Merge branch 'develop' into features/r2_11_2/JAL-3829_3dbeacons

diff --combined src/jalview/gui/SequenceFetcher.java
index 7f9d4c7,a4e7952..caecbba
--- 1/src/jalview/gui/SequenceFetcher.java
--- 2/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@@ -27,7 -27,6 +27,7 @@@ import jalview.datamodel.DBRefEntry
  import jalview.datamodel.SequenceI;
  import jalview.fts.core.GFTSPanel;
  import jalview.fts.service.pdb.PDBFTSPanel;
 +import jalview.fts.service.threedbeacons.TDBeaconsFTSPanel;
  import jalview.fts.service.uniprot.UniprotFTSPanel;
  import jalview.io.FileFormatI;
  import jalview.io.gff.SequenceOntologyI;
@@@ -196,11 -195,6 +196,11 @@@ public class SequenceFetcher extends JP
            frame.dispose();
            new UniprotFTSPanel(SequenceFetcher.this);
          }
 +        else if ("3d-beacons".equalsIgnoreCase(currentSelection))
 +        {
 +          frame.dispose();
 +          new TDBeaconsFTSPanel(SequenceFetcher.this);
 +        }
          else
          {
            otherSourceAction();
@@@ -803,15 -797,8 +803,15 @@@
    {
      return "Retrieved from " + database.getSelectedItem();
    }
 -
 -  AlignmentI parseResult(AlignmentI al, String title,
 +  /**
 +   * constructs an alignment frame given the data and metadata
 +   * @param al
 +   * @param title
 +   * @param currentFileFormat
 +   * @param preferredFeatureColours
 +   * @return the alignment 
 +   */
 +  public AlignmentI parseResult(AlignmentI al, String title,
            FileFormatI currentFileFormat,
            FeatureSettingsModelI preferredFeatureColours)
    {
@@@ -844,10 -831,7 +844,7 @@@
            }
          }
  
-         if (preferredFeatureColours != null)
-         {
-           af.getViewport().applyFeaturesStyle(preferredFeatureColours);
-         }
+         af.getViewport().applyFeaturesStyle(preferredFeatureColours);
          if (Cache.getDefault("HIDE_INTRONS", true))
          {
            af.hideFeatureColumns(SequenceOntologyI.EXON, false);

diff --combined src/jalview/structures/models/AAStructureBindingModel.java
index 289d340,da86ca5..5a7b448
--- 1/src/jalview/structures/models/AAStructureBindingModel.java
--- 2/src/jalview/structures/models/AAStructureBindingModel.java
+++ b/src/jalview/structures/models/AAStructureBindingModel.java
@@@ -1096,10 -1096,7 +1096,10 @@@ public abstract class AAStructureBindin
          for (StructureCommandI cmd : cmds)
          {
            List<String> replies = executeCommand(cmd, true);
 -          response.addAll(replies);
 +          if (replies != null)
 +          {
 +            response.addAll(replies);
 +          }
          }
          return response;
        } finally
@@@ -1216,8 -1213,7 +1216,7 @@@
    }
  
    /**
-    * Returns the FeatureRenderer for the given alignment view, or null if
-    * feature display is turned off in the view.
+    * Returns the FeatureRenderer for the given alignment view
     * 
     * @param avp
     * @return
@@@ -1230,9 -1226,7 +1229,7 @@@
      {
        return null;
      }
-     return ap.getAlignViewport().isShowSequenceFeatures()
-             ? ap.getFeatureRenderer()
-             : null;
+     return ap.getFeatureRenderer();
    }
  
    protected void setStructureCommands(StructureCommandsI cmd)