JAL-961, JAL-1115 - pending test to ensure only one worker waits around for another...

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

diff --git a/src/jalview/workers/StrucConsensusThread.java b/src/jalview/workers/StrucConsensusThread.java
index ea900dc..a7f919b 100644 (file)
--- a/src/jalview/workers/StrucConsensusThread.java
+++ b/src/jalview/workers/StrucConsensusThread.java
@@ -2,7 +2,6 @@ package jalview.workers;
 
 import java.util.Hashtable;
 
-import jalview.analysis.AAFrequency;
 import jalview.analysis.StructureFrequency;
 import jalview.api.AlignCalcWorkerI;
 import jalview.api.AlignViewportI;
@@ -29,6 +28,10 @@ public class StrucConsensusThread extends AlignCalcWorker implements
   {
     try
     {
+      if (calcMan.isPending(this))
+      {
+        return;
+      }
       calcMan.notifyStart(this);
       while (!calcMan.notifyWorking(this))
       {
@@ -36,7 +39,7 @@ public class StrucConsensusThread extends AlignCalcWorker implements
         {
           if (ap != null)
           {
-            ap.paintAlignment(false);
+            // ap.paintAlignment(false);
           }
 
           Thread.sleep(200);
@@ -85,9 +88,15 @@ public class StrucConsensusThread extends AlignCalcWorker implements
         return;
       }
 
-      jalview.analysis.StructureFrequency.calculate(
+      try {
+              jalview.analysis.StructureFrequency.calculate(
               alignment.getSequencesArray(), 0, alignment.getWidth(),
               hStrucConsensus, true, rnaStruc);
+      } catch (ArrayIndexOutOfBoundsException x)
+      {
+        calcMan.workerComplete(this);
+        return;
+      }
       alignViewport.setRnaStructureConsensusHash(hStrucConsensus);
       // TODO AlignmentAnnotation rnaStruc!!!
       updateResultAnnotation(true);
@@ -103,12 +112,13 @@ public class StrucConsensusThread extends AlignCalcWorker implements
       // consensus = null;
       // hconsensus = null;
       ap.raiseOOMWarning("calculating RNA structure consensus", error);
-    }
-
-    calcMan.workerComplete(this);
-    if (ap != null)
+    } finally
     {
-      ap.paintAlignment(true);
+      calcMan.workerComplete(this);
+      if (ap != null)
+      {
+        ap.paintAlignment(true);
+      }
     }
 
   }