uniform the output format
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 e4317f0..a1a15a6 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
@@ -4,7 +4,6 @@
import org.apache.hadoop.io.WritableComparable;
-import edu.uci.ics.genomix.pregelix.operator.NaiveAlgorithmForPathMergeVertex;
import edu.uci.ics.genomix.pregelix.type.State;
import edu.uci.ics.genomix.type.GeneCode;
import edu.uci.ics.genomix.type.KmerBytesWritable;
@@ -19,7 +18,7 @@
public ValueStateWritable() {
state = State.NON_VERTEX;
- mergeChain = new VKmerBytesWritable(-1);
+ mergeChain = new VKmerBytesWritable(0);
}
public ValueStateWritable(byte adjMap, byte state, VKmerBytesWritable mergeChain) {
@@ -53,7 +52,7 @@
public int getLengthOfMergeChain() {
return mergeChain.getKmerLength();
}
-
+
public VKmerBytesWritable getMergeChain() {
return mergeChain;
}
@@ -87,8 +86,8 @@
@Override
public String toString() {
- if(mergeChain.getKmerLength() == -1 || mergeChain.getKmerLength() == 0)
- return GeneCode.getSymbolFromBitMap(adjMap);
+ //if(mergeChain.getKmerLength() == -1 || mergeChain.getKmerLength() == 0)
+ // return GeneCode.getSymbolFromBitMap(adjMap);
return GeneCode.getSymbolFromBitMap(adjMap) + "\t" +
getLengthOfMergeChain() + "\t" +
mergeChain.toString();
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/NaiveAlgorithmForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/NaiveAlgorithmForPathMergeVertex.java
index 6db02c7..5187f1c 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/NaiveAlgorithmForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/NaiveAlgorithmForPathMergeVertex.java
@@ -156,6 +156,10 @@
@Override
public void compute(Iterator<NaiveAlgorithmMessageWritable> msgIterator) {
initVertex();
+ /*if(getVertexId().toString().equals("TCCTACGAATTAATGCTCTCCCACGCAACATCACCATATCTTCACGGGAGAGCCG"))
+ System.out.println();
+ if(getVertexId().toString().equals("ATCCTACGAATTAATGCTCTCCCACGCAACATCACCATATCTTCACGGGAGAGCC"))
+ System.out.println();*/
if (getSuperstep() == 1) {
if(GraphVertexOperation.isHeadVertex(getVertexValue().getAdjMap())){
msg.set(getVertexId(), chainVertexId, getVertexId(), (byte)0, false);
@@ -171,12 +175,8 @@
//head node sends message to path node
else if(getSuperstep()%2 == 1 && getSuperstep() <= maxIteration){
while (msgIterator.hasNext()){
- //if(getSuperstep() == 3 && GraphVertexOperation.isRearVertex(getVertexValue().getAdjMap()))
- // voteToHalt();
- //else{
msg = msgIterator.next();
sendMsgToPathVertex();
- //}
}
}
//path node sends message back to head node
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/TwoStepLogAlgorithmForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/TwoStepLogAlgorithmForPathMergeVertex.java
index 0ac4345..712b614 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/TwoStepLogAlgorithmForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/TwoStepLogAlgorithmForPathMergeVertex.java
@@ -177,7 +177,7 @@
* path send message to head
*/
public void responseMsgToHeadVertex(){
- if(getVertexValue().getLengthOfMergeChain() == -1){
+ if(getVertexValue().getLengthOfMergeChain() == 0){
getVertexValue().setMergeChain(getVertexId());
setVertexValue(getVertexValue());
}
@@ -327,6 +327,10 @@
@Override
public void compute(Iterator<LogAlgorithmMessageWritable> msgIterator) {
initVertex();
+ /*if(getVertexId().toString().equals("TCCTACGAATTAATGCTCTCCCACGCAACATCACCATATCTTCACGGGAGAGCCG"))
+ System.out.println();
+ if(getVertexId().toString().equals("ATCCTACGAATTAATGCTCTCCCACGCAACATCACCATATCTTCACGGGAGAGCC"))
+ System.out.println();*/
if (getSuperstep() == 1)
startSendMsg();
else if(getSuperstep() == 2)
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
index c17abc9..88bec61 100644
--- 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
@@ -1,7 +1,9 @@
package edu.uci.ics.genomix.pregelix.sequencefile;
+import java.io.File;
import java.io.IOException;
+import org.apache.commons.io.FileUtils;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
@@ -39,10 +41,12 @@
*/
public static void main(String[] args) throws IOException {
// TODO Auto-generated method stub
- Path dir = new Path("data");
+ Path dir = new Path("data/test8m");
+ Path outDir = new Path("data/input/test");
+ FileUtils.cleanDirectory(new File("data/input/test"));
Path inFile = new Path(dir, "part-0");
- Path outFile = new Path(dir, "part-0-out-20000000");
- generateNumOfLinesFromBigFile(inFile,outFile,20000000);
+ Path outFile = new Path(outDir, "part-0-out-100");
+ generateNumOfLinesFromBigFile(inFile,outFile,100);
}
}
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 50f1679..79538b8 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
@@ -56,20 +56,20 @@
OutputStreamWriter writer;
try {
writer = new OutputStreamWriter(new FileOutputStream("graph/55/SinglePath_55"));
- writer.write(simplePath(55,320,1));
+ writer.write(simplePath(55,60,1));
writer.close();
- /*writer = new OutputStreamWriter(new FileOutputStream("graph/55/SimplePath_55"));
+ writer = new OutputStreamWriter(new FileOutputStream("graph/55/SimplePath_55"));
writer.write(simplePath(55,60,3));
writer.close();
- writer = new OutputStreamWriter(new FileOutputStream("graph/55/TreePath"));
+ writer = new OutputStreamWriter(new FileOutputStream("graph/55/TreePath_55"));
writer.write(treePath(55, 5, 5, 3));
writer.close();
- writer = new OutputStreamWriter(new FileOutputStream("graph/55/CyclePath"));
+ writer = new OutputStreamWriter(new FileOutputStream("graph/55/CyclePath_55"));
writer.write(cyclePath(55,60));
writer.close();
- writer = new OutputStreamWriter(new FileOutputStream("graph/55/BridgePath"));
+ writer = new OutputStreamWriter(new FileOutputStream("graph/55/BridgePath_55"));
writer.write(bridgePath(55,2));
- writer.close();*/
+ writer.close();
} catch (IOException e) {
e.printStackTrace();
}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/GraphBuildTest.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/GraphBuildTest.java
index b3ba49d..d79bb91 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/GraphBuildTest.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/GraphBuildTest.java
@@ -34,15 +34,14 @@
private static final String ACTUAL_RESULT_DIR = "graphbuildresult";
private static final String PATH_TO_HADOOP_CONF = "src/test/resources/hadoop/conf";
- private static final String DATA_PATH = "data/TwoKmer";
- private static final String HDFS_INPUT_PATH = "/CyclePath2";
- private static final String HDFS_OUTPUT_PATH = "/CyclePath2_result";
+ private static final String DATA_PATH = "data/TreePath_55";
+ private static final String HDFS_INPUT_PATH = "/test";
+ private static final String HDFS_OUTPUT_PATH = "/result";
private static final String DUMPED_RESULT = ACTUAL_RESULT_DIR
+ HDFS_OUTPUT_PATH + "/result.txt";
- private static final String CONVERT_RESULT = DUMPED_RESULT + ".txt";
+ private static final String CONVERT_RESULT = "graph/result.txt.txt";
private static final String EXPECTED_PATH = "src/test/resources/expected/result2";
- private static final String EXPECTED_REVERSE_PATH = "src/test/resources/expected/result_reverse";
private static final String HADOOP_CONF_PATH = ACTUAL_RESULT_DIR
+ File.separator + "conf.xml";
@@ -65,7 +64,7 @@
FileInputFormat.setInputPaths(conf, HDFS_INPUT_PATH);
FileOutputFormat.setOutputPath(conf, new Path(HDFS_OUTPUT_PATH));
- conf.setInt(GenomixJob.KMER_LENGTH, 5);
+ conf.setInt(GenomixJob.KMER_LENGTH, 55);
driver = new Driver(
edu.uci.ics.hyracks.hdfs.utils.HyracksUtils.CC_HOST,
edu.uci.ics.hyracks.hdfs.utils.HyracksUtils.TEST_HYRACKS_CC_CLIENT_PORT,
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/MergePathTest.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/MergePathTest.java
index 353fc6d..217f59a 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/MergePathTest.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/MergePathTest.java
@@ -19,8 +19,10 @@
public class MergePathTest {
public static final String PATH_TO_TESTSTORE = "testcase/pathmerge/";
- public static final String NAIVE_DATA_INPUT = "genomix_result/pathmerge/naive_35";
- public static final String LOG_DATA_INPUT = "genomix_result/pathmerge/log_12";
+ //"genomix_result/pathmerge/new_naive";
+ public static final String NAIVE_DATA_INPUT = "genomix_result/pathmerge/new_naive";//"actual/NaiveAlgorithmForMergeGraph/BinaryOutput/test";
+ //"genomix_result/pathmerge/new_log";
+ public static final String LOG_DATA_INPUT = "genomix_result/pathmerge/new_log";//"actual/TwoStepLogAlgorithmForMergeGraph/BinaryOutput/test";
public static final String TEXT_OUTPUT = PATH_TO_TESTSTORE + "textfile";
public static final String CHAIN_OUTPUT = PATH_TO_TESTSTORE + "chain";
@@ -56,14 +58,13 @@
if (key == null || value == null){
break;
}
- if(value.getLengthOfMergeChain() != -1
- && value.getState() == State.FINAL_VERTEX){
- bw.write(value.getLengthOfMergeChain() + "\t" +
- value.getMergeChain().toString() + "\t" +
- GeneCode.getSymbolFromBitMap(value.getAdjMap()));
-
- bw.newLine();
- }
+ /*bw.write(value.getLengthOfMergeChain() + "\t" +
+ value.getMergeChain().toString() + "\t" +
+ GeneCode.getSymbolFromBitMap(value.getAdjMap()) + "\t" +
+ key.toString());*/
+ bw.write(key.toString() + "\t" +
+ value.toString());
+ bw.newLine();
}
reader.close();
}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/PathMergeSmallTestCase.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/PathMergeSmallTestCase.java
index 67b6f21..4b6d367 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/PathMergeSmallTestCase.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/PathMergeSmallTestCase.java
@@ -77,7 +77,7 @@
private void compareResults() throws Exception {
dfs.copyToLocalFile(FileOutputFormat.getOutputPath(job), new Path(
resultFileDir));
- GenerateTextFile.generateFromPathmergeResult(5, resultFileDir, textFileDir);
+ GenerateTextFile.generateFromPathmergeResult(55, resultFileDir, textFileDir);
// TestUtils.compareWithResultDir(new File(expectedFileDir), new
// File(resultFileDir));
}
diff --git a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/PathMergeSmallTestSuite.java b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/PathMergeSmallTestSuite.java
index 43555c5..eee9e39 100644
--- a/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/PathMergeSmallTestSuite.java
+++ b/genomix/genomix-pregelix/src/test/java/edu/uci/ics/genomix/pregelix/pathmerge/PathMergeSmallTestSuite.java
@@ -20,7 +20,6 @@
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.FileReader;
-import java.io.FilenameFilter;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
@@ -31,7 +30,6 @@
import junit.framework.TestSuite;
import org.apache.commons.io.FileUtils;
-import org.apache.commons.io.filefilter.WildcardFileFilter;
import org.apache.hadoop.conf.Configuration;
import org.apache.hadoop.fs.FileSystem;
import org.apache.hadoop.fs.Path;
@@ -46,18 +44,19 @@
private static final Logger LOGGER = Logger
.getLogger(PathMergeSmallTestSuite.class.getName());
- public static final String PreFix = "data/PathTestSet";
+ public static final String PreFix = "data/input";
public static final String[] TestDir = { PreFix + File.separator
- + "TwoKmer", PreFix + File.separator
+ + "test"};
+ /*+ "TwoKmer", PreFix + File.separator
+ "ThreeKmer", PreFix + File.separator
+ "SinglePath", PreFix + File.separator
+ "SimplePath", PreFix + File.separator
+ "Path", PreFix + File.separator
+ "BridgePath", PreFix + File.separator
+ "CyclePath", PreFix + File.separator
- + "CyclePath2", PreFix + File.separator
+ + "RingPath", PreFix + File.separator
+ "LongPath", PreFix + File.separator
- + "TreePath"};
+ + "TreePath"};*/
private static final String ACTUAL_RESULT_DIR = "actual";
private static final String PATH_TO_HADOOP_CONF = "src/test/resources/hadoop/conf";
private static final String PATH_TO_CLUSTER_STORE = "src/test/resources/cluster/stores.properties";