NodeWritable: refactor getListFromDir to getEdgeList
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 6e69677..d005d7e 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
@@ -103,7 +103,7 @@
return kmer.getKmerLetterLength();
}
- public VKmerListWritable getListFromDir(byte dir) {
+ public VKmerListWritable getEdgeList(byte dir) {
return edges[dir & DirectionFlag.DIR_MASK];
}
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 716b3d6..3a21bae 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
@@ -40,7 +40,7 @@
tmpNode.set(values.next());
outputNode.getNodeIdList().unionUpdate(tmpNode.getNodeIdList());
for (byte d: DirectionFlag.values) {
- outputNode.getListFromDir(d).unionUpdate(tmpNode.getListFromDir(d));
+ outputNode.getEdgeList(d).unionUpdate(tmpNode.getEdgeList(d));
}
averageCoverage += tmpNode.getAvgCoverage();
}
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 bad818b..d92dc18 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
@@ -69,22 +69,22 @@
public static String convertEdgeToGraph(String outputNode, NodeWritable value){
String outputEdge = "";
Iterator<VKmerBytesWritable> kmerIterator;
- kmerIterator = value.getListFromDir(DirectionFlag.DIR_FF).iterator();
+ kmerIterator = value.getEdgeList(DirectionFlag.DIR_FF).iterator();
while(kmerIterator.hasNext()){
VKmerBytesWritable edge = kmerIterator.next();
outputEdge += outputNode + " -> " + edge.toString() + "[color = \"black\" label =\"FF\"]\n";
}
- kmerIterator = value.getListFromDir(DirectionFlag.DIR_FR).iterator();
+ kmerIterator = value.getEdgeList(DirectionFlag.DIR_FR).iterator();
while(kmerIterator.hasNext()){
VKmerBytesWritable edge = kmerIterator.next();
outputEdge += outputNode + " -> " + edge.toString() + "[color = \"blue\" label =\"FR\"]\n";
}
- kmerIterator = value.getListFromDir(DirectionFlag.DIR_RF).iterator();
+ kmerIterator = value.getEdgeList(DirectionFlag.DIR_RF).iterator();
while(kmerIterator.hasNext()){
VKmerBytesWritable edge = kmerIterator.next();
outputEdge += outputNode + " -> " + edge.toString() + "[color = \"green\" label =\"RF\"]\n";
}
- kmerIterator = value.getListFromDir(DirectionFlag.DIR_RR).iterator();
+ kmerIterator = value.getEdgeList(DirectionFlag.DIR_RR).iterator();
while(kmerIterator.hasNext()){
VKmerBytesWritable edge = kmerIterator.next();
outputEdge += outputNode + " -> " + edge.toString() + "[color = \"red\" label =\"RR\"]\n";
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 81f5576..88c76ce 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
@@ -178,20 +178,20 @@
public void setEdgeListForCurAndNextKmer(KmerDir curKmerDir, NodeWritable curNode, KmerDir nextKmerDir,
NodeWritable nextNode) {
if (curKmerDir == KmerDir.FORWARD && nextKmerDir == KmerDir.FORWARD) {
- curNode.getListFromDir(DirectionFlag.DIR_FF).append(kmerSize, nextForwardKmer);
- nextNode.getListFromDir(DirectionFlag.DIR_RR).append(kmerSize, curForwardKmer);
+ curNode.getEdgeList(DirectionFlag.DIR_FF).append(kmerSize, nextForwardKmer);
+ nextNode.getEdgeList(DirectionFlag.DIR_RR).append(kmerSize, curForwardKmer);
}
if (curKmerDir == KmerDir.FORWARD && nextKmerDir == KmerDir.REVERSE) {
- curNode.getListFromDir(DirectionFlag.DIR_FR).append(kmerSize, nextReverseKmer);
- nextNode.getListFromDir(DirectionFlag.DIR_FR).append(kmerSize, curForwardKmer);
+ curNode.getEdgeList(DirectionFlag.DIR_FR).append(kmerSize, nextReverseKmer);
+ nextNode.getEdgeList(DirectionFlag.DIR_FR).append(kmerSize, curForwardKmer);
}
if (curKmerDir == KmerDir.REVERSE && nextKmerDir == KmerDir.FORWARD) {
- curNode.getListFromDir(DirectionFlag.DIR_RF).append(kmerSize, nextForwardKmer);
- nextNode.getListFromDir(DirectionFlag.DIR_RF).append(kmerSize, curReverseKmer);
+ curNode.getEdgeList(DirectionFlag.DIR_RF).append(kmerSize, nextForwardKmer);
+ nextNode.getEdgeList(DirectionFlag.DIR_RF).append(kmerSize, curReverseKmer);
}
if (curKmerDir == KmerDir.REVERSE && nextKmerDir == KmerDir.REVERSE) {
- curNode.getListFromDir(DirectionFlag.DIR_RR).append(kmerSize, nextReverseKmer);
- nextNode.getListFromDir(DirectionFlag.DIR_FF).append(kmerSize, curReverseKmer);
+ curNode.getEdgeList(DirectionFlag.DIR_RR).append(kmerSize, nextReverseKmer);
+ nextNode.getEdgeList(DirectionFlag.DIR_FF).append(kmerSize, curReverseKmer);
}
}
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/aggregators/AggregateKmerAggregateFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/aggregators/AggregateKmerAggregateFactory.java
index eb367a1..1d204f1 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/aggregators/AggregateKmerAggregateFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/aggregators/AggregateKmerAggregateFactory.java
@@ -80,7 +80,7 @@
readNode.setAsReference(accessor.getBuffer().array(), getOffSet(accessor, tIndex, 1));
localUniNode.getNodeIdList().appendList(readNode.getNodeIdList());
for (byte d: DirectionFlag.values) {
- localUniNode.getListFromDir(d).appendList(readNode.getListFromDir(d));
+ localUniNode.getEdgeList(d).appendList(readNode.getEdgeList(d));
}
localUniNode.addCoverage(readNode);
// make an empty field
@@ -94,7 +94,7 @@
readNode.setAsReference(accessor.getBuffer().array(), getOffSet(accessor, tIndex, 1));
localUniNode.getNodeIdList().appendList(readNode.getNodeIdList());
for (byte d: DirectionFlag.values) {
- localUniNode.getListFromDir(d).appendList(readNode.getListFromDir(d));
+ localUniNode.getEdgeList(d).appendList(readNode.getEdgeList(d));
}
localUniNode.addCoverage(readNode);
}
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/aggregators/MergeKmerAggregateFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/aggregators/MergeKmerAggregateFactory.java
index 89a0e35..3d072db 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/aggregators/MergeKmerAggregateFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/aggregators/MergeKmerAggregateFactory.java
@@ -73,7 +73,7 @@
readNode.setAsReference(accessor.getBuffer().array(), getOffSet(accessor, tIndex, 1));
localUniNode.getNodeIdList().unionUpdate(readNode.getNodeIdList());
for (byte d: DirectionFlag.values) {
- localUniNode.getListFromDir(d).unionUpdate(readNode.getListFromDir(d));
+ localUniNode.getEdgeList(d).unionUpdate(readNode.getEdgeList(d));
}
localUniNode.addCoverage(readNode);
//make a fake feild to cheat caller
@@ -92,7 +92,7 @@
readNode.setAsReference(accessor.getBuffer().array(), getOffSet(accessor, tIndex, 1));
localUniNode.getNodeIdList().unionUpdate(readNode.getNodeIdList());
for (byte d: DirectionFlag.values) {
- localUniNode.getListFromDir(d).unionUpdate(readNode.getListFromDir(d));
+ localUniNode.getEdgeList(d).unionUpdate(readNode.getEdgeList(d));
}
localUniNode.addCoverage(readNode);
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/InitialGraphCleanInputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/InitialGraphCleanInputFormat.java
index 7a09c3c..ca6a3e4 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/InitialGraphCleanInputFormat.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/InitialGraphCleanInputFormat.java
@@ -72,10 +72,10 @@
*/
node.set(getRecordReader().getCurrentValue());
vertexValue.setNodeIdList(node.getNodeIdList());
- vertexValue.setFFList(node.getListFromDir(DirectionFlag.DIR_FF));
- vertexValue.setFRList(node.getListFromDir(DirectionFlag.DIR_FR));
- vertexValue.setRFList(node.getListFromDir(DirectionFlag.DIR_RF));
- vertexValue.setRRList(node.getListFromDir(DirectionFlag.DIR_RR));
+ vertexValue.setFFList(node.getEdgeList(DirectionFlag.DIR_FF));
+ vertexValue.setFRList(node.getEdgeList(DirectionFlag.DIR_FR));
+ vertexValue.setRFList(node.getEdgeList(DirectionFlag.DIR_RF));
+ vertexValue.setRRList(node.getEdgeList(DirectionFlag.DIR_RR));
// TODO make this more efficient (don't use toString)
vertexValue.setActualKmer(new VKmerBytesWritable(vertexId));
vertexValue.setState(State.IS_NON);
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 b60d33f..91f0109 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
@@ -122,22 +122,22 @@
public static String convertEdgeToGraph(String outputNode, NodeWritable value){
String outputEdge = "";
Iterator<VKmerBytesWritable> kmerIterator;
- kmerIterator = value.getListFromDir(DirectionFlag.DIR_FF).iterator();
+ kmerIterator = value.getEdgeList(DirectionFlag.DIR_FF).iterator();
while(kmerIterator.hasNext()){
VKmerBytesWritable edge = kmerIterator.next();
outputEdge += outputNode + " -> " + edge.toString() + "[color = \"black\" label =\"FF\"]\n";
}
- kmerIterator = value.getListFromDir(DirectionFlag.DIR_FR).iterator();
+ kmerIterator = value.getEdgeList(DirectionFlag.DIR_FR).iterator();
while(kmerIterator.hasNext()){
VKmerBytesWritable edge = kmerIterator.next();
outputEdge += outputNode + " -> " + edge.toString() + "[color = \"blue\" label =\"FR\"]\n";
}
- kmerIterator = value.getListFromDir(DirectionFlag.DIR_RF).iterator();
+ kmerIterator = value.getEdgeList(DirectionFlag.DIR_RF).iterator();
while(kmerIterator.hasNext()){
VKmerBytesWritable edge = kmerIterator.next();
outputEdge += outputNode + " -> " + edge.toString() + "[color = \"green\" label =\"RF\"]\n";
}
- kmerIterator = value.getListFromDir(DirectionFlag.DIR_RR).iterator();
+ kmerIterator = value.getEdgeList(DirectionFlag.DIR_RR).iterator();
while(kmerIterator.hasNext()){
VKmerBytesWritable edge = kmerIterator.next();
outputEdge += outputNode + " -> " + edge.toString() + "[color = \"red\" label =\"RR\"]\n";