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;
26 public jalview.api.FeatureRenderer getFeatureRenderer()
28 if (appletJmolBinding.ap.av.showSequenceFeatures)
30 if (appletJmolBinding.fr == null)
32 appletJmolBinding.fr = new jalview.appletgui.FeatureRenderer(appletJmolBinding.ap.av);
35 appletJmolBinding.fr.transferSettings(appletJmolBinding.ap.seqPanel.seqCanvas.getFeatureRenderer());
38 return appletJmolBinding.fr;
41 public jalview.api.SequenceRenderer getSequenceRenderer()
43 return new SequenceRenderer(appletJmolBinding.ap.av);
46 public void sendConsoleEcho(String strEcho)
48 if (appletJmolBinding.scriptWindow == null)
49 appletJmolBinding.showConsole(true);
51 appletJmolBinding.history.append("\n" + strEcho);
54 public void sendConsoleMessage(String strStatus)
56 if (appletJmolBinding.history != null && strStatus != null
57 && !strStatus.equals("Script completed"))
59 appletJmolBinding.history.append("\n" + strStatus);
63 public void showUrl(String url, String target)
65 appletJmolBinding.ap.alignFrame.showURL(url, target);
69 public void updateUI()
71 appletJmolBinding.updateTitleAndMenus();
74 public void updateColours(Object source)
76 AlignmentPanel ap = (AlignmentPanel) source;
77 colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
80 public void showUrl(String url)
84 appletJmolBinding.ap.av.applet.getAppletContext().showDocument(new java.net.URL(url),
86 } catch (java.net.MalformedURLException ex)
91 public void newJmolPopup(boolean translateLocale, String menuName, boolean asPopup)
94 jmolpopup = JmolPopup.newJmolPopup(viewer,translateLocale, menuName,asPopup);
97 public void notifyScriptTermination(String strStatus, int msWalltime)