new update for new version graph-building
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/experiment/KmerVertexID.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/experiment/KmerVertexID.java
deleted file mode 100644
index 9a01e36..0000000
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/experiment/KmerVertexID.java
+++ /dev/null
@@ -1,69 +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.experiment;
-
-import java.io.DataInput;
-import java.io.DataOutput;
-import java.io.IOException;
-
-import org.apache.hadoop.io.Writable;
-
-public class KmerVertexID implements Writable {
- private int readID;
- private byte posInRead;
-
- public KmerVertexID(int readID, byte posInRead) {
- set(readID, posInRead);
- }
-
- public KmerVertexID() {
- readID = -1;
- posInRead = -1;
- }
-
- @Override
- public void readFields(DataInput arg0) throws IOException {
- readID = arg0.readInt();
- posInRead = arg0.readByte();
- }
-
- @Override
- public void write(DataOutput arg0) throws IOException {
- arg0.writeInt(readID);
- arg0.writeByte(posInRead);
- }
-
- @Override
- public String toString() {
- return String.valueOf(readID) + '\t' + String.valueOf(posInRead);
- }
-
- public void set(int readID, byte posInRead) {
- this.readID = readID;
- this.posInRead = posInRead;
- }
-
- public int getReadID() {
- return readID;
- }
-
- public void setReadID(int readID) {
- this.readID = readID;
- }
-
- public byte getPosInRead() {
- return posInRead;
- }
-}
\ No newline at end of file
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/experiment/VertexAdjacentWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/experiment/VertexAdjacentWritable.java
index 191aacf..4145a3b 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/experiment/VertexAdjacentWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/experiment/VertexAdjacentWritable.java
@@ -19,7 +19,7 @@
this(null, 0, EMPTY_BYTES);
}
- public VertexAdjacentWritable(VertexIDList right, int kmerSize, byte[] bytes) {
+ public VertexAdjacentWritable(PositionList right, int kmerSize, byte[] bytes) {
if (right != null)
this.adjVertexList = new VertexIDListWritable(right);
else
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/experiment/VertexIDList.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/experiment/VertexIDList.java
deleted file mode 100644
index f799b00..0000000
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/experiment/VertexIDList.java
+++ /dev/null
@@ -1,183 +0,0 @@
-package edu.uci.ics.genomix.experiment;
-
-public class VertexIDList {
-
- private int[] readIDList;
- private byte[] posInReadList;
- private static final int[] EMPTY_INTS = {};
- private static final byte[] EMPTY_BYTES = {};
-
- private int usedSize;
- private int arraySize;
-
- public VertexIDList() {
- this(0, 0, EMPTY_INTS, EMPTY_BYTES);
- }
-
- public VertexIDList(int usedSize, int arraySize, int[] rList, byte[] pList) {
- this.usedSize = usedSize;
- this.arraySize = arraySize;
- if (arraySize > 0) {
- this.readIDList = rList;
- this.posInReadList = pList;
- if (this.readIDList.length != arraySize | this.posInReadList.length != arraySize) {
- throw new ArrayIndexOutOfBoundsException("the arraySize doesn't corespond to the array");
- }
- if (this.readIDList.length < usedSize | this.posInReadList.length < usedSize) {
- throw new ArrayIndexOutOfBoundsException("the usedSize doesn't corespond to the array");
- }
- } else {
- this.readIDList = rList;
- this.posInReadList = pList;
- this.arraySize = 0;
- this.usedSize = 0;
- }
- }
-
- public VertexIDList(int arraySize) {
- this.arraySize = arraySize;
- this.usedSize = 0;
- if (arraySize > 0) {
- this.readIDList = new int[this.arraySize];
- this.posInReadList = new byte[this.arraySize];
- } else {
- this.readIDList = EMPTY_INTS;
- this.posInReadList = EMPTY_BYTES;
- }
- }
-
- public VertexIDList(VertexIDList right) {
- if (right != null) {
- this.usedSize = right.usedSize;
- this.arraySize = right.arraySize;
- this.readIDList = new int[right.arraySize];
- this.posInReadList = new byte[right.arraySize];
- if (this.readIDList.length != arraySize | this.posInReadList.length != arraySize) {
- throw new ArrayIndexOutOfBoundsException("the arraySize doesn't corespond to the array");
- }
- if (this.readIDList.length < usedSize | this.posInReadList.length < usedSize) {
- throw new ArrayIndexOutOfBoundsException("the usedSize doesn't corespond to the array");
- }
- set(right);
- } else {
- this.arraySize = 0;
- this.usedSize = 0;
- this.readIDList = EMPTY_INTS;
- this.posInReadList = EMPTY_BYTES;
- }
- }
-
- public void set(VertexIDList newData) {
- set(newData.readIDList, 0, newData.posInReadList, 0, newData.usedSize);
- }
-
- public void set(int[] rIDList, int rOffset, byte[] pReadList, int pOffset, int copySize) {
- setArraySize(0);
- setArraySize(copySize);
- System.arraycopy(rIDList, rOffset, this.readIDList, 0, copySize);
- System.arraycopy(pReadList, pOffset, this.posInReadList, 0, copySize);
- this.usedSize = copySize;
- }
-
- public void setArraySize(int arraySize) {
- if (arraySize > getCapacity()) {
- setCapacity((arraySize * 2));
- }
- this.arraySize = arraySize;
- }
-
- public int getCapacity() {
- return this.arraySize;
- }
-
- public void setCapacity(int new_cap) {
- if (new_cap != getCapacity()) {
- int[] newRList = new int[new_cap];
- byte[] newPList = new byte[new_cap];
- if (new_cap < this.arraySize) {
- this.arraySize = new_cap;
- }
- if (this.arraySize != 0) {
- System.arraycopy(this.readIDList, 0, newRList, 0, this.usedSize);
- System.arraycopy(this.posInReadList, 0, newPList, 0, this.usedSize);
- }
- this.readIDList = newRList;
- this.posInReadList = newPList;
- }
- }
-
- public int getReadListElement(int position) {
- if (position < this.usedSize) {
- return this.readIDList[position];
- } else {
- throw new ArrayIndexOutOfBoundsException("position exceed for the usedSize");
- }
- }
-
- public byte getPosinReadListElement(int position) {
- if (position < this.usedSize) {
- return this.posInReadList[position];
- } else {
- throw new ArrayIndexOutOfBoundsException("position exceed for the usedSize");
- }
- }
-
- public int findReadListElement(int rContent) {
- for (int i = 0; i < this.usedSize; i++) {
- if (this.readIDList[i] == rContent)
- return i;
- }
- return -1;
- }
-
- public int findPosinReadListElement(int pContent) {
- for (int i = 0; i < this.usedSize; i++) {
- if (this.usedSize == pContent)
- return i;
- }
- return -1;
- }
-
- public void addELementToList(int rContent, byte pContent) {
- if (this.usedSize < this.arraySize) {
- this.readIDList[this.usedSize] = rContent;
- this.posInReadList[this.usedSize] = pContent;
- this.usedSize++;
- } else {
- setCapacity((this.arraySize * 2));
- this.readIDList[this.usedSize] = rContent;
- this.posInReadList[this.usedSize] = pContent;
- this.usedSize++;
- }
- }
-
- public void deleteElementFromTwoList(int position) {
- if (position < this.usedSize) {
- for (int i = position; i < this.usedSize; i++) {
- this.readIDList[i] = this.readIDList[i + 1];
- this.posInReadList[i] = this.posInReadList[i + 1];
- }
- this.readIDList[this.usedSize - 1] = -1;
- this.posInReadList[this.usedSize - 1] = (byte) -1;
- this.usedSize--;
- } else {
- throw new ArrayIndexOutOfBoundsException("position exceed for the usedSize");
- }
- }
-
- public int[] getReadIDList() {
- return this.readIDList;
- }
-
- public byte[] getPosInReadList() {
- return this.posInReadList;
- }
-
- public int getUsedSize() {
- return this.usedSize;
- }
-
- public int getArraySize() {
- return this.arraySize;
- }
-}
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/experiment/VertexIDListWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/experiment/VertexIDListWritable.java
index f7d917a..d8763e9 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/experiment/VertexIDListWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/experiment/VertexIDListWritable.java
@@ -7,26 +7,26 @@
public class VertexIDListWritable implements Writable {
- private VertexIDList vertexIDList;
+ private PositionList vertexIDList;
private int[] tempReadIDList = null;
private byte[] tempPosInReadList = null;
public VertexIDListWritable() {
- this.vertexIDList = new VertexIDList();
+ this.vertexIDList = new PositionList();
}
- public VertexIDListWritable(VertexIDList right) {
- this.vertexIDList = new VertexIDList(right);
+ public VertexIDListWritable(PositionList right) {
+ this.vertexIDList = new PositionList(right);
}
public VertexIDListWritable(int length) {
- this.vertexIDList = new VertexIDList(length);
+ this.vertexIDList = new PositionList(length);
}
public void set(VertexIDListWritable right) {
set(right.get());
}
- public void set(VertexIDList right) {
+ public void set(PositionList right) {
this.vertexIDList.set(right);
}
@@ -46,8 +46,13 @@
}
}
+// Position [] pos = new Position();
@Override
public void write(DataOutput out) throws IOException {
+// out.writeInt(length);
+// for ( int i: length){
+// pos[i].write(out);
+// }
// TODO Auto-generated method stub
out.writeInt(vertexIDList.getArraySize());
out.writeInt(vertexIDList.getUsedSize());
@@ -60,7 +65,7 @@
}
}
- public VertexIDList get() {
+ public PositionList get() {
return vertexIDList;
}
}
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/MergePathValueWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/MergePathValueWritable.java
deleted file mode 100644
index 4e8199a..0000000
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/MergePathValueWritable.java
+++ /dev/null
@@ -1,118 +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.type;
-
-import java.io.DataInput;
-import java.io.DataOutput;
-import java.io.IOException;
-
-import org.apache.hadoop.io.BinaryComparable;
-import org.apache.hadoop.io.WritableComparable;
-
-import edu.uci.ics.genomix.type.GeneCode;
-import edu.uci.ics.genomix.type.VKmerBytesWritable;
-
-public class MergePathValueWritable extends BinaryComparable implements WritableComparable<BinaryComparable> {
-
- private static final byte[] EMPTY_BYTES = {};
- private byte adjBitMap;
- private byte flag;
- private VKmerBytesWritable kmer;
-
- public MergePathValueWritable() {
- this((byte) 0, (byte) 0, 0, EMPTY_BYTES);
- }
-
- public MergePathValueWritable(int k) {
- this.adjBitMap = 0;
- this.flag = 0;
- this.kmer = new VKmerBytesWritable(k);
- }
-
- public MergePathValueWritable(byte adjBitMap, byte flag, int kmerSize, byte[] bytes) {
- this.adjBitMap = adjBitMap;
- this.flag = flag;
- this.kmer = new VKmerBytesWritable(kmerSize, bytes);
- kmer.set(bytes, 0, bytes.length);
- }
-
- public void set(MergePathValueWritable right) {
- set(right.getAdjBitMap(), right.getFlag(), right.getKmer());
- }
-
- public void set(byte adjBitMap, byte flag, VKmerBytesWritable kmer) {
- this.kmer.set(kmer);
- this.adjBitMap = adjBitMap;
- this.flag = flag;
- }
-
- @Override
- public void readFields(DataInput arg0) throws IOException {
- // TODO Auto-generated method stub
- kmer.readFields(arg0);
- adjBitMap = arg0.readByte();
- flag = arg0.readByte();
- }
-
- @Override
- public void write(DataOutput arg0) throws IOException {
- // TODO Auto-generated method stub
-
- kmer.write(arg0);
- arg0.writeByte(adjBitMap);
- arg0.writeByte(flag);
- }
-
- public VKmerBytesWritable getKmer() {
- if (kmer.getLength() != 0) {
- return kmer;
- }
- return null;
- }
-
- public byte getAdjBitMap() {
- return this.adjBitMap;
- }
-
- public byte getFlag() {
- return this.flag;
- }
-
- public String toString() {
- return GeneCode.getSymbolFromBitMap(adjBitMap) + '\t' + String.valueOf(flag);
- }
-
- public String pureToString() {
- return GeneCode.getSymbolFromBitMap(adjBitMap);
- }
- @Override
- public byte[] getBytes() {
- // TODO Auto-generated method stub
- if (kmer.getLength() != 0) {
- return kmer.getBytes();
- } else
- return null;
-
- }
-
- public int getKmerLength() {
- return kmer.getKmerLength();
- }
-
- @Override
- public int getLength() {
- return kmer.getLength();
- }
-}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/experiments/DeepGraphBuildingMapper.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/experiments/DeepGraphBuildingMapper.java
index d2aa96e..254d891 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/experiments/DeepGraphBuildingMapper.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/experiments/DeepGraphBuildingMapper.java
@@ -6,7 +6,7 @@
import org.apache.hadoop.mapred.Mapper;
import org.apache.hadoop.mapred.OutputCollector;
import org.apache.hadoop.mapred.Reporter;
-import edu.uci.ics.genomix.experiment.VertexIDList;
+import edu.uci.ics.genomix.experiment.PositionList;
import edu.uci.ics.genomix.experiment.VertexIDListWritable;
import edu.uci.ics.genomix.type.KmerBytesWritable;
@@ -14,7 +14,7 @@
public class DeepGraphBuildingMapper extends MapReduceBase implements
Mapper<KmerBytesWritable, VertexIDListWritable, IntWritable, LineBasedmappingWritable> {
IntWritable numLine = new IntWritable();
- VertexIDList vertexList = new VertexIDList(1);
+ PositionList vertexList = new PositionList(1);
LineBasedmappingWritable lineBasedWriter = new LineBasedmappingWritable();
@Override
public void map(KmerBytesWritable key, VertexIDListWritable value, OutputCollector<IntWritable, LineBasedmappingWritable> output,
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/experiments/DeepGraphBuildingReducer.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/experiments/DeepGraphBuildingReducer.java
index 0a3270e..cace3d2 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/experiments/DeepGraphBuildingReducer.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/experiments/DeepGraphBuildingReducer.java
@@ -9,9 +9,9 @@
import org.apache.hadoop.mapred.OutputCollector;
import org.apache.hadoop.mapred.Reducer;
import org.apache.hadoop.mapred.Reporter;
-import edu.uci.ics.genomix.experiment.KmerVertexID;
+import edu.uci.ics.genomix.experiment.Position;
import edu.uci.ics.genomix.experiment.VertexAdjacentWritable;
-import edu.uci.ics.genomix.experiment.VertexIDList;
+import edu.uci.ics.genomix.experiment.PositionList;
import edu.uci.ics.genomix.experiment.VertexIDListWritable;
import edu.uci.ics.genomix.type.KmerBytesWritable;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
@@ -19,20 +19,20 @@
@SuppressWarnings("deprecation")
public class DeepGraphBuildingReducer extends MapReduceBase implements
- Reducer<IntWritable, LineBasedmappingWritable, KmerVertexID, VertexAdjacentWritable> {
+ Reducer<IntWritable, LineBasedmappingWritable, Position, VertexAdjacentWritable> {
public ArrayList<LineBasedmappingWritable> lineElementsSet = new ArrayList<LineBasedmappingWritable>();
- public KmerVertexID outputVerID = new KmerVertexID();
+ public Position outputVerID = new Position();
public VertexAdjacentWritable outputAdjacentList = new VertexAdjacentWritable();
- public VertexIDList srcVtexAdjList = new VertexIDList();
- public VertexIDList desVtexAdjList = new VertexIDList();
+ public PositionList srcVtexAdjList = new PositionList();
+ public PositionList desVtexAdjList = new PositionList();
public VertexIDListWritable srcAdjListWritable = new VertexIDListWritable();
public VKmerBytesWritable desKmer = new VKmerBytesWritable(1);
public VKmerBytesWritableFactory kmerFactory = new VKmerBytesWritableFactory(1);
public VKmerBytesWritable srcKmer = new VKmerBytesWritable(1);
@Override
public void reduce(IntWritable key, Iterator<LineBasedmappingWritable> values,
- OutputCollector<KmerVertexID, VertexAdjacentWritable> output, Reporter reporter) throws IOException {
+ OutputCollector<Position, VertexAdjacentWritable> output, Reporter reporter) throws IOException {
while (values.hasNext()) {
lineElementsSet.add(values.next());
}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/experiments/GraphKmerInvertedIndexMapper.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/experiments/GraphKmerInvertedIndexMapper.java
index fe63012..9b5fec2 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/experiments/GraphKmerInvertedIndexMapper.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/experiments/GraphKmerInvertedIndexMapper.java
@@ -10,26 +10,26 @@
import org.apache.hadoop.mapred.Mapper;
import org.apache.hadoop.mapred.OutputCollector;
import org.apache.hadoop.mapred.Reporter;
-import edu.uci.ics.genomix.experiment.KmerVertexID;
+import edu.uci.ics.genomix.experiment.Position;
import edu.uci.ics.genomix.type.GeneCode;
import edu.uci.ics.genomix.type.KmerBytesWritable;
import edu.uci.ics.genomix.type.KmerCountValue;
public class GraphKmerInvertedIndexMapper extends MapReduceBase implements
- Mapper<LongWritable, Text, KmerBytesWritable, KmerVertexID> {
+ Mapper<LongWritable, Text, KmerBytesWritable, Position> {
public static int KMER_SIZE;
- public KmerVertexID outputVertexID;
+ public Position outputVertexID;
public KmerBytesWritable outputKmer;
@Override
public void configure(JobConf job) {
KMER_SIZE = Integer.parseInt(job.get("sizeKmer"));
- outputVertexID = new KmerVertexID();
+ outputVertexID = new Position();
outputKmer = new KmerBytesWritable(KMER_SIZE);
}
@Override
- public void map(LongWritable key, Text value, OutputCollector<KmerBytesWritable, KmerVertexID> output,
+ public void map(LongWritable key, Text value, OutputCollector<KmerBytesWritable, Position> output,
Reporter reporter) throws IOException {
String geneLine = value.toString();
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/experiments/GraphKmerInvertedIndexReducer.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/experiments/GraphKmerInvertedIndexReducer.java
index a228a3c..a4a579b 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/experiments/GraphKmerInvertedIndexReducer.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/experiments/GraphKmerInvertedIndexReducer.java
@@ -7,22 +7,22 @@
import org.apache.hadoop.mapred.OutputCollector;
import org.apache.hadoop.mapred.Reducer;
import org.apache.hadoop.mapred.Reporter;
-import edu.uci.ics.genomix.experiment.KmerVertexID;
-import edu.uci.ics.genomix.experiment.VertexIDList;
+import edu.uci.ics.genomix.experiment.Position;
+import edu.uci.ics.genomix.experiment.PositionList;
import edu.uci.ics.genomix.experiment.VertexIDListWritable;
import edu.uci.ics.genomix.type.KmerBytesWritable;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
@SuppressWarnings({ "deprecation", "unused" })
public class GraphKmerInvertedIndexReducer extends MapReduceBase implements
- Reducer<KmerBytesWritable, KmerVertexID, KmerBytesWritable, VertexIDListWritable> {
- VertexIDList vertexList = new VertexIDList(1);
+ Reducer<KmerBytesWritable, Position, KmerBytesWritable, VertexIDListWritable> {
+ PositionList vertexList = new PositionList(1);
VertexIDListWritable listWritable = new VertexIDListWritable();
@Override
- public void reduce(KmerBytesWritable key, Iterator<KmerVertexID> values,
+ public void reduce(KmerBytesWritable key, Iterator<Position> values,
OutputCollector<KmerBytesWritable, VertexIDListWritable> output, Reporter reporter) throws IOException {
while (values.hasNext()) {
- KmerVertexID vertexID = values.next();
+ Position vertexID = values.next();
vertexList.addELementToList(vertexID.getReadID(), vertexID.getPosInRead());
}
listWritable.set(vertexList);
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/experiments/LineBasedmappingWritable.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/experiments/LineBasedmappingWritable.java
index 658d56d..aa9413c 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/experiments/LineBasedmappingWritable.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/experiments/LineBasedmappingWritable.java
@@ -5,7 +5,7 @@
import java.io.IOException;
import edu.uci.ics.genomix.experiment.VertexAdjacentWritable;
-import edu.uci.ics.genomix.experiment.VertexIDList;
+import edu.uci.ics.genomix.experiment.PositionList;
import edu.uci.ics.genomix.experiment.VertexIDListWritable;
import edu.uci.ics.genomix.type.KmerBytesWritable;
import edu.uci.ics.genomix.type.VKmerBytesWritable;
@@ -18,7 +18,7 @@
this.posInInvertedIndex = -1;
}
- public LineBasedmappingWritable(int posInInvertedIndex, VertexIDList right, int kmerSize, byte[] bytes) {
+ public LineBasedmappingWritable(int posInInvertedIndex, PositionList right, int kmerSize, byte[] bytes) {
super(right, kmerSize, bytes);
this.posInInvertedIndex = posInInvertedIndex;
}