From e683768e084c5e2999846de881b3903f62417919 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Mon, 13 Sep 2010 19:55:05 +0000
Subject: [PATCH] refactored to remove App reference in Applet (JAL-638)

---
 src/jalview/appletgui/AppletJmolBinding.java |   11 +++++++++++
 src/jalview/appletgui/ExtJmol.java           |   10 ++++++++++
 src/jalview/ext/jmol/JalviewJmolBinding.java |    8 ++++++--
 src/jalview/gui/AppJmolBinding.java          |   10 ++++++++++
 4 files changed, 37 insertions(+), 2 deletions(-)

diff --git a/src/jalview/appletgui/AppletJmolBinding.java b/src/jalview/appletgui/AppletJmolBinding.java
index 3a2abcf..d6be32d 100644
--- a/src/jalview/appletgui/AppletJmolBinding.java
+++ b/src/jalview/appletgui/AppletJmolBinding.java
@@ -3,11 +3,14 @@
  */
 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
@@ -119,4 +122,12 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
     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
diff --git a/src/jalview/appletgui/ExtJmol.java b/src/jalview/appletgui/ExtJmol.java
index b7fb311..63c1ca7 100644
--- a/src/jalview/appletgui/ExtJmol.java
+++ b/src/jalview/appletgui/ExtJmol.java
@@ -1,9 +1,11 @@
 package jalview.appletgui;
 
+import java.awt.Container;
 import java.util.BitSet;
 import java.util.Hashtable;
 import java.util.Vector;
 
+import org.jmol.api.JmolAppConsoleInterface;
 import org.jmol.api.JmolViewer;
 
 import jalview.api.FeatureRenderer;
@@ -128,4 +130,12 @@ public class ExtJmol extends JalviewJmolBinding
     // This never gets called because we haven't overriden the associated Jmol's console
     System.err.println("WARNING: unexpected call to ExtJmol's showConsole method. (showConsole="+show);
   }
+
+  @Override
+  protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
+          Container consolePanel, String buttonsToShow)
+  {
+    // TODO Auto-generated method stub
+    return null;
+  }
 }
diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index c852a1a..8e72380 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -39,7 +39,6 @@ import org.jmol.adapter.smarter.SmarterJmolAdapter;
 import org.jmol.popup.*;
 import org.jmol.viewer.JmolConstants;
 import org.jmol.viewer.Viewer;
-import org.openscience.jmol.app.jmolpanel.AppConsole;
 
 import jalview.schemes.*;
 
@@ -1333,8 +1332,10 @@ public abstract class JalviewJmolBinding implements StructureListener,
             (jmolfileio ? new SmarterJmolAdapter() : null), htmlName
                     + ((Object) this).toString(), documentBase, codeBase,
             commandOptions, this);
-      console = new AppConsole(viewer, null, consolePanel,
+      
+      console = createJmolConsole(viewer, consolePanel,
               buttonsToShow);
+      
       viewer.setConsole(new JmolAppConsoleInterface() {
 
         @Override
@@ -1398,6 +1399,9 @@ public abstract class JalviewJmolBinding implements StructureListener,
       
   }
     
+    protected abstract JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
+             Container consolePanel, String buttonsToShow);
+
   protected org.jmol.api.JmolAppConsoleInterface console = null;
 
   public void setLoadingFromArchive(boolean loadingFromArchive)
diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index 2a0e2a7..babffed 100644
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -3,6 +3,7 @@
  */
 package jalview.gui;
 
+import java.awt.Container;
 import java.util.BitSet;
 
 import javax.swing.JPanel;
@@ -11,6 +12,8 @@ import jalview.bin.Cache;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 
+import org.jmol.api.JmolAppConsoleInterface;
+import org.jmol.api.JmolViewer;
 import org.jmol.popup.JmolPopup;
 import org.openscience.jmol.app.jmolpanel.AppConsole;
 
@@ -160,4 +163,11 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
       }
     }
   }
+
+  @Override
+  protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
+          Container consolePanel, String buttonsToShow)
+  {
+    return new AppConsole(viewer, null, consolePanel, buttonsToShow);
+  }
 }
\ No newline at end of file
-- 
1.7.10.2