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This class is an extention of Canvas. Runs its own thread.
paint methods cannot be called directly by browser (good)
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import java.awt.*;
import java.awt.event.MouseMotionListener;
import java.awt.event.MouseListener;
import java.awt.event.MouseEvent;
import java.awt.image.BufferedImage;
import java.text.DecimalFormat;

//! @brief This class shows a sort of video of the actual AFM at work

/// It looks only as good as you make it.
class Animation extends Canvas implements Runnable {
    private Thread myThread;
    private AFMSimulator afmSim;
    private BufferedImage image;
    private int ind, time;
    private final int W = 500, H = 300;
    private final double INTERVAL = (double) W / AFMConstants.SAMPLES;
    private int delay = 100;
    private int k = 6; // speed of animation (skip rate)
    private int surface_periods = 1;
    private int zoom = 1000; // don't need this. remove.
    private final int X_AXIS = H/2 + 100;
    private Color backgroundColor;
    private Color textColor;

    public Animation() {
        setSize(W, H);
        afmSim = new AFMSimulator();
        afmSim.setParams(AFMApplet.params[0], AFMApplet.params[1], AFMApplet.params[2], AFMApplet.params[3], AFMApplet.params[4], AFMApplet.params[5], AFMApplet.params[6], AFMApplet.params[7], AFMApplet.params[8]);
        afmSim.resetSim();
        image = new BufferedImage(W, H, BufferedImage.TYPE_INT_RGB);
        textColor = AFMConstants.text_color;
        backgroundColor = AFMConstants.BG_color;
        Graphics back = image.getGraphics();
        back.setColor(backgroundColor);
        back.fillRect(0, 0, W, H);
        back.setColor(textColor);
        back.drawString("AFM Animation", 400, 20);
        ind = 0; time = 0;
        AFMApplet.drawSurface(image, afmSim, surface_periods, AFMConstants.surface_color);
        addMouseListener(new MouseCoordListener());
        addMouseMotionListener(new MouseCoordListener());
    }

    public Animation(int _delay) {
        this();
        delay = _delay;
    }

    public void start() {
        if (myThread != null) stop();
        myThread = new Thread(this);
        myThread.start();
        AFMApplet.drawSurface(image, afmSim, surface_periods, AFMConstants.surface_color);
    }//end start

    public void reset() {
        image = new BufferedImage(W, H, BufferedImage.TYPE_INT_RGB);
        ind = 0; time = 0;
        Graphics back = image.getGraphics();
        back.setColor(backgroundColor);     // background color
        back.fillRect(0, 0, W, H);
        back.setColor(textColor);     // title text color
        back.drawString("AFM Animation", 400, 20);
        afmSim = new AFMSimulator();
        afmSim.setParams(AFMApplet.params[0], AFMApplet.params[1], AFMApplet.params[2], AFMApplet.params[3], AFMApplet.params[4], AFMApplet.params[5], AFMApplet.params[6], AFMApplet.params[7], AFMApplet.params[8]);
        afmSim.resetSim();
        AFMApplet.drawSurface(image, afmSim, surface_periods, AFMConstants.surface_color);
    }

    public void resume() {
        start();
    }

    public void run() {
        while (myThread != null) {
            repaint();
            try {
                Thread.sleep(delay);
            }
            catch (InterruptedException e) {
                this.stop();
            }
        }
    }//end run

    public void stop() {
        myThread = null;
    }

    public void cleanup() {
        myThread = null;
        afmSim = null;
        image = null;
        backgroundColor = null;
        textColor = null;
    }

    public void setState(AFMSimulator afmSim) {
        this.afmSim = afmSim;
    }

    public void clear() {
        Graphics back = image.getGraphics();
        back.setColor(backgroundColor);
        back.fillRect(0, 0, W, H);
    }

    public void update(Graphics g) {
        Graphics back = image.getGraphics();
        back.setColor(backgroundColor);
        back.fillRect(0, 0, W, H);

        back = image.getGraphics();
        back.setColor(textColor);
        back.drawString("AFM Animation", 400, 20);

        int old;
        if (ind > 0)
            old = ind - k;
        else
            old = k * (AFMConstants.SAMPLES / k);
        for (int i = 0; i < AFMConstants.SAMPLES; i++) {
            int xOld = W / 2 + (int) (i * INTERVAL);
            int j = AFMMath.mod((i + ind + AFMSimulator.STROBE_OFFSET), AFMConstants.SAMPLES); //if(j>=AFMConstants.SAMPLES) j-=AFMConstants.SAMPLES;
            int yNew = AFMApplet.SURFACE_HEIGHT - (int) Math.round(afmSim.getSurface().getY(j) * 500 / surface_periods);
            if (xOld > W) xOld -= W;
            back.setColor(AFMConstants.surface_color);
            back.drawOval(xOld, yNew, 0, 0);
        }
        back.setColor(backgroundColor);
        DecimalFormat dec = new DecimalFormat("0.###");
        String t = dec.format(afmSim.getAFM().getTime(old));
        back.drawString("Time = " + time + " = " + t, 20, 290); //afmSim.getAFM().getTime(old), others (0) ind-1-->time
        paint(g);
    }

    public void paint(Graphics g) {
        Graphics back = image.getGraphics();

        if (AFMMath.dif(AFMConstants.SAMPLES, ind, 20))        /**** and selection is STROBOSCOPIC,... ****/
            back.setColor(textColor);
        else
            back.setColor(AFMConstants.info_color);
        DecimalFormat dec = new DecimalFormat("0.###");
        String t = dec.format(afmSim.getAFM().getTime(ind));
        back.drawString("Time = " + time + " = " + t + " ms", 20, 290); //afmSim.getAFM().getTime(ind)

        int tipX = (int) (W / 2 + (afmSim.getAFM().getX(ind) - afmSim.getAFM().getV() * afmSim.getAFM().getT(ind)) * AFMConstants.SAMPLES / (Surface.L));
        int tipY = AFMApplet.SURFACE_HEIGHT - (int) Math.round(afmSim.getAFM().getY(ind) * 500 / surface_periods);
        // draw AFM tip (triangle)
        int x[] = {tipX - 5, tipX, tipX + 5}, y[] = {tipY - 7, tipY, tipY - 7};
        back.fillPolygon(x, y, 3);
        // draw AFM cantilever
        back.setColor(AFMConstants.AFMspring_color);
        //back.drawLine((int) (W / 2 + (afmSim.getAFM().getX(ind) - afmSim.getAFM().getV() * afmSim.getAFM().getT(ind)) * AFMConstants.SAMPLES / Surface.L), (int) (AFMApplet.SURFACE_HEIGHT - (int) Math.round(afmSim.getAFM().getY(ind) * 500 / surface_periods) - 8), W / 2, 0);
        back.drawArc((int) (W / 2 + (afmSim.getAFM().getX(ind) - afmSim.getAFM().getV() * afmSim.getAFM().getT(ind)) * AFMConstants.SAMPLES / Surface.L), (int) (AFMApplet.SURFACE_HEIGHT - (int) Math.round(afmSim.getAFM().getY(ind) * 500 / surface_periods) - 38), W*3/2, 55, 90, 90);
        //back.drawLine((int) (W / 2 + (afmSim.getAFM().getX(ind) - afmSim.getAFM().getV() * afmSim.getAFM().getT(ind)) * AFMConstants.SAMPLES / Surface.L), (int) (AFMApplet.SURFACE_HEIGHT - (int) Math.round(afmSim.getAFM().getY(ind) * 500 / surface_periods) - 8), W, (int) (AFMApplet.SURFACE_HEIGHT - (int) Math.round(afmSim.getAFM().getY(ind) * 500 / surface_periods) - 8));
        g.drawImage(image, 0, 0, this);
        ind += k;
        if (ind >= AFMConstants.SAMPLES) {
            afmSim.getMore();              // add a warning when there is dragging
            ind = 0; time++;
        }
    }//end paint

        private class MouseCoordListener implements MouseMotionListener, MouseListener {

        private String lastInfo = "";

        public void mouseDragged(MouseEvent e) {
            //To change body of implemented methods use File | Settings | File Templates.
        }

        public void mouseMoved(MouseEvent event) {
            Graphics back = image.getGraphics();
            double x = event.getPoint().getX();
            double y = event.getPoint().getY();
            double x_realValue = (double) (x - W / 2) * Surface.L / W;        // x_center holds *actual* x center value (in the system, not on the display)
            if(x_realValue > 1) x_realValue -= 1;
            double y_realValue = (double) (X_AXIS - y) / zoom;
            back.setColor(backgroundColor);
            back.drawString(lastInfo, 20, 270);
            DecimalFormat dec = new DecimalFormat("0.###");
            dec.setMaximumFractionDigits((int)Math.round(AFMMath.log2(zoom/100)) + 4);
            back.setColor(AFMConstants.info_color);
            lastInfo = "(" + dec.format(x_realValue) + ", " + dec.format(y_realValue) + ")";
            back.drawString(lastInfo, 20, 270);
            /***ADD CODE HERE***/
        }

        public void mouseClicked(MouseEvent event) {
            if(AFMApplet.zoomTool.isSelected()) {
                if (event.getButton() != MouseEvent.BUTTON1)
                    surface_periods *= 2;
                else
                    surface_periods /= 2;
                if(surface_periods<1) surface_periods = 1;
                //Graphics back = surface_image.getGraphics();
                //back.setColor(backgroundColor);
                //back.fillRect(0,0,W,H);
                //AFMApplet.drawSurface(surface_image, afmSim, surface_periods, AFMConstants.surface_color);
                clear();
                repaint();
            }
        }


        public void mouseEntered(MouseEvent e) {
            //To change body of implemented methods use File | Settings | File Templates.
        }

        public void mouseExited(MouseEvent e) {
            //To change body of implemented methods use File | Settings | File Templates.
        }

        public void mousePressed(MouseEvent e) {
            //To change body of implemented methods use File | Settings | File Templates.
        }

        public void mouseReleased(MouseEvent e) {
            //To change body of implemented methods use File | Settings | File Templates.
        }
    }// end MouseListener

}//end Animation