Examples with MinLongHeap org.cytoscape.util.intr.MinLongHeap used on opensource projects

Example 1 with MinLongHeap

use of org.cytoscape.util.intr.MinLongHeap in project cytoscape-impl by cytoscape.

the class RTreeQueryPerformance method main.

/**
 * For given N, creates N rectangles whose centers are in the space
 * [0,1] X [0,1].  Each rectangle has width and height no greater
 * than 1/sqrt(N).  The location of the centers of the rectangles
 * and the choice of width and height for each rectangle is determined
 * by the input stream, which in most cases will be a randomly generated
 * stream of bytes.  Please see the actual code for an explanation of
 * how the input stream of bytes is converted into the rectangle
 * information.
 */
public static void main(String[] args) throws Exception {
    final RTree tree;
    // Populate the tree with entries.
    {
        int branches = Integer.parseInt(args[0]);
        int N = Integer.parseInt(args[1]);
        tree = new RTree(branches);
        double sqrtN = Math.sqrt((double) N);
        InputStream in = System.in;
        byte[] buff = new byte[16];
        int inx = 0;
        int off = 0;
        int read;
        while ((inx < N) && ((read = in.read(buff, off, buff.length - off)) > 0)) {
            off += read;
            if (off < buff.length)
                continue;
            else
                off = 0;
            int nonnegative = 0x7fffffff & assembleInt(buff, 0);
            double centerX = ((double) nonnegative) / ((double) 0x7fffffff);
            nonnegative = 0x7fffffff & assembleInt(buff, 4);
            double centerY = ((double) nonnegative) / ((double) 0x7fffffff);
            nonnegative = 0x7fffffff & assembleInt(buff, 8);
            double width = (((double) nonnegative) / ((double) 0x7fffffff)) / sqrtN;
            nonnegative = 0x7fffffff & assembleInt(buff, 12);
            double height = (((double) nonnegative) / ((double) 0x7fffffff)) / sqrtN;
            tree.insert(inx, (float) (centerX - (width / 2.0d)), (float) (centerY - (height / 2.0d)), (float) (centerX + (width / 2.0d)), (float) (centerY + (height / 2.0d)), 0.0);
            inx++;
        }
        if (inx < N)
            throw new IOException("premature end of input");
    }
    final MinLongHeap[] pointQueries;
    // Test 121 Point queries.
    {
        pointQueries = new MinLongHeap[121];
        for (int i = 0; i < pointQueries.length; i++) pointQueries[i] = new MinLongHeap();
        for (int i = 0; i < 3; i++) {
            System.gc();
            Thread.sleep(1000);
        }
        final long millisBegin = System.currentTimeMillis();
        int inx = 0;
        float currX = -0.1f;
        for (int i = 0; i < 11; i++) {
            currX += 0.1f;
            float currY = -0.1f;
            for (int j = 0; j < 11; j++) {
                currY += 0.1f;
                final LongEnumerator iter = tree.queryOverlap(currX, currY, currX, currY, null, 0, false);
                final MinLongHeap heap = pointQueries[inx++];
                while (iter.numRemaining() > 0) heap.toss(iter.nextLong());
            }
        }
        final long millisEnd = System.currentTimeMillis();
        System.err.println("point queries took " + (millisEnd - millisBegin) + " milliseconds");
    }
    final MinLongHeap[] areaQueries;
    // Test 5 area queries - each area is 0.1 X 0.1.
    {
        areaQueries = new MinLongHeap[5];
        for (int i = 0; i < areaQueries.length; i++) areaQueries[i] = new MinLongHeap();
        for (int i = 0; i < 3; i++) {
            System.gc();
            Thread.sleep(1000);
        }
        final long millisBegin = System.currentTimeMillis();
        for (int i = 0; i < 5; i++) {
            final LongEnumerator iter = tree.queryOverlap(((float) i) * 0.1f, ((float) i) * 0.1f, ((float) (i + 1)) * 0.1f, ((float) (i + 1)) * 0.1f, null, 0, false);
            final MinLongHeap heap = areaQueries[i];
            while (iter.numRemaining() > 0) heap.toss(iter.nextLong());
        }
        final long millisEnd = System.currentTimeMillis();
        System.err.println("area queries took " + (millisEnd - millisBegin) + " milliseconds");
    }
    final int[] countQueries;
    // Test 5 count queries - each area is 0.6 X 0.6.
    {
        countQueries = new int[5];
        for (int i = 0; i < 3; i++) {
            System.gc();
            Thread.sleep(1000);
        }
        final long millisBegin = System.currentTimeMillis();
        for (int i = 0; i < 5; i++) {
            final LongEnumerator iter = tree.queryOverlap(((float) i) * 0.1f, ((float) i) * 0.1f, ((float) (i + 6)) * 0.1f, ((float) (i + 6)) * 0.1f, null, 0, false);
            countQueries[i] = iter.numRemaining();
        }
        final long millisEnd = System.currentTimeMillis();
        System.err.println("count queries took " + (millisEnd - millisBegin) + " milliseconds");
    }
    for (int i = 0; i < pointQueries.length; i++) {
        final MinLongHeap heap = pointQueries[i];
        while (heap.size() > 0) System.out.print(" " + heap.deleteMin());
        System.out.println();
    }
    for (int i = 0; i < areaQueries.length; i++) {
        final MinLongHeap heap = areaQueries[i];
        while (heap.size() > 0) System.out.print(" " + heap.deleteMin());
        System.out.println();
    }
    for (int i = 0; i < countQueries.length; i++) {
        System.out.println(countQueries[i]);
    }
}