4 package jalview.appletgui;
6 import java.util.BitSet;
8 import jalview.datamodel.PDBEntry;
9 import jalview.datamodel.SequenceI;
11 import org.jmol.popup.JmolPopup;
13 class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
17 * Window that contains the bound Jmol instance
19 private AppletJmol appletJmolBinding;
21 public AppletJmolBinding(AppletJmol appletJmol, PDBEntry[] pdbentry, SequenceI[][] seq,
22 String[][] chains, String protocol)
24 super(pdbentry, seq, chains, protocol);
25 appletJmolBinding = appletJmol;
28 public jalview.api.FeatureRenderer getFeatureRenderer()
30 if (appletJmolBinding.ap.av.showSequenceFeatures)
32 if (appletJmolBinding.fr == null)
34 appletJmolBinding.fr = new jalview.appletgui.FeatureRenderer(appletJmolBinding.ap.av);
37 appletJmolBinding.fr.transferSettings(appletJmolBinding.ap.seqPanel.seqCanvas.getFeatureRenderer());
40 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);
65 public void showUrl(String url, String target)
67 appletJmolBinding.ap.alignFrame.showURL(url, target);
71 public void refreshGUI()
73 appletJmolBinding.updateTitleAndMenus();
76 public void updateColours(Object source)
78 AlignmentPanel ap = (AlignmentPanel) source;
79 colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
82 public void showUrl(String url)
86 appletJmolBinding.ap.av.applet.getAppletContext().showDocument(new java.net.URL(url),
88 } catch (java.net.MalformedURLException ex)
93 public void newJmolPopup(boolean translateLocale, String menuName, boolean asPopup)
96 jmolpopup = JmolPopup.newJmolPopup(viewer,translateLocale, menuName,asPopup);
99 public void notifyScriptTermination(String strStatus, int msWalltime)
104 public void selectionChanged(BitSet arg0)
106 // TODO Auto-generated method stub
110 public void refreshPdbEntries()
112 // TODO Auto-generated method stub