clean up interface for VKmer setByRead
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritableFactory.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritableFactory.java
index 16df821..c287c1b 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritableFactory.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritableFactory.java
@@ -31,8 +31,7 @@
* @param start
*/
public VKmerBytesWritable getKmerByRead(int k, byte[] array, int start) {
- kmer.reset(k);
- kmer.setByRead(array, start);
+ kmer.setByRead(k, array, start);
return kmer;
}
@@ -44,8 +43,7 @@
* @param start
*/
public VKmerBytesWritable getKmerByReadReverse(int k, byte[] array, int start) {
- kmer.reset(k);
- kmer.setByReadReverse(array, start);
+ kmer.setByReadReverse(k, array, start);
return kmer;
}
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/VKmerBytesWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/VKmerBytesWritable.java
index 73edd9d..af5b2ed 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/VKmerBytesWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/VKmerBytesWritable.java
@@ -441,7 +441,7 @@
* @param stringBytes
* @param start
*/
- public void setByRead(byte[] stringBytes, int start) {
+ private void setByRead(byte[] stringBytes, int start) {
byte l = 0;
int bytecount = 0;
int bcount = this.bytesUsed - 1;
@@ -474,7 +474,7 @@
* @param start
* position
*/
- public void setByReadReverse(byte[] array, int start) {
+ private void setByReadReverse(byte[] array, int start) {
byte l = 0;
int bytecount = 0;
int bcount = bytesUsed - 1;
diff --git a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableFactoryTest.java b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableFactoryTest.java
index 7808719..36115d3 100644
--- a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableFactoryTest.java
+++ b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableFactoryTest.java
@@ -29,8 +29,8 @@
@Test
public void TestGetLastKmer() {
- VKmerBytesWritable kmer = new VKmerBytesWritable(9);
- kmer.setByRead(array, 0);
+ VKmerBytesWritable kmer = new VKmerBytesWritable();
+ kmer.setByRead(9, array, 0);
Assert.assertEquals("AGCTGACCG", kmer.toString());
VKmerBytesWritable lastKmer;
for (int i = 8; i > 0; i--) {
@@ -50,8 +50,8 @@
@Test
public void TestGetFirstKmer() {
- VKmerBytesWritable kmer = new VKmerBytesWritable(9);
- kmer.setByRead(array, 0);
+ VKmerBytesWritable kmer = new VKmerBytesWritable();
+ kmer.setByRead(9, array, 0);
Assert.assertEquals("AGCTGACCG", kmer.toString());
VKmerBytesWritable firstKmer;
for (int i = 8; i > 0; i--) {
@@ -71,8 +71,8 @@
@Test
public void TestGetSubKmer() {
- VKmerBytesWritable kmer = new VKmerBytesWritable(9);
- kmer.setByRead(array, 0);
+ VKmerBytesWritable kmer = new VKmerBytesWritable();
+ kmer.setByRead(9, array, 0);
Assert.assertEquals("AGCTGACCG", kmer.toString());
VKmerBytesWritable subKmer;
for (int istart = 0; istart < kmer.getKmerLetterLength() - 1; istart++) {
@@ -85,8 +85,8 @@
@Test
public void TestMergeNext() {
- VKmerBytesWritable kmer = new VKmerBytesWritable(9);
- kmer.setByRead(array, 0);
+ VKmerBytesWritable kmer = new VKmerBytesWritable();
+ kmer.setByRead(9, array, 0);
Assert.assertEquals("AGCTGACCG", kmer.toString());
String text = "AGCTGACCG";
@@ -106,8 +106,8 @@
@Test
public void TestMergePre() {
- VKmerBytesWritable kmer = new VKmerBytesWritable(9);
- kmer.setByRead(array, 0);
+ VKmerBytesWritable kmer = new VKmerBytesWritable();
+ kmer.setByRead(9, array, 0);
Assert.assertEquals("AGCTGACCG", kmer.toString());
String text = "AGCTGACCG";
for (byte x = GeneCode.A; x <= GeneCode.T; x++) {
@@ -126,11 +126,11 @@
@Test
public void TestMergeTwoKmer() {
- VKmerBytesWritable kmer1 = new VKmerBytesWritable(9);
- kmer1.setByRead(array, 0);
+ VKmerBytesWritable kmer1 = new VKmerBytesWritable();
+ kmer1.setByRead(9, array, 0);
String text1 = "AGCTGACCG";
- VKmerBytesWritable kmer2 = new VKmerBytesWritable(9);
- kmer2.setByRead(array, 1);
+ VKmerBytesWritable kmer2 = new VKmerBytesWritable();
+ kmer2.setByRead(9, array, 1);
String text2 = "GCTGACCGT";
Assert.assertEquals(text1, kmer1.toString());
Assert.assertEquals(text2, kmer2.toString());
@@ -138,8 +138,8 @@
VKmerBytesWritable merged = kmerFactory.mergeTwoKmer(kmer1, kmer2);
Assert.assertEquals(text1 + text2, merged.toString());
- VKmerBytesWritable kmer3 = new VKmerBytesWritable(3);
- kmer3.setByRead(array, 1);
+ VKmerBytesWritable kmer3 = new VKmerBytesWritable();
+ kmer3.setByRead(3, array, 1);
String text3 = "GCT";
Assert.assertEquals(text3, kmer3.toString());
@@ -148,17 +148,17 @@
merged = kmerFactory.mergeTwoKmer(kmer3, kmer1);
Assert.assertEquals(text3 + text1, merged.toString());
- VKmerBytesWritable kmer4 = new VKmerBytesWritable(8);
- kmer4.setByRead(array, 0);
+ VKmerBytesWritable kmer4 = new VKmerBytesWritable();
+ kmer4.setByRead(8, array, 0);
String text4 = "AGCTGACC";
Assert.assertEquals(text4, kmer4.toString());
merged = kmerFactory.mergeTwoKmer(kmer4, kmer3);
Assert.assertEquals(text4 + text3, merged.toString());
- VKmerBytesWritable kmer5 = new VKmerBytesWritable(7);
- kmer5.setByRead(array, 0);
+ VKmerBytesWritable kmer5 = new VKmerBytesWritable();
+ kmer5.setByRead(7, array, 0);
String text5 = "AGCTGAC";
- VKmerBytesWritable kmer6 = new VKmerBytesWritable(9);
+ VKmerBytesWritable kmer6 = new VKmerBytesWritable();
kmer6.setByRead(9, array, 1);
String text6 = "GCTGACCGT";
merged = kmerFactory.mergeTwoKmer(kmer5, kmer6);
@@ -192,17 +192,16 @@
@Test
public void TestReverseKmer() {
- VKmerBytesWritable kmer = new VKmerBytesWritable(7);
- kmer.setByRead(array, 0);
+ VKmerBytesWritable kmer = new VKmerBytesWritable();
+ kmer.setByRead(7, array, 0);
Assert.assertEquals(kmer.toString(), "AGCTGAC");
VKmerBytesWritable reversed = kmerFactory.reverse(kmer);
Assert.assertEquals(reversed.toString(), "CAGTCGA");
- kmer.reset(8);
- kmer.setByRead(("AATAGAAC").getBytes(), 0);
+ kmer.setByRead(8, ("AATAGAAC").getBytes(), 0);
Assert.assertEquals(kmer.toString(), "AATAGAAC");
reversed.reset(8);
reversed = kmerFactory.reverse(kmer);
- Assert.assertEquals(reversed.toString(), "GTTCTATT");
+ Assert.assertEquals(reversed.toString(), "CAAGATAA");
}
}
diff --git a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerListWritableTest.java b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerListWritableTest.java
index 9ca4488..fc97664 100644
--- a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerListWritableTest.java
+++ b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerListWritableTest.java
@@ -23,7 +23,7 @@
kmer = new VKmerBytesWritable(i);
String randomString = generaterRandomString(i);
byte[] array = randomString.getBytes();
- kmer.setByRead(array, 0);
+ kmer.setByRead(i, array, 0);
kmerList.reset();
kmerList.append(kmer);
Assert.assertEquals(randomString, kmerList.getPosition(0).toString());
@@ -36,7 +36,7 @@
kmer = new VKmerBytesWritable(5);
String randomString = generaterRandomString(5);
byte[] array = randomString.getBytes();
- kmer.setByRead(array, 0);
+ kmer.setByRead(5, array, 0);
kmerList.append(kmer);
Assert.assertEquals(kmerList.getPosition(i).toString(), randomString);
Assert.assertEquals(i + 1, kmerList.getCountOfPosition());
@@ -62,7 +62,7 @@
kmer = new VKmerBytesWritable(5);
String randomString = generaterRandomString(5);
byte[] array = randomString.getBytes();
- kmer.setByRead(array, 0);
+ kmer.setByRead(5, array, 0);
kmerList.append(kmer);
Assert.assertEquals(randomString, kmerList.getPosition(i).toString());
Assert.assertEquals(i + 1, kmerList.getCountOfPosition());
@@ -78,7 +78,7 @@
iterator = copyList.iterator();
byte[] array = kmerList.getPosition(j).toString().getBytes();
VKmerBytesWritable deletePos = new VKmerBytesWritable(5);
- deletePos.setByRead(array, 0);
+ deletePos.setByRead(5, array, 0);
boolean removed = false;
while(iterator.hasNext()){
tmpKmer = iterator.next();
@@ -109,9 +109,9 @@
VKmerListWritable edgeList = new VKmerListWritable();
VKmerBytesWritable k = new VKmerBytesWritable(3);
- k.setByRead(("AAA").getBytes(), 0);
+ k.setByRead(3, ("AAA").getBytes(), 0);
edgeList.append(k);
- k.setByRead(("CCC").getBytes(), 0);
+ k.setByRead(3, ("CCC").getBytes(), 0);
edgeList.append(k);
for(VKmerBytesWritable edge : edgeList){
System.out.println(edge.toString());
diff --git a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/VKmerBytesWritableTest.java b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/VKmerBytesWritableTest.java
index 2493b7e..1b60c3c 100644
--- a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/VKmerBytesWritableTest.java
+++ b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/VKmerBytesWritableTest.java
@@ -37,17 +37,17 @@
@Test
public void TestCompressKmer() {
VKmerBytesWritable kmer = new VKmerBytesWritable(k);
- kmer.setByRead(array, 0);
+ kmer.setByRead(k, array, 0);
Assert.assertEquals(kmer.toString(), "AATAGAA");
- kmer.setByRead(array, 1);
+ kmer.setByRead(k, array, 1);
Assert.assertEquals(kmer.toString(), "ATAGAAG");
}
@Test
public void TestMoveKmer() {
VKmerBytesWritable kmer = new VKmerBytesWritable(k);
- kmer.setByRead(array, 0);
+ kmer.setByRead(k, array, 0);
Assert.assertEquals(kmer.toString(), "AATAGAA");
for (int i = k; i < array.length - 1; i++) {
@@ -63,17 +63,17 @@
@Test
public void TestCompressKmerReverse() {
VKmerBytesWritable kmer = new VKmerBytesWritable(k);
- kmer.setByRead(array, 0);
+ kmer.setByRead(k, array, 0);
Assert.assertEquals(kmer.toString(), "AATAGAA");
- kmer.setByReadReverse(array, 1);
+ kmer.setByReadReverse(k, array, 1);
Assert.assertEquals(kmer.toString(), "CTTCTAT");
}
@Test
public void TestMoveKmerReverse() {
VKmerBytesWritable kmer = new VKmerBytesWritable(k);
- kmer.setByRead(array, 0);
+ kmer.setByRead(k, array, 0);
Assert.assertEquals(kmer.toString(), "AATAGAA");
for (int i = k; i < array.length - 1; i++) {
@@ -91,7 +91,7 @@
VKmerBytesWritable kmer = new VKmerBytesWritable(9);
String text = "AGCTGACCG";
byte[] array = { 'A', 'G', 'C', 'T', 'G', 'A', 'C', 'C', 'G' };
- kmer.setByRead(array, 0);
+ kmer.setByRead(9, array, 0);
for (int i = 0; i < 9; i++) {
Assert.assertEquals(text.charAt(i), (char) (GeneCode.getSymbolFromCode(kmer.getGeneCodeAtPosition(i))));
@@ -105,7 +105,7 @@
for (int k = 3; k <= 10; k++) {
VKmerBytesWritable kmer = new VKmerBytesWritable(k);
VKmerBytesWritable kmerAppend = new VKmerBytesWritable(k);
- kmer.setByRead(array, 0);
+ kmer.setByRead(k, array, 0);
Assert.assertEquals(string.substring(0, k), kmer.toString());
for (int b = 0; b < k; b++) {
byte byteActual = KmerBytesWritable.getOneByteFromKmerAtPosition(b, kmer.getBytes(),
@@ -127,12 +127,12 @@
byte[] array = { 'A', 'G', 'C', 'T', 'G', 'A', 'C', 'C', 'G', 'T' };
String text = "AGCTGACCGT";
VKmerBytesWritable kmer1 = new VKmerBytesWritable(8);
- kmer1.setByRead(array, 0);
+ kmer1.setByRead(8, array, 0);
String text1 = "AGCTGACC";
Assert.assertEquals(text1, kmer1.toString());
VKmerBytesWritable kmer2 = new VKmerBytesWritable(8);
- kmer2.setByRead(array, 1);
+ kmer2.setByRead(8, array, 1);
String text2 = "GCTGACCG";
Assert.assertEquals(text2, kmer2.toString());
@@ -151,8 +151,8 @@
for (int jk = 1; jk <= 10; jk++) {
kmer1 = new VKmerBytesWritable(ik);
kmer2 = new VKmerBytesWritable(jk);
- kmer1.setByRead(array, 0);
- kmer2.setByRead(array, 0);
+ kmer1.setByRead(ik, array, 0);
+ kmer2.setByRead(jk, array, 0);
text1 = text.substring(0, ik);
text2 = text.substring(0, jk);
Assert.assertEquals(text1, kmer1.toString());
@@ -174,13 +174,13 @@
String text1 = "AAGCTAA";
VKmerBytesWritable kmer1 = new VKmerBytesWritable(text1.length());
- kmer1.setByRead(resultArray, 0);
+ kmer1.setByRead(text1.length(), resultArray, 0);
Assert.assertEquals(text1, kmer1.toString());
// kmer2 is the rc of the end of the read
String text2 = "GGTTGTT";
VKmerBytesWritable kmer2 = new VKmerBytesWritable(text2.length());
- kmer2.setByReadReverse(resultArray, result.length() - text2.length());
+ kmer2.setByReadReverse(text2.length(), resultArray, result.length() - text2.length());
Assert.assertEquals(text2, kmer2.toString());
VKmerBytesWritable merge = new VKmerBytesWritable(kmer1);
@@ -211,13 +211,13 @@
String text1 = "AACAACCC";
VKmerBytesWritable kmer1 = new VKmerBytesWritable(text1.length());
- kmer1.setByRead(resultArray, 5);
+ kmer1.setByRead(text1.length(), resultArray, 5);
Assert.assertEquals(text1, kmer1.toString());
// kmer2 is the rc of the end of the read
String text2 = "TTGTGCC";
VKmerBytesWritable kmer2 = new VKmerBytesWritable(text2.length());
- kmer2.setByReadReverse(resultArray, 0);
+ kmer2.setByReadReverse(text2.length(), resultArray, 0);
Assert.assertEquals(text2, kmer2.toString());
VKmerBytesWritable merge = new VKmerBytesWritable(kmer1);
@@ -253,8 +253,8 @@
String test4 = "AGA"; // rc = TCT
VKmerBytesWritable k3 = new VKmerBytesWritable(3);
VKmerBytesWritable k4 = new VKmerBytesWritable(3);
- k3.setByRead(test3.getBytes(), 0);
- k4.setByRead(test4.getBytes(), 0);
+ k3.setByRead(3, test3.getBytes(), 0);
+ k4.setByRead(3, test4.getBytes(), 0);
k3.mergeWithRFKmer(3, k4);
Assert.assertEquals("TCTA", k3.toString());
// Assert.assertEquals("CTAT", k3); // this is an incorrect test case--
@@ -266,8 +266,8 @@
test2 = "AGA";
VKmerBytesWritable k1 = new VKmerBytesWritable(3);
VKmerBytesWritable k2 = new VKmerBytesWritable(3);
- k1.setByRead(test1.getBytes(), 0);
- k2.setByRead(test2.getBytes(), 0);
+ k1.setByRead(3, test1.getBytes(), 0);
+ k2.setByRead(3, test2.getBytes(), 0);
k1.mergeWithRFKmer(3, k2);
Assert.assertEquals("TCTA", k1.toString());
@@ -277,8 +277,8 @@
test2 = "ATA"; //TAT
k1 = new VKmerBytesWritable(3);
k2 = new VKmerBytesWritable(3);
- k1.setByRead(test1.getBytes(), 0);
- k2.setByRead(test2.getBytes(), 0);
+ k1.setByRead(3, test1.getBytes(), 0);
+ k2.setByRead(3, test2.getBytes(), 0);
k1.mergeWithFRKmer(3, k2);
Assert.assertEquals("CTAT", k1.toString());
@@ -286,8 +286,8 @@
test2 = "CTA"; //TAT
k1 = new VKmerBytesWritable(3);
k2 = new VKmerBytesWritable(3);
- k1.setByRead(test1.getBytes(), 0);
- k2.setByRead(test2.getBytes(), 0);
+ k1.setByRead(3, test1.getBytes(), 0);
+ k2.setByRead(3, test2.getBytes(), 0);
k1.mergeWithFRKmer(3, k2);
Assert.assertEquals("ATAG", k1.toString());
@@ -295,8 +295,8 @@
test2 = "GAAC";
k1 = new VKmerBytesWritable(5);
k2 = new VKmerBytesWritable(4);
- k1.setByRead(test1.getBytes(), 0);
- k2.setByRead(test2.getBytes(), 0);
+ k1.setByRead(5, test1.getBytes(), 0);
+ k2.setByRead(4, test2.getBytes(), 0);
k1.mergeWithRFKmer(3, k2);
Assert.assertEquals("GTTCTAT", k1.toString());
}
@@ -306,10 +306,10 @@
byte[] array = { 'A', 'G', 'C', 'T', 'G', 'A', 'C', 'C', 'G', 'T' };
String text = "AGCTGACCGT";
VKmerBytesWritable kmer1 = new VKmerBytesWritable(8);
- kmer1.setByRead(array, 0);
+ kmer1.setByRead(8, array, 0);
String text1 = "AGCTGACC";
VKmerBytesWritable kmer2 = new VKmerBytesWritable(8);
- kmer2.setByRead(array, 1);
+ kmer2.setByRead(8, array, 1);
String text2 = "GCTGACCG";
Assert.assertEquals(text2, kmer2.toString());
VKmerBytesWritable merge = new VKmerBytesWritable(kmer2);
@@ -327,8 +327,8 @@
for (int jk = 1; jk <= 10; jk++) {
kmer1 = new VKmerBytesWritable(ik);
kmer2 = new VKmerBytesWritable(jk);
- kmer1.setByRead(array, 0);
- kmer2.setByRead(array, 0);
+ kmer1.setByRead(ik, array, 0);
+ kmer2.setByRead(jk, array, 0);
text1 = text.substring(0, ik);
text2 = text.substring(0, jk);
Assert.assertEquals(text1, kmer1.toString());
@@ -350,9 +350,9 @@
VKmerBytesWritable k1 = new VKmerBytesWritable(5);
VKmerBytesWritable k2 = new VKmerBytesWritable(5);
VKmerBytesWritable k3 = new VKmerBytesWritable(5);
- k1.setByRead(test1.getBytes(), 0);
- k2.setByRead(test2.getBytes(), 0);
- k3.setByRead(test3.getBytes(), 0);
+ k1.setByRead(5, test1.getBytes(), 0);
+ k2.setByRead(5, test2.getBytes(), 0);
+ k3.setByRead(5, test3.getBytes(), 0);
k1.mergeWithRFKmer(5, k2);
Assert.assertEquals("CTAGAT", k1.toString());
k1.mergeWithRRKmer(5, k3);
@@ -367,9 +367,9 @@
VKmerBytesWritable k1 = new VKmerBytesWritable(5);
VKmerBytesWritable k2 = new VKmerBytesWritable(5);
VKmerBytesWritable k3 = new VKmerBytesWritable(5);
- k1.setByRead(test1.getBytes(), 0);
- k2.setByRead(test2.getBytes(), 0);
- k3.setByRead(test3.getBytes(), 0);
+ k1.setByRead(5, test1.getBytes(), 0);
+ k2.setByRead(5, test2.getBytes(), 0);
+ k3.setByRead(5, test3.getBytes(), 0);
k1.mergeWithRFKmer(5, k2);
Assert.assertEquals("CTAGAT", k1.toString());
k1.mergeWithRFKmer(5, k3);
@@ -384,9 +384,9 @@
VKmerBytesWritable k1 = new VKmerBytesWritable(5);
VKmerBytesWritable k2 = new VKmerBytesWritable(5);
VKmerBytesWritable k3 = new VKmerBytesWritable(5);
- k1.setByRead(test1.getBytes(), 0);
- k2.setByRead(test2.getBytes(), 0);
- k3.setByRead(test3.getBytes(), 0);
+ k1.setByRead(5, test1.getBytes(), 0);
+ k2.setByRead(5, test2.getBytes(), 0);
+ k3.setByRead(5, test3.getBytes(), 0);
k2.mergeWithRFKmer(5, k1);
Assert.assertEquals("ATCTAG", k2.toString());
k2.mergeWithFRKmer(5, k3);
@@ -401,9 +401,9 @@
VKmerBytesWritable k1 = new VKmerBytesWritable(5);
VKmerBytesWritable k2 = new VKmerBytesWritable(5);
VKmerBytesWritable k3 = new VKmerBytesWritable(5);
- k1.setByRead(test1.getBytes(), 0);
- k2.setByRead(test2.getBytes(), 0);
- k3.setByRead(test3.getBytes(), 0);
+ k1.setByRead(5, test1.getBytes(), 0);
+ k2.setByRead(5, test2.getBytes(), 0);
+ k3.setByRead(5, test3.getBytes(), 0);
k2.mergeWithRFKmer(5, k1);
Assert.assertEquals("ATCTAG", k2.toString());
k2.mergeWithFFKmer(5, k3);
@@ -418,9 +418,9 @@
VKmerBytesWritable k1 = new VKmerBytesWritable(5);
VKmerBytesWritable k2 = new VKmerBytesWritable(5);
VKmerBytesWritable k3 = new VKmerBytesWritable(5);
- k1.setByRead(test1.getBytes(), 0);
- k2.setByRead(test2.getBytes(), 0);
- k3.setByRead(test3.getBytes(), 0);
+ k1.setByRead(5, test1.getBytes(), 0);
+ k2.setByRead(5, test2.getBytes(), 0);
+ k3.setByRead(5, test3.getBytes(), 0);
k2.mergeWithRFKmer(5, k1);
Assert.assertEquals("ATCTAG", k2.toString());
k2.mergeWithFFKmer(5, k3);
@@ -435,9 +435,9 @@
VKmerBytesWritable k1 = new VKmerBytesWritable(5);
VKmerBytesWritable k2 = new VKmerBytesWritable(5);
VKmerBytesWritable k3 = new VKmerBytesWritable(5);
- k1.setByRead(test1.getBytes(), 0);
- k2.setByRead(test2.getBytes(), 0);
- k3.setByRead(test3.getBytes(), 0);
+ k1.setByRead(5, test1.getBytes(), 0);
+ k2.setByRead(5, test2.getBytes(), 0);
+ k3.setByRead(5, test3.getBytes(), 0);
k1.mergeWithRFKmer(5, k2);
Assert.assertEquals("CTAGAT", k1.toString());
k1.mergeWithRFKmer(5, k3);
@@ -465,7 +465,7 @@
index = msgString.indexOf(match);
// does this test belong in VKmer so it can have variable-length kmers?
// kmer.reset(msgString.length() - index);
- kmer.setByRead(msgString.substring(index).getBytes(), 0);
+ kmer.setByRead(kmerSize, msgString.substring(index).getBytes(), 0);
System.out.println(kmer.toString());
//FR test
@@ -474,7 +474,7 @@
msgString = GeneCode.reverseComplement(R2);
index = msgString.indexOf(match);
kmer.reset(msgString.length() - index);
- kmer.setByRead(msgString.substring(index).getBytes(), 0);
+ kmer.setByRead(kmerSize, msgString.substring(index).getBytes(), 0);
System.out.println(kmer.toString());
//RF test
@@ -483,7 +483,7 @@
msgString = GeneCode.reverseComplement(F2);
index = msgString.lastIndexOf(match) + kmerSize - 2;
kmer.reset(index + 1);
- kmer.setByReadReverse(msgString.substring(0, index + 1).getBytes(), 0);
+ kmer.setByReadReverse(kmerSize, msgString.substring(0, index + 1).getBytes(), 0);
System.out.println(kmer.toString());
//RR test
@@ -492,7 +492,7 @@
msgString = R2;
index = msgString.lastIndexOf(match) + kmerSize - 2;
kmer.reset(index + 1);
- kmer.setByRead(msgString.substring(0, index + 1).getBytes(), 0);
+ kmer.setByRead(kmerSize, msgString.substring(0, index + 1).getBytes(), 0);
System.out.println(kmer.toString());
String[][] connectedTable = new String[][]{
@@ -521,21 +521,21 @@
Map<VKmerBytesWritable, Set<Long>> map = new HashMap<VKmerBytesWritable, Set<Long>>();
VKmerBytesWritable k1 = new VKmerBytesWritable(3);
Set<Long> set1 = new HashSet<Long>();
- k1.setByRead(("CTA").getBytes(), 0);
+ k1.setByRead(3, ("CTA").getBytes(), 0);
set1.add((long)1);
map.put(k1, set1);
VKmerBytesWritable k2 = new VKmerBytesWritable(3);
- k2.setByRead(("GTA").getBytes(), 0);
+ k2.setByRead(3, ("GTA").getBytes(), 0);
Set<Long> set2 = new HashSet<Long>();
set2.add((long) 2);
map.put(k2, set2);
VKmerBytesWritable k3 = new VKmerBytesWritable(3);
- k3.setByRead(("ATG").getBytes(), 0);
+ k3.setByRead(3, ("ATG").getBytes(), 0);
Set<Long> set3 = new HashSet<Long>();
set3.add((long) 2);
map.put(k3, set3);
VKmerBytesWritable k4 = new VKmerBytesWritable(3);
- k4.setByRead(("AAT").getBytes(), 0);
+ k4.setByRead(3, ("AAT").getBytes(), 0);
Set<Long> set4 = new HashSet<Long>();
set4.add((long) 1);
map.put(k4, set4);