(JAL-980,JAL-982) - applet console only allows console to be popped up in own window

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

diff --git a/src/jalview/appletgui/AppletJmolBinding.java b/src/jalview/appletgui/AppletJmolBinding.java
index 009cefd..808e30b 100644 (file)
--- a/src/jalview/appletgui/AppletJmolBinding.java
+++ b/src/jalview/appletgui/AppletJmolBinding.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -17,15 +17,16 @@
  */
 package jalview.appletgui;
 
-import java.awt.Container;
-import java.util.BitSet;
-
+import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
+import jalview.structure.StructureSelectionManager;
+
+import java.awt.Container;
+import java.util.BitSet;
 
 import org.jmol.api.JmolAppConsoleInterface;
 import org.jmol.api.JmolViewer;
-import org.jmol.applet.AppletConsole;
 import org.jmol.popup.JmolPopup;
 
 class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
@@ -36,15 +37,16 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
    */
   private AppletJmol appletJmolBinding;
 
-  public AppletJmolBinding(AppletJmol appletJmol, PDBEntry[] pdbentry,
+  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)
@@ -61,9 +63,9 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
     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)
@@ -97,7 +99,7 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   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)
@@ -115,7 +117,8 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
           boolean asPopup)
   {
 
-    jmolpopup = JmolPopup.newJmolPopup(viewer, translateLocale, menuName,
+    jmolpopup = new JmolPopup();
+    jmolpopup.initialize(viewer, translateLocale, menuName,
             asPopup);
   }
 
@@ -146,7 +149,9 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
   protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
           Container consolePanel, String buttonsToShow)
   {
-    return new AppletConsole(viewer2, consolePanel);
+    //return new org.jmol.console.AppletConsole(viewer2, consolePanel);
+    JmolAppConsoleInterface appc = new org.jmol.console.AppletConsole().getAppConsole(viewer2);
+    return appc;
   }
 
   @Override
@@ -169,4 +174,14 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
 
   }
 
+  @Override
+  public void releaseReferences(Object svl)
+  {
+  }
+  @Override
+  public void resizeInnerPanel(String data)
+  {
+    // TODO Auto-generated method stub
+    
+  }
 }