Code review: refactor offset name
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 c6360a9..7fed5c7 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
@@ -133,17 +133,17 @@
*
* @param newData
* : byte array to copy (should have a header)
- * @param offset
+ * @param blockOffset
*/
- public void setAsReference(byte[] newData, int offset) {
+ public void setAsReference(byte[] newData, int blockOffset) {
this.bytes = newData;
- this.offset = offset + HEADER_SIZE;
- int kRequested = Marshal.getInt(newData, offset);
+ this.offset = blockOffset + HEADER_SIZE;
+ int kRequested = Marshal.getInt(newData, blockOffset);
int bytesRequested = KmerUtil.getByteNumFromK(kRequested) + HEADER_SIZE;
- if (newData.length - offset < bytesRequested) {
+ if (newData.length - blockOffset < bytesRequested) {
throw new IllegalArgumentException("Requested " + bytesRequested
+ " bytes (k=" + kRequested + ") but buffer has only "
- + (newData.length - offset) + " bytes");
+ + (newData.length - blockOffset) + " bytes");
}
setKmerLength(kRequested);
}
@@ -214,6 +214,9 @@
Marshal.putInt(lettersInKmer, bytes, offset - HEADER_SIZE);
}
+ /**
+ * write the entire byte array including the header
+ */
@Override
public void write(DataOutput out) throws IOException {
out.write(bytes, offset - HEADER_SIZE, bytesUsed + HEADER_SIZE);