patch for JAL-699 so conservation/consensus threads restart correctly

[jalview.git] / src / jalview / gui / ConservationThread.java

diff --git a/src/jalview/gui/ConservationThread.java b/src/jalview/gui/ConservationThread.java
index fa70bcc..5ed536c 100644 (file)
--- a/src/jalview/gui/ConservationThread.java
+++ b/src/jalview/gui/ConservationThread.java
@@ -60,9 +60,12 @@ class ConservationThread extends Thread
 
       AlignViewport.UPDATING_CONSERVATION = true;
 
-      int alWidth = this.alignViewport.alignment.getWidth();
-      if (alWidth < 0)
+      int alWidth;
+      
+      if (alignViewport==null || alignViewport.alignment==null || (alWidth=alignViewport.alignment.getWidth())< 0)
       {
+        this.alignViewport.updatingConservation = false;
+        AlignViewport.UPDATING_CONSERVATION = false;
         return;
       }
 
@@ -85,7 +88,6 @@ class ConservationThread extends Thread
 
       this.alignViewport.conservation = null;
       this.alignViewport.quality = null;
-
     }
 
     AlignViewport.UPDATING_CONSERVATION = false;