commit be0a038966f849795de62ee13079ec8936a8743b
author Nan Zhang <zhangnan2920214@gmail.com> Fri Jul 26 16:59:52 2013 -0700
committer Nan Zhang <zhangnan2920214@gmail.com> Fri Jul 26 16:59:52 2013 -0700
tree 182d388571f9ba0e8794b4b701bb1f388510e82b
parent fe8cb0f7c8dc053cee406a904ca491baf96a759d

modify the jobGeBrujinGraph

genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/job/JobGenBrujinGraph.java

diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/job/JobGenBrujinGraph.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/job/JobGenBrujinGraph.java
index 96e31b8..99885a7 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/job/JobGenBrujinGraph.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/job/JobGenBrujinGraph.java
@@ -29,13 +29,11 @@
 import edu.uci.ics.genomix.hyracks.data.accessors.ReadIDPartitionComputerFactory;
 import edu.uci.ics.genomix.hyracks.data.primitive.KmerPointable;
 import edu.uci.ics.genomix.hyracks.dataflow.ConnectorPolicyAssignmentPolicy;
-import edu.uci.ics.genomix.hyracks.dataflow.MapKmerPositionToReadOperator;
-import edu.uci.ics.genomix.hyracks.dataflow.MapReadToNodeOperator;
-import edu.uci.ics.genomix.hyracks.dataflow.ReadsKeyValueParserFactory;
-import edu.uci.ics.genomix.hyracks.dataflow.aggregators.AggregateKmerAggregateFactory;
-import edu.uci.ics.genomix.hyracks.dataflow.aggregators.AggregateReadIDAggregateFactory;
-import edu.uci.ics.genomix.hyracks.dataflow.aggregators.MergeKmerAggregateFactory;
-import edu.uci.ics.genomix.hyracks.dataflow.aggregators.MergeReadIDAggregateFactory;
+import edu.uci.ics.genomix.hyracks.newgraph.dataflow.ReadsKeyValueParserFactory;
+import edu.uci.ics.genomix.hyracks.newgraph.dataflow.aggregators.AggregateKmerAggregateFactory;
+import edu.uci.ics.genomix.hyracks.newgraph.dataflow.aggregators.MergeKmerAggregateFactory;
+
+
 import edu.uci.ics.genomix.hyracks.dataflow.io.KMerSequenceWriterFactory;
 import edu.uci.ics.genomix.hyracks.dataflow.io.KMerTextWriterFactory;
 import edu.uci.ics.genomix.hyracks.dataflow.io.NodeSequenceWriterFactory;
@@ -103,7 +101,7 @@
     protected int tableSize;
     protected GroupbyType groupbyType;
     protected OutputFormat outputFormat;
-    protected boolean bGenerateReversedKmer;
+
 
     protected void logDebug(String status) {
         LOG.debug(status + " nc nodes:" + ncNodeNames.length);
@@ -173,7 +171,7 @@
 
             return new HDFSReadOperatorDescriptor(jobSpec, ReadsKeyValueParserFactory.readKmerOutputRec,
                     hadoopJobConfFactory.getConf(), splits, readSchedule, new ReadsKeyValueParserFactory(readLength,
-                            kmerSize, bGenerateReversedKmer));
+                            kmerSize));
         } catch (Exception e) {
             throw new HyracksDataException(e);
         }