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Replace BitVector by BitSet and remove legacy library #258

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Merged
mbastian merged 4 commits into from
Oct 26, 2025
Merged

Replace BitVector by BitSet and remove legacy library #258

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6456df4
Replace BitVector by BitSet and remove legacy library
mbastian Oct 25, 2025
4101284
Performance optimisation with bitset operations
mbastian Oct 26, 2025
805f588
Update README
mbastian Oct 26, 2025
98364f1
Add some defensive checks when elements are removed
mbastian Oct 26, 2025
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -53,7 +53,7 @@ compile 'org.gephi:graphstore:0.8.0'

## Dependencies

GraphStore is built for JRE 17+ and depends on FastUtil and Colt.
GraphStore is built for JRE 17+ and depends on FastUtil.

For a complete list of dependencies, consult the `pom.xml` file.

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5 changes: 0 additions & 5 deletions pom.xml
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Expand Up @@ -67,11 +67,6 @@
<artifactId>fastutil</artifactId>
<version>8.5.16</version>
</dependency>
<dependency>
<groupId>colt</groupId>
<artifactId>colt</artifactId>
<version>1.2.0</version>
</dependency>
</dependencies>

<build>
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21 changes: 6 additions & 15 deletions src/main/java/org/gephi/graph/impl/ColumnObserverImpl.java
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Expand Up @@ -15,8 +15,7 @@
*/
package org.gephi.graph.impl;

import cern.colt.bitvector.BitVector;
import cern.colt.bitvector.QuickBitVector;
import java.util.BitSet;
import it.unimi.dsi.fastutil.objects.ObjectArrayList;
import it.unimi.dsi.fastutil.objects.ObjectList;
import it.unimi.dsi.fastutil.objects.ObjectLists;
Expand All @@ -40,7 +39,7 @@ public class ColumnObserverImpl implements ColumnObserver {
protected boolean destroyed;
// Config
protected final boolean withDiff;
protected BitVector bitVector;
protected BitSet bitVector;
// Cache
protected ColumnDiffImpl columnDiff;

Expand Down Expand Up @@ -109,7 +108,7 @@ private void refreshDiff() {
boolean node = AttributeUtils.isNodeColumn(column);
columnDiff = node ? new NodeColumnDiffImpl() : new EdgeColumnDiffImpl();

int size = bitVector.size();
int size = bitVector.length();

for (int i = 0; i < size; i++) {
boolean t = bitVector.get(i);
Expand Down Expand Up @@ -179,19 +178,11 @@ public EdgeIterable getTouchedElements() {
private void ensureVectorSize(ElementImpl element) {
int sid = element.getStoreId();
if (bitVector == null) {
bitVector = new BitVector(sid + 1);
} else if (sid >= bitVector.size()) {
int newSize = Math.min(Math
int initialSize = Math.min(Math
.max(sid + 1, (int) (sid * GraphStoreConfiguration.COLUMNDIFF_GROWING_FACTOR)), Integer.MAX_VALUE);
bitVector = growBitVector(bitVector, newSize);
bitVector = new BitSet(initialSize);
}
}

private BitVector growBitVector(BitVector bitVector, int size) {
long[] elements = bitVector.elements();
long[] newElements = QuickBitVector.makeBitVector(size, 1);
System.arraycopy(elements, 0, newElements, 0, elements.length);
return new BitVector(newElements, size);
// BitSet grows automatically when setting bits, no need to manually grow
}

private void readLock() {
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