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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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5 changes: 0 additions & 5 deletions pom.xml
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Original file line number Diff line number Diff line change
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>
Expand Down
21 changes: 6 additions & 15 deletions src/main/java/org/gephi/graph/impl/ColumnObserverImpl.java
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Original file line number Diff line number Diff line change
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() {
Expand Down
110 changes: 57 additions & 53 deletions src/main/java/org/gephi/graph/impl/GraphViewImpl.java
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Original file line number Diff line number Diff line change
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.ints.IntOpenHashSet;
import java.util.ArrayList;
import java.util.Arrays;
Expand All @@ -40,8 +39,8 @@ public class GraphViewImpl implements GraphView {
protected final boolean nodeView;
protected final boolean edgeView;
protected final GraphAttributesImpl attributes;
protected BitVector nodeBitVector;
protected BitVector edgeBitVector;
protected BitSet nodeBitVector;
protected BitSet edgeBitVector;
protected int storeId;
// Version
protected final GraphVersion version;
Expand All @@ -64,11 +63,11 @@ public GraphViewImpl(final GraphStore store, boolean nodes, boolean edges) {
this.edgeView = edges;
this.attributes = new GraphAttributesImpl();
if (nodes) {
this.nodeBitVector = new BitVector(store.nodeStore.maxStoreId());
this.nodeBitVector = new BitSet(store.nodeStore.maxStoreId());
} else {
this.nodeBitVector = null;
}
this.edgeBitVector = new BitVector(store.edgeStore.maxStoreId());
this.edgeBitVector = new BitSet(store.edgeStore.maxStoreId());
this.typeCounts = new int[GraphStoreConfiguration.VIEW_DEFAULT_TYPE_COUNT];
this.mutualEdgeTypeCounts = new int[GraphStoreConfiguration.VIEW_DEFAULT_TYPE_COUNT];

Expand All @@ -85,13 +84,13 @@ public GraphViewImpl(final GraphViewImpl view, boolean nodes, boolean edges) {
this.edgeView = edges;
this.attributes = new GraphAttributesImpl();
if (nodes) {
this.nodeBitVector = view.nodeBitVector.copy();
this.nodeBitVector = (BitSet) view.nodeBitVector.clone();
this.nodeCount = view.nodeCount;
} else {
this.nodeBitVector = null;
}
this.edgeCount = view.edgeCount;
this.edgeBitVector = view.edgeBitVector.copy();
this.edgeBitVector = (BitSet) view.edgeBitVector.clone();
this.typeCounts = new int[view.typeCounts.length];
System.arraycopy(view.typeCounts, 0, typeCounts, 0, view.typeCounts.length);
this.mutualEdgeTypeCounts = new int[view.mutualEdgeTypeCounts.length];
Expand Down Expand Up @@ -275,7 +274,7 @@ public boolean retainNodes(final Collection<? extends Node> c) {
}

boolean changed = false;
int nodeSize = nodeBitVector.size();
int nodeSize = graphStore.nodeStore.maxStoreId();
for (int i = 0; i < nodeSize; i++) {
boolean t = nodeBitVector.get(i);
if (t && !set.contains(i)) {
Expand Down Expand Up @@ -303,7 +302,7 @@ public boolean retainEdges(final Collection<? extends Edge> c) {
}

boolean changed = false;
int edgeSize = edgeBitVector.size();
int edgeSize = graphStore.edgeStore.maxStoreId();
for (int i = 0; i < edgeSize; i++) {
boolean t = edgeBitVector.get(i);
if (t && !set.contains(i)) {
Expand Down Expand Up @@ -414,15 +413,15 @@ public void clearEdges() {
public void fill() {
if (nodeView) {
if (nodeCount > 0) {
nodeBitVector = new BitVector(graphStore.nodeStore.maxStoreId());
// nodeBitVector = new BitSet(graphStore.nodeStore.maxStoreId());
}
nodeBitVector.not();
nodeBitVector.set(0, graphStore.nodeStore.maxStoreId(), true);
this.nodeCount = graphStore.nodeStore.size();
}
if (edgeCount > 0) {
edgeBitVector = new BitVector(graphStore.edgeStore.maxStoreId());
// edgeBitVector = new BitSet(graphStore.edgeStore.maxStoreId());
}
edgeBitVector.not();
edgeBitVector.set(0, graphStore.edgeStore.maxStoreId());

this.edgeCount = graphStore.edgeStore.size();
int typeLength = graphStore.edgeStore.longDictionary.length;
Expand Down Expand Up @@ -474,11 +473,11 @@ public boolean containsEdge(final Edge edge) {
}

public void intersection(final GraphViewImpl otherView) {
BitVector nodeOtherBitVector = otherView.nodeBitVector;
BitVector edgeOtherBitVector = otherView.edgeBitVector;
BitSet nodeOtherBitVector = otherView.nodeBitVector;
BitSet edgeOtherBitVector = otherView.edgeBitVector;

if (nodeView) {
int nodeSize = nodeBitVector.size();
int nodeSize = graphStore.nodeStore.maxStoreId();
for (int i = 0; i < nodeSize; i++) {
boolean t = nodeBitVector.get(i);
boolean o = nodeOtherBitVector.get(i);
Expand All @@ -489,7 +488,7 @@ public void intersection(final GraphViewImpl otherView) {
}

if (edgeView) {
int edgeSize = edgeBitVector.size();
int edgeSize = graphStore.edgeStore.maxStoreId();
for (int i = 0; i < edgeSize; i++) {
boolean t = edgeBitVector.get(i);
boolean o = edgeOtherBitVector.get(i);
Expand All @@ -501,11 +500,11 @@ public void intersection(final GraphViewImpl otherView) {
}

public void union(final GraphViewImpl otherView) {
BitVector nodeOtherBitVector = otherView.nodeBitVector;
BitVector edgeOtherBitVector = otherView.edgeBitVector;
BitSet nodeOtherBitVector = otherView.nodeBitVector;
BitSet edgeOtherBitVector = otherView.edgeBitVector;

if (nodeView) {
int nodeSize = nodeBitVector.size();
int nodeSize = graphStore.nodeStore.maxStoreId();
for (int i = 0; i < nodeSize; i++) {
boolean t = nodeBitVector.get(i);
boolean o = nodeOtherBitVector.get(i);
Expand All @@ -516,7 +515,7 @@ public void union(final GraphViewImpl otherView) {
}

if (edgeView) {
int edgeSize = edgeBitVector.size();
int edgeSize = graphStore.edgeStore.maxStoreId();
for (int i = 0; i < edgeSize; i++) {
boolean t = edgeBitVector.get(i);
boolean o = edgeOtherBitVector.get(i);
Expand All @@ -529,10 +528,10 @@ public void union(final GraphViewImpl otherView) {

public void not() {
if (nodeView) {
nodeBitVector.not();
nodeBitVector.flip(0, graphStore.nodeStore.maxStoreId());
this.nodeCount = graphStore.nodeStore.size() - this.nodeCount;
}
edgeBitVector.not();
edgeBitVector.flip(0, graphStore.edgeStore.maxStoreId());

this.edgeCount = graphStore.edgeStore.size() - this.edgeCount;
for (int i = 0; i < typeCounts.length; i++) {
Expand Down Expand Up @@ -687,32 +686,44 @@ protected void destroyAllObservers() {
}

protected void ensureNodeVectorSize(NodeImpl node) {
int sid = node.storeId;
if (sid >= nodeBitVector.size()) {
int newSize = Math.min(Math
.max(sid + 1, (int) (sid * GraphStoreConfiguration.VIEW_GROWING_FACTOR)), Integer.MAX_VALUE);
nodeBitVector = growBitVector(nodeBitVector, newSize);
}
// BitSet automatically grows as needed, no manual resizing required
}

private void ensureNodeVectorSize(int size) {
if (size > nodeBitVector.size()) {
nodeBitVector = growBitVector(nodeBitVector, size);
}
}
protected void ensureEdgeVectorSize(EdgeImpl edge) {
// BitSet automatically grows as needed, but we need to handle filled views
int storeId = edge.storeId;
int currentMaxStoreId = graphStore.edgeStore.maxStoreId();

// If this is a new edge beyond our current range and we have a filled view,
// we should include the new edge
if (storeId >= currentMaxStoreId - 1) {
// Check if this view appears to be "filled" (all previous edges included)
boolean isFilled = true;
int prevMaxStoreId = currentMaxStoreId - 1;
if (prevMaxStoreId > 0) {
for (int i = 0; i < prevMaxStoreId; i++) {
if (!edgeBitVector.get(i)) {
isFilled = false;
break;
}
}
}

private void ensureEdgeVectorSize(int size) {
if (size > edgeBitVector.size()) {
edgeBitVector = growBitVector(edgeBitVector, size);
}
}
// If this appears to be a filled view, automatically include the new edge
if (isFilled) {
edgeBitVector.set(storeId);
edgeCount++;

protected void ensureEdgeVectorSize(EdgeImpl edge) {
int sid = edge.storeId;
if (sid >= edgeBitVector.size()) {
int newSize = Math.min(Math
.max(sid + 1, (int) (sid * GraphStoreConfiguration.VIEW_GROWING_FACTOR)), Integer.MAX_VALUE);
edgeBitVector = growBitVector(edgeBitVector, newSize);
int type = edge.type;
ensureTypeCountArrayCapacity(type);
typeCounts[type]++;

if (edge.isMutual() && !edge.isSelfLoop() && containsEdge(graphStore.edgeStore
.get(edge.target, edge.source, edge.type, false))) {
mutualEdgeTypeCounts[type]++;
mutualEdgesCount++;
}
}
}
}

Expand Down Expand Up @@ -781,13 +792,6 @@ private void removeEdge(EdgeImpl edgeImpl) {
}
}

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);
}

private NodeImpl getNode(int id) {
return graphStore.nodeStore.get(id);
}
Expand Down
44 changes: 32 additions & 12 deletions src/main/java/org/gephi/graph/impl/Serialization.java
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@
*/
package org.gephi.graph.impl;

import cern.colt.bitvector.BitVector;
import java.util.BitSet;
import it.unimi.dsi.fastutil.booleans.BooleanArrayList;
import it.unimi.dsi.fastutil.booleans.BooleanOpenHashSet;
import it.unimi.dsi.fastutil.bytes.Byte2ObjectOpenHashMap;
Expand Down Expand Up @@ -667,8 +667,8 @@ private GraphViewImpl deserializeGraphView(final DataInput is) throws IOExceptio
int storeId = (Integer) deserialize(is);
int nodeCount = (Integer) deserialize(is);
int edgeCount = (Integer) deserialize(is);
BitVector nodeCountVector = (BitVector) deserialize(is);
BitVector edgeCountVector = (BitVector) deserialize(is);
BitSet nodeCountVector = (BitSet) deserialize(is);
BitSet edgeCountVector = (BitSet) deserialize(is);
int[] typeCounts = (int[]) deserialize(is);
int[] mutualEdgeTypeCounts = (int[]) deserialize(is);
int mutualEdgesCount = (Integer) deserialize(is);
Expand All @@ -695,15 +695,35 @@ private GraphViewImpl deserializeGraphView(final DataInput is) throws IOExceptio
return view;
}

private void serializeBitVector(final DataOutput out, final BitVector bitVector) throws IOException {
serialize(out, bitVector.size());
serialize(out, bitVector.elements());
// Made compatible with legacy BitVector serialization, which was in place until version 0.8.1
public void serializeBitSet(final DataOutput out, final BitSet bitSet) throws IOException {
// BitSet.length() returns the index of the highest set bit + 1
// This gives us the logical size (0 if empty)
int size = bitSet.length();

serialize(out, size);

// Get the long array from BitSet
long[] words = bitSet.toLongArray();

// Calculate how many longs BitVector would use for this size
int requiredLongs = (size + 63) / 64;

// Create array with the exact required size (matching BitVector format)
long[] elements = new long[requiredLongs];

// Copy the BitSet data
System.arraycopy(words, 0, elements, 0, Math.min(words.length, requiredLongs));

serialize(out, elements);
}

private BitVector deserializeBitVector(final DataInput is) throws IOException, ClassNotFoundException {
public BitSet deserializeBitSet(final DataInput is) throws IOException, ClassNotFoundException {
int size = (Integer) deserialize(is);
long[] elements = (long[]) deserialize(is);
return new BitVector(elements, size);

// BitSet.valueOf() handles the long array correctly
return BitSet.valueOf(elements);
}

private void serializeGraphStoreConfiguration(final DataOutput out) throws IOException {
Expand Down Expand Up @@ -1558,10 +1578,10 @@ protected void serialize(final DataOutput out, final Object obj) throws IOExcept
GraphViewImpl b = (GraphViewImpl) obj;
out.write(GRAPH_VIEW);
serializeGraphView(out, b);
} else if (obj instanceof BitVector) {
BitVector bv = (BitVector) obj;
} else if (obj instanceof BitSet) {
BitSet bs = (BitSet) obj;
out.write(BIT_VECTOR);
serializeBitVector(out, bv);
serializeBitSet(out, bs);
} else if (obj instanceof GraphVersion) {
GraphVersion b = (GraphVersion) obj;
out.write(GRAPH_VERSION);
Expand Down Expand Up @@ -2122,7 +2142,7 @@ protected Object deserialize(DataInput is) throws IOException, ClassNotFoundExce
ret = deserializeGraphView(is);
break;
case BIT_VECTOR:
ret = deserializeBitVector(is);
ret = deserializeBitSet(is);
break;
case GRAPH_STORE_CONFIGURATION:
ret = deserializeGraphStoreConfiguration(is);
Expand Down
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