Fix numerous warnings (#37)

* Fix warnings

CHANGELOG.md

@@ -3,6 +3,7 @@
 ## Unreleased
 
 - getStats() for empty trees fails. [#36](https://github.com/tzaeschke/phtree/pull/36)
+- Fix some warnings. [#37](https://github.com/tzaeschke/phtree/pull/37)
 
 ## 2.8.0 - 2023-07-29
 

src/main/java/ch/ethz/globis/phtree/nv/PhTreeNVSolidF.java

@@ -169,7 +169,7 @@ public PHREntryIterator queryInclude(double[] lower, double[] upper) {
 		long[] lLow = new long[lower.length << 1];
 		pre.pre(lower, lower, lLow);
 		pre.pre(upper, upper, lUpp);
-		return new PHREntryIterator((PhIteratorNV) pht.query(lLow, lUpp), DIM);
+		return new PHREntryIterator(pht.query(lLow, lUpp), DIM);
 	}
 
 	/**
@@ -183,7 +183,7 @@ public PHREntryIterator queryIntersect(double[] lower, double[] upper) {
 		long[] lLow = new long[lower.length << 1];
 		pre.pre(MIN, lower, lLow);
 		pre.pre(upper, MAX, lUpp);
-		return new PHREntryIterator((PhIteratorNV) pht.query(lLow, lUpp), DIM);
+		return new PHREntryIterator(pht.query(lLow, lUpp), DIM);
 	}
 
 	public class PHREntryIterator implements Iterator<PHREntry> {

src/main/java/ch/ethz/globis/phtree/nv/PhTreeVProxy.java

@@ -34,7 +34,7 @@ public PhTreeVProxy(int dim) {
 	}
 
 	public PhTreeVProxy(PhTree<Object> tree) {
-		this.tree = (PhTree<Object>) tree;
+		this.tree = tree;
 	}
 
 	@Override

src/main/java/ch/ethz/globis/phtree/util/BitsInt.java

@@ -168,7 +168,7 @@ public static void insertBits(int[] ba, final int start, final int nBits) {
 			ba[dstByteStart] = (ba[dstByteStart] & ~mask0) |
 					(Integer.rotateRight(ba[srcByteStart], localShift) & mask0);
 			//write second part
-			int mask1 = (int) mask0 >>> -srcLocalStart; //(UNIT_BITS-srcLocalStart);
+			int mask1 = mask0 >>> -srcLocalStart; //(UNIT_BITS-srcLocalStart);
 			ba[dstByteStart] = (ba[dstByteStart] & ~mask1) | ((buf1 >>> localShift) & mask1);
 		} else {
 			//write first part
@@ -359,7 +359,7 @@ public static void copyBitsLeft1(int[] src, int posSrc, int[] dst, int posDst, i
 				//TODO? if (localEnd==0) localEnd==32;
 				int leftMask = (int) (dstLocalEnd==0 ? UNIT_0xFF : ~(UNIT_0xFF >>> dstLocalEnd)); // e.g. 1111.1110
 				int rightMask = (int) (UNIT_0xFF >>> (dstLocalEnd-srcLocalEnd));
-				int maskPost = (int) leftMask & rightMask;
+				int maskPost = leftMask & rightMask;
 				//TODO
 				//TODO local mask should go from dstLocalStart to dstLocalEnd only.
 				//TODO

src/main/java/ch/ethz/globis/phtree/util/JmxTools.java

@@ -212,7 +212,8 @@ private static void processNotification(ObjectName name) {
 		totalDiff += mi.diff;
 		totalTime += mi.duration;
 	}
-
+
+	@SuppressWarnings("unchecked")
 	public static void gcCheck() {
 		try {
 			MBeanServer server = ManagementFactory.getPlatformMBeanServer();

src/main/java/ch/ethz/globis/phtree/util/Refs.java

@@ -9,6 +9,7 @@
 import java.io.IOException;
 import java.io.ObjectInput;
 import java.io.ObjectOutput;
+import java.lang.reflect.Array;
 import java.util.Arrays;
 
 import ch.ethz.globis.phtree.PhTreeHelper;
@@ -140,7 +141,7 @@ public static <T> T[] arrayCreate(int size) {
      * @return Same array or expanded array.
      * @param <T> array type
      */
-    @Deprecated
+    // TODO remove? was @Deprecated
     public static <T> T[] arrayEnsureSize(T[] oldA, int requiredSize) {
     	if (isCapacitySufficient(oldA, requiredSize)) {
     		return oldA;
@@ -177,8 +178,8 @@ public static <T> T[] arrayClone(T[] oldA) {
     private static <T> boolean isCapacitySufficient(T[] a, int requiredSize) {
     	return a.length >= requiredSize;
     }
-    
-    @Deprecated
+
+	// TODO remove? was @Deprecated
     @SuppressWarnings("unchecked")
 	public static <T> T[] arrayTrim(T[] oldA, int requiredSize) {
     	int reqSize = calcArraySize(requiredSize);
@@ -191,7 +192,7 @@ public static <T> T[] arrayTrim(T[] oldA, int requiredSize) {
     	return newA;
     }
 
-    @Deprecated
+	// TODO remove? was @Deprecated
 	public static <T> void insertAtPos(T[] values, int pos, T value) {
 		copyRight(values, pos, values, pos+1, values.length-pos-1);
 		values[pos] = value;
@@ -216,8 +217,8 @@ public static <T> T[] insertSpaceAtPos(T[] values, int pos, int requiredSize) {
 		copyRight(values, pos, dst, pos+1, requiredSize-1-pos);
 		return dst;
 	}
-	
-	@Deprecated
+
+	// TODO remove? was @Deprecated
 	public static <T> void removeAtPos(T[] values, int pos) {
 		if (pos < values.length-1) {
 			copyLeft(values, pos+1, values, pos, values.length-pos-1);
@@ -300,5 +301,14 @@ public static <T> T[] read(ObjectInput in) throws IOException {
 		}
 		return ret;
 	}
-
+
+	@SuppressWarnings("unchecked")
+	public static <T> T[] newArray(int size) {
+		return (T[]) new Object[size];
+	}
+
+	@SuppressWarnings("unchecked")
+	public static <T> T[] newArray(Class<T> c, int size) {
+		return (T[]) Array.newInstance(c, size);
+	}
 }

src/main/java/ch/ethz/globis/phtree/v11/NodeIteratorListReuse.java

@@ -11,6 +11,7 @@
 import ch.ethz.globis.pht64kd.MaxKTreeI.NtEntry;
 import ch.ethz.globis.phtree.PhEntry;
 import ch.ethz.globis.phtree.PhTreeHelper;
+import ch.ethz.globis.phtree.util.Refs;
 import ch.ethz.globis.phtree.v11.nt.NtIteratorMask;
 
 /**
@@ -31,7 +32,8 @@ public class NodeIteratorListReuse<T, R> {
 
 	private class PhIteratorStack {
 		@SuppressWarnings("unchecked")
-		private final NodeIterator[] stack = new NodeIteratorListReuse.NodeIterator[64];
+		private final NodeIterator[] stack =
+				Refs.newArray(NodeIteratorListReuse.NodeIterator.class, 64);
 		private int size = 0;
 
 
@@ -70,14 +72,9 @@ private final class NodeIterator {
 
 		/**
 		 * 
-		 * @param node
-		 * @param dims
-		 * @param valTemplate A null indicates that no values are to be extracted.
+		 * @param node node
 		 * @param lower The minimum HC-Pos that a value should have.
-		 * @param upper
-		 * @param minValue The minimum value that any found value should have. 
-		 * 				   If the found value is lower, the search continues.
-		 * @param maxValue
+		 * @param upper The maximum HC-Pos that a value should have.
 		 */
 		void reinitAndRun(Node node, long lower, long upper) {
 			this.node = node;

src/main/java/ch/ethz/globis/phtree/v11/PhIteratorFullNoGC.java

@@ -11,6 +11,7 @@
 import ch.ethz.globis.phtree.PhEntry;
 import ch.ethz.globis.phtree.PhFilter;
 import ch.ethz.globis.phtree.PhTree.PhExtent;
+import ch.ethz.globis.phtree.util.Refs;
 
 /**
  * This PhIterator uses a loop instead of recursion in findNextElement();. 
@@ -32,7 +33,7 @@ private class PhIteratorStack {
 
 		@SuppressWarnings("unchecked")
 		public PhIteratorStack() {
-			stack = new NodeIteratorFullNoGC[PhTree11.DEPTH_64];
+			stack = Refs.newArray(NodeIteratorFullNoGC.class, PhTree11.DEPTH_64);
 		}
 
 		public boolean isEmpty() {

src/main/java/ch/ethz/globis/phtree/v11/PhIteratorNoGC.java

@@ -12,6 +12,7 @@
 import ch.ethz.globis.phtree.PhFilter;
 import ch.ethz.globis.phtree.PhTree.PhQuery;
 import ch.ethz.globis.phtree.PhTreeHelper;
+import ch.ethz.globis.phtree.util.Refs;
 
 /**
  * This PhIterator uses a loop instead of recursion in findNextElement();. 
@@ -33,7 +34,7 @@ private class PhIteratorStack {
 
 		@SuppressWarnings("unchecked")
 		public PhIteratorStack() {
-			stack = new NodeIteratorNoGC[PhTree11.DEPTH_64];
+			stack = Refs.newArray(NodeIteratorNoGC.class, PhTree11.DEPTH_64);
 		}
 
 		public boolean isEmpty() {

src/main/java/ch/ethz/globis/phtree/v11/PhQueryKnnMbbPPList.java

@@ -15,6 +15,7 @@
 import ch.ethz.globis.phtree.PhFilterDistance;
 import ch.ethz.globis.phtree.PhTree.PhExtent;
 import ch.ethz.globis.phtree.PhTree.PhKnnQuery;
+import ch.ethz.globis.phtree.util.Refs;
 
 /**
  * kNN query implementation that uses preprocessors and distance functions.
@@ -302,7 +303,7 @@ void reset(int newSize, long[] center) {
 			this.center = center;
 			maxDistance = Double.MAX_VALUE;
 			if (data == null) {
-				data = new PhEntryDist[newSize];
+				data = Refs.newArray(PhEntryDist.class, newSize);
 				distData = new double[newSize];
 				for (int i = 0; i < data.length; i++) {
 					data[i] = createEntry();

src/main/java/ch/ethz/globis/phtree/v11/PhTree11.java

@@ -133,6 +133,9 @@ public int size() {
 
 	@Override
 	public PhTreeStats getStats() {
+		if (getRoot() == null) {
+			return new PhTreeStats(DEPTH_64);
+		}
 		return getStats(0, getRoot(), new PhTreeStats(DEPTH_64));
 	}
 

src/main/java/ch/ethz/globis/phtree/v11/nt/NtIteratorMask.java

@@ -11,6 +11,7 @@
 import ch.ethz.globis.pht64kd.MaxKTreeI;
 import ch.ethz.globis.pht64kd.MaxKTreeI.NtEntry;
 import ch.ethz.globis.pht64kd.MaxKTreeI.PhIterator64;
+import ch.ethz.globis.phtree.util.Refs;
 
 
 /**
@@ -34,7 +35,7 @@ private class PhIteratorStack {
 
 		@SuppressWarnings("unchecked")
 		public PhIteratorStack(int depth) {
-			stack = new NtNodeIteratorMask[depth];
+			stack = Refs.newArray(NtNodeIteratorMask.class, depth);
 		}
 
 		public boolean isEmpty() {

src/main/java/ch/ethz/globis/phtree/v11/nt/NtIteratorMinMax.java

@@ -11,6 +11,7 @@
 import ch.ethz.globis.pht64kd.MaxKTreeI;
 import ch.ethz.globis.pht64kd.MaxKTreeI.NtEntry;
 import ch.ethz.globis.pht64kd.MaxKTreeI.PhIterator64;
+import ch.ethz.globis.phtree.util.Refs;
 
 
 /**
@@ -34,7 +35,7 @@ private class PhIteratorStack {
 
 		@SuppressWarnings("unchecked")
 		public PhIteratorStack(int depth) {
-			stack = new NtNodeIteratorMinMax[depth];
+			stack = Refs.newArray(NtNodeIteratorMinMax.class, depth);
 		}
 
 		public boolean isEmpty() {

src/main/java/ch/ethz/globis/phtree/v11/nt/NtNodePool.java

@@ -7,6 +7,7 @@
 package ch.ethz.globis.phtree.v11.nt;
 
 import ch.ethz.globis.phtree.PhTreeHelper;
+import ch.ethz.globis.phtree.util.Refs;
 
 /**
  * Manipulation methods and pool for NtNodes.
@@ -15,8 +16,8 @@
  */
 public class NtNodePool {
 
-	private static final NtNode<?>[] POOL = 
-			new NtNode[PhTreeHelper.MAX_OBJECT_POOL_SIZE];
+	private static final NtNode<?>[] POOL =
+			Refs.newArray(NtNode.class, PhTreeHelper.MAX_OBJECT_POOL_SIZE);
 	private static int poolSize;
 	/** Nodes currently used outside the pool. */
 	private static int activeNodes = 0;

src/main/java/ch/ethz/globis/phtree/v13/NodeIteratorListReuse.java

@@ -22,6 +22,7 @@
 import java.util.List;
 
 import ch.ethz.globis.phtree.PhEntry;
+import ch.ethz.globis.phtree.util.Refs;
 
 /**
  * A NodeIterator that returns a list instead of an Iterator AND reuses the NodeIterator.
@@ -41,7 +42,8 @@ public class NodeIteratorListReuse<T, R> {
 
 	private class PhIteratorStack {
 		@SuppressWarnings("unchecked")
-		private final NodeIterator[] stack = new NodeIteratorListReuse.NodeIterator[64];
+		private final NodeIterator[] stack =
+				Refs.newArray(NodeIteratorListReuse.NodeIterator.class,64);
 		private int size = 0;
 
 

src/main/java/ch/ethz/globis/phtree/v13/PhIteratorFullNoGC.java

@@ -13,6 +13,7 @@
 import ch.ethz.globis.phtree.PhEntry;
 import ch.ethz.globis.phtree.PhFilter;
 import ch.ethz.globis.phtree.PhTree.PhExtent;
+import ch.ethz.globis.phtree.util.Refs;
 
 /**
  * This PhIterator uses a loop instead of recursion in findNextElement();. 
@@ -34,7 +35,7 @@ private class PhIteratorStack {
 
 		@SuppressWarnings("unchecked")
 		PhIteratorStack() {
-			stack = new NodeIteratorFullNoGC[PhTree13.DEPTH_64];
+			stack = Refs.newArray(NodeIteratorFullNoGC.class, PhTree13.DEPTH_64);
 		}
 
 		public boolean isEmpty() {

src/main/java/ch/ethz/globis/phtree/v13/PhIteratorKnn.java

@@ -66,7 +66,7 @@ public boolean isValid(int bitsToIgnore, long[] prefix) {
     }
 
     @Override
-    public PhKnnQuery<T> reset(int minResults, PhDistance distFn, long[] center) {
+    public PhKnnQuery<T> reset(int minResults, PhDistance distFn, long ... center) {
         this.center = center;
         this.distFn = distFn == null ? this.distFn : distFn;
         this.currentDistance = Double.MAX_VALUE;

src/main/java/ch/ethz/globis/phtree/v13/PhIteratorNoGC.java

@@ -14,6 +14,7 @@
 import ch.ethz.globis.phtree.PhFilter;
 import ch.ethz.globis.phtree.PhTree.PhQuery;
 import ch.ethz.globis.phtree.PhTreeHelper;
+import ch.ethz.globis.phtree.util.Refs;
 
 /**
  * This PhIterator uses a loop instead of recursion in findNextElement();. 
@@ -35,7 +36,7 @@ private class PhIteratorStack {
 
 		@SuppressWarnings("unchecked")
 		PhIteratorStack() {
-			stack = new NodeIteratorNoGC[PhTree13.DEPTH_64];
+			stack = Refs.newArray(NodeIteratorNoGC.class, PhTree13.DEPTH_64);
 		}
 
 		public boolean isEmpty() {

src/main/java/ch/ethz/globis/phtree/v13/PhTree13.java

@@ -44,46 +44,46 @@
 
 /**
  * n-dimensional index (quad-/oct-/n-tree).
- *
+ * <p>
  *
  * Version 13:
  * Version 13SP: Based on Version 11. Some optimizations, for example store HC-Pos in postFix.
  * 				Version 13SP has 'synchronized' object pools and NT nodes for high dim.
  * 			    Version 13 has local unsynchronized pools. It also has the NT tree removed.
- * 
+ * <p>
  * Version 12: This was an attempt at a persistent version.
- * 
+ * <p>
  * Version 11: Use of NtTree for Nodes
  *             'null' values are replaced by NULL, this allows removal of AHC-exists bitmap
  *             Removal of recursion (and reimplementation) for get/insert/delete/update 
- * 
+ * <p>
  * Version 10b: Moved infix into parent node.
- * 
+ * <p>
  * Version 10: Store sub-nodes and postfixes in a common structure (one list/HC of key, one array)
  *             Advantages: much easier iteration through node, replacement of sub/post during 
  *             updates w/o bit shifting, can check infix without accessing sub-node (good for I/O).
- * 
+ * <p>
  * Version 8b: Extended array pooling to all arrays
- * 
+ * <p>
  * Version 8: Use 64bit depth everywhere. This should simplify a number of methods, especially
  *            regarding negative values.
- * 
+ * <p>
  * Version 7: Uses PhEntry to store/return keys.
- *
+ * <p>
  * Version 5: moved postCnt/subCnt into node.
- *
+ * <p>
  * Version 4: Using long[] instead of int[]
- *
+ * <p>
  * Version 3: This includes values for each key.
- *
+ * <p>
  * Storage:
  * - classic: One node per combination of bits. Unused nodes can be cut off.
  * - use prefix-truncation: a node may contain a series of unique bit combinations
- *
+ * <p>
  * Hypercube: expanded byte array that contains 2^DIM references to sub-nodes (and posts, depending 
  * on implementation)
  * Linearization: Storing Hypercube as paired array of index / non_null_reference 
- *
+ * <p>
  * See also : T. Zaeschke, C. Zimmerli, M.C. Norrie; 
  * "The PH-Tree -- A Space-Efficient Storage Structure and Multi-Dimensional Index", 
  * (SIGMOD 2014)