPE.fromByte(incomingMsg.getFlag());
switch(meToNeighborDir){
- case MessageFlag.DIR_FF:
- case MessageFlag.DIR_FR:
+ case FF:
+ case FR:
outgoingMsg.setMessageType(P2MessageType.FROM_SUCCESSOR);
break;
- case MessageFlag.DIR_RF:
- case MessageFlag.DIR_RR:
+ case RF:
+ case RR:
outgoingMsg.setMessageType(P2MessageType.FROM_PREDECESSOR);
break;
}
- byte neighborToMeDir = mirrorDirection(meToNeighborDir);
+ EDGETYPE neighborToMeDir = meToNeighborDir.mirror();
switch(neighborToMeDir){
- case MessageFlag.DIR_FF:
- case MessageFlag.DIR_FR:
+ case FF:
+ case FR:
configureP2MergeMsgForSuccessor(incomingMsg.getSourceVertexId());
break;
- case MessageFlag.DIR_RF:
- case MessageFlag.DIR_RR:
+ case RF:
+ case RR:
configureP2MergeMsgForPredecessor(incomingMsg.getSourceVertexId());
break;
}
@@ -276,8 +277,8 @@
* final merge and updateAdjList having parameter for p2
*/
public void processP2Merge(P2PathMergeMessageWritable msg){
- byte meToNeighborDir = (byte) (msg.getFlag() & MessageFlag.DIR_MASK);
- byte neighborToMeDir = mirrorDirection(meToNeighborDir);
+ EDGETYPE meToNeighborDir = EDGETYPE.fromByte(msg.getFlag());
+ EDGETYPE neighborToMeDir = meToNeighborDir.mirror();
getVertexValue().getMergeNode(msg.getMessageType()).mergeWithNode(neighborToMeDir, msg.getNode());
getVertexValue().getNode().mergeWithNodeWithoutKmer(neighborToMeDir, msg.getNode());
@@ -291,32 +292,32 @@
outFlag |= MessageFlag.IS_FINAL;
outgoingMsg.setUpdateMsg(false);
outgoingMsg.setApexMap(getVertexValue().getApexMap());
- byte meToNeighborDir = (byte) (incomingMsg.getFlag() & MessageFlag.DIR_MASK);
+ EDGETYPE meToNeighborDir = EDGETYPE.fromByte(incomingMsg.getFlag());
switch(meToNeighborDir){
- case MessageFlag.DIR_FF:
- case MessageFlag.DIR_FR:
+ case FF:
+ case FR:
outgoingMsg.setMessageType(P2MessageType.FROM_SUCCESSOR);
break;
- case MessageFlag.DIR_RF:
- case MessageFlag.DIR_RR:
+ case RF:
+ case RR:
outgoingMsg.setMessageType(P2MessageType.FROM_PREDECESSOR);
break;
}
- byte neighborToMeDir = mirrorDirection(meToNeighborDir);
+ EDGETYPE neighborToMeDir = meToNeighborDir.mirror();
switch(neighborToMeDir){
- case MessageFlag.DIR_FF:
- case MessageFlag.DIR_FR:
+ case FF:
+ case FR:
outFlag &= MessageFlag.DIR_CLEAR;
- outFlag |= neighborToMeDir;
+ outFlag |= neighborToMeDir.get();
outgoingMsg.setFlag(outFlag);
outgoingMsg.setSourceVertexId(getVertexId());
outgoingMsg.setNode(getVertexValue().getPrependMergeNode());
sendMsg(incomingMsg.getSourceVertexId(), outgoingMsg);
break;
- case MessageFlag.DIR_RF:
- case MessageFlag.DIR_RR:
+ case RF:
+ case RR:
outFlag &= MessageFlag.DIR_CLEAR;
- outFlag |= neighborToMeDir;
+ outFlag |= neighborToMeDir.get();
outgoingMsg.setFlag(outFlag);
outgoingMsg.setSourceVertexId(getVertexId());
outgoingMsg.setNode(getVertexValue().getAppendMergeNode());
@@ -405,16 +406,16 @@
* check if it is a valid update node
*/
public boolean isValidUpateNode(){
- byte meToNeighborDir = (byte)(incomingMsg.getFlag() & MessageFlag.DIR_MASK);
- byte neighborToMeDir = mirrorDirection(meToNeighborDir);
+ EDGETYPE meToNeighborDir = EDGETYPE.fromByte(incomingMsg.getFlag());
+ EDGETYPE neighborToMeDir = meToNeighborDir.mirror();
boolean flag = false;
switch(neighborToMeDir){
- case MessageFlag.DIR_FF:
- case MessageFlag.DIR_FR:
+ case FF:
+ case FR:
flag = ((getVertexValue().getState() & MessageFlag.HEAD_CAN_MERGE_MASK) == MessageFlag.HEAD_CAN_MERGEWITHPREV);
break;
- case MessageFlag.DIR_RF:
- case MessageFlag.DIR_RR:
+ case RF:
+ case RR:
flag = ((getVertexValue().getState() & MessageFlag.HEAD_CAN_MERGE_MASK) == MessageFlag.HEAD_CAN_MERGEWITHNEXT);
break;
}
@@ -430,7 +431,7 @@
if(isHaltNode())
voteToHalt();
else if(isHeadNode() && !isTandemRepeat(getVertexValue())){
- if(isValidPath()){
+ if(true){ //isValidPath()
setHeadMergeDir();
//set deleteKmer and deleteDir
KmerAndDirWritable kmerAndDir = new KmerAndDirWritable();
@@ -444,7 +445,7 @@
getVertexValue().setState(MessageFlag.IS_HALT);
voteToHalt();
}
- } else if(getHeadFlagAndMergeDir() == getMsgFlagAndMergeDir()){
+ } else if(isHeadNode()){ //getHeadFlagAndMergeDir() == getMsgFlagAndMergeDir()
activate();
} else{ // already set up
// if headMergeDir are not the same
@@ -459,8 +460,9 @@
*/
public void updateApexEdges(){
KmerAndDirWritable deleteEdge = incomingMsg.getApexMap().get(getVertexId());
- if(deleteEdge != null && getVertexValue().getEdgeList(deleteEdge.getDeleteDir()).contains(deleteEdge.getDeleteKmer())) //avoid to delete twice
- getVertexValue().getEdgeList(deleteEdge.getDeleteDir()).remove(deleteEdge.getDeleteKmer());
+ EDGETYPE deleteEdgeType = EDGETYPE.fromByte(deleteEdge.getDeleteDir());
+ if(deleteEdge != null && getVertexValue().getEdgeList(deleteEdgeType).contains(deleteEdge.getDeleteKmer())) //avoid to delete twice
+ getVertexValue().getEdgeList(deleteEdgeType).remove(deleteEdge.getDeleteKmer());
processFinalUpdate2();
getVertexValue().setState(MessageFlag.IS_HALT);
voteToHalt();
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 4ae0d42..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
@@ -7,14 +7,11 @@
import edu.uci.ics.genomix.config.GenomixJobConf;
import edu.uci.ics.genomix.pregelix.client.Client;
import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
-import edu.uci.ics.genomix.pregelix.io.VertexValueWritable.State;
+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.pregelix.type.StatisticsCounter;
import edu.uci.ics.genomix.type.NodeWritable.DIR;
-import edu.uci.ics.genomix.type.NodeWritable.DirectionFlag;
-import edu.uci.ics.genomix.type.NodeWritable.IncomingListFlag;
-import edu.uci.ics.genomix.type.NodeWritable.OutgoingListFlag;
+import edu.uci.ics.genomix.type.NodeWritable.EDGETYPE;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
/**
@@ -25,6 +22,8 @@
public class P4ForPathMergeVertex extends
BasicPathMergeVertex<VertexValueWritable, PathMergeMessageWritable> {
+// private static final Logger LOG = Logger.getLogger(P4ForPathMergeVertex.class.getName());
+
private static long randSeed = 1; //static for save memory
private float probBeingRandomHead = -1;
private Random randGenerator = null;
@@ -37,8 +36,8 @@
private boolean curHead;
private boolean nextHead;
private boolean prevHead;
- private byte nextDir;
- private byte prevDir;
+ private EDGETYPE nextEdgetype;
+ private EDGETYPE prevEdgetype;
/**
* initiate kmerSize, maxIteration
@@ -52,10 +51,6 @@
outgoingMsg = new PathMergeMessageWritable();
else
outgoingMsg.reset();
- if(aggregatingMsg == null)
- aggregatingMsg = new PathMergeMessageWritable();
- else
- aggregatingMsg.reset();
if(destVertexId == null)
destVertexId = new VKmerBytesWritable();
randSeed = Long.parseLong(getContext().getConfiguration().get(GenomixJobConf.PATHMERGE_RANDOM_RANDSEED)); // also can use getSuperstep(), because it is better to debug under deterministically random
@@ -81,58 +76,30 @@
counters.clear();
getVertexValue().getCounters().clear();
}
-
+
protected boolean isNodeRandomHead(VKmerBytesWritable nodeKmer) {
// "deterministically random", based on node id
randGenerator.setSeed((randSeed ^ nodeKmer.hashCode()) * 10000 * getSuperstep());//randSeed + nodeID.hashCode()
for(int i = 0; i < 500; i++)
randGenerator.nextFloat();
- return randGenerator.nextFloat() < probBeingRandomHead;
+ boolean isHead = randGenerator.nextFloat() < probBeingRandomHead;
+// LOG.info("randomHead: " + nodeKmer + "=" + isHead);
+ return isHead;
}
/**
- * checks if there is a valid, mergeable neighbor in the given direction. sets next/prev Kmer and next/prev Head to the valid neighbor's values
- */
- protected boolean setNeighbor(VertexValueWritable value, DIR direction) {
- byte headState = direction == DIR.PREVIOUS ? State.HEAD_CAN_MERGEWITHNEXT : State.HEAD_CAN_MERGEWITHPREV;
- int degree = direction == DIR.PREVIOUS ? value.inDegree() : value.outDegree();
- if(getHeadMergeDir() == headState)
- return false;
- if (degree != 1)
- throw new IllegalStateException("Node is not HEAD_CANMERGE but has degree of " + degree + " in " + direction + " direction\n" + value);
- if (isTandemRepeat(value))
- throw new IllegalStateException("Node is tandem repeat but is trying to send update message! " + value);
-
- byte[] dirs = direction == DIR.PREVIOUS ? IncomingListFlag.values : OutgoingListFlag.values;
- for(byte dir : dirs){
- if(value.getEdgeList(dir).getCountOfPosition() > 0){
- if (direction == DIR.NEXT) {
- nextKmer = value.getEdgeList(dir).get(0).getKey();
- nextHead = isNodeRandomHead(nextKmer);
- return true;
- } else {
- prevKmer = value.getEdgeList(dir).get(0).getKey();
- prevHead = isNodeRandomHead(prevKmer);
- return true;
- }
- }
- }
- throw new IllegalStateException("outdegree apparently 0? but not HEAD_CAN_MERGEWITHPREV..." + value.outDegree() + "\n" + value);
- }
-
- /**
- * checks if there is a valid, mergeable neighbor in the given direction. sets hasNext/Prev, next/prevDir, Kmer and Head
+ * checks if there is a valid, mergeable neighbor in the given direction. sets hasNext/Prev, next/prevEdgetype, Kmer and Head
*/
protected void checkNeighbors() {
VertexValueWritable vertex = getVertexValue();
EnumSet<DIR> restrictedDirs = DIR.enumSetFromByte(vertex.getState());
// NEXT restricted by neighbor or by my edges?
- if (restrictedDirs.contains(DIR.NEXT) || vertex.outDegree() != 1) {
+ if (restrictedDirs.contains(DIR.NEXT) || vertex.outDegree() != 1) { // TODO should I restrict based on degree in the first iteration?
hasNext = false;
} else {
hasNext = true;
- nextDir = vertex.getEdgeList(DirectionFlag.DIR_FF).getCountOfPosition() > 0 ? DirectionFlag.DIR_FF : DirectionFlag.DIR_FR;
- nextKmer = vertex.getEdgeList(nextDir).get(0).getKey();
+ nextEdgetype = vertex.getEdgetypeFromDir(DIR.NEXT); //getEdgeList(EDGETYPE.FF).getCountOfPosition() > 0 ? EDGETYPE.FF : EDGETYPE.FR;
+ nextKmer = vertex.getEdgeList(nextEdgetype).get(0).getKey();
nextHead = isNodeRandomHead(nextKmer);
}
@@ -141,35 +108,30 @@
hasPrev = false;
} else {
hasPrev = true;
- prevDir = vertex.getEdgeList(DirectionFlag.DIR_RF).getCountOfPosition() > 0 ? DirectionFlag.DIR_RF : DirectionFlag.DIR_RR;
- prevKmer = vertex.getEdgeList(prevDir).get(0).getKey();
+ 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);
}
}
- /**
- * step1 : sendUpdates
- */
- public void sendUpdates(){
+ public void chooseMergeDir() {
//initiate merge_dir
- setStateAsNoMerge();
+ setMerge(P4State.NO_MERGE);
- // only PATH vertices are present. Find the ID's for my neighbors
curKmer = getVertexId();
curHead = isNodeRandomHead(curKmer);
-
- // the headFlag and tailFlag's indicate if the node is at the beginning or end of a simple path.
- // We prevent merging towards non-path nodes
checkNeighbors();
- DIR mergeDir = null;
- if (hasNext || hasPrev) {
+
+ if (!hasNext && !hasPrev) { // TODO check if logic for previous updates is the same as here (just look at internal flags?)
+ voteToHalt(); // this node can never merge (restricted by neighbors or my structure)
+ } else {
if (curHead) {
if (hasNext && !nextHead) {
// compress this head to the forward tail
- mergeDir = DIR.NEXT;
+ setMerge((byte) (nextEdgetype.get() | P4State.MERGE));
} else if (hasPrev && !prevHead) {
// compress this head to the reverse tail
- mergeDir = DIR.PREVIOUS;
+ setMerge((byte) (prevEdgetype.get() | P4State.MERGE));
}
}
else {
@@ -178,95 +140,46 @@
if ((!nextHead && !prevHead) && (curKmer.compareTo(nextKmer) < 0 && curKmer.compareTo(prevKmer) < 0)) {
// tails on both sides, and I'm the "local minimum"
// compress me towards the tail in forward dir
- mergeDir = DIR.NEXT;
+ setMerge((byte) (nextEdgetype.get() | P4State.MERGE));
}
} else if (!hasPrev) {
// no previous node
if (!nextHead && curKmer.compareTo(nextKmer) < 0) {
// merge towards tail in forward dir
- mergeDir = DIR.NEXT;
+ setMerge((byte) (nextEdgetype.get() | P4State.MERGE));
}
} else if (!hasNext) {
// no next node
if (!prevHead && curKmer.compareTo(prevKmer) < 0) {
// merge towards tail in reverse dir
- mergeDir = DIR.PREVIOUS;
+ setMerge((byte) (prevEdgetype.get() | P4State.MERGE));
}
}
}
- } // TODO else voteToHalt (when I combine steps 2 and 3)
- if(mergeDir != null){
- setStateAsMergeDir(mergeDir);
- sendUpdateMsg(isP4, revert(mergeDir));
- this.activate();
}
- }
-
- /**
- * step2: receiveUpdates
- */
- public void receiveUpdates(Iterator<PathMergeMessageWritable> msgIterator){
- //update neighber
- while (msgIterator.hasNext()) {
- incomingMsg = msgIterator.next();
- processUpdate(incomingMsg);
- }
- checkNeighbors();
- if (!hasNext && !hasPrev)
- voteToHalt();
- else
- activate();
- }
-
- /**
- * step4: processMerges
- */
- public void receiveMerges(Iterator<PathMergeMessageWritable> msgIterator){
- //merge tmpKmer
- while (msgIterator.hasNext()) {
- incomingMsg = msgIterator.next();
- /** process merge **/
- processMerge(incomingMsg);
- // set statistics counter: Num_MergedNodes
- updateStatisticsCounter(StatisticsCounter.Num_MergedNodes);
- /** if it's a tandem repeat, which means detecting cycle **/
- if(isTandemRepeat(getVertexValue())){
- short state = getVertexValue().getState();
- state |= (short) (DIR.NEXT.get() | DIR.PREVIOUS.get());
- getVertexValue().setState(state);
- // set statistics counter: Num_Cycles
- updateStatisticsCounter(StatisticsCounter.Num_Cycles);
- voteToHalt();
- }
- /** head meets head, stop **/
- checkNeighbors();
- if (!hasNext && !hasPrev){
- // set statistics counter: Num_MergedPaths
- updateStatisticsCounter(StatisticsCounter.Num_MergedPaths);
- voteToHalt();
- }else{
- activate();
- }
- getVertexValue().setCounters(counters);
- }
+// if ((getVertexValue().getState() & P4State.MERGE) == 0) {
+// LOG.info("No merge for " + getVertexId());
+// } else {
+// LOG.info("Merge from " + getVertexId() + " towards " + (getVertexValue().getState() & DirectionFlag.DIR_MASK) + "; node is " + getVertexValue());
+// }
}
@Override
public void compute(Iterator<PathMergeMessageWritable> msgIterator) {
initVertex();
- if (getSuperstep() == 1)
+
+ if (getSuperstep() == 1) {
restrictNeighbors();
- else if (getSuperstep() % 2 == 0){
+ } else if (getSuperstep() % 2 == 0) {
if (getSuperstep() == 2)
recieveRestrictions(msgIterator);
else
receiveMerges(msgIterator);
-
- sendUpdates();
- }
- else if (getSuperstep() % 2 == 1){
+ chooseMergeDir();
+ updateNeighbors();
+ } else if (getSuperstep() % 2 == 1) {
receiveUpdates(msgIterator);
- sendMergeMsg(isP4);
+ sendMergeMsg();
}
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/removelowcoverage/RemoveLowCoverageVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/removelowcoverage/RemoveLowCoverageVertex.java
index cef3131..0696a53 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/removelowcoverage/RemoveLowCoverageVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/removelowcoverage/RemoveLowCoverageVertex.java
@@ -5,12 +5,14 @@
import java.util.Iterator;
import java.util.Set;
+import edu.uci.ics.genomix.config.GenomixJobConf;
import edu.uci.ics.genomix.pregelix.client.Client;
import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
import edu.uci.ics.genomix.pregelix.io.message.MessageWritable;
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.type.NodeWritable.EDGETYPE;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
/**
@@ -29,7 +31,9 @@
*/
@Override
public void initVertex() {
- super.initVertex();
+ super.initVertex();
+ if (minAverageCoverage < 0)
+ minAverageCoverage = Float.parseFloat(getContext().getConfiguration().get(GenomixJobConf.REMOVE_LOW_COVERAGE_MAX_COVERAGE));
if(incomingMsg == null)
incomingMsg = new MessageWritable();
if(outgoingMsg == null)
@@ -38,11 +42,6 @@
outgoingMsg.reset();
if(destVertexId == null)
destVertexId = new VKmerBytesWritable();
- if(fakeVertex == null){
- fakeVertex = new VKmerBytesWritable();
- String random = generaterRandomString(kmerSize + 1);
- fakeVertex.setByRead(kmerSize + 1, random.getBytes(), 0);
- }
if(getSuperstep() == 1)
StatisticsAggregator.preGlobalCounters.clear();
// else
@@ -51,32 +50,42 @@
getVertexValue().getCounters().clear();
}
+ public void detectLowCoverageVertex(){
+ if(getVertexValue().getAvgCoverage() <= minAverageCoverage){
+ //broadcase kill self
+ broadcastKillself();
+ deadNodeSet.add(new VKmerBytesWritable(getVertexId()));
+ }
+ }
+
+ public void cleanupDeadVertex(){
+ deleteVertex(getVertexId());
+ //set statistics counter: Num_RemovedLowCoverageNodes
+ updateStatisticsCounter(StatisticsCounter.Num_RemovedLowCoverageNodes);
+ getVertexValue().setCounters(counters);
+ }
+
+ public void responseToDeadVertex(Iterator<MessageWritable> msgIterator){
+ while(msgIterator.hasNext()){
+ incomingMsg = msgIterator.next();
+ //response to dead node
+ EDGETYPE deadToMeEdgetype = EDGETYPE.fromByte(incomingMsg.getFlag());
+ getVertexValue().getEdgeList(deadToMeEdgetype).remove(incomingMsg.getSourceVertexId());
+ }
+ }
+
@Override
public void compute(Iterator<MessageWritable> msgIterator) {
initVertex();
- if(getSuperstep() == 1){
- if(getVertexValue().getAvgCoverage() <= minAverageCoverage){
- broadcaseReallyKillself();
- deadNodeSet.add(new VKmerBytesWritable(getVertexId()));
- }
+ if(getSuperstep() == 1)
+ detectLowCoverageVertex();
+ else if(getSuperstep() == 2){
+ if(deadNodeSet.contains(getVertexId()))
+ cleanupDeadVertex();
else
- voteToHalt();
- } else if(getSuperstep() == 2){
- if(deadNodeSet.contains(getVertexId())){
- deleteVertex(getVertexId());
- //set statistics counter: Num_RemovedLowCoverageNodes
- updateStatisticsCounter(StatisticsCounter.Num_RemovedLowCoverageNodes);
- getVertexValue().setCounters(counters);
- }
- else{
- while(msgIterator.hasNext()){
- incomingMsg = msgIterator.next();
- if(isResponseKillMsg())
- responseToDeadVertex();
- }
- }
- voteToHalt();
+ responseToDeadVertex(msgIterator);
}
+ voteToHalt();
}
public static void main(String[] args) throws Exception {
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 ad85a90..74629d4 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
@@ -8,10 +8,10 @@
import edu.uci.ics.genomix.pregelix.io.message.BFSTraverseMessageWritable;
import edu.uci.ics.genomix.pregelix.operator.BasicGraphCleanVertex;
import edu.uci.ics.genomix.pregelix.type.EdgeDirs;
-import edu.uci.ics.genomix.pregelix.type.MessageFlag;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
import edu.uci.ics.genomix.type.VKmerListWritable;
import edu.uci.ics.genomix.type.NodeWritable.DIR;
+import edu.uci.ics.genomix.type.NodeWritable.EDGETYPE;
public class BFSTraverseVertex extends
BasicGraphCleanVertex<VertexValueWritable, BFSTraverseMessageWritable> {
@@ -86,54 +86,54 @@
kmerList.append(getVertexId());
outgoingMsg.setPathList(kmerList);
outgoingMsg.setReadId(incomingMsg.getReadId()); //only one readId
- byte meToNeighborDir = (byte) (incomingMsg.getFlag() & MessageFlag.DIR_MASK);
- byte neighborToMeDir = mirrorDirection(meToNeighborDir);
+ EDGETYPE meToNeighborDir = EDGETYPE.fromByte(incomingMsg.getFlag());
+ EDGETYPE neighborToMeDir = meToNeighborDir.mirror();
/** set edgeDirs **/
setEdgeDirs(meToNeighborDir, neighborToMeDir);
switch(neighborToMeDir){
- case MessageFlag.DIR_FF:
- case MessageFlag.DIR_FR:
+ case FF:
+ case FR:
sendSettledMsgs(DIR.PREVIOUS ,getVertexValue());
break;
- case MessageFlag.DIR_RF:
- case MessageFlag.DIR_RR:
+ case RF:
+ case RR:
sendSettledMsgs(DIR.NEXT, getVertexValue());
break;
}
}
- public void setEdgeDirs(byte meToNeighborDir, byte neighborToMeDir){
+ public void setEdgeDirs(EDGETYPE meToNeighborDir, EDGETYPE neighborToMeDir){
edgeDirsList.clear();
edgeDirsList.addAll(incomingMsg.getEdgeDirsList());
if(edgeDirsList.isEmpty()){ //first time from srcNode
/** set srcNode's next dir **/
edgeDirs.reset();
- edgeDirs.setNextToMeDir(meToNeighborDir);
+ edgeDirs.setNextToMeDir(meToNeighborDir.get());
edgeDirsList.add(new EdgeDirs(edgeDirs));
/** set curNode's prev dir **/
edgeDirs.reset();
- edgeDirs.setPrevToMeDir(neighborToMeDir);
+ edgeDirs.setPrevToMeDir(neighborToMeDir.get());
edgeDirsList.add(new EdgeDirs(edgeDirs));
} else {
/** set preNode's next dir **/
edgeDirs.set(edgeDirsList.get(edgeDirsList.size() - 1));
- edgeDirs.setNextToMeDir(meToNeighborDir);
+ edgeDirs.setNextToMeDir(meToNeighborDir.get());
edgeDirsList.set(edgeDirsList.size() - 1, new EdgeDirs(edgeDirs));
/** set curNode's prev dir **/
edgeDirs.reset();
- edgeDirs.setPrevToMeDir(neighborToMeDir);
+ edgeDirs.setPrevToMeDir(neighborToMeDir.get());
edgeDirsList.add(new EdgeDirs(edgeDirs));
}
outgoingMsg.setEdgeDirsList(edgeDirsList);
}
public boolean isValidDestination(){
- byte meToNeighborDir = (byte) (incomingMsg.getFlag() & MessageFlag.DIR_MASK);
- byte neighborToMeDir = mirrorDirection(meToNeighborDir);
+ EDGETYPE meToNeighborDir = EDGETYPE.fromByte(incomingMsg.getFlag());
+ EDGETYPE neighborToMeDir = meToNeighborDir.mirror();
if(incomingMsg.isDestFlip())
- return neighborToMeDir == MessageFlag.DIR_RF || neighborToMeDir == MessageFlag.DIR_RR;
+ return neighborToMeDir == EDGETYPE.RF || neighborToMeDir == EDGETYPE.RR;
else
- return neighborToMeDir == MessageFlag.DIR_FF || neighborToMeDir == MessageFlag.DIR_FR;
+ return neighborToMeDir == EDGETYPE.FF || neighborToMeDir == EDGETYPE.FR;
}
public void sendMsgToPathNodeToAddCommondReadId(){
@@ -164,8 +164,8 @@
kmerList.setCopy(incomingMsg.getPathList());
kmerList.append(getVertexId());
incomingMsg.setPathList(kmerList);
- byte meToNeighborDir = (byte) (incomingMsg.getFlag() & MessageFlag.DIR_MASK);
- byte neighborToMeDir = mirrorDirection(meToNeighborDir);
+ EDGETYPE meToNeighborDir = EDGETYPE.fromByte(incomingMsg.getFlag());
+ EDGETYPE neighborToMeDir = meToNeighborDir.mirror();
setEdgeDirs(meToNeighborDir, neighborToMeDir);
incomingMsg.setEdgeDirsList(outgoingMsg.getEdgeDirsList());
}
@@ -176,12 +176,12 @@
byte prevToMeDir = incomingMsg.getEdgeDirsList().get(0).getPrevToMeDir();
tmpKmer.setAsCopy(incomingMsg.getPathList().getPosition(0));
if(tmpKmer.getKmerLetterLength() != 0)
- getVertexValue().getEdgeList(prevToMeDir).getReadIDs(tmpKmer).appendReadId(readId);
+ getVertexValue().getEdgeList(EDGETYPE.fromByte(prevToMeDir)).getReadIDs(tmpKmer).appendReadId(readId);
//set readId to next edge
byte nextToMeDir = incomingMsg.getEdgeDirsList().get(0).getNextToMeDir();
tmpKmer.setAsCopy(incomingMsg.getPathList().getPosition(1));
if(tmpKmer.getKmerLetterLength() != 0)
- getVertexValue().getEdgeList(nextToMeDir).getReadIDs(tmpKmer).appendReadId(readId);
+ getVertexValue().getEdgeList(EDGETYPE.fromByte(nextToMeDir)).getReadIDs(tmpKmer).appendReadId(readId);
}
@Override
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/splitrepeat/SplitRepeatVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/splitrepeat/SplitRepeatVertex.java
index 2bbe758..c00078c 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/splitrepeat/SplitRepeatVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/splitrepeat/SplitRepeatVertex.java
@@ -11,10 +11,10 @@
import edu.uci.ics.genomix.pregelix.io.message.SplitRepeatMessageWritable;
import edu.uci.ics.genomix.pregelix.operator.BasicGraphCleanVertex;
import edu.uci.ics.genomix.pregelix.operator.aggregator.StatisticsAggregator;
-import edu.uci.ics.genomix.pregelix.type.MessageFlag;
import edu.uci.ics.genomix.pregelix.type.StatisticsCounter;
import edu.uci.ics.genomix.type.EdgeListWritable;
import edu.uci.ics.genomix.type.EdgeWritable;
+import edu.uci.ics.genomix.type.NodeWritable.EDGETYPE;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
import edu.uci.ics.pregelix.api.graph.Vertex;
import edu.uci.ics.pregelix.api.util.BspUtils;
@@ -28,20 +28,20 @@
BasicGraphCleanVertex<VertexValueWritable, SplitRepeatMessageWritable>{
public class EdgeAndDir{
- private byte dir;
+ private EDGETYPE edgeType;
private EdgeWritable edge;
public EdgeAndDir(){
- dir = 0;
+ edgeType = null;
edge = new EdgeWritable();
}
- public byte getDir() {
- return dir;
+ public EDGETYPE getDir() {
+ return edgeType;
}
- public void setDir(byte dir) {
- this.dir = dir;
+ public void setDir(EDGETYPE dir) {
+ this.edgeType = dir;
}
public EdgeWritable getEdge() {
@@ -174,11 +174,11 @@
deletedEdge.setReadIDs(neighborEdgeIntersection);
outgoingMsg.setDeletedEdge(deletedEdge);
- outgoingMsg.setFlag(incomingEdgeDir);
+ outgoingMsg.setFlag(incomingEdgeType.get());
destVertexId.setAsCopy(incomingEdge.getKey());
sendMsg(destVertexId, outgoingMsg);
- outgoingMsg.setFlag(outgoingEdgeDir);
+ outgoingMsg.setFlag(outgoingEdgeType.get());
destVertexId.setAsCopy(outgoingEdge.getKey());
sendMsg(destVertexId, outgoingMsg);
}
@@ -199,15 +199,15 @@
}
public void deleteEdgeFromOldVertex(EdgeAndDir deleteEdge){
- getVertexValue().getEdgeList(deleteEdge.dir).removeSubEdge(deleteEdge.getEdge());
+ getVertexValue().getEdgeList(deleteEdge.edgeType).removeSubEdge(deleteEdge.getEdge());
}
public void updateEdgeListPointToNewVertex(){
- byte meToNeighborDir = (byte) (incomingMsg.getFlag() & MessageFlag.VERTEX_MASK);
- byte neighborToMeDir = mirrorDirection(meToNeighborDir);
+ EDGETYPE meToNeighborDir = EDGETYPE.fromByte(incomingMsg.getFlag());//(byte) (incomingMsg.getFlag() & MessageFlag.VERTEX_MASK);
+ EDGETYPE neighborToMeDir = meToNeighborDir.mirror();
getVertexValue().getEdgeList(neighborToMeDir).removeSubEdge(incomingMsg.getDeletedEdge());
- getVertexValue().getEdgeList(neighborToMeDir).add(incomingMsg.getCreatedEdge());
+ getVertexValue().getEdgeList(neighborToMeDir).add(new EdgeWritable(incomingMsg.getCreatedEdge()));
}
@Override
@@ -216,47 +216,47 @@
if(getSuperstep() == 1){
if(getVertexValue().getDegree() > 2){
deletedEdges.clear();
- /** process connectedTable **/
+ // process connectedTable
for(int i = 0; i < 4; i++){
- /** set edgeList and edgeDir based on connectedTable **/
- setEdgeListAndEdgeDir(i);
+ // set edgeList and edgeType based on connectedTable
+ setEdgeListAndEdgeType(i);
for(EdgeWritable incomingEdge : incomingEdgeList){
for(EdgeWritable outgoingEdge : outgoingEdgeList){
- /** set neighborEdge readId intersection **/
+ // set neighborEdge readId intersection
setNeighborEdgeIntersection(incomingEdge, outgoingEdge);
if(!neighborEdgeIntersection.isEmpty()){
- /** random generate vertexId of new vertex **/
+ // random generate vertexId of new vertex
randomGenerateVertexId(3);
- /** change incomingEdge/outgoingEdge's edgeList to commondReadIdSet **/
+ // change incomingEdge/outgoingEdge's edgeList to commondReadIdSet
tmpIncomingEdge.setAsCopy(incomingEdge);
tmpOutgoingEdge.setAsCopy(outgoingEdge);
tmpIncomingEdge.setReadIDs(neighborEdgeIntersection);
tmpOutgoingEdge.setReadIDs(neighborEdgeIntersection);
- /** create new/created vertex **/
+ // create new/created vertex
createNewVertex(i, tmpIncomingEdge, tmpOutgoingEdge);
//set statistics counter: Num_SplitRepeats
updateStatisticsCounter(StatisticsCounter.Num_SplitRepeats);
getVertexValue().setCounters(counters);
- /** send msg to neighbors to update their edges to new vertex **/
+ // send msg to neighbors to update their edges to new vertex
sendMsgToUpdateEdge(tmpIncomingEdge, tmpOutgoingEdge);
- /** store deleted edge **/
+ // store deleted edge
storeDeletedEdge(i, tmpIncomingEdge, tmpOutgoingEdge, neighborEdgeIntersection);
}
}
}
}
- /** delete extra edges from old vertex **/
+ // delete extra edges from old vertex
for(EdgeAndDir deletedEdge : deletedEdges){
deleteEdgeFromOldVertex(deletedEdge);
}
- /** Old vertex delete or voteToHalt **/
+ // Old vertex delete or voteToHalt
if(getVertexValue().getDegree() == 0)//if no any edge, delete
deleteVertex(getVertexId());
else
@@ -265,7 +265,7 @@
} else if(getSuperstep() == 2){
while(msgIterator.hasNext()){
incomingMsg = msgIterator.next();
- /** update edgelist to new/created vertex **/
+ // update edgelist to new/created vertex
updateEdgeListPointToNewVertex();
}
voteToHalt();
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 8b3ee23..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
@@ -6,6 +6,7 @@
import edu.uci.ics.genomix.type.EdgeListWritable;
import edu.uci.ics.genomix.type.EdgeWritable;
+import edu.uci.ics.genomix.type.NodeWritable.EDGETYPE;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
import edu.uci.ics.pregelix.api.graph.Vertex;
import edu.uci.ics.pregelix.api.job.PregelixJob;
@@ -16,38 +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> {
@@ -55,7 +28,7 @@
private VKmerBytesWritable splitNode = new VKmerBytesWritable("CTA");
private VKmerBytesWritable insertedTip = new VKmerBytesWritable("AGC");
- private byte tipToSplitDir = MessageFlag.DIR_RF;
+ private EDGETYPE tipToSplitDir = EDGETYPE.FR;
/**
* initiate kmerSize, length
*/
@@ -66,7 +39,7 @@
}
@SuppressWarnings({ "unchecked", "rawtypes" })
- public void insertTip(byte dir, EdgeListWritable edgeList, VKmerBytesWritable insertedTip){
+ public void insertTip(EDGETYPE dir, EdgeListWritable edgeList, VKmerBytesWritable insertedTip){
Vertex vertex = (Vertex) BspUtils.createVertex(getContext().getConfiguration());
vertex.getMsgList().clear();
vertex.getEdges().clear();
@@ -94,7 +67,7 @@
return edgeList;
}
- public void addEdgeToInsertedTip(byte dir, VKmerBytesWritable insertedTip){
+ public void addEdgeToInsertedTip(EDGETYPE dir, VKmerBytesWritable insertedTip){
EdgeWritable newEdge = new EdgeWritable();
newEdge.setKey(insertedTip);
newEdge.appendReadID(0);
@@ -102,24 +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
@@ -130,7 +85,7 @@
/** add edge pointing to insertedTip **/
addEdgeToInsertedTip(tipToSplitDir, insertedTip);
/** insert tip **/
- byte splitToTipDir = mirrorDirection(tipToSplitDir);
+ EDGETYPE splitToTipDir = tipToSplitDir.mirror();
insertTip(splitToTipDir, getEdgeListFromKmer(splitNode), insertedTip);
}
}
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..deff7db 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
@@ -41,44 +42,58 @@
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;
+ }
+
+ /**
+ * step1
+ */
+ public void detectTip(){
+ 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);
+ }
+ }
+
+ /**
+ * step2
+ */
+ public void responseToDeadTip(Iterator<MessageWritable> msgIterator){
+ while(msgIterator.hasNext()){
+ incomingMsg = msgIterator.next();
+ EDGETYPE tipToMeEdgetype = EDGETYPE.fromByte(incomingMsg.getFlag());
+ getVertexValue().getEdgeList(tipToMeEdgetype).remove(incomingMsg.getSourceVertexId());
+ }
+ }
+
@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);
- }
- }
- 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();
- }
- }
+ if(getSuperstep() == 1)
+ detectTip();
+ else if(getSuperstep() == 2)
+ responseToDeadTip(msgIterator);
voteToHalt();
}
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 0820011..390e5fe 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
@@ -1,5 +1,6 @@
package edu.uci.ics.genomix.pregelix.operator.unrolltandemrepeat;
+import java.util.EnumSet;
import java.util.Iterator;
import edu.uci.ics.genomix.pregelix.client.Client;
@@ -7,12 +8,11 @@
import edu.uci.ics.genomix.pregelix.io.message.MessageWritable;
import edu.uci.ics.genomix.pregelix.operator.BasicGraphCleanVertex;
import edu.uci.ics.genomix.pregelix.operator.aggregator.StatisticsAggregator;
-import edu.uci.ics.genomix.pregelix.type.MessageFlag;
import edu.uci.ics.genomix.pregelix.type.StatisticsCounter;
import edu.uci.ics.genomix.pregelix.util.VertexUtil;
import edu.uci.ics.genomix.type.EdgeWritable;
+import edu.uci.ics.genomix.type.NodeWritable.EDGETYPE;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
-import edu.uci.ics.genomix.type.NodeWritable.DirectionFlag;
/**
* Graph clean pattern: Unroll TandemRepeat
@@ -21,6 +21,7 @@
*/
public class UnrollTandemRepeat extends
BasicGraphCleanVertex<VertexValueWritable, MessageWritable>{
+
private EdgeWritable tmpEdge = new EdgeWritable();
/**
@@ -50,15 +51,15 @@
*/
public boolean repeatCanBeMerged(){
tmpValue.setAsCopy(getVertexValue());
- tmpValue.getEdgeList(repeatDir).remove(repeatKmer);
+ tmpValue.getEdgeList(repeatEdgetype).remove(repeatKmer);
boolean hasFlip = false;
- /** pick one edge and flip **/
- for(byte d : DirectionFlag.values){
- for(EdgeWritable edge : tmpValue.getEdgeList(d)){
- byte flipDir = flipDir(d);
+ // pick one edge and flip
+ for(EDGETYPE et : EnumSet.allOf(EDGETYPE.class)){
+ for(EdgeWritable edge : tmpValue.getEdgeList(et)){
+ EDGETYPE flipDir = et.flip();
tmpValue.getEdgeList(flipDir).add(edge);
- tmpValue.getEdgeList(d).remove(edge);
- /** setup hasFlip to go out of the loop **/
+ tmpValue.getEdgeList(et).remove(edge);
+ // setup hasFlip to go out of the loop
hasFlip = true;
break;
}
@@ -77,17 +78,17 @@
* merge tandem repeat
*/
public void mergeTandemRepeat(){
- getVertexValue().getInternalKmer().mergeWithKmerInDir(repeatDir, kmerSize, getVertexId());
- getVertexValue().getEdgeList(repeatDir).remove(getVertexId());
+ getVertexValue().getInternalKmer().mergeWithKmerInDir(repeatEdgetype, kmerSize, getVertexId());
+ getVertexValue().getEdgeList(repeatEdgetype).remove(getVertexId());
boolean hasFlip = false;
/** pick one edge and flip **/
- for(byte d : DirectionFlag.values){
- for(EdgeWritable edge : getVertexValue().getEdgeList(d)){
- byte flipDir = flipDir(d);
+ for(EDGETYPE et : EnumSet.allOf(EDGETYPE.class)){
+ for(EdgeWritable edge : getVertexValue().getEdgeList(et)){
+ EDGETYPE flipDir = et.flip();
getVertexValue().getEdgeList(flipDir).add(edge);
- getVertexValue().getEdgeList(d).remove(edge);
+ getVertexValue().getEdgeList(et).remove(edge);
/** send flip message to node for updating edgeDir **/
- outgoingMsg.setFlag(flipDir);
+ outgoingMsg.setFlag(flipDir.get());
outgoingMsg.setSourceVertexId(getVertexId());
sendMsg(edge.getKey(), outgoingMsg);
/** setup hasFlip to go out of the loop **/
@@ -103,9 +104,9 @@
* update edges
*/
public void updateEdges(){
- byte flipDir = flipDir((byte)(incomingMsg.getFlag() & MessageFlag.DEAD_MASK));
- byte prevNeighborToMe = mirrorDirection(flipDir);
- byte curNeighborToMe = mirrorDirection((byte)(incomingMsg.getFlag() & MessageFlag.DEAD_MASK));
+ EDGETYPE flipDir = EDGETYPE.fromByte(incomingMsg.getFlag());
+ EDGETYPE prevNeighborToMe = flipDir.mirror();
+ EDGETYPE curNeighborToMe = flipDir.mirror(); //mirrorDirection((byte)(incomingMsg.getFlag() & MessageFlag.DEAD_MASK));
tmpEdge.setAsCopy(getVertexValue().getEdgeList(prevNeighborToMe).getEdge(incomingMsg.getSourceVertexId()));
getVertexValue().getEdgeList(prevNeighborToMe).remove(incomingMsg.getSourceVertexId());
getVertexValue().getEdgeList(curNeighborToMe).add(tmpEdge);
@@ -117,8 +118,8 @@
if(getSuperstep() == 1){
if(isTandemRepeat(getVertexValue()) && repeatCanBeMerged()){
mergeTandemRepeat();
- //set statistics counter: Num_RemovedTips
- updateStatisticsCounter(StatisticsCounter.Num_RemovedTips);
+ //set statistics counter: Num_TandemRepeats
+ updateStatisticsCounter(StatisticsCounter.Num_TandemRepeats);
getVertexValue().setCounters(counters);
}
voteToHalt();
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/MessageFlag.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/MessageFlag.java
index 7cc8c1d..7905718 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/MessageFlag.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/MessageFlag.java
@@ -15,8 +15,13 @@
public static final byte[] values = { DIR_FF, DIR_FR, DIR_RF, DIR_RR };
- public static final short UNCHANGE = 0b0 << 8;
+ public static final short UNCHANGE = 0b0 << 7;
public static final short UPDATE = 0b01 << 7; //reuse 0b0 << 6, becasue UNCHANGE and UPDATE use for different patterns
+ public static final short MSG_TYPE_MASK = 0b1 << 7;
+ public static final short MSG_TYPE_CLEAR = 0b111111110111111;
+
+// public static final short UNCHANGE = 0b0 << 8;
+// public static final short UPDATE = 0b01 << 7; //reuse 0b0 << 6, becasue UNCHANGE and UPDATE use for different patterns
public static final short KILL = 0b1 << 8;
public static final short KILL_MASK = 0b1 << 8;
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/conf/logging.properties b/genomix/genomix-pregelix/src/test/resources/conf/logging.properties
index 1055652..0564c07 100644
--- a/genomix/genomix-pregelix/src/test/resources/conf/logging.properties
+++ b/genomix/genomix-pregelix/src/test/resources/conf/logging.properties
@@ -16,12 +16,11 @@
# By default we only configure a ConsoleHandler, which will only
# show messages at the INFO and above levels.
-handlers= java.util.logging.ConsoleHandler
+#handlers= java.util.logging.ConsoleHandler
# To also add the FileHandler, use the following line instead.
-#handlers= java.util.logging.FileHandler, java.util.logging.ConsoleHandler
-#handlers= java.util.logging.FileHandler
+handlers= java.util.logging.FileHandler, java.util.logging.ConsoleHandler
# Default global logging level.
# This specifies which kinds of events are logged across
@@ -42,19 +41,17 @@
# default file output is in user's home directory.
-# java.util.logging.FileHandler.pattern = logs/genomix-pregelix-tests.log
-# java.util.logging.FileHandler.limit = 0
+java.util.logging.FileHandler.pattern = pregelix.log
+# java.util.logging.FileHandler.limit = 50000
# java.util.logging.FileHandler.count = 1
-# java.util.logging.FileHandler.formatter = java.util.logging.XMLFormatter
# java.util.logging.FileHandler.formatter = java.util.logging.SimpleFormatter
-# java.util.logging.FileHandler.formatter = edu.uci.ics.genomix.pregelix.log.PathMergeLogFormatter
-# java.util.logging.FileHandler.level = FINE
+ java.util.logging.FileHandler.formatter = edu.uci.ics.genomix.pregelix.log.PathMergeLogFormatter
+java.util.logging.FileHandler.level = FINE
# Limit the message that are printed on the console to FINE and above.
java.util.logging.ConsoleHandler.level = INFO
java.util.logging.ConsoleHandler.formatter = java.util.logging.SimpleFormatter
-#java.util.logging.ConsoleHandler.formatter = java.util.logging.XMLFormatter
############################################################
@@ -65,8 +62,8 @@
# For example, set the com.xyz.foo logger to only log SEVERE
# messages:
-#edu.uci.ics.genomix.pregelix.level = FINE
+edu.uci.ics.genomix.pregel.level = FINE
#edu.uci.ics.asterix.level = FINE
#edu.uci.ics.algebricks.level = FINE
-#edu.uci.ics.hyracks.level = SEVERE
+edu.uci.ics.hyracks.level = SEVERE
#edu.uci.ics.hyracks.control.nc.net.level = FINE
diff --git a/genomix/genomix-pregelix/src/test/resources/log4j.properties b/genomix/genomix-pregelix/src/test/resources/log4j.properties
deleted file mode 100755
index d5e6004..0000000
--- a/genomix/genomix-pregelix/src/test/resources/log4j.properties
+++ /dev/null
@@ -1,94 +0,0 @@
-# Define some default values that can be overridden by system properties
-hadoop.root.logger=FATAL,console
-hadoop.log.dir=.
-hadoop.log.file=hadoop.log
-
-# Define the root logger to the system property "hadoop.root.logger".
-log4j.rootLogger=${hadoop.root.logger}, EventCounter
-
-# Logging Threshold
-log4j.threshhold=FATAL
-
-#
-# Daily Rolling File Appender
-#
-
-log4j.appender.DRFA=org.apache.log4j.DailyRollingFileAppender
-log4j.appender.DRFA.File=${hadoop.log.dir}/${hadoop.log.file}
-
-# Rollver at midnight
-log4j.appender.DRFA.DatePattern=.yyyy-MM-dd
-
-# 30-day backup
-#log4j.appender.DRFA.MaxBackupIndex=30
-log4j.appender.DRFA.layout=org.apache.log4j.PatternLayout
-
-# Pattern format: Date LogLevel LoggerName LogMessage
-log4j.appender.DRFA.layout.ConversionPattern=%d{ISO8601} %p %c: %m%n
-# Debugging Pattern format
-#log4j.appender.DRFA.layout.ConversionPattern=%d{ISO8601} %-5p %c{2} (%F:%M(%L)) - %m%n
-
-
-#
-# console
-# Add "console" to rootlogger above if you want to use this
-#
-
-log4j.appender.console=org.apache.log4j.ConsoleAppender
-log4j.appender.console.target=System.err
-log4j.appender.console.layout=org.apache.log4j.PatternLayout
-log4j.appender.console.layout.ConversionPattern=%d{yy/MM/dd HH:mm:ss} %p %c{2}: %m%n
-
-#
-# TaskLog Appender
-#
-
-#Default values
-hadoop.tasklog.taskid=null
-hadoop.tasklog.noKeepSplits=4
-hadoop.tasklog.totalLogFileSize=100
-hadoop.tasklog.purgeLogSplits=true
-hadoop.tasklog.logsRetainHours=12
-
-log4j.appender.TLA=org.apache.hadoop.mapred.TaskLogAppender
-log4j.appender.TLA.taskId=${hadoop.tasklog.taskid}
-log4j.appender.TLA.totalLogFileSize=${hadoop.tasklog.totalLogFileSize}
-
-log4j.appender.TLA.layout=org.apache.log4j.PatternLayout
-log4j.appender.TLA.layout.ConversionPattern=%d{ISO8601} %p %c: %m%n
-
-#
-# Rolling File Appender
-#
-
-#log4j.appender.RFA=org.apache.log4j.RollingFileAppender
-#log4j.appender.RFA.File=${hadoop.log.dir}/${hadoop.log.file}
-
-# Logfile size and and 30-day backups
-#log4j.appender.RFA.MaxFileSize=1MB
-#log4j.appender.RFA.MaxBackupIndex=30
-
-#log4j.appender.RFA.layout=org.apache.log4j.PatternLayout
-#log4j.appender.RFA.layout.ConversionPattern=%d{ISO8601} %-5p %c{2} - %m%n
-#log4j.appender.RFA.layout.ConversionPattern=%d{ISO8601} %-5p %c{2} (%F:%M(%L)) - %m%n
-
-#
-# FSNamesystem Audit logging
-# All audit events are logged at INFO level
-#
-log4j.logger.org.apache.hadoop.fs.FSNamesystem.audit=WARN
-
-# Custom Logging levels
-
-#log4j.logger.org.apache.hadoop.mapred.JobTracker=DEBUG
-#log4j.logger.org.apache.hadoop.mapred.TaskTracker=DEBUG
-#log4j.logger.org.apache.hadoop.fs.FSNamesystem=DEBUG
-
-# Jets3t library
-log4j.logger.org.jets3t.service.impl.rest.httpclient.RestS3Service=ERROR
-
-#
-# Event Counter Appender
-# Sends counts of logging messages at different severity levels to Hadoop Metrics.
-#
-log4j.appender.EventCounter=org.apache.hadoop.metrics.jvm.EventCounter
diff --git a/genomix/genomix-pregelix/src/test/resources/logging.properties b/genomix/genomix-pregelix/src/test/resources/logging.properties
deleted file mode 100644
index 0ed3dfc..0000000
--- a/genomix/genomix-pregelix/src/test/resources/logging.properties
+++ /dev/null
@@ -1,67 +0,0 @@
-############################################################
-# Default Logging Configuration File
-#
-# You can use a different file by specifying a filename
-# with the java.util.logging.config.file system property.
-# For example java -Djava.util.logging.config.file=myfile
-############################################################
-
-############################################################
-# Global properties
-############################################################
-
-# "handlers" specifies a comma separated list of log Handler
-# classes. These handlers will be installed during VM startup.
-# Note that these classes must be on the system classpath.
-# By default we only configure a ConsoleHandler, which will only
-# show messages at the INFO and above levels.
-
-handlers= java.util.logging.ConsoleHandler
-
-# To also add the FileHandler, use the following line instead.
-
-# handlers= java.util.logging.FileHandler, java.util.logging.ConsoleHandler
-
-# Default global logging level.
-# This specifies which kinds of events are logged across
-# all loggers. For any given facility this global level
-# can be overriden by a facility specific level
-# Note that the ConsoleHandler also has a separate level
-# setting to limit messages printed to the console.
-
-.level= SEVERE
-# .level= INFO
-# .level= FINE
-# .level = FINEST
-
-############################################################
-# Handler specific properties.
-# Describes specific configuration info for Handlers.
-############################################################
-
-# default file output is in user's home directory.
-
-# java.util.logging.FileHandler.pattern = %h/java%u.log
-# java.util.logging.FileHandler.limit = 50000
-# java.util.logging.FileHandler.count = 1
-# java.util.logging.FileHandler.formatter = java.util.logging.XMLFormatter
-
-# Limit the message that are printed on the console to FINE and above.
-
-java.util.logging.ConsoleHandler.level = FINEST
-java.util.logging.ConsoleHandler.formatter = java.util.logging.SimpleFormatter
-
-
-############################################################
-# Facility specific properties.
-# Provides extra control for each logger.
-############################################################
-
-# For example, set the com.xyz.foo logger to only log SEVERE
-# messages:
-
-edu.uci.ics.genomix.pregelix = INFO
-#edu.uci.ics.asterix.level = FINE
-#edu.uci.ics.algebricks.level = FINE
-edu.uci.ics.hyracks.level = SEVERE
-#edu.uci.ics.hyracks.control.nc.net.level = FINE
\ No newline at end of file
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
