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Description: changing some imports linked to fastutil classes
Goby 3.3.1 was written for an old fastutil library.
Author: Pierre Gruet <pgt@debian.org>
Forwarded: not-needed
Last-Update: 2021-08-04
--- a/goby-distribution/src/main/java/org/campagnelab/goby/alignments/ConcatSortedAlignmentReader.java
+++ b/goby-distribution/src/main/java/org/campagnelab/goby/alignments/ConcatSortedAlignmentReader.java
@@ -20,7 +20,7 @@
package org.campagnelab.goby.alignments;
-import it.unimi.dsi.fastutil.AbstractPriorityQueue;
+import it.unimi.dsi.fastutil.PriorityQueue;
import it.unimi.dsi.fastutil.objects.ObjectArrayPriorityQueue;
import it.unimi.dsi.fastutil.objects.ObjectHeapPriorityQueue;
import org.apache.commons.logging.Log;
@@ -40,7 +40,7 @@
*/
public class ConcatSortedAlignmentReader extends ConcatAlignmentReader {
- AbstractPriorityQueue<Bucket> entryHeap;
+ PriorityQueue<Bucket> entryHeap;
private static AlignmentPositionComparator comparator = new AlignmentPositionComparator();
private boolean[] nextLoadedForReader;
private Bucket[] buckets;
--- a/goby-distribution/src/main/java/org/campagnelab/goby/alignments/processors/LocalSortProcessor.java
+++ b/goby-distribution/src/main/java/org/campagnelab/goby/alignments/processors/LocalSortProcessor.java
@@ -21,7 +21,7 @@
import edu.cornell.med.icb.identifier.IndexedIdentifier;
import org.campagnelab.goby.alignments.Alignments;
import org.campagnelab.goby.reads.RandomAccessSequenceInterface;
-import it.unimi.dsi.fastutil.AbstractPriorityQueue;
+import it.unimi.dsi.fastutil.PriorityQueue;
import it.unimi.dsi.fastutil.objects.ObjectHeapPriorityQueue;
import java.io.IOException;
@@ -38,7 +38,7 @@
* Time: 10:49 AM
*/
public class LocalSortProcessor implements AlignmentProcessorInterface {
- AbstractPriorityQueue<Alignments.AlignmentEntry> entryHeap;
+ PriorityQueue<Alignments.AlignmentEntry> entryHeap;
AlignmentProcessorInterface delegate;
/**
* We store at most alignments for 30 consecutive genomic positions. 30 is chosen because it is much larger than
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