Merge branch 'bugs/JAL-2777_whitespaceChain' into develop

diff --combined src/jalview/gui/FeatureSettings.java
index c5454ab,63f1b13..b768339
--- 1/src/jalview/gui/FeatureSettings.java
--- 2/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@@ -131,6 -131,11 +131,11 @@@ public class FeatureSettings extends JP
    private static final int MIN_WIDTH = 400;
  
    private static final int MIN_HEIGHT = 400;
+   
+   /**
+    * when true, constructor is still executing - so ignore UI events
+    */
+   protected volatile boolean inConstruction = true;
  
    /**
     * Constructor
@@@ -303,6 -308,7 +308,7 @@@
                };
              });
      frame.setLayer(JLayeredPane.PALETTE_LAYER);
+     inConstruction = false;
    }
  
    protected void popupSort(final int selectedRow, final String type,
@@@ -1058,7 -1064,7 +1064,7 @@@
    {
      if (fr.setFeaturePriority(data, visibleNew))
      {
 -      af.alignPanel.paintAlignment(true);
 +      af.alignPanel.paintAlignment(true, true);
      }
    }
  
@@@ -1237,8 -1243,11 +1243,11 @@@
        @Override
        public void stateChanged(ChangeEvent evt)
        {
-         fr.setTransparency((100 - transparency.getValue()) / 100f);
-         af.alignPanel.paintAlignment(true, true);
+         if (!inConstruction)
+         {
+           fr.setTransparency((100 - transparency.getValue()) / 100f);
 -          af.alignPanel.paintAlignment(true);
++          af.alignPanel.paintAlignment(true,true);
+         }
        }
      });