JAL-2177 Jmol update from: Jmol-14.2.14_2015.06.11 to Jmol-14.6.4_2016.10.26

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

diff --git a/src/jalview/appletgui/AppletJmolBinding.java b/src/jalview/appletgui/AppletJmolBinding.java
index 7844f57..ea3d3fa 100644 (file)
--- a/src/jalview/appletgui/AppletJmolBinding.java
+++ b/src/jalview/appletgui/AppletJmolBinding.java
@@ -29,12 +29,9 @@ import jalview.structure.StructureSelectionManager;
 import java.awt.Container;
 import java.util.Map;
 
-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 +85,7 @@ class AppletJmolBinding extends JalviewJmolBinding
       appletJmolBinding.showConsole(true);
     }
 
-    appletJmolBinding.history.append("\n" + strEcho);
+    appletJmolBinding.addToHistory(strEcho);
   }
 
   @Override
@@ -97,7 +94,7 @@ class AppletJmolBinding extends JalviewJmolBinding
     if (appletJmolBinding.history != null && strStatus != null
             && !strStatus.equals("Script completed"))
     {
-      appletJmolBinding.history.append("\n" + strStatus);
+      appletJmolBinding.addToHistory(strStatus);
     }
   }
 
@@ -114,12 +111,14 @@ class AppletJmolBinding extends JalviewJmolBinding
     appletJmolBinding.updateTitleAndMenus();
   }
 
+  @Override
   public void updateColours(Object source)
   {
     AlignmentPanel ap = (AlignmentPanel) source;
-    colourBySequence(ap.av.isShowSequenceFeatures(), ap);
+    colourBySequence(ap);
   }
 
+  @Override
   public void showUrl(String url)
   {
     try
@@ -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
@@ -145,6 +143,7 @@ class AppletJmolBinding extends JalviewJmolBinding
     // do nothing.
   }
 
+  @Override
   public void selectionChanged(BS arg0)
   {
     // TODO Auto-generated method stub
@@ -185,7 +184,7 @@ class AppletJmolBinding extends JalviewJmolBinding
   }
 
   @Override
-  public Dimension resizeInnerPanel(String data)
+  public int[] resizeInnerPanel(String data)
   {
     // TODO Auto-generated method stub
     return null;