make genomix-hadoop genomix-hyracks compilable
diff --git a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/example/kmer/KmerBytesWritableTest.java b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/example/kmer/KmerBytesWritableTest.java
index ea1d0c2..f21da91 100644
--- a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/example/kmer/KmerBytesWritableTest.java
+++ b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/example/kmer/KmerBytesWritableTest.java
@@ -8,73 +8,71 @@
import edu.uci.ics.genomix.type.KmerBytesWritable;
public class KmerBytesWritableTest {
- static byte[] array = { 'A', 'A', 'T', 'A', 'G', 'A', 'A', 'G' };
- static int k = 7;
-
- @Test
- public void TestCompressKmer() {
- KmerBytesWritable kmer = new KmerBytesWritable(k);
- kmer.setByRead( array, 0);
- Assert.assertEquals(kmer.toString(), "AATAGAA");
-
- kmer.setByRead( array, 1);
- Assert.assertEquals(kmer.toString(), "ATAGAAG");
- }
-
- @Test
- public void TestMoveKmer(){
- KmerBytesWritable kmer = new KmerBytesWritable(k);
- kmer.setByRead( array, 0);
- Assert.assertEquals(kmer.toString(), "AATAGAA");
-
- for (int i = k; i < array.length-1; i++) {
- kmer.shiftKmerWithNextCode(array[i]);
- Assert.assertTrue(false);
- }
+ static byte[] array = { 'A', 'A', 'T', 'A', 'G', 'A', 'A', 'G' };
+ static int k = 7;
- byte out = kmer.shiftKmerWithNextChar( array[array.length - 1]);
- Assert.assertEquals(out, GeneCode.getAdjBit((byte) 'A'));
- Assert.assertEquals(kmer.toString(), "ATAGAAG");
- }
-
-
- @Test
- public void TestCompressKmerReverse() {
- KmerBytesWritable kmer = new KmerBytesWritable(k);
- kmer.setByRead( array, 0);
- Assert.assertEquals(kmer.toString(), "AATAGAA");
-
- kmer.setByReadReverse( array, 1);
- Assert.assertEquals(kmer.toString(), "GAAGATA");
- }
-
- @Test
- public void TestMoveKmerReverse(){
- KmerBytesWritable kmer = new KmerBytesWritable(k);
- kmer.setByRead( array, 0);
- Assert.assertEquals(kmer.toString(), "AATAGAA");
-
- for (int i = k; i < array.length-1; i++) {
- kmer.shiftKmerWithPreChar( array[i]);
- Assert.assertTrue(false);
- }
+ @Test
+ public void TestCompressKmer() {
+ KmerBytesWritable kmer = new KmerBytesWritable(k);
+ kmer.setByRead(array, 0);
+ Assert.assertEquals(kmer.toString(), "AATAGAA");
- byte out = kmer.shiftKmerWithPreChar(array[array.length - 1]);
- Assert.assertEquals(out, GeneCode.getAdjBit((byte) 'A'));
- Assert.assertEquals(kmer.toString(), "GAATAGA");
- }
+ kmer.setByRead(array, 1);
+ Assert.assertEquals(kmer.toString(), "ATAGAAG");
+ }
- @Test
- public void TestGetGene(){
- KmerBytesWritable kmer = new KmerBytesWritable(9);
- String text = "AGCTGACCG";
- byte[] array = { 'A', 'G', 'C', 'T', 'G', 'A', 'C', 'C','G' };
- kmer.setByRead( array, 0);
-
- for(int i =0; i < 9; i++){
- Assert.assertEquals(text.charAt(i),
- (char)(GeneCode.getSymbolFromCode(kmer.getGeneCodeAtPosition(i))));
- }
- }
+ @Test
+ public void TestMoveKmer() {
+ KmerBytesWritable kmer = new KmerBytesWritable(k);
+ kmer.setByRead(array, 0);
+ Assert.assertEquals(kmer.toString(), "AATAGAA");
+
+ for (int i = k; i < array.length - 1; i++) {
+ kmer.shiftKmerWithNextCode(array[i]);
+ Assert.assertTrue(false);
+ }
+
+ byte out = kmer.shiftKmerWithNextChar(array[array.length - 1]);
+ Assert.assertEquals(out, GeneCode.getAdjBit((byte) 'A'));
+ Assert.assertEquals(kmer.toString(), "ATAGAAG");
+ }
+
+ @Test
+ public void TestCompressKmerReverse() {
+ KmerBytesWritable kmer = new KmerBytesWritable(k);
+ kmer.setByRead(array, 0);
+ Assert.assertEquals(kmer.toString(), "AATAGAA");
+
+ kmer.setByReadReverse(array, 1);
+ Assert.assertEquals(kmer.toString(), "GAAGATA");
+ }
+
+ @Test
+ public void TestMoveKmerReverse() {
+ KmerBytesWritable kmer = new KmerBytesWritable(k);
+ kmer.setByRead(array, 0);
+ Assert.assertEquals(kmer.toString(), "AATAGAA");
+
+ for (int i = k; i < array.length - 1; i++) {
+ kmer.shiftKmerWithPreChar(array[i]);
+ Assert.assertTrue(false);
+ }
+
+ byte out = kmer.shiftKmerWithPreChar(array[array.length - 1]);
+ Assert.assertEquals(out, GeneCode.getAdjBit((byte) 'A'));
+ Assert.assertEquals(kmer.toString(), "GAATAGA");
+ }
+
+ @Test
+ public void TestGetGene() {
+ KmerBytesWritable kmer = new KmerBytesWritable(9);
+ String text = "AGCTGACCG";
+ byte[] array = { 'A', 'G', 'C', 'T', 'G', 'A', 'C', 'C', 'G' };
+ kmer.setByRead(array, 0);
+
+ for (int i = 0; i < 9; i++) {
+ Assert.assertEquals(text.charAt(i), (char) (GeneCode.getSymbolFromCode(kmer.getGeneCodeAtPosition(i))));
+ }
+ }
}
diff --git a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/example/kmer/VKmerBytesWritableFactoryTest.java b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/example/kmer/VKmerBytesWritableFactoryTest.java
index a0b8845..c40729c 100644
--- a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/example/kmer/VKmerBytesWritableFactoryTest.java
+++ b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/example/kmer/VKmerBytesWritableFactoryTest.java
@@ -9,150 +9,150 @@
import edu.uci.ics.genomix.type.VKmerBytesWritableFactory;
public class VKmerBytesWritableFactoryTest {
- static byte[] array = { 'A', 'G', 'C', 'T', 'G', 'A', 'C', 'C','G','T'};
-
- VKmerBytesWritableFactory kmerFactory = new VKmerBytesWritableFactory(8);
-
- @Test
- public void TestDegree(){
- Assert.assertTrue(GeneCode.inDegree((byte) 0xff) == 4);
- Assert.assertTrue(GeneCode.outDegree((byte) 0xff) == 4);
- Assert.assertTrue(GeneCode.inDegree((byte) 0x3f) == 2);
- Assert.assertTrue(GeneCode.outDegree((byte) 0x01) == 1);
- Assert.assertTrue(GeneCode.inDegree((byte) 0x01) == 0);
- }
-
- @Test
- public void TestGetLastKmer(){
- KmerBytesWritable kmer = new KmerBytesWritable(9);
- kmer.setByRead( array, 0);
- Assert.assertEquals("AGCTGACCG", kmer.toString());
- KmerBytesWritable lastKmer ;
- for(int i = 8; i>0 ; i--){
- lastKmer = kmerFactory.getLastKmerFromChain(i, kmer);
- Assert.assertEquals("AGCTGACCG".substring(9-i), lastKmer.toString());
- }
- VKmerBytesWritable vlastKmer ;
- for(int i = 8; i>0 ; i--){
- vlastKmer = kmerFactory.getLastKmerFromChain(i, kmer);
- Assert.assertEquals("AGCTGACCG".substring(9-i), vlastKmer.toString());
- }
- }
-
- @Test
- public void TestMergeNext(){
- KmerBytesWritable kmer = new KmerBytesWritable(9);
- kmer.setByRead(array, 0);
- Assert.assertEquals("AGCTGACCG", kmer.toString());
-
- String text = "AGCTGACCG";
- for(byte x = GeneCode.A; x<= GeneCode.T ; x++){
- KmerBytesWritable newkmer = kmerFactory.mergeKmerWithNextCode(kmer, x);
- text = text + (char)GeneCode.GENE_SYMBOL[x];
- Assert.assertEquals(text, newkmer.toString());
- kmer = new KmerBytesWritable(newkmer);
- }
- for(byte x = GeneCode.A; x<= GeneCode.T ; x++){
- KmerBytesWritable newkmer = kmerFactory.mergeKmerWithNextCode(kmer, x);
- text = text + (char)GeneCode.GENE_SYMBOL[x];
- Assert.assertEquals(text, newkmer.toString());
- kmer = new KmerBytesWritable(newkmer);
- }
- }
-
- @Test
- public void TestMergePre(){
- KmerBytesWritable kmer = new KmerBytesWritable(9);
- kmer.setByRead(array, 0);
- Assert.assertEquals("AGCTGACCG", kmer.toString());
- String text = "AGCTGACCG";
- for(byte x = GeneCode.A; x<= GeneCode.T ; x++){
- KmerBytesWritable newkmer = kmerFactory.mergeKmerWithPreCode(kmer, x);
- text = (char)GeneCode.GENE_SYMBOL[x] + text;
- Assert.assertEquals(text , newkmer.toString());
- kmer = new KmerBytesWritable(newkmer);
- }
- for(byte x = GeneCode.A; x<= GeneCode.T ; x++){
- KmerBytesWritable newkmer = kmerFactory.mergeKmerWithPreCode(kmer, x);
- text = (char)GeneCode.GENE_SYMBOL[x] + text;
- Assert.assertEquals(text , newkmer.toString());
- kmer = new KmerBytesWritable(newkmer);
- }
- }
-
- @Test
- public void TestMergeTwoKmer(){
- KmerBytesWritable kmer1 = new KmerBytesWritable(9);
- kmer1.setByRead( array, 0);
- String text1 = "AGCTGACCG";
- KmerBytesWritable kmer2 = new KmerBytesWritable(9);
- kmer2.setByRead(array, 1);
- String text2 = "GCTGACCGT";
- Assert.assertEquals(text1, kmer1.toString());
- Assert.assertEquals(text2, kmer2.toString());
-
- KmerBytesWritable merged = kmerFactory.mergeTwoKmer(kmer1, kmer2);
- Assert.assertEquals(text1+text2, merged.toString());
-
- KmerBytesWritable kmer3 = new KmerBytesWritable(3);
- kmer3.setByRead(array, 1);
- String text3 = "GCT";
- Assert.assertEquals(text3, kmer3.toString());
-
- merged = kmerFactory.mergeTwoKmer(kmer1, kmer3);
- Assert.assertEquals(text1+text3, merged.toString());
- merged = kmerFactory.mergeTwoKmer( kmer3, kmer1);
- Assert.assertEquals(text3+text1, merged.toString());
-
- KmerBytesWritable kmer4 = new KmerBytesWritable(8);
- kmer4.setByRead( array, 0);
- String text4 = "AGCTGACC";
- Assert.assertEquals(text4, kmer4.toString());
- merged = kmerFactory.mergeTwoKmer(kmer4, kmer3);
- Assert.assertEquals(text4+text3, merged.toString());
-
- KmerBytesWritable kmer5 = new KmerBytesWritable(7);
- kmer5.setByRead( array, 0);
- String text5 = "AGCTGAC";
- VKmerBytesWritable kmer6 = new VKmerBytesWritable(9);
- kmer6.setByRead(9, array, 1);
- String text6 = "GCTGACCGT";
- merged = kmerFactory.mergeTwoKmer(kmer5, kmer6);
- Assert.assertEquals(text5+text6, merged.toString());
-
- kmer6.setByRead(6, array, 1);
- String text7 = "GCTGAC";
- merged = kmerFactory.mergeTwoKmer(kmer5, kmer6);
- Assert.assertEquals(text5+text7, merged.toString());
-
- kmer6.setByRead(4, array, 1);
- String text8 = "GCTG";
- merged = kmerFactory.mergeTwoKmer( kmer5, kmer6);
- Assert.assertEquals(text5+text8, merged.toString());
+ static byte[] array = { 'A', 'G', 'C', 'T', 'G', 'A', 'C', 'C', 'G', 'T' };
- }
- @Test
- public void TestShift(){
- VKmerBytesWritable kmer = new VKmerBytesWritable(kmerFactory.getKmerByRead(9, array, 0));
- String text = "AGCTGACCG";
- Assert.assertEquals(text, kmer.toString());
-
- VKmerBytesWritable kmerForward = kmerFactory.shiftKmerWithNextCode(kmer,GeneCode.A);
- Assert.assertEquals(text, kmer.toString());
- Assert.assertEquals("GCTGACCGA", kmerForward.toString());
- VKmerBytesWritable kmerBackward = kmerFactory.shiftKmerWithPreCode(kmer,GeneCode.C);
- Assert.assertEquals(text, kmer.toString());
- Assert.assertEquals("CAGCTGACC", kmerBackward.toString());
-
- }
+ VKmerBytesWritableFactory kmerFactory = new VKmerBytesWritableFactory(8);
-
- @Test
- public void TestReverseKmer(){
- KmerBytesWritable kmer = new KmerBytesWritable(7);
- kmer.setByRead( array, 0);
- Assert.assertEquals(kmer.toString(), "AGCTGAC");
- KmerBytesWritable reversed = kmerFactory.reverse(kmer);
- Assert.assertEquals(reversed.toString(), "CAGTCGA");
- }
+ @Test
+ public void TestDegree() {
+ Assert.assertTrue(GeneCode.inDegree((byte) 0xff) == 4);
+ Assert.assertTrue(GeneCode.outDegree((byte) 0xff) == 4);
+ Assert.assertTrue(GeneCode.inDegree((byte) 0x3f) == 2);
+ Assert.assertTrue(GeneCode.outDegree((byte) 0x01) == 1);
+ Assert.assertTrue(GeneCode.inDegree((byte) 0x01) == 0);
+ }
+
+ @Test
+ public void TestGetLastKmer() {
+ KmerBytesWritable kmer = new KmerBytesWritable(9);
+ kmer.setByRead(array, 0);
+ Assert.assertEquals("AGCTGACCG", kmer.toString());
+ KmerBytesWritable lastKmer;
+ for (int i = 8; i > 0; i--) {
+ lastKmer = kmerFactory.getLastKmerFromChain(i, kmer);
+ Assert.assertEquals("AGCTGACCG".substring(9 - i), lastKmer.toString());
+ }
+ VKmerBytesWritable vlastKmer;
+ for (int i = 8; i > 0; i--) {
+ vlastKmer = kmerFactory.getLastKmerFromChain(i, kmer);
+ Assert.assertEquals("AGCTGACCG".substring(9 - i), vlastKmer.toString());
+ }
+ }
+
+ @Test
+ public void TestMergeNext() {
+ KmerBytesWritable kmer = new KmerBytesWritable(9);
+ kmer.setByRead(array, 0);
+ Assert.assertEquals("AGCTGACCG", kmer.toString());
+
+ String text = "AGCTGACCG";
+ for (byte x = GeneCode.A; x <= GeneCode.T; x++) {
+ KmerBytesWritable newkmer = kmerFactory.mergeKmerWithNextCode(kmer, x);
+ text = text + (char) GeneCode.GENE_SYMBOL[x];
+ Assert.assertEquals(text, newkmer.toString());
+ kmer = new KmerBytesWritable(newkmer);
+ }
+ for (byte x = GeneCode.A; x <= GeneCode.T; x++) {
+ KmerBytesWritable newkmer = kmerFactory.mergeKmerWithNextCode(kmer, x);
+ text = text + (char) GeneCode.GENE_SYMBOL[x];
+ Assert.assertEquals(text, newkmer.toString());
+ kmer = new KmerBytesWritable(newkmer);
+ }
+ }
+
+ @Test
+ public void TestMergePre() {
+ KmerBytesWritable kmer = new KmerBytesWritable(9);
+ kmer.setByRead(array, 0);
+ Assert.assertEquals("AGCTGACCG", kmer.toString());
+ String text = "AGCTGACCG";
+ for (byte x = GeneCode.A; x <= GeneCode.T; x++) {
+ KmerBytesWritable newkmer = kmerFactory.mergeKmerWithPreCode(kmer, x);
+ text = (char) GeneCode.GENE_SYMBOL[x] + text;
+ Assert.assertEquals(text, newkmer.toString());
+ kmer = new KmerBytesWritable(newkmer);
+ }
+ for (byte x = GeneCode.A; x <= GeneCode.T; x++) {
+ KmerBytesWritable newkmer = kmerFactory.mergeKmerWithPreCode(kmer, x);
+ text = (char) GeneCode.GENE_SYMBOL[x] + text;
+ Assert.assertEquals(text, newkmer.toString());
+ kmer = new KmerBytesWritable(newkmer);
+ }
+ }
+
+ @Test
+ public void TestMergeTwoKmer() {
+ KmerBytesWritable kmer1 = new KmerBytesWritable(9);
+ kmer1.setByRead(array, 0);
+ String text1 = "AGCTGACCG";
+ KmerBytesWritable kmer2 = new KmerBytesWritable(9);
+ kmer2.setByRead(array, 1);
+ String text2 = "GCTGACCGT";
+ Assert.assertEquals(text1, kmer1.toString());
+ Assert.assertEquals(text2, kmer2.toString());
+
+ KmerBytesWritable merged = kmerFactory.mergeTwoKmer(kmer1, kmer2);
+ Assert.assertEquals(text1 + text2, merged.toString());
+
+ KmerBytesWritable kmer3 = new KmerBytesWritable(3);
+ kmer3.setByRead(array, 1);
+ String text3 = "GCT";
+ Assert.assertEquals(text3, kmer3.toString());
+
+ merged = kmerFactory.mergeTwoKmer(kmer1, kmer3);
+ Assert.assertEquals(text1 + text3, merged.toString());
+ merged = kmerFactory.mergeTwoKmer(kmer3, kmer1);
+ Assert.assertEquals(text3 + text1, merged.toString());
+
+ KmerBytesWritable kmer4 = new KmerBytesWritable(8);
+ kmer4.setByRead(array, 0);
+ String text4 = "AGCTGACC";
+ Assert.assertEquals(text4, kmer4.toString());
+ merged = kmerFactory.mergeTwoKmer(kmer4, kmer3);
+ Assert.assertEquals(text4 + text3, merged.toString());
+
+ KmerBytesWritable kmer5 = new KmerBytesWritable(7);
+ kmer5.setByRead(array, 0);
+ String text5 = "AGCTGAC";
+ VKmerBytesWritable kmer6 = new VKmerBytesWritable(9);
+ kmer6.setByRead(9, array, 1);
+ String text6 = "GCTGACCGT";
+ merged = kmerFactory.mergeTwoKmer(kmer5, kmer6);
+ Assert.assertEquals(text5 + text6, merged.toString());
+
+ kmer6.setByRead(6, array, 1);
+ String text7 = "GCTGAC";
+ merged = kmerFactory.mergeTwoKmer(kmer5, kmer6);
+ Assert.assertEquals(text5 + text7, merged.toString());
+
+ kmer6.setByRead(4, array, 1);
+ String text8 = "GCTG";
+ merged = kmerFactory.mergeTwoKmer(kmer5, kmer6);
+ Assert.assertEquals(text5 + text8, merged.toString());
+
+ }
+
+ @Test
+ public void TestShift() {
+ VKmerBytesWritable kmer = new VKmerBytesWritable(kmerFactory.getKmerByRead(9, array, 0));
+ String text = "AGCTGACCG";
+ Assert.assertEquals(text, kmer.toString());
+
+ VKmerBytesWritable kmerForward = kmerFactory.shiftKmerWithNextCode(kmer, GeneCode.A);
+ Assert.assertEquals(text, kmer.toString());
+ Assert.assertEquals("GCTGACCGA", kmerForward.toString());
+ VKmerBytesWritable kmerBackward = kmerFactory.shiftKmerWithPreCode(kmer, GeneCode.C);
+ Assert.assertEquals(text, kmer.toString());
+ Assert.assertEquals("CAGCTGACC", kmerBackward.toString());
+
+ }
+
+ @Test
+ public void TestReverseKmer() {
+ KmerBytesWritable kmer = new KmerBytesWritable(7);
+ kmer.setByRead(array, 0);
+ Assert.assertEquals(kmer.toString(), "AGCTGAC");
+ KmerBytesWritable reversed = kmerFactory.reverse(kmer);
+ Assert.assertEquals(reversed.toString(), "CAGTCGA");
+ }
}
diff --git a/genomix/genomix-data/src/test/resources/hadoop/conf/core-site.xml b/genomix/genomix-data/src/test/resources/hadoop/conf/core-site.xml
index 47dfac5..3e5bacb 100644
--- a/genomix/genomix-data/src/test/resources/hadoop/conf/core-site.xml
+++ b/genomix/genomix-data/src/test/resources/hadoop/conf/core-site.xml
@@ -5,14 +5,14 @@
<configuration>
-<property>
- <name>fs.default.name</name>
- <value>hdfs://127.0.0.1:31888</value>
-</property>
-<property>
- <name>hadoop.tmp.dir</name>
- <value>/tmp/hadoop</value>
-</property>
+ <property>
+ <name>fs.default.name</name>
+ <value>hdfs://127.0.0.1:31888</value>
+ </property>
+ <property>
+ <name>hadoop.tmp.dir</name>
+ <value>/tmp/hadoop</value>
+ </property>
</configuration>
diff --git a/genomix/genomix-data/src/test/resources/hadoop/conf/hdfs-site.xml b/genomix/genomix-data/src/test/resources/hadoop/conf/hdfs-site.xml
index 8d29b1d..b1b1902 100644
--- a/genomix/genomix-data/src/test/resources/hadoop/conf/hdfs-site.xml
+++ b/genomix/genomix-data/src/test/resources/hadoop/conf/hdfs-site.xml
@@ -5,14 +5,14 @@
<configuration>
-<property>
- <name>dfs.replication</name>
- <value>1</value>
-</property>
+ <property>
+ <name>dfs.replication</name>
+ <value>1</value>
+ </property>
-<property>
- <name>dfs.block.size</name>
- <value>65536</value>
-</property>
+ <property>
+ <name>dfs.block.size</name>
+ <value>65536</value>
+ </property>
</configuration>
diff --git a/genomix/genomix-data/src/test/resources/hadoop/conf/mapred-site.xml b/genomix/genomix-data/src/test/resources/hadoop/conf/mapred-site.xml
index 39b6505..525e7d5 100644
--- a/genomix/genomix-data/src/test/resources/hadoop/conf/mapred-site.xml
+++ b/genomix/genomix-data/src/test/resources/hadoop/conf/mapred-site.xml
@@ -5,21 +5,21 @@
<configuration>
- <property>
- <name>mapred.job.tracker</name>
- <value>localhost:29007</value>
- </property>
- <property>
- <name>mapred.tasktracker.map.tasks.maximum</name>
- <value>20</value>
- </property>
- <property>
- <name>mapred.tasktracker.reduce.tasks.maximum</name>
- <value>20</value>
- </property>
- <property>
- <name>mapred.max.split.size</name>
- <value>2048</value>
- </property>
+ <property>
+ <name>mapred.job.tracker</name>
+ <value>localhost:29007</value>
+ </property>
+ <property>
+ <name>mapred.tasktracker.map.tasks.maximum</name>
+ <value>20</value>
+ </property>
+ <property>
+ <name>mapred.tasktracker.reduce.tasks.maximum</name>
+ <value>20</value>
+ </property>
+ <property>
+ <name>mapred.max.split.size</name>
+ <value>2048</value>
+ </property>
</configuration>