JAL-3148 show/hide features on structure independent of alignment

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

diff --git a/src/jalview/appletgui/AppletJmolBinding.java b/src/jalview/appletgui/AppletJmolBinding.java
index 9b8a235..696a272 100644 (file)
--- a/src/jalview/appletgui/AppletJmolBinding.java
+++ b/src/jalview/appletgui/AppletJmolBinding.java
@@ -24,6 +24,7 @@ import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.ext.jmol.JalviewJmolBinding;
+import jalview.gui.IProgressIndicator;
 import jalview.io.DataSourceType;
 import jalview.structure.StructureSelectionManager;
 
@@ -58,13 +59,6 @@ class AppletJmolBinding extends JalviewJmolBinding
   }
 
   @Override
-  public jalview.api.SequenceRenderer getSequenceRenderer(
-          AlignmentViewPanel alignment)
-  {
-    return new SequenceRenderer(((AlignmentPanel) alignment).av);
-  }
-
-  @Override
   public void sendConsoleEcho(String strEcho)
   {
     if (appletJmolBinding.scriptWindow == null)
@@ -102,7 +96,7 @@ class AppletJmolBinding extends JalviewJmolBinding
   public void updateColours(Object source)
   {
     AlignmentPanel ap = (AlignmentPanel) source;
-    colourBySequence(ap);
+    colourBySequence(ap, ap.av.isShowSequenceFeatures());
   }
 
   @Override
@@ -110,8 +104,8 @@ class AppletJmolBinding extends JalviewJmolBinding
   {
     try
     {
-      appletJmolBinding.ap.av.applet.getAppletContext().showDocument(
-              new java.net.URL(url), "jmol");
+      appletJmolBinding.ap.av.applet.getAppletContext()
+              .showDocument(new java.net.URL(url), "jmol");
     } catch (java.net.MalformedURLException ex)
     {
     }
@@ -183,4 +177,11 @@ class AppletJmolBinding extends JalviewJmolBinding
     // TODO Auto-generated method stub
     return null;
   }
+
+  @Override
+  protected IProgressIndicator getIProgressIndicator()
+  {
+    // no progress indicators on the applet
+    return null;
+  }
 }