more cleanup of setByRead interface
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 782869a..d9d6642 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
@@ -11,7 +11,7 @@
import org.apache.hadoop.io.SequenceFile;
import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
public class GenerateGraphViz {
@@ -31,7 +31,7 @@
String outputEdge = "";
for (File f : srcPath.listFiles((FilenameFilter) (new WildcardFileFilter("part*")))) {
SequenceFile.Reader reader = new SequenceFile.Reader(fileSys, new Path(f.getAbsolutePath()), conf);
- KmerBytesWritable key = new KmerBytesWritable();
+ VKmerBytesWritable key = new VKmerBytesWritable();
VertexValueWritable value = new VertexValueWritable();
while (reader.next(key, value)) {
@@ -58,25 +58,25 @@
public String convertEdgeToGraph(String outputNode, VertexValueWritable value){
String outputEdge = "";
- Iterator<KmerBytesWritable> kmerIterator;
+ Iterator<VKmerBytesWritable> kmerIterator;
kmerIterator = value.getFFList().iterator();
while(kmerIterator.hasNext()){
- KmerBytesWritable edge = kmerIterator.next();
+ VKmerBytesWritable edge = kmerIterator.next();
outputEdge += outputNode + " -> " + edge.toString() + "[color = \"black\" label =\"FF\"]\n";
}
kmerIterator = value.getFRList().iterator();
while(kmerIterator.hasNext()){
- KmerBytesWritable edge = kmerIterator.next();
+ VKmerBytesWritable edge = kmerIterator.next();
outputEdge += outputNode + " -> " + edge.toString() + "[color = \"black\" label =\"FR\"]\n";
}
kmerIterator = value.getRFList().iterator();
while(kmerIterator.hasNext()){
- KmerBytesWritable edge = kmerIterator.next();
+ VKmerBytesWritable edge = kmerIterator.next();
outputEdge += outputNode + " -> " + edge.toString() + "[color = \"red\" label =\"RF\"]\n";
}
kmerIterator = value.getRRList().iterator();
while(kmerIterator.hasNext()){
- KmerBytesWritable edge = kmerIterator.next();
+ VKmerBytesWritable edge = kmerIterator.next();
outputEdge += outputNode + " -> " + edge.toString() + "[color = \"red\" label =\"RR\"]\n";
}
return outputEdge;
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 5cb6aac..3f4e409 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
@@ -72,7 +72,7 @@
if(getSuperstep() == 1){
if(getVertexId().toString().equals("ATA")){
VKmerBytesWritable vertexId = new VKmerBytesWritable(kmerSize);
- vertexId.setByRead("GTA".getBytes(), 0);
+ vertexId.setByRead(kmerSize, "GTA".getBytes(), 0);
getVertexValue().getFRList().append(vertexId);
//add bridge vertex
@@ -92,7 +92,7 @@
kmerFRList.append(getVertexId());
vertexValue.setFRList(kmerFRList);
VKmerBytesWritable otherVertexId = new VKmerBytesWritable(kmerSize);
- otherVertexId.setByRead("ACG".getBytes(), 0);
+ otherVertexId.setByRead(kmerSize, "ACG".getBytes(), 0);
VKmerListWritable kmerRFList = new VKmerListWritable();
kmerRFList.append(otherVertexId);
vertexValue.setRFList(kmerRFList);
@@ -103,7 +103,7 @@
}
else if(getVertexId().toString().equals("ACG")){
VKmerBytesWritable brdgeVertexId = new VKmerBytesWritable(kmerSize);
- brdgeVertexId.setByRead("GTA".getBytes(), 0);
+ brdgeVertexId.setByRead(kmerSize, "GTA".getBytes(), 0);
getVertexValue().getRFList().append(brdgeVertexId);
}
}
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 3df090c..0c96412 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
@@ -65,7 +65,7 @@
if(getSuperstep() == 1){
if(getVertexId().toString().equals("ATA")){
VKmerBytesWritable vertexId = new VKmerBytesWritable(kmerSize);
- vertexId.setByRead("GTA".getBytes(), 0);
+ vertexId.setByRead(kmerSize, "GTA".getBytes(), 0);
getVertexValue().getFRList().append(vertexId);
//add bridge vertex
@@ -85,7 +85,7 @@
kmerFRList.append(getVertexId());
vertexValue.setFRList(kmerFRList);
VKmerBytesWritable otherVertexId = new VKmerBytesWritable(kmerSize);
- otherVertexId.setByRead("AGA".getBytes(), 0);
+ otherVertexId.setByRead(kmerSize, "AGA".getBytes(), 0);
VKmerListWritable kmerRFList = new VKmerListWritable();
kmerRFList.append(otherVertexId);
vertexValue.setRFList(kmerRFList);
@@ -96,7 +96,7 @@
}
else if(getVertexId().toString().equals("AGA")){
VKmerBytesWritable brdgeVertexId = new VKmerBytesWritable(kmerSize);
- brdgeVertexId.setByRead("GTA".getBytes(), 0);
+ brdgeVertexId.setByRead(kmerSize, "GTA".getBytes(), 0);
getVertexValue().getRFList().append(brdgeVertexId);
}
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicGraphCleanVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicGraphCleanVertex.java
index ca4b088..ece573c 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicGraphCleanVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicGraphCleanVertex.java
@@ -653,32 +653,28 @@
match = selfString.substring(selfString.length() - kmerSize + 1,selfString.length());
msgString = msg.getActualKmer().toString();
index = msgString.indexOf(match);
-// tmpKmer.reset(msgString.length() - index);
- tmpKmer.setByRead(msgString.substring(index).getBytes(), 0);
+ tmpKmer.setByRead(msgString.length() - index, msgString.substring(index).getBytes(), 0);
break;
case MessageFlag.DIR_FR:
selfString = getVertexValue().getKmer().toString();
match = selfString.substring(selfString.length() - kmerSize + 1,selfString.length());
msgString = GeneCode.reverseComplement(msg.getActualKmer().toString());
index = msgString.indexOf(match);
-// tmpKmer.reset(msgString.length() - index);
- tmpKmer.setByReadReverse(msgString.substring(index).getBytes(), 0);
+ tmpKmer.setByReadReverse(msgString.length() - index, msgString.substring(index).getBytes(), 0);
break;
case MessageFlag.DIR_RF:
selfString = getVertexValue().getKmer().toString();
match = selfString.substring(0,kmerSize - 1);
msgString = GeneCode.reverseComplement(msg.getActualKmer().toString());
index = msgString.lastIndexOf(match) + kmerSize - 2;
-// tmpKmer.reset(index + 1);
- tmpKmer.setByReadReverse(msgString.substring(0, index + 1).getBytes(), 0);
+ tmpKmer.setByReadReverse(index + 1, msgString.substring(0, index + 1).getBytes(), 0);
break;
case MessageFlag.DIR_RR:
selfString = getVertexValue().getKmer().toString();
match = selfString.substring(0,kmerSize - 1);
msgString = msg.getActualKmer().toString();
index = msgString.lastIndexOf(match) + kmerSize - 2;
-// tmpKmer.reset(index + 1); // TODO: fix ALL of these resets (only if you need to)
- tmpKmer.setByRead(msgString.substring(0, index + 1).getBytes(), 0);
+ tmpKmer.setByRead(index + 1, msgString.substring(0, index + 1).getBytes(), 0);
break;
}
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 027d295..1c981f2 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
@@ -49,10 +49,9 @@
else
kmerList.reset();
if(fakeVertex == null){
-// fakeVertex = new KmerBytesWritable(kmerSize + 1); // TODO check if merge is correct
fakeVertex = new VKmerBytesWritable();
String random = generaterRandomString(kmerSize + 1);
- fakeVertex.setByRead(random.getBytes(), 0);
+ fakeVertex.setByRead(kmerSize + 1, random.getBytes(), 0);
}
if(destVertexId == null)
destVertexId = new VKmerBytesWritable(kmerSize);
@@ -108,9 +107,8 @@
incomingMsg = msgIterator.next();
String kmerString = incomingMsg.getActualKmer().toString();
tmpKmer.reset(kmerString.length());
-// reverseKmer.reset(kmerString.length());//kmerbyteswritable
- tmpKmer.setByRead(kmerString.getBytes(), 0);
- reverseKmer.setByReadReverse(kmerString.getBytes(), 0);
+ tmpKmer.setByRead(kmerString.length(), kmerString.getBytes(), 0);
+ reverseKmer.setByReadReverse(kmerString.length(), kmerString.getBytes(), 0);
if(reverseKmer.compareTo(tmpKmer) < 0)
tmpKmer.setAsCopy(reverseKmer);
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 da83dcf..6b7ad1f 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
@@ -76,7 +76,7 @@
// fakeVertex = new KmerBytesWritable(kmerSize + 1);
fakeVertex = new VKmerBytesWritable();
String random = generaterRandomString(kmerSize + 1);
- fakeVertex.setByRead(random.getBytes(), 0);
+ fakeVertex.setByRead(kmerSize + 1, random.getBytes(), 0);
}
isFakeVertex = ((byte)getVertexValue().getState() & State.FAKEFLAG_MASK) > 0 ? true : false;
if(destVertexId == 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 e4e797f..83958fe 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
@@ -341,9 +341,9 @@
if(!neighborEdgeIntersection.isEmpty()){
if(count == 0)
- createdVertexId.setByRead("AAA".getBytes(), 0);//kmerSize + 1 generaterRandomString(kmerSize).getBytes()
+ createdVertexId.setByRead("AAA".length(), "AAA".getBytes(), 0);//kmerSize + 1 generaterRandomString(kmerSize).getBytes()
else
- createdVertexId.setByRead("GGG".getBytes(), 0);
+ createdVertexId.setByRead("GGG".length(), "GGG".getBytes(), 0);
count++;
/** create new/created vertex **/
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 4a540b8..cff87c7 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
@@ -69,7 +69,7 @@
if(getSuperstep() == 1){
if(getVertexId().toString().equals("CTA")){
VKmerBytesWritable vertexId = new VKmerBytesWritable(kmerSize);
- vertexId.setByRead("AGC".getBytes(), 0);
+ vertexId.setByRead(kmerSize, "AGC".getBytes(), 0);
getVertexValue().getRFList().append(vertexId);
//add tip vertex
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/MergePathTest.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/MergePathTest.java
index e8ca60f..9daeaa3 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/MergePathTest.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/MergePathTest.java
@@ -14,7 +14,7 @@
import edu.uci.ics.genomix.pregelix.io.VertexValueWritable;
import edu.uci.ics.genomix.pregelix.type.State2;
-import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
public class MergePathTest {
public static final String PATH_TO_TESTSTORE = "testcase/pathmerge/";
@@ -50,7 +50,7 @@
for (int i = 0; i < nc; i++) {
Path path = new Path(input + "/part-" + i);
SequenceFile.Reader reader = new SequenceFile.Reader(fileSys, path, conf);
- KmerBytesWritable key = new KmerBytesWritable(kmerSize);
+ VKmerBytesWritable key = new VKmerBytesWritable(kmerSize);
VertexValueWritable value = new VertexValueWritable();
while (reader.next(key, value)) {
@@ -90,7 +90,7 @@
for (int i = 0; i < nc; i++) {
Path path = new Path(input + "/part-" + i);
SequenceFile.Reader reader = new SequenceFile.Reader(fileSys, path, conf);
- KmerBytesWritable key = new KmerBytesWritable(kmerSize);
+ VKmerBytesWritable key = new VKmerBytesWritable(kmerSize);
VertexValueWritable value = new VertexValueWritable();
while (reader.next(key, value)) {
@@ -115,7 +115,7 @@
for (int i = 0; i < nc; i++) {
Path path = new Path(input + "/part-" + i);
SequenceFile.Reader reader = new SequenceFile.Reader(fileSys, path, conf);
- KmerBytesWritable key = new KmerBytesWritable(kmerSize);
+ VKmerBytesWritable key = new VKmerBytesWritable(kmerSize);
VertexValueWritable value = new VertexValueWritable();
while (reader.next(key, value)) {