Merge branch 'features/JAL-1605_html-svg-export' into develop

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

diff --git a/src/jalview/appletgui/ExtJmol.java b/src/jalview/appletgui/ExtJmol.java
index 705b510..1efb971 100644 (file)
--- a/src/jalview/appletgui/ExtJmol.java
+++ b/src/jalview/appletgui/ExtJmol.java
@@ -1,19 +1,22 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * 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;
 
@@ -28,7 +31,6 @@ import org.jmol.api.JmolViewer;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureRenderer;
 import jalview.api.SequenceRenderer;
-import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.ext.jmol.JalviewJmolBinding;
@@ -48,7 +50,8 @@ public class ExtJmol extends JalviewJmolBinding
           PDBEntry[] pdbentry, SequenceI[][] seq, String[][] chains,
           String protocol)
   {
-    super(alframe.alignPanel.getStructureSelectionManager(), pdbentry, seq, chains, protocol);
+    super(alframe.alignPanel.getStructureSelectionManager(), pdbentry, seq,
+            chains, protocol);
   }
 
   public ExtJmol(JmolViewer viewer, AlignmentPanel alignPanel,
@@ -74,8 +77,8 @@ public class ExtJmol extends JalviewJmolBinding
 
   public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
   {
-    AlignmentPanel ap = (AlignmentPanel)alignment;
-    if (ap.av.showSequenceFeatures)
+    AlignmentPanel ap = (AlignmentPanel) alignment;
+    if (ap.av.isShowSequenceFeatures())
     {
       return ap.getFeatureRenderer();
     }
@@ -87,7 +90,7 @@ public class ExtJmol extends JalviewJmolBinding
 
   public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
   {
-    return ((AlignmentPanel)alignment).getSequenceRenderer();
+    return ((AlignmentPanel) alignment).getSequenceRenderer();
   }
 
   public void notifyScriptTermination(String strStatus, int msWalltime)
@@ -189,7 +192,7 @@ public class ExtJmol extends JalviewJmolBinding
   public void releaseReferences(Object svl)
   {
     // TODO Auto-generated method stub
-    
+
   }
 
 }