src/jalview/appletgui/AppletJmolBinding.java

   1 /**
   2  *
   3  */
   4 package jalview.appletgui;
   5
   6 import java.awt.Container;
   7 import java.util.BitSet;
   8
   9 import jalview.datamodel.PDBEntry;
  10 import jalview.datamodel.SequenceI;
  11
  12 import org.jmol.api.JmolAppConsoleInterface;
  13 import org.jmol.api.JmolViewer;
  14 import org.jmol.applet.AppletConsole;
  15 import org.jmol.popup.JmolPopup;
  16
  17 class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
  18 {
  19
  20   /**
  21    * Window that contains the bound Jmol instance
  22    */
  23   private AppletJmol appletJmolBinding;
  24
  25   public AppletJmolBinding(AppletJmol appletJmol, PDBEntry[] pdbentry, SequenceI[][] seq,
  26           String[][] chains, String protocol)
  27   {
  28     super(pdbentry, seq, chains, protocol);
  29     appletJmolBinding = appletJmol;
  30   }
  31
  32   public jalview.api.FeatureRenderer getFeatureRenderer()
  33   {
  34     if (appletJmolBinding.ap.av.showSequenceFeatures)
  35     {
  36       if (appletJmolBinding.fr == null)
  37       {
  38         appletJmolBinding.fr = new jalview.appletgui.FeatureRenderer(appletJmolBinding.ap.av);
  39       }
  40
  41       appletJmolBinding.fr.transferSettings(appletJmolBinding.ap.seqPanel.seqCanvas.getFeatureRenderer());
  42     }
  43
  44     return appletJmolBinding.fr;
  45   }
  46
  47   public jalview.api.SequenceRenderer getSequenceRenderer()
  48   {
  49     return new SequenceRenderer(appletJmolBinding.ap.av);
  50   }
  51
  52   public void sendConsoleEcho(String strEcho)
  53   {
  54     if (appletJmolBinding.scriptWindow == null)
  55       appletJmolBinding.showConsole(true);
  56
  57     appletJmolBinding.history.append("\n" + strEcho);
  58   }
  59
  60   public void sendConsoleMessage(String strStatus)
  61   {
  62     if (appletJmolBinding.history != null && strStatus != null
  63             && !strStatus.equals("Script completed"))
  64     {
  65       appletJmolBinding.history.append("\n" + strStatus);
  66     }
  67   }
  68
  69   public void showUrl(String url, String target)
  70   {
  71     appletJmolBinding.ap.alignFrame.showURL(url, target);
  72
  73   }
  74
  75   public void refreshGUI()
  76   {
  77     appletJmolBinding.updateTitleAndMenus();
  78   }
  79
  80   public void updateColours(Object source)
  81   {
  82     AlignmentPanel ap = (AlignmentPanel) source;
  83     colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
  84   }
  85
  86   public void showUrl(String url)
  87   {
  88     try
  89     {
  90       appletJmolBinding.ap.av.applet.getAppletContext().showDocument(new java.net.URL(url),
  91               "jmol");
  92     } catch (java.net.MalformedURLException ex)
  93     {
  94     }
  95   }
  96
  97   public void newJmolPopup(boolean translateLocale, String menuName, boolean asPopup)
  98   {
  99
 100     jmolpopup = JmolPopup.newJmolPopup(viewer,translateLocale, menuName,asPopup);
 101   }
 102
 103   public void notifyScriptTermination(String strStatus, int msWalltime)
 104   {
 105     // do nothing.
 106   }
 107
 108   public void selectionChanged(BitSet arg0)
 109   {
 110     // TODO Auto-generated method stub
 111
 112   }
 113
 114   public void refreshPdbEntries()
 115   {
 116     // TODO Auto-generated method stub
 117
 118   }
 119
 120   @Override
 121   public void showConsole(boolean show)
 122   {
 123     appletJmolBinding.showConsole(show);
 124   }
 125
 126   @Override
 127   protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
 128           Container consolePanel, String buttonsToShow)
 129   {
 130     return new AppletConsole(viewer2, consolePanel);
 131   }
 132   @Override
 133   protected void releaseUIResources()
 134   {
 135     appletJmolBinding = null;
 136     if (console!=null) {
 137       try {
 138         console.setVisible(false);
 139       } catch (Error e) {} catch (Exception x) {};
 140       console=null;
 141     }
 142
 143   }
 144
 145 }