X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FConservationThread.java;fp=src%2Fjalview%2Fworkers%2FConservationThread.java;h=54b0191169f79e21eebc431d55d75c3dbf5efc9c;hb=0efc6021e63ff62bb2e275501586c1900561b303;hp=571234cb749388a0fe8f2a875301e25aae5918b7;hpb=771d1758a42abc6e3e330dd6c5117734acf0067f;p=jalview.git

diff --git a/src/jalview/workers/ConservationThread.java b/src/jalview/workers/ConservationThread.java
index 571234c..54b0191 100644
--- a/src/jalview/workers/ConservationThread.java
+++ b/src/jalview/workers/ConservationThread.java
@@ -75,7 +75,7 @@ public class ConservationThread extends AlignCalcWorker
         abortAndDestroy();
         return;
       }
-      List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
+      List<AlignmentAnnotation> ourAnnot = new ArrayList<>();
       AlignmentI alignment = alignViewport.getAlignment();
       conservation = alignViewport.getAlignmentConservationAnnotation();
       quality = alignViewport.getAlignmentQualityAnnot();
@@ -123,7 +123,7 @@ public class ConservationThread extends AlignCalcWorker
     }
     if (ap != null)
     {
-      ap.paintAlignment(true);
+      ap.paintAlignment(true, true);
     }
 
   }