Updated Genomix
git-svn-id: https://hyracks.googlecode.com/svn/branches/fullstack_genomix@2947 123451ca-8445-de46-9d55-352943316053
diff --git a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/normalizers/VLongNormalizedKeyComputerFactory.java b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/normalizers/VLongNormalizedKeyComputerFactory.java
index f8134dc..969431c 100644
--- a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/normalizers/VLongNormalizedKeyComputerFactory.java
+++ b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/normalizers/VLongNormalizedKeyComputerFactory.java
@@ -21,7 +21,7 @@
long r = 0;
for (int i = 0; i < n; i++) {
r <<= 8;
- r += (long) (bytes[offset + 1] & 0xff);
+ r += (long) (bytes[offset + i + 1] & 0xff);
}
return r;
diff --git a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/std/primitive/VLongPointable.java b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/std/primitive/VLongPointable.java
index b7f9c25..ffa6fc6 100644
--- a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/std/primitive/VLongPointable.java
+++ b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/data/std/primitive/VLongPointable.java
@@ -85,13 +85,12 @@
int n = this.bytes[be];
int l = (int) Math.ceil(n / 4);
- for (int i = 0; i <= l; i++) {
+ for (int i = l; i > 0; i--) {
if (this.bytes[be + i] < bytes[start + i]) {
return -1;
} else if (this.bytes[be + i] > bytes[start + i]) {
return 1;
}
-
}
return 0;
}
diff --git a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/aggregators/DistributedMergeLmerAggregateFactory.java b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/aggregators/DistributedMergeLmerAggregateFactory.java
index a16dcea..d7ab7f7 100644
--- a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/aggregators/DistributedMergeLmerAggregateFactory.java
+++ b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/aggregators/DistributedMergeLmerAggregateFactory.java
@@ -21,7 +21,7 @@
public class DistributedMergeLmerAggregateFactory implements
IAggregatorDescriptorFactory {
private static final long serialVersionUID = 1L;
- private static final int max = 255;
+ private static final int max = 127;
public DistributedMergeLmerAggregateFactory() {
}
diff --git a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/aggregators/MergeKmerAggregateFactory.java b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/aggregators/MergeKmerAggregateFactory.java
index b2f94dc..76b04d1 100644
--- a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/aggregators/MergeKmerAggregateFactory.java
+++ b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/dataflow/aggregators/MergeKmerAggregateFactory.java
@@ -20,7 +20,7 @@
*/
public class MergeKmerAggregateFactory implements IAggregatorDescriptorFactory {
private static final long serialVersionUID = 1L;
- private static final int max = 255;
+ private static final int max = 127;
public MergeKmerAggregateFactory() {
}
@@ -100,6 +100,9 @@
+ stateAccessor.getFieldSlotsLength() + statefieldStart;
count += 1;
+ if(count > max){
+ count = max;
+ }
byte[] data = stateAccessor.getBuffer().array();
diff --git a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/job/JobGenBrujinGraph.java b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/job/JobGenBrujinGraph.java
index a67f42f..d6c72da 100644
--- a/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/job/JobGenBrujinGraph.java
+++ b/genomix/genomix-core/src/main/java/edu/uci/ics/genomix/job/JobGenBrujinGraph.java
@@ -123,7 +123,7 @@
recordSizeInBytes,
tableSize,
new IBinaryComparatorFactory[] { PointableBinaryComparatorFactory
- .of(LongPointable.FACTORY) },
+ .of(VLongPointable.FACTORY) },
new IBinaryHashFunctionFamily[] { new VLongBinaryHashFunctionFamily() },
hashfuncStartLevel,
new VLongNormalizedKeyComputerFactory(),
@@ -157,7 +157,7 @@
jobSpec,
keyFields,
new IBinaryComparatorFactory[] { PointableBinaryComparatorFactory
- .of(LongPointable.FACTORY) },
+ .of(VLongPointable.FACTORY) },
new DistributedMergeLmerAggregateFactory(), outputRec);
break;
case HYBRIDHASH: