Merge branch 'KDTree' into 'TeamB'

Kd tree

See merge request schankuc/2XB3!6

src/biotree/Data.java

+package biotree;
+
+import sort.KDT;
+
+public class Data {
+	KDT data = new KDT<Integer>();
+	
+	public static void initialize(Record rec) {
+		
+	}
+}

src/sandbox/Point.java

+package sandbox;
+
+public class Point implements Comparable<Point> {
+	private final int x;
+	private final int y;
+	
+	public Point(int x, int y) {
+		this.x = x;
+		this.y = y;
+	}
+	
+	public int getX() {
+		return this.x;
+	}
+	
+	public int getY() {
+		return this.y;
+	}
+	
+	public String toString() {
+		return String.format("(%d,%d)", x, y);
+	}
+
+	@Override
+	public int compareTo(Point o) {
+		// TODO Auto-generated method stub
+		return 0;
+	}
+}

src/sort/Bound.java

+package sort;
+
+public enum Bound {
+	LOWER, UPPER, LOWHIGH, ANY;
+}

src/sort/GeneralCompare.java

 package sort;
 
 public interface GeneralCompare<T> {
+	/**
+	 * Compare two Comparable elements based on an arbitrary ordering definition.
+	 * @param a1 The first value to be compared.
+	 * @param a2 The second value to be compared
+	 * @return Integer < 0 if a1 is less than a2, 0 if equal and > 0 if a1 is bigger than a2
+	 */
 	public int compare(Comparable<T> a1, Comparable<T> a2);
 }

src/sort/GeneralRange.java

+package sort;
+
+public interface GeneralRange<T extends Comparable<T>> {
+	/**
+	 * Compare two Comparable elements based on an arbitrary ordering definition.
+	 * @param a1 The first value to be compared.
+	 * @param a2 The second value to be compared
+	 * @return Integer < 0 if a1 is less than a2, 0 if equal and > 0 if a1 is bigger than a2
+	 */
+	public int isInBounds(T a1);
+}

src/sort/KDT.java

+package sort;
+
+import sandbox.Point;
+import java.util.ArrayList;
+
+public class KDT<KeyVal extends Comparable<KeyVal>> {
+	Node root;
+	ArrayList<GeneralCompare<KeyVal>> axes;
+	
+	public static void main(String[] args) {
+		GeneralCompare<Point> compX = (p1, p2) -> ((Point) p1).getX() - ((Point) p2).getX();
+		GeneralCompare<Point> compY = (p1, p2) -> ((Point) p1).getY() - ((Point) p2).getY();
+		
+		//(2,3), (4,7), (5,4), (7,2), (8,1), (9,6)
+		//(8,1), (7,2), (2,3), (5,4), (9,6), (4,7)
+		Point p1 = new Point(2,3);
+		Point p2 = new Point(5,4);
+		Point p3 = new Point(9,6);
+		Point p4 = new Point(4,7);
+		Point p5 = new Point(8,1);
+		Point p6 = new Point(7,2);
+		
+		ArrayList<GeneralCompare<Point>> axes = new ArrayList<GeneralCompare<Point>>();
+		axes.add(compX);
+		axes.add(compY);
+		
+		Point[] pts = {p1, p2, p3, p4, p5, p6};
+		
+		KDT<Point> kdt = new KDT<Point>(axes, pts);
+		System.out.println(kdt.size());
+		System.out.println(kdt.height());
+		
+		//GeneralRange<Point> xRange = p -> 4 <= p.getX() && p.getX() <= 6;
+		//GeneralRange<Point> yRange = p -> 3 <= p.getY() && p.getY() <= 5;
+		
+		GeneralRange<Point> xRange = p -> p.getX() < 2 ? -1 : (p.getX() > 7 ? 1 : 0);
+		GeneralRange<Point> yRange = p -> 0;//p.getY() < 3 ? -1 : (p.getY() > 6 ? 1 : 0);
+		
+		ArrayList<GeneralRange<Point>> ranges = new ArrayList<GeneralRange<Point>>();
+		ranges.add(xRange);
+		ranges.add(yRange);
+		
+		Iterable<Point> results = kdt.rangeSearch(ranges);
+		
+		System.out.println("Results");
+		for (Point p : results) {
+			System.out.println(p);
+		}
+
+		System.out.println(kdt.toString());
+	}
+	
+	private class Node{
+		private KeyVal keyval;
+		private Node left, right;
+		private int n;
+		
+		public Node(KeyVal keyval, int n) {
+			this.keyval = keyval;
+			this.n = n;
+		}
+	}
+	
+	/**
+	 * Create a new KD-tree from an array of key-value paired objects.
+	 * @param axes A sequence of k GeneralCompare functions which compare based on each of the k axes.
+	 * For example, to order a point based on x in the first axis and y in the second, the two
+	 * GeneralCompares should correspond to x and y respectively. The length k of this list also
+	 * defines the number of axes contained within the tree (the number of unique values on which
+	 * to index the data).
+	 * @param keyvals An array of key-value pairs to be inserted into the tree initially.
+	 */
+	public KDT(ArrayList<GeneralCompare<KeyVal>> axes, Comparable<KeyVal>[] keyvals) {
+		this.axes = axes;
+		root = buildTree(keyvals, 0, keyvals.length - 1, 0);
+	}
+	
+	private Node buildTree(Comparable<KeyVal>[] keyvals, int lo, int hi, int depth) {
+		if (lo > hi) return null;
+		int axis = depth % getK();
+		
+		int mid = (lo + hi) / 2;
+		MergeSort.sort(keyvals, lo, hi, axes.get(axis));
+		KeyVal median = (KeyVal) keyvals[mid];
+		
+		System.out.println(median);
+		
+		//TODO: fix size
+		Node newNode = new Node(median, 0);
+		newNode.left = buildTree(keyvals, lo, mid - 1, depth + 1);
+		newNode.right = buildTree(keyvals, mid + 1, hi, depth + 1);
+		
+		newNode.n = size(newNode.left) + size(newNode.right) + 1;
+		return newNode;
+	}
+	
+	/**
+	 * Range search by providing k GeneralRange functions.
+	 * @param range An ArrayList sequence of k GeneralRange functions for searching on
+	 * each of the k axes. Must equal the number of axes used in the current tree.
+	 * @return An Iterable object of all results found within the range specified.
+	 */
+	public Iterable<KeyVal> rangeSearch(ArrayList<GeneralRange<KeyVal>> range){
+		ArrayList<KeyVal> result = new ArrayList<KeyVal>();
+		rangeSearch(root, range, result, 0);
+		return result;
+	}
+	
+	private void rangeSearch(Node x, ArrayList<GeneralRange<KeyVal>> range, ArrayList<KeyVal> result, int depth) {
+		if (x == null) return;
+		int axis = depth % getK();
+		GeneralRange<KeyVal> rg = range.get(axis);
+		
+		System.out.println("Try: " + x.keyval);
+		
+		int bounds = rg.isInBounds((KeyVal) x.keyval);
+		if (bounds == 0) {
+			System.out.println(pointInside(x.keyval, range));
+			if (pointInside(x.keyval, range)) {
+				result.add(x.keyval);
+			}
+			rangeSearch(x.left, range, result, depth + 1);
+			rangeSearch(x.right, range, result, depth + 1);
+		} else if (bounds > 0) {
+			rangeSearch(x.left, range, result, depth + 1);
+		} else if (bounds < 0)
+			rangeSearch(x.right, range, result, depth + 1);
+		
+		return;
+	}
+	
+	private boolean pointInside(KeyVal pt, ArrayList<GeneralRange<KeyVal>> range) {
+		for (int i = 0; i < axes.size(); i++)
+			if (range.get(i).isInBounds(pt) != 0) return false;
+		return true;
+	}
+	
+	public int size() {
+		return size(root);
+	}
+	
+	public int height() {
+		return height(root);
+	}
+	
+	private int height(Node x) {
+		if (x == null) return 0;
+		return 1 + Math.max(height(x.left), height(x.right));
+	}
+	
+	private int size(Node x) {
+		if (x == null) return 0;
+		else return x.n;
+	}
+	
+	/**
+	 * Get the number of axes in this tree.
+	 * @return The number of axes, k, in the current tree.
+	 */
+	public int getK() {
+		return axes.size();
+	}
+	
+	public String toString() {
+		return toString(root, "");
+	}
+	
+	private String toString(Node x, String depth) {
+		if (x == null) return depth + "null\n";
+		String result = "";
+		result += depth + x.keyval.toString() + "\n";
+		result += toString(x.left, depth + "    ");
+		result += toString(x.right, depth + "    ");
+		return result;
+	}
+}

src/sort/MergeSort.java

@@ -37,7 +37,7 @@ public class MergeSort{
 		int mid = lo + (n/2);
 
 		// Fill auxiliary array
-		System.out.println("lo, mid, hi: " + lo + ", " + mid + ", " + hi);
+		//System.out.println("lo, mid, hi: " + lo + ", " + mid + ", " + hi);
 		
 		for(int k = lo; k <= hi; k++){
 			aux[k] = x[k];

src/sort/Range.java

+package sort;
+
+public class Range<Key extends Comparable<Key>> {
+	private final Bound boundType;
+	private final Key lower;
+	private final Key upper;
+	
+	public Range(Bound bt) throws Exception {
+		if (bt == Bound.ANY) {
+			boundType = bt;
+			lower = null;
+			upper = null;
+		}
+		else
+			throw new Exception("Must provide ANY bound.");
+	}
+	
+	public Range(Bound bt, Key upperOrLower) throws Exception {
+		if (bt == Bound.UPPER) {
+			upper = upperOrLower;
+			lower = null;
+		} else if (bt == Bound.LOWER) {
+			upper = upperOrLower;
+			lower = null;
+		}
+		else 
+			throw new Exception("Must provide UPPER OR LOWER bound.");
+		boundType = bt;
+	}
+	
+	public Range(Bound bt, Key lower, Key upper) throws Exception {
+		if (bt == Bound.LOWHIGH) {
+			this.lower = lower;
+			this.upper = upper;
+		} else
+			throw new Exception("Must provide LOWHIGH bound.");
+		this.boundType = bt;
+	}
+	
+	public <T> boolean inBounds(T key) {
+		if (boundType == Bound.ANY) return true;
+		else if (boundType == Bound.LOWER) 	return gc.compare(lower, key) <= 0;
+		else if (boundType == Bound.UPPER) 	return gc.compare(upper, key) >= 0;
+		else									return gc.compare(lower, key) <= 0 && gc.compare(upper, key) >= 0;
+	}
+}