delete the endnodefile
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/pathmergingh2/ENodeInitialReducer.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/pathmergingh2/ENodeInitialReducer.java
deleted file mode 100644
index 651476c..0000000
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/pathmergingh2/ENodeInitialReducer.java
+++ /dev/null
@@ -1,72 +0,0 @@
-/*
- * Copyright 2009-2012 by The Regents of the University of California
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * you may obtain a copy of the License from
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package edu.uci.ics.genomix.pathmergingh2;
-
-import java.io.IOException;
-import java.util.Iterator;
-import org.apache.hadoop.io.BytesWritable;
-import org.apache.hadoop.mapred.JobConf;
-import org.apache.hadoop.mapred.MapReduceBase;
-import org.apache.hadoop.mapred.OutputCollector;
-import org.apache.hadoop.mapred.Reducer;
-import org.apache.hadoop.mapred.Reporter;
-import edu.uci.ics.genomix.type.KmerUtil;
-
-@SuppressWarnings("deprecation")
-public class ENodeInitialReducer extends MapReduceBase implements
- Reducer<BytesWritable, MergePathValueWritable, BytesWritable, MergePathValueWritable> {
- public BytesWritable outputKmer = new BytesWritable();
- public MergePathValueWritable outputAdjList = new MergePathValueWritable();
-
- @Override
- public void reduce(BytesWritable key, Iterator<MergePathValueWritable> values,
- OutputCollector<BytesWritable, MergePathValueWritable> output, Reporter reporter) throws IOException {
- outputAdjList = values.next();
- outputKmer.set(key);
- if (values.hasNext() == true) {
- byte bitFlag = outputAdjList.getFlag();
- bitFlag = (byte) (bitFlag & 0xFE);
- if (bitFlag == 2) {
- bitFlag = (byte) (0x80 | outputAdjList.getFlag());
- outputAdjList.set(outputAdjList.getAdjBitMap(), bitFlag, null);
- output.collect(outputKmer, outputAdjList);
-
- } else {
- boolean flag = false;
- while (values.hasNext()) {
- outputAdjList = values.next();
- if (outputAdjList.getFlag() == 2) {
- flag = true;
- break;
- }
- }
- if (flag == true) {
- bitFlag = (byte) (0x80 | outputAdjList.getFlag());
- outputAdjList.set(outputAdjList.getAdjBitMap(), bitFlag, null);
- output.collect(outputKmer, outputAdjList);
- }
- }
- } else {
- byte bitFlag = outputAdjList.getFlag();
- bitFlag = (byte) (bitFlag & 0xFE);
- if (bitFlag == 2) {
- bitFlag = 0;
- outputAdjList.set(outputAdjList.getAdjBitMap(), bitFlag, null);
- output.collect(outputKmer, outputAdjList);
- }
- }
- }
-}
-