JAL-3521 Change grouped Jalview windows on linux taskbar to have name Jalview

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

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index f822358..3432911 100644 (file)
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -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);
@@ -198,13 +205,9 @@ public class AppJmolBinding extends JalviewJmolBinding
   public jalview.api.FeatureRenderer getFeatureRenderer(
           AlignmentViewPanel alignment)
   {
-    AlignmentPanel ap = (alignment == null) ? appJmolWindow
-            .getAlignmentPanel() : (AlignmentPanel) alignment;
-    if (ap.av.isShowSequenceFeatures())
-    {
-      return ap.av.getAlignPanel().getSeqPanel().seqCanvas.fr;
-    }
-
-    return null;
+    AlignmentPanel ap = (alignment == null)
+            ? appJmolWindow.getAlignmentPanel()
+            : (AlignmentPanel) alignment;
+    return ap.av.getAlignPanel().getFeatureRenderer();
   }
 }