JAL-2136 merged develop into branch to fix build failure

diff --cc resources/lang/Messages.properties
Simple merge

diff --cc src/MCview/AppletPDBCanvas.java
Simple merge

diff --cc src/MCview/PDBCanvas.java
Simple merge

diff --cc src/jalview/appletgui/AlignFrame.java
Simple merge

diff --cc src/jalview/appletgui/AppletJmolBinding.java
Simple merge

diff --cc src/jalview/appletgui/ExtJmol.java
Simple merge

diff --cc src/jalview/ext/jmol/JalviewJmolBinding.java
Simple merge

diff --cc src/jalview/ext/jmol/JmolCommands.java
Simple merge

diff --cc src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
index 745b1e1,fad3137..ecf93d3
--- 1/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
--- 2/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@@ -1110,17 -1101,8 +1101,8 @@@ public abstract class JalviewChimeraBin
    {
      // TODO refactor as required to pull up to an interface
      AlignmentI alignment = avp.getAlignment();
-     FeatureRenderer fr = getFeatureRenderer(avp);
- 
-     /*
-      * fr is null if feature display is turned off
-      */
-     if (fr == null)
-     {
-       return 0;
-     }
  
 -    String[] files = getPdbFile();
 +    String[] files = getStructureFiles();
      if (files == null)
      {
        return 0;

diff --cc src/jalview/gui/AlignFrame.java
Simple merge

diff --cc src/jalview/gui/AppJmolBinding.java
index 2227978,f822358..0c5f469
--- 1/src/jalview/gui/AppJmolBinding.java
--- 2/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@@ -50,31 -48,6 +48,12 @@@ public class AppJmolBinding extends Jal
    }
  
    @Override
 +  protected IProgressIndicator getIProgressIndicator()
 +  {
 +    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)
    {
      return new SequenceRenderer(((AlignmentPanel) alignment).av);

diff --cc src/jalview/gui/ChimeraViewFrame.java
Simple merge

diff --cc src/jalview/gui/Jalview2XML.java
Simple merge

diff --cc src/jalview/javascript/MouseOverStructureListener.java
Simple merge

diff --cc src/jalview/structures/models/AAStructureBindingModel.java
Simple merge

diff --cc test/jalview/structures/models/AAStructureBindingModelTest.java
Simple merge

diff --cc test/jalview/ws/sifts/SiftsClientTest.java
index 6a1fa1f,7f8adc9..fc07749
--- 1/test/jalview/ws/sifts/SiftsClientTest.java
--- 2/test/jalview/ws/sifts/SiftsClientTest.java
+++ b/test/jalview/ws/sifts/SiftsClientTest.java
@@@ -282,16 -282,19 +283,18 @@@ public class SiftsClientTes
                "A", testSeq, null);
        Assert.assertEquals(testSeq.getStart(), 1);
        Assert.assertEquals(testSeq.getEnd(), 147);
-       // Assert.assertEquals(actualMapping, expectedMapping);
+       // Can't do Assert.assertEquals(actualMapping, expectedMapping);
+       // because this fails in our version of TestNG
        Assert.assertEquals(actualMapping.size(), expectedMapping.size());
-       // Test key set
-       Assert.assertEquals(actualMapping.keySet(), expectedMapping.keySet());
-       // Test entry set
-       for (int key : expectedMapping.keySet())
+       Iterator<Map.Entry<Integer, int[]>> it = expectedMapping.entrySet()
+               .iterator();
+       while (it.hasNext())
        {
-         Assert.assertTrue(Arrays.equals(expectedMapping.get(key),
-                 actualMapping.get(key)));
+         Map.Entry<Integer, int[]> pair = it.next();
+         Assert.assertTrue(actualMapping.containsKey(pair.getKey()));
+         Assert.assertEquals(actualMapping.get(pair.getKey()),
+                 pair.getValue());
        }
 -
      } catch (Exception e)
      {
        e.printStackTrace();