X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAppletJmolBinding.java;h=80fafe3697fefc143b7a608bf42338d31e56401b;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=009cefd90f6c8bd38ab42c2420724924ff2276ac;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git

diff --git a/src/jalview/appletgui/AppletJmolBinding.java b/src/jalview/appletgui/AppletJmolBinding.java
index 009cefd..80fafe3 100644
--- a/src/jalview/appletgui/AppletJmolBinding.java
+++ b/src/jalview/appletgui/AppletJmolBinding.java
@@ -1,31 +1,35 @@
 /*
- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 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
@@ -36,16 +40,19 @@ 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)
   {
-    if (appletJmolBinding.ap.av.showSequenceFeatures)
+    AlignmentPanel ap = (AlignmentPanel) alignment;
+    if (appletJmolBinding.ap.av.isShowSequenceFeatures())
     {
       if (appletJmolBinding.fr == null)
       {
@@ -61,15 +68,18 @@ 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)
   {
     if (appletJmolBinding.scriptWindow == null)
+    {
       appletJmolBinding.showConsole(true);
+    }
 
     appletJmolBinding.history.append("\n" + strEcho);
   }
@@ -97,7 +107,7 @@ 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.isShowSequenceFeatures(), ap);
   }
 
   public void showUrl(String url)
@@ -115,8 +125,8 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
           boolean asPopup)
   {
 
-    jmolpopup = JmolPopup.newJmolPopup(viewer, translateLocale, menuName,
-            asPopup);
+    jmolpopup = new JmolPopup();
+    jmolpopup.initialize(viewer, translateLocale, menuName, asPopup);
   }
 
   public void notifyScriptTermination(String strStatus, int msWalltime)
@@ -130,10 +140,10 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
 
   }
 
+  @Override
   public void refreshPdbEntries()
   {
-    // TODO Auto-generated method stub
-
+    // noop
   }
 
   @Override
@@ -146,27 +156,28 @@ 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
   protected void releaseUIResources()
   {
     appletJmolBinding = null;
-    if (console != null)
-    {
-      try
-      {
-        console.setVisible(false);
-      } catch (Error e)
-      {
-      } catch (Exception x)
-      {
-      }
-      ;
-      console = null;
-    }
+    closeConsole();
+  }
 
+  @Override
+  public void releaseReferences(Object svl)
+  {
   }
 
+  @Override
+  public void resizeInnerPanel(String data)
+  {
+    // TODO Auto-generated method stub
+
+  }
 }