Fixed synchr. problem.

pfeiferd · Dec 20, 2024 · 69cc745 · 69cc745
1 parent 1baa13c
commit 69cc745
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Showing 2 changed files with 12 additions and 1 deletion.
diff --git a/src/main/java/org/metagene/genestrip/goals/refseq/DBGoal.java b/src/main/java/org/metagene/genestrip/goals/refseq/DBGoal.java
@@ -145,7 +145,10 @@ protected void doMakeThis() {
 				}
 			}
 			store.fix();
-			set(new Database((KMerSortedArray<String>) store, wrapper.getTaxTree()));
+			set(new Database(store, wrapper.getTaxTree()));
+			if (getLogger().isTraceEnabled()) {
+				getLogger().trace("KMers moved: " + store.getKMersMoved());
+			}
 		} catch (IOException e) {
 			throw new RuntimeException(e);
 		} finally {

diff --git a/src/main/java/org/metagene/genestrip/store/KMerSortedArray.java b/src/main/java/org/metagene/genestrip/store/KMerSortedArray.java
@@ -74,6 +74,8 @@ public class KMerSortedArray<V extends Serializable> implements KMerStore<V> {
 	private boolean useFilter;
 	private Object2LongMap<V> kmerPersTaxid;
 
+	private transient long kmersMoved;
+
 	public KMerSortedArray(int k, double fpp, List<V> initialValues, boolean enforceLarge) {
 		this(k, fpp, initialValues, enforceLarge, new MurmurCGATBloomFilter(k, fpp));
 	}
@@ -100,6 +102,11 @@ protected KMerSortedArray(int k, double fpp, List<V> initialValues, boolean enfo
 		this.filter = filter;
 		this.useFilter = filter != null;
 		this.kmerPersTaxid = null;
+		this.kmersMoved = 0;
+	}
+
+	public long getKMersMoved() {
+		return kmersMoved;
 	}
 
 	@SuppressWarnings("unchecked")
@@ -368,6 +375,7 @@ public boolean update(long kmer, UpdateValueProvider<V> provider) {
 				// This is important in the multi-threading context:
 				synchronized (valueMap) {
 					index = getAddValueIndex(newValue);
+					kmersMoved++;
 				}
 				if (largeKmers != null) {
 					BigArrays.set(largeValueIndexes, pos, index);