start dependency refactor
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 1ad6cf0..833462c 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
@@ -17,6 +17,7 @@
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.VKmerBytesWritable;
@SuppressWarnings("deprecation")
public class GenomixMapper extends MapReduceBase implements
@@ -49,17 +50,18 @@
@Override
public void configure(JobConf job) {
KMER_SIZE = Integer.parseInt(job.get("sizeKmer"));
- preForwardKmer = new KmerBytesWritable(KMER_SIZE);
- preReverseKmer = new KmerBytesWritable(KMER_SIZE);
- curForwardKmer = new KmerBytesWritable(KMER_SIZE);
- curReverseKmer = new KmerBytesWritable(KMER_SIZE);
- nextForwardKmer = new KmerBytesWritable(KMER_SIZE);
- nextReverseKmer = new KmerBytesWritable(KMER_SIZE);
+ KmerBytesWritable.setGlobalKmerLength(KMER_SIZE);
+ preForwardKmer = new KmerBytesWritable();
+ preReverseKmer = new KmerBytesWritable();
+ curForwardKmer = new KmerBytesWritable();
+ curReverseKmer = new KmerBytesWritable();
+ nextForwardKmer = new KmerBytesWritable();
+ nextReverseKmer = new KmerBytesWritable();
nodeId = new PositionWritable();
nodeIdList = new PositionListWritable();
- edgeListForPreKmer = new KmerListWritable(KMER_SIZE);
- edgeListForNextKmer = new KmerListWritable(KMER_SIZE);
- outputNode = new NodeWritable(KMER_SIZE);
+ edgeListForPreKmer = new KmerListWritable();
+ edgeListForNextKmer = new KmerListWritable();
+ outputNode = new NodeWritable();
preKmerDir = KmerDir.FORWARD;
curKmerDir = KmerDir.FORWARD;
nextKmerDir = KmerDir.FORWARD;
@@ -86,7 +88,7 @@
}
/** first kmer **/
- outputNode.reset(KMER_SIZE);
+ outputNode.reset();
curForwardKmer.setByRead(array, 0);
curReverseKmer.setByReadReverse(array, 0);
curKmerDir = curForwardKmer.compareTo(curReverseKmer) <= 0 ? KmerDir.FORWARD : KmerDir.REVERSE;
@@ -100,7 +102,7 @@
/** middle kmer **/
for (int i = KMER_SIZE + 1; i < array.length; i++) {
- outputNode.reset(KMER_SIZE);
+ outputNode.reset();
setPreKmerByOldCurKmer();
setCurKmerByOldNextKmer();
setNextKmer(array[i]);
@@ -114,7 +116,7 @@
}
/** last kmer **/
- outputNode.reset(KMER_SIZE);
+ outputNode.reset();
setPreKmerByOldCurKmer();
setCurKmerByOldNextKmer();
//set value.nodeId
@@ -138,12 +140,12 @@
case FORWARD:
switch(preKmerDir){
case FORWARD:
- edgeListForPreKmer.reset(KMER_SIZE);
+ edgeListForPreKmer.reset();
edgeListForPreKmer.append(preForwardKmer);
outputNode.setRRList(edgeListForPreKmer);
break;
case REVERSE:
- edgeListForPreKmer.reset(KMER_SIZE);
+ edgeListForPreKmer.reset();
edgeListForPreKmer.append(preReverseKmer);
outputNode.setRFList(edgeListForPreKmer);
break;
@@ -152,12 +154,12 @@
case REVERSE:
switch(preKmerDir){
case FORWARD:
- edgeListForPreKmer.reset(KMER_SIZE);
+ edgeListForPreKmer.reset();
edgeListForPreKmer.append(preForwardKmer);
outputNode.setFRList(edgeListForPreKmer);
break;
case REVERSE:
- edgeListForPreKmer.reset(KMER_SIZE);
+ edgeListForPreKmer.reset();
edgeListForPreKmer.append(preReverseKmer);
outputNode.setFFList(edgeListForPreKmer);
break;
@@ -171,12 +173,12 @@
case FORWARD:
switch(nextKmerDir){
case FORWARD:
- edgeListForNextKmer.reset(KMER_SIZE);
+ edgeListForNextKmer.reset();
edgeListForNextKmer.append(nextForwardKmer);
outputNode.setFFList(edgeListForNextKmer);
break;
case REVERSE:
- edgeListForNextKmer.reset(KMER_SIZE);
+ edgeListForNextKmer.reset();
edgeListForNextKmer.append(nextReverseKmer);
outputNode.setFRList(edgeListForNextKmer);
break;
@@ -185,12 +187,12 @@
case REVERSE:
switch(nextKmerDir){
case FORWARD:
- edgeListForNextKmer.reset(KMER_SIZE);
+ edgeListForNextKmer.reset();
edgeListForNextKmer.append(nextForwardKmer);
outputNode.setRFList(edgeListForNextKmer);
break;
case REVERSE:
- edgeListForNextKmer.reset(KMER_SIZE);
+ edgeListForNextKmer.reset();
edgeListForNextKmer.append(nextReverseKmer);
outputNode.setRRList(edgeListForNextKmer);
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 1633c26..f39cdcb 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
@@ -23,15 +23,16 @@
@Override
public void configure(JobConf job) {
KMER_SIZE = GenomixMapper.KMER_SIZE;
- outputNode = new NodeWritable(KMER_SIZE);
- tmpNode = new NodeWritable(KMER_SIZE);
+ KmerBytesWritable.setGlobalKmerLength(KMER_SIZE);
+ outputNode = new NodeWritable();
+ tmpNode = new NodeWritable();
}
@Override
public void reduce(KmerBytesWritable key, Iterator<NodeWritable> values,
OutputCollector<KmerBytesWritable, NodeWritable> output,
Reporter reporter) throws IOException {
- outputNode.reset(KMER_SIZE);
+ outputNode.reset();
while (values.hasNext()) {
tmpNode.set(values.next());
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h3/MergePathsH3.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h3/MergePathsH3.java
index 8736fe3..b28328f 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h3/MergePathsH3.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/mergepaths/h3/MergePathsH3.java
@@ -27,6 +27,7 @@
import edu.uci.ics.genomix.hadoop.pmcommon.PathNodeInitial.PathNodeFlag;
import edu.uci.ics.genomix.oldtype.NodeWritable;
import edu.uci.ics.genomix.oldtype.PositionWritable;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
@SuppressWarnings("deprecation")
public class MergePathsH3 extends Configured implements Tool {
@@ -58,12 +59,14 @@
private boolean finalMerge;
public void configure(JobConf conf) {
+ KMER_SIZE = conf.getInt("sizeKmer", 0);
+ KmerBytesWritable.setGlobalKmerLength(KMER_SIZE);
+
randSeed = conf.getLong("randomSeed", 0);
randGenerator = new Random(randSeed);
probBeingRandomHead = conf.getFloat("probBeingRandomHead", 0.5f);
finalMerge = conf.getBoolean("finalMerge", false);
- KMER_SIZE = conf.getInt("sizeKmer", 0);
outputValue = new NodeWithFlagWritable(KMER_SIZE);
outputKey = new PositionWritable();
curNode = new NodeWritable(KMER_SIZE);
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 5c8f9c2..6695abe 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
@@ -70,7 +70,7 @@
* set the vertex value
*/
node.set(getRecordReader().getCurrentValue());
- vertexValue.setKmerlength(node.getKmerlength());
+ vertexValue.setKmerlength(node.getKmerLength());
vertexValue.setNodeIdList(node.getNodeIdList());
vertexValue.setFFList(node.getFFList());
vertexValue.setFRList(node.getFRList());