- public void run()
- {
- try
- {
- EBIFetchClient ebi = new EBIFetchClient();
- String query = "pdb:" + pdb.getId();
- tmpPDBFile = ebi.fetchDataAsFile(query, "default", "raw").getAbsolutePath();
- if (tmpPDBFile != null)
- {
- PDBfile pdbfile = new PDBfile(tmpPDBFile,
- jalview.io.AppletFormatAdapter.FILE);
- pdbcanvas.setPDBFile(pdbfile);
- }
- else
- {
- throw new Exception("Empty result for WSDbFetch Query: " + query);
- }
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- showErrorMessage("Failed to retrieve PDB structure.");
-// this.dispose();
- }
- }
-
-
- setContentPane(pdbcanvas);
- StringBuffer title = new StringBuffer(sequence.getName() + ":" + pdb.getId());
- if (pdb.getProperty() != null)
- {
- if (pdb.getProperty().get("method") != null)
- {
- title.append(" Method: ");
- title.append(pdb.getProperty().get("method"));
- }
- if (pdb.getProperty().get("chains") != null)
- {
- title.append(" Chain:");
- title.append(pdb.getProperty().get("chains"));
- }
- }
- */
-
- Container contentPane = getContentPane();
- JmolPanel jmolPanel = new JmolPanel();
- contentPane.add(jmolPanel);
-
- JmolViewer viewer = jmolPanel.viewer;
-
-
- System.out.println(entry.getFile()+" "+entry.getId());
- viewer.openFile(entry.getFile());
-
-
- StringBuffer string = new StringBuffer();
-
- for(int i=0; i<seq.getLength(); i++)
- {
- Color col = seqcanvas.getSequenceRenderer().getResidueBoxColour(seq, i);
-
- string.append("select " + i + "B; color [" +
- col.getRed()+","
- +col.getGreen()+","
- +col.getBlue()+"]; ");
- }
- System.out.println(string);
-
- viewer.evalString(string.toString());
-
-
- String strError = viewer.getOpenFileError();
- if (strError != null)
- Logger.error(strError);
-
-
- // Desktop.addInternalFrame(this,
- // seq.getName() + ":1GAQ"
- // , 400, 400);
-
- }
-
-
-
-
- static class JmolPanel
- extends JPanel implements JmolSelectionListener
- {
- JmolViewer viewer;
- JmolAdapter adapter;
- JmolPanel()
- {
- adapter = new SmarterJmolAdapter(null);
- viewer = org.jmol.viewer.Viewer.allocateViewer(this, adapter);
- viewer.addSelectionListener(this);
-
- MyStatusListener myStatusListener;
- myStatusListener = new MyStatusListener();
- viewer.setJmolStatusListener(myStatusListener);
-
- JFrame frame = new JFrame("script window");
- // scriptWindow = new ScriptWindow(viewer, frame);
-
- myStatusListener.jmolpopup = JmolPopup.newJmolPopup(viewer);
- }
- public ScriptWindow scriptWindow;
- class MyStatusListener implements JmolStatusListener
- {
-
- JmolPopup jmolpopup ;
-
-
- public String eval(String strEval) {
- return "# 'eval' is implemented only for the applet.";
- }
-
- public void createImage(String file, String type, int quality) {
- System.out.println("CREATE IMAGE");
- // ImageCreator c = new ImageCreator(viewer, status);
- // c.createImage(file, type, quality);
- }
-
- public void setCallbackFunction(String callbackType, String callbackFunction) {
- // applet only?
- }
-
- public void notifyFileLoaded(String fullPathName, String fileName,
- String modelName, Object clientFile,
- String errorMsg) {
-
- }
-
- public void notifyFrameChanged(int frameNo) {
- // Note: twos-complement. To get actual frame number, use
- // Math.max(frameNo, -2 - frameNo)
- // -1 means all frames are now displayed
-
- boolean isAnimationRunning = (frameNo <= -2);
-
- }
-
- public void notifyScriptStart(String statusMessage, String additionalInfo) {
- //System.out.println("notifyScriptStart:" + statusMessage + (additionalInfo == "" ? "" : additionalInfo));
- }
-
- public void sendConsoleEcho(String strEcho) {
- if (scriptWindow != null)
- scriptWindow.sendConsoleEcho(strEcho);
- }
-
- public void sendConsoleMessage(String strStatus) {
- if (scriptWindow != null)
- scriptWindow.sendConsoleMessage(strStatus);
- }
-
- public void notifyScriptTermination(String strStatus, int msWalltime) {
- if (scriptWindow != null)
- scriptWindow.notifyScriptTermination(strStatus, msWalltime);
- }
-
- public void handlePopupMenu(int x, int y) {
- jmolpopup.show(x, y);
- }
-
- public void notifyNewPickingModeMeasurement(int iatom, String strMeasure) {
- notifyAtomPicked(iatom, strMeasure);
- }
-
- public void notifyNewDefaultModeMeasurement(int count, String strInfo) {
- // measurementTable.updateTables();
- }
-
- public void notifyAtomPicked(int atomIndex, String strInfo) {
-
- System.out.println("ATOM PICKED "+atomIndex+" "+strInfo);
- if (scriptWindow != null) {
- scriptWindow.sendConsoleMessage(strInfo);
- scriptWindow.sendConsoleMessage("\n");
- }
- }
-
- public void notifyAtomHovered(int atomIndex, String strInfo) {
-System.out.println("HOVER "+atomIndex+" "+strInfo);
- }
-
- public void sendSyncScript(String script, String appletName) {
- }
-
- public void showUrl(String url) {
- }
-
- public void showConsole(boolean showConsole) {
- System.out.println("SHOW CONSOLE" +(scriptWindow==null));
- if (scriptWindow == null)
- return;
-
- scriptWindow.setVisible(showConsole);
- }
-
- public float functionXY(String functionName, int x, int y) {
- return 0; // for user-defined isosurface functions (testing only -- bob hanson)
- }
-
- }
-
-
- class ScriptWindowAction extends AbstractAction {
-
- public ScriptWindowAction() {
- super("BLAH");
- }
-
- public void actionPerformed(ActionEvent e) {
- if (scriptWindow != null)
- scriptWindow.show();
- }
- }
-
- /**
- * Called when the selected atoms change
- * @param selection bit set giving selection of atom indexes
- */
- public void selectionChanged(BitSet selection)