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   public jalview.api.FeatureRenderer getFeatureRenderer()
  27   {
  28     if (appletJmolBinding.ap.av.showSequenceFeatures)
  29     {
  30       if (appletJmolBinding.fr == null)
  31       {
  32         appletJmolBinding.fr = new jalview.appletgui.FeatureRenderer(appletJmolBinding.ap.av);
  33       }
  34
  35       appletJmolBinding.fr.transferSettings(appletJmolBinding.ap.seqPanel.seqCanvas.getFeatureRenderer());
  36     }
  37
  38     return appletJmolBinding.fr;
  39   }
  40
  41   public jalview.api.SequenceRenderer getSequenceRenderer()
  42   {
  43     return new SequenceRenderer(appletJmolBinding.ap.av);
  44   }
  45
  46   public void sendConsoleEcho(String strEcho)
  47   {
  48     if (appletJmolBinding.scriptWindow == null)
  49       appletJmolBinding.showConsole(true);
  50
  51     appletJmolBinding.history.append("\n" + strEcho);
  52   }
  53
  54   public void sendConsoleMessage(String strStatus)
  55   {
  56     if (appletJmolBinding.history != null && strStatus != null
  57             && !strStatus.equals("Script completed"))
  58     {
  59       appletJmolBinding.history.append("\n" + strStatus);
  60     }
  61   }
  62
  63   public void showUrl(String url, String target)
  64   {
  65     appletJmolBinding.ap.alignFrame.showURL(url, target);
  66
  67   }
  68
  69   public void updateUI()
  70   {
  71     appletJmolBinding.updateTitleAndMenus();
  72   }
  73
  74   public void updateColours(Object source)
  75   {
  76     AlignmentPanel ap = (AlignmentPanel) source;
  77     colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
  78   }
  79
  80   public void showUrl(String url)
  81   {
  82     try
  83     {
  84       appletJmolBinding.ap.av.applet.getAppletContext().showDocument(new java.net.URL(url),
  85               "jmol");
  86     } catch (java.net.MalformedURLException ex)
  87     {
  88     }
  89   }
  90
  91   public void newJmolPopup(boolean translateLocale, String menuName, boolean asPopup)
  92   {
  93
  94     jmolpopup = JmolPopup.newJmolPopup(viewer,translateLocale, menuName,asPopup);
  95   }
  96
  97   public void notifyScriptTermination(String strStatus, int msWalltime)
  98   {
  99     // do nothing.
 100   }
 101
 102 }