X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=750e82372157b0ee5d63d88836ebb1ce8f397b5d;hb=6288934c2b3c469369bfb8ee09fea627dafd7776;hp=59d7b97b137954cc055126aace22ac9f9f447169;hpb=8fc51088adad6a0d5a66acf1747d0257380429c3;p=jalview.git

diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 59d7b97..750e823 100755
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1327,6 +1327,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
   public void updateAnnotation(boolean applyGlobalSettings)
   {
+    // TODO: this should be merged with other annotation update stuff - that sits on AlignViewport
     boolean updateCalcs = false;
     boolean conv = av.isShowGroupConservation();
     boolean cons = av.isShowGroupConsensus();
@@ -1343,6 +1344,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
 
     AlignmentAnnotation[] aan = av.alignment.getAlignmentAnnotation();
     Hashtable oldrfs = new Hashtable();
+    if (aan != null)
+    {
     for (int an = 0; an < aan.length; an++)
     {
       if (aan[an].autoCalculated && aan[an].groupRef != null)
@@ -1352,7 +1355,10 @@ public class AlignmentPanel extends GAlignmentPanel implements
         aan[an] = null;
       }
     }
+    }
     SequenceGroup sg;
+    if (gr != null)
+    {
     for (int g = 0; g < gr.size(); g++)
     {
       updateCalcs = false;
@@ -1379,6 +1385,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
         sg.recalcConservation();
       }
     }
+    }
     oldrfs.clear();
     adjustAnnotationHeight();
   }