JAL-2089 patch broken merge to master for Release 2.10.0b1

[jalview.git] / src / jalview / gui / AppJmolBinding.java

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index 1283019..1c54a5e 100644 (file)
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -32,7 +32,6 @@ import java.util.Map;
 
 import org.jmol.api.JmolAppConsoleInterface;
 import org.jmol.java.BS;
-import org.jmol.popup.JmolAwtPopup;
 import org.openscience.jmol.app.jmolpanel.console.AppConsole;
 
 public class AppJmolBinding extends JalviewJmolBinding
@@ -50,11 +49,10 @@ public class AppJmolBinding extends JalviewJmolBinding
   }
 
   @Override
-  public FeatureRenderer getFeatureRenderer(
-          AlignmentViewPanel alignment)
+  public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
   {
-    AlignmentPanel ap = (alignment == null) ? appJmolWindow.getAlignmentPanel()
-            : (AlignmentPanel) alignment;
+    AlignmentPanel ap = (alignment == null) ? appJmolWindow
+            .getAlignmentPanel() : (AlignmentPanel) alignment;
     if (ap.av.isShowSequenceFeatures())
     {
       if (fr == null)
@@ -71,8 +69,7 @@ public class AppJmolBinding extends JalviewJmolBinding
   }
 
   @Override
-  public SequenceRenderer getSequenceRenderer(
-          AlignmentViewPanel alignment)
+  public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
   {
     return new SequenceRenderer(((AlignmentPanel) alignment).av);
   }
@@ -126,7 +123,7 @@ public class AppJmolBinding extends JalviewJmolBinding
 
   public void updateColours(Object source)
   {
-    AlignmentPanel ap = (AlignmentPanel) source, topap;
+    AlignmentPanel ap = (AlignmentPanel) source;
     // ignore events from panels not used to colour this view
     if (!appJmolWindow.isUsedforcolourby(ap))
     {
@@ -134,7 +131,7 @@ public class AppJmolBinding extends JalviewJmolBinding
     }
     if (!isLoadingFromArchive())
     {
-      colourBySequence(ap.av.isShowSequenceFeatures(), ap);
+      colourBySequence(ap);
     }
   }
 
@@ -154,8 +151,8 @@ public class AppJmolBinding extends JalviewJmolBinding
 
   public void newJmolPopup(String menuName)
   {
-    jmolpopup = new JmolAwtPopup();
-    jmolpopup.jpiInitialize((viewer), menuName);
+    // jmolpopup = new JmolAwtPopup();
+    // jmolpopup.jpiInitialize((viewer), menuName);
   }
 
   @Override