Merge branch 'releases/Release_2_11_1_Branch' into merge/JAL_1842+JAL-3509+releases_R...

diff --combined src/jalview/gui/AlignViewport.java
index e6ac07e,ba7aad4..8e12ff5
--- 1/src/jalview/gui/AlignViewport.java
--- 2/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@@ -59,7 -59,6 +59,6 @@@ import java.awt.FontMetrics
  import java.awt.Rectangle;
  import java.util.ArrayList;
  import java.util.Hashtable;
- import java.util.Iterator;
  import java.util.List;
  
  import javax.swing.JInternalFrame;
@@@ -446,31 -445,6 +445,6 @@@ public class AlignViewport extends Alig
    }
  
    /**
-    * returns the visible column regions of the alignment
-    * 
-    * @param selectedRegionOnly
-    *          true to just return the contigs intersecting with the selected
-    *          area
-    * @return
-    */
-   public Iterator<int[]> getViewAsVisibleContigs(boolean selectedRegionOnly)
-   {
-     int start = 0;
-     int end = 0;
-     if (selectedRegionOnly && selectionGroup != null)
-     {
-       start = selectionGroup.getStartRes();
-       end = selectionGroup.getEndRes() + 1;
-     }
-     else
-     {
-       end = alignment.getWidth();
-     }
-     return (alignment.getHiddenColumns().getVisContigsIterator(start, end,
-             false));
-   }
- 
-   /**
     * get hash of undo and redo list for the alignment
     * 
     * @return long[] { historyList.hashCode, redoList.hashCode };
@@@ -1018,8 -992,8 +992,8 @@@
      
      FeatureRenderer fr = getAlignPanel().getSeqPanel().seqCanvas
              .getFeatureRenderer();
 -    List<String> origRenderOrder = new ArrayList(),
 -            origGroups = new ArrayList();
 +    List<String> origRenderOrder = new ArrayList<>();
 +    List<String> origGroups = new ArrayList<>();
      // preserve original render order - allows differentiation between user configured colours and autogenerated ones
      origRenderOrder.addAll(fr.getRenderOrder());
      origGroups.addAll(fr.getFeatureGroups());
@@@ -1030,7 -1004,7 +1004,7 @@@
      if (!mergeOnly)
      {
        // only clear displayed features if we are mergeing
 -      displayed.clear();
 +      // displayed.clear();
      }
      // TODO this clears displayed.featuresRegistered - do we care?
      //
@@@ -1062,10 -1036,6 +1036,10 @@@
          {
            displayed.setVisible(type);
          }
 +        else if (featureSettings.isFeatureHidden(type))
 +        {
 +          displayed.setHidden(type);
 +        }
        }
      }
  
@@@ -1094,8 -1064,6 +1068,8 @@@
        fr.orderFeatures(featureSettings);
      }
      fr.setTransparency(featureSettings.getTransparency());
 +
 +    fr.notifyFeaturesChanged();
    }
  
    public String getViewName()