X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FStrucConsensusThread.java;h=61ec3d09b119e13cba7fa3b9ba107c52894df567;hb=5b833c4ea17f7e45fe1532b36219fcbfba3c0e4a;hp=1944e7698b0735ed735a28a7833d4677c1f6b4de;hpb=25551bf7f81cd62e7b427f5787f2879eab2afed7;p=jalview.git

diff --git a/src/jalview/workers/StrucConsensusThread.java b/src/jalview/workers/StrucConsensusThread.java
index 1944e76..61ec3d0 100644
--- a/src/jalview/workers/StrucConsensusThread.java
+++ b/src/jalview/workers/StrucConsensusThread.java
@@ -94,12 +94,15 @@ public class StrucConsensusThread extends AlignCalcWorker
               .getAlignmentAnnotation();
       AlignmentAnnotation rnaStruc = null;
       // select rna struct to use for calculation
-      for (int i = 0; i < aa.length; i++)
+      if (aa != null)
       {
-        if (aa[i].visible && aa[i].isRNA() && aa[i].isValidStruc())
+        for (int i = 0; i < aa.length; i++)
         {
-          rnaStruc = aa[i];
-          break;
+          if (aa[i].visible && aa[i].isRNA() && aa[i].isValidStruc())
+          {
+            rnaStruc = aa[i];
+            break;
+          }
         }
       }
       // check to see if its valid
@@ -136,7 +139,7 @@ public class StrucConsensusThread extends AlignCalcWorker
       calcMan.workerComplete(this);
       if (ap != null)
       {
-        ap.paintAlignment(true);
+        ap.paintAlignment(true, true);
       }
     }