Conservation etc have autoCalculated flag set true

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index be7f8f4..8b929c7 100755 (executable)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -199,6 +199,7 @@ public class AlignViewport
                 11f,
                 AlignmentAnnotation.BAR_GRAPH);
             conservation.hasText = true;
+            conservation.autoCalculated = true;
 
 
             if (Cache.getDefault("SHOW_CONSERVATION", true))
@@ -215,6 +216,7 @@ public class AlignViewport
                                                 11f,
                                                 AlignmentAnnotation.BAR_GRAPH);
               quality.hasText = true;
+              quality.autoCalculated = true;
 
               alignment.addAnnotation(quality);
             }
@@ -224,6 +226,7 @@ public class AlignViewport
                                                new Annotation[1], 0f, 100f,
                                                AlignmentAnnotation.BAR_GRAPH);
           consensus.hasText = true;
+          consensus.autoCalculated = true;
 
            if (Cache.getDefault("SHOW_IDENTITY", true))
            {
@@ -1599,7 +1602,7 @@ public class AlignViewport
 
         resetAllColourSchemes();
 
-        alignment.adjustSequenceAnnotations();
+       // alignment.adjustSequenceAnnotations();
     }