4 package jalview.appletgui;
6 import jalview.datamodel.PDBEntry;
7 import jalview.datamodel.SequenceI;
9 import org.jmol.popup.JmolPopup;
11 class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
17 private AppletJmol appletJmolBinding;
19 public AppletJmolBinding(AppletJmol appletJmol, PDBEntry[] pdbentry, SequenceI[] seq,
20 String[] chains, String protocol)
22 super(pdbentry, seq, chains, protocol);
23 appletJmolBinding = appletJmol;
27 public jalview.api.FeatureRenderer getFeatureRenderer()
29 if (appletJmolBinding.ap.av.showSequenceFeatures)
31 if (appletJmolBinding.fr == null)
33 appletJmolBinding.fr = new jalview.appletgui.FeatureRenderer(appletJmolBinding.ap.av);
36 appletJmolBinding.fr.transferSettings(appletJmolBinding.ap.seqPanel.seqCanvas.getFeatureRenderer());
39 return appletJmolBinding.fr;
43 public jalview.api.SequenceRenderer getSequenceRenderer()
45 return new SequenceRenderer(appletJmolBinding.ap.av);
48 public void sendConsoleEcho(String strEcho)
50 if (appletJmolBinding.scriptWindow == null)
51 appletJmolBinding.showConsole(true);
53 appletJmolBinding.history.append("\n" + strEcho);
56 public void sendConsoleMessage(String strStatus)
58 if (appletJmolBinding.history != null && strStatus != null
59 && !strStatus.equals("Script completed"))
61 appletJmolBinding.history.append("\n" + strStatus);
66 public void showUrl(String url, String target)
68 appletJmolBinding.ap.alignFrame.showURL(url, target);
73 public void updateUI()
75 appletJmolBinding.updateTitleAndMenus();
78 public void updateColours(Object source)
80 AlignmentPanel ap = (AlignmentPanel) source;
81 colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
84 public void showUrl(String url)
88 appletJmolBinding.ap.av.applet.getAppletContext().showDocument(new java.net.URL(url),
90 } catch (java.net.MalformedURLException ex)
95 public void newJmolPopup(boolean translateLocale, String menuName, boolean asPopup)
98 jmolpopup = JmolPopup.newJmolPopup(viewer,translateLocale, menuName,asPopup);
102 public void notifyScriptTermination(String strStatus, int msWalltime)