src/jalview/appletgui/AppletJmolBinding.java

   1 /**
   2  *
   3  */
   4 package jalview.appletgui;
   5
   6 import java.util.BitSet;
   7
   8 import jalview.datamodel.PDBEntry;
   9 import jalview.datamodel.SequenceI;
  10
  11 import org.jmol.popup.JmolPopup;
  12
  13 class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
  14 {
  15
  16   /**
  17    * Window that contains the bound Jmol instance
  18    */
  19   private AppletJmol appletJmolBinding;
  20
  21   public AppletJmolBinding(AppletJmol appletJmol, PDBEntry[] pdbentry, SequenceI[][] seq,
  22           String[][] chains, String protocol)
  23   {
  24     super(pdbentry, seq, chains, protocol);
  25     appletJmolBinding = appletJmol;
  26   }
  27
  28   public jalview.api.FeatureRenderer getFeatureRenderer()
  29   {
  30     if (appletJmolBinding.ap.av.showSequenceFeatures)
  31     {
  32       if (appletJmolBinding.fr == null)
  33       {
  34         appletJmolBinding.fr = new jalview.appletgui.FeatureRenderer(appletJmolBinding.ap.av);
  35       }
  36
  37       appletJmolBinding.fr.transferSettings(appletJmolBinding.ap.seqPanel.seqCanvas.getFeatureRenderer());
  38     }
  39
  40     return appletJmolBinding.fr;
  41   }
  42
  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   public void showUrl(String url, String target)
  66   {
  67     appletJmolBinding.ap.alignFrame.showURL(url, target);
  68
  69   }
  70
  71   public void refreshGUI()
  72   {
  73     appletJmolBinding.updateTitleAndMenus();
  74   }
  75
  76   public void updateColours(Object source)
  77   {
  78     AlignmentPanel ap = (AlignmentPanel) source;
  79     colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
  80   }
  81
  82   public void showUrl(String url)
  83   {
  84     try
  85     {
  86       appletJmolBinding.ap.av.applet.getAppletContext().showDocument(new java.net.URL(url),
  87               "jmol");
  88     } catch (java.net.MalformedURLException ex)
  89     {
  90     }
  91   }
  92
  93   public void newJmolPopup(boolean translateLocale, String menuName, boolean asPopup)
  94   {
  95
  96     jmolpopup = JmolPopup.newJmolPopup(viewer,translateLocale, menuName,asPopup);
  97   }
  98
  99   public void notifyScriptTermination(String strStatus, int msWalltime)
 100   {
 101     // do nothing.
 102   }
 103
 104   public void selectionChanged(BitSet arg0)
 105   {
 106     // TODO Auto-generated method stub
 107
 108   }
 109
 110   public void refreshPdbEntries()
 111   {
 112     // TODO Auto-generated method stub
 113
 114   }
 115
 116 }