GH-420 quads (#425)

HDTq MSDL, DiffCat, GenDisk implementation and add tests

qendpoint-core/src/main/java/com/the_qa_company/qendpoint/core/compact/bitmap/AddSnapshotBitmap.java

@@ -64,15 +64,15 @@ public interface AddSnapshotDeltaBitmap extends Bitmap, AutoCloseable {
 		 * @return the roaring bitmap associated with this snapshot, can be null
 		 *         for empty value
 		 */
-		RoaringBitmap roaringBitmap();
+		RoaringBitmap64 roaringBitmap();
 	}
 
 	private class DeltaBitmap implements SimpleBitmap, AddSnapshotDeltaBitmap {
 		private boolean closed;
 		/**
 		 * compressed memory bitmap storing the delta
 		 */
-		final RoaringBitmap snapshot = new RoaringBitmap();
+		final RoaringBitmap64 snapshot = new RoaringBitmap64();
 		/**
 		 * next snapshot created after this one
 		 */
@@ -94,7 +94,7 @@ private class DeltaBitmap implements SimpleBitmap, AddSnapshotDeltaBitmap {
 		}
 
 		@Override
-		public RoaringBitmap roaringBitmap() {
+		public RoaringBitmap64 roaringBitmap() {
 			return snapshot;
 		}
 

qendpoint-core/src/main/java/com/the_qa_company/qendpoint/core/compact/bitmap/Bitmap64Big.java

@@ -162,12 +162,24 @@ public boolean access(long bitIndex) {
 
 	@Override
 	public long rank1(long pos) {
-		throw new NotImplementedException();
+		long c = 0;
+		for (int i = 0; i < pos; i++) {
+			if (access(i)) {
+				c++;
+			}
+		}
+		return c;
 	}
 
 	@Override
 	public long rank0(long pos) {
-		throw new NotImplementedException();
+		long c = 0;
+		for (int i = 0; i < pos; i++) {
+			if (!access(i)) {
+				c++;
+			}
+		}
+		return c;
 	}
 
 	@Override
@@ -264,7 +276,7 @@ public String getType() {
 	}
 
 	public long selectPrev1(long start) {
-		throw new NotImplementedException();
+		return select1(rank1(start));
 	}
 
 	public long getNumBits() {

qendpoint-core/src/main/java/com/the_qa_company/qendpoint/core/compact/bitmap/BitmapFactoryImpl.java

@@ -36,7 +36,7 @@ public class BitmapFactoryImpl extends BitmapFactory {
 	protected ModifiableBitmap doCreateModifiableBitmap(String type) {
 		return switch (Objects.requireNonNullElse(type, HDTVocabulary.BITMAP_TYPE_PLAIN)) {
 		case HDTVocabulary.BITMAP_TYPE_PLAIN -> Bitmap375Big.memory(0);
-		case HDTVocabulary.BITMAP_TYPE_ROARING -> new RoaringBitmap();
+		case HDTVocabulary.BITMAP_TYPE_ROARING -> new RoaringBitmap64();
 		default -> throw new IllegalArgumentException("Implementation not found for Bitmap with type " + type);
 		};
 	}

qendpoint-core/src/main/java/com/the_qa_company/qendpoint/core/compact/bitmap/GraphDeleteBitmap.java

@@ -0,0 +1,124 @@
+package com.the_qa_company.qendpoint.core.compact.bitmap;
+
+import com.the_qa_company.qendpoint.core.exceptions.NotImplementedException;
+import com.the_qa_company.qendpoint.core.util.io.Closer;
+
+import java.io.Closeable;
+import java.io.IOException;
+
+/**
+ * Bitmap to delete inside a graph, all the ids are mapped on a bitmap with the
+ * formula
+ *
+ * <pre>
+ * (id, graph) -> id * graphs + graph
+ * </pre>
+ *
+ * @author Antoine Willerval
+ */
+public class GraphDeleteBitmap implements SimpleModifiableBitmap, Closeable {
+	/**
+	 * create empty graph delete bitmap
+	 *
+	 * @param graphs graphs count
+	 * @param size   triples count
+	 * @return gdb
+	 */
+	public static GraphDeleteBitmap empty(long graphs, long size) {
+		return new GraphDeleteBitmap(EmptyBitmap.of(size * graphs), graphs);
+	}
+
+	/**
+	 * create memory graph delete bitmap
+	 *
+	 * @param graphs graphs count
+	 * @param size   triples count
+	 * @return gdb
+	 */
+	public static GraphDeleteBitmap memory(long graphs, long size) {
+		return new GraphDeleteBitmap(MultiRoaringBitmap.memory(size * graphs), graphs);
+	}
+
+	/**
+	 * wrap a bitmap to create a {@link GraphDeleteBitmap}
+	 *
+	 * @param bitmap bitmap
+	 * @param graphs graphs count
+	 * @return bitmap if already instanceof graph delete bitmap and contains the
+	 *         right graphs number or wrap into GraphDeleteBitmap
+	 */
+	public static GraphDeleteBitmap wrap(Bitmap bitmap, long graphs) {
+		if (bitmap instanceof GraphDeleteBitmap gdb && gdb.graphs == graphs) {
+			// use directly the bitmap
+			return gdb;
+		}
+		return new GraphDeleteBitmap(bitmap, graphs);
+	}
+
+	private final Bitmap store;
+	private final long graphs;
+
+	private GraphDeleteBitmap(Bitmap store, long graphs) {
+		this.store = store;
+		this.graphs = graphs;
+	}
+
+	/**
+	 * access a bit in a graph
+	 *
+	 * @param graph    graph
+	 * @param position position
+	 * @return bit value
+	 */
+	public boolean access(long graph, long position) {
+		return access(position * graphs + graph);
+	}
+
+	/**
+	 * set a bit in a graph
+	 *
+	 * @param graph    graph
+	 * @param position position
+	 * @param value    value
+	 * @throws ClassCastException if the wrapped bitmap isn't a modifiable
+	 *                            bitmap
+	 */
+	public void set(int graph, long position, boolean value) {
+		set(position * graphs + graph, value);
+	}
+
+	@Override
+	public boolean access(long position) {
+		return store.access(position);
+	}
+
+	@Override
+	public void set(long position, boolean value) {
+		((ModifiableBitmap) store).set(position, value);
+	}
+
+	@Override
+	public long getNumBits() {
+		return store.getNumBits();
+	}
+
+	@Override
+	public long getSizeBytes() {
+		return store.getSizeBytes();
+	}
+
+	@Override
+	public String getType() {
+		return store.getType();
+	}
+
+	@Override
+	public void append(boolean value) {
+		throw new NotImplementedException();
+	}
+
+	@Override
+	public void close() throws IOException {
+		Closer.closeSingle(store);
+	}
+}

qendpoint-core/src/main/java/com/the_qa_company/qendpoint/core/compact/bitmap/MappedRoaringBitmap.java

@@ -0,0 +1,101 @@
+package com.the_qa_company.qendpoint.core.compact.bitmap;
+
+import com.the_qa_company.qendpoint.core.hdt.HDTVocabulary;
+import com.the_qa_company.qendpoint.core.listener.ProgressListener;
+import com.the_qa_company.qendpoint.core.util.io.CloseMappedByteBuffer;
+import com.the_qa_company.qendpoint.core.util.io.IOUtil;
+import org.roaringbitmap.buffer.ImmutableRoaringBitmap;
+
+import java.io.Closeable;
+import java.io.DataOutputStream;
+import java.io.IOException;
+import java.io.OutputStream;
+
+/**
+ * Mapped {@link Bitmap} wrapper for the {@link ImmutableRoaringBitmap}, not
+ * compatible with {@link RoaringBitmap64}
+ *
+ * @author Antoine Willerval
+ */
+public class MappedRoaringBitmap implements SimpleBitmap, Closeable {
+	private final CloseMappedByteBuffer buffer;
+	private final ImmutableRoaringBitmap rbm;
+
+	public MappedRoaringBitmap(CloseMappedByteBuffer buffer) {
+		this.buffer = buffer;
+		this.rbm = new ImmutableRoaringBitmap(buffer.getInternalBuffer());
+	}
+
+	public ImmutableRoaringBitmap getHandle() {
+		return rbm;
+	}
+
+	@Override
+	public boolean access(long position) {
+		return rbm.contains((int) position);
+	}
+
+	@Override
+	public long getNumBits() {
+		return rbm.last();
+	}
+
+	@Override
+	public long getSizeBytes() {
+		return rbm.serializedSizeInBytes() + 8;
+	}
+
+	@Override
+	public void save(OutputStream output, ProgressListener listener) throws IOException {
+		long size = rbm.serializedSizeInBytes();
+		IOUtil.writeLong(output, size);
+		rbm.serialize(new DataOutputStream(output));
+	}
+
+	@Override
+	public String getType() {
+		return HDTVocabulary.BITMAP_TYPE_ROARING;
+	}
+
+	@Override
+	public long select1(long n) {
+		long position = n - 1;
+		if (position == -1)
+			return -1;
+		if (position < rbm.getLongCardinality()) {
+			return rbm.select((int) position);
+		} else {
+			return rbm.select((int) rbm.getLongCardinality() - 1) + 1;
+		}
+	}
+
+	@Override
+	public long rank1(long position) {
+		if (position >= 0)
+			return rbm.rankLong((int) position);
+		return 0;
+	}
+
+	@Override
+	public long countOnes() {
+		return rbm.getLongCardinality();
+	}
+
+	@Override
+	public long selectPrev1(long start) {
+		return select1(rank1(start));
+	}
+
+	@Override
+	public long selectNext1(long start) {
+		long pos = rank1(start - 1);
+		if (pos < rbm.getLongCardinality())
+			return select1(pos + 1);
+		return -1;
+	}
+
+	@Override
+	public void close() throws IOException {
+		buffer.close();
+	}
+}