4 package jalview.appletgui;
6 import java.awt.Container;
7 import java.util.BitSet;
9 import jalview.datamodel.PDBEntry;
10 import jalview.datamodel.SequenceI;
12 import org.jmol.api.JmolAppConsoleInterface;
13 import org.jmol.api.JmolViewer;
14 import org.jmol.popup.JmolPopup;
16 class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
20 * Window that contains the bound Jmol instance
22 private AppletJmol appletJmolBinding;
24 public AppletJmolBinding(AppletJmol appletJmol, PDBEntry[] pdbentry, SequenceI[][] seq,
25 String[][] chains, String protocol)
27 super(pdbentry, seq, chains, protocol);
28 appletJmolBinding = appletJmol;
31 public jalview.api.FeatureRenderer getFeatureRenderer()
33 if (appletJmolBinding.ap.av.showSequenceFeatures)
35 if (appletJmolBinding.fr == null)
37 appletJmolBinding.fr = new jalview.appletgui.FeatureRenderer(appletJmolBinding.ap.av);
40 appletJmolBinding.fr.transferSettings(appletJmolBinding.ap.seqPanel.seqCanvas.getFeatureRenderer());
43 return appletJmolBinding.fr;
46 public jalview.api.SequenceRenderer getSequenceRenderer()
48 return new SequenceRenderer(appletJmolBinding.ap.av);
51 public void sendConsoleEcho(String strEcho)
53 if (appletJmolBinding.scriptWindow == null)
54 appletJmolBinding.showConsole(true);
56 appletJmolBinding.history.append("\n" + strEcho);
59 public void sendConsoleMessage(String strStatus)
61 if (appletJmolBinding.history != null && strStatus != null
62 && !strStatus.equals("Script completed"))
64 appletJmolBinding.history.append("\n" + strStatus);
68 public void showUrl(String url, String target)
70 appletJmolBinding.ap.alignFrame.showURL(url, target);
74 public void refreshGUI()
76 appletJmolBinding.updateTitleAndMenus();
79 public void updateColours(Object source)
81 AlignmentPanel ap = (AlignmentPanel) source;
82 colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
85 public void showUrl(String url)
89 appletJmolBinding.ap.av.applet.getAppletContext().showDocument(new java.net.URL(url),
91 } catch (java.net.MalformedURLException ex)
96 public void newJmolPopup(boolean translateLocale, String menuName, boolean asPopup)
99 jmolpopup = JmolPopup.newJmolPopup(viewer,translateLocale, menuName,asPopup);
102 public void notifyScriptTermination(String strStatus, int msWalltime)
107 public void selectionChanged(BitSet arg0)
109 // TODO Auto-generated method stub
113 public void refreshPdbEntries()
115 // TODO Auto-generated method stub
120 public void showConsole(boolean show)
122 appletJmolBinding.showConsole(show);
126 protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
127 Container consolePanel, String buttonsToShow)
129 // TODO Auto-generated method stub