X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmolBinding.java;h=eeb48887fb4ee2244ada8e0566f712008fb8a38e;hb=26b115b0a77d521da92a06572d9b7819c2d0d49a;hp=f822358ebd1990c0e53a0a413374389349604fcc;hpb=2888e7307e1f7c8239234941498cb86e8c65ab36;p=jalview.git

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index f822358..eeb4888 100644
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -33,7 +33,7 @@ import java.awt.Container;
 import java.util.Map;
 
 import org.jmol.api.JmolAppConsoleInterface;
-import org.jmol.java.BS;
+import javajs.util.BS;
 import org.openscience.jmol.app.jmolpanel.console.AppConsole;
 
 public class AppJmolBinding extends JalviewJmolBinding
@@ -41,13 +41,20 @@ public class AppJmolBinding extends JalviewJmolBinding
   private AppJmol appJmolWindow;
 
   public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
-          PDBEntry[] pdbentry, SequenceI[][] sequenceIs, DataSourceType protocol)
+          PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
+          DataSourceType protocol)
   {
     super(sSm, pdbentry, sequenceIs, protocol);
     appJmolWindow = appJmol;
   }
 
   @Override
+  protected IProgressIndicator getIProgressIndicator()
+  {
+    return appJmolWindow.progressBar;
+  }
+
+  @Override
   public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
   {
     return new SequenceRenderer(((AlignmentPanel) alignment).av);
@@ -162,7 +169,7 @@ public class AppJmolBinding extends JalviewJmolBinding
           Container consolePanel, String buttonsToShow)
   {
     viewer.setJmolCallbackListener(this);
-    return new AppConsole(viewer, consolePanel, buttonsToShow);
+    return null;//BH can't do this yet. new AppConsole(viewer, consolePanel, buttonsToShow);
   }
 
   @Override
@@ -198,8 +205,9 @@ public class AppJmolBinding extends JalviewJmolBinding
   public jalview.api.FeatureRenderer getFeatureRenderer(
           AlignmentViewPanel alignment)
   {
-    AlignmentPanel ap = (alignment == null) ? appJmolWindow
-            .getAlignmentPanel() : (AlignmentPanel) alignment;
+    AlignmentPanel ap = (alignment == null)
+            ? appJmolWindow.getAlignmentPanel()
+            : (AlignmentPanel) alignment;
     if (ap.av.isShowSequenceFeatures())
     {
       return ap.av.getAlignPanel().getSeqPanel().seqCanvas.fr;