X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FExtJmol.java;h=47469320c4e502deaa09feca82855892b0e4293c;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=d3dad58f982edccc05f422578f0e94b0eae4b445;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git

diff --git a/src/jalview/appletgui/ExtJmol.java b/src/jalview/appletgui/ExtJmol.java
index d3dad58..4746932 100644
--- a/src/jalview/appletgui/ExtJmol.java
+++ b/src/jalview/appletgui/ExtJmol.java
@@ -1,19 +1,22 @@
 /*
- * 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 2.8.2b1)
+ * Copyright (C) 2014 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;
 
@@ -25,6 +28,7 @@ import java.util.Vector;
 import org.jmol.api.JmolAppConsoleInterface;
 import org.jmol.api.JmolViewer;
 
+import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
 import jalview.datamodel.PDBEntry;
@@ -46,13 +50,14 @@ public class ExtJmol extends JalviewJmolBinding
           PDBEntry[] pdbentry, SequenceI[][] seq, String[][] chains,
           String protocol)
   {
-    super(pdbentry, seq, chains, protocol);
+    super(alframe.alignPanel.getStructureSelectionManager(), pdbentry, seq,
+            chains, protocol);
   }
 
   public ExtJmol(JmolViewer viewer, AlignmentPanel alignPanel,
           SequenceI[][] seqs)
   {
-    super(viewer);
+    super(alignPanel.getStructureSelectionManager(), viewer);
     ap = alignPanel;
     this.sequence = seqs;
     notifyFileLoaded(null, null, null, null, 0);
@@ -70,8 +75,9 @@ public class ExtJmol extends JalviewJmolBinding
     showUrl(arg0, "jmol");
   }
 
-  public FeatureRenderer getFeatureRenderer()
+  public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
   {
+    AlignmentPanel ap = (AlignmentPanel) alignment;
     if (ap.av.showSequenceFeatures)
     {
       return ap.getFeatureRenderer();
@@ -82,9 +88,9 @@ public class ExtJmol extends JalviewJmolBinding
     }
   }
 
-  public SequenceRenderer getSequenceRenderer()
+  public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
   {
-    return ap.getSequenceRenderer();
+    return ((AlignmentPanel) alignment).getSequenceRenderer();
   }
 
   public void notifyScriptTermination(String strStatus, int msWalltime)
@@ -182,4 +188,11 @@ public class ExtJmol extends JalviewJmolBinding
 
   }
 
+  @Override
+  public void releaseReferences(Object svl)
+  {
+    // TODO Auto-generated method stub
+
+  }
+
 }