Merge branch 'genomix/fullstack_genomix' of https://code.google.com/p/hyracks into genomix/fullstack_genomix
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
new file mode 100644
index 0000000..9a01e36
--- /dev/null
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/experiment/KmerVertexID.java
@@ -0,0 +1,69 @@
+/*
+ * 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
new file mode 100644
index 0000000..191aacf
--- /dev/null
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/experiment/VertexAdjacentWritable.java
@@ -0,0 +1,66 @@
+package edu.uci.ics.genomix.experiment;
+
+import java.io.DataInput;
+import java.io.DataOutput;
+import java.io.IOException;
+
+import org.apache.hadoop.io.Writable;
+
+import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
+
+public class VertexAdjacentWritable implements Writable {
+
+ private static final byte[] EMPTY_BYTES = {};
+ private VertexIDListWritable adjVertexList;
+ private VKmerBytesWritable kmer;
+
+ public VertexAdjacentWritable() {
+ this(null, 0, EMPTY_BYTES);
+ }
+
+ public VertexAdjacentWritable(VertexIDList right, int kmerSize, byte[] bytes) {
+ if (right != null)
+ this.adjVertexList = new VertexIDListWritable(right);
+ else
+ this.adjVertexList = new VertexIDListWritable();
+ this.kmer = new VKmerBytesWritable(kmerSize, bytes);
+ kmer.set(bytes, 0, bytes.length);
+ }
+
+ public void set(VertexAdjacentWritable right) {
+ set(right.getAdjVertexList(), right.getVkmer());
+ }
+
+ public void set(VertexIDListWritable vIDList, KmerBytesWritable kmer) {
+ this.adjVertexList.set(vIDList);
+ this.kmer.set(kmer);
+ }
+
+ public void set(VertexIDListWritable vIDList, VKmerBytesWritable kmer) {
+ this.adjVertexList.set(vIDList);
+ this.kmer.set(kmer);
+ }
+
+ @Override
+ public void readFields(DataInput arg0) throws IOException {
+ // TODO Auto-generated method stub
+ adjVertexList.readFields(arg0);
+ kmer.readFields(arg0);
+ }
+
+ @Override
+ public void write(DataOutput arg0) throws IOException {
+ // TODO Auto-generated method stub
+ adjVertexList.write(arg0);
+ kmer.write(arg0);
+ }
+
+ public VertexIDListWritable getAdjVertexList() {
+ return this.adjVertexList;
+ }
+
+ public VKmerBytesWritable getVkmer() {
+ return this.kmer;
+ }
+}
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
new file mode 100644
index 0000000..f799b00
--- /dev/null
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/experiment/VertexIDList.java
@@ -0,0 +1,183 @@
+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
new file mode 100644
index 0000000..f7d917a
--- /dev/null
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/experiment/VertexIDListWritable.java
@@ -0,0 +1,66 @@
+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 VertexIDListWritable implements Writable {
+
+ private VertexIDList vertexIDList;
+ private int[] tempReadIDList = null;
+ private byte[] tempPosInReadList = null;
+
+ public VertexIDListWritable() {
+ this.vertexIDList = new VertexIDList();
+ }
+
+ public VertexIDListWritable(VertexIDList right) {
+ this.vertexIDList = new VertexIDList(right);
+ }
+
+ public VertexIDListWritable(int length) {
+ this.vertexIDList = new VertexIDList(length);
+ }
+
+ public void set(VertexIDListWritable right) {
+ set(right.get());
+ }
+ public void set(VertexIDList right) {
+ this.vertexIDList.set(right);
+ }
+
+ @Override
+ public void readFields(DataInput in) throws IOException {
+ // TODO Auto-generated method stub
+ int arraySize = in.readInt();
+ int usedSize = in.readInt();
+ if(usedSize > 0) {
+ this.tempReadIDList = new int[arraySize];
+ this.tempPosInReadList = new byte[arraySize];
+ for(int i = 0; i < arraySize; i++){
+ this.tempReadIDList[i] = in.readInt();
+ }
+ in.readFully(this.tempPosInReadList, 0, arraySize);
+ this.vertexIDList.set(this.tempReadIDList, 0, this.tempPosInReadList, 0, usedSize);
+ }
+ }
+
+ @Override
+ public void write(DataOutput out) throws IOException {
+ // TODO Auto-generated method stub
+ out.writeInt(vertexIDList.getArraySize());
+ out.writeInt(vertexIDList.getUsedSize());
+ if(vertexIDList.getUsedSize() > 0) {
+ int[] readIDList = vertexIDList.getReadIDList();
+ for(int i = 0 ; i < vertexIDList.getArraySize(); i ++ ){
+ out.writeInt(readIDList[i]);
+ }
+ out.write(vertexIDList.getPosInReadList(), 0, vertexIDList.getArraySize());
+ }
+ }
+
+ public VertexIDList get() {
+ return vertexIDList;
+ }
+}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/graphbuilding/GenomixMapper.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/graphbuilding/GenomixMapper.java
index b9b9aec..70d1f7a 100755
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/graphbuilding/GenomixMapper.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/graphbuilding/GenomixMapper.java
@@ -38,14 +38,9 @@
public class GenomixMapper extends MapReduceBase implements
Mapper<LongWritable, Text, KmerBytesWritable, KmerCountValue> {
- public class CurrenByte {
- public byte curByte;
- public byte preMarker;
- }
-
public static int KMER_SIZE;
- public KmerCountValue outputAdjList;
- public KmerBytesWritable outputKmer;
+ public KmerCountValue outputAdjList;
+ public KmerBytesWritable outputKmer;
@Override
public void configure(JobConf job) {
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
new file mode 100644
index 0000000..d2aa96e
--- /dev/null
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/experiments/DeepGraphBuildingMapper.java
@@ -0,0 +1,29 @@
+package edu.uci.ics.genomix.hadoop.experiments;
+
+import java.io.IOException;
+import org.apache.hadoop.io.IntWritable;
+import org.apache.hadoop.mapred.MapReduceBase;
+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.VertexIDListWritable;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
+
+@SuppressWarnings("deprecation")
+public class DeepGraphBuildingMapper extends MapReduceBase implements
+ Mapper<KmerBytesWritable, VertexIDListWritable, IntWritable, LineBasedmappingWritable> {
+ IntWritable numLine = new IntWritable();
+ VertexIDList vertexList = new VertexIDList(1);
+ LineBasedmappingWritable lineBasedWriter = new LineBasedmappingWritable();
+ @Override
+ public void map(KmerBytesWritable key, VertexIDListWritable value, OutputCollector<IntWritable, LineBasedmappingWritable> output,
+ Reporter reporter) throws IOException {
+ vertexList.set(value.get());
+ for(int i = 0; i < vertexList.getUsedSize(); i++) {
+ numLine.set(vertexList.getReadListElement(i));
+ lineBasedWriter.set(i, value, key);
+ output.collect(numLine, lineBasedWriter);
+ }
+ }
+}
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
new file mode 100644
index 0000000..0a3270e
--- /dev/null
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/experiments/DeepGraphBuildingReducer.java
@@ -0,0 +1,92 @@
+package edu.uci.ics.genomix.hadoop.experiments;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Iterator;
+
+import org.apache.hadoop.io.IntWritable;
+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.experiment.KmerVertexID;
+import edu.uci.ics.genomix.experiment.VertexAdjacentWritable;
+import edu.uci.ics.genomix.experiment.VertexIDList;
+import edu.uci.ics.genomix.experiment.VertexIDListWritable;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritableFactory;
+
+@SuppressWarnings("deprecation")
+public class DeepGraphBuildingReducer extends MapReduceBase implements
+ Reducer<IntWritable, LineBasedmappingWritable, KmerVertexID, VertexAdjacentWritable> {
+
+ public ArrayList<LineBasedmappingWritable> lineElementsSet = new ArrayList<LineBasedmappingWritable>();
+ public KmerVertexID outputVerID = new KmerVertexID();
+ public VertexAdjacentWritable outputAdjacentList = new VertexAdjacentWritable();
+ public VertexIDList srcVtexAdjList = new VertexIDList();
+ public VertexIDList desVtexAdjList = new VertexIDList();
+ 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 {
+ while (values.hasNext()) {
+ lineElementsSet.add(values.next());
+ }
+ int[] orderLineTable = new int[lineElementsSet.size()];
+ for (int i = 0; i < lineElementsSet.size(); i++) {
+ int posInInvertedIndex = lineElementsSet.get(i).getPosInInvertedIndex();
+ orderLineTable[lineElementsSet.get(i).getAdjVertexList().get().getPosinReadListElement(posInInvertedIndex)] = i;
+ }
+ //the first node in this read
+ int posInInvertedIndex = lineElementsSet.get(orderLineTable[0]).getPosInInvertedIndex();
+ outputVerID.set(
+ lineElementsSet.get(orderLineTable[0]).getAdjVertexList().get().getReadListElement(posInInvertedIndex),
+ (byte) 0);
+ desVtexAdjList.set(lineElementsSet.get(orderLineTable[1]).getAdjVertexList().get());
+ for (int i = 0; i < desVtexAdjList.getUsedSize(); i++) {
+ if (desVtexAdjList.getPosinReadListElement(i) == (byte) 0) {
+ srcVtexAdjList.addELementToList(desVtexAdjList.getReadListElement(i), (byte) 0);
+ }
+ }
+ srcVtexAdjList.addELementToList(key.get(), (byte) 1);
+ outputVerID.set(
+ lineElementsSet.get(orderLineTable[0]).getAdjVertexList().get().getReadListElement(posInInvertedIndex),
+ (byte) 0);
+ srcAdjListWritable.set(srcVtexAdjList);
+ outputAdjacentList.set(srcAdjListWritable, lineElementsSet.get(orderLineTable[0]).getVkmer());
+ output.collect(outputVerID, outputAdjacentList);
+ //srcVtexAdjList reset!!!!
+
+ for (int i = 1; i < lineElementsSet.size(); i++) {
+ desVtexAdjList.set(lineElementsSet.get(orderLineTable[i + 1]).getAdjVertexList().get());
+ boolean flag = false;
+ for (int j = 0; j < desVtexAdjList.getUsedSize(); j++) {
+ if (desVtexAdjList.getPosinReadListElement(j) == (byte) 0) {
+ srcVtexAdjList.addELementToList(desVtexAdjList.getReadListElement(i), (byte) 0);
+ flag = true;
+ }
+ }
+ if (flag = true) {
+ //doesm't merge
+ srcVtexAdjList.addELementToList(key.get(), (byte) (i + 1));
+ outputVerID.set(
+ lineElementsSet.get(orderLineTable[i]).getAdjVertexList().get()
+ .getReadListElement(posInInvertedIndex), lineElementsSet.get(orderLineTable[i])
+ .getAdjVertexList().get().getPosinReadListElement(posInInvertedIndex));
+ srcAdjListWritable.set(srcVtexAdjList);
+ outputAdjacentList.set(srcAdjListWritable, lineElementsSet.get(orderLineTable[i]).getVkmer());
+ }
+ else {
+ //merge
+ desKmer.set(kmerFactory.getFirstKmerFromChain(1, lineElementsSet.get(orderLineTable[i+1]).getVkmer()));
+ srcKmer.set(lineElementsSet.get(orderLineTable[i]).getVkmer());
+ lineElementsSet.get(orderLineTable[i+1]).getVkmer().set(kmerFactory.mergeTwoKmer(srcKmer, desKmer));
+ orderLineTable[i+1] = orderLineTable[i];
+ }
+ }
+ }
+}
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
new file mode 100644
index 0000000..fe63012
--- /dev/null
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/experiments/GraphKmerInvertedIndexMapper.java
@@ -0,0 +1,60 @@
+package edu.uci.ics.genomix.hadoop.experiments;
+
+import java.io.IOException;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+import org.apache.hadoop.io.LongWritable;
+import org.apache.hadoop.io.Text;
+import org.apache.hadoop.mapred.JobConf;
+import org.apache.hadoop.mapred.MapReduceBase;
+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.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> {
+
+ public static int KMER_SIZE;
+ public KmerVertexID outputVertexID;
+ public KmerBytesWritable outputKmer;
+
+ @Override
+ public void configure(JobConf job) {
+ KMER_SIZE = Integer.parseInt(job.get("sizeKmer"));
+ outputVertexID = new KmerVertexID();
+ outputKmer = new KmerBytesWritable(KMER_SIZE);
+ }
+ @Override
+ public void map(LongWritable key, Text value, OutputCollector<KmerBytesWritable, KmerVertexID> output,
+ Reporter reporter) throws IOException {
+
+ String geneLine = value.toString();
+ /** first kmer */
+// byte count = 1;
+ byte[] array = geneLine.getBytes();
+ outputKmer.setByRead(array, 0);
+ byte pre = 0;
+ //byte next = GeneCode.getAdjBit(array[KMER_SIZE]);
+ //byte adj = GeneCode.mergePreNextAdj(pre, next);
+ outputVertexID.set((int)key.get(), (byte)0);
+ output.collect(outputKmer, outputVertexID);
+ /** middle kmer */
+ for (int i = KMER_SIZE; i < array.length - 1; i++) {
+ pre = GeneCode.getBitMapFromGeneCode(outputKmer.shiftKmerWithNextChar(array[i]));
+// next = GeneCode.getAdjBit(array[i + 1]);
+// adj = GeneCode.mergePreNextAdj(pre, next);
+ outputVertexID.set((int)key.get(), (byte)(i - KMER_SIZE + 1));
+ output.collect(outputKmer, outputVertexID);
+ }
+ /** last kmer */
+ pre = GeneCode.getBitMapFromGeneCode(outputKmer.shiftKmerWithNextChar(array[array.length - 1]));
+// next = 0;
+// adj = GeneCode.mergePreNextAdj(pre, next);
+ outputVertexID.set((int)key.get(), (byte)(array.length - 1 + 1));
+ output.collect(outputKmer, outputVertexID);
+ }
+}
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
new file mode 100644
index 0000000..a228a3c
--- /dev/null
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/experiments/GraphKmerInvertedIndexReducer.java
@@ -0,0 +1,31 @@
+package edu.uci.ics.genomix.hadoop.experiments;
+
+import java.io.IOException;
+import java.util.Iterator;
+import org.apache.hadoop.mapred.MapReduceBase;
+import org.apache.hadoop.mapred.Mapper;
+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.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);
+ VertexIDListWritable listWritable = new VertexIDListWritable();
+ @Override
+ public void reduce(KmerBytesWritable key, Iterator<KmerVertexID> values,
+ OutputCollector<KmerBytesWritable, VertexIDListWritable> output, Reporter reporter) throws IOException {
+ while (values.hasNext()) {
+ KmerVertexID vertexID = values.next();
+ vertexList.addELementToList(vertexID.getReadID(), vertexID.getPosInRead());
+ }
+ listWritable.set(vertexList);
+ output.collect(key, listWritable);
+ }
+}
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
new file mode 100644
index 0000000..658d56d
--- /dev/null
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/experiments/LineBasedmappingWritable.java
@@ -0,0 +1,56 @@
+package edu.uci.ics.genomix.hadoop.experiments;
+
+import java.io.DataInput;
+import java.io.DataOutput;
+import java.io.IOException;
+
+import edu.uci.ics.genomix.experiment.VertexAdjacentWritable;
+import edu.uci.ics.genomix.experiment.VertexIDList;
+import edu.uci.ics.genomix.experiment.VertexIDListWritable;
+import edu.uci.ics.genomix.type.KmerBytesWritable;
+import edu.uci.ics.genomix.type.VKmerBytesWritable;
+
+public class LineBasedmappingWritable extends VertexAdjacentWritable{
+ int posInInvertedIndex;
+
+ public LineBasedmappingWritable() {
+ super();
+ this.posInInvertedIndex = -1;
+ }
+
+ public LineBasedmappingWritable(int posInInvertedIndex, VertexIDList right, int kmerSize, byte[] bytes) {
+ super(right, kmerSize, bytes);
+ this.posInInvertedIndex = posInInvertedIndex;
+ }
+
+ public void set(int posInInvertedIndex, VertexAdjacentWritable right) {
+ super.set(right.getAdjVertexList(), right.getVkmer());
+ this.posInInvertedIndex = posInInvertedIndex;
+ }
+
+ public void set(int posInInvertedIndex, VertexIDListWritable vIDList, VKmerBytesWritable kmer) {
+ super.set(vIDList, kmer);
+ this.posInInvertedIndex = posInInvertedIndex;
+ }
+
+ public void set(int posInInvertedIndex, VertexIDListWritable vIDList, KmerBytesWritable kmer) {
+ super.set(vIDList, kmer);
+ this.posInInvertedIndex = posInInvertedIndex;
+ }
+
+ @Override
+ public void readFields(DataInput in) throws IOException {
+ super.readFields(in);
+ this.posInInvertedIndex = in.readInt();
+ }
+
+ @Override
+ public void write(DataOutput out) throws IOException {
+ super.write(out);
+ out.writeInt(this.posInInvertedIndex);
+ }
+
+ public int getPosInInvertedIndex() {
+ return this.posInInvertedIndex;
+ }
+}