refactored to remove App reference in Applet (JAL-638)

[jalview.git] / src / jalview / appletgui / AppletJmolBinding.java

diff --git a/src/jalview/appletgui/AppletJmolBinding.java b/src/jalview/appletgui/AppletJmolBinding.java
index 745e8f7..d6be32d 100644 (file)
--- a/src/jalview/appletgui/AppletJmolBinding.java
+++ b/src/jalview/appletgui/AppletJmolBinding.java
@@ -3,27 +3,31 @@
  */
 package jalview.appletgui;
 
+import java.awt.Container;
+import java.util.BitSet;
+
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 
+import org.jmol.api.JmolAppConsoleInterface;
+import org.jmol.api.JmolViewer;
 import org.jmol.popup.JmolPopup;
 
 class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
 {
 
   /**
-   * 
+   * Window that contains the bound Jmol instance
    */
   private AppletJmol appletJmolBinding;
 
-  public AppletJmolBinding(AppletJmol appletJmol, PDBEntry[] pdbentry, SequenceI[] seq,
-          String[] chains, String protocol)
+  public AppletJmolBinding(AppletJmol appletJmol, PDBEntry[] pdbentry, SequenceI[][] seq,
+          String[][] chains, String protocol)
   {
     super(pdbentry, seq, chains, protocol);
     appletJmolBinding = appletJmol;
   }
 
-  @Override
   public jalview.api.FeatureRenderer getFeatureRenderer()
   {
     if (appletJmolBinding.ap.av.showSequenceFeatures)
@@ -39,7 +43,6 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
     return appletJmolBinding.fr;
   }
 
-  @Override
   public jalview.api.SequenceRenderer getSequenceRenderer()
   {
     return new SequenceRenderer(appletJmolBinding.ap.av);
@@ -62,15 +65,13 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
     }
   }
 
-  @Override
   public void showUrl(String url, String target)
   {
     appletJmolBinding.ap.alignFrame.showURL(url, target);
 
   }
 
-  @Override
-  public void updateUI()
+  public void refreshGUI()
   {
     appletJmolBinding.updateTitleAndMenus();
   }
@@ -98,10 +99,35 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
     jmolpopup = JmolPopup.newJmolPopup(viewer,translateLocale, menuName,asPopup);
   }
 
-  @Override
   public void notifyScriptTermination(String strStatus, int msWalltime)
   {
     // do nothing.
   }
 
+  public void selectionChanged(BitSet arg0)
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
+  public void refreshPdbEntries()
+  {
+    // TODO Auto-generated method stub
+    
+  }
+
+  @Override
+  public void showConsole(boolean show)
+  {
+    appletJmolBinding.showConsole(show);
+  }
+
+  @Override
+  protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
+          Container consolePanel, String buttonsToShow)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
+
 }
\ No newline at end of file