JAL-2136 merged develop into branch to fix build failure

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

diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index aebdc21..0c5f469 100644 (file)
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -21,10 +21,12 @@
 package jalview.gui;
 
 import jalview.api.AlignmentViewPanel;
+import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Cache;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.ext.jmol.JalviewJmolBinding;
+import jalview.io.DataSourceType;
 import jalview.structure.StructureSelectionManager;
 
 import java.awt.Container;
@@ -38,13 +40,10 @@ public class AppJmolBinding extends JalviewJmolBinding
 {
   private AppJmol appJmolWindow;
 
-  private FeatureRenderer fr = null;
-
   public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
-          PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
-          String protocol)
+          PDBEntry[] pdbentry, SequenceI[][] sequenceIs, DataSourceType protocol)
   {
-    super(sSm, pdbentry, sequenceIs, chains, protocol);
+    super(sSm, pdbentry, sequenceIs, protocol);
     appJmolWindow = appJmol;
   }
 
@@ -53,25 +52,6 @@ public class AppJmolBinding extends JalviewJmolBinding
   {
     return appJmolWindow.progressBar;
   }
-  @Override
-  public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
-  {
-    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;
-  }
 
   @Override
   public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
@@ -213,4 +193,24 @@ 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;
+  }
 }