Merge branch 'Release_2_9_0b1_Branch'

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

diff --git a/src/jalview/appletgui/AppletJmolBinding.java b/src/jalview/appletgui/AppletJmolBinding.java
index 7844f57..6c30eed 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 ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -34,7 +34,6 @@ import javajs.awt.Dimension;
 import org.jmol.api.JmolAppConsoleInterface;
 import org.jmol.console.AppletConsole;
 import org.jmol.java.BS;
-import org.jmol.popup.JmolAwtPopup;
 
 class AppletJmolBinding extends JalviewJmolBinding
 {
@@ -88,7 +87,7 @@ class AppletJmolBinding extends JalviewJmolBinding
       appletJmolBinding.showConsole(true);
     }
 
-    appletJmolBinding.history.append("\n" + strEcho);
+    appletJmolBinding.addToHistory(strEcho);
   }
 
   @Override
@@ -97,7 +96,7 @@ class AppletJmolBinding extends JalviewJmolBinding
     if (appletJmolBinding.history != null && strStatus != null
             && !strStatus.equals("Script completed"))
     {
-      appletJmolBinding.history.append("\n" + strStatus);
+      appletJmolBinding.addToHistory(strStatus);
     }
   }
 
@@ -117,7 +116,7 @@ class AppletJmolBinding extends JalviewJmolBinding
   public void updateColours(Object source)
   {
     AlignmentPanel ap = (AlignmentPanel) source;
-    colourBySequence(ap.av.isShowSequenceFeatures(), ap);
+    colourBySequence(ap);
   }
 
   public void showUrl(String url)
@@ -134,9 +133,8 @@ class AppletJmolBinding extends JalviewJmolBinding
   public void newJmolPopup(boolean translateLocale, String menuName,
           boolean asPopup)
   {
-    jmolpopup = new JmolAwtPopup(); // is this used?
-    jmolpopup.jpiInitialize((viewer), menuName);
-
+    // jmolpopup = new JmolAwtPopup(); // is this used?
+    // jmolpopup.jpiInitialize((viewer), menuName);
   }
 
   @Override