Refactor KmerBytesWritable to use internal length
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/oldtype/NodeWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/oldtype/NodeWritable.java
index 9fc1829..b2ba461 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/oldtype/NodeWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/oldtype/NodeWritable.java
@@ -68,7 +68,7 @@
forwardReverseList.set(FRList);
reverseForwardList.set(RFList);
reverseReverseList.set(RRList);
- kmer.set(kmer);
+ kmer.setAsCopy(kmer);
}
public void set(PositionWritable nodeID, PositionListWritable FFList, PositionListWritable FRList,
@@ -78,7 +78,7 @@
this.forwardReverseList.set(FRList);
this.reverseForwardList.set(RFList);
this.reverseReverseList.set(RRList);
- this.kmer.set(kmer);
+ this.kmer.setAsCopy(kmer);
}
public void setNodeID(PositionWritable ref) {
@@ -90,7 +90,7 @@
}
public void setKmer(KmerBytesWritable right) {
- this.kmer.set(right);
+ this.kmer.setAsCopy(right);
}
public void reset(int kmerSize) {
@@ -163,7 +163,7 @@
this.forwardReverseList.set(node.forwardReverseList);
this.reverseForwardList.set(node.reverseForwardList);
this.reverseReverseList.set(node.reverseReverseList);
- this.kmer.set(node.kmer);
+ this.kmer.setAsCopy(node.kmer);
}
@Override
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritable.java
index 95bcaf8..b42b8f0 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerBytesWritable.java
@@ -25,6 +25,7 @@
import org.apache.hadoop.io.WritableComparator;
import edu.uci.ics.genomix.data.KmerUtil;
+import edu.uci.ics.genomix.data.Marshal;
import edu.uci.ics.genomix.oldtype.NodeWritable.DirectionFlag;
/**
@@ -33,92 +34,92 @@
* Thus the kmerByteSize of bytes doesn't change either.
*/
public class KmerBytesWritable extends BinaryComparable implements Serializable, WritableComparable<BinaryComparable> {
- /**
- *
- */
+
private static final long serialVersionUID = 1L;
- private static final byte[] EMPTY_BYTES = {};
+ private static final byte[] EMPTY_BYTES = { 0, 0, 0, 0 }; // int indicating 0 length
+ private static final int HEADER_SIZE = 4; // number of bytes for header info
- public int kmerByteSize;
- protected byte[] bytes;
- protected int offset;
- protected int kmerlength;
+ private int lettersInKmer;
+ private int bytesUsed;
+ private byte[] bytes;
+ private int offset;
+ /**
+ * Initialize as empty kmer
+ */
public KmerBytesWritable() {
- this(0, EMPTY_BYTES, 0);
- }
-
- public KmerBytesWritable(int k, byte[] storage, int offset) {
- setNewReference(k, storage, offset);
- }
-
- public KmerBytesWritable(int k, String kmer) {
- setNewReference(kmer.length(), kmer.getBytes(), 0);
+ this(EMPTY_BYTES, 0);
}
/**
- * Initial Kmer space by kmerlength
- *
- * @param k
- * kmerlengthz
+ * Copy contents of kmer string
+ */
+ public KmerBytesWritable(String kmer) {
+ bytes = new byte[HEADER_SIZE + KmerUtil.getByteNumFromK(kmer.length())];
+ setAsCopy(kmer);
+ }
+
+ /**
+ * Set as reference to given data
+ */
+ public KmerBytesWritable(byte[] storage, int offset) {
+ setAsReference(storage, offset);
+ }
+
+ /**
+ * Reserve space for k letters
*/
public KmerBytesWritable(int k) {
- this.kmerlength = k;
- this.kmerByteSize = KmerUtil.getByteNumFromK(kmerlength);
if (k > 0) {
- this.bytes = new byte[this.kmerByteSize];
+ this.bytes = new byte[HEADER_SIZE + KmerUtil.getByteNumFromK(k)];
} else {
this.bytes = EMPTY_BYTES;
}
this.offset = 0;
+ setKmerLength(k);
}
- public KmerBytesWritable(KmerBytesWritable right) {
- this(right.kmerlength);
- set(right);
+ /**
+ * copy kmer in other
+ *
+ * @param other
+ */
+ public KmerBytesWritable(KmerBytesWritable other) {
+ this(other.lettersInKmer);
+ setAsCopy(other);
}
/**
* Deep copy of the given kmer
*
- * @param newData
+ * @param other
*/
- public void set(KmerBytesWritable newData) {
- if (newData == null) {
- this.set(0, EMPTY_BYTES, 0);
- } else {
- this.set(newData.kmerlength, newData.bytes, newData.getOffset());
+ public void setAsCopy(KmerBytesWritable other) {
+ reset(other.lettersInKmer);
+ if (lettersInKmer > 0) {
+ System.arraycopy(other.bytes, other.offset + HEADER_SIZE, bytes, this.offset + HEADER_SIZE, lettersInKmer);
}
}
/**
+ * set from String kmer
+ */
+ public void setAsCopy(String kmer) {
+ int k = kmer.length();
+ reset(k);
+ System.arraycopy(kmer.getBytes(), 0, bytes, offset + HEADER_SIZE, k);
+ }
+
+ /**
* Deep copy of the given bytes data
- * It will not change the kmerlength
*
* @param newData
* @param offset
*/
- public void set(byte[] newData, int offset) {
- if (kmerlength > 0) {
- System.arraycopy(newData, offset, bytes, this.offset, kmerByteSize);
- }
- }
-
- /**
- * Deep copy of the given data, and also set to new kmerlength
- *
- * @param k
- * : new kmer length
- * @param newData
- * : data storage
- * @param offset
- * : start offset
- */
- public void set(int k, byte[] newData, int offset) {
+ public void setAsCopy(byte[] newData, int offset) {
+ int k = Marshal.getInt(newData, offset);
reset(k);
- if (k > 0) {
- System.arraycopy(newData, offset, bytes, this.offset, kmerByteSize);
- }
+ System.arraycopy(newData, offset + HEADER_SIZE, bytes, this.offset + HEADER_SIZE, k);
}
/**
@@ -127,47 +128,36 @@
* @param k
*/
public void reset(int k) {
- this.kmerlength = k;
- setSize(KmerUtil.getByteNumFromK(k));
+ setKmerLength(k);
+ setSize(bytesUsed);
clearLeadBit();
}
/**
* Point this datablock to the given bytes array
* It works like the pointer to new datablock.
- * kmerlength will not change
+ * NOTE: kmerlength is NOT updated
*
* @param newData
* @param offset
*/
- public void setNewReference(byte[] newData, int offset) {
+ public void setAsReference(byte[] newData, int offset) {
this.bytes = newData;
this.offset = offset;
- if (newData.length - offset < kmerByteSize) {
- throw new IllegalArgumentException("Not given enough space");
+ int kRequested = Marshal.getInt(newData, offset);
+ int bytesRequested = KmerUtil.getByteNumFromK(kRequested);
+ if (newData.length - offset < bytesRequested) {
+ throw new IllegalArgumentException("Requested " + bytesRequested + " bytes (k=" + kRequested
+ + ") but buffer has only " + (newData.length - offset) + " bytes");
}
- }
-
- /**
- * Point this datablock to the given bytes array
- * It works like the pointer to new datablock.
- * It also set the new kmerlength
- *
- * @param k
- * @param newData
- * @param offset
- */
- public void setNewReference(int k, byte[] newData, int offset) {
- this.kmerlength = k;
- this.kmerByteSize = KmerUtil.getByteNumFromK(k);
- setNewReference(newData, offset);
+ setKmerLength(kRequested);
}
protected void setSize(int size) {
if (size > getCapacity()) {
setCapacity((size * 3 / 2));
}
- this.kmerByteSize = size;
+ this.bytesUsed = size;
}
protected int getCapacity() {
@@ -177,11 +167,11 @@
protected void setCapacity(int new_cap) {
if (new_cap != getCapacity()) {
byte[] new_data = new byte[new_cap];
- if (new_cap < kmerByteSize) {
- kmerByteSize = new_cap;
+ if (new_cap < bytesUsed) {
+ bytesUsed = new_cap;
}
- if (kmerByteSize != 0) {
- System.arraycopy(bytes, offset, new_data, 0, kmerByteSize);
+ if (bytesUsed != 0) {
+ System.arraycopy(bytes, offset, new_data, 0, bytesUsed);
}
bytes = new_data;
offset = 0;
@@ -196,21 +186,27 @@
* @return
*/
public byte getGeneCodeAtPosition(int pos) {
- if (pos >= kmerlength) {
+ if (pos >= lettersInKmer) {
throw new IllegalArgumentException("gene position out of bound");
}
return geneCodeAtPosition(pos);
}
-
+
// unchecked version of above. Used when kmerlength is inaccurate (mid-merge)
private byte geneCodeAtPosition(int pos) {
int posByte = pos / 4;
int shift = (pos % 4) << 1;
- return (byte) ((bytes[offset + kmerByteSize - 1 - posByte] >> shift) & 0x3);
+ return (byte) ((bytes[offset + bytesUsed - 1 - posByte] >> shift) & 0x3);
}
-
+
+ public void setKmerLength(int k) {
+ this.bytesUsed = HEADER_SIZE + KmerUtil.getByteNumFromK(k);
+ this.lettersInKmer = k;
+ Marshal.putInt(k, bytes, offset);
+ }
+
public int getKmerLength() {
- return this.kmerlength;
+ return lettersInKmer;
}
@Override
@@ -224,7 +220,7 @@
@Override
public int getLength() {
- return kmerByteSize;
+ return bytesUsed;
}
/**
@@ -232,25 +228,26 @@
* [0x000G, 0xATAA]
*
* @param k
- * @param array
+ * @param stringBytes
+ * : byte array from a _string_. Meaning there's no header
* @param start
*/
- public void setByRead(byte[] array, int start) {
+ public void setByRead(byte[] stringBytes, int start) {
byte l = 0;
int bytecount = 0;
- int bcount = this.kmerByteSize - 1;
- for (int i = start; i < start + kmerlength && i < array.length; i++) {
- byte code = GeneCode.getCodeFromSymbol(array[i]);
+ int bcount = this.bytesUsed - 1;
+ for (int i = start; i < start + lettersInKmer && i < stringBytes.length; i++) {
+ byte code = GeneCode.getCodeFromSymbol(stringBytes[i]);
l |= (byte) (code << bytecount);
bytecount += 2;
if (bytecount == 8) {
- bytes[offset + bcount--] = l;
+ bytes[offset + HEADER_SIZE + bcount--] = l;
l = 0;
bytecount = 0;
}
}
if (bcount >= 0) {
- bytes[offset] = l;
+ bytes[offset + HEADER_SIZE] = l;
}
}
@@ -272,20 +269,20 @@
public void setByReadReverse(byte[] array, int start) {
byte l = 0;
int bytecount = 0;
- int bcount = kmerByteSize - 1;
-// for (int i = start + kmerlength - 1; i >= 0 && i < array.length; i--) {
- for (int i = start + kmerlength - 1; i >= start && i < array.length; i--) {
+ int bcount = bytesUsed - 1;
+ // for (int i = start + kmerlength - 1; i >= 0 && i < array.length; i--) {
+ for (int i = start + lettersInKmer - 1; i >= start && i < array.length; i--) {
byte code = GeneCode.getPairedCodeFromSymbol(array[i]);
l |= (byte) (code << bytecount);
bytecount += 2;
if (bytecount == 8) {
- bytes[offset + bcount--] = l;
+ bytes[offset + HEADER_SIZE + bcount--] = l;
l = 0;
bytecount = 0;
}
}
if (bcount >= 0) {
- bytes[offset] = l;
+ bytes[offset + HEADER_SIZE] = l;
}
}
@@ -313,14 +310,14 @@
* @return the shift out gene, in gene code format
*/
public byte shiftKmerWithNextCode(byte c) {
- byte output = (byte) (bytes[offset + kmerByteSize - 1] & 0x03);
- for (int i = kmerByteSize - 1; i > 0; i--) {
- byte in = (byte) (bytes[offset + i - 1] & 0x03);
- bytes[offset + i] = (byte) (((bytes[offset + i] >>> 2) & 0x3f) | (in << 6));
+ byte output = (byte) (bytes[offset + HEADER_SIZE + bytesUsed - 1] & 0x03);
+ for (int i = bytesUsed - 1; i > 0; i--) {
+ byte in = (byte) (bytes[offset + HEADER_SIZE + i - 1] & 0x03);
+ bytes[offset + HEADER_SIZE + i] = (byte) (((bytes[offset + HEADER_SIZE + i] >>> 2) & 0x3f) | (in << 6));
}
- int pos = ((kmerlength - 1) % 4) << 1;
+ int pos = ((lettersInKmer - 1) % 4) << 1;
byte code = (byte) (c << pos);
- bytes[offset] = (byte) (((bytes[offset] >>> 2) & 0x3f) | code);
+ bytes[offset + HEADER_SIZE] = (byte) (((bytes[offset + HEADER_SIZE] >>> 2) & 0x3f) | code);
clearLeadBit();
return output;
}
@@ -344,13 +341,13 @@
* @return the shiftout gene, in gene code format
*/
public byte shiftKmerWithPreCode(byte c) {
- int pos = ((kmerlength - 1) % 4) << 1;
- byte output = (byte) ((bytes[offset] >> pos) & 0x03);
- for (int i = 0; i < kmerByteSize - 1; i++) {
- byte in = (byte) ((bytes[offset + i + 1] >> 6) & 0x03);
- bytes[offset + i] = (byte) ((bytes[offset + i] << 2) | in);
+ int pos = ((lettersInKmer - 1) % 4) << 1;
+ byte output = (byte) ((bytes[offset + HEADER_SIZE] >> pos) & 0x03);
+ for (int i = 0; i < bytesUsed - 1; i++) {
+ byte in = (byte) ((bytes[offset + HEADER_SIZE + i + 1] >> 6) & 0x03);
+ bytes[offset + HEADER_SIZE + i] = (byte) ((bytes[offset + HEADER_SIZE + i] << 2) | in);
}
- bytes[offset + kmerByteSize - 1] = (byte) ((bytes[offset + kmerByteSize - 1] << 2) | c);
+ bytes[offset + HEADER_SIZE + bytesUsed - 1] = (byte) ((bytes[offset + HEADER_SIZE + bytesUsed - 1] << 2) | c);
clearLeadBit();
return output;
}
@@ -366,16 +363,16 @@
* : the next kmer
*/
public void mergeWithFFKmer(int initialKmerSize, KmerBytesWritable kmer) {
- int preKmerLength = kmerlength;
- int preSize = kmerByteSize;
- this.kmerlength += kmer.kmerlength - initialKmerSize + 1;
- setSize(KmerUtil.getByteNumFromK(kmerlength));
+ int preKmerLength = lettersInKmer;
+ int preSize = bytesUsed;
+ lettersInKmer += kmer.lettersInKmer - initialKmerSize + 1;
+ setSize(KmerUtil.getByteNumFromK(lettersInKmer));
for (int i = 1; i <= preSize; i++) {
- bytes[offset + kmerByteSize - i] = bytes[offset + preSize - i];
+ bytes[offset + HEADER_SIZE + bytesUsed - i] = bytes[offset + preSize - i];
}
for (int k = initialKmerSize - 1; k < kmer.getKmerLength(); k += 4) {
byte onebyte = getOneByteFromKmerAtPosition(k, kmer.getBytes(), kmer.getOffset(), kmer.getLength());
- appendOneByteAtPosition(preKmerLength + k - initialKmerSize + 1, onebyte, bytes, offset, kmerByteSize);
+ appendOneByteAtPosition(preKmerLength + k - initialKmerSize + 1, onebyte, bytes, offset + HEADER_SIZE, bytesUsed);
}
clearLeadBit();
}
@@ -384,8 +381,7 @@
* Merge Kmer with the next connected Kmer, when that Kmer needs to be reverse-complemented
* e.g. AAGCTAA merge with GGTTGTT, if the initial kmerSize = 3
* then it will return AAGCTAACAACC
- *
- * A merge B => A B~
+ * A merge B => A B~
*
* @param initialKmerSize
* : the initial kmerSize
@@ -393,31 +389,31 @@
* : the next kmer
*/
public void mergeWithFRKmer(int initialKmerSize, KmerBytesWritable kmer) {
- int preSize = kmerByteSize;
- int preKmerLength = kmerlength;
- this.kmerlength += kmer.kmerlength - initialKmerSize + 1;
- setSize(KmerUtil.getByteNumFromK(kmerlength));
+ int preSize = bytesUsed;
+ int preKmerLength = lettersInKmer;
+ lettersInKmer += kmer.lettersInKmer - initialKmerSize + 1;
+ setSize(KmerUtil.getByteNumFromK(lettersInKmer));
// copy prefix into right-side of buffer
for (int i = 1; i <= preSize; i++) {
- bytes[offset + kmerByteSize - i] = bytes[offset + preSize - i];
+ bytes[offset + HEADER_SIZE + bytesUsed - i] = bytes[offset + HEADER_SIZE + preSize - i];
}
int bytecount = (preKmerLength % 4) * 2;
- int bcount = kmerByteSize - preSize - bytecount / 8; // may overlap previous kmer
- byte l = bcount == kmerByteSize - preSize ? bytes[offset + bcount] : 0x00;
+ int bcount = bytesUsed - preSize - bytecount / 8; // may overlap previous kmer
+ byte l = bcount == bytesUsed - preSize ? bytes[offset + bcount] : 0x00;
bytecount %= 8;
- for (int i = kmer.kmerlength - initialKmerSize; i >= 0; i--) {
+ for (int i = kmer.lettersInKmer - initialKmerSize; i >= 0; i--) {
byte code = GeneCode.getPairedGeneCode(kmer.getGeneCodeAtPosition(i));
l |= (byte) (code << bytecount);
bytecount += 2;
if (bytecount == 8) {
- bytes[offset + bcount--] = l;
+ bytes[offset + HEADER_SIZE + bcount--] = l;
l = 0;
bytecount = 0;
}
}
if (bcount >= 0) {
- bytes[offset] = l;
+ bytes[offset + HEADER_SIZE] = l;
}
}
@@ -432,18 +428,18 @@
* : the previous kmer
*/
public void mergeWithRFKmer(int initialKmerSize, KmerBytesWritable preKmer) {
- int preKmerLength = kmerlength;
- int preSize = kmerByteSize;
- this.kmerlength += preKmer.kmerlength - initialKmerSize + 1;
- setSize(KmerUtil.getByteNumFromK(kmerlength));
+ int preKmerLength = lettersInKmer;
+ int preSize = bytesUsed;
+ lettersInKmer += preKmer.lettersInKmer - initialKmerSize + 1;
+ setSize(KmerUtil.getByteNumFromK(lettersInKmer));
// byte cacheByte = getOneByteFromKmerAtPosition(0, bytes, offset, preSize);
- int byteIndex = kmerByteSize - 1;
+ int byteIndex = bytesUsed - 1;
byte cacheByte = 0x00;
int posnInByte = 0;
// copy rc of preKmer into high bytes
- for (int i = preKmer.kmerlength - 1; i >= initialKmerSize - 1; i--) {
+ for (int i = preKmer.lettersInKmer - 1; i >= initialKmerSize - 1; i--) {
byte code = GeneCode.getPairedGeneCode(preKmer.getGeneCodeAtPosition(i));
cacheByte |= (byte) (code << posnInByte);
posnInByte += 2;
@@ -453,11 +449,11 @@
posnInByte = 0;
}
}
-
+
// copy my kmer into low positions of bytes
for (int i = 0; i < preKmerLength; i++) {
- // expanding the capacity makes this offset incorrect. It's off by the # of additional bytes added.
- int newposn = i + (kmerByteSize - preSize) * 4;
+ // expanding the capacity makes this offset incorrect. It's off by the # of additional bytes added.
+ int newposn = i + (bytesUsed - preSize) * 4;
byte code = geneCodeAtPosition(newposn);
cacheByte |= (byte) (code << posnInByte);
posnInByte += 2;
@@ -467,7 +463,7 @@
posnInByte = 0;
}
}
- bytes[offset] = cacheByte;
+ bytes[offset + HEADER_SIZE] = cacheByte;
clearLeadBit();
}
@@ -482,31 +478,32 @@
* : the previous kmer
*/
public void mergeWithRRKmer(int initialKmerSize, KmerBytesWritable preKmer) {
- int preKmerLength = kmerlength;
- int preSize = kmerByteSize;
- this.kmerlength += preKmer.kmerlength - initialKmerSize + 1;
- setSize(KmerUtil.getByteNumFromK(kmerlength));
+ int preKmerLength = lettersInKmer;
+ int preSize = bytesUsed;
+ lettersInKmer += preKmer.lettersInKmer - initialKmerSize + 1;
+ setSize(KmerUtil.getByteNumFromK(lettersInKmer));
byte cacheByte = getOneByteFromKmerAtPosition(0, bytes, offset, preSize);
// copy prekmer
- for (int k = 0; k < preKmer.kmerlength - initialKmerSize + 1; k += 4) {
- byte onebyte = getOneByteFromKmerAtPosition(k, preKmer.bytes, preKmer.offset, preKmer.kmerByteSize);
- appendOneByteAtPosition(k, onebyte, bytes, offset, kmerByteSize);
+ for (int k = 0; k < preKmer.lettersInKmer - initialKmerSize + 1; k += 4) {
+ byte onebyte = getOneByteFromKmerAtPosition(k, preKmer.bytes, preKmer.offset, preKmer.bytesUsed);
+ appendOneByteAtPosition(k, onebyte, bytes, offset + HEADER_SIZE, bytesUsed);
}
// copy current kmer
int k = 4;
for (; k < preKmerLength; k += 4) {
byte onebyte = getOneByteFromKmerAtPosition(k, bytes, offset, preSize);
- appendOneByteAtPosition(preKmer.kmerlength - initialKmerSize + k - 4 + 1, cacheByte, bytes, offset, kmerByteSize);
+ appendOneByteAtPosition(preKmer.lettersInKmer - initialKmerSize + k - 4 + 1, cacheByte, bytes, offset + HEADER_SIZE,
+ bytesUsed);
cacheByte = onebyte;
}
- appendOneByteAtPosition(preKmer.kmerlength - initialKmerSize + k - 4 + 1, cacheByte, bytes, offset, kmerByteSize);
+ appendOneByteAtPosition(preKmer.lettersInKmer - initialKmerSize + k - 4 + 1, cacheByte, bytes, offset + HEADER_SIZE, bytesUsed);
clearLeadBit();
}
-
+
public void mergeWithKmerInDir(byte dir, int initialKmerSize, KmerBytesWritable kmer) {
- switch(dir & DirectionFlag.DIR_MASK) {
+ switch (dir & DirectionFlag.DIR_MASK) {
case DirectionFlag.DIR_FF:
mergeWithFFKmer(initialKmerSize, kmer);
break;
@@ -520,7 +517,7 @@
mergeWithRRKmer(initialKmerSize, kmer);
break;
default:
- throw new RuntimeException("Direciotn not recognized: " + dir);
+ throw new RuntimeException("Direction not recognized: " + dir);
}
}
@@ -552,61 +549,62 @@
}
protected void clearLeadBit() {
- if (kmerlength % 4 != 0) {
- bytes[offset] &= (1 << ((kmerlength % 4) << 1)) - 1;
+ if (lettersInKmer % 4 != 0) {
+ bytes[offset + HEADER_SIZE] &= (1 << ((lettersInKmer % 4) << 1)) - 1;
}
}
@Override
public void readFields(DataInput in) throws IOException {
- this.kmerlength = in.readInt();
- this.kmerByteSize = KmerUtil.getByteNumFromK(kmerlength);
- if (this.kmerlength > 0) {
- if (this.bytes.length < this.kmerByteSize) {
- this.bytes = new byte[this.kmerByteSize];
+ lettersInKmer = in.readInt();
+ bytesUsed = KmerUtil.getByteNumFromK(lettersInKmer);
+ if (lettersInKmer > 0) {
+ if (this.bytes.length < this.bytesUsed) {
+ this.bytes = new byte[this.bytesUsed];
this.offset = 0;
+
}
- in.readFully(bytes, offset, kmerByteSize);
+ in.readFully(bytes, offset + HEADER_SIZE, bytesUsed - HEADER_SIZE);
}
+ Marshal.putInt(lettersInKmer, bytes, offset);
}
@Override
public void write(DataOutput out) throws IOException {
- out.writeInt(kmerlength);
- if (kmerlength > 0) {
- out.write(bytes, offset, kmerByteSize);
+ out.writeInt(lettersInKmer);
+ if (lettersInKmer > 0) {
+ out.write(bytes, offset + HEADER_SIZE, bytesUsed - HEADER_SIZE);
}
}
@Override
public int hashCode() {
- return super.hashCode() * 31 + this.kmerlength;
+ return super.hashCode() * 31 + this.lettersInKmer;
}
@Override
public boolean equals(Object right_obj) {
if (right_obj instanceof KmerBytesWritable)
- return this.kmerlength == ((KmerBytesWritable) right_obj).kmerlength && super.equals(right_obj);
+ return this.lettersInKmer == ((KmerBytesWritable) right_obj).lettersInKmer && super.equals(right_obj);
return false;
}
@Override
public String toString() {
- return KmerUtil.recoverKmerFrom(this.kmerlength, this.getBytes(), offset, this.getLength());
+ return KmerUtil.recoverKmerFrom(this.lettersInKmer, this.getBytes(), offset + HEADER_SIZE, this.getLength());
}
public static class Comparator extends WritableComparator {
- public final int LEAD_BYTES = 4;
public Comparator() {
super(KmerBytesWritable.class);
}
public int compare(byte[] b1, int s1, int l1, byte[] b2, int s2, int l2) {
- int kmerlength1 = readInt(b1, s1);
- int kmerlength2 = readInt(b2, s2);
+ int kmerlength1 = Marshal.getInt(b1, s1);
+ int kmerlength2 = Marshal.getInt(b2, s2);
if (kmerlength1 == kmerlength2) {
- return compareBytes(b1, s1 + LEAD_BYTES, l1 - LEAD_BYTES, b2, s2 + LEAD_BYTES, l2 - LEAD_BYTES);
+ return compareBytes(b1, s1 + HEADER_SIZE, l1 - HEADER_SIZE, b2, s2 + HEADER_SIZE, l2 - HEADER_SIZE);
}
return kmerlength1 - kmerlength2;
}
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 d2e3a94..f805610 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
@@ -64,7 +64,7 @@
return null;
}
if (lastK == kmerChain.getKmerLength()) {
- kmer.set(kmerChain);
+ kmer.setAsCopy(kmerChain);
return kmer;
}
kmer.reset(lastK);
@@ -100,7 +100,7 @@
return null;
}
if (firstK == kmerChain.getKmerLength()) {
- kmer.set(kmerChain);
+ kmer.setAsCopy(kmerChain);
return kmer;
}
kmer.reset(firstK);
@@ -124,7 +124,7 @@
return null;
}
if (startK == 0 && kSize == kmerChain.getKmerLength()) {
- kmer.set(kmerChain);
+ kmer.setAsCopy(kmerChain);
return kmer;
}
kmer.reset(kSize);
@@ -256,7 +256,7 @@
* @return new created kmer that shifted by afterCode, the K will not change
*/
public KmerBytesWritable shiftKmerWithNextCode(final KmerBytesWritable kmer, byte afterCode) {
- this.kmer.set(kmer);
+ this.kmer.setAsCopy(kmer);
this.kmer.shiftKmerWithNextCode(afterCode);
return this.kmer;
}
@@ -274,7 +274,7 @@
* @return new created kmer that shifted by preCode, the K will not change
*/
public KmerBytesWritable shiftKmerWithPreCode(final KmerBytesWritable kmer, byte preCode) {
- this.kmer.set(kmer);
+ this.kmer.setAsCopy(kmer);
this.kmer.shiftKmerWithPreCode(preCode);
return this.kmer;
}
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerListWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerListWritable.java
index 88bb79c..e434989 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerListWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/KmerListWritable.java
@@ -116,7 +116,7 @@
if (i >= valueCount) {
throw new ArrayIndexOutOfBoundsException("No such positions");
}
- posIter.setNewReference(kmerlength, storage, offset + i * kmerByteSize);
+ posIter.setAsReference(kmerlength, storage, offset + i * kmerByteSize);
return posIter;
}
diff --git a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/NodeWritable.java b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/NodeWritable.java
index efa87f7..98e37dc 100644
--- a/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/NodeWritable.java
+++ b/genomix/genomix-data/src/main/java/edu/uci/ics/genomix/type/NodeWritable.java
@@ -63,7 +63,7 @@
this.forwardReverseList.set(FRList);
this.reverseForwardList.set(RFList);
this.reverseReverseList.set(RRList);
- this.kmer.set(kmer);
+ this.kmer.setAsCopy(kmer);
}
public void reset(int kmerSize) {
@@ -90,7 +90,7 @@
}
public void setKmer(KmerBytesWritable kmer) {
- this.kmer.set(kmer);
+ this.kmer.setAsCopy(kmer);
}
public int getKmerlength() {
diff --git a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java
index b4361ac..3a8fb93 100644
--- a/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java
+++ b/genomix/genomix-data/src/test/java/edu/uci/ics/genomix/data/test/KmerBytesWritableTest.java
@@ -131,7 +131,7 @@
Assert.assertEquals(text1 + text2.substring(kmerSize - 1), merge.toString());
for (int i = 1; i < 8; i++) {
- merge.set(kmer1);
+ merge.setAsCopy(kmer1);
merge.mergeWithFFKmer(i, kmer2);
Assert.assertEquals(text1 + text2.substring(i - 1), merge.toString());
}
@@ -147,7 +147,7 @@
Assert.assertEquals(text1, kmer1.toString());
Assert.assertEquals(text2, kmer2.toString());
for (int x = 1; x < jk; x++) {
- merge.set(kmer1);
+ merge.setAsCopy(kmer1);
merge.mergeWithFFKmer(x, kmer2);
Assert.assertEquals(text1 + text2.substring(x - 1), merge.toString());
}
@@ -177,17 +177,17 @@
Assert.assertEquals(result, merge.toString());
int i = 1;
- merge.set(kmer1);
+ merge.setAsCopy(kmer1);
merge.mergeWithFRKmer(i, kmer2);
Assert.assertEquals("AAGCTAAAACAACC", merge.toString());
i = 2;
- merge.set(kmer1);
+ merge.setAsCopy(kmer1);
merge.mergeWithFRKmer(i, kmer2);
Assert.assertEquals("AAGCTAAACAACC", merge.toString());
i = 3;
- merge.set(kmer1);
+ merge.setAsCopy(kmer1);
merge.mergeWithFRKmer(i, kmer2);
Assert.assertEquals("AAGCTAACAACC", merge.toString());
}
@@ -215,17 +215,17 @@
Assert.assertEquals(result, merge.toString());
int i = 1;
- merge.set(kmer1);
+ merge.setAsCopy(kmer1);
merge.mergeWithRFKmer(i, kmer2);
Assert.assertEquals("GGCACAAAACAACCC", merge.toString());
i = 2;
- merge.set(kmer1);
+ merge.setAsCopy(kmer1);
merge.mergeWithRFKmer(i, kmer2);
Assert.assertEquals("GGCACAAACAACCC", merge.toString());
i = 3;
- merge.set(kmer1);
+ merge.setAsCopy(kmer1);
merge.mergeWithRFKmer(i, kmer2);
Assert.assertEquals("GGCACAACAACCC", merge.toString());
@@ -258,7 +258,7 @@
Assert.assertEquals(text1 + text2.substring(kmerSize - 1), merge.toString());
for (int i = 1; i < 8; i++) {
- merge.set(kmer2);
+ merge.setAsCopy(kmer2);
merge.mergeWithRRKmer(i, kmer1);
Assert.assertEquals(text1.substring(0, text1.length() - i + 1) + text2, merge.toString());
}
@@ -274,7 +274,7 @@
Assert.assertEquals(text1, kmer1.toString());
Assert.assertEquals(text2, kmer2.toString());
for (int x = 1; x < ik; x++) {
- merge.set(kmer2);
+ merge.setAsCopy(kmer2);
merge.mergeWithRRKmer(x, kmer1);
Assert.assertEquals(text1.substring(0, text1.length() - x + 1) + text2, merge.toString());
}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixMapper.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixMapper.java
index 98f561f..1ad6cf0 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixMapper.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/contrailgraphbuilding/GenomixMapper.java
@@ -201,7 +201,7 @@
//set preKmer by shifting curKmer with preChar
public void setPreKmer(byte preChar){
- preForwardKmer.set(curForwardKmer);
+ preForwardKmer.setAsCopy(curForwardKmer);
preForwardKmer.shiftKmerWithPreChar(preChar);
preReverseKmer.setByReadReverse(preForwardKmer.toString().getBytes(), preForwardKmer.getOffset());
preKmerDir = preForwardKmer.compareTo(preReverseKmer) <= 0 ? KmerDir.FORWARD : KmerDir.REVERSE;
@@ -209,7 +209,7 @@
//set nextKmer by shifting curKmer with nextChar
public void setNextKmer(byte nextChar){
- nextForwardKmer.set(curForwardKmer);
+ nextForwardKmer.setAsCopy(curForwardKmer);
nextForwardKmer.shiftKmerWithNextChar(nextChar);
nextReverseKmer.setByReadReverse(nextForwardKmer.toString().getBytes(), nextForwardKmer.getOffset());
nextKmerDir = nextForwardKmer.compareTo(nextReverseKmer) <= 0 ? KmerDir.FORWARD : KmerDir.REVERSE;
@@ -218,15 +218,15 @@
//old curKmer becomes current preKmer
public void setPreKmerByOldCurKmer(){
preKmerDir = curKmerDir;
- preForwardKmer.set(curForwardKmer);
- preReverseKmer.set(curReverseKmer);
+ preForwardKmer.setAsCopy(curForwardKmer);
+ preReverseKmer.setAsCopy(curReverseKmer);
}
//old nextKmer becomes current curKmer
public void setCurKmerByOldNextKmer(){
curKmerDir = nextKmerDir;
- curForwardKmer.set(nextForwardKmer);
- curReverseKmer.set(nextReverseKmer);
+ curForwardKmer.setAsCopy(nextForwardKmer);
+ curReverseKmer.setAsCopy(nextReverseKmer);
}
public void setMapperOutput(OutputCollector<KmerBytesWritable, NodeWritable> output) throws IOException{
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/removetips/RemoveTips.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/removetips/RemoveTips.java
index 83fe200..f1bfec6 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/removetips/RemoveTips.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/graphclean/removetips/RemoveTips.java
@@ -60,7 +60,7 @@
// kill this node by NOT mapping it. Update my neighbors with a suicide note
//TODO: update neighbors by removing me from its list
} else {
- outputValue.set(MergeMessageFlag.MSG_SELF, curNode);
+ outputValue.setAsCopy(MergeMessageFlag.MSG_SELF, curNode);
output.collect(key, value);
}
}
diff --git a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/PositionListAndKmerWritable.java b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/PositionListAndKmerWritable.java
index 943b505..550cc7c 100644
--- a/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/PositionListAndKmerWritable.java
+++ b/genomix/genomix-hadoop/src/main/java/edu/uci/ics/genomix/hadoop/velvetgraphbuilding/PositionListAndKmerWritable.java
@@ -54,12 +54,12 @@
public void set(PositionListAndKmerWritable right) {
this.countOfKmer = right.countOfKmer;
this.vertexIDList.set(right.vertexIDList);
- this.kmer.set(right.kmer);
+ this.kmer.setAsCopy(right.kmer);
}
public void set(PositionListWritable list, KmerBytesWritable kmer) {
this.vertexIDList.set(list);
- this.kmer.set(kmer);
+ this.kmer.setAsCopy(kmer);
}
@Override
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/contrail/graph/AggregateKmerAggregateFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/contrail/graph/AggregateKmerAggregateFactory.java
index d9efd75..d14405e 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/contrail/graph/AggregateKmerAggregateFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/contrail/graph/AggregateKmerAggregateFactory.java
@@ -88,7 +88,7 @@
reverseForwardList.reset(kmerSize);
reverseReverseList.reset(kmerSize);
- kmer.set(accessor.getBuffer().array(), getOffSet(accessor, tIndex, 1));//??从1算起？？
+ kmer.setAsCopy(accessor.getBuffer().array(), getOffSet(accessor, tIndex, 1));//??从1算起？？
nodeIdList.setNewReference(1, accessor.getBuffer().array(), getOffSet(accessor, tIndex, 2));
int ffCount = Marshal.getInt(accessor.getBuffer().array(), getOffSet(accessor, tIndex, 3));//??
forwardForwardList.setNewReference(ffCount, accessor.getBuffer().array(), getOffSet(accessor, tIndex, 4));
@@ -100,7 +100,7 @@
reverseForwardList.setNewReference(rrCount, accessor.getBuffer().array(), getOffSet(accessor, tIndex, 10));
nodeAggreter.set(nodeIdList, forwardForwardList, forwardReverseList, reverseForwardList, reverseForwardList, kmer);
- inputVal.getKmer().set(kmer);
+ inputVal.getKmer().setAsCopy(kmer);
inputVal.getNodeIdList().appendList(nodeIdList);
inputVal.getFFList().appendList(forwardForwardList);
inputVal.getFRList().appendList(forwardReverseList);
@@ -115,7 +115,7 @@
public void aggregate(IFrameTupleAccessor accessor, int tIndex, IFrameTupleAccessor stateAccessor,
int stateTupleIndex, AggregateState state) throws HyracksDataException {
NodeWritable inputVal = (NodeWritable) state.state;
- kmer.set(accessor.getBuffer().array(), getOffSet(accessor, tIndex, 1));//??从1算起？？
+ kmer.setAsCopy(accessor.getBuffer().array(), getOffSet(accessor, tIndex, 1));//??从1算起？？
nodeIdList.setNewReference(1, accessor.getBuffer().array(), getOffSet(accessor, tIndex, 2));
int ffCount = Marshal.getInt(accessor.getBuffer().array(), getOffSet(accessor, tIndex, 3));//??
forwardForwardList.setNewReference(ffCount, accessor.getBuffer().array(), getOffSet(accessor, tIndex, 4));
@@ -127,7 +127,7 @@
reverseForwardList.setNewReference(rrCount, accessor.getBuffer().array(), getOffSet(accessor, tIndex, 10));
nodeAggreter.set(nodeIdList, forwardForwardList, forwardReverseList, reverseForwardList, reverseForwardList, kmer);
- inputVal.getKmer().set(kmer);
+ inputVal.getKmer().setAsCopy(kmer);
inputVal.getNodeIdList().appendList(nodeIdList);
inputVal.getFFList().appendList(forwardForwardList);
inputVal.getFRList().appendList(forwardReverseList);
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/contrail/graph/ReadsKeyValueParserFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/contrail/graph/ReadsKeyValueParserFactory.java
index 7280dff..3adf8a0 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/contrail/graph/ReadsKeyValueParserFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/contrail/graph/ReadsKeyValueParserFactory.java
@@ -150,10 +150,10 @@
}
/** first kmer **/
curForwardKmer.setByRead(array, 0);
- curReverseKmer.set(kmerFactory.reverse(curForwardKmer));
+ curReverseKmer.setAsCopy(kmerFactory.reverse(curForwardKmer));
curKmerDir = curForwardKmer.compareTo(curReverseKmer) >= 0 ? KmerDir.FORWARD : KmerDir.REVERSE;
setNextKmer(array[kmerSize]);
- readId.set(mateId, readID);
+ readId.setAsCopy(mateId, readID);
outputNode.setreadId(readId);
setEdgeListForNextKmer();
switch (curKmerDir) {
@@ -170,7 +170,7 @@
setCurKmerByOldNextKmer();
setNextKmer(array[i]);
//set value.readId
- readId.set(mateId, readID);
+ readId.setAsCopy(mateId, readID);
outputNode.setreadId(readId);
//set value.edgeList
setEdgeListForPreKmer();
@@ -189,7 +189,7 @@
setPreKmerByOldCurKmer();
setCurKmerByOldNextKmer();
//set value.readId
- readId.set(mateId, readID);
+ readId.setAsCopy(mateId, readID);
outputNode.setreadId(readId);
//set value.edgeList
setEdgeListForPreKmer();
@@ -205,32 +205,32 @@
}
public void setPreKmer(byte preChar){
- preForwardKmer.set(curForwardKmer);
+ preForwardKmer.setAsCopy(curForwardKmer);
preForwardKmer.shiftKmerWithPreChar(preChar);
- preReverseKmer.set(preForwardKmer);
- preReverseKmer.set(kmerFactory.reverse(nextForwardKmer));
+ preReverseKmer.setAsCopy(preForwardKmer);
+ preReverseKmer.setAsCopy(kmerFactory.reverse(nextForwardKmer));
preKmerDir = preForwardKmer.compareTo(preReverseKmer) >= 0 ? KmerDir.FORWARD : KmerDir.REVERSE;
}
public void setNextKmer(byte nextChar) {
- nextForwardKmer.set(curForwardKmer);
+ nextForwardKmer.setAsCopy(curForwardKmer);
nextForwardKmer.shiftKmerWithNextChar(nextChar);
- nextReverseKmer.set(nextForwardKmer);
- nextReverseKmer.set(kmerFactory.reverse(nextForwardKmer));
+ nextReverseKmer.setAsCopy(nextForwardKmer);
+ nextReverseKmer.setAsCopy(kmerFactory.reverse(nextForwardKmer));
nextKmerDir = nextForwardKmer.compareTo(nextReverseKmer) >= 0 ? KmerDir.FORWARD : KmerDir.REVERSE;
}
public void setPreKmerByOldCurKmer() {
preKmerDir = curKmerDir;
- preForwardKmer.set(curForwardKmer);
- preReverseKmer.set(curReverseKmer);
+ preForwardKmer.setAsCopy(curForwardKmer);
+ preReverseKmer.setAsCopy(curReverseKmer);
}
//old nextKmer becomes current curKmer
public void setCurKmerByOldNextKmer() {
curKmerDir = nextKmerDir;
- curForwardKmer.set(nextForwardKmer);
- preReverseKmer.set(nextReverseKmer);
+ curForwardKmer.setAsCopy(nextForwardKmer);
+ preReverseKmer.setAsCopy(nextReverseKmer);
}
public void setEdgeListForNextKmer() {
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/MapReadToNodeOperator.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/MapReadToNodeOperator.java
index 0f0aa29..f376f71 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/MapReadToNodeOperator.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/MapReadToNodeOperator.java
@@ -186,7 +186,7 @@
throw new IllegalArgumentException("kmer kmerByteSize is invalid");
}
offset += INT_LENGTH;
- kmer.set(buffer.array(), offset);
+ kmer.setAsCopy(buffer.array(), offset);
}
private void connect(NodeReference curNode, NodeReference nextNode) {
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/KMerSequenceWriterFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/KMerSequenceWriterFactory.java
index f6c2cf9..aabdb3f 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/KMerSequenceWriterFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/KMerSequenceWriterFactory.java
@@ -70,7 +70,7 @@
if (reEnterKey.getLength() > tuple.getFieldLength(InputKmerField)) {
throw new IllegalArgumentException("Not enough kmer bytes");
}
- reEnterKey.setNewReference(tuple.getFieldData(InputKmerField), tuple.getFieldStart(InputKmerField));
+ reEnterKey.setAsReference(tuple.getFieldData(InputKmerField), tuple.getFieldStart(InputKmerField));
int countOfPos = tuple.getFieldLength(InputPositionListField) / PositionWritable.LENGTH;
if (tuple.getFieldLength(InputPositionListField) % PositionWritable.LENGTH != 0) {
throw new IllegalArgumentException("Invalid count of position byte");
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/KMerTextWriterFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/KMerTextWriterFactory.java
index e7526ed..91f10be 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/KMerTextWriterFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/KMerTextWriterFactory.java
@@ -49,7 +49,7 @@
if (kmer.getLength() > tuple.getFieldLength(KMerSequenceWriterFactory.InputKmerField)) {
throw new IllegalArgumentException("Not enough kmer bytes");
}
- kmer.setNewReference(tuple.getFieldData(KMerSequenceWriterFactory.InputKmerField),
+ kmer.setAsReference(tuple.getFieldData(KMerSequenceWriterFactory.InputKmerField),
tuple.getFieldStart(KMerSequenceWriterFactory.InputKmerField));
int countOfPos = tuple.getFieldLength(KMerSequenceWriterFactory.InputPositionListField)
/ PositionWritable.LENGTH;
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/NodeSequenceWriterFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/NodeSequenceWriterFactory.java
index 77efcf8..1651d4a 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/NodeSequenceWriterFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/NodeSequenceWriterFactory.java
@@ -94,7 +94,7 @@
node.getRRList().setNewReference(tuple.getFieldLength(InputRRField) / PositionWritable.LENGTH,
tuple.getFieldData(InputRRField), tuple.getFieldStart(InputRRField));
- node.getKmer().setNewReference(
+ node.getKmer().setAsReference(
Marshal.getInt(tuple.getFieldData(NodeSequenceWriterFactory.InputCountOfKmerField),
tuple.getFieldStart(NodeSequenceWriterFactory.InputCountOfKmerField)),
tuple.getFieldData(InputKmerBytesField), tuple.getFieldStart(InputKmerBytesField));
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/NodeTextWriterFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/NodeTextWriterFactory.java
index dffd3a9..3ca4a9d 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/NodeTextWriterFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/dataflow/io/NodeTextWriterFactory.java
@@ -69,7 +69,7 @@
tuple.getFieldData(NodeSequenceWriterFactory.InputRRField),
tuple.getFieldStart(NodeSequenceWriterFactory.InputRRField));
- node.getKmer().setNewReference(
+ node.getKmer().setAsReference(
Marshal.getInt(tuple.getFieldData(NodeSequenceWriterFactory.InputCountOfKmerField),
tuple.getFieldStart(NodeSequenceWriterFactory.InputCountOfKmerField)),
tuple.getFieldData(NodeSequenceWriterFactory.InputKmerBytesField),
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenCheckReader.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenCheckReader.java
index c3ec3c7..07d16f8 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenCheckReader.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenCheckReader.java
@@ -89,7 +89,7 @@
.getFieldLength(ReadsKeyValueParserFactory.OutputKmerField)) {
throw new IllegalArgumentException("Not enough kmer bytes");
}
- kmer.setNewReference(
+ kmer.setAsReference(
tuple.getFieldData(ReadsKeyValueParserFactory.OutputKmerField),
tuple.getFieldStart(ReadsKeyValueParserFactory.OutputKmerField));
pos.setNewReference(tuple.getFieldData(ReadsKeyValueParserFactory.OutputPosition),
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenGroupbyReadID.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenGroupbyReadID.java
index 559060a..fa5360c 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenGroupbyReadID.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenGroupbyReadID.java
@@ -121,7 +121,7 @@
throw new IllegalArgumentException("kmerlength is invalid");
}
fieldOffset += 4;
- kmer.setNewReference(buffer, fieldOffset);
+ kmer.setAsReference(buffer, fieldOffset);
fieldOffset += kmer.getLength();
kmerString = kmer.toString();
}
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenMapKmerToRead.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenMapKmerToRead.java
index e9aede5..09b1680 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenMapKmerToRead.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/job/JobGenMapKmerToRead.java
@@ -93,7 +93,7 @@
.getFieldLength(MapKmerPositionToReadOperator.OutputKmerField)) {
throw new IllegalArgumentException("Not enough kmer bytes");
}
- kmer.setNewReference(
+ kmer.setAsReference(
tuple.getFieldData(MapKmerPositionToReadOperator.OutputKmerField),
tuple.getFieldStart(MapKmerPositionToReadOperator.OutputKmerField));
kmerString = kmer.toString();
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/ReadsKeyValueParserFactory.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/ReadsKeyValueParserFactory.java
index 1b123f1..22b2ae7 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/ReadsKeyValueParserFactory.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/dataflow/ReadsKeyValueParserFactory.java
@@ -169,7 +169,7 @@
}
public void setNextKmer(byte nextChar){
- nextForwardKmer.set(curForwardKmer);
+ nextForwardKmer.setAsCopy(curForwardKmer);
nextForwardKmer.shiftKmerWithNextChar(nextChar);
nextReverseKmer.setByReadReverse(nextForwardKmer.toString().getBytes(), nextForwardKmer.getOffset());
nextKmerDir = nextForwardKmer.compareTo(nextReverseKmer) <= 0 ? KmerDir.FORWARD : KmerDir.REVERSE;
@@ -177,14 +177,14 @@
public void setPreKmerByOldCurKmer(){
preKmerDir = curKmerDir;
- preForwardKmer.set(curForwardKmer);
- preReverseKmer.set(curReverseKmer);
+ preForwardKmer.setAsCopy(curForwardKmer);
+ preReverseKmer.setAsCopy(curReverseKmer);
}
public void setCurKmerByOldNextKmer(){
curKmerDir = nextKmerDir;
- curForwardKmer.set(nextForwardKmer);
- curReverseKmer.set(nextReverseKmer);
+ curForwardKmer.setAsCopy(nextForwardKmer);
+ curReverseKmer.setAsCopy(nextReverseKmer);
}
public void writeToFrame(IFrameWriter writer) {
diff --git a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/job/JobGenCheckReader.java b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/job/JobGenCheckReader.java
index 6026ac1..6d64cfd 100644
--- a/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/job/JobGenCheckReader.java
+++ b/genomix/genomix-hyracks/src/main/java/edu/uci/ics/genomix/hyracks/newgraph/job/JobGenCheckReader.java
@@ -88,10 +88,10 @@
throw new IllegalArgumentException("Not enough kmer bytes");
}
//kemr
- kmer.setNewReference(
+ kmer.setAsReference(
tuple.getFieldData(ReadsKeyValueParserFactory.OutputKmerField),
tuple.getFieldStart(ReadsKeyValueParserFactory.OutputKmerField));
- kmerList.setNewReference(tuple.getFieldLength(ReadsKeyValueParserFactory.OutputNodeIdField),
+ kmerList.setAsReference(tuple.getFieldLength(ReadsKeyValueParserFactory.OutputNodeIdField),
tuple.getFieldData(ReadsKeyValueParserFactory.OutputNodeIdField),
tuple.getFieldStart(ReadsKeyValueParserFactory.OutputNodeIdField));
// //nodeId
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/GraphCleanInputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/GraphCleanInputFormat.java
index e36e344..e8a72ce 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/GraphCleanInputFormat.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/GraphCleanInputFormat.java
@@ -60,7 +60,7 @@
/**
* set the src vertex id
*/
- vertexId.set(getRecordReader().getCurrentKey());
+ vertexId.setAsCopy(getRecordReader().getCurrentKey());
vertex.setVertexId(vertexId);
/**
* set the vertex value
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/InitialGraphCleanInputFormat.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/InitialGraphCleanInputFormat.java
index 0d685de..5c8f9c2 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/InitialGraphCleanInputFormat.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/format/InitialGraphCleanInputFormat.java
@@ -64,7 +64,7 @@
/**
* set the src vertex id
*/
- vertexId.set(getRecordReader().getCurrentKey());
+ vertexId.setAsCopy(getRecordReader().getCurrentKey());
vertex.setVertexId(vertexId);
/**
* set the vertex value
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MergeBubbleMessageWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MergeBubbleMessageWritable.java
index c3b4710..c3e02a0 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MergeBubbleMessageWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/MergeBubbleMessageWritable.java
@@ -42,7 +42,7 @@
}
if (chainVertexId != null) {
checkMessage |= CheckMessage.CHAIN;
- this.chainVertexId.set(msg.getChainVertexId());
+ this.chainVertexId.setAsCopy(msg.getChainVertexId());
}
if (neighberNode != null) {
checkMessage |= CheckMessage.NEIGHBER;
@@ -63,7 +63,7 @@
}
if (chainVertexId != null) {
checkMessage |= CheckMessage.CHAIN;
- this.chainVertexId.set(chainVertexId);
+ this.chainVertexId.setAsCopy(chainVertexId);
}
if (neighberNode != null) {
checkMessage |= CheckMessage.NEIGHBER;
@@ -101,7 +101,7 @@
public void setChainVertexId(KmerBytesWritable chainVertexId) {
if (chainVertexId != null) {
checkMessage |= CheckMessage.CHAIN;
- this.chainVertexId.set(chainVertexId);
+ this.chainVertexId.setAsCopy(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 1c5f325..ea91144 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
@@ -49,11 +49,11 @@
checkMessage = 0;
if (sourceVertexId != null) {
checkMessage |= CheckMessage.SOURCE;
- this.sourceVertexId.set(msg.getSourceVertexId());
+ this.sourceVertexId.setAsCopy(msg.getSourceVertexId());
}
if (kmer != null) {
checkMessage |= CheckMessage.CHAIN;
- this.kmer.set(msg.getKmer());
+ this.kmer.setAsCopy(msg.getKmer());
}
if (neighberNode != null) {
checkMessage |= CheckMessage.NEIGHBER;
@@ -68,11 +68,11 @@
checkMessage = 0;
if (sourceVertexId != null) {
checkMessage |= CheckMessage.SOURCE;
- this.sourceVertexId.set(sourceVertexId);
+ this.sourceVertexId.setAsCopy(sourceVertexId);
}
if (chainVertexId != null) {
checkMessage |= CheckMessage.CHAIN;
- this.kmer.set(chainVertexId);
+ this.kmer.setAsCopy(chainVertexId);
}
if (neighberNode != null) {
checkMessage |= CheckMessage.NEIGHBER;
@@ -102,7 +102,7 @@
public void setSourceVertexId(KmerBytesWritable sourceVertexId) {
if (sourceVertexId != null) {
checkMessage |= CheckMessage.SOURCE;
- this.sourceVertexId.set(sourceVertexId);
+ this.sourceVertexId.setAsCopy(sourceVertexId);
}
}
@@ -113,7 +113,7 @@
public void setChainVertexId(KmerBytesWritable chainVertexId) {
if (chainVertexId != null) {
checkMessage |= CheckMessage.CHAIN;
- this.kmer.set(chainVertexId);
+ this.kmer.setAsCopy(chainVertexId);
}
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
index 5d06234..d472fd1 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/io/VertexValueWritable.java
@@ -74,7 +74,7 @@
this.outgoingList.setForwardList(forwardForwardList);
this.outgoingList.setReverseList(forwardReverseList);
this.state = state;
- this.kmer.set(kmer);
+ this.kmer.setAsCopy(kmer);
}
public void set(VertexValueWritable value) {
@@ -157,7 +157,7 @@
}
public void setKmer(KmerBytesWritable kmer) {
- this.kmer.set(kmer);
+ this.kmer.setAsCopy(kmer);
}
public KmerBytesWritable getMergeDest() {
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/LogAlgorithmLogFormatter.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/LogAlgorithmLogFormatter.java
index 5f6440f..27e2683 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/LogAlgorithmLogFormatter.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/LogAlgorithmLogFormatter.java
@@ -32,8 +32,8 @@
public void set(long step, KmerBytesWritable sourceVertexId, KmerBytesWritable destVertexId,
MessageWritable msg, byte state) {
this.step = step;
- this.sourceVertexId.set(sourceVertexId);
- this.destVertexId.set(destVertexId);
+ this.sourceVertexId.setAsCopy(sourceVertexId);
+ this.destVertexId.setAsCopy(destVertexId);
this.msg = msg;
this.state = state;
this.operation = 0;
@@ -42,15 +42,15 @@
public void setMergeChain(long step, KmerBytesWritable sourceVertexId, KmerBytesWritable mergeChain) {
this.reset();
this.step = step;
- this.sourceVertexId.set(sourceVertexId);
- this.mergeChain.set(mergeChain);
+ this.sourceVertexId.setAsCopy(sourceVertexId);
+ this.mergeChain.setAsCopy(mergeChain);
this.operation = 2;
}
public void setVotoToHalt(long step, KmerBytesWritable sourceVertexId) {
this.reset();
this.step = step;
- this.sourceVertexId.set(sourceVertexId);
+ this.sourceVertexId.setAsCopy(sourceVertexId);
this.operation = 3;
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/NaiveAlgorithmLogFormatter.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/NaiveAlgorithmLogFormatter.java
index 4a5850a..6b23074 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/NaiveAlgorithmLogFormatter.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/log/NaiveAlgorithmLogFormatter.java
@@ -15,8 +15,8 @@
public void set(long step, KmerBytesWritable sourceVertexId, KmerBytesWritable destVertexId) {
this.step = step;
- this.sourceVertexId.set(sourceVertexId);
- this.destVertexId.set(destVertexId);
+ this.sourceVertexId.setAsCopy(sourceVertexId);
+ this.destVertexId.setAsCopy(destVertexId);
}
public String format(LogRecord record) {
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicPathMergeVertex.java
index 937fa42..9acba97 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/BasicPathMergeVertex.java
@@ -128,12 +128,12 @@
public void sendMsgToAllNextNodes(VertexValueWritable value) {
posIterator = value.getFFList().iterator(); // FFList
while(posIterator.hasNext()){
- destVertexId.set(posIterator.next());
+ destVertexId.setAsCopy(posIterator.next());
sendMsg(destVertexId, outgoingMsg);
}
posIterator = value.getFRList().iterator(); // FRList
while(posIterator.hasNext()){
- destVertexId.set(posIterator.next());
+ destVertexId.setAsCopy(posIterator.next());
sendMsg(destVertexId, outgoingMsg);
}
}
@@ -144,12 +144,12 @@
public void sendMsgToAllPreviousNodes(VertexValueWritable value) {
posIterator = value.getRFList().iterator(); // RFList
while(posIterator.hasNext()){
- destVertexId.set(posIterator.next());
+ destVertexId.setAsCopy(posIterator.next());
sendMsg(destVertexId, outgoingMsg);
}
posIterator = value.getRRList().iterator(); // RRList
while(posIterator.hasNext()){
- destVertexId.set(posIterator.next());
+ destVertexId.setAsCopy(posIterator.next());
sendMsg(destVertexId, outgoingMsg);
}
}
@@ -160,22 +160,22 @@
public void sendMsgToAllNeighborNodes(VertexValueWritable value){
posIterator = value.getFFList().iterator(); // FFList
while(posIterator.hasNext()){
- destVertexId.set(posIterator.next());
+ destVertexId.setAsCopy(posIterator.next());
sendMsg(destVertexId, outgoingMsg);
}
posIterator = value.getFRList().iterator(); // FRList
while(posIterator.hasNext()){
- destVertexId.set(posIterator.next());
+ destVertexId.setAsCopy(posIterator.next());
sendMsg(destVertexId, outgoingMsg);
}
posIterator = value.getFFList().iterator(); // FFList
while(posIterator.hasNext()){
- destVertexId.set(posIterator.next());
+ destVertexId.setAsCopy(posIterator.next());
sendMsg(destVertexId, outgoingMsg);
}
posIterator = value.getFRList().iterator(); // FRList
while(posIterator.hasNext()){
- destVertexId.set(posIterator.next());
+ destVertexId.setAsCopy(posIterator.next());
sendMsg(destVertexId, outgoingMsg);
}
}
@@ -188,14 +188,14 @@
while(posIterator.hasNext()){
outgoingMsg.setFlag(AdjMessage.FROMFF);
outgoingMsg.setSourceVertexId(getVertexId());
- destVertexId.set(posIterator.next());
+ destVertexId.setAsCopy(posIterator.next());
sendMsg(destVertexId, outgoingMsg);
}
posIterator = value.getFRList().iterator(); // FRList
while(posIterator.hasNext()){
outgoingMsg.setFlag(AdjMessage.FROMFR);
outgoingMsg.setSourceVertexId(getVertexId());
- destVertexId.set(posIterator.next());
+ destVertexId.setAsCopy(posIterator.next());
sendMsg(destVertexId, outgoingMsg);
}
}
@@ -208,14 +208,14 @@
while(posIterator.hasNext()){
outgoingMsg.setFlag(AdjMessage.FROMRF);
outgoingMsg.setSourceVertexId(getVertexId());
- destVertexId.set(posIterator.next());
+ destVertexId.setAsCopy(posIterator.next());
sendMsg(destVertexId, outgoingMsg);
}
posIterator = value.getRRList().iterator(); // RRList
while(posIterator.hasNext()){
outgoingMsg.setFlag(AdjMessage.FROMRR);
outgoingMsg.setSourceVertexId(getVertexId());
- destVertexId.set(posIterator.next());
+ destVertexId.setAsCopy(posIterator.next());
sendMsg(destVertexId, outgoingMsg);
}
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java
index 7185616..feb22aa 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/LogAlgorithmForPathMergeVertex.java
@@ -67,7 +67,7 @@
//send wantToMerge to next
tempPostition = getNextDestVertexIdAndSetFlag(getVertexValue());
if(tempPostition != null){
- destVertexId.set(tempPostition);
+ destVertexId.setAsCopy(tempPostition);
outgoingMsg.setFlag(outFlag);
outgoingMsg.setSourceVertexId(getVertexId());
sendMsg(destVertexId, outgoingMsg);
@@ -76,7 +76,7 @@
////send wantToMerge to prev
tempPostition = getPreDestVertexIdAndSetFlag(getVertexValue());
if(tempPostition != null){
- destVertexId.set(tempPostition);
+ destVertexId.setAsCopy(tempPostition);
outgoingMsg.setFlag(outFlag);
outgoingMsg.setSourceVertexId(getVertexId());
sendMsg(destVertexId, outgoingMsg);
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/NaiveAlgorithmForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/NaiveAlgorithmForPathMergeVertex.java
index a65f556..ac43c62 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/NaiveAlgorithmForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/NaiveAlgorithmForPathMergeVertex.java
@@ -184,7 +184,7 @@
*/
public void mergeChainVertex() {
//merge chain
- lastKmer.set(kmerFactory.getLastKmerFromChain(incomingMsg.getLengthOfChain() - kmerSize + 1,
+ lastKmer.setAsCopy(kmerFactory.getLastKmerFromChain(incomingMsg.getLengthOfChain() - kmerSize + 1,
incomingMsg.getKmer()));
getVertexValue().setKmer(kmerFactory.mergeTwoKmer(getVertexValue().getKmer(), lastKmer));
getVertexValue().setOutgoingList(incomingMsg.getNeighberNode());
@@ -225,7 +225,7 @@
outgoingMsg.setChainVertexId(getVertexValue().getKmer());
if (getVertexValue().getState() == State.IS_HEAD)//is_tail
outgoingMsg.setFlag(Message.STOP);
- destVertexId.set(incomingMsg.getSourceVertexId());
+ destVertexId.setAsCopy(incomingMsg.getSourceVertexId());
sendMsg(destVertexId, outgoingMsg);
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P3ForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P3ForPathMergeVertex.java
index f2bb3db..fd3a1db 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P3ForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P3ForPathMergeVertex.java
@@ -230,7 +230,7 @@
* merge chain vertex
*/
public void mergeChainVertex(){
- lastKmer.set(kmerFactory.getLastKmerFromChain(incomingMsg.getLengthOfChain() - kmerSize + 1,
+ lastKmer.setAsCopy(kmerFactory.getLastKmerFromChain(incomingMsg.getLengthOfChain() - kmerSize + 1,
incomingMsg.getKmer()));
getVertexValue().setKmer(
kmerFactory.mergeTwoKmer(getVertexValue().getKmer(),
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P4ForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P4ForPathMergeVertex.java
index 94428ca..e6c5f34 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P4ForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P4ForPathMergeVertex.java
@@ -111,12 +111,12 @@
*/
protected boolean setNextInfo(VertexValueWritable value) {
if (value.getFFList().getCountOfPosition() > 0) {
- nextKmer.set(value.getFFList().getPosition(0));
+ nextKmer.setAsCopy(value.getFFList().getPosition(0));
nextHead = isNodeRandomHead(nextKmer);
return true;
}
if (value.getFRList().getCountOfPosition() > 0) {
- nextKmer.set(value.getFRList().getPosition(0));
+ nextKmer.setAsCopy(value.getFRList().getPosition(0));
nextHead = isNodeRandomHead(nextKmer);
return true;
}
@@ -128,12 +128,12 @@
*/
protected boolean setPrevInfo(VertexValueWritable value) {
if (value.getRRList().getCountOfPosition() > 0) {
- prevKmer.set(value.getRRList().getPosition(0));
+ prevKmer.setAsCopy(value.getRRList().getPosition(0));
prevHead = isNodeRandomHead(prevKmer);
return true;
}
if (value.getRFList().getCountOfPosition() > 0) {
- prevKmer.set(value.getRFList().getPosition(0));
+ prevKmer.setAsCopy(value.getRFList().getPosition(0));
prevHead = isNodeRandomHead(prevKmer);
return true;
}
@@ -156,7 +156,7 @@
setStateAsNoMerge();
// only PATH vertices are present. Find the ID's for my neighbors
- curKmer.set(getVertexId());
+ curKmer.setAsCopy(getVertexId());
curHead = isNodeRandomHead(curKmer);
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P5ForPathMergeVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P5ForPathMergeVertex.java
index 8a2a301..7f8a832 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P5ForPathMergeVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/pathmerge/P5ForPathMergeVertex.java
@@ -113,12 +113,12 @@
*/
protected boolean setNextInfo(VertexValueWritable value) {
if (value.getFFList().getCountOfPosition() > 0) {
- nextID.set(value.getFFList().getPosition(0));
+ nextID.setAsCopy(value.getFFList().getPosition(0));
nextHead = isNodeRandomHead(nextID);
return true;
}
if (value.getFRList().getCountOfPosition() > 0) {
- nextID.set(value.getFRList().getPosition(0));
+ nextID.setAsCopy(value.getFRList().getPosition(0));
nextHead = isNodeRandomHead(nextID);
return true;
}
@@ -130,12 +130,12 @@
*/
protected boolean setPrevInfo(VertexValueWritable value) {
if (value.getRRList().getCountOfPosition() > 0) {
- prevID.set(value.getRRList().getPosition(0));
+ prevID.setAsCopy(value.getRRList().getPosition(0));
prevHead = isNodeRandomHead(prevID);
return true;
}
if (value.getRFList().getCountOfPosition() > 0) {
- prevID.set(value.getRFList().getPosition(0));
+ prevID.setAsCopy(value.getRFList().getPosition(0));
prevHead = isNodeRandomHead(prevID);
return true;
}
diff --git a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipRemoveVertex.java b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipRemoveVertex.java
index 7141ae7..9b83d19 100644
--- a/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipRemoveVertex.java
+++ b/genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/tipremove/TipRemoveVertex.java
@@ -71,7 +71,7 @@
else if(getVertexValue().getFRList().getCountOfPosition() > 0)
outgoingMsg.setFlag(AdjMessage.FROMFR);
outgoingMsg.setSourceVertexId(getVertexId());
- destVertexId.set(getNextDestVertexId(getVertexValue()));
+ destVertexId.setAsCopy(getNextDestVertexId(getVertexValue()));
sendMsg(destVertexId, outgoingMsg);
deleteVertex(getVertexId());
}
@@ -83,7 +83,7 @@
else if(getVertexValue().getRRList().getCountOfPosition() > 0)
outgoingMsg.setFlag(AdjMessage.FROMRR);
outgoingMsg.setSourceVertexId(getVertexId());
- destVertexId.set(getPreDestVertexId(getVertexValue()));
+ destVertexId.setAsCopy(getPreDestVertexId(getVertexValue()));
sendMsg(destVertexId, outgoingMsg);
deleteVertex(getVertexId());
}