merge develop

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 ffce90c,745b1e1..daf6131
--- 1/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
--- 2/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
+++ b/src/jalview/ext/rbvi/chimera/JalviewChimeraBinding.java
@@@ -1099,8 -1110,17 +1099,8 @@@ 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 f822358,2227978..0c5f469
--- 1/src/jalview/gui/AppJmolBinding.java
--- 2/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@@ -48,6 -50,31 +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 src/jalview/ws/sifts/SiftsClient.java
Simple merge

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

diff --cc test/jalview/ws/sifts/SiftsClientTest.java
index 7f8adc9,6a1fa1f..b50baff
--- 1/test/jalview/ws/sifts/SiftsClientTest.java
--- 2/test/jalview/ws/sifts/SiftsClientTest.java
+++ b/test/jalview/ws/sifts/SiftsClientTest.java
@@@ -37,9 -38,8 +38,10 @@@ import jalview.xml.binding.sifts.Entry.
  import java.io.File;
  import java.io.IOException;
  import java.util.ArrayList;
+ import java.util.Arrays;
  import java.util.HashMap;
 +import java.util.Iterator;
 +import java.util.Map;
  
  import org.testng.Assert;
  import org.testng.FileAssert;
@@@ -282,19 -282,16 +284,32 @@@ public class SiftsClientTes
                "A", testSeq, null);
        Assert.assertEquals(testSeq.getStart(), 1);
        Assert.assertEquals(testSeq.getEnd(), 147);
++<<<<<<< HEAD
 +      // Can't do Assert.assertEquals(actualMapping, expectedMapping);
 +      // because this fails in our version of TestNG
 +      Assert.assertEquals(actualMapping.size(), expectedMapping.size());
 +      Iterator<Map.Entry<Integer, int[]>> it = expectedMapping.entrySet()
 +              .iterator();
 +      while (it.hasNext())
 +      {
 +        Map.Entry<Integer, int[]> pair = it.next();
 +        Assert.assertTrue(actualMapping.containsKey(pair.getKey()));
 +        Assert.assertEquals(actualMapping.get(pair.getKey()),
 +                pair.getValue());
 +      }
 +
++=======
+       // Assert.assertEquals(actualMapping, expectedMapping);
+       Assert.assertEquals(actualMapping.size(), expectedMapping.size());
+       // Test key set
+       Assert.assertEquals(actualMapping.keySet(), expectedMapping.keySet());
+       // Test entry set
+       for (int key : expectedMapping.keySet())
+       {
+         Assert.assertTrue(Arrays.equals(expectedMapping.get(key),
+                 actualMapping.get(key)));
+       }
++>>>>>>> f80180a53bf16dc72ecdd4ace0f70c83cb0d274a
      } catch (Exception e)
      {
        e.printStackTrace();
@@@ -414,19 -412,17 +430,33 @@@ groups = { "Network" }
      Assert.assertEquals(strucMapping.getMappingDetailsOutput(),
              expectedMappingOutput);
  
++<<<<<<< HEAD
 +    // Can't do Assert.assertEquals(strucMapping.getMapping(), expectedMapping);
 +    // because this fails in our version of TestNG
 +    Assert.assertEquals(strucMapping.getMapping().size(),
 +            expectedMapping.size());
 +    Iterator<Map.Entry<Integer, int[]>> it = expectedMapping.entrySet()
 +            .iterator();
 +    while (it.hasNext())
 +    {
 +      Map.Entry<Integer, int[]> pair = it.next();
 +      Assert.assertTrue(strucMapping.getMapping()
 +              .containsKey(pair.getKey()));
 +      Assert.assertEquals(strucMapping.getMapping().get(pair.getKey()),
 +              pair.getValue());
++=======
+     // Assert.assertEquals(strucMapping.getMapping(), expectedMapping);
+     Assert.assertEquals(strucMapping.getMapping().size(),
+             expectedMapping.size());
+     // Test key set
+     Assert.assertEquals(strucMapping.getMapping().keySet(),
+             expectedMapping.keySet());
+     // Test entry set
+     for (int key : expectedMapping.keySet())
+     {
+       Assert.assertTrue(Arrays.equals(expectedMapping.get(key),
+               strucMapping.getMapping().get(key)));
++>>>>>>> f80180a53bf16dc72ecdd4ace0f70c83cb0d274a
      }
    }