refactor KmerList -> VKmerList
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 362c12e..d61f679 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
@@ -17,10 +17,10 @@
public static final NodeWritable EMPTY_NODE = new NodeWritable();
private PositionListWritable nodeIdList;
- private KmerListWritable forwardForwardList;
- private KmerListWritable forwardReverseList;
- private KmerListWritable reverseForwardList;
- private KmerListWritable reverseReverseList;
+ private VKmerListWritable forwardForwardList;
+ private VKmerListWritable forwardReverseList;
+ private VKmerListWritable reverseForwardList;
+ private VKmerListWritable reverseReverseList;
private VKmerBytesWritable kmer;
// merge/update directions
@@ -34,15 +34,15 @@
public NodeWritable() {
nodeIdList = new PositionListWritable();
- forwardForwardList = new KmerListWritable();
- forwardReverseList = new KmerListWritable();
- reverseForwardList = new KmerListWritable();
- reverseReverseList = new KmerListWritable();
+ forwardForwardList = new VKmerListWritable();
+ forwardReverseList = new VKmerListWritable();
+ reverseForwardList = new VKmerListWritable();
+ reverseReverseList = new VKmerListWritable();
kmer = new VKmerBytesWritable(); // in graph construction - not set kmerlength Optimization: VKmer
}
- public NodeWritable(PositionListWritable nodeIdList, KmerListWritable FFList, KmerListWritable FRList,
- KmerListWritable RFList, KmerListWritable RRList, VKmerBytesWritable kmer) {
+ public NodeWritable(PositionListWritable nodeIdList, VKmerListWritable FFList, VKmerListWritable FRList,
+ VKmerListWritable RFList, VKmerListWritable RRList, VKmerBytesWritable kmer) {
this();
set(nodeIdList, FFList, FRList, RFList, RRList, kmer);
}
@@ -52,8 +52,8 @@
node.reverseReverseList, node.kmer);
}
- public void set(PositionListWritable nodeIdList, KmerListWritable FFList, KmerListWritable FRList,
- KmerListWritable RFList, KmerListWritable RRList, VKmerBytesWritable kmer2) {
+ public void set(PositionListWritable nodeIdList, VKmerListWritable FFList, VKmerListWritable FRList,
+ VKmerListWritable RFList, VKmerListWritable RRList, VKmerBytesWritable kmer2) {
this.nodeIdList.set(nodeIdList);
this.forwardForwardList.setCopy(FFList);
this.forwardReverseList.setCopy(FRList);
@@ -92,39 +92,39 @@
return kmer.getKmerLetterLength();
}
- public KmerListWritable getFFList() {
+ public VKmerListWritable getFFList() {
return forwardForwardList;
}
- public KmerListWritable getFRList() {
+ public VKmerListWritable getFRList() {
return forwardReverseList;
}
- public KmerListWritable getRFList() {
+ public VKmerListWritable getRFList() {
return reverseForwardList;
}
- public KmerListWritable getRRList() {
+ public VKmerListWritable getRRList() {
return reverseReverseList;
}
- public void setFFList(KmerListWritable forwardForwardList) {
+ public void setFFList(VKmerListWritable forwardForwardList) {
this.forwardForwardList.setCopy(forwardForwardList);
}
- public void setFRList(KmerListWritable forwardReverseList) {
+ public void setFRList(VKmerListWritable forwardReverseList) {
this.forwardReverseList.setCopy(forwardReverseList);
}
- public void setRFList(KmerListWritable reverseForwardList) {
+ public void setRFList(VKmerListWritable reverseForwardList) {
this.reverseForwardList.setCopy(reverseForwardList);
}
- public void setRRList(KmerListWritable reverseReverseList) {
+ public void setRRList(VKmerListWritable reverseReverseList) {
this.reverseReverseList.setCopy(reverseReverseList);
}
- public KmerListWritable getListFromDir(byte dir) {
+ public VKmerListWritable getListFromDir(byte dir) {
switch (dir & DirectionFlag.DIR_MASK) {
case DirectionFlag.DIR_FF:
return getFFList();
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerListWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/VKmerListWritable.java
similarity index 95%
rename from genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerListWritable.java
rename to genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/VKmerListWritable.java
index 2aee32d..44b2772 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerListWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/VKmerListWritable.java
@@ -15,7 +15,7 @@
/**
* A list of fixed-length kmers. The length of this list is stored internally.
*/
-public class KmerListWritable implements Writable, Iterable<KmerBytesWritable>, Serializable {
+public class VKmerListWritable implements Writable, Iterable<KmerBytesWritable>, Serializable {
private static final long serialVersionUID = 1L;
protected static final byte[] EMPTY_BYTES = { 0, 0, 0, 0 };
protected static final int HEADER_SIZE = 4;
@@ -27,18 +27,18 @@
private KmerBytesWritable posIter = new KmerBytesWritable();
- public KmerListWritable() {
+ public VKmerListWritable() {
storage = EMPTY_BYTES;
valueCount = 0;
offset = 0;
storageMaxSize = storage.length;
}
- public KmerListWritable(byte[] data, int offset) {
+ public VKmerListWritable(byte[] data, int offset) {
setNewReference(data, offset);
}
- public KmerListWritable(List<KmerBytesWritable> kmers) {
+ public VKmerListWritable(List<KmerBytesWritable> kmers) {
this();
setSize(kmers.size() * KmerBytesWritable.getBytesPerKmer() + HEADER_SIZE); // reserve space for all elements
for (KmerBytesWritable kmer : kmers) {
@@ -69,7 +69,7 @@
/*
* Append the otherList to the end of myList
*/
- public void appendList(KmerListWritable otherList) {
+ public void appendList(VKmerListWritable otherList) {
if (otherList.valueCount > 0) {
setSize((valueCount + otherList.valueCount) * KmerBytesWritable.getBytesPerKmer() + HEADER_SIZE);
// copy contents of otherList into the end of my storage
@@ -85,7 +85,7 @@
* Save the union of my list and otherList. Uses a temporary HashSet for
* uniquefication
*/
- public void unionUpdate(KmerListWritable otherList) {
+ public void unionUpdate(VKmerListWritable otherList) {
int newSize = valueCount + otherList.valueCount;
HashSet<KmerBytesWritable> uniqueElements = new HashSet<KmerBytesWritable>(newSize);
for (KmerBytesWritable kmer : this) {
@@ -136,7 +136,7 @@
return posIter;
}
- public void setCopy(KmerListWritable otherList) {
+ public void setCopy(VKmerListWritable otherList) {
setCopy(otherList.storage, otherList.offset);
}
diff --git a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerListWritableTest.java b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerListWritableTest.java
index 2f7bba8..25e74bd 100644
--- a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerListWritableTest.java
+++ b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerListWritableTest.java
@@ -8,13 +8,13 @@
import org.junit.Test;
import edu.uci.ics.genomix.type.KmerBytesWritable;
-import edu.uci.ics.genomix.type.KmerListWritable;
+import edu.uci.ics.genomix.type.VKmerListWritable;
public class KmerListWritableTest {
@Test
public void TestInitial() {
- KmerListWritable kmerList = new KmerListWritable();
+ VKmerListWritable kmerList = new VKmerListWritable();
Assert.assertEquals(kmerList.getCountOfPosition(), 0);
//one kmer in list and reset each time
@@ -47,7 +47,7 @@
byte [] another = new byte [kmerList.getLength()*2];
int start = 20;
System.arraycopy(kmerList.getByteArray(), kmerList.getStartOffset(), another, start, kmerList.getLength());
- KmerListWritable plist2 = new KmerListWritable(another, start);
+ VKmerListWritable plist2 = new VKmerListWritable(another, start);
for(int i = 0; i < plist2.getCountOfPosition(); i++){
Assert.assertEquals(kmerList.getPosition(i).toString(), plist2.getPosition(i).toString());
}
@@ -55,7 +55,7 @@
@Test
public void TestRemove() {
- KmerListWritable kmerList = new KmerListWritable();
+ VKmerListWritable kmerList = new VKmerListWritable();
Assert.assertEquals(kmerList.getCountOfPosition(), 0);
int i;
@@ -74,7 +74,7 @@
//delete one element each time
KmerBytesWritable tmpKmer = new KmerBytesWritable();
i = 0;
- KmerListWritable copyList = new KmerListWritable();
+ VKmerListWritable copyList = new VKmerListWritable();
copyList.setCopy(kmerList);
Iterator<KmerBytesWritable> iterator;
for(int j = 0; j < 5; j++){
@@ -108,7 +108,7 @@
Assert.assertEquals(0, kmerList.getCountOfPosition());
KmerBytesWritable.setGlobalKmerLength(3);
- KmerListWritable edgeList = new KmerListWritable();
+ VKmerListWritable edgeList = new VKmerListWritable();
KmerBytesWritable k = new KmerBytesWritable();
k.setByRead(("AAA").getBytes(), 0);
edgeList.append(k);
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 833462c..0c7cc20 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
@@ -13,7 +13,7 @@
import org.apache.hadoop.mapred.Reporter;
import edu.uci.ics.genomix.type.KmerBytesWritable;
-import edu.uci.ics.genomix.type.KmerListWritable;
+import edu.uci.ics.genomix.type.VKmerListWritable;
import edu.uci.ics.genomix.type.NodeWritable;
import edu.uci.ics.genomix.type.PositionListWritable;
import edu.uci.ics.genomix.type.PositionWritable;
@@ -37,8 +37,8 @@
private KmerBytesWritable nextReverseKmer;
private PositionWritable nodeId;
private PositionListWritable nodeIdList;
- private KmerListWritable edgeListForPreKmer;
- private KmerListWritable edgeListForNextKmer;
+ private VKmerListWritable edgeListForPreKmer;
+ private VKmerListWritable edgeListForNextKmer;
private NodeWritable outputNode;
private KmerDir preKmerDir;
@@ -59,8 +59,8 @@
nextReverseKmer = new KmerBytesWritable();
nodeId = new PositionWritable();
nodeIdList = new PositionListWritable();
- edgeListForPreKmer = new KmerListWritable();
- edgeListForNextKmer = new KmerListWritable();
+ edgeListForPreKmer = new VKmerListWritable();
+ edgeListForNextKmer = new VKmerListWritable();
outputNode = new NodeWritable();
preKmerDir = KmerDir.FORWARD;
curKmerDir = KmerDir.FORWARD;
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/ReadsKeyValueParserFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/ReadsKeyValueParserFactory.java
index 84f9fe0..42d8db6 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/ReadsKeyValueParserFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/ReadsKeyValueParserFactory.java
@@ -25,7 +25,7 @@
import org.apache.hadoop.io.Text;
import edu.uci.ics.genomix.type.KmerBytesWritable;
-import edu.uci.ics.genomix.type.KmerListWritable;
+import edu.uci.ics.genomix.type.VKmerListWritable;
import edu.uci.ics.genomix.type.NodeWritable;
import edu.uci.ics.genomix.type.PositionListWritable;
import edu.uci.ics.genomix.type.PositionWritable;
@@ -76,8 +76,8 @@
private PositionWritable nodeId = new PositionWritable();
private PositionListWritable nodeIdList = new PositionListWritable();
- private KmerListWritable edgeListForPreKmer = new KmerListWritable();
- private KmerListWritable edgeListForNextKmer = new KmerListWritable();
+ private VKmerListWritable edgeListForPreKmer = new VKmerListWritable();
+ private VKmerListWritable edgeListForNextKmer = new VKmerListWritable();
private NodeWritable outputNode = new NodeWritable();
// private NodeWritable outputNode2 = new NodeWritable();
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/AdjacencyListWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/AdjacencyListWritable.java
index b19a0cf..09e98fa 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/AdjacencyListWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/AdjacencyListWritable.java
@@ -7,20 +7,20 @@
import org.apache.hadoop.io.WritableComparable;
import edu.uci.ics.genomix.oldtype.PositionListWritable;
-import edu.uci.ics.genomix.type.KmerListWritable;
+import edu.uci.ics.genomix.type.VKmerListWritable;
public class AdjacencyListWritable implements WritableComparable<AdjacencyListWritable>{
- private KmerListWritable forwardList;
- private KmerListWritable reverseList;
+ private VKmerListWritable forwardList;
+ private VKmerListWritable reverseList;
public AdjacencyListWritable(){
- forwardList = new KmerListWritable();
- reverseList = new KmerListWritable();
+ forwardList = new VKmerListWritable();
+ reverseList = new VKmerListWritable();
}
public AdjacencyListWritable(int kmerSize){
- forwardList = new KmerListWritable();
- reverseList = new KmerListWritable();
+ forwardList = new VKmerListWritable();
+ reverseList = new VKmerListWritable();
}
public void set(AdjacencyListWritable adjacencyList){
@@ -42,19 +42,19 @@
return forwardList.getCountOfPosition() + reverseList.getCountOfPosition();
}
- public KmerListWritable getForwardList() {
+ public VKmerListWritable getForwardList() {
return forwardList;
}
- public void setForwardList(KmerListWritable forwardList) {
+ public void setForwardList(VKmerListWritable forwardList) {
this.forwardList = forwardList;
}
- public KmerListWritable getReverseList() {
+ public VKmerListWritable getReverseList() {
return reverseList;
}
- public void setReverseList(KmerListWritable reverseList) {
+ public void setReverseList(VKmerListWritable reverseList) {
this.reverseList = reverseList;
}
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 9cdac8f..83f286c 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
@@ -8,7 +8,7 @@
import edu.uci.ics.genomix.pregelix.type.MessageFlag;
import edu.uci.ics.genomix.type.KmerBytesWritable;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
-import edu.uci.ics.genomix.type.KmerListWritable;
+import edu.uci.ics.genomix.type.VKmerListWritable;
public class VertexValueWritable implements WritableComparable<VertexValueWritable> {
@@ -66,16 +66,16 @@
kmer = new VKmerBytesWritable();
}
- public VertexValueWritable(PositionListWritable nodeIdList, KmerListWritable forwardForwardList, KmerListWritable forwardReverseList,
- KmerListWritable reverseForwardList, KmerListWritable reverseReverseList,
+ public VertexValueWritable(PositionListWritable nodeIdList, VKmerListWritable forwardForwardList, VKmerListWritable forwardReverseList,
+ VKmerListWritable reverseForwardList, VKmerListWritable reverseReverseList,
byte state, VKmerBytesWritable kmer) {
set(nodeIdList, forwardForwardList, forwardReverseList,
reverseForwardList, reverseReverseList,
state, kmer);
}
- public void set(PositionListWritable nodeIdList, KmerListWritable forwardForwardList, KmerListWritable forwardReverseList,
- KmerListWritable reverseForwardList, KmerListWritable reverseReverseList,
+ public void set(PositionListWritable nodeIdList, VKmerListWritable forwardForwardList, VKmerListWritable forwardReverseList,
+ VKmerListWritable reverseForwardList, VKmerListWritable reverseReverseList,
byte state, VKmerBytesWritable kmer) {
this.kmerlength = kmer.getKmerLetterLength();
this.incomingList.setForwardList(reverseForwardList);
@@ -101,35 +101,35 @@
this.nodeIdList.set(nodeIdList);
}
- public KmerListWritable getFFList() {
+ public VKmerListWritable getFFList() {
return outgoingList.getForwardList();
}
- public KmerListWritable getFRList() {
+ public VKmerListWritable getFRList() {
return outgoingList.getReverseList();
}
- public KmerListWritable getRFList() {
+ public VKmerListWritable getRFList() {
return incomingList.getForwardList();
}
- public KmerListWritable getRRList() {
+ public VKmerListWritable getRRList() {
return incomingList.getReverseList();
}
- public void setFFList(KmerListWritable forwardForwardList){
+ public void setFFList(VKmerListWritable forwardForwardList){
outgoingList.setForwardList(forwardForwardList);
}
- public void setFRList(KmerListWritable forwardReverseList){
+ public void setFRList(VKmerListWritable forwardReverseList){
outgoingList.setReverseList(forwardReverseList);
}
- public void setRFList(KmerListWritable reverseForwardList){
+ public void setRFList(VKmerListWritable reverseForwardList){
incomingList.setForwardList(reverseForwardList);
}
- public void setRRList(KmerListWritable reverseReverseList){
+ public void setRRList(VKmerListWritable reverseReverseList){
incomingList.setReverseList(reverseReverseList);
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/MapReduceVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/MapReduceVertex.java
index ecd3c4f..99cd3c2 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/MapReduceVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/MapReduceVertex.java
@@ -13,7 +13,7 @@
import edu.uci.ics.genomix.pregelix.io.VertexValueWritable.State;
import edu.uci.ics.genomix.pregelix.type.MessageFlag;
//import edu.uci.ics.genomix.type.KmerBytesWritable;
-import edu.uci.ics.genomix.type.KmerListWritable;
+import edu.uci.ics.genomix.type.VKmerListWritable;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
import edu.uci.ics.pregelix.api.graph.Vertex;
import edu.uci.ics.pregelix.api.job.PregelixJob;
@@ -26,8 +26,8 @@
protected static VKmerBytesWritable fakeVertex = null;
protected VKmerBytesWritable reverseKmer;
- protected KmerListWritable kmerList = null;
- protected Map<VKmerBytesWritable, KmerListWritable> kmerMapper = new HashMap<VKmerBytesWritable, KmerListWritable>();
+ protected VKmerListWritable kmerList = null;
+ protected Map<VKmerBytesWritable, VKmerListWritable> kmerMapper = new HashMap<VKmerBytesWritable, VKmerListWritable>();
/**
* initiate kmerSize, maxIteration
@@ -46,7 +46,7 @@
if(reverseKmer == null)
reverseKmer = new VKmerBytesWritable();
if(kmerList == null)
- kmerList = new KmerListWritable();
+ kmerList = new VKmerListWritable();
else
kmerList.reset();
if(fakeVertex == null){
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 ef39a23..c9942a2 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
@@ -13,7 +13,7 @@
import edu.uci.ics.genomix.pregelix.type.MessageFlag;
import edu.uci.ics.genomix.pregelix.type.MessageFromHead;
import edu.uci.ics.genomix.type.KmerBytesWritable;
-import edu.uci.ics.genomix.type.KmerListWritable;
+import edu.uci.ics.genomix.type.VKmerListWritable;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
/*
* vertexId: BytesWritable
@@ -70,7 +70,7 @@
if(reverseKmer == null)
reverseKmer = new VKmerBytesWritable();
if(kmerList == null)
- kmerList = new KmerListWritable();
+ kmerList = new VKmerListWritable();
else
kmerList.reset();
if(fakeVertex == null){
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 8546bb6..33b62c3 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
@@ -12,7 +12,7 @@
import edu.uci.ics.genomix.pregelix.operator.pathmerge.BasicGraphCleanVertex;
import edu.uci.ics.genomix.pregelix.type.MessageFlag;
import edu.uci.ics.genomix.type.KmerBytesWritable;
-import edu.uci.ics.genomix.type.KmerListWritable;
+import edu.uci.ics.genomix.type.VKmerListWritable;
import edu.uci.ics.genomix.type.PositionWritable;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
import edu.uci.ics.pregelix.api.graph.Vertex;