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