X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAppletJmolBinding.java;h=ffe00b54f535937c457a89fc577f8bb9d3aa902b;hb=74e0948bc8efef9a573f037e8c037c46fade0c6f;hp=7490edcd249d1078bcbec46334570783527163ca;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/appletgui/AppletJmolBinding.java b/src/jalview/appletgui/AppletJmolBinding.java
index 7490edc..ffe00b5 100644
--- a/src/jalview/appletgui/AppletJmolBinding.java
+++ b/src/jalview/appletgui/AppletJmolBinding.java
@@ -20,8 +20,11 @@ package jalview.appletgui;
 import java.awt.Container;
 import java.util.BitSet;
 
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.structure.StructureSelectionManager;
 
 import org.jmol.api.JmolAppConsoleInterface;
 import org.jmol.api.JmolViewer;
@@ -36,31 +39,35 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
    */
   private AppletJmol appletJmolBinding;
 
-  public AppletJmolBinding(AppletJmol appletJmol, PDBEntry[] pdbentry, SequenceI[][] seq,
-          String[][] chains, String protocol)
+  public AppletJmolBinding(AppletJmol appletJmol, StructureSelectionManager sSm, PDBEntry[] pdbentry,
+          SequenceI[][] seq, String[][] chains, String protocol)
   {
-    super(pdbentry, seq, chains, protocol);
+    super(sSm, pdbentry, seq, chains, protocol);
     appletJmolBinding = appletJmol;
   }
 
-  public jalview.api.FeatureRenderer getFeatureRenderer()
+  public jalview.api.FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
   {
+    AlignmentPanel ap = (AlignmentPanel)alignment;
     if (appletJmolBinding.ap.av.showSequenceFeatures)
     {
       if (appletJmolBinding.fr == null)
       {
-        appletJmolBinding.fr = new jalview.appletgui.FeatureRenderer(appletJmolBinding.ap.av);
+        appletJmolBinding.fr = new jalview.appletgui.FeatureRenderer(
+                appletJmolBinding.ap.av);
       }
 
-      appletJmolBinding.fr.transferSettings(appletJmolBinding.ap.seqPanel.seqCanvas.getFeatureRenderer());
+      appletJmolBinding.fr
+              .transferSettings(appletJmolBinding.ap.seqPanel.seqCanvas
+                      .getFeatureRenderer());
     }
 
     return appletJmolBinding.fr;
   }
 
-  public jalview.api.SequenceRenderer getSequenceRenderer()
+  public jalview.api.SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
   {
-    return new SequenceRenderer(appletJmolBinding.ap.av);
+    return new SequenceRenderer(((AlignmentPanel)alignment).av);
   }
 
   public void sendConsoleEcho(String strEcho)
@@ -90,28 +97,30 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   {
     appletJmolBinding.updateTitleAndMenus();
   }
-  
+
   public void updateColours(Object source)
   {
     AlignmentPanel ap = (AlignmentPanel) source;
-    colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
+    colourBySequence(ap.av.getShowSequenceFeatures(), ap);
   }
 
   public void showUrl(String url)
   {
     try
     {
-      appletJmolBinding.ap.av.applet.getAppletContext().showDocument(new java.net.URL(url),
-              "jmol");
+      appletJmolBinding.ap.av.applet.getAppletContext().showDocument(
+              new java.net.URL(url), "jmol");
     } catch (java.net.MalformedURLException ex)
     {
     }
   }
 
-  public void newJmolPopup(boolean translateLocale, String menuName, boolean asPopup)
+  public void newJmolPopup(boolean translateLocale, String menuName,
+          boolean asPopup)
   {
-    
-    jmolpopup = JmolPopup.newJmolPopup(viewer,translateLocale, menuName,asPopup);
+
+    jmolpopup = JmolPopup.newJmolPopup(viewer, translateLocale, menuName,
+            asPopup);
   }
 
   public void notifyScriptTermination(String strStatus, int msWalltime)
@@ -122,13 +131,13 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   public void selectionChanged(BitSet arg0)
   {
     // TODO Auto-generated method stub
-    
+
   }
 
   public void refreshPdbEntries()
   {
     // TODO Auto-generated method stub
-    
+
   }
 
   @Override
@@ -143,17 +152,30 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   {
     return new AppletConsole(viewer2, consolePanel);
   }
+
   @Override
   protected void releaseUIResources()
   {
     appletJmolBinding = null;
-    if (console!=null) {
-      try {
+    if (console != null)
+    {
+      try
+      {
         console.setVisible(false);
-      } catch (Error e) {} catch (Exception x) {};
-      console=null;
+      } catch (Error e)
+      {
+      } catch (Exception x)
+      {
+      }
+      ;
+      console = null;
     }
-    
+
+  }
+
+  @Override
+  public void releaseReferences(Object svl)
+  {
   }
 
 }