Visualizing HIV Envelope Proteins: Week 7 Project Status

1. Visualizing HIV Envelope Proteins: Week 7 Project Status Phil Heller CMP 261 Spring 2010

2. Jmol • Open source • 498 source files • 190,000 lines • Mean ~400 lpf but • Biggest file is 14,523 lines • Several > 3k lines • Many > 2k lines

3. Tasks • ~ 6 main frames rather than 1 • Multiplex all spatial events • Inject markup scripts • Generate markup scripts from lab data

4. Status

5. Java’s Event Model • Class XXXEvent • Source • Low-level details • Semantics • Interface XXXListener • 1 method for each semantic category • No convention for method names • Method args are events • Event source • addXXXListener() • removeXXXListener()

6. Using the Model class ReportingListener implements MouseListener { public void mouseClicked(MouseEvente) { System.out.println(“CLICK at “ + e.getX() + e.getY()); } // other event handlers } class SamplePanel extends JPanel { SamplePanel() { ReportingListenerrl = new ReportingListener (); addMouseListener(rl); } }

7. How to share Jmol events? • Modify existing event handlers • High degree of convolution • Evidence of “black-box maintenance” • Hard to prove correctness of my changes • LBTW bugs • Preserve existing event handlers, add my own • Can’t break what I don’t touch

8. My Solution: Event Echoing public class MouseEventEcho extends MouseEvent { // Just a little housekeeping here } Class EchoingListener implements MouseListener { // You’ll see … }

9. addActionListener (theEchoingListener) EchoingListener

10. The Echoing Listener Receives an Event Done Echo Event? yes no Build echo event from original For each Jmol except the sender Inject echo into Jmol’sdispatcher

11. Scenario: Mouse Event in Green Jmol • Green dispatcher sends event to green handler • Green dispatcher sends event to echoing listener • Echoing listener makes echo event • Echoing listener sends echo event to red dispatcher : • Red dispatcher sends event to red handler • Red dispatcher sends event to echoing listener (no-op) • Echoing listener sends echo event to yellow dispatcher • … and to blue dispatcher • … and to purple dispatcher • … and to orange dispatcher 0 changes to Jmol

12. What’s next • Map features to molecule colors • Convert Hxb2 coordinates to 2B4c coordinates • Predicate view