src/jalview/appletgui/AppletJmolBinding.java

   1 /**
   2  *
   3  */
   4 package jalview.appletgui;
   5
   6 import jalview.datamodel.PDBEntry;
   7 import jalview.datamodel.SequenceI;
   8
   9 import org.jmol.popup.JmolPopup;
  10
  11 class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
  12 {
  13
  14   /**
  15    *
  16    */
  17   private AppletJmol appletJmolBinding;
  18
  19   public AppletJmolBinding(AppletJmol appletJmol, PDBEntry[] pdbentry, SequenceI[] seq,
  20           String[] chains, String protocol)
  21   {
  22     super(pdbentry, seq, chains, protocol);
  23     appletJmolBinding = appletJmol;
  24   }
  25
  26   @Override
  27   public jalview.api.FeatureRenderer getFeatureRenderer()
  28   {
  29     if (appletJmolBinding.ap.av.showSequenceFeatures)
  30     {
  31       if (appletJmolBinding.fr == null)
  32       {
  33         appletJmolBinding.fr = new jalview.appletgui.FeatureRenderer(appletJmolBinding.ap.av);
  34       }
  35
  36       appletJmolBinding.fr.transferSettings(appletJmolBinding.ap.seqPanel.seqCanvas.getFeatureRenderer());
  37     }
  38
  39     return appletJmolBinding.fr;
  40   }
  41
  42   @Override
  43   public jalview.api.SequenceRenderer getSequenceRenderer()
  44   {
  45     return new SequenceRenderer(appletJmolBinding.ap.av);
  46   }
  47
  48   public void sendConsoleEcho(String strEcho)
  49   {
  50     if (appletJmolBinding.scriptWindow == null)
  51       appletJmolBinding.showConsole(true);
  52
  53     appletJmolBinding.history.append("\n" + strEcho);
  54   }
  55
  56   public void sendConsoleMessage(String strStatus)
  57   {
  58     if (appletJmolBinding.history != null && strStatus != null
  59             && !strStatus.equals("Script completed"))
  60     {
  61       appletJmolBinding.history.append("\n" + strStatus);
  62     }
  63   }
  64
  65   @Override
  66   public void showUrl(String url, String target)
  67   {
  68     appletJmolBinding.ap.alignFrame.showURL(url, target);
  69
  70   }
  71
  72   @Override
  73   public void updateUI()
  74   {
  75     appletJmolBinding.updateTitleAndMenus();
  76   }
  77
  78   public void updateColours(Object source)
  79   {
  80     AlignmentPanel ap = (AlignmentPanel) source;
  81     colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
  82   }
  83
  84   public void showUrl(String url)
  85   {
  86     try
  87     {
  88       appletJmolBinding.ap.av.applet.getAppletContext().showDocument(new java.net.URL(url),
  89               "jmol");
  90     } catch (java.net.MalformedURLException ex)
  91     {
  92     }
  93   }
  94
  95   public void newJmolPopup(boolean translateLocale, String menuName, boolean asPopup)
  96   {
  97
  98     jmolpopup = JmolPopup.newJmolPopup(viewer,translateLocale, menuName,asPopup);
  99   }
 100
 101   @Override
 102   public void notifyScriptTermination(String strStatus, int msWalltime)
 103   {
 104     // do nothing.
 105   }
 106
 107 }