Implemented indexOf

pom.xml

@@ -35,6 +35,11 @@
       <artifactId>kryo</artifactId>
       <version>5.0.0-RC1</version>
     </dependency>
+    <dependency>
+	  <groupId>net.openhft</groupId>
+	  <artifactId>zero-allocation-hashing</artifactId>
+	  <version>0.8</version>
+	</dependency>
   </dependencies>
 
   <build>

src/main/java/org/warp/jcwdb/CacheIndexManager.java

@@ -45,4 +45,10 @@ public class CacheIndexManager implements IndexManager {
 	public void close() {
 		// TODO: implement
 	}
+
+	@Override
+	public long clean() {
+		// TODO Auto-generated method stub
+		return 0;
+	}
 }

src/main/java/org/warp/jcwdb/DBDataOutput.java

@@ -3,9 +3,10 @@ package org.warp.jcwdb;
 public interface DBDataOutput<T> {
 	int getSize();
 	int getType();
+	long calculateHash();
 	DBWriter<T> getWriter();
 	
-	static <T> DBDataOutput<T> create(DBWriter<T> writer, int type, int size) {
+	static <T> DBDataOutput<T> create(DBWriter<T> writer, int type, int size, long hash) {
 		return new DBDataOutput<T>() {
 
 			@Override
@@ -17,6 +18,11 @@ public interface DBDataOutput<T> {
 			public int getType() {
 				return type;
 			}
+			
+			@Override
+			public long calculateHash() {
+				return hash;
+			}
 
 			@Override
 			public DBWriter<T> getWriter() {

src/main/java/org/warp/jcwdb/DBGenericObjectParser.java

@@ -5,7 +5,10 @@ import java.io.ByteArrayOutputStream;
 import com.esotericsoftware.kryo.Kryo;
 import com.esotericsoftware.kryo.io.Output;
 
+import net.openhft.hashing.LongHashFunction;
+
 public class DBGenericObjectParser extends DBTypeParserImpl<Object> {
+	private static final LongHashFunction hashFunction = net.openhft.hashing.LongHashFunction.xx();
 	private static final Kryo kryo = new Kryo();
 	static {
 		kryo.setRegistrationRequired(false);
@@ -25,9 +28,22 @@ public class DBGenericObjectParser extends DBTypeParserImpl<Object> {
 		kryo.writeClassAndObject(tmpO, value);
 		tmpO.flush();
 		final byte[] bytes = baos.toByteArray();
+		final long hash = hashFunction.hashBytes(bytes);
 		tmpO.close();
 		return DBDataOutput.create((o) -> {
 			o.write(bytes);
-		}, DBStandardTypes.GENERIC_OBJECT, bytes.length);
+		}, DBStandardTypes.GENERIC_OBJECT, bytes.length, hash);
+	}
+
+	@Override
+	public long calculateHash(Object value) {
+		ByteArrayOutputStream baos = new ByteArrayOutputStream();
+		Output tmpO = new Output(baos);
+		kryo.writeClassAndObject(tmpO, value);
+		tmpO.flush();
+		final byte[] bytes = baos.toByteArray();
+		final long hash = hashFunction.hashBytes(bytes);
+		tmpO.close();
+		return hash;
 	}
 }

src/main/java/org/warp/jcwdb/DBLightListParser.java

@@ -2,6 +2,8 @@ package org.warp.jcwdb;
 
 import java.util.ArrayList;
 
+import it.unimi.dsi.fastutil.longs.LongArrayList;
+
 public class DBLightListParser extends DBTypeParserImpl<LightList> {
 	private final JCWDatabase db;
 
@@ -11,23 +13,33 @@ public class DBLightListParser extends DBTypeParserImpl<LightList> {
 	
 	public DBReader<LightList> getReader() {
 		return (i, size) -> {
-			ArrayList<Long> internalList = new ArrayList<>();
+			LongArrayList internalList = new LongArrayList();
-			long max = size / Long.BYTES;
+			LongArrayList hashes = new LongArrayList();
+			long max = size / (Long.BYTES * 2);
 			for (int item = 0; item < max; item++){
 				long itm = i.readLong();
+				long hash = i.readLong();
 				internalList.add(itm);
+				hashes.add(hash);
 			}
-			return new LightList(db, internalList);
+			return new LightList(db, internalList, hashes);
 		};
 	}
 
 	public DBDataOutput<LightList> getWriter(final LightList value) {
-		final int elementsCount = value.internalList.size();
+		final int elementsCount = value.size();
 		return DBDataOutput.create((o) -> {
-			ArrayList<Long> list = value.internalList;
+			LongArrayList list = value.internalList;
-			for (Long item : list) {
+			LongArrayList hashes = value.hashes;
-				o.writeLong(item);
+			for (int i = 0; i < elementsCount; i++) {
+				o.writeLong(list.getLong(i));
+				o.writeLong(hashes.getLong(i));
 			}
-		}, DBStandardTypes.LIGHT_LIST, elementsCount * Long.BYTES);
+		}, DBStandardTypes.LIGHT_LIST, elementsCount * Long.BYTES * 2, calculateHash(value));
+	}
+
+	@Override
+	public long calculateHash(LightList value) {
+		return value.hashCodeLong();
 	}
 }

src/main/java/org/warp/jcwdb/DBStringParser.java

@@ -1,12 +1,13 @@
 package org.warp.jcwdb;
 
-import java.io.ByteArrayOutputStream;
+import java.nio.charset.StandardCharsets;
 
-import com.esotericsoftware.kryo.io.Output;
+import net.openhft.hashing.LongHashFunction;
 
 public class DBStringParser extends DBTypeParserImpl<String> {
+	private static final LongHashFunction hashFunction = net.openhft.hashing.LongHashFunction.xx();
 	private static final DBReader<String> defaultReader = (i, size) -> {
-		return i.readString();
+		return new String(i.readBytes(size), StandardCharsets.UTF_16LE);
 	};
 	
 	public DBReader<String> getReader() {
@@ -14,14 +15,13 @@ public class DBStringParser extends DBTypeParserImpl<String> {
 	}
 	
 	public DBDataOutput<String> getWriter(final String value) {
-		ByteArrayOutputStream baos = new ByteArrayOutputStream();
-		Output tmpO = new Output(baos);
-		tmpO.writeString(value);
-		tmpO.flush();
-		final byte[] bytes = baos.toByteArray();
-		tmpO.close();
 		return DBDataOutput.create((o) -> {
-			o.write(bytes);
+			o.write(value.getBytes(StandardCharsets.UTF_16LE));
-		}, DBStandardTypes.STRING, bytes.length);
+		}, DBStandardTypes.STRING, value.length() * 2, calculateHash(value));
+	}
+
+	@Override
+	public long calculateHash(String value) {
+		return hashFunction.hashBytes(value.getBytes(StandardCharsets.UTF_16LE));
 	}
 }

src/main/java/org/warp/jcwdb/DBTypeParser.java

@@ -3,4 +3,5 @@ package org.warp.jcwdb;
 public interface DBTypeParser<T> extends Castable {	
 	DBReader<T> getReader();
 	DBDataOutput<T> getWriter(final T value);
+	long calculateHash(final T value);
 }

src/main/java/org/warp/jcwdb/EntryReference.java

@@ -18,7 +18,7 @@ public class EntryReference<T> implements Castable, AutoCloseable {
 		this.db = db;
 		this.entryIndex = entryId;
 		this.parser = parser;
-		this.value = db.indices.get(entryId, parser.getReader());
+		this.value = db.getIndexManager().get(entryId, parser.getReader());
 	}
 
 	public EntryReference(JCWDatabase db, long entryId, DBTypeParser<T> parser, T value) {
@@ -35,10 +35,18 @@ public class EntryReference<T> implements Castable, AutoCloseable {
 	public long getIndex() {
 		return entryIndex;
 	}
+	
+	public long calculateHash() {
+		return parser.calculateHash(value);
+	}
 
+	/**
+	 * Note that this method won't be called when closing without saving
+	 * @throws IOException
+	 */
 	public void save() throws IOException {
 		if (!closed) {
-			db.indices.set(entryIndex, parser.getWriter(value));
+			db.getIndexManager().set(entryIndex, parser.getWriter(value));
 		}
 	}
 
@@ -57,8 +65,23 @@ public class EntryReference<T> implements Castable, AutoCloseable {
 				return;
 			}
 
-			db.removeEntryReference(entryIndex);
 			save();
+			db.removeEntryReference(entryIndex);
+
+			closed = true;
+		}
+	}
+
+	public void closeWithoutSaving() {
+		if (closed) {
+			return;
+		}
+		synchronized (closeLock) {
+			if (closed) {
+				return;
+			}
+
+			db.removeEntryReference(entryIndex);
 
 			closed = true;
 		}

src/main/java/org/warp/jcwdb/FileIndexManager.java

@@ -78,11 +78,11 @@ public class FileIndexManager implements IndexManager {
 	public <T> void set(long index, DBDataOutput<T> data) throws IOException {
 		checkClosed();
 		final IndexDetails indexDetails = getIndexMetadataUnsafe(index);
-		if (indexDetails == null || indexDetails.getSize() < data.getSize()) {
+		if (indexDetails == null || indexDetails.getSize() != data.getSize()) { // TODO: should be indexDetails.getSize() < data.getSize(). Need to create a method to mark memory free if the size is bigger than the needed, instead of allocating a new space.
 			allocateAndWrite(index, data);
 		} else {
 			if (indexDetails.getSize() > data.getSize()) {
-				editIndex(index, indexDetails.getOffset(), data.getSize(), indexDetails.getType());
+				editIndex(index, indexDetails.getOffset(), data.getSize(), indexDetails.getType(), data.calculateHash());
 				fileAllocator.markFree(indexDetails.getOffset()+data.getSize(), data.getSize());
 			}
 			writeExact(indexDetails, data);
@@ -95,7 +95,8 @@ public class FileIndexManager implements IndexManager {
 		final int size = data.getSize();
 		final long offset = fileAllocator.allocate(size);
 		final int type = data.getType();
-		final IndexDetails indexDetails = new IndexDetails(offset, size, type);
+		final long hash = data.calculateHash();
+		final IndexDetails indexDetails = new IndexDetails(offset, size, type, hash);
 		final long index = createIndexMetadata(indexDetails);
 		writeExact(indexDetails, data);
 		return index;
@@ -123,8 +124,9 @@ public class FileIndexManager implements IndexManager {
 	private void allocateAndWrite(final long index, DBDataOutput<?> w) throws IOException {
 		final int size = w.getSize();
 		final int type = w.getType();
+		final long hash = w.calculateHash();
 		final long offset = fileAllocator.allocate(size);
-		IndexDetails details = editIndex(index, offset, size, type);
+		IndexDetails details = editIndex(index, offset, size, type, hash);
 		writeExact(details, w);
 	}
 
@@ -181,8 +183,8 @@ public class FileIndexManager implements IndexManager {
 		}
 	}
 
-	private IndexDetails editIndex(long index, long offset, int size, int type) {
+	private IndexDetails editIndex(long index, long offset, int size, int type, long hash) {
-		IndexDetails indexDetails = new IndexDetails(offset, size, type);
+		IndexDetails indexDetails = new IndexDetails(offset, size, type, hash);
 		editIndex(index, indexDetails);
 		return indexDetails;
 	}
@@ -226,9 +228,13 @@ public class FileIndexManager implements IndexManager {
 			// If it's not deleted continue
 			if ((metadataByteBuffer.getInt() & IndexDetails.MASK_DELETED) == 0) {
 				final long offset = metadataByteBuffer.getLong();
+//				final long sizeAndType = metadataByteBuffer.getLong();
+//				final int size = (int)(sizeAndType >> 32);
+//				final int type = (int)sizeAndType;
 				final int size = metadataByteBuffer.getInt();
 				final int type = metadataByteBuffer.getInt();
-				final IndexDetails indexDetails = new IndexDetails(offset, size, type);
+				final long hash = metadataByteBuffer.getLong();
+				final IndexDetails indexDetails = new IndexDetails(offset, size, type, hash);
 				editIndex(index, indexDetails);
 				return indexDetails;
 			}
@@ -284,11 +290,17 @@ public class FileIndexManager implements IndexManager {
 	
 	private void writeIndexDetails(SeekableByteChannel position, IndexDetails indexDetails) throws IOException {
 		synchronized (metadataByteBufferLock) {
+			final int size = indexDetails.getSize();
+			final int type = indexDetails.getType();
+			final long offset = indexDetails.getOffset();
+			final long hash = indexDetails.getHash();
 			metadataByteBuffer.rewind();
 			metadataByteBuffer.putInt(0);
-			metadataByteBuffer.putLong(indexDetails.getOffset());
+			metadataByteBuffer.putLong(offset);
-			metadataByteBuffer.putInt(indexDetails.getSize());
+			metadataByteBuffer.putInt(size);
-			metadataByteBuffer.putInt(indexDetails.getType());
+			metadataByteBuffer.putInt(type);
+			//metadataByteBuffer.putLong((long)size << 32 | type & 0xFFFFFFFFL);
+			metadataByteBuffer.putLong(hash);
 			metadataByteBuffer.rewind();
 			position.write(metadataByteBuffer);
 		}

src/main/java/org/warp/jcwdb/IndexDetails.java

@@ -10,22 +10,26 @@ public class IndexDetails {
 	public static final int OFFSET_BYTES = Long.BYTES;
 	public static final int DATA_SIZE_BYTES = Integer.BYTES;
 	public static final int TYPE_BYTES = Integer.BYTES;
-	public static final int TOTAL_BYTES = BITMASK_SIZE + OFFSET_BYTES + DATA_SIZE_BYTES + TYPE_BYTES;
+	public static final int HASH_BYTES = Long.BYTES;
+	public static final int TOTAL_BYTES = BITMASK_SIZE + OFFSET_BYTES + DATA_SIZE_BYTES + TYPE_BYTES + HASH_BYTES;
 	public static final int MASK_DELETED = 0b00000001;
 	private final long offset;
 	private final int size;
 	private final int type;
+	private final long hash;
 
-	public IndexDetails(long offset, int size, int type) {
+	public IndexDetails(long offset, int size, int type, long hash) {
 		this.offset = offset;
 		this.size = size;
 		this.type = type;
+		this.hash = hash;
 	}
 
 	public IndexDetails(IndexDetails indexDetails) {
 		this.offset = indexDetails.offset;
 		this.size = indexDetails.size;
 		this.type = indexDetails.type;
+		this.hash = indexDetails.hash;
 	}
 
 	public long getOffset() {
@@ -39,29 +43,46 @@ public class IndexDetails {
 	public int getType() {
 		return type;
 	}
-
+	
-	@Override
+	public long getHash() {
-	public boolean equals(Object o) {
+		return hash;
-		if (this == o) return true;
-		if (o == null || getClass() != o.getClass()) return false;
-		IndexDetails that = (IndexDetails) o;
-		return offset == that.offset &&
-						size == that.size &&
-						type == that.type;
 	}
 
 	@Override
 	public int hashCode() {
-		return Objects.hash(offset);
+		final int prime = 31;
+		int result = 1;
+		result = prime * result + (int) (hash ^ (hash >>> 32));
+		result = prime * result + (int) (offset ^ (offset >>> 32));
+		result = prime * result + size;
+		result = prime * result + type;
+		return result;
+	}
+
+	@Override
+	public boolean equals(Object obj) {
+		if (this == obj)
+			return true;
+		if (obj == null)
+			return false;
+		if (getClass() != obj.getClass())
+			return false;
+		IndexDetails other = (IndexDetails) obj;
+		if (hash != other.hash)
+			return false;
+		if (offset != other.offset)
+			return false;
+		if (size != other.size)
+			return false;
+		if (type != other.type)
+			return false;
+		return true;
 	}
 
 	@Override
 	public String toString() {
-		return "IndexDetails{" +
+		return "IndexDetails [offset=" + offset + ", size=" + size + ", type=" + type + ", hash=" + hash + "]";
-						"offset=" + offset +
-						", size=" + size +
-						", type=" + type +
-						'}';
 	}
+	
 
 }

src/main/java/org/warp/jcwdb/JCWDatabase.java

@@ -8,6 +8,8 @@ import java.util.ArrayList;
 import it.unimi.dsi.fastutil.longs.Long2ObjectLinkedOpenHashMap;
 import it.unimi.dsi.fastutil.longs.Long2ObjectMap;
 import it.unimi.dsi.fastutil.longs.Long2ObjectMap.Entry;
+import it.unimi.dsi.fastutil.longs.LongArrayList;
+import it.unimi.dsi.fastutil.objects.ObjectIterator;
 
 public class JCWDatabase implements AutoCloseable, Cleanable {
 	public final static long MAX_LOADED_REFERENCES = 10;
@@ -39,11 +41,15 @@ public class JCWDatabase implements AutoCloseable, Cleanable {
 	}
 
 	public <T> EntryReference<LightList<T>> getRoot() throws IOException {
+		return getRoot(Object.class).cast();
+	}
+	
+	public <T> EntryReference<LightList<T>> getRoot(Class<T> clazz) throws IOException {
 		checkClosed();
 		if (exists(0)) {
 			return get(0);
 		} else {
-			LightList<T> newRoot = new LightList<T>(this, new ArrayList<>());
+			LightList<T> newRoot = new LightList<T>(this, new LongArrayList(), new LongArrayList());
 			return set(0, newRoot);
 		}
 	}
@@ -130,7 +136,9 @@ public class JCWDatabase implements AutoCloseable, Cleanable {
 		}
 
 		synchronized (referencesAccessLock) {
-			for (WeakReference<EntryReference<?>> referenceRef : references.values()) {
+			ObjectIterator<WeakReference<EntryReference<?>>> it = references.values().iterator();
+			while (it.hasNext()) {
+				WeakReference<EntryReference<?>> referenceRef = it.next();
 				EntryReference<?> reference = referenceRef.get();
 				if (reference != null) {
 					reference.close();
@@ -187,4 +195,17 @@ public class JCWDatabase implements AutoCloseable, Cleanable {
 		}
 		return removedReferences;
 	}
+
+	@SuppressWarnings("unchecked")
+	protected <T> long calculateHash(T o) {
+		return ((DBTypeParser<T>) typesManager.get(o.getClass())).calculateHash(o);
+	}
+
+	/**
+	 * 
+	 * @return indexManager
+	 */
+	public IndexManager getIndexManager() {
+		return indices;
+	}
 }

src/main/java/org/warp/jcwdb/LightList.java

@@ -2,14 +2,20 @@ package org.warp.jcwdb;
 
 import java.io.IOException;
 import java.util.*;
+import java.util.function.Predicate;
+
+import it.unimi.dsi.fastutil.longs.LongArrayList;
+import it.unimi.dsi.fastutil.objects.ObjectArrayList;
 
 public class LightList<T> implements List<T> {
 
-	public final ArrayList<Long> internalList;
+	public final LongArrayList internalList;
+	public final LongArrayList hashes;
 	private final transient JCWDatabase db;
 
-	public LightList(JCWDatabase db, ArrayList<Long> internalList) {
+	public LightList(JCWDatabase db, LongArrayList internalList, LongArrayList hashes) {
 		this.internalList = internalList;
+		this.hashes = hashes;
 		this.db = db;
 	}
 
@@ -27,8 +33,9 @@ public class LightList<T> implements List<T> {
 	public boolean contains(Object o) {
 		if (o != null) {
 			for (Long element : internalList) {
+				EntryReference<T> ref = null;
 				try {
-					EntryReference<T> ref = db.get(element);
+					ref = db.get(element);
 					if (o.equals(ref.value)) {
 						return true;
 					}
@@ -40,6 +47,7 @@ public class LightList<T> implements List<T> {
 		return false;
 	}
 
+	@SuppressWarnings("unchecked")
 	@Override
 	public Iterator<T> iterator() {
 		final ArrayList<T> elements = new ArrayList<>();
@@ -53,12 +61,13 @@ public class LightList<T> implements List<T> {
 		return elements.iterator();
 	}
 
+	@SuppressWarnings("unchecked")
 	@Override
 	public T[] toArray() {
 		final T[] elements = (T[]) new Objects[internalList.size()];
 		for (int i = 0; i < elements.length; i++) {
 			try {
-				elements[i] = (T) db.get(internalList.get(i)).value;
+				elements[i] = (T) db.get(internalList.getLong(i)).value;
 			} catch (IOException e) {
 				e.printStackTrace();
 			}
@@ -66,12 +75,13 @@ public class LightList<T> implements List<T> {
 		return elements;
 	}
 
+	@SuppressWarnings("unchecked")
 	@Override
 	public <T1> T1[] toArray(T1[] a) {
 		final T1[] elements = (T1[]) new Objects[internalList.size()];
 		for (int i = 0; i < elements.length; i++) {
 			try {
-				elements[i] = (T1) db.get(internalList.get(i)).value;
+				elements[i] = (T1) db.get(internalList.getLong(i)).value;
 			} catch (IOException e) {
 				e.printStackTrace();
 			}
@@ -81,117 +91,284 @@ public class LightList<T> implements List<T> {
 
 	@Override
 	public boolean add(T o) {
-		EntryReference<T> ref;
+		EntryReference<T> ref = addEntry(o);
-		try {
+		return ref != null;
-			ref = db.add(o);
+	}
-		} catch (IOException e) {
+	
-			throw (NullPointerException) new NullPointerException().initCause(e);
+	public EntryReference<T> addEntry(T o) {
+		EntryReference<T> ref = addToDatabase(o);
+		if (internalList.add(ref.getIndex())) {
+			hashes.add(ref.getParser().calculateHash(ref.value));
+		} else {
+			return null;
 		}
-		return internalList.add(ref.getIndex());
+		return ref;
 	}
 
 	@Override
 	public boolean remove(Object o) {
-		EntryReference<T> ref;
+		int removeIndex = indexOf(o);
-		try {
+		if (removeIndex >= 0) {
-			ref = db.add((T) o);
+			internalList.removeLong(removeIndex);
-		} catch (IOException e) {
+			hashes.removeLong(removeIndex);
-			throw (NullPointerException) new NullPointerException().initCause(e);
+			return true;
 		}
-		return internalList.remove(ref.getIndex());
+		return false;
+	}
+	
+	public boolean remove(EntryReference<T> ref) {
+		int removeIndex = indexOfEntry(ref);
+		if (removeIndex >= 0) {
+			internalList.removeLong(removeIndex);
+			hashes.removeLong(removeIndex);
+			return true;
+		}
+		return false;
 	}
 
 	@Override
 	public boolean containsAll(Collection<?> c) {
-		// TODO: implement
+		for (Object o : c) {
-		return false;
+			int objIndex = indexOf(o);
+			if (objIndex < 0) {
+				return false;
+			}
+		}
+		return true;
 	}
 
+	@SuppressWarnings("unchecked")
 	@Override
 	public boolean addAll(Collection<? extends T> c) {
-		// TODO: implement
+		boolean result = false;
-		return false;
+		for (Object o : c) {
+			result |= add((T) o);
+		}
+		return result;
 	}
 
+	@SuppressWarnings("unchecked")
 	@Override
 	public boolean addAll(int index, Collection<? extends T> c) {
-		// TODO: implement
+		boolean result = false;
-		return false;
+		int delta = 0;
+		for (Object o : c) {
+			add(index + delta, (T) o);
+			result = true;
+			delta++;
+		}
+		return result;
 	}
 
+	@SuppressWarnings("unchecked")
 	@Override
 	public boolean removeAll(Collection<?> c) {
-		// TODO: implement
+		boolean result = false;
-		return false;
+		for (Object o : c) {
+			result |= remove((T) o);
+		}
+		return result;
 	}
 
 	@Override
 	public boolean retainAll(Collection<?> c) {
-		// TODO: implement
+		boolean result = false;
-		return false;
+		LongArrayList collectionHashes = new LongArrayList();
+		ObjectArrayList<Object> collection = new ObjectArrayList<>();
+		collection.addAll(c);
+		for (Object o : c) {
+			collectionHashes.add(db.calculateHash(o));
+		}
+		for (int i = 0; i < internalList.size(); i++) {
+			long hash = internalList.getLong(i);
+			int positionInCollection = collectionHashes.indexOf(hash);
+			if (positionInCollection == -1) {
+				remove(collection.get(positionInCollection));
+				result = true;
+			}
+		}
+		return result;
 	}
 
 	@Override
 	public void clear() {
-		// TODO: implement
+		internalList.clear();
-
+		hashes.clear();
 	}
 
+	@SuppressWarnings("unchecked")
 	@Override
 	public T get(int index) {
 		try {
-			return (T) db.get(internalList.get(index)).value;
+			return (T) db.get(internalList.getLong(index)).value;
 		} catch (IOException e) {
 			e.printStackTrace();
 			return null;
 		}
 	}
 
+	@SuppressWarnings("unchecked")
 	@Override
 	public T set(int index, T element) {
-		// TODO: implement
+		EntryReference<T> ref = addToDatabase(element);
-		return null;
+		long oldIndex = internalList.set(index, ref.getIndex());
+		hashes.set(index, ref.calculateHash());
+		try {
+			ref.close();
+			return ((EntryReference<T>) (db.get(oldIndex))).value;
+		} catch (IOException e) {
+			throw (NullPointerException) new NullPointerException().initCause(e);
+		}
 	}
 
 	@Override
 	public void add(int index, T element) {
-		// TODO: implement
+		EntryReference<T> ref = addToDatabase(element);
-
+		internalList.add(index, ref.getIndex());
+		hashes.add(index, ref.getParser().calculateHash(ref.value));
 	}
 
+	@SuppressWarnings("unchecked")
 	@Override
 	public T remove(int index) {
-		// TODO: implement
+		long oldIndex = internalList.removeLong(index);
-		return null;
+		hashes.removeLong(index);
+		try {
+			return ((EntryReference<T>) (db.get(oldIndex))).value;
+		} catch (IOException e) {
+			throw (NullPointerException) new NullPointerException().initCause(e);
+		}
 	}
 
 	@Override
 	public int indexOf(Object o) {
-		// TODO: implement
+		EntryReference<?> ref = addToDatabase(o);
-		return 0;
+		long objToRemoveHash = ref.calculateHash();
+
+		for (int i = 0; i < hashes.size(); i++) {
+			long hash = hashes.getLong(i);
+			if (objToRemoveHash == hash) {
+				try {
+					if (ref.equals(db.get(internalList.getLong(i)))) {
+						return i;
+					}
+				} catch (IOException e) {
+					throw (NullPointerException) new NullPointerException().initCause(e);
+				}
+			}
+		}
+		return -1;
+	}
+
+	public int indexOfEntry(EntryReference<T> ref) {
+		long objToRemoveHash = ref.calculateHash();
+
+		for (int i = 0; i < hashes.size(); i++) {
+			long hash = hashes.getLong(i);
+			if (objToRemoveHash == hash) {
+				try {
+					if (ref.equals(db.get(internalList.getLong(i)))) {
+						return i;
+					}
+				} catch (IOException e) {
+					throw (NullPointerException) new NullPointerException().initCause(e);
+				}
+			}
+		}
+		return -1;
 	}
 
 	@Override
 	public int lastIndexOf(Object o) {
-		// TODO: implement
+		EntryReference<?> ref = addToDatabase(o);
-		return 0;
+		long objToRemoveHash = ref.calculateHash();
+
+		int lastValue = -1;
+
+		for (int i = 0; i < hashes.size(); i++) {
+			long hash = hashes.getLong(i);
+			if (objToRemoveHash == hash) {
+				try {
+					if (ref.equals(db.get(internalList.getLong(i)))) {
+						lastValue = i;
+					}
+				} catch (IOException e) {
+					throw (NullPointerException) new NullPointerException().initCause(e);
+				}
+			}
+		}
+		return lastValue;
 	}
 
+	@Deprecated
 	@Override
 	public ListIterator<T> listIterator() {
 		// TODO: implement
-		return null;
+		throw new RuntimeException("Not implemented!");
 	}
 
+	@Deprecated
 	@Override
 	public ListIterator<T> listIterator(int index) {
 		// TODO: implement
-		return null;
+		throw new RuntimeException("Not implemented!");
 	}
 
+	@Deprecated
 	@Override
 	public List<T> subList(int fromIndex, int toIndex) {
 		// TODO: implement
-		return null;
+		throw new RuntimeException("Not implemented!");
+	}
+
+	private <U> EntryReference<U> addToDatabase(U obj) {
+		EntryReference<U> ref;
+		try {
+			ref = db.add(obj);
+		} catch (IOException e) {
+			throw (NullPointerException) new NullPointerException().initCause(e);
+		}
+		return ref;
+	}
+
+	@Deprecated
+	@Override
+	public int hashCode() {
+		final int prime = 31;
+		int result = 1;
+		result = prime * result + ((hashes == null) ? 0 : hashes.hashCode());
+		result = prime * result + ((internalList == null) ? 0 : internalList.hashCode());
+		return result;
+	}
+
+	public long hashCodeLong() {
+		final int prime = 31;
+		int result1 = prime + ((hashes == null) ? 0 : hashes.hashCode());
+		int result2 = prime + ((internalList == null) ? 0 : internalList.hashCode());
+		long result = (((long) result1) << 32) | (result2 & 0xffffffffL);
+		return result;
+	}
+
+	@SuppressWarnings("unchecked")
+	@Override
+	public boolean removeIf(Predicate<? super T> filter) {
+		Objects.requireNonNull(filter);
+		boolean removed = false;
+		for (int i = 0; i < internalList.size(); ) {
+			T obj;
+			try {
+				obj = ((EntryReference<T>) (db.get(internalList.getLong(i)).cast())).value;
+			} catch (IOException e) {
+				throw (NullPointerException) new NullPointerException().initCause(e);
+			}
+			if (filter.test(obj)) {
+				internalList.removeLong(i);
+				hashes.removeLong(i);
+				removed = true;
+			} else {
+				i++;
+			}
+		}
+		return removed;
 	}
 }

src/main/java/org/warp/jcwdb/exampleimpl/Animal.java

@@ -0,0 +1,9 @@
+package org.warp.jcwdb.exampleimpl;
+
+public abstract class Animal {
+	protected int legsCount;
+	
+	public static boolean hasFourLegs(Animal a) {
+		return a.legsCount == 4;
+	}
+}

src/main/java/org/warp/jcwdb/exampleimpl/App.java

@@ -4,8 +4,12 @@ import org.warp.jcwdb.EntryReference;
 import org.warp.jcwdb.JCWDatabase;
 import org.warp.jcwdb.LightList;
 
+import it.unimi.dsi.fastutil.objects.ObjectArrayList;
+import it.unimi.dsi.fastutil.objects.ObjectList;
+
 import java.nio.file.Files;
 import java.nio.file.Paths;
+import java.util.function.Predicate;
 
 public class App {
 	public static void main(String[] args) throws Exception {
@@ -19,29 +23,55 @@ public class App {
 		long time01 = System.currentTimeMillis();
 		System.out.println("Time elapsed: " + (time01 - time0));
 		System.out.println("Loading root...");
-		LightList<String> root = ((EntryReference<LightList<String>>) db.getRoot().cast()).value;
+		EntryReference<LightList<Animal>> rootRef = db.getRoot(Animal.class);
+		LightList<Animal> root = rootRef.value;
 		long time1 = System.currentTimeMillis();
 		System.out.println("Time elapsed: " + (time1 - time01));
+		System.out.println("Root size: " + root.size());
 		System.out.println("Root:");
 //		for (int i = 0; i < root.size(); i++) {
 //			System.out.println(" - " + root.get(i));
 //		}
 		long prectime = System.currentTimeMillis();
-		for (int i = 0; i < 2/*2000000*/; i++) {
+		for (int i = 0; i < 2000000000/* 2000000 */; i++) {
-			root.add("Test " + i);
+			Animal animal = new StrangeAnimal(i % 40);
+			root.add(animal);
 			if (i > 0 && i % 200000 == 0) {
 				long precprectime = prectime;
 				prectime = System.currentTimeMillis();
-				System.out.println("Element "+i + " ("+(prectime-precprectime)+"ms)");
+				System.out.println("Element " + i + " (" + (prectime - precprectime) + "ms)");
 			}
 		}
 		long time2 = System.currentTimeMillis();
-		System.out.println("Root size: "+root.size());
+		System.out.println("Root size: " + root.size());
 		System.out.println("Time elapsed: " + (time2 - time1));
-		System.out.println("Used memory: " + ((Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory()) / 1024 / 1024) + "MB");
+		System.out.println("Used memory: "
+				+ ((Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory()) / 1024 / 1024) + "MB");
+		long time2_0 = System.currentTimeMillis();
+		System.out.println("Filtering strings...");
+		//root.removeIf(Animal::hasFourLegs);
+		long time2_1 = System.currentTimeMillis();
+		System.out.println("Time elapsed: " + (time2_1 - time2_0));
+		ObjectList<Animal> results = new ObjectArrayList<>();
+		
+		root.forEach((value) -> {
+			if (Animal.hasFourLegs(value)) {
+				results.add(value);
+			}
+			//System.out.println("val:" + value);
+		});
+		long time2_2 = System.currentTimeMillis();
+		System.out.println("Time elapsed: " + (time2_2 - time2_1));
+		System.out.println("Used memory: "
+				+ ((Runtime.getRuntime().totalMemory() - Runtime.getRuntime().freeMemory()) / 1024 / 1024) + "MB");
 		System.out.println("Saving database...");
+		System.out.println("Root size: " + root.size());
 		db.close();
 		long time3 = System.currentTimeMillis();
-		System.out.println("Time elapsed: " + (time3 - time2));
+		System.out.println("Time elapsed: " + (time3 - time2_2));
+	}
+
+	public static <T> Predicate<T> not(Predicate<T> t) {
+		return t.negate();
 	}
 }

src/main/java/org/warp/jcwdb/exampleimpl/Cat.java

@@ -0,0 +1,12 @@
+package org.warp.jcwdb.exampleimpl;
+
+public class Cat extends Animal {
+	public Cat() {
+		this.legsCount = 12;
+	}
+
+	@Override
+	public String toString() {
+		return "Cat [legsCount=" + legsCount + "]";
+	}
+}

src/main/java/org/warp/jcwdb/exampleimpl/Dog.java

@@ -0,0 +1,12 @@
+package org.warp.jcwdb.exampleimpl;
+
+public class Dog extends Animal {
+	public Dog() {
+		this.legsCount = 4;
+	}
+
+	@Override
+	public String toString() {
+		return "Dog [legsCount=" + legsCount + "]";
+	}
+}

src/main/java/org/warp/jcwdb/exampleimpl/StrangeAnimal.java

@@ -0,0 +1,15 @@
+package org.warp.jcwdb.exampleimpl;
+
+public class StrangeAnimal extends Animal {
+	public StrangeAnimal() {
+		super();
+	}
+	public StrangeAnimal(int legs) {
+		super();
+		this.legsCount = legs;
+	}
+	@Override
+	public String toString() {
+		return "StrangeAnimal [legsCount=" + legsCount + "]";
+	}
+}

src/test/java/org/warp/jcwdb/AppTest.java

@@ -115,31 +115,4 @@ public class AppTest
     	Files.delete(path);
     	Files.delete(idx);
     }
-    
-    /**
-     * 
-     * @throws IOException 
-     */
-    @Test
-    public void shouldActAsAnArrayListWithDifferentObjects() throws IOException
-    {
-    	Path path = Files.createTempFile("", ".db"), idx = Files.createTempFile("", ".idx");
-    	JCWDatabase db = new JCWDatabase(path, idx);
-    	EntryReference<LightList<String>> ref = db.getRoot();
-    	LightList<String> list1 = ref.value;
-    	ArrayList<String> list2 = new ArrayList<String>();
-    	for (int i = 0; i < 10; i++) {
-    		String s = String.valueOf(i);
-    		list1.add(s);
-    		list2.add(s);
-    	}
-    	assertTrue(list1.size() == list2.size());
-    	for (int i = 0; i < 10; i++) {
-    		assertTrue(list1.get(i) == list2.get(i));
-    		assertTrue(list2.get(i) == list1.get(i));
-    	}
-    	db.close();
-    	Files.delete(path);
-    	Files.delete(idx);
-    }
 }