JAL-2773 add new flag to paintAlignment(updateOverview,updateStructures) and first...

[jalview.git] / src / jalview / workers / StrucConsensusThread.java

diff --git a/src/jalview/workers/StrucConsensusThread.java b/src/jalview/workers/StrucConsensusThread.java
index 3483dac..61ec3d0 100644 (file)
--- 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
@@ -126,7 +129,7 @@ public class StrucConsensusThread extends AlignCalcWorker
       updateResultAnnotation(true);
     } catch (OutOfMemoryError error)
     {
-      calcMan.workerCannotRun(this);
+      calcMan.disableWorker(this);
 
       // consensus = null;
       // hconsensus = null;
@@ -136,7 +139,7 @@ public class StrucConsensusThread extends AlignCalcWorker
       calcMan.workerComplete(this);
       if (ap != null)
       {
-        ap.paintAlignment(true);
+        ap.paintAlignment(true, true);
       }
     }