Merge branch 'fullstack_genomix' of https://code.google.com/p/hyracks into fullstack_genomix
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/LogAlgorithmForMergeGraphVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/LogAlgorithmForMergeGraphVertex.java
index 757d8f8..d55e64e 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/LogAlgorithmForMergeGraphVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/LogAlgorithmForMergeGraphVertex.java
@@ -45,9 +45,11 @@
* The succeed node and precursor node will be stored in vertexValue and we don't use edgeValue.
* The details about message are in edu.uci.ics.pregelix.example.io.MessageWritable.
*/
-public class LogAlgorithmForMergeGraphVertex extends Vertex<BytesWritable, ValueStateWritable, NullWritable, LogAlgorithmMessageWritable>{
+public class LogAlgorithmForMergeGraphVertex extends Vertex<BytesWritable, ValueStateWritable, NullWritable, LogAlgorithmMessageWritable>{
public static final String KMER_SIZE = "LogAlgorithmForMergeGraphVertex.kmerSize";
+ public static final String ITERATIONS = "MergeGraphVertex.iteration";
public static int kmerSize = -1;
+ private int maxIteration = -1;
private byte[] tmpVertexId;
private byte[] tmpDestVertexId;
@@ -60,18 +62,15 @@
/**
* Log Algorithm for path merge graph
*/
-
/**
- * Load KmerSize
+ * Load KmerSize, MaxIteration
*/
- public LogAlgorithmForMergeGraphVertex(){
-
- }
-
@Override
public void compute(Iterator<LogAlgorithmMessageWritable> msgIterator) {
if(kmerSize == -1)
kmerSize = getContext().getConfiguration().getInt(KMER_SIZE, 5);
+ if (maxIteration < 0)
+ maxIteration = getContext().getConfiguration().getInt(ITERATIONS, 100);
tmpVertexId = GraphVertexOperation.generateValidDataFromBytesWritable(getVertexId());
tmpVal = getVertexValue();
if (getSuperstep() == 1) {
@@ -103,12 +102,12 @@
tmpVal.setState(State.MID_VERTEX);
setVertexValue(tmpVal);
}
- if(!GraphVertexOperation.isHeadVertex(tmpVal.getValue())
+ /*if(!GraphVertexOperation.isHeadVertex(tmpVal.getValue())
&& !GraphVertexOperation.isRearVertex(tmpVal.getValue())
&& !GraphVertexOperation.isRearVertex(tmpVal.getValue()))
- voteToHalt();
+ voteToHalt();*/
}
- else if(getSuperstep() == 2){
+ else if(getSuperstep() == 2 && getSuperstep() <= maxIteration){
while(msgIterator.hasNext()){
if(!GraphVertexOperation.isPathVertex(tmpVal.getValue())){
msgIterator.next();
@@ -116,7 +115,8 @@
}
else{
tmpMsg = msgIterator.next();
- if(tmpMsg.getMessage() == Message.START && tmpVal.getState() == State.MID_VERTEX){
+ if(tmpMsg.getMessage() == Message.START &&
+ (tmpVal.getState() == State.MID_VERTEX || tmpVal.getState() == State.END_VERTEX)){
tmpVal.setState(State.START_VERTEX);
setVertexValue(tmpVal);
}
@@ -131,7 +131,7 @@
}
}
//head node sends message to path node
- else if(getSuperstep()%3 == 0){
+ else if(getSuperstep()%3 == 0 && getSuperstep() <= maxIteration){
if(getSuperstep() == 3){
tmpMsg = new LogAlgorithmMessageWritable();
if(Kmer.GENE_CODE.getGeneCodeFromBitMap((byte)(tmpVal.getValue() & 0x0F)) == -1)
@@ -162,12 +162,12 @@
tmpVal.getLengthOfMergeChain(),
tmpVal.getMergeChain(),
0, tmpVal.getMergeChain().length);
- if(Kmer.GENE_CODE.getGeneCodeFromBitMap((byte)(tmpVal.getValue() & 0x0F)) == -1)
+ if(Kmer.GENE_CODE.getGeneCodeFromBitMap((byte)(tmpVal.getValue() & 0x0F)) == -1 || lastKmer == null)
voteToHalt();
else{
tmpDestVertexId = KmerUtil.shiftKmerWithNextCode(kmerSize, lastKmer,
0, lastKmer.length,
- Kmer.GENE_CODE.getGeneCodeFromBitMap((byte)(tmpVal.getValue() & 0x0F))); //tmpMsg.getNeighberInfo()
+ Kmer.GENE_CODE.getGeneCodeFromBitMap((byte)(tmpVal.getValue() & 0x0F)));
destVertexId.set(tmpDestVertexId, 0, tmpDestVertexId.length);
if(tmpVal.getState() == State.START_VERTEX){
tmpMsg.setMessage(Message.START);
@@ -186,7 +186,7 @@
}
//path node sends message back to head node
- else if(getSuperstep()%3 == 1){
+ else if(getSuperstep()%3 == 1 && getSuperstep() <= maxIteration){
if(msgIterator.hasNext()){
tmpMsg = msgIterator.next();
int message = tmpMsg.getMessage();
@@ -217,17 +217,23 @@
}
destVertexId.set(tmpMsg.getSourceVertexId(), 0, tmpMsg.getSourceVertexId().length);
sendMsg(destVertexId,tmpMsg);
- voteToHalt();
+ //voteToHalt();
}
else{
- if(getVertexValue().getState() != State.START_VERTEX
- && getVertexValue().getState() != State.END_VERTEX && getVertexValue().getState() != State.FINAL_DELETE)
+ if(getVertexValue().getState() != State.START_VERTEX && getVertexValue().getState() != State.NON_EXIST
+ && getVertexValue().getState() != State.END_VERTEX && getVertexValue().getState() != State.FINAL_DELETE){
+ tmpVal.setState(State.NON_EXIST);
+ setVertexValue(tmpVal);
deleteVertex(getVertexId()); //killSelf because it doesn't receive any message
+ }
}
}
- else if(getSuperstep()%3 == 2){
- if(tmpVal.getState() == State.TODELETE)
+ else if(getSuperstep()%3 == 2 && getSuperstep() <= maxIteration){
+ if(tmpVal.getState() == State.TODELETE && getVertexValue().getState() != State.NON_EXIST){
+ tmpVal.setState(State.NON_EXIST);
+ setVertexValue(tmpVal);
deleteVertex(getVertexId()); //killSelf
+ }
else{
if(msgIterator.hasNext()){
tmpMsg = msgIterator.next();
@@ -268,14 +274,13 @@
sendMsg(getVertexId(),tmpMsg);
}
}
- if(tmpVal.getState() == State.END_VERTEX || tmpVal.getState() == State.FINAL_DELETE)
+ if(tmpVal.getState() == State.END_VERTEX || tmpVal.getState() == State.FINAL_DELETE || tmpVal.getState() == State.NON_EXIST)
voteToHalt();
if(tmpVal.getState() == State.FINAL_VERTEX){
//String source = Kmer.recoverKmerFrom(tmpVal.getLengthOfMergeChain(), tmpVal.getMergeChain(), 0, tmpVal.getMergeChain().length);
voteToHalt();
}
}
-
}
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/MergeGraphVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/MergeGraphVertex.java
index 0f244dc..067b70d 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/MergeGraphVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/MergeGraphVertex.java
@@ -63,7 +63,7 @@
* @throws
*/
/**
- * Load KmerSize
+ * Load KmerSize, MaxIteration
*/
@Override
public void compute(Iterator<MessageWritable> msgIterator) {
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/LogAlgorithmForMergeGraphOutputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/LogAlgorithmForMergeGraphOutputFormat.java
index aa81066..24fca7b 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/LogAlgorithmForMergeGraphOutputFormat.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/LogAlgorithmForMergeGraphOutputFormat.java
@@ -7,11 +7,13 @@
import org.apache.hadoop.mapreduce.RecordWriter;
import org.apache.hadoop.mapreduce.TaskAttemptContext;
+import edu.uci.ics.genomix.pregelix.GraphVertexOperation;
import edu.uci.ics.genomix.pregelix.api.io.binary.BinaryVertexOutputFormat;
import edu.uci.ics.pregelix.api.graph.Vertex;
import edu.uci.ics.pregelix.api.io.VertexWriter;
import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
import edu.uci.ics.genomix.pregelix.type.State;
+import edu.uci.ics.genomix.type.Kmer;
public class LogAlgorithmForMergeGraphOutputFormat extends
BinaryVertexOutputFormat<BytesWritable, ValueStateWritable, NullWritable> {
@@ -37,7 +39,8 @@
@Override
public void writeVertex(Vertex<BytesWritable, ValueStateWritable, NullWritable, ?> vertex) throws IOException,
InterruptedException {
- if(vertex.getVertexValue().getState() != State.FINAL_DELETE)
+ if(vertex.getVertexValue().getState() != State.FINAL_DELETE
+ && vertex.getVertexValue().getState() != State.END_VERTEX)
getRecordWriter().write(vertex.getVertexId(),vertex.getVertexValue());
}
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/LogAlgorithmMessageWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/LogAlgorithmMessageWritable.java
index 42f1269..3d07c5b 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/LogAlgorithmMessageWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/LogAlgorithmMessageWritable.java
@@ -122,7 +122,7 @@
public void readFields(DataInput in) throws IOException {
// TODO Auto-generated method stub
lengthOfChain = in.readInt();
- if(lengthOfChain != 0){
+ if(lengthOfChain > 0){
chainVertexId = new byte[(lengthOfChain-1)/4 + 1];
in.readFully(chainVertexId);
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MessageWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MessageWritable.java
index 2976c87..3872514 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MessageWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MessageWritable.java
@@ -113,7 +113,7 @@
public void readFields(DataInput in) throws IOException {
// TODO Auto-generated method stub
lengthOfChain = in.readInt();
- if(lengthOfChain != 0){
+ if(lengthOfChain > 0){
chainVertexId = new byte[(lengthOfChain-1)/4 + 1];
in.readFully(chainVertexId);
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/ValueStateWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/ValueStateWritable.java
index 9acda4e..f101d7f 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/ValueStateWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/ValueStateWritable.java
@@ -5,6 +5,7 @@
import org.apache.hadoop.io.WritableComparable;
import edu.uci.ics.genomix.pregelix.type.State;
+import edu.uci.ics.genomix.type.Kmer;
public class ValueStateWritable implements WritableComparable<ValueStateWritable> {
@@ -63,6 +64,8 @@
value = in.readByte();
state = in.readInt();
lengthOfMergeChain = in.readInt();
+ if(lengthOfMergeChain < 0)
+ System.out.println();
if(lengthOfMergeChain != 0){
mergeChain = new byte[(lengthOfMergeChain-1)/4 + 1];
in.readFully(mergeChain);
@@ -86,4 +89,14 @@
return 0;
}
+ @Override
+ public String toString() {
+ if(lengthOfMergeChain == 0)
+ return Kmer.GENE_CODE.getSymbolFromBitMap(value);
+ return Kmer.GENE_CODE.getSymbolFromBitMap(value) + "\t" +
+ lengthOfMergeChain + "\t" +
+ Kmer.recoverKmerFrom(lengthOfMergeChain, mergeChain, 0, mergeChain.length) + "\t" +
+ state;
+ }
+
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/GenerateTextFile.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/GenerateTextFile.java
new file mode 100644
index 0000000..8ab6990
--- /dev/null
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/GenerateTextFile.java
@@ -0,0 +1,50 @@
+package edu.uci.ics.genomix.pregelix.sequencefile;
+
+import java.io.BufferedWriter;
+import java.io.FileWriter;
+import java.io.IOException;
+
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
+import org.apache.hadoop.io.BytesWritable;
+import org.apache.hadoop.io.SequenceFile;
+
+import edu.uci.ics.genomix.pregelix.io.ValueStateWritable;
+import edu.uci.ics.genomix.type.Kmer;
+
+public class GenerateTextFile {
+
+ public static void generate() throws IOException{
+ BufferedWriter bw = new BufferedWriter(new FileWriter("text/naive_CyclePath"));
+ Configuration conf = new Configuration();
+ FileSystem fileSys = FileSystem.get(conf);
+ for(int i = 0; i < 2; i++){
+ Path path = new Path("output/part-" + i);
+ SequenceFile.Reader reader = new SequenceFile.Reader(fileSys, path, conf);
+ BytesWritable key = new BytesWritable();
+ ValueStateWritable value = new ValueStateWritable();
+
+ while(reader.next(key, value)){
+ if (key == null || value == null){
+ break;
+ }
+ bw.write(Kmer.recoverKmerFrom(5, key.getBytes(), 0,
+ key.getLength())
+ + "\t" + value.toString());
+ bw.newLine();
+ }
+ reader.close();
+ }
+ bw.close();
+ }
+ /**
+ * @param args
+ * @throws IOException
+ */
+ public static void main(String[] args) throws IOException {
+ // TODO Auto-generated method stub
+ generate();
+ }
+
+}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/generateSmallFile.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/generateSmallFile.java
deleted file mode 100644
index 45329d0..0000000
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/sequencefile/generateSmallFile.java
+++ /dev/null
@@ -1,48 +0,0 @@
-package edu.uci.ics.genomix.pregelix.sequencefile;
-
-import java.io.IOException;
-
-import org.apache.hadoop.conf.Configuration;
-import org.apache.hadoop.fs.FileSystem;
-import org.apache.hadoop.fs.Path;
-import org.apache.hadoop.io.BytesWritable;
-import org.apache.hadoop.io.SequenceFile;
-import org.apache.hadoop.io.SequenceFile.CompressionType;
-
-import edu.uci.ics.genomix.type.KmerCountValue;
-
-public class generateSmallFile {
-
- public static void generateNumOfLinesFromBigFile(Path inFile, Path outFile, int numOfLines) throws IOException{
- Configuration conf = new Configuration();
- FileSystem fileSys = FileSystem.get(conf);
-
- SequenceFile.Reader reader = new SequenceFile.Reader(fileSys, inFile, conf);
- SequenceFile.Writer writer = SequenceFile.createWriter(fileSys, conf,
- outFile, BytesWritable.class, KmerCountValue.class,
- CompressionType.NONE);
- BytesWritable outKey = new BytesWritable();
- KmerCountValue outValue = new KmerCountValue();
- int i = 0;
-
- for(i = 0; i < numOfLines; i++){
- //System.out.println(i);
- reader.next(outKey, outValue);
- writer.append(outKey, outValue);
- }
- writer.close();
- reader.close();
- }
- /**
- * @param args
- * @throws IOException
- */
- public static void main(String[] args) throws IOException {
- // TODO Auto-generated method stub
- Path dir = new Path("data/webmap");
- Path inFile = new Path(dir, "part-2");
- Path outFile = new Path(dir, "part-2-out-20000");
- generateNumOfLinesFromBigFile(inFile,outFile,20000);
- }
-
-}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/testcase/GenerateTestInput.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/testcase/GenerateTestInput.java
index 8ff5589..6d81b74 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/testcase/GenerateTestInput.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/testcase/GenerateTestInput.java
@@ -61,15 +61,15 @@
writer = new OutputStreamWriter(new FileOutputStream("graph/55/SimplePath_55"));
writer.write(simplePath(55,60,3));
writer.close();
- /*writer = new OutputStreamWriter(new FileOutputStream("TreePath"));
- writer.write(treePath(5, 5, 5, 3));
+ writer = new OutputStreamWriter(new FileOutputStream("graph/55/TreePath"));
+ writer.write(treePath(55, 5, 5, 3));
writer.close();
- writer = new OutputStreamWriter(new FileOutputStream("CyclePath"));
- writer.write(cyclePath(5,10));
+ writer = new OutputStreamWriter(new FileOutputStream("graph/55/CyclePath"));
+ writer.write(cyclePath(55,60));
writer.close();
- writer = new OutputStreamWriter(new FileOutputStream("BridgePath"));
- writer.write(bridgePath(5,2));
- writer.close();*/
+ writer = new OutputStreamWriter(new FileOutputStream("graph/55/BridgePath"));
+ writer.write(bridgePath(55,2));
+ writer.close();
} catch (IOException e) {
e.printStackTrace();
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/State.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/State.java
index 5447d26..999b431 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/State.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/type/State.java
@@ -8,6 +8,7 @@
public static final int TODELETE = 4;
public static final int FINAL_VERTEX = 5;
public static final int FINAL_DELETE = 6;
+ public static final int NON_EXIST = 7;
public final static class STATE_CONTENT{
@@ -35,6 +36,9 @@
case FINAL_DELETE:
r = "FINAL_DELETE";
break;
+ case NON_EXIST:
+ r = "NON_EXIST";
+ break;
}
return r;
}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java
index 53340dc..763d46e 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobGen/JobGenerator.java
@@ -71,7 +71,7 @@
job.setOutputValueClass(ValueStateWritable.class);
FileInputFormat.setInputPaths(job, HDFS_INPUTPATH);
FileOutputFormat.setOutputPath(job, new Path(HDFS_OUTPUTPAH));
- job.getConfiguration().setInt(LogAlgorithmForMergeGraphVertex.KMER_SIZE, 55);
+ job.getConfiguration().setInt(LogAlgorithmForMergeGraphVertex.KMER_SIZE, 5);
job.getConfiguration().writeXml(new FileOutputStream(new File(outputPath)));
}
@@ -86,8 +86,8 @@
public static void main(String[] args) throws IOException {
// TODO Auto-generated method stub
//genLoadGraph();
- genMergeGraph();
- //genLogAlgorithmForMergeGraph();
+ //genMergeGraph();
+ genLogAlgorithmForMergeGraph();
//genSequenceLoadGraph();
//genBasicBinaryLoadGraph();
}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/RunJobTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/RunJobTestSuite.java
index ba0f4c3..ffc1a25 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/RunJobTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/JobRun/RunJobTestSuite.java
@@ -40,7 +40,7 @@
private static final String PATH_TO_ONLY = "src/test/resources/only.txt";
private static final String FILE_EXTENSION_OF_RESULTS = "result";
- private static final String DATA_PATH = "data/input/part-1-out-500000";// sequenceShortFileMergeTest
+ private static final String DATA_PATH = "data/result/TreePath";// sequenceShortFileMergeTest
private static final String HDFS_PATH = "/webmap/";
private static final String HYRACKS_APP_NAME = "pregelix";
diff --git a/genomix/genomix-pregelix/src/test/resources/hadoop/conf/hdfs-site.xml b/genomix/genomix-pregelix/src/test/resources/hadoop/conf/hdfs-site.xml
index 8d29b1d..a36b6d7 100644
--- a/genomix/genomix-pregelix/src/test/resources/hadoop/conf/hdfs-site.xml
+++ b/genomix/genomix-pregelix/src/test/resources/hadoop/conf/hdfs-site.xml
@@ -12,7 +12,7 @@
<property>
<name>dfs.block.size</name>
- <value>65536</value>
+ <value>655360</value>
</property>
</configuration>
diff --git a/genomix/genomix-pregelix/text/BridgePath/log_BridgePath b/genomix/genomix-pregelix/text/BridgePath/log_BridgePath
new file mode 100644
index 0000000..cab1281
--- /dev/null
+++ b/genomix/genomix-pregelix/text/BridgePath/log_BridgePath
@@ -0,0 +1,6 @@
+TTCCA T|C
+CCGTG CT|
+TCCAC T|CT
+CCACC T|G 9 CCACCCCGT 5
+TTTCC |A
+CCACT T|G 9 CCACTCCGT 5
diff --git a/genomix/genomix-pregelix/text/BridgePath/naive_BridgePath b/genomix/genomix-pregelix/text/BridgePath/naive_BridgePath
new file mode 100644
index 0000000..c669dba
--- /dev/null
+++ b/genomix/genomix-pregelix/text/BridgePath/naive_BridgePath
@@ -0,0 +1,6 @@
+TTCCA T|C 5 TTCCA 1
+CCGTG CT|
+TCCAC T|CT
+CCACC T|G 9 CCACCCCGT 1
+TTTCC |A
+CCACT T|C
diff --git a/genomix/genomix-pregelix/text/CyclePath/log_CyclePath b/genomix/genomix-pregelix/text/CyclePath/log_CyclePath
new file mode 100644
index 0000000..d0ee84f
--- /dev/null
+++ b/genomix/genomix-pregelix/text/CyclePath/log_CyclePath
@@ -0,0 +1,3 @@
+GCAAC |T
+AACTT C|T 12 AACTTCATCAAC 5
+CAACT GT|T
diff --git a/genomix/genomix-pregelix/text/CyclePath/naive_CyclePath b/genomix/genomix-pregelix/text/CyclePath/naive_CyclePath
new file mode 100644
index 0000000..5cdb7c2
--- /dev/null
+++ b/genomix/genomix-pregelix/text/CyclePath/naive_CyclePath
@@ -0,0 +1,3 @@
+GCAAC |T
+AACTT C|T 12 AACTTCATCAAC 1
+CAACT GT|T
diff --git a/genomix/genomix-pregelix/text/LongPath/log_LongPath b/genomix/genomix-pregelix/text/LongPath/log_LongPath
new file mode 100644
index 0000000..98cb21e
--- /dev/null
+++ b/genomix/genomix-pregelix/text/LongPath/log_LongPath
@@ -0,0 +1,3 @@
+GCCTC G|G 15 GCCTCAGTACGCCCG 5
+CCCGG G|
+GGCCT |C
diff --git a/genomix/genomix-pregelix/text/LongPath/naive_LongPath b/genomix/genomix-pregelix/text/LongPath/naive_LongPath
new file mode 100644
index 0000000..c1a472e
--- /dev/null
+++ b/genomix/genomix-pregelix/text/LongPath/naive_LongPath
@@ -0,0 +1,3 @@
+GCCTC G|G 15 GCCTCAGTACGCCCG 1
+CCCGG G|
+GGCCT |C
diff --git a/genomix/genomix-pregelix/text/Path/log_Path b/genomix/genomix-pregelix/text/Path/log_Path
new file mode 100644
index 0000000..3a46528
--- /dev/null
+++ b/genomix/genomix-pregelix/text/Path/log_Path
@@ -0,0 +1,3 @@
+GCCTC G|G 10 GCCTCAGTAC 5
+GGCCT |C
+GTACG A|
diff --git a/genomix/genomix-pregelix/text/Path/naive_Path b/genomix/genomix-pregelix/text/Path/naive_Path
new file mode 100644
index 0000000..b8d2aeb
--- /dev/null
+++ b/genomix/genomix-pregelix/text/Path/naive_Path
@@ -0,0 +1,3 @@
+GCCTC G|G 10 GCCTCAGTAC 1
+GGCCT |C
+GTACG A|
diff --git a/genomix/genomix-pregelix/text/SimplePath/log_SimplePath b/genomix/genomix-pregelix/text/SimplePath/log_SimplePath
new file mode 100644
index 0000000..5c149ac
--- /dev/null
+++ b/genomix/genomix-pregelix/text/SimplePath/log_SimplePath
@@ -0,0 +1,9 @@
+CGGCA G|A 8 CGGCAAGA 5
+AGCAC C|
+AAGAC |A
+GCGGC |A
+GCATC C|
+ATATC |G
+TATCG A|C 8 TATCGCAT 5
+AAGAA C|
+AGACA A|C 8 AGACAGCA 5
diff --git a/genomix/genomix-pregelix/text/SimplePath/naive_SimplePath b/genomix/genomix-pregelix/text/SimplePath/naive_SimplePath
new file mode 100644
index 0000000..cf53cc8
--- /dev/null
+++ b/genomix/genomix-pregelix/text/SimplePath/naive_SimplePath
@@ -0,0 +1,9 @@
+CGGCA G|A 8 CGGCAAGA 1
+AGCAC C|
+AAGAC |A
+GCGGC |A
+GCATC C|
+ATATC |G
+TATCG A|C 8 TATCGCAT 1
+AAGAA C|
+AGACA A|C 8 AGACAGCA 1
diff --git a/genomix/genomix-pregelix/text/SinglePath/log_SinglePath b/genomix/genomix-pregelix/text/SinglePath/log_SinglePath
new file mode 100644
index 0000000..f1371ec
--- /dev/null
+++ b/genomix/genomix-pregelix/text/SinglePath/log_SinglePath
@@ -0,0 +1,3 @@
+ACAGT A|
+GACAA A|T 8 GACAACAG 5
+AGACA |A
diff --git a/genomix/genomix-pregelix/text/SinglePath/naive_SinglePath b/genomix/genomix-pregelix/text/SinglePath/naive_SinglePath
new file mode 100644
index 0000000..b736667
--- /dev/null
+++ b/genomix/genomix-pregelix/text/SinglePath/naive_SinglePath
@@ -0,0 +1,3 @@
+ACAGT A|
+GACAA A|T 8 GACAACAG 1
+AGACA |A
diff --git a/genomix/genomix-pregelix/text/TreePath/log_TreePath b/genomix/genomix-pregelix/text/TreePath/log_TreePath
new file mode 100644
index 0000000..0b9f198
--- /dev/null
+++ b/genomix/genomix-pregelix/text/TreePath/log_TreePath
@@ -0,0 +1,9 @@
+CAGTA T|AC
+AGTAC C|G 10 AGTACGCCCG 5
+ATCCC T|
+GCCTC G|A 8 GCCTCAGT 5
+CCCGG G|
+GGCCT |CG
+AGTAA C|C 10 AGTAACTAAA 5
+TAAAC C|
+GCCTG G|C 12 GCCTGGCTATCC 5
diff --git a/genomix/genomix-pregelix/text/TreePath/naive_TreePath b/genomix/genomix-pregelix/text/TreePath/naive_TreePath
new file mode 100644
index 0000000..39dcbaa
--- /dev/null
+++ b/genomix/genomix-pregelix/text/TreePath/naive_TreePath
@@ -0,0 +1,9 @@
+CAGTA T|AC
+AGTAC C|G 10 AGTACGCCCG 1
+ATCCC T|
+GCCTC G|A 8 GCCTCAGT 1
+CCCGG G|
+GGCCT |CG
+AGTAA C|C 10 AGTAACTAAA 1
+TAAAC C|
+GCCTG G|C 12 GCCTGGCTATCC 1