Merge branch 'genomix/fullstack_genomix' into wbiesing/refactor_p4
use static final values "debug" and "problemKmers" to log all actions
for given set of kmers
Conflicts:
genomix/genomix-
pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P4ForPathMergeVertex.java
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/config/GenomixJobConf.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/config/GenomixJobConf.java
index 4e8fd4f..14423e1 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/config/GenomixJobConf.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/config/GenomixJobConf.java
@@ -111,7 +111,7 @@
private int clusterWaitTime = -1;
@Option(name = "-drawStatistics", usage = "Plot coverage statistics after graphbuilding stages", required = false)
- private boolean drawStatistics = false;
+ private boolean drawStatistics = false; // TODO make this a proper map-reduce job
// Graph cleaning
@Option(name = "-bridgeRemove_maxLength", usage = "Nodes with length <= bridgeRemoveLength that bridge separate paths are removed from the graph", required = false)
@@ -121,7 +121,7 @@
private float bubbleMerge_maxDissimilarity = -1;
@Option(name = "-graphCleanMaxIterations", usage = "The maximum number of iterations any graph cleaning job is allowed to run for", required = false)
- private int graphCleanMaxIterations = -1;
+ private int graphCleanMaxIterations = -1; // TODO respect this value in pregelix
@Option(name = "-pathMergeRandom_randSeed", usage = "The seed used in the random path-merge algorithm", required = false)
private long pathMergeRandom_randSeed = -1;
@@ -139,6 +139,7 @@
private int maxReadIDsPerEdge = -1;
// Hyracks/Pregelix Setup
+ // TODO remove ip and port? (refactor Nan's driver)
@Option(name = "-ip", usage = "IP address of the cluster controller", required = false)
private String ipAddress;
@@ -161,7 +162,7 @@
/**
* the set of patterns that can be applied to the graph
*/
- public static enum Patterns {
+ public static enum Patterns { // TODO static needed for other place we use enum?
BUILD,
BUILD_HYRACKS,
BUILD_HADOOP,
@@ -233,13 +234,13 @@
// public static final String FRAME_SIZE = "genomix.framesize";
public static final String FRAME_SIZE = "pregelix.framesize";
public static final String FRAME_LIMIT = "genomix.framelimit";
- public static final String GROUPBY_TYPE = "genomix.graph.groupby.type";
+ public static final String GROUPBY_TYPE = "genomix.graph.groupby.type"; // TODO strip this out
public static final String OUTPUT_FORMAT = "genomix.graph.output";
- public static final String GROUPBY_TYPE_PRECLUSTER = "precluster";
+ public static final String GROUPBY_TYPE_PRECLUSTER = "precluster"; // TODO remove
- public static final String JOB_PLAN_GRAPHBUILD = "graphbuild";
- public static final String JOB_PLAN_GRAPHSTAT = "graphstat";
+ public static final String JOB_PLAN_GRAPHBUILD = "graphbuild"; // TODO remove
+ public static final String JOB_PLAN_GRAPHSTAT = "graphstat"; // TODO remove
public static final String OUTPUT_FORMAT_BINARY = "genomix.outputformat.binary";
public static final String OUTPUT_FORMAT_TEXT = "genomix.outputformat.text";
@@ -257,7 +258,7 @@
Patterns.SCAFFOLD, Patterns.MERGE
};
- private String[] extraArguments = {};
+ private String[] extraArguments = {}; // TODO remove extraArguments
private static Map<String, Long> tickTimes = new HashMap<String, Long>();
@@ -295,7 +296,7 @@
/**
* retrieve any unparsed arguments from parseArguments. Returns an empty array if we weren't initialized use fromArguments()
*/
- public String[] getExtraArguments() {
+ public String[] getExtraArguments() { // TODO remove
return extraArguments;
}
@@ -457,7 +458,7 @@
return System.currentTimeMillis() - time;
}
- public static void setGlobalStaticConstants(Configuration conf) {
+ public static void setGlobalStaticConstants(Configuration conf) { // TODO make sure everyone uses this version
KmerBytesWritable.setGlobalKmerLength(Integer.parseInt(conf.get(GenomixJobConf.KMER_LENGTH)));
// EdgeWritable.MAX_READ_IDS_PER_EDGE = Integer.parseInt(conf.get(GenomixJobConf.MAX_READIDS_PER_EDGE));
}
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/minicluster/GenomixClusterManager.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/minicluster/GenomixClusterManager.java
index 9a520b9..28a742c 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/minicluster/GenomixClusterManager.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/minicluster/GenomixClusterManager.java
@@ -236,6 +236,7 @@
Path jarDestDir = new Path(conf.get(GenomixJobConf.HDFS_WORK_PATH) + "/jar-dependencies");
// dist cache requires absolute paths. we have to use the working directory if HDFS_WORK_PATH is relative
if (!jarDestDir.isAbsolute()) {
+ // TODO move this to a single function
// working dir is the correct base, but we must use the path version (not a URI). Get URI and strip out leading identifiers
String hostNameRE = "([a-zA-Z0-9]|[a-zA-Z0-9][a-zA-Z0-9\\-]{0,61}[a-zA-Z0-9])(\\.([a-zA-Z0-9]|[a-zA-Z0-9][a-zA-Z0-9\\-]{0,61}[a-zA-Z0-9]))*";
String[] workDirs = dfs.getWorkingDirectory().toString()
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 4ad48e4..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
@@ -246,7 +246,7 @@
};
return it;
}
-
+
public Iterable<VKmerBytesWritable> getKeys() {
return new Iterable<VKmerBytesWritable>() {
@Override
@@ -255,7 +255,7 @@
}
};
}
-
+
public PositionListWritable getReadIDs(VKmerBytesWritable key) {
for (EdgeWritable e : this) {
if (e.getKey().equals(key))
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 1c0a023..0250a73 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
@@ -78,7 +78,14 @@
b |= NEXT.val;
return b;
}
+ 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)
@@ -100,8 +107,182 @@
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();
@@ -121,151 +302,12 @@
// public String previous;
// public int stepCount;
// merge/update directions
- public static class DirectionFlag { // TODO change to "EdgeType" and make enum-based
- 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 };
-
- /**
- * Returns the edge dir for B->A when the A->B edge is type @dir
- */
- public static byte mirrorEdge(byte edgeType) {
- switch (edgeType) {
- case DIR_FF:
- return DIR_RR;
- case DIR_FR:
- return DIR_FR;
- case DIR_RF:
- return DIR_RF;
- case DIR_RR:
- return DIR_FF;
- default:
- throw new RuntimeException("Unrecognized direction in mirrorDirection: " + edgeType);
- }
- }
-
- public static DIR dirFromEdgeType(byte b) {
- switch(b & DirectionFlag.DIR_MASK) {
- case DIR_FF:
- case DIR_FR:
- return DIR.NEXT;
- case DIR_RF:
- case DIR_RR:
- return DIR.PREVIOUS;
- default:
- throw new RuntimeException("Unrecognized direction in dirFromEdgeType: " + b);
-
- }
- }
-
- /**
- * 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 byte resolveLinkThroughMiddleNode(byte BtoA, byte BtoC) {
- BtoA &= DIR_MASK;
- BtoC &= DIR_MASK;
- byte AtoB = mirrorEdge(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 DIR_FF:
- switch (BtoC) {
- case DIR_FF:
- case DIR_FR:
- return BtoC;
- case DIR_RF:
- case DIR_RR:
- throw new IllegalArgumentException("Tried to resolve an invalid link type: A --" + AtoB + "--> B --" + BtoC + "--> C");
- }
- break;
- case DIR_FR:
- switch (BtoC) {
- case DIR_FF:
- case DIR_FR:
- throw new IllegalArgumentException("Tried to resolve an invalid link type: A --" + AtoB + "--> B --" + BtoC + "--> C");
- case DIR_RF:
- return DIR_FF;
- case DIR_RR:
- return DIR_FR;
- }
- break;
- case DIR_RF:
- switch (BtoC) {
- case DIR_FF:
- return DIR_RF;
- case DIR_FR:
- return DIR_RR;
- case DIR_RF:
- case DIR_RR:
- throw new IllegalArgumentException("Tried to resolve an invalid link type: A --" + AtoB + "--> B --" + BtoC + "--> C");
- }
- break;
- case DIR_RR:
- switch (BtoC) {
- case DIR_FF:
- case DIR_FR:
- throw new IllegalArgumentException("Tried to resolve an invalid link type: A --" + AtoB + "--> B --" + BtoC + "--> C");
- case DIR_RF:
- return DIR_RF;
- case DIR_RR:
- return DIR_RR;
- }
- break;
- }
- throw new IllegalStateException("Logic Error or unrecognized direction... original values were: " + BtoA + " and " + BtoC);
- }
-
- public static boolean causesFlip(byte direction) {
- direction &= DIR_MASK;
- switch (direction) {
- case DIR_FF:
- case DIR_RR:
- return false;
- case DIR_FR:
- case DIR_RF:
- return true;
- default:
- throw new IllegalArgumentException("unrecognized direction: " + direction);
- }
- }
- }
-
-
-
- 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();
@@ -299,8 +341,8 @@
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);
@@ -309,8 +351,8 @@
}
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();
@@ -329,13 +371,25 @@
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() {
@@ -407,8 +461,8 @@
*/
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();
@@ -429,9 +483,9 @@
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();
@@ -444,9 +498,9 @@
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();
@@ -460,8 +514,8 @@
@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);
@@ -472,8 +526,8 @@
@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);
@@ -504,8 +558,8 @@
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;
}
@@ -517,8 +571,8 @@
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');
@@ -543,23 +597,23 @@
* @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);
}
@@ -601,91 +655,76 @@
}
}
}
-
+//
/**
* 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);
- 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) {
@@ -695,7 +734,7 @@
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) {
@@ -705,7 +744,7 @@
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)
@@ -723,7 +762,7 @@
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) {
@@ -743,24 +782,26 @@
}
/**
- * Debug helper function to find the edge associated with the given kmer
+ * Debug helper function to find the edge associated with the given kmer.
+ *
+ * Note: may be very slow-- does a linear scan of all edges!
*/
- public Map.Entry<Byte, EdgeWritable> findEdge(final VKmerBytesWritable kmer) {
- for (byte dir : DirectionFlag.values) {
- for (EdgeWritable e : edges[dir]) {
+ public Map.Entry<EDGETYPE, EdgeWritable> findEdge(final VKmerBytesWritable kmer) {
+ for (EDGETYPE dir : EDGETYPE.values()) {
+ for (EdgeWritable e : edges[dir.get()]) {
if (e.getKey().equals(kmer))
- return new AbstractMap.SimpleEntry<Byte, EdgeWritable>(dir, e);
+ return new AbstractMap.SimpleEntry<EDGETYPE, EdgeWritable>(dir, e);
}
}
return null;
}
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 ea561ed..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;
/**
@@ -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 bb15cb1..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
@@ -1,22 +1,28 @@
package edu.uci.ics.genomix.data.test;
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.DataInputStream;
+import java.io.DataOutputStream;
import java.io.IOException;
+import java.io.InputStream;
+import java.util.ArrayList;
import java.util.Arrays;
import java.util.Iterator;
+import java.util.List;
import junit.framework.Assert;
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 {
@@ -45,18 +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;
@@ -69,4 +75,235 @@
Assert.assertTrue("Didn't find element " + i, found);
}
}
+
+ @Test
+ public void TestConstructor() throws IOException {
+ String kmerSample = "ATGCATGCGCTAGCTAGCTAGACTACGATGCATGCTAGCTAATCGATCGATCGAT";
+ VKmerBytesWritable kSample = new VKmerBytesWritable(kmerSample);
+ EdgeWritable sample = new EdgeWritable();
+ PositionListWritable positionsSample = new PositionListWritable();
+ long numelements = 89432;
+ for (long i = 0; i < numelements; i++) {
+ positionsSample.appendReadId(i);
+ }
+ sample.setAsCopy(kSample, positionsSample);
+ ArrayList<EdgeWritable> sampleList = new ArrayList<EdgeWritable>();
+ sampleList.add(sample);
+ EdgeListWritable toTest = new EdgeListWritable(sampleList);
+ //begin test
+ Assert.assertEquals(numelements, toTest.get(0).getReadIDs().getCountOfPosition());
+ Assert.assertEquals(kmerSample, toTest.get(0).getKey().toString());
+ for(long i = 0; i < numelements; i++) {
+ Assert.assertEquals(i, toTest.get(0).getReadIDs().getPosition((int)i).getReadId());
+ }
+ //finish test
+ }
+
+ @Test
+ public void TestSetAsCopy() throws IOException {
+ String oldkmerSample = "ATGCATGCGCTAGCTAGCTAGACTACGATGCATGCTAGCTAATCGATCGATCGAT";
+ VKmerBytesWritable oldKSample = new VKmerBytesWritable(oldkmerSample);
+ EdgeWritable sample = new EdgeWritable();
+ PositionListWritable positionsSample = new PositionListWritable();
+ long numelements = 89432;
+ for (long i = 0; i < numelements; i++) {
+ positionsSample.appendReadId(i);
+ }
+ sample.setAsCopy(oldKSample, positionsSample);
+ ArrayList<EdgeWritable> sampleList = new ArrayList<EdgeWritable>();
+ sampleList.add(sample);
+ EdgeListWritable source = new EdgeListWritable(sampleList);
+ //begin test
+ EdgeListWritable target = new EdgeListWritable();
+ target.setAsCopy(source);
+ String newKmerSample = "GCTAGACTAC";
+ VKmerBytesWritable newKSample = new VKmerBytesWritable(newKmerSample);
+ source.get(0).setKey(newKSample);
+ Assert.assertEquals(oldkmerSample, target.get(0).getKey().toString());
+ //finish test
+ }
+
+ @Test
+ public void TestAdd() throws IOException {
+ String oldkmerSample = "ATGCATGCGCTAGCTAGCTAGACTACGATGCATGCTAGCTAATCGATCGATCGAT";
+ VKmerBytesWritable oldKSample = new VKmerBytesWritable(oldkmerSample);
+ EdgeWritable sample = new EdgeWritable();
+ PositionListWritable positionsSample = new PositionListWritable();
+ long numelements = 89432;
+ for (long i = 0; i < numelements; i++) {
+ positionsSample.appendReadId(i);
+ }
+ sample.setAsCopy(oldKSample, positionsSample);
+ EdgeListWritable toTest = new EdgeListWritable();
+ //begin test
+ toTest.add(sample);
+ sample.getReadIDs().resetPosition(100, 999999);
+ String oldReadId = "(100-0_0)";
+ Assert.assertEquals(oldReadId,toTest.get(0).getReadIDs().getPosition(100).toString());
+ }
+
+ @Test
+ public void Testset() throws IOException {
+ String oldkmerSample = "ATGCATGCGCTAGCTAGCTAGACTACGATGCATGCTAGCTAATCGATCGATCGAT";
+ VKmerBytesWritable oldKSample = new VKmerBytesWritable(oldkmerSample);
+ EdgeWritable sample = new EdgeWritable();
+ PositionListWritable positionsSample = new PositionListWritable();
+ long numelements = 89432;
+ for (long i = 0; i < numelements; i++) {
+ positionsSample.appendReadId(i);
+ }
+ sample.setAsCopy(oldKSample, positionsSample);
+ EdgeListWritable toTest = new EdgeListWritable();
+ toTest.add(sample);
+ String newkmerSample = "ATGCATGCGCTACCCCCCCCTAGCTAGACTACG";
+ VKmerBytesWritable newSample = new VKmerBytesWritable(newkmerSample);
+ sample.setKey(newSample);
+ //begin test
+ toTest.set(0, sample);
+ Assert.assertEquals(newkmerSample, toTest.get(0).getKey().toString());
+ }
+
+ @Test
+ public void TestgetEdge() throws IOException {
+ String oldkmerSample = "ATGCATGCGCTAGCTAGCTAGACTACGATGCATGCTAGCTAATCGATCGATCGAT";
+ VKmerBytesWritable oldKSample = new VKmerBytesWritable(oldkmerSample);
+ EdgeWritable sample = new EdgeWritable();
+ PositionListWritable positionsSample = new PositionListWritable();
+ long numelements = 89432;
+ for (long i = 0; i < numelements; i++) {
+ positionsSample.appendReadId(i);
+ }
+ sample.setAsCopy(oldKSample, positionsSample);
+ EdgeListWritable toTest = new EdgeListWritable();
+ toTest.add(sample);
+ String oldReadId = "(100-0_0)";
+ Assert.assertEquals(oldReadId, toTest.getEdge(oldKSample).getReadIDs().getPosition(100).toString());
+ }
+
+ @Test
+ public void TestByteStreamReadWrite() throws IOException {
+ String oldkmerSample = "ATGCATGCGCTAGCTAGCTAGACTACGATGCATGCTAGCTAATCGATCGATCGAT";
+ VKmerBytesWritable oldKSample = new VKmerBytesWritable(oldkmerSample);
+ EdgeWritable sample = new EdgeWritable();
+ PositionListWritable positionsSample = new PositionListWritable();
+ long numelements = 898852;
+ for (long i = 0; i < numelements; i++) {
+ positionsSample.appendReadId(i);
+ }
+ sample.setAsCopy(oldKSample, positionsSample);
+ ArrayList<EdgeWritable> sampleList = new ArrayList<EdgeWritable>();
+ sampleList.add(sample);
+ EdgeListWritable toTest = new EdgeListWritable(sampleList);
+ //begin test
+ ByteArrayOutputStream baos = new ByteArrayOutputStream(toTest.getLength());
+ DataOutputStream out = new DataOutputStream(baos);
+ toTest.write(out);
+ InputStream inputStream = new ByteArrayInputStream(baos.toByteArray());
+ DataInputStream in = new DataInputStream(inputStream);
+ EdgeListWritable toTest2 = new EdgeListWritable();
+ toTest2.readFields(in);
+ String oldReadId = "(123-0_0)";
+ Assert.assertEquals(oldReadId, toTest2.getEdge(oldKSample).getReadIDs().getPosition(123).toString());
+ }
+
+ @Test
+ public void TestCompareTo() throws IOException {
+ String oldkmerSample = "ATGCATGCGCTAGCTAGCTAGACTACGATGCATGCTAGCTAATCGATCGATCGAT";
+ VKmerBytesWritable oldKSample = new VKmerBytesWritable(oldkmerSample);
+ EdgeWritable sample = new EdgeWritable();
+ PositionListWritable positionsSample = new PositionListWritable();
+ long numelements = 898852;
+ for (long i = 0; i < numelements; i++) {
+ positionsSample.appendReadId(i);
+ }
+ sample.setAsCopy(oldKSample, positionsSample);
+ ArrayList<EdgeWritable> sampleList = new ArrayList<EdgeWritable>();
+ sampleList.add(sample);
+ EdgeListWritable toTest = new EdgeListWritable(sampleList);
+ //begin test
+
+ String newkmerSample = "TTTTTTGCGCTAGCTAGCTAGACTACGATGCATGCTAGCTAATCGATCGATCGAT";
+ VKmerBytesWritable newKSample = new VKmerBytesWritable(newkmerSample);
+ EdgeWritable sample2 = new EdgeWritable();
+ PositionListWritable newpositionsSample = new PositionListWritable();
+ long numnewelements = 999;
+ for (long i = 0; i < numnewelements; i++) {
+ newpositionsSample.appendReadId(i);
+ }
+ sample2.setAsCopy(newKSample, newpositionsSample);
+ ArrayList<EdgeWritable> sampleList2 = new ArrayList<EdgeWritable>();
+ sampleList2.add(sample2);
+ EdgeListWritable toTest2 = new EdgeListWritable(sampleList2);
+ Assert.assertEquals(new String("should true"), false, toTest.compareTo(toTest2) < 0 ? false : true);
+ }
+
+ @Test
+ public void TestRemoveSubEdge() throws IOException {
+ String oldkmerSample = "ATGCATGCGCTAGCTAGCTAGACTACGATGCATGCTAGCTAATCGATCGATCGAT";
+ VKmerBytesWritable oldKSample = new VKmerBytesWritable(oldkmerSample);
+ EdgeWritable sample = new EdgeWritable();
+ PositionListWritable positionsSample = new PositionListWritable();
+ long numelements = 898852;
+ for (long i = 0; i < numelements; i++) {
+ positionsSample.appendReadId(i);
+ }
+ sample.setAsCopy(oldKSample, positionsSample);
+ ArrayList<EdgeWritable> sampleList = new ArrayList<EdgeWritable>();
+ sampleList.add(sample);
+ EdgeListWritable toTest = new EdgeListWritable(sampleList);
+ //begin test
+ PositionListWritable positionsSample2 = new PositionListWritable();
+ long removeElements = 99;
+ for (long i = 0; i < removeElements; i++) {
+ positionsSample2.appendReadId(i * i * 2);
+ }
+ sample.setAsCopy(oldKSample, positionsSample2);
+ toTest.removeSubEdge(sample);
+ boolean flag = false;
+
+ for(long i = 0 ; i < removeElements; i++) {
+ PositionWritable forCompare = new PositionWritable((byte)0, i*i*2, 0);
+ if(toTest.get(0).getReadIDs().getPosition((int) i) == forCompare){
+ flag = true;
+ break;
+ }
+ }
+ Assert.assertFalse(flag);
+ }
+
+ @Test
+ public void TestUnionUpdate() throws IOException {
+ String kmerSample = "ATGCATGCGCTAGCTAGCTAGACTACGATGCATGCTAGCTAATCGATCGATCGAT";
+ VKmerBytesWritable KSample = new VKmerBytesWritable(kmerSample);
+ EdgeWritable sample = new EdgeWritable();
+ PositionListWritable positionsSample = new PositionListWritable();
+ long numelements = 100;
+ for (long i = 0; i < numelements; i++) {
+ positionsSample.appendReadId(i % 50);
+ }
+ sample.setAsCopy(KSample, positionsSample);
+ EdgeWritable sample2 = new EdgeWritable();
+ for (long i = 0; i < numelements; i++) {
+ positionsSample.appendReadId(i % 30);
+ }
+ sample2.setAsCopy(KSample, positionsSample);
+ ArrayList<EdgeWritable> sampleList = new ArrayList<EdgeWritable>();
+ sampleList.add(sample);
+ ArrayList<EdgeWritable> sampleList2 = new ArrayList<EdgeWritable>();
+ sampleList2.add(sample2);
+ EdgeListWritable toTest = new EdgeListWritable(sampleList);
+ EdgeListWritable toTest2 = new EdgeListWritable(sampleList2);
+ toTest.unionUpdate(toTest2);
+ PositionListWritable targetSample = new PositionListWritable();
+ numelements = 50;
+ for (long i = 0; i < 50; i++) {
+ targetSample.appendReadId(i);
+ }
+ EdgeWritable targetEdge = new EdgeWritable();
+ targetEdge.setAsCopy(KSample, targetSample);
+ ArrayList<EdgeWritable> targeList = new ArrayList<EdgeWritable>();
+ targeList.add(targetEdge);
+ EdgeListWritable toTarget = new EdgeListWritable(targeList);
+ Assert.assertEquals(true, toTarget.equals(toTest));
+ }
}
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-driver/src/main/java/edu/uci/ics/genomix/driver/GenomixDriver.java b/genomix/genomix-driver/src/main/java/edu/uci/ics/genomix/driver/GenomixDriver.java
index 9d3c591..831cc17 100644
--- a/genomix/genomix-driver/src/main/java/edu/uci/ics/genomix/driver/GenomixDriver.java
+++ b/genomix/genomix-driver/src/main/java/edu/uci/ics/genomix/driver/GenomixDriver.java
@@ -64,11 +64,11 @@
private String prevOutput;
private String curOutput;
private int stepNum;
- private List<PregelixJob> pregelixJobs;
+ private List<PregelixJob> pregelixJobs; // TODO add sanity checks to pipeline order
private boolean followingBuild = false; // need to adapt the graph immediately after building
- private boolean runLocal;
- private int numCoresPerMachine;
- private int numMachines;
+ private boolean runLocal = false;
+ private int numCoresPerMachine; // TODO remove ?
+ private int numMachines; // TODO remove ?
private GenomixClusterManager manager;
private edu.uci.ics.genomix.hyracks.graph.driver.Driver hyracksDriver;
@@ -78,12 +78,14 @@
LOG.info("Building Graph using Hyracks...");
manager.startCluster(ClusterType.HYRACKS);
GenomixJobConf.tick("buildGraphWithHyracks");
+ // TODO move this to parser
conf.set(GenomixJobConf.OUTPUT_FORMAT, Boolean.parseBoolean(conf.get(GenomixJobConf.HYRACKS_BUILD_OUTPUT_TEXT)) ? GenomixJobConf.OUTPUT_FORMAT_TEXT : GenomixJobConf.OUTPUT_FORMAT_BINARY);
conf.set(GenomixJobConf.GROUPBY_TYPE, GenomixJobConf.GROUPBY_TYPE_PRECLUSTER);
+
String hyracksIP = runLocal ? GenomixClusterManager.LOCAL_IP : conf.get(GenomixJobConf.IP_ADDRESS);
int hyracksPort = runLocal ? GenomixClusterManager.LOCAL_HYRACKS_CLIENT_PORT : Integer.parseInt(conf.get(GenomixJobConf.PORT));
hyracksDriver = new edu.uci.ics.genomix.hyracks.graph.driver.Driver(hyracksIP, hyracksPort, numCoresPerMachine);
- hyracksDriver.runJob(conf, Plan.BUILD_UNMERGED_GRAPH, Boolean.parseBoolean(conf.get(GenomixJobConf.PROFILE)));
+ hyracksDriver.runJob(conf, Plan.BUILD_UNMERGED_GRAPH, Boolean.parseBoolean(conf.get(GenomixJobConf.PROFILE))); // TODO fix name of plan
followingBuild = true;
manager.stopCluster(ClusterType.HYRACKS);
LOG.info("Building the graph took " + GenomixJobConf.tock("buildGraphWithHyracks") + "ms");
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%
rename from genomix/genomix-pregelix/data/TestSet/TipRemove/SmallGenome/.txt.crc
rename to genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/.statistics.crc
diff --git a/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/bin/.part-0.crc b/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/bin/.part-0.crc
index bf60a71..de75c33 100644
--- a/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/bin/.part-0.crc
+++ b/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/bin/.part-0.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/bin/.part-1.crc b/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/bin/.part-1.crc
index 744fbef..7120be2 100644
--- a/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/bin/.part-1.crc
+++ b/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/bin/.part-1.crc
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/bin/part-0 b/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/bin/part-0
index 7934715..89795c2 100755
--- a/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/bin/part-0
+++ b/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/bin/part-0
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/bin/part-1 b/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/bin/part-1
index fc82ad0..0ca2113 100755
--- a/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/bin/part-1
+++ b/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/bin/part-1
Binary files differ
diff --git a/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/graphviz.svg b/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/graphviz.svg
new file mode 100644
index 0000000..a9f1169
--- /dev/null
+++ b/genomix/genomix-pregelix/data/TestSet/TipRemove/FR_Tip/graphviz.svg
@@ -0,0 +1,151 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN"
+ "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd">
+<!-- Generated by graphviz version 2.26.3 (20100126.1600)
+ -->
+<!-- Title: G Pages: 1 -->
+<svg width="620pt" height="286pt"
+ viewBox="0.00 0.00 620.00 286.00" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink">
+<g id="graph1" class="graph" transform="scale(1 1) rotate(0) translate(4 282)">
+<title>G</title>
+<polygon fill="white" stroke="white" points="-4,5 -4,-282 617,-282 617,5 -4,5"/>
+<!-- GAA -->
+<g id="node1" class="node"><title>GAA</title>
+<polygon fill="none" stroke="black" points="0,-75 0,-205 56,-205 56,-75 0,-75"/>
+<text text-anchor="middle" x="28" y="-188.4" font-family="Times Roman,serif" font-size="14.00">GAA</text>
+<polyline fill="none" stroke="black" points="0,-179 56,-179 "/>
+<text text-anchor="middle" x="28" y="-162.4" font-family="Times Roman,serif" font-size="14.00">5':[]</text>
+<polyline fill="none" stroke="black" points="0,-153 56,-153 "/>
+<text text-anchor="middle" x="28" y="-136.4" font-family="Times Roman,serif" font-size="14.00">~5':[]</text>
+<polyline fill="none" stroke="black" points="0,-127 56,-127 "/>
+<text text-anchor="middle" x="28" y="-110.4" font-family="Times Roman,serif" font-size="14.00">1.0</text>
+<polyline fill="none" stroke="black" points="0,-101 56,-101 "/>
+<text text-anchor="middle" x="28" y="-84.4" font-family="Times Roman,serif" font-size="14.00">GAA</text>
+</g>
+<!-- AGA -->
+<g id="node3" class="node"><title>AGA</title>
+<polygon fill="none" stroke="black" points="140,-75 140,-205 196,-205 196,-75 140,-75"/>
+<text text-anchor="middle" x="168" y="-188.4" font-family="Times Roman,serif" font-size="14.00">AGA</text>
+<polyline fill="none" stroke="black" points="140,-179 196,-179 "/>
+<text text-anchor="middle" x="168" y="-162.4" font-family="Times Roman,serif" font-size="14.00">5':[]</text>
+<polyline fill="none" stroke="black" points="140,-153 196,-153 "/>
+<text text-anchor="middle" x="168" y="-136.4" font-family="Times Roman,serif" font-size="14.00">~5':[]</text>
+<polyline fill="none" stroke="black" points="140,-127 196,-127 "/>
+<text text-anchor="middle" x="168" y="-110.4" font-family="Times Roman,serif" font-size="14.00">1.0</text>
+<polyline fill="none" stroke="black" points="140,-101 196,-101 "/>
+<text text-anchor="middle" x="168" y="-84.4" font-family="Times Roman,serif" font-size="14.00">AGA</text>
+</g>
+<!-- GAA->AGA -->
+<g id="edge2" class="edge"><title>GAA->AGA</title>
+<path fill="none" stroke="red" d="M56.3311,-140C77.3945,-140 106.372,-140 129.53,-140"/>
+<polygon fill="red" stroke="red" points="129.711,-143.5 139.711,-140 129.711,-136.5 129.711,-143.5"/>
+<text text-anchor="middle" x="98" y="-145.4" font-family="Times Roman,serif" font-size="14.00">RR: [1]</text>
+</g>
+<!-- AGA->GAA -->
+<g id="edge4" class="edge"><title>AGA->GAA</title>
+<path fill="none" stroke="black" d="M139.511,-123.987C133.868,-121.508 127.871,-119.332 122,-118 101.195,-113.281 94.8048,-113.281 74,-118 71.3399,-118.603 68.6538,-119.38 65.9864,-120.28"/>
+<polygon fill="black" stroke="black" points="64.5325,-117.09 56.4893,-123.987 67.0775,-123.611 64.5325,-117.09"/>
+<text text-anchor="middle" x="98" y="-123.4" font-family="Times Roman,serif" font-size="14.00">FF: [1]</text>
+</g>
+<!-- CTA -->
+<g id="node6" class="node"><title>CTA</title>
+<polygon fill="none" stroke="black" points="278,-75 278,-205 334,-205 334,-75 278,-75"/>
+<text text-anchor="middle" x="306" y="-188.4" font-family="Times Roman,serif" font-size="14.00">CTA</text>
+<polyline fill="none" stroke="black" points="278,-179 334,-179 "/>
+<text text-anchor="middle" x="306" y="-162.4" font-family="Times Roman,serif" font-size="14.00">5':[]</text>
+<polyline fill="none" stroke="black" points="278,-153 334,-153 "/>
+<text text-anchor="middle" x="306" y="-136.4" font-family="Times Roman,serif" font-size="14.00">~5':[]</text>
+<polyline fill="none" stroke="black" points="278,-127 334,-127 "/>
+<text text-anchor="middle" x="306" y="-110.4" font-family="Times Roman,serif" font-size="14.00">1.0</text>
+<polyline fill="none" stroke="black" points="278,-101 334,-101 "/>
+<text text-anchor="middle" x="306" y="-84.4" font-family="Times Roman,serif" font-size="14.00">CTA</text>
+</g>
+<!-- AGA->CTA -->
+<g id="edge6" class="edge"><title>AGA->CTA</title>
+<path fill="none" stroke="green" d="M196.259,-140C216.818,-140 244.894,-140 267.501,-140"/>
+<polygon fill="green" stroke="green" points="267.778,-143.5 277.778,-140 267.778,-136.5 267.778,-143.5"/>
+<text text-anchor="middle" x="237" y="-145.4" font-family="Times Roman,serif" font-size="14.00">RF: [1]</text>
+</g>
+<!-- CTA->AGA -->
+<g id="edge20" class="edge"><title>CTA->AGA</title>
+<path fill="none" stroke="green" d="M277.511,-123.987C271.868,-121.508 265.871,-119.332 260,-118 240.062,-113.478 233.938,-113.478 214,-118 211.34,-118.603 208.654,-119.38 205.986,-120.28"/>
+<polygon fill="green" stroke="green" points="204.532,-117.09 196.489,-123.987 207.078,-123.611 204.532,-117.09"/>
+<text text-anchor="middle" x="237" y="-123.4" font-family="Times Roman,serif" font-size="14.00">RF: [1]</text>
+</g>
+<!-- ATA -->
+<g id="node7" class="node"><title>ATA</title>
+<polygon fill="none" stroke="black" points="416,-148 416,-278 472,-278 472,-148 416,-148"/>
+<text text-anchor="middle" x="444" y="-261.4" font-family="Times Roman,serif" font-size="14.00">ATA</text>
+<polyline fill="none" stroke="black" points="416,-252 472,-252 "/>
+<text text-anchor="middle" x="444" y="-235.4" font-family="Times Roman,serif" font-size="14.00">5':[]</text>
+<polyline fill="none" stroke="black" points="416,-226 472,-226 "/>
+<text text-anchor="middle" x="444" y="-209.4" font-family="Times Roman,serif" font-size="14.00">~5':[]</text>
+<polyline fill="none" stroke="black" points="416,-200 472,-200 "/>
+<text text-anchor="middle" x="444" y="-183.4" font-family="Times Roman,serif" font-size="14.00">1.0</text>
+<polyline fill="none" stroke="black" points="416,-174 472,-174 "/>
+<text text-anchor="middle" x="444" y="-157.4" font-family="Times Roman,serif" font-size="14.00">ATA</text>
+</g>
+<!-- CTA->ATA -->
+<g id="edge16" class="edge"><title>CTA->ATA</title>
+<path fill="none" stroke="blue" d="M334.238,-175.156C339.685,-180.371 345.68,-185.245 352,-189 368.218,-198.635 388.29,-204.451 405.543,-207.937"/>
+<polygon fill="blue" stroke="blue" points="405.396,-211.467 415.862,-209.819 406.653,-204.581 405.396,-211.467"/>
+<text text-anchor="middle" x="375" y="-212.4" font-family="Times Roman,serif" font-size="14.00">FR: [1]</text>
+</g>
+<!-- AGC -->
+<g id="node11" class="node"><title>AGC</title>
+<polygon fill="none" stroke="black" points="416,-0 416,-130 472,-130 472,-0 416,-0"/>
+<text text-anchor="middle" x="444" y="-113.4" font-family="Times Roman,serif" font-size="14.00">AGC</text>
+<polyline fill="none" stroke="black" points="416,-104 472,-104 "/>
+<text text-anchor="middle" x="444" y="-87.4" font-family="Times Roman,serif" font-size="14.00">5':[]</text>
+<polyline fill="none" stroke="black" points="416,-78 472,-78 "/>
+<text text-anchor="middle" x="444" y="-61.4" font-family="Times Roman,serif" font-size="14.00">~5':[]</text>
+<polyline fill="none" stroke="black" points="416,-52 472,-52 "/>
+<text text-anchor="middle" x="444" y="-35.4" font-family="Times Roman,serif" font-size="14.00">0.0</text>
+<polyline fill="none" stroke="black" points="416,-26 472,-26 "/>
+<text text-anchor="middle" x="444" y="-9.4" font-family="Times Roman,serif" font-size="14.00"> </text>
+</g>
+<!-- CTA->AGC -->
+<g id="edge18" class="edge"><title>CTA->AGC</title>
+<path fill="none" stroke="blue" d="M334.075,-128.859C352.667,-121.079 377.341,-109.974 398,-98 401.162,-96.1672 404.376,-94.1705 407.561,-92.0962"/>
+<polygon fill="blue" stroke="blue" points="409.539,-94.9835 415.864,-86.4835 405.619,-89.1841 409.539,-94.9835"/>
+<text text-anchor="middle" x="375" y="-126.4" font-family="Times Roman,serif" font-size="14.00">FR: [0]</text>
+</g>
+<!-- ATA->CTA -->
+<g id="edge8" class="edge"><title>ATA->CTA</title>
+<path fill="none" stroke="blue" d="M415.758,-183.923C410.185,-179.17 404.149,-174.624 398,-171 381.37,-161.201 361.207,-153.965 344.001,-148.96"/>
+<polygon fill="blue" stroke="blue" points="344.832,-145.559 334.261,-146.269 342.967,-152.306 344.832,-145.559"/>
+<text text-anchor="middle" x="375" y="-176.4" font-family="Times Roman,serif" font-size="14.00">FR: [1]</text>
+</g>
+<!-- AAT -->
+<g id="node10" class="node"><title>AAT</title>
+<polygon fill="grey" stroke="black" points="556,-147 556,-277 612,-277 612,-147 556,-147"/>
+<text text-anchor="middle" x="584" y="-260.4" font-family="Times Roman,serif" font-size="14.00">AAT</text>
+<polyline fill="none" stroke="black" points="556,-251 612,-251 "/>
+<text text-anchor="middle" x="584" y="-234.4" font-family="Times Roman,serif" font-size="14.00">5':[1]</text>
+<polyline fill="none" stroke="black" points="556,-225 612,-225 "/>
+<text text-anchor="middle" x="584" y="-208.4" font-family="Times Roman,serif" font-size="14.00">~5':[]</text>
+<polyline fill="none" stroke="black" points="556,-199 612,-199 "/>
+<text text-anchor="middle" x="584" y="-182.4" font-family="Times Roman,serif" font-size="14.00">1.0</text>
+<polyline fill="none" stroke="black" points="556,-173 612,-173 "/>
+<text text-anchor="middle" x="584" y="-156.4" font-family="Times Roman,serif" font-size="14.00">AAT</text>
+</g>
+<!-- ATA->AAT -->
+<g id="edge10" class="edge"><title>ATA->AAT</title>
+<path fill="none" stroke="red" d="M472.331,-212.798C493.395,-212.647 522.372,-212.44 545.53,-212.275"/>
+<polygon fill="red" stroke="red" points="545.736,-215.773 555.711,-212.202 545.686,-208.774 545.736,-215.773"/>
+<text text-anchor="middle" x="514" y="-218.4" font-family="Times Roman,serif" font-size="14.00">RR: [1]</text>
+</g>
+<!-- AAT->ATA -->
+<g id="edge14" class="edge"><title>AAT->ATA</title>
+<path fill="none" stroke="black" d="M555.947,-196.92C550.165,-194.468 544.005,-192.306 538,-191 517.154,-186.467 510.805,-186.281 490,-191 487.34,-191.603 484.654,-192.38 481.986,-193.28"/>
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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 @@
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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%
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copy to genomix/genomix-pregelix/data/TestSet/TipRemove/RF_Tip/.statistics.crc
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old mode 100644
new mode 100755
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copy from genomix/genomix-pregelix/data/TestSet/TipRemove/SmallGenome/.txt.crc
copy to genomix/genomix-pregelix/data/TestSet/TipRemove/RF_Tip/statistics
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-newpath 4598.52 671.13 moveto
-4588.14 673.24 lineto
-4597.57 678.06 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-4606 696.97 moveto 204 (FR: [8,31,42,50,66,69,78,86]) alignedtext
-grestore
-% ACT->TCA
-gsave
-1 setlinewidth
-0 1 1 edgecolor
-newpath 5080.04 696.97 moveto
-5372.53 693.28 6913.07 673.85 7261.78 669.46 curveto
-stroke
-0 1 1 edgecolor
-newpath 7262.04 672.95 moveto
-7271.99 669.33 lineto
-7261.95 665.96 lineto
-closepath fill
-1 setlinewidth
-solid
-0 1 1 edgecolor
-newpath 7262.04 672.95 moveto
-7271.99 669.33 lineto
-7261.95 665.96 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-6296.5 687.97 moveto 187 (RR: [1,3,4,20,27,41,51,67]) alignedtext
-grestore
-% ACT->CTC
-gsave
-1 setlinewidth
-0 0 0 edgecolor
-newpath 5080.38 690.07 moveto
-5125.26 683.4 5193.99 673.89 5254 668.57 curveto
-6511.79 557.14 6830.09 580.71 8092 535.57 curveto
-9127.32 498.54 10388.88 475.93 10696.12 470.73 curveto
-stroke
-0 0 0 edgecolor
-newpath 10696.28 474.23 moveto
-10706.22 470.56 lineto
-10696.16 467.23 lineto
-closepath fill
-1 setlinewidth
-solid
-0 0 0 edgecolor
-newpath 10696.28 474.23 moveto
-10706.22 470.56 lineto
-10696.16 467.23 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-8117.5 540.97 moveto 229 (FF: [1,3,4,20,27,35,41,44,51,67]) alignedtext
-grestore
-% ACT->CCA
-gsave
-1 setlinewidth
-0 1 1 edgecolor
-newpath 5080.05 701.98 moveto
-5124.99 706.03 5194.02 712.07 5254 716.57 curveto
-5412.11 728.44 5453.37 714.95 5610 739.57 curveto
-5698.58 753.5 5799.16 781.42 5858.73 799.27 curveto
-stroke
-0 1 1 edgecolor
-newpath 5858.06 802.72 moveto
-5868.64 802.26 lineto
-5860.08 796.02 lineto
-closepath fill
-1 setlinewidth
-solid
-0 1 1 edgecolor
-newpath 5858.06 802.72 moveto
-5868.64 802.26 lineto
-5860.08 796.02 lineto
-closepath stroke
-0 0 0 edgecolor
-14 /Times-Roman set_font
-5307 744.97 moveto 250 (RR: [8,19,26,31,42,50,69,78,86,92]) alignedtext
-grestore
-endpage
-showpage
-grestore
-%%PageTrailer
-%%EndPage: 1
-%%Trailer
-%%Pages: 1
-%%BoundingBox: 36 36 12234 2334
-end
-restore
-%%EOF
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 @@
-AAA {[{AAA:[93]},{AAG:[81,83,89,93,94,97]},{AAT:[2,4,9,14,27,30,41,49,64,75,81,83,94,97]}] [] [] [{AAA:[93]},{GAA:[1,2,4,9,14,27,30,41,49,54,64,67,75,81,83,94,97]},{TAA:[49,81,83,89,93,94,97]}] {5':[], ~5':[(1-0_0),(49-0_0),(54-0_0),(67-0_0)]} AAA 25.0x}
-GAA {[{AAA:[1,2,4,9,14,27,30,41,49,54,64,67,75,81,83,94,97]},{AAG:[8,25,32,36,42,46,47,52,53,62,66,71,76,78,80,84,86,87]},{AAT:[13,15,17,23,33,45,48,59,77,96,98]}] [] [{TCA:[1,4,20,27,30,41,64,67]}] [{AGA:[8,25,42,46,66,70,78,80,86]},{CGA:[13,17,32,33,38,45,47,52,59,62,71,76,77,84,91,96,98]},{GGA:[2,10,14,49,54,63,75,81,94,97]}] {5':[(36-0_0),(53-0_0)], ~5':[(38-0_0),(63-0_0),(70-0_0),(91-0_0)]} GAA 52.0x}
-AGA {[{GAA:[8,25,42,46,66,70,78,80,86]},{GAC:[29,79,89]}] [{CTC:[10,43,54,63,65,99,100]}] [] [{AAG:[79,83,89]},{CAG:[2,8,10,14,25,42,43,46,54,63,65,66,70,78,80,86,100]}] {5':[(29-0_0),(99-0_0)], ~5':[(14-0_0),(83-0_0)]} AGA 22.0x}
-GGA {[{GAA:[2,10,14,49,54,63,75,81,94,97]},{GAC:[9,13,17,18,33,45,74,77,98]}] [{ATC:[11,16,37,56,82,85]},{CTC:[1,3,4,20,35,44,51,67]}] [{CCA:[2,10,14,43,49,54,63,75]},{CCC:[1,3,20,28,35,44,51,67,95]},{CCG:[9,11,16,18,30,33,45,56,64,74,77,82,85]}] [] {5':[(4-0_0),(17-0_0),(37-0_0),(81-0_0)], ~5':[(28-0_0),(30-0_0),(64-0_0)]} GGA 38.0x}
-ATA {[{TAA:[49,75,81,83,89,94,97]}] [{ATA:[22,28,29,34,55,57,68,73,79,95]}] [{ATC:[22,28,29,34,35,44,55,57,68,73,95]}] [{AAT:[2,14,22,28,29,34,49,55,57,68,73,75,79,81,83,89,94,95,97]}] {5':[(79-0_0)], ~5':[(2-0_0),(35-0_0),(44-0_0)]} ATA 31.0x}
-GAC {[{CAA:[22,29,34,55,57,68,79]},{ACG:[13,17,18,33,45,59,74,77,98]}] [] [] [{AGA:[29,79,89]},{GGA:[9,13,17,18,33,45,74,77,98]}] {5':[(59-0_0)], ~5':[(9-0_0)]} GAC 14.0x}
-ACC {[{CCG:[5,7,15,21,23,37,40,48,56]}] [] [{TAA:[7,11,37,40,56]}] [] {5':[(5-0_0),(15-1_0),(23-1_0),(48-1_0)], ~5':[]} TACC 8.5x}
-GCC {[{CCA:[19,26,31,50,69,90,92]},{CCC:[6,36,53,70,76,87]},{CCG:[5,7,15,21,23,40,48,96]}] [{AGG:[12,24,39,58,61,88]}] [] [{AGC:[6,12,19,24,25,26,31,36,46,50,53,58,60,61,69,70,72,76,80,87,88,90,92,99]},{ATG:[5,13,15,17,21,23,48,59,96,98]}] {5':[(39-0_0),(40-0_0)], ~5':[]} GCC 34.0x}
-AGC {[{GCC:[6,12,19,24,25,26,31,36,46,50,53,58,60,61,69,70,72,76,80,87,88,90,92,99]}] [{AGC:[10,24,43,58,63,65,99,100]},{CGC:[16,32,38,39,47,52,62,71,82,84,85,91,93]}] [{CTA:[12,16,24,43,58,61,65,82,85,88,93,99,100]},{CTC:[6,10,25,36,43,46,53,54,58,63,65,66,70,76,80,87,99,100]}] [{AAG:[32,38,39,47,52,62,71,84,88,91]},{CAG:[19,26,31,50,60,69,72,90,92]}] {5':[(10-0_0),(24-0_0)], ~5':[(61-0_0),(66-0_0),(88-0_0)]} AGC 59.0x}
-ATC {[{TCA:[19,26,60,72,90,92]}] [{CGA:[9,18,22,28,30,34,35,44,55,57,64,68,73,74,95]},{GGA:[11,16,37,56,82,85]}] [{ATA:[22,28,29,34,35,44,55,57,68,73,95]},{ATC:[19,60,72,90,92]}] [{AAT:[7,9,11,16,18,27,30,37,40,41,56,64,74,82,85]}] {5':[], ~5':[(7-0_0),(19-0_0)]} ATC 37.0x}
-AAG {[{AGA:[79,83,89]},{AGC:[32,38,39,47,52,62,71,84,88,91]},{AGG:[6,32,36,47,52,53,62,76,84,87]}] [{ACT:[8,31,42,50,66,69,78,86]}] [] [{AAA:[81,83,89,93,94,97]},{GAA:[8,25,32,36,42,46,47,52,53,62,66,71,76,78,80,84,86,87]},{TAA:[38,39,47,52,71,88,91]}] {5':[(6-0_0),(50-0_0),(62-0_0)], ~5':[(25-0_0),(46-0_0),(71-0_0),(80-0_0),(94-0_0),(97-0_0)]} AAG 39.0x}
-ACG {[{CGA:[13,17,18,33,45,59,74,77,98]}] [] [] [{GAC:[13,17,18,33,45,59,74,77,98]}] {5':[], ~5':[]} ACG 9.0x}
-AGG {[] [{CCC:[6,32,36,53,62,76,84,87]},{GCC:[12,24,39,58,61,88]}] [{CTA:[12,24,38,39,61,88,91]}] [{AAG:[6,32,36,47,52,53,62,76,84,87]}] {5':[], ~5':[(52-0_0)]} AGG 18.0x}
-ATG {[{GCC:[5,15,21,23,48,59,96]}] [] [] [{AAT:[5,13,15,17,21,23,45,48,59,77,96,98]}] {5':[], ~5':[(13-1_0),(45-0_0),(77-0_0),(98-1_0)]} ATGC 11.0x}
-AAT {[{ATA:[2,14,22,28,29,34,49,55,57,68,73,75,79,81,83,89,94,95,97]},{ATC:[7,9,11,16,18,27,30,37,40,41,56,64,74,82,85]},{ATG:[5,13,15,17,21,23,45,48,59,77,96,98]}] [] [] [{AAA:[2,4,9,14,27,30,41,49,64,75,81,83,94,97]},{CAA:[22,29,34,55,57,68,73,79]},{GAA:[13,15,17,23,33,45,48,59,77,96,98]},{TAA:[7,11,37,40,56,85]}] {5':[(16-0_0),(18-0_0),(21-0_0),(74-0_0),(82-0_0),(89-0_0),(95-0_0)], ~5':[(33-0_0)]} AAT 48.0x}
-ACT {[{CTC:[1,3,4,20,27,35,41,44,51,67]}] [{AAG:[8,31,42,50,66,69,78,86]}] [] [{CCA:[8,19,26,31,42,50,69,78,86,92]},{TCA:[1,3,4,20,27,41,51,67]}] {5':[], ~5':[(26-1_0),(92-0_0)]} CACT 18.5x}
-CAA {[{AAT:[22,29,34,55,57,68,73,79]}] [] [] [{GAC:[29,55,79,89]}] {5':[(22-0_0),(34-0_0),(57-0_0)], ~5':[]} ACAA 8.0x}
-TAA {[{AAA:[49,81,83,89,93,94,97]},{AAG:[38,39,47,52,71,88,91]},{AAT:[7,11,37,40,56,85]}] [] [{ACC:[5,7,11,21,37,40,56]}] [{ATA:[49,75,81,83,89,94,97]},{CTA:[12,16,38,39,61,71,82,88,91,93]}] {5':[(47-0_0)], ~5':[(12-0_0),(75-0_0)]} TAA 25.0x}
-CCA {[{CAG:[2,10,14,43,54,63,75,100]},{ACT:[1,3,4,8,20,26,27,31,41,42,50,51,67,69,78,86]}] [] [{GGA:[2,10,14,43,49,54,63,75]}] [{GCC:[19,26,31,50,69,90,92]}] {5':[(78-0_0),(86-0_0)], ~5':[]} CCA 20.0x}
-TCA {[{CAG:[6,8,19,25,26,31,42,46,50,60,66,69,70,72,78,80,86,90,92]},{ACT:[1,3,4,8,20,26,27,31,41,42,50,51,67,69,78,86]}] [] [{GAA:[1,4,20,27,30,41,64,67]}] [{ATC:[19,26,60,72,90,92]},{CTC:[6,25,36,46,53,66,70,80,87]}] {5':[(8-0_0),(31-0_0),(42-0_0),(69-0_0)], ~5':[(87-0_0),(90-0_0)]} TCA 35.0x}
-CGA {[{GAA:[13,17,32,33,38,45,47,52,59,62,71,76,77,84,91,96,98]}] [{ATC:[9,18,22,28,30,34,35,44,55,57,64,68,73,74,95]}] [{CGC:[32,38,39,47,52,62,71,84,91]}] [{ACG:[13,17,18,33,45,59,74,77,98]},{CCG:[3,9,18,22,28,30,33,34,35,44,51,57,64,68,73,74,95]}] {5':[(55-0_0),(76-0_0)], ~5':[(3-0_0),(51-0_0)]} CGA 38.0x}
-CTA {[{TAA:[12,16,38,39,61,71,82,88,91,93]}] [{CTA:[12,24,58,61,65,99,100]}] [{AGC:[12,16,24,43,58,61,65,82,85,88,93,99,100]},{AGG:[12,24,38,39,61,88,91]}] [] {5':[(100-0_0)], ~5':[(43-0_0),(85-0_0)]} CTA 28.0x}
-CCC {[{CCG:[3,20,28,35,44,51,73,95]}] [{AGG:[6,32,36,53,62,76,84,87]}] [{GGA:[1,3,20,28,35,44,51,67,95]}] [{GCC:[6,36,53,70,76,87]}] {5':[(32-0_0),(73-0_0),(84-0_0)], ~5':[]} CCC 19.0x}
-CGC {[] [{AGC:[16,32,38,39,47,52,62,71,82,84,85,91,93]}] [{CGA:[32,38,39,47,52,62,71,84,91]}] [{CCG:[11,16,82,85,93]}] {5':[], ~5':[(11-0_0)]} CGC 14.0x}
-CTC {[{TCA:[6,25,36,46,53,66,70,80,87]}] [{AGA:[10,43,54,63,65,99,100]},{GGA:[1,3,4,20,35,44,51,67]}] [{AGC:[6,10,25,36,43,46,53,54,58,63,65,66,70,76,80,87,99,100]}] [{ACT:[1,3,4,20,27,35,41,44,51,67]}] {5':[], ~5':[(27-0_0),(41-0_0),(58-0_0)]} CTC 28.0x}
-CAG {[{AGA:[2,8,10,14,25,42,43,46,54,63,65,66,70,78,80,86,100]},{AGC:[19,26,31,50,60,69,72,90,92]}] [] [] [{CCA:[2,10,14,43,54,63,75,100]},{TCA:[6,8,19,25,26,31,42,46,50,60,66,69,70,72,78,80,86,90,92]}] {5':[(65-0_0)], ~5':[(60-0_0),(72-0_0)]} CAG 30.0x}
-CCG {[{CGA:[3,9,18,22,28,30,33,34,35,44,51,57,64,68,73,74,95]},{CGC:[11,16,82,85,93]}] [{CCG:[5,7,15,21,23,37,40,48,96]}] [{GGA:[9,11,16,18,30,33,45,56,64,74,77,82,85]}] [{ACC:[5,7,15,21,23,37,40,48,56]},{CCC:[3,20,28,35,44,51,73,95]},{GCC:[5,7,15,21,23,40,48,96]}] {5':[(68-0_0),(93-0_0),(96-0_0)], ~5':[(20-0_0),(56-0_0)]} CCG 45.0x}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/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 9e07213..4eee225 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;
@@ -18,7 +17,7 @@
private static final long serialVersionUID = 1L;
public static class HeadMergeDir{
- public static final byte NON_HEAD = 0b00 << 2;
+ public static final byte PATH_NON_HEAD = 0b00 << 2;
public static final byte HEAD_CANNOT_MERGE = 0b01 << 2;
public static final byte HEAD_CAN_MERGEWITHPREV = 0b10 << 2; //use for initiating head
public static final byte HEAD_CAN_MERGEWITHNEXT = 0b11 << 2;
@@ -27,6 +26,13 @@
}
public static class VertexStateFlag extends HeadMergeDir{
+ public static final byte TO_UPDATE = 0b01 << 5;
+ public static final byte TO_OTHER = 0b10 << 5;
+ public static final byte TO_NEIGHBOR = 0b11 << 5;
+ public static final byte MSG_MASK = 0b11 << 5;
+ public static final byte MSG_CLEAR = (byte)0011111;
+
+ //TODO clean up code
public static final byte IS_NON = 0b000 << 4;
public static final byte IS_HEAD = 0b001 << 4;
public static final byte IS_FINAL = 0b010 << 4;
@@ -97,11 +103,6 @@
scaffoldingMap = new HashMapWritable<VLongWritable, KmerListAndFlagListWritable>();
}
-// TODO: figure out why can't use
-// public VertexValueWritable get(){
-// return this;
-// }
-
public void setAsCopy(VertexValueWritable other){
setNode(other.getNode());
state = other.getState();
@@ -118,35 +119,35 @@
}
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() {
@@ -252,53 +253,23 @@
/**
* 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);
}
-
-// /**
-// * Process any changes to value. This is for edge updates. nodeToAdd should be only edge
-// */
-// public void processUpdates(byte deleteDir, VKmerBytesWritable toDelete, byte updateDir, NodeWritable other){
-// // TODO remove this function (use updateEdges)
-// byte replaceDir = mirrorDirection(deleteDir);
-// this.getNode().updateEdges(deleteDir, toDelete, updateDir, replaceDir, other, true);
-// }
-
- 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
- mergeDir = (byte)(mergeDir & MessageFlag.DIR_MASK); // TODO move this dir outside and remove this function
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..77e421a 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{
@@ -24,6 +25,11 @@
updateMsg = false;
}
+ public PathMergeMessageWritable(PathMergeMessageWritable other){
+ this();
+ this.setAsCopy(other);
+ }
+
public void setAsCopy(PathMergeMessageWritable other){
super.setAsCopy(other);
this.node.setAsCopy(other.getNode());
@@ -46,20 +52,20 @@
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 5349b1c..dcae00a 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
@@ -1,9 +1,10 @@
package edu.uci.ics.genomix.pregelix.operator;
import java.io.IOException;
+import java.util.Arrays;
+import java.util.EnumSet;
import java.util.Iterator;
-import java.util.Map.Entry;
-import java.util.AbstractMap.SimpleEntry;
+import java.util.List;
import java.util.Random;
import java.util.logging.Logger;
@@ -28,12 +29,10 @@
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> {
@@ -48,21 +47,22 @@
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;
protected M outgoingMsg = null;
+ protected M aggregatingMsg = null;
protected VKmerBytesWritable destVertexId = null;
protected VertexValueWritable tmpValue = new VertexValueWritable();
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;
@@ -70,8 +70,22 @@
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 static final List<VKmerBytesWritable> problemKmers = Arrays.asList(
+// new VKmerBytesWritable("CCCGGCCTCCAGCGTGGGATACGCGAAGATGCCGCCGTAGGTGAGAATCTGGTTC"),
+// new VKmerBytesWritable("GCAGGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"),
+// new VKmerBytesWritable("GAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"),
+// new VKmerBytesWritable("GAGCAGGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"),
+// new VKmerBytesWritable("GGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"),
+// new VKmerBytesWritable("AGGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"),
+// new VKmerBytesWritable("GCGACGTGCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"),
+// new VKmerBytesWritable("GTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"),
+ new VKmerBytesWritable("AACACCGAGGGCGTGCCGACGAACCCCGAGGCCTACGCGAAGATGCGCGGCTGGA")
+ );
+ protected static final boolean debug = false;
+ protected boolean verbose = false;
protected HashMapWritable<ByteWritable, VLongWritable> counters = new HashMapWritable<ByteWritable, VLongWritable>();
/**
@@ -83,6 +97,10 @@
if (maxIteration < 0)
maxIteration = Integer.parseInt(getContext().getConfiguration().get(GenomixJobConf.GRAPH_CLEAN_MAX_ITERATIONS));
GenomixJobConf.setGlobalStaticConstants(getContext().getConfiguration());
+
+ verbose = false;
+ for (VKmerBytesWritable problemKmer : problemKmers)
+ verbose |= debug && (getVertexValue().getNode().findEdge(problemKmer) != null || getVertexId().equals(problemKmer));
}
public boolean isHeadNode(){
@@ -120,22 +138,22 @@
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
@@ -196,34 +214,6 @@
/**
* get destination vertex
*/
- public VKmerBytesWritable getPrevDestVertexId() {
- // TODO check length of RF and RR == 1; throw exception otherwise
- if (!getVertexValue().getRFList().isEmpty()){ //#RFList() > 0
- kmerIterator = getVertexValue().getRFList().getKeyIterator();
- return kmerIterator.next();
- } else if (!getVertexValue().getRRList().isEmpty()){ //#RRList() > 0
- kmerIterator = getVertexValue().getRRList().getKeyIterator();
- return kmerIterator.next();
- } else {
- return null;
- }
- }
-
- public VKmerBytesWritable getNextDestVertexId() {
- if (!getVertexValue().getFFList().isEmpty()){ //#FFList() > 0
- kmerIterator = getVertexValue().getFFList().getKeyIterator();
- return kmerIterator.next();
- } else if (!getVertexValue().getFRList().isEmpty()){ //#FRList() > 0
- kmerIterator = getVertexValue().getFRList().getKeyIterator();
- return kmerIterator.next();
- } else {
- return null;
- }
- }
-
- /**
- * get destination vertex
- */
public VKmerBytesWritable getPrevDestVertexIdAndSetFlag() {
if (!getVertexValue().getRFList().isEmpty()){ // #RFList() > 0
kmerIterator = getVertexValue().getRFList().getKeyIterator();
@@ -268,7 +258,7 @@
else if(!getVertexValue().getRRList().isEmpty())
outgoingMsg.setFlag(MessageFlag.DIR_RR);
outgoingMsg.setSourceVertexId(getVertexId());
- destVertexId.setAsCopy(getPrevDestVertexId());
+ destVertexId.setAsCopy(getDestVertexId(DIR.PREVIOUS));
sendMsg(destVertexId, outgoingMsg);
}
}
@@ -284,22 +274,22 @@
else if(!getVertexValue().getFRList().isEmpty())
outgoingMsg.setFlag(MessageFlag.DIR_FR);
outgoingMsg.setSourceVertexId(getVertexId());
- destVertexId.setAsCopy(getNextDestVertexId());
+ destVertexId.setAsCopy(getDestVertexId(DIR.NEXT));
sendMsg(destVertexId, outgoingMsg);
}
}
/**
- * head send message to all neighbor nodes
+ * send message to all neighbor nodes
*/
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());
@@ -314,38 +304,72 @@
}
/**
+ * head send message to all neighbor nodes
+ */
+ public void headSendSettledMsgs(DIR direction, VertexValueWritable value){
+ //TODO THE less context you send, the better (send simple messages)
+ 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;
+ EDGETYPE meToNeighborEdgeType = e.mirror();
+ switch(meToNeighborEdgeType){
+ case FF:
+ case FR:
+ outFlag |= MessageFlag.HEAD_CAN_MERGEWITHPREV;
+ break;
+ case RF:
+ case RR:
+ outFlag |= MessageFlag.HEAD_CAN_MERGEWITHNEXT;
+ break;
+ }
+ outgoingMsg.setFlag(outFlag);
+ outgoingMsg.setSourceVertexId(getVertexId());
+ destVertexId.setAsCopy(kmerIterator.next());
+ sendMsg(destVertexId, outgoingMsg);
+ }
+ }
+ }
+
+ public void headSendSettledMsgToAllNeighborNodes(VertexValueWritable value) {
+ headSendSettledMsgs(DIR.PREVIOUS, value);
+ headSendSettledMsgs(DIR.NEXT, value);
+ }
+
+ /**
* get a copy of the original Kmer without TandemRepeat
* @param destVertex
*/
public void copyWithoutTandemRepeats(V srcVertex, VertexValueWritable destVertex){
destVertex.setAsCopy(srcVertex);
- destVertex.getEdgeList(repeatDir).remove(repeatKmer);
+ destVertex.getEdgeList(repeatEdgetype).remove(repeatKmer);
while(isTandemRepeat(destVertex))
- destVertex.getEdgeList(repeatDir).remove(repeatKmer);
+ 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
*/
- public boolean ifFlipWithNeighbor(boolean withPrecessor){
- if(withPrecessor){
+ public boolean ifFlipWithNeighbor(DIR direction){
+ if(direction == DIR.PREVIOUS){
if(getVertexValue().getRRList().isEmpty())
return true;
else
@@ -395,17 +419,14 @@
/**
* set neighborToMe Dir
*/
- public void setNeighborToMeDir(DIR predecessorToMe){
- if(getVertexValue().getDegree(predecessorToMe) != 1)
+ public void setNeighborToMeDir(DIR direction){
+ if(getVertexValue().getDegree(direction) != 1)
throw new IllegalArgumentException("In merge dir, the degree is not 1");
- byte[] dirs = predecessorToMe == 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();
}
/**
@@ -433,7 +454,7 @@
/**
* 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;
@@ -497,8 +518,8 @@
* 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());
}
@@ -548,48 +569,17 @@
/**
* Look inside of vertex for the given edge, returning the direction we found it in (or null)
*/
- public static Byte findEdge(VKmerBytesWritable id, VertexValueWritable vertex){
+ public static EDGETYPE findEdge(VKmerBytesWritable id, VertexValueWritable vertex){
// TODO move into Node?
- for(byte d : DirectionFlag.values){
- for (VKmerBytesWritable curKey : vertex.getEdgeList(d).getKeys()) {
+ for(EDGETYPE e : EnumSet.allOf(EDGETYPE.class)){
+ for (VKmerBytesWritable curKey : vertex.getEdgeList(e).getKeys()) {
if(curKey.equals(id)) // points to self
- return d;
+ return e;
}
}
return null;
}
- 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;
- }
- }
- }
- 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);
- }
- }
-
/**
* set statistics counter
*/
@@ -639,9 +629,9 @@
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);
@@ -693,12 +683,67 @@
* 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 ce770e3..47b71a1 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
@@ -1,26 +1,31 @@
package edu.uci.ics.genomix.pregelix.operator.pathmerge;
+import java.util.ArrayList;
import java.util.EnumSet;
import java.util.Iterator;
+import java.util.logging.Logger;
+
+import org.apache.commons.lang3.StringUtils;
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.DirectionFlag;
-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
BasicGraphCleanVertex<V, M>{
+
+ private static final Logger LOG = Logger.getLogger(BasicPathMergeVertex.class.getName());
+
protected static final boolean isP1 = true;
protected static final boolean isP2 = false;
protected static final boolean isP4 = true;
@@ -32,22 +37,9 @@
public byte getMsgMergeDir(){
return (byte) (incomingMsg.getFlag() & MessageFlag.HEAD_CAN_MERGE_MASK);
}
-
- public void setHeadMergeDir(){
- byte state = 0;
- byte meToNeighborDir = (byte) (incomingMsg.getFlag() & MessageFlag.DIR_MASK);
- byte neighborToMeDir = mirrorDirection(meToNeighborDir);
- switch(neighborToMeDir){
- case MessageFlag.DIR_FF:
- case MessageFlag.DIR_FR:
- state |= State.HEAD_CAN_MERGEWITHPREV;
- break;
- case MessageFlag.DIR_RF:
- case MessageFlag.DIR_RR:
- state |= State.HEAD_CAN_MERGEWITHNEXT;
- break;
- }
- getVertexValue().setState(state);
+
+ public byte getAggregatingMsgMergeDir(){
+ return (byte) (aggregatingMsg.getFlag() & MessageFlag.HEAD_CAN_MERGE_MASK);
}
public boolean isHeadUnableToMerge(){
@@ -55,28 +47,154 @@
return state == State.HEAD_CANNOT_MERGE;
}
- 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();
+ public DIR revert(DIR direction){
+ return direction == DIR.PREVIOUS ? DIR.NEXT : DIR.PREVIOUS;
}
+
+ /**
+ * send UPDATE msg boolean: true == P4, false == P2
+ */
+ public void sendUpdateMsg(boolean isP4, DIR direction){
+ // TODO pass in the vertexId rather than isP4 (removes this block）
+// if(isP4)
+// outgoingMsg.setFlip(ifFlipWithNeighbor(revertDirection)); //ifFilpWithSuccessor()
+// else
+// outgoingMsg.setFlip(ifFilpWithSuccessor(incomingMsg.getSourceVertexId()));
+ DIR revertDirection = revert(direction);
+ 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());
+
+ //set replaceDir
+ setReplaceDir(mergeDirs);
+
+ for(EDGETYPE dir : updateDirs){
+ kmerIterator = getVertexValue().getEdgeList(dir).getKeyIterator();
+ while(kmerIterator.hasNext()){
+ //set deleteDir
+ EDGETYPE deleteDir = setDeleteDir(dir);
+ //set mergeDir, so it won't need flip
+ setMergeDir(deleteDir, revertDirection);
+ outgoingMsg.setFlag(outFlag);
+ destVertexId = kmerIterator.next(); //TODO does destVertexId need deep copy?
+ sendMsg(destVertexId, outgoingMsg);
+ }
+ }
+ }
+
/**
* updateAdjList
*/
public void processUpdate(M msg){
// A -> B -> C with B merging with C
inFlag = msg.getFlag();
- byte meToNeighborDir = (byte) (inFlag & MessageFlag.DIR_MASK); // A -> B dir
- byte neighborToMeDir = mirrorDirection(meToNeighborDir); // B -> A 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
- // TODO if you want, this logic could be figured out when sending the update from B
- byte neighborToMergeDir = flipDirection(neighborToMeDir, msg.isFlip()); // A -> C after the merge
- byte replaceDir = mirrorDirection(neighborToMeDir); // C -> A dir
- getVertexValue().getNode().updateEdges(neighborToMeDir, msg.getSourceVertexId(),
- neighborToMergeDir, replaceDir, msg.getNode(), true);
+ getVertexValue().getNode().updateEdges(deleteDir, msg.getSourceVertexId(),
+ mergeDir, replaceDir, msg.getNode(), true);
+ }
+
+ /**
+ * send MERGE msg
+ */
+ public void sendMergeMsg(boolean isP4){
+ byte restrictedDirs = (byte)(getVertexValue().getState() & DIR.MASK);
+ outFlag |= restrictedDirs;
+
+ DIR direction = null;
+ byte mergeDir = (byte)(getVertexValue().getState() & State.CAN_MERGE_MASK);
+ if(mergeDir == State.CAN_MERGEWITHPREV)
+ direction = DIR.PREVIOUS;
+ else if(mergeDir == State.CAN_MERGEWITHNEXT)
+ direction = DIR.NEXT;
+ if(direction != null){
+ setNeighborToMeDir(direction);
+ outgoingMsg.setFlag(outFlag);
+ outgoingMsg.setSourceVertexId(getVertexId());
+ outgoingMsg.setNode(getVertexValue().getNode()); //half of edges are enough
+ destVertexId = getDestVertexId(direction);
+ sendMsg(destVertexId, outgoingMsg);
+
+ if(isP4)
+ deleteVertex(getVertexId());
+ else{
+ getVertexValue().setState(State.IS_DEAD);
+ activate();
+ }
+ }
+ }
+
+ public void aggregateMsg(Iterator<M> msgIterator){
+ while (msgIterator.hasNext()) {
+ incomingMsg = msgIterator.next();
+ //aggregate all the incomingMsgs first
+ switch(getAggregatingMsgMergeDir()){
+ case State.PATH_NON_HEAD:
+ aggregatingMsg.setFlag(getMsgMergeDir());
+ activate();
+ break;
+ case State.HEAD_CAN_MERGEWITHPREV:
+ case State.HEAD_CAN_MERGEWITHNEXT:
+ if (getAggregatingMsgMergeDir() != getMsgMergeDir())
+ aggregatingMsg.setFlag(State.HEAD_CANNOT_MERGE);
+ break;
+ case State.HEAD_CANNOT_MERGE:
+ break;
+ }
+ }
+ }
+
+ public void updateState(){
+ switch(getHeadMergeDir()){
+ case State.PATH_NON_HEAD:
+ getVertexValue().setState(getAggregatingMsgMergeDir());
+ activate();
+ break;
+ case State.HEAD_CAN_MERGEWITHPREV:
+ case State.HEAD_CAN_MERGEWITHNEXT:
+ if (getHeadMergeDir() != getAggregatingMsgMergeDir()){
+ getVertexValue().setState(State.HEAD_CANNOT_MERGE);
+ voteToHalt();
+ }
+ break;
+ case State.HEAD_CANNOT_MERGE:
+ voteToHalt();
+ break;
+ }
+ }
+
+ 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)
+ throw new IllegalStateException("Only can sendUpdateMsg to degree = 1 direction!");
+ outgoingMsg.getNode().setEdgeList(dir, getVertexValue().getEdgeList(dir));
+ replaceDir = dir;
+ break;
+ }
+ }
+ outFlag &= MessageFlag.REPLACE_DIR_CLEAR;
+ outFlag |= replaceDir.get();
+ }
+
+ public EDGETYPE setDeleteDir(EDGETYPE dir){
+ EDGETYPE deleteDir = dir.mirror();
+ outFlag &= MessageFlag.DELETE_DIR_CLEAR;
+ outFlag |= deleteDir.get();
+ return deleteDir;
+ }
+
+ public void setMergeDir(EDGETYPE deleteDir, DIR revertDirection){
+ EDGETYPE mergeDir = ifFlipWithNeighbor(revertDirection) ? deleteDir.flip() : deleteDir;
+ outFlag &= MessageFlag.MERGE_DIR_CLEAR;
+ outFlag |= mergeDir.get();
}
/**
@@ -84,10 +202,10 @@
*/
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());
}
@@ -96,8 +214,8 @@
*/
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());
@@ -105,20 +223,6 @@
getVertexValue().getEdgeList(neighborToMeDir).unionAdd(edge);
}
- public byte flipHeadMergeDir(byte d, boolean isFlip){
- if(isFlip){
- switch(d){
- case State.HEAD_CAN_MERGEWITHPREV:
- return State.HEAD_CAN_MERGEWITHNEXT;
- case State.HEAD_CAN_MERGEWITHNEXT:
- return State.HEAD_CAN_MERGEWITHPREV;
- default:
- return 0;
- }
- } else
- return d;
- }
-
public boolean isDifferentDirWithMergeKmer(byte neighborToMeDir){
return neighborToMeDir == MessageFlag.DIR_FR || neighborToMeDir == MessageFlag.DIR_RF;
}
@@ -144,50 +248,16 @@
*/
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));
+ getVertexValue().setState(state);
getVertexValue().processMerges(neighborToMeDir, msg.getNode(), kmerSize);
}
-
- /**
- * send UPDATE msg boolean: true == P4, false == P2
- */
- public void sendUpdateMsg(boolean isP4, DIR direction){
- outgoingMsg.setSourceVertexId(getVertexId());
- // TODO pass in the vertexId rather than isP4 (removes this block）
- if(isP4)
- outgoingMsg.setFlip(ifFlipWithNeighbor(direction == DIR.NEXT)); //ifFilpWithSuccessor()
- else
- outgoingMsg.setFlip(ifFilpWithSuccessor(incomingMsg.getSourceVertexId()));
-
- byte[] mergeDirs = direction == DIR.PREVIOUS ? OutgoingListFlag.values : IncomingListFlag.values;
- byte[] updateDirs = direction == DIR.PREVIOUS ? IncomingListFlag.values : OutgoingListFlag.values;
-
- for(byte dir : mergeDirs)
- outgoingMsg.getNode().setEdgeList(dir, getVertexValue().getEdgeList(dir));
-
- for(byte dir : updateDirs){
- kmerIterator = getVertexValue().getEdgeList(dir).getKeyIterator();
- while(kmerIterator.hasNext()){
- outFlag &= MessageFlag.DIR_CLEAR;
- outFlag |= dir;
- outgoingMsg.setFlag(outFlag);
- destVertexId.setAsCopy(kmerIterator.next()); //TODO does destVertexId need deep copy?
- sendMsg(destVertexId, outgoingMsg);
- }
- }
- }
-
/**
* override sendUpdateMsg and use incomingMsg as parameter automatically
*/
@@ -206,15 +276,15 @@
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;
}
@@ -240,57 +310,43 @@
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());
- sendMsg(getNextDestVertexId(), outgoingMsg);
+ sendMsg(getDestVertexId(DIR.NEXT), outgoingMsg);
}
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;
}
}
/**
- * send MERGE msg
- */
- public void sendMergeMsg(boolean toPredecessor, VKmerBytesWritable mergeDest){
- setNeighborToMeDir(DIR.PREVIOUS);
- outgoingMsg.setFlag(outFlag);
- outgoingMsg.setSourceVertexId(getVertexId());
-// for(byte d: OutgoingListFlag.values)
-// outgoingMsg.setEdgeList(d, getVertexValue().getEdgeList(d));
- outgoingMsg.setNode(getVertexValue().getNode());
- sendMsg(mergeDest, outgoingMsg);
- }
-
- /**
* configure MERGE msg TODO: delete edgelist, merge configureMergeMsgForPredecessor and configureMergeMsgForPredecessorByIn...
*/
public void configureMergeMsgForPredecessor(VKmerBytesWritable mergeDest){
@@ -313,36 +369,6 @@
sendMsg(mergeDest, outgoingMsg);
}
-
- /**
- * send merge message to neighber for P4, send message to the merge object and kill self
- */
- public void broadcastMergeMsg(boolean isP4){
- outFlag |= getHeadMergeDir();
- switch(getVertexValue().getState() & State.CAN_MERGE_MASK) {
- case State.CAN_MERGEWITHNEXT:
- // configure merge msg for successor
- configureMergeMsgForSuccessor(getNextDestVertexId()); // TODO getDestVertexId(DIRECTION), then remove the switch statement, sendMergeMsg(DIRECTION)
- if(isP4)
- deleteVertex(getVertexId());
- else{
- getVertexValue().setState(State.IS_DEAD);
- activate();
- }
- break;
- case State.CAN_MERGEWITHPREV:
- // configure merge msg for predecessor
- configureMergeMsgForPredecessor(getPrevDestVertexId());
- if(isP4)
- deleteVertex(getVertexId());
- else{
- getVertexValue().setState(State.IS_DEAD);
- activate();
- }
- break;
- }
- }
-
public byte revertHeadMergeDir(byte headMergeDir){
switch(headMergeDir){
case MessageFlag.HEAD_CAN_MERGEWITHPREV:
@@ -369,4 +395,249 @@
String logMessage = LogUtil.getMessageLog(loggingType, getSuperstep(), getVertexId(), msg, dest);
logger.fine(logMessage);
}
+
+ /*
+ * garbage
+ */
+ public void setHeadMergeDir(){
+ byte state = 0;
+ EDGETYPE meToNeighborDir = EDGETYPE.fromByte(incomingMsg.getFlag());
+ EDGETYPE neighborToMeDir = meToNeighborDir.mirror();
+ switch(neighborToMeDir){
+ case FF:
+ case FR:
+ state |= State.HEAD_CAN_MERGEWITHPREV;
+ break;
+ 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()) {
+ if (debug)
+ for (VKmerBytesWritable problemKmer : problemKmers)
+ verbose |= destId.equals(problemKmer);
+ outgoingMsg.reset();
+ outgoingMsg.setFlag(et.mirror().dir().get());
+
+ if (verbose)
+ LOG.fine("send restriction from " + getVertexId() + " to " + destId +
+ " in my " + et + " and their " + et.mirror() +
+ " (" + EDGETYPE.dir(et.mirror()) +
+ "); I am " + getVertexValue());
+ sendMsg(destId, outgoingMsg);
+ }
+ }
+ }
+ }
+
+ /**
+ * initiate head, rear and path node
+ */
+ public void recieveRestrictions(Iterator<M> msgIterator) {
+ short restrictedDirs = getVertexValue().getState(); // the directions (NEXT/PREVIOUS) that I'm not allowed to merge in
+ boolean updated = false;
+ while (msgIterator.hasNext()) {
+ if (verbose)
+ LOG.fine("before restriction " + getVertexId() + ": " + DIR.fromByte(restrictedDirs));
+ incomingMsg = msgIterator.next();
+ restrictedDirs |= incomingMsg.getFlag();
+ if (verbose)
+ LOG.fine("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());
+ outFlag = 0;
+ outFlag |= MessageFlag.TO_UPDATE | updateEdge.mirror().get(); // neighbor's edge to me (so he can remove me)
+ outgoingMsg.setFlag(outFlag);
+ for (EDGETYPE mergeEdge : mergeEdges) {
+ EDGETYPE newEdgetype = EDGETYPE.resolveLinkThroughMiddleNode(updateEdge, mergeEdge);
+ outgoingMsg.getNode().setEdgeList(newEdgetype, getVertexValue().getEdgeList(mergeEdge)); // copy into outgoingMsg
+ }
+ if (debug)
+ for (VKmerBytesWritable problemKmer : problemKmers)
+ verbose |= outgoingMsg.getNode().findEdge(problemKmer) != null;
+
+ // 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()) {
+ if (verbose)
+ LOG.fine("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;
+ ArrayList<PathMergeMessageWritable> allSeenMsgs = new ArrayList<PathMergeMessageWritable>();
+ while (msgIterator.hasNext()) {
+ incomingMsg = msgIterator.next();
+ if (debug)
+ for (VKmerBytesWritable problemKmer : problemKmers)
+ verbose |= incomingMsg.getNode().findEdge(problemKmer) != null || incomingMsg.getSourceVertexId().equals(problemKmer);
+ if (verbose)
+ LOG.fine("before update from neighbor: " + getVertexValue());
+ // 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;
+ if (verbose) {
+ LOG.fine("after update from neighbor: " + getVertexValue());
+ allSeenMsgs.add(incomingMsg);
+ }
+ }
+ if (verbose)
+ LOG.fine("All recieved updates: \n{\n" + StringUtils.join(allSeenMsgs, "\n") + "\n}\n");
+ 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();
+ sendMsg(dest, outgoingMsg);
+ deleteVertex(getVertexId());
+
+ if (verbose) {
+ LOG.fine("send merge mesage from " + getVertexId() + " to " + dest + ": " + outgoingMsg + "; my restrictions are: " + DIR.enumSetFromByte(vertex.getState()) + ", their restrictions are: " + DIR.enumSetFromByte(outgoingMsg.getFlag()));
+ LOG.fine("killing self: " + 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()) {
+ incomingMsg = msgIterator.next();
+ if (debug)
+ for (VKmerBytesWritable problemKmer : problemKmers)
+ verbose |= incomingMsg.getNode().findEdge(problemKmer) != null;
+ if (verbose)
+ LOG.fine("before merge: " + getVertexValue() + " restrictions: " + DIR.enumSetFromByte(state));
+ senderEdgetype = EDGETYPE.fromByte(incomingMsg.getFlag());
+ node.mergeWithNode(senderEdgetype, incomingMsg.getNode());
+ state |= (byte) (incomingMsg.getFlag() & DIR.MASK); // update incoming restricted directions
+ numMerged++;
+ updated = true;
+ if (verbose)
+ LOG.fine("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;
+ if (verbose)
+ LOG.fine("recieveMerges is a tandem repeat: " + getVertexId() + " " + getVertexValue());
+// 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..672d9ac
--- /dev/null
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P0ForPathMergeVertex.java
@@ -0,0 +1,393 @@
+package edu.uci.ics.genomix.pregelix.operator.pathmerge;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+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;
+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.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
+ * @author anbangx
+ *
+ */
+public class P0ForPathMergeVertex extends
+ MapReduceVertex<VertexValueWritable, PathMergeMessageWritable> {
+
+ private ArrayList<PathMergeMessageWritable> receivedMsg = new ArrayList<PathMergeMessageWritable>();
+ private HashMap<VKmerBytesWritable, ArrayList<Byte>> dirMapper = new HashMap<VKmerBytesWritable, ArrayList<Byte>>();
+
+ private EdgeWritable tmpEdge = new EdgeWritable();
+ /**
+ * initiate kmerSize, maxIteration
+ */
+ 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();
+ inFlag = 0;
+ outFlag = 0;
+ if(repeatKmer == null)
+ repeatKmer = new VKmerBytesWritable();
+ tmpValue.reset();
+ synchronized(lock){
+ if(fakeVertex == null){
+ fakeVertex = new VKmerBytesWritable();
+ String fake = generateString(kmerSize + 1);//generaterRandomString(kmerSize + 1);
+ fakeVertex.setByRead(kmerSize + 1, fake.getBytes(), 0);
+ }
+ }
+ if(tmpKmer == null)
+ tmpKmer = new VKmerBytesWritable();
+ if(reverseKmer == null)
+ reverseKmer = new VKmerBytesWritable();
+ if(kmerList == null)
+ kmerList = new VKmerListWritable();
+ else
+ kmerList.reset();
+ if(getSuperstep() == 1)
+ StatisticsAggregator.preGlobalCounters.clear();
+// else
+// StatisticsAggregator.preGlobalCounters = BasicGraphCleanVertex.readStatisticsCounterResult(getContext().getConfiguration());
+ counters.clear();
+ getVertexValue().getCounters().clear();
+ }
+
+ /**
+ * map reduce in FakeNode
+ */
+ public void aggregateMsgAndGroupInFakeNode(Iterator<PathMergeMessageWritable> msgIterator){
+ kmerMapper.clear();
+ dirMapper.clear();
+ /** Mapper **/
+ mapKeyByInternalKmer(msgIterator);
+ /** Reducer **/
+ reduceKeyByInternalKmer();
+ }
+
+ /**
+ * typical for P1
+ */
+ @Override
+ public void mapKeyByInternalKmer(Iterator<PathMergeMessageWritable> msgIterator){
+ byte dir = 0;
+ while(msgIterator.hasNext()){
+ incomingMsg = msgIterator.next();
+ String kmerString = incomingMsg.getInternalKmer().toString();
+ tmpKmer.setByRead(kmerString.length(), kmerString.getBytes(), 0);
+ reverseKmer.setByReadReverse(kmerString.length(), kmerString.getBytes(), 0);
+
+ VKmerBytesWritable kmer = new VKmerBytesWritable();
+ kmerList = new VKmerListWritable();
+ if(reverseKmer.compareTo(tmpKmer) > 0){
+ dir = KmerDir.FORWARD;
+ kmer.setAsCopy(tmpKmer);
+ }
+ else{
+ dir = KmerDir.REVERSE;
+ kmer.setAsCopy(reverseKmer);
+ }
+ if(!kmerMapper.containsKey(kmer)){
+ //kmerList.reset();
+ kmerList.append(incomingMsg.getSourceVertexId());
+ kmerMapper.put(kmer, kmerList);
+ } else{
+ kmerList.setCopy(kmerMapper.get(kmer));
+ kmerList.append(incomingMsg.getSourceVertexId());
+ kmerMapper.put(kmer, kmerList);
+ }
+ //dirMapper
+ ArrayList<Byte> dirList = new ArrayList<Byte>();
+ if(!dirMapper.containsKey(kmer)){
+ dirList.clear();
+ dirList.add(dir);
+ dirMapper.put(kmer, dirList);
+ } else{
+ dirList.clear();
+ dirList.addAll(dirMapper.get(kmer));
+ dirList.add(dir);
+ dirMapper.put(kmer, dirList);
+ }
+ }
+ }
+
+ /**
+ * typical for P1
+ */
+ @Override
+ public void reduceKeyByInternalKmer(){
+ for (VKmerBytesWritable key : kmerMapper.keySet()) {
+ kmerList = kmerMapper.get(key);
+ //always delete kmerList(1), keep kmerList(0)
+
+ //send kill message to kmerList(1), and carry with kmerList(0) to update edgeLists of kmerList(1)'s neighbor
+ outgoingMsg.setFlag(MessageFlag.KILL);
+ outgoingMsg.getNode().setInternalKmer(kmerList.getPosition(0));
+ boolean isFlip = dirMapper.get(key).get(0) == dirMapper.get(key).get(1) ? false : true;
+ outgoingMsg.setFlip(isFlip);
+ destVertexId.setAsCopy(kmerList.getPosition(1));
+ sendMsg(destVertexId, outgoingMsg);
+ }
+ }
+
+ /**
+ * typical for P1
+ * do some remove operations on adjMap after receiving the info about dead Vertex
+ */
+ public void responseToDeadVertexAndUpdateEdges(){
+ 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()));
+
+ getVertexValue().getEdgeList(neighborToMeDir).remove(incomingMsg.getSourceVertexId());
+ }
+ tmpEdge.setKey(incomingMsg.getNode().getInternalKmer());
+ EDGETYPE updateDir = incomingMsg.isFlip() ? neighborToMeDir.flip() : neighborToMeDir;
+ getVertexValue().getEdgeList(updateDir).unionAdd(tmpEdge);
+ }
+
+ /**
+ * head send update message
+ */
+ public void headSendUpdateMsg(){
+ if(isHeadNode()){
+ byte headMergeDir = (byte)(getVertexValue().getState() & State.HEAD_CAN_MERGE_MASK);
+ switch(headMergeDir){
+ case State.HEAD_CAN_MERGEWITHPREV:
+ sendUpdateMsg(isP1, DIR.NEXT);
+ break;
+ case State.HEAD_CAN_MERGEWITHNEXT:
+ sendUpdateMsg(isP1, DIR.PREVIOUS);
+ break;
+ }
+ } else
+ voteToHalt();
+ }
+
+ /**
+ * process update when receiving update msg
+ */
+ public void processUpdateOnceReceiveMsg(Iterator<PathMergeMessageWritable> msgIterator){
+ while(msgIterator.hasNext()){
+ incomingMsg = msgIterator.next();
+ processUpdate(incomingMsg);
+ if(isHaltNode())
+ voteToHalt();
+ else
+ activate();
+ }
+ }
+ /**
+ * aggregate received msg
+ */
+ public void aggregateReceivedMsg(Iterator<PathMergeMessageWritable> msgIterator){
+ receivedMsg.clear();
+ while(msgIterator.hasNext()){
+ incomingMsg = msgIterator.next();
+ receivedMsg.add(incomingMsg);
+ }
+ }
+
+ /**
+ * process message directly
+ */
+ public void processMessageDirectly(){
+ for(int i = 0; i < 2; i++)
+ processMerge(receivedMsg.get(i));
+ //final vertex
+ getVertexValue().setState(MessageFlag.IS_HALT);
+ voteToHalt();
+ }
+
+ /**
+ * processMerge and sendMsgToFake
+ */
+ public void processMergeAndSendMsgToFake(){
+ boolean isHead = isHeadNode();
+ boolean isDead = isDeadNode();
+ processMerge(receivedMsg.get(0));
+ if(isHead || isDead){
+ // NON-FAKE and Final vertice send msg to FAKE vertex
+ sendMsgToFakeVertex();
+ //final vertex
+ getVertexValue().setState(MessageFlag.IS_HALT);
+ voteToHalt();
+ } else
+ activate();
+ }
+
+ /**
+ * if receive kill msg, broadcaseKillself
+ */
+ public void broadcaseKillselfOnceReceiveKillMsg(Iterator<PathMergeMessageWritable> msgIterator){
+ while(msgIterator.hasNext()){
+ incomingMsg = msgIterator.next();
+ if(isReceiveKillMsg()){
+ outgoingMsg.setInternalKmer(incomingMsg.getNode().getInternalKmer());
+ outgoingMsg.setFlip(incomingMsg.isFlip());
+ broadcaseKillself();
+ }
+ }
+ }
+
+ /**
+ * if receive dead msg, responseToDeadVertexAndUpdateEdges
+ */
+ public void responseToDeadVertexAndUpdateEdgesOnceReceiveDeadMsg(Iterator<PathMergeMessageWritable> msgIterator){
+ while(msgIterator.hasNext()){
+ incomingMsg = msgIterator.next();
+ if(isResponseKillMsg())
+ responseToDeadVertexAndUpdateEdges();
+ }
+ if(isHeadNode())
+ activate();
+ else
+ 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();
+ if (getSuperstep() == 1) {
+ addFakeVertex();
+ startSendMsg();
+ } else if (getSuperstep() == 2)
+ if(!isFakeVertex())
+ initState(msgIterator);
+ else voteToHalt();
+ else if (getSuperstep() % 7 == 3 && getSuperstep() <= maxIteration) {
+ //head send update message
+ headSendUpdateMsg();
+ } else if (getSuperstep() % 7 == 4 && getSuperstep() <= maxIteration) {
+ //process update when receiving updateMsg
+ processUpdateOnceReceiveMsg(msgIterator);
+ } else if (getSuperstep() % 7 == 5 && getSuperstep() <= maxIteration) {
+ //head broadcastMergeMsg, while non-head voteToHalt
+ if(isHeadNode())
+ sendMergeMsg(isP1);
+ else
+ voteToHalt();
+ } else if (getSuperstep() % 7 == 6 && getSuperstep() <= maxIteration) {
+ if(!msgIterator.hasNext() && isDeadNode())
+ deleteVertex(getVertexId());
+ else{
+ //aggregate received msg
+ aggregateReceivedMsg(msgIterator);
+ if(receivedMsg.size() == 2){ //#incomingMsg == even
+ //processMerge directly
+ processMessageDirectly();
+ } else if(receivedMsg.size() == 1){
+ //processMerge and sendMsgToFake
+ processMergeAndSendMsgToFake();
+ }
+ }
+ } else if (getSuperstep() % 7 == 0 && getSuperstep() <= maxIteration){
+ if(isFakeVertex()){//is FakeVertex
+ // Fake vertex agregates message and group them by actual kmer (1)
+ aggregateMsgAndGroupInFakeNode(msgIterator);
+ voteToHalt();
+ }
+ } else if (getSuperstep() % 7 == 1 && getSuperstep() <= maxIteration){
+ //if receive kill msg, broadcaseKillself
+ broadcaseKillselfOnceReceiveKillMsg(msgIterator);
+ } else if (getSuperstep() % 7 == 2 && getSuperstep() <= maxIteration){
+ //if receive dead msg, responseToDeadVertexAndUpdateEdges
+ responseToDeadVertexAndUpdateEdgesOnceReceiveDeadMsg(msgIterator);
+ }
+ else
+ voteToHalt();
+ }
+
+ public static void main(String[] args) throws Exception {
+ Client.run(args, getConfiguredJob(null, P0ForPathMergeVertex.class));
+ }
+}
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 d6e488c..3210698 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
@@ -1,36 +1,32 @@
package edu.uci.ics.genomix.pregelix.operator.pathmerge;
import java.util.ArrayList;
-import java.util.HashMap;
+import java.util.EnumSet;
+import java.util.HashSet;
import java.util.Iterator;
-import edu.uci.ics.genomix.type.EdgeWritable;
-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.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.MessageFlag;
-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.NodeWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
+import edu.uci.ics.genomix.type.NodeWritable.DIR;
-/**
- * Graph clean pattern: P1(Naive-algorithm) for path merge
- * @author anbangx
- *
- */
public class P1ForPathMergeVertex extends
- MapReduceVertex<VertexValueWritable, PathMergeMessageWritable> {
+ BasicPathMergeVertex<VertexValueWritable, PathMergeMessageWritable> {
- private ArrayList<PathMergeMessageWritable> receivedMsg = new ArrayList<PathMergeMessageWritable>();
- private HashMap<VKmerBytesWritable, ArrayList<Byte>> dirMapper = new HashMap<VKmerBytesWritable, ArrayList<Byte>>();
-
- private EdgeWritable tmpEdge = new EdgeWritable();
+ private HashSet<PathMergeMessageWritable> updateMsgs = new HashSet<PathMergeMessageWritable>();
+ private HashSet<PathMergeMessageWritable> otherMsgs = new HashSet<PathMergeMessageWritable>();
+ private HashSet<PathMergeMessageWritable> neighborMsgs = new HashSet<PathMergeMessageWritable>();
/**
* initiate kmerSize, maxIteration
*/
+ @Override
public void initVertex() {
super.initVertex();
if(incomingMsg == null)
@@ -41,26 +37,8 @@
outgoingMsg.reset();
if(destVertexId == null)
destVertexId = new VKmerBytesWritable();
- inFlag = 0;
- outFlag = 0;
if(repeatKmer == null)
repeatKmer = new VKmerBytesWritable();
- tmpValue.reset();
- synchronized(lock){
- if(fakeVertex == null){
- fakeVertex = new VKmerBytesWritable();
- String fake = generateString(kmerSize + 1);//generaterRandomString(kmerSize + 1);
- fakeVertex.setByRead(kmerSize + 1, fake.getBytes(), 0);
- }
- }
- if(tmpKmer == null)
- tmpKmer = new VKmerBytesWritable();
- if(reverseKmer == null)
- reverseKmer = new VKmerBytesWritable();
- if(kmerList == null)
- kmerList = new VKmerListWritable();
- else
- kmerList.reset();
if(getSuperstep() == 1)
StatisticsAggregator.preGlobalCounters.clear();
// else
@@ -69,321 +47,212 @@
getVertexValue().getCounters().clear();
}
- /**
- * map reduce in FakeNode
- */
- public void aggregateMsgAndGroupInFakeNode(Iterator<PathMergeMessageWritable> msgIterator){
- kmerMapper.clear();
- dirMapper.clear();
- /** Mapper **/
- mapKeyByInternalKmer(msgIterator);
- /** Reducer **/
- reduceKeyByInternalKmer();
- }
-
- /**
- * typical for P1
- */
- @Override
- public void mapKeyByInternalKmer(Iterator<PathMergeMessageWritable> msgIterator){
- byte dir = 0;
- while(msgIterator.hasNext()){
- incomingMsg = msgIterator.next();
- String kmerString = incomingMsg.getInternalKmer().toString();
- tmpKmer.setByRead(kmerString.length(), kmerString.getBytes(), 0);
- reverseKmer.setByReadReverse(kmerString.length(), kmerString.getBytes(), 0);
-
- VKmerBytesWritable kmer = new VKmerBytesWritable();
- kmerList = new VKmerListWritable();
- if(reverseKmer.compareTo(tmpKmer) > 0){
- dir = KmerDir.FORWARD;
- kmer.setAsCopy(tmpKmer);
- }
- else{
- dir = KmerDir.REVERSE;
- kmer.setAsCopy(reverseKmer);
- }
- if(!kmerMapper.containsKey(kmer)){
- //kmerList.reset();
- kmerList.append(incomingMsg.getSourceVertexId());
- kmerMapper.put(kmer, kmerList);
- } else{
- kmerList.setCopy(kmerMapper.get(kmer));
- kmerList.append(incomingMsg.getSourceVertexId());
- kmerMapper.put(kmer, kmerList);
- }
- //dirMapper
- ArrayList<Byte> dirList = new ArrayList<Byte>();
- if(!dirMapper.containsKey(kmer)){
- dirList.clear();
- dirList.add(dir);
- dirMapper.put(kmer, dirList);
- } else{
- dirList.clear();
- dirList.addAll(dirMapper.get(kmer));
- dirList.add(dir);
- dirMapper.put(kmer, dirList);
- }
- }
- }
-
- /**
- * typical for P1
- */
- @Override
- public void reduceKeyByInternalKmer(){
- for (VKmerBytesWritable key : kmerMapper.keySet()) {
- kmerList = kmerMapper.get(key);
- //always delete kmerList(1), keep kmerList(0)
-
- //send kill message to kmerList(1), and carry with kmerList(0) to update edgeLists of kmerList(1)'s neighbor
- outgoingMsg.setFlag(MessageFlag.KILL);
- outgoingMsg.getNode().setInternalKmer(kmerList.getPosition(0));
- boolean isFlip = dirMapper.get(key).get(0) == dirMapper.get(key).get(1) ? false : true;
- outgoingMsg.setFlip(isFlip);
- destVertexId.setAsCopy(kmerList.getPosition(1));
- sendMsg(destVertexId, outgoingMsg);
- }
- }
-
- /**
- * typical for P1
- * 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);
+ 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);
- if(getVertexValue().getEdgeList(neighborToMeDir).getEdge(incomingMsg.getSourceVertexId()) != null){
- tmpEdge.setAsCopy(getVertexValue().getEdgeList(neighborToMeDir).getEdge(incomingMsg.getSourceVertexId()));
-
- getVertexValue().getEdgeList(neighborToMeDir).remove(incomingMsg.getSourceVertexId());
+ //choose merge dir -- principle: only merge with nextDir
+ if(restrictedDirs.size() == 1){
+ if((restrictedDirs.contains(DIR.PREVIOUS) && vertex.getDegree(DIR.NEXT) == 1)
+ || (restrictedDirs.contains(DIR.NEXT) && vertex.getDegree(DIR.PREVIOUS) == 1)){
+ EDGETYPE edgeType = restrictedDirs.contains(DIR.PREVIOUS) ? vertex.getEdgetypeFromDir(DIR.NEXT) : vertex.getEdgetypeFromDir(DIR.PREVIOUS);
+ state |= P4State.MERGE | edgeType.get();
+ updated = true;
+ }
}
- tmpEdge.setKey(incomingMsg.getNode().getInternalKmer());
- byte updateDir = flipDirection(neighborToMeDir, incomingMsg.isFlip());
- getVertexValue().getEdgeList(updateDir).unionAdd(tmpEdge);
- }
-
- /**
- * head send update message
- */
- public void headSendUpdateMsg(){
- if(isHeadNode()){
- byte headMergeDir = (byte)(getVertexValue().getState() & State.HEAD_CAN_MERGE_MASK);
- switch(headMergeDir){
- case State.HEAD_CAN_MERGEWITHPREV:
- sendUpdateMsg(isP1, DIR.NEXT);
- break;
- case State.HEAD_CAN_MERGEWITHNEXT:
- sendUpdateMsg(isP1, DIR.PREVIOUS);
- break;
- }
- } else
+
+ getVertexValue().setState(state);
+ if (updated)
+ activate();
+ else
voteToHalt();
}
/**
- * process update when receiving update msg
+ * step4: receive and process Merges for P0
*/
- public void processUpdateOnceReceiveMsg(Iterator<PathMergeMessageWritable> msgIterator){
- while(msgIterator.hasNext()){
- incomingMsg = msgIterator.next();
- processUpdate(incomingMsg);
- if(isHaltNode())
+ public void receiveMerges(Iterator<PathMergeMessageWritable> msgIterator) {
+ VertexValueWritable vertex = getVertexValue();
+ NodeWritable node = vertex.getNode();
+ short state = vertex.getState();
+ boolean updated = false;
+ EDGETYPE senderEdgetype;
+ @SuppressWarnings("unused")
+ int numMerged = 0;
+ // aggregate incomingMsg
+ ArrayList<PathMergeMessageWritable> receivedMsgList = new ArrayList<PathMergeMessageWritable>();
+ while(msgIterator.hasNext())
+ receivedMsgList.add(new PathMergeMessageWritable(msgIterator.next()));
+
+ if(receivedMsgList.size() > 2)
+ throw new IllegalStateException("In path merge, it is impossible to receive more than 2 messages!");
+
+ // odd number of nodes
+ if(receivedMsgList.size() == 2){
+ for(PathMergeMessageWritable msg : receivedMsgList){
+ senderEdgetype = EDGETYPE.fromByte(msg.getFlag());
+ node.mergeWithNode(senderEdgetype, msg.getNode());
+ state |= (byte) (msg.getFlag() & DIR.MASK); // update incoming restricted directions
+ numMerged++;
+ updated = true;
+ deleteVertex(msg.getSourceVertexId());
+ }
+ } else if(receivedMsgList.size() == 1){ // even number of nodes
+ PathMergeMessageWritable msg = receivedMsgList.get(0);
+ senderEdgetype = EDGETYPE.fromByte(msg.getFlag());
+ state |= (byte) (msg.getFlag() & DIR.MASK); // update incoming restricted directions
+ VKmerBytesWritable me = getVertexId();
+ VKmerBytesWritable other = msg.getSourceVertexId();
+ // determine if merge. if head msg meets head and #receiveMsg = 1
+ if (DIR.enumSetFromByte(state).containsAll(EnumSet.allOf(DIR.class))){
+ if(me.compareTo(other) < 0){
+ node.mergeWithNode(senderEdgetype, msg.getNode());
+ numMerged++;
+ updated = true;
+ deleteVertex(other);
+ } else{
+ // broadcast kill self and update pointer to new kmer, update edge from toMe to toOther
+ node.mergeWithNode(senderEdgetype, msg.getNode());
+ outgoingMsg.setSourceVertexId(me);
+ outgoingMsg.getNode().setInternalKmer(other);
+ outFlag = 0;
+ outFlag |= MessageFlag.TO_NEIGHBOR;
+ for(EDGETYPE et : EnumSet.allOf(EDGETYPE.class)){
+ for(VKmerBytesWritable kmer : vertex.getEdgeList(et).getKeys()){
+ EDGETYPE meToNeighbor = et.mirror();
+ EDGETYPE otherToNeighbor = senderEdgetype.causesFlip() ? meToNeighbor.flip() : meToNeighbor;
+ outFlag &= EDGETYPE.CLEAR;
+ outFlag &= MessageFlag.MERGE_DIR_CLEAR;
+ outFlag |= meToNeighbor.get() | otherToNeighbor.get() << 9;
+ outgoingMsg.setFlag(outFlag);
+ destVertexId = kmer;
+ sendMsg(destVertexId, outgoingMsg);
+ }
+ }
+
+ state |= P4State.NO_MERGE;
+ vertex.setState(state);
+ voteToHalt();
+ }
+ } else{
+ node.mergeWithNode(senderEdgetype, msg.getNode());
+ numMerged++;
+ updated = true;
+ deleteVertex(other);
+ }
+ }
+
+ 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
+ else
activate();
}
}
- /**
- * aggregate received msg
- */
- public void aggregateReceivedMsg(Iterator<PathMergeMessageWritable> msgIterator){
- receivedMsg.clear();
+
+ public void catagorizeMsg(Iterator<PathMergeMessageWritable> msgIterator){
+ updateMsgs.clear();
+ otherMsgs.clear();
+ neighborMsgs.clear();
while(msgIterator.hasNext()){
incomingMsg = msgIterator.next();
- receivedMsg.add(incomingMsg);
- }
- }
-
- /**
- * process message directly
- */
- public void processMessageDirectly(){
- for(int i = 0; i < 2; i++)
- processMerge(receivedMsg.get(i));
- //final vertex
- getVertexValue().setState(MessageFlag.IS_HALT);
- voteToHalt();
- }
-
- /**
- * processMerge and sendMsgToFake
- */
- public void processMergeAndSendMsgToFake(){
- boolean isHead = isHeadNode();
- boolean isDead = isDeadNode();
- processMerge(receivedMsg.get(0));
- if(isHead || isDead){
- // NON-FAKE and Final vertice send msg to FAKE vertex
- sendMsgToFakeVertex();
- //final vertex
- getVertexValue().setState(MessageFlag.IS_HALT);
- voteToHalt();
- } else
- activate();
- }
-
- /**
- * if receive kill msg, broadcaseKillself
- */
- public void broadcaseKillselfOnceReceiveKillMsg(Iterator<PathMergeMessageWritable> msgIterator){
- while(msgIterator.hasNext()){
- incomingMsg = msgIterator.next();
- if(isReceiveKillMsg()){
- outgoingMsg.setInternalKmer(incomingMsg.getNode().getInternalKmer());
- outgoingMsg.setFlip(incomingMsg.isFlip());
- broadcaseKillself();
- }
- }
- }
-
- /**
- * if receive dead msg, responseToDeadVertexAndUpdateEdges
- */
- public void responseToDeadVertexAndUpdateEdgesOnceReceiveDeadMsg(Iterator<PathMergeMessageWritable> msgIterator){
- while(msgIterator.hasNext()){
- incomingMsg = msgIterator.next();
- if(isResponseKillMsg())
- responseToDeadVertexAndUpdateEdges();
- }
- if(isHeadNode())
- activate();
- else
- 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.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 (getHeadFlagAndMergeDir() != getMsgFlagAndMergeDir()){
- getVertexValue().setState(State.HEAD_CANNOT_MERGE);
- voteToHalt();
- }
- break;
- case State.HEAD_CANNOT_MERGE:
- voteToHalt();
- break;
- }
- }
- }
+ byte msgType = (byte) (incomingMsg.getFlag() & MessageFlag.MSG_MASK);
+ switch(msgType){
+ case MessageFlag.TO_UPDATE:
+ updateMsgs.add(new PathMergeMessageWritable(incomingMsg));
+ break;
+ case MessageFlag.TO_NEIGHBOR:
+ neighborMsgs.add(new PathMergeMessageWritable(incomingMsg));
+ break;
+ default:
+ throw new IllegalStateException("Message types are allowd for only TO_UPDATE, TO_OTHER and TO_NEIGHBOR!");
}
-
+ }
+ }
+
+ public void receiveToNeighbor(Iterator<PathMergeMessageWritable> msgIterator){
+ VertexValueWritable value = getVertexValue();
+ while(msgIterator.hasNext()){
+ incomingMsg = msgIterator.next();
+ EDGETYPE deleteToMe = EDGETYPE.fromByte(incomingMsg.getFlag());
+ EDGETYPE aliveToMe = EDGETYPE.fromByte((short) (incomingMsg.getFlag() >> 9));
+
+ VKmerBytesWritable deletedKmer = incomingMsg.getSourceVertexId();
+ if(value.getEdgeList(deleteToMe).contains(deletedKmer)){
+ EdgeWritable deletedEdge = value.getEdgeList(deleteToMe).getEdge(deletedKmer);
+ value.getEdgeList(deleteToMe).remove(deletedKmer);
+
+ deletedEdge.setKey(incomingMsg.getInternalKmer());
+ value.getEdgeList(aliveToMe).unionAdd(deletedEdge);
+ }
+ voteToHalt();
+ }
+ }
+
+ /**
+ * for P0
+ */
+ 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());
+ state |= P4State.NO_MERGE;
+ vertex.setState(state);
+ voteToHalt();
+ }
+ }
@Override
- public void compute(Iterator<PathMergeMessageWritable> msgIterator) {
+ public void compute(Iterator<PathMergeMessageWritable> msgIterator) throws Exception {
initVertex();
+
if (getSuperstep() == 1) {
- addFakeVertex();
- startSendMsg();
- } else if (getSuperstep() == 2)
- if(!isFakeVertex())
- initState(msgIterator);
- else voteToHalt();
- else if (getSuperstep() % 7 == 3 && getSuperstep() <= maxIteration) {
- //head send update message
- headSendUpdateMsg();
- } else if (getSuperstep() % 7 == 4 && getSuperstep() <= maxIteration) {
- //process update when receiving updateMsg
- processUpdateOnceReceiveMsg(msgIterator);
- } else if (getSuperstep() % 7 == 5 && getSuperstep() <= maxIteration) {
- //head broadcastMergeMsg, while non-head voteToHalt
- if(isHeadNode())
- broadcastMergeMsg(false);
+ restrictNeighbors();
+ } else if (getSuperstep() % 2 == 0) {
+ if (getSuperstep() == 2)
+ recieveRestrictions(msgIterator);
else
- voteToHalt();
- } else if (getSuperstep() % 7 == 6 && getSuperstep() <= maxIteration) {
- if(!msgIterator.hasNext() && isDeadNode())
- deleteVertex(getVertexId());
- else{
- //aggregate received msg
- aggregateReceivedMsg(msgIterator);
- if(receivedMsg.size() == 2){ //#incomingMsg == even
- //processMerge directly
- processMessageDirectly();
- } else if(receivedMsg.size() == 1){
- //processMerge and sendMsgToFake
- processMergeAndSendMsgToFake();
- }
- }
- } else if (getSuperstep() % 7 == 0 && getSuperstep() <= maxIteration){
- if(isFakeVertex()){//is FakeVertex
- // Fake vertex agregates message and group them by actual kmer (1)
- aggregateMsgAndGroupInFakeNode(msgIterator);
- voteToHalt();
- }
- } else if (getSuperstep() % 7 == 1 && getSuperstep() <= maxIteration){
- //if receive kill msg, broadcaseKillself
- broadcaseKillselfOnceReceiveKillMsg(msgIterator);
- } else if (getSuperstep() % 7 == 2 && getSuperstep() <= maxIteration){
- //if receive dead msg, responseToDeadVertexAndUpdateEdges
- responseToDeadVertexAndUpdateEdgesOnceReceiveDeadMsg(msgIterator);
- }
- else
- voteToHalt();
+ receiveMerges(msgIterator);
+ chooseMergeDir();
+ updateNeighbors();
+ } else if (getSuperstep() % 2 == 1) {
+ catagorizeMsg(msgIterator);
+
+ receiveUpdates(updateMsgs.iterator());
+ receiveToNeighbor(neighborMsgs.iterator());
+
+ sendMergeMsg();
+ }
}
public static void main(String[] args) throws Exception {
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 6b4171e..824d0da 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
@@ -1,10 +1,8 @@
package edu.uci.ics.genomix.pregelix.operator.pathmerge;
import java.util.ArrayList;
-import java.util.Arrays;
import java.util.EnumSet;
import java.util.Iterator;
-import java.util.List;
import java.util.Random;
import java.util.logging.Logger;
@@ -15,17 +13,10 @@
import edu.uci.ics.genomix.pregelix.client.Client;
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.PathMergeMessageWritable;
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.NodeWritable;
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;
import edu.uci.ics.hyracks.api.exceptions.HyracksDataException;
@@ -51,20 +42,8 @@
private boolean curHead;
private boolean nextHead;
private boolean prevHead;
- private byte nextDir;
- private byte prevDir;
-
- private static final List<VKmerBytesWritable> problemKmers = Arrays.asList(
- new VKmerBytesWritable("CCCGGCCTCCAGCGTGGGATACGCGAAGATGCCGCCGTAGGTGAGAATCTGGTTC"),
- new VKmerBytesWritable("GCAGGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"),
- new VKmerBytesWritable("GAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"),
- new VKmerBytesWritable("GAGCAGGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"),
- new VKmerBytesWritable("GGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"),
- new VKmerBytesWritable("AGGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"),
- new VKmerBytesWritable("GCGACGTGCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"),
- new VKmerBytesWritable("GTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA")
- );
- private boolean verbose;
+ private EDGETYPE nextEdgetype;
+ private EDGETYPE prevEdgetype;
/**
* initiate kmerSize, maxIteration
@@ -102,88 +81,6 @@
// StatisticsAggregator.preGlobalCounters = BasicGraphCleanVertex.readStatisticsCounterResult(getContext().getConfiguration());
counters.clear();
getVertexValue().getCounters().clear();
-
- verbose = false;
- for (VKmerBytesWritable pk : problemKmers)
- verbose |= getVertexValue().getNode().findEdge(pk) != null || getVertexId().equals(pk);
- if (verbose)
- LOG.fine("iteration " + getSuperstep());
- }
-
- /**
- * 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 (byte d : NodeWritable.edgeTypesInDir(dir)) {
- for (VKmerBytesWritable destId : vertex.getEdgeList(d).getKeys()) {
- for (VKmerBytesWritable pk : problemKmers)
- verbose |= destId.equals(pk);
- outgoingMsg.reset();
- outgoingMsg.setFlag(DirectionFlag.dirFromEdgeType(DirectionFlag.mirrorEdge(d)).get());
- if (verbose)
- LOG.fine("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<PathMergeMessageWritable> msgIterator) {
- short restrictedDirs = 0; // the directions (NEXT/PREVIOUS) that I'm not allowed to merge in
- boolean updated = false;
- while (msgIterator.hasNext()) {
- incomingMsg = msgIterator.next();
- for (VKmerBytesWritable pk : problemKmers)
- verbose |= incomingMsg.getNode().findEdge(pk) != null || incomingMsg.getSourceVertexId().equals(pk);
- if (verbose)
- LOG.fine("before restriction " + getVertexId() + ": " + DIR.fromByte(restrictedDirs));
- restrictedDirs |= incomingMsg.getFlag();
- if (verbose)
- LOG.fine("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();
- }
}
protected boolean isNodeRandomHead(VKmerBytesWritable nodeKmer) {
@@ -198,7 +95,7 @@
}
/**
- * 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();
@@ -208,8 +105,8 @@
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);
}
@@ -218,8 +115,8 @@
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);
}
}
@@ -238,10 +135,10 @@
if (curHead) {
if (hasNext && !nextHead) {
// compress this head to the forward tail
- setMerge((byte) (nextDir | P4State.MERGE));
+ setMerge((byte) (nextEdgetype.get() | P4State.MERGE));
} else if (hasPrev && !prevHead) {
// compress this head to the reverse tail
- setMerge((byte) (prevDir | P4State.MERGE));
+ setMerge((byte) (prevEdgetype.get() | P4State.MERGE));
}
}
else {
@@ -250,177 +147,29 @@
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
- setMerge((byte) (nextDir | P4State.MERGE));
+ setMerge((byte) (nextEdgetype.get() | P4State.MERGE));
}
} else if (!hasPrev) {
// no previous node
if (!nextHead && curKmer.compareTo(nextKmer) < 0) {
// merge towards tail in forward dir
- setMerge((byte) (nextDir | P4State.MERGE));
+ setMerge((byte) (nextEdgetype.get() | P4State.MERGE));
}
} else if (!hasNext) {
// no next node
if (!prevHead && curKmer.compareTo(prevKmer) < 0) {
// merge towards tail in reverse dir
- setMerge((byte) (prevDir | P4State.MERGE));
+ setMerge((byte) (prevEdgetype.get() | P4State.MERGE));
}
}
}
}
if (verbose) {
- if ((getVertexValue().getState() & P4State.MERGE) == 0) {
- LOG.fine("No merge for " + getVertexId());
- } else {
- LOG.fine("Merge from " + getVertexId() + " towards " + (getVertexValue().getState() & DirectionFlag.DIR_MASK) + "; node is " + getVertexValue());
- }
- }
- }
-
- public void updateNeighbors() {
- VertexValueWritable vertex = getVertexValue();
- short state = vertex.getState();
- if ((state & P4State.MERGE) == 0) {
- return; // no merge requested; don't have to update neighbors
- }
-
- DIR mergeDir = DirectionFlag.dirFromEdgeType((byte)state);
- byte[] mergeEdges = NodeWritable.edgeTypesInDir(mergeDir);
-
- DIR updateDir = mergeDir.mirror();
- byte[] updateEdges = NodeWritable.edgeTypesInDir(updateDir); //
-
- // 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 (byte updateEdge : updateEdges) {
- outgoingMsg.reset();
- outgoingMsg.setSourceVertexId(getVertexId());
- outgoingMsg.setFlag(DirectionFlag.mirrorEdge(updateEdge)); // neighbor's edge to me (so he can remove me)
- for (byte mergeEdge : mergeEdges) {
- byte newDir = DirectionFlag.resolveLinkThroughMiddleNode(updateEdge, mergeEdge);
- outgoingMsg.getNode().setEdgeList(newDir, getVertexValue().getEdgeList(mergeEdge)); // copy into outgoingMsg
- }
- for (VKmerBytesWritable pk : problemKmers)
- verbose |= outgoingMsg.getNode().findEdge(pk) != null;
-
- // 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()) {
- if (verbose)
- LOG.fine("send update message from " + getVertexId() + " to " + dest + ": " + outgoingMsg);
- sendMsg(dest, outgoingMsg);
- }
- }
- }
-
- public void receiveUpdates(Iterator<PathMergeMessageWritable> msgIterator) throws HyracksDataException{
- VertexValueWritable vertex = getVertexValue();
- NodeWritable node = vertex.getNode();
- boolean updated = false;
- ArrayList<PathMergeMessageWritable> allSeenMsgs = new ArrayList<PathMergeMessageWritable>();
- while (msgIterator.hasNext()) {
- incomingMsg = msgIterator.next();
- for (VKmerBytesWritable pk : problemKmers)
- verbose |= incomingMsg.getNode().findEdge(pk) != null || incomingMsg.getSourceVertexId().equals(pk);
- if (verbose)
- LOG.fine("before update from neighbor: " + getVertexValue());
- // remove the edge to the node that will merge elsewhere
- try {
- node.getEdgeList((byte)(incomingMsg.getFlag() & DirectionFlag.DIR_MASK)).remove(incomingMsg.getSourceVertexId());
- } catch (ArrayIndexOutOfBoundsException e) {
- throw new HyracksDataException("In update, tried to remove an edge that doesn't exist...\nvertex: " + vertex + "\nremoving " + incomingMsg.getSourceVertexId() + " from dir " + (incomingMsg.getFlag() & DirectionFlag.DIR_MASK) + "\nupdate node: " + incomingMsg.getNode() + "\npreviously recieved messages this iteration: \n{\n" + StringUtils.join(allSeenMsgs, "\n") + "\n}\n", e);
- }
- // add the node this neighbor will merge into
- for (byte dir : DirectionFlag.values) {
- node.getEdgeList(dir).unionUpdate(incomingMsg.getEdgeList(dir));
- }
- updated = true;
- allSeenMsgs.add(incomingMsg);
- if (verbose)
- LOG.fine("after update from neighbor: " + getVertexValue());
- }
- if (verbose)
- LOG.fine("All recieved updates: \n{\n" + StringUtils.join(allSeenMsgs, "\n") + "\n}\n");
- if (updated) {
- if (DIR.enumSetFromByte(vertex.getState()).containsAll(EnumSet.allOf(DIR.class)))
- voteToHalt();
- else
- activate();
- }
-
-// checkNeighbors();
-// if (!hasNext && !hasPrev)
-// voteToHalt();
-// else
-// activate();
- }
-
- public void broadcastMerge() {
- 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)
- byte mergeDir = (byte)(vertex.getState() & DirectionFlag.DIR_MASK);
- byte neighborRestrictions = DIR.fromSet(DirectionFlag.causesFlip(mergeDir) ? DIR.flipSetFromByte(state) : DIR.enumSetFromByte(state));
-
- outgoingMsg.setFlag((short) (DirectionFlag.mirrorEdge(mergeDir) | neighborRestrictions));
- outgoingMsg.setSourceVertexId(getVertexId());
- outgoingMsg.setNode(vertex.getNode());
- if (vertex.getDegree(DirectionFlag.dirFromEdgeType(mergeDir)) != 1)
- throw new IllegalStateException("Merge attempted in node with degree in " + mergeDir + " direction != 1!\n" + vertex);
- VKmerBytesWritable dest = vertex.getEdgeList(mergeDir).get(0).getKey();
- for (VKmerBytesWritable pk : problemKmers)
- verbose |= outgoingMsg.getNode().findEdge(pk) != null || dest.equals(pk);
- if (verbose)
- LOG.fine("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);
-
- if (verbose)
- LOG.fine("killing self: " + getVertexId());
- deleteVertex(getVertexId());
- }
- }
-
- /**
- * step4: processMerges
- */
- public void receiveMerges(Iterator<PathMergeMessageWritable> msgIterator) {
- VertexValueWritable vertex = getVertexValue();
- NodeWritable node = vertex.getNode();
- short state = vertex.getState();
- boolean updated = false;
- byte senderDir;
- int numMerged = 0;
- while (msgIterator.hasNext()) {
- incomingMsg = msgIterator.next();
- for (VKmerBytesWritable pk : problemKmers)
- verbose |= incomingMsg.getNode().findEdge(pk) != null;
- if (verbose)
- LOG.fine("before merge: " + getVertexValue() + " restrictions: " + DIR.enumSetFromByte(state));
- senderDir = (byte) (incomingMsg.getFlag() & DirectionFlag.DIR_MASK);
- node.mergeWithNode(senderDir, incomingMsg.getNode());
- state |= (byte) (incomingMsg.getFlag() & DIR.MASK); // update incoming restricted directions
- numMerged++;
- updated = true;
- if (verbose)
- LOG.fine("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;
- if (verbose)
- LOG.fine("recieveMerges is a tandem repeat: " + getVertexId() + " " + getVertexValue());
-// 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();
+// if ((getVertexValue().getState() & P4State.MERGE) == 0) {
+// LOG.fine("No merge for " + getVertexId());
+// } else {
+ LOG.fine("Merge from " + getVertexId() + " towards " + (EDGETYPE.fromByte(getVertexValue().getState())) + "; node is " + getVertexValue());
+// }
}
}
@@ -439,7 +188,7 @@
updateNeighbors();
} else if (getSuperstep() % 2 == 1) {
receiveUpdates(msgIterator);
- broadcastMerge();
+ 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 fc38f4d..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
@@ -10,11 +10,18 @@
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 short REPLACE_DIR_MASK = 0b11 << 0;
+ public static final short REPLACE_DIR_CLEAR = 0b11111111111100 << 0;
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;
@@ -22,6 +29,20 @@
public static final short DIR_FROM_DEADVERTEX = 0b1 << 7;
public static final short DEAD_MASK = 0b1 << 7;
+ public static final short MERGE_DIR_FF = 0b00 << 9;
+ public static final short MERGE_DIR_FR = 0b01 << 9;
+ public static final short MERGE_DIR_RF = 0b10 << 9;
+ public static final short MERGE_DIR_RR = 0b11 << 9;
+ public static final short MERGE_DIR_MASK = 0b11 << 9;
+ public static final short MERGE_DIR_CLEAR = 0b11100111111111;
+
+ public static final short DELETE_DIR_FF = 0b00 << 11;
+ public static final short DELETE_DIR_FR = 0b01 << 11;
+ public static final short DELETE_DIR_RF = 0b10 << 11;
+ public static final short DELETE_DIR_RR = 0b11 << 11;
+ public static final short DELETE_DIR_MASK = 0b11 << 11;
+ public static final short DELETE_DIR_CLEAR = 0b10011111111111;
+
public static String getFlagAsString(byte code) {
return "ERROR_BAD_MESSAGE";
}
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 71444a6..a2a305e 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/PathMergeTestSuite.java
@@ -6,8 +6,10 @@
public static Test suite() throws Exception {
String pattern ="PathMerge";
- String testSet[] = {"ThreeNodesCycle", "RingPath", "SimpleTreePath", "RingPath", "CyclePath", "9", "P2_8", "ComplexTandemRepeat"
-// "2", "3", "4", "5", "6", "7", "8", "9", "head_6", "head_7",
+ String testSet[] = {"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",
// "LeftAdj", "RightAdj",
// "FR", "RF", "head_FR", "head_RF", "twohead_FR", "twohead_RF",
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 55f6060..0564c07 100644
--- a/genomix/genomix-pregelix/src/test/resources/conf/logging.properties
+++ b/genomix/genomix-pregelix/src/test/resources/conf/logging.properties
@@ -62,7 +62,7 @@
# For example, set the com.xyz.foo logger to only log SEVERE
# messages:
-edu.uci.ics.genomix.pregelix = 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
diff --git a/genomix/genomix-pregelix/src/test/resources/only_PathMerge.txt b/genomix/genomix-pregelix/src/test/resources/only_PathMerge.txt
index 3d007d2..b27e516 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
+P1ForMergeGraph.xml
