X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmolBinding.java;h=724cec1b8cbe0804661870885359c51151ae934d;hb=e29f805236e7328f34c0664e72f46925d7d28e07;hp=6e520e5b527affe21b2f88a852fe375a70356361;hpb=230fac58c5afe1843bf7177834fe1bd1d7e6f9d5;p=jalview.git

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index 6e520e5..724cec1 100644
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -21,6 +21,7 @@
 package jalview.gui;
 
 import jalview.api.AlignmentViewPanel;
+import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
@@ -39,34 +40,18 @@ public class AppJmolBinding extends JalviewJmolBinding
 {
   private AppJmol appJmolWindow;
 
-  private FeatureRenderer fr = null;
-
   public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
-          PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
+          PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
           DataSourceType protocol)
   {
-    super(sSm, pdbentry, sequenceIs, chains, protocol);
+    super(sSm, pdbentry, sequenceIs, protocol);
     appJmolWindow = appJmol;
   }
 
   @Override
-  public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
+  protected IProgressIndicator getIProgressIndicator()
   {
-    AlignmentPanel ap = (alignment == null) ? appJmolWindow
-            .getAlignmentPanel() : (AlignmentPanel) alignment;
-    if (ap.av.isShowSequenceFeatures())
-    {
-      if (fr == null)
-      {
-        fr = (jalview.gui.FeatureRenderer) ap.cloneFeatureRenderer();
-      }
-      else
-      {
-        ap.updateFeatureRenderer(fr);
-      }
-    }
-
-    return fr;
+    return appJmolWindow.progressBar;
   }
 
   @Override
@@ -209,4 +194,25 @@ public class AppJmolBinding extends JalviewJmolBinding
     // TODO Auto-generated method stub
     return null;
   }
+
+  @Override
+  public JalviewStructureDisplayI getViewer()
+  {
+    return appJmolWindow;
+  }
+
+  @Override
+  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;
+  }
 }