X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FConservationThread.java;h=8f4a6a67ff02a98f8a9c4b62fde6e2a4660e5591;hb=691798cf6a90094f4c83e79fd5c703457b1135b0;hp=4b921ac3f26ddd11696adbc95d15df912c940dfc;hpb=23d1e9604a788400fe2115c58b122556e1fb92a9;p=jalview.git

diff --git a/src/jalview/gui/ConservationThread.java b/src/jalview/gui/ConservationThread.java
index 4b921ac..8f4a6a6 100644
--- a/src/jalview/gui/ConservationThread.java
+++ b/src/jalview/gui/ConservationThread.java
@@ -1,5 +1,19 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * 
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  */
 package jalview.gui;
 
@@ -14,6 +28,7 @@ class ConservationThread extends Thread
    * 
    */
   private AlignViewport alignViewport;
+
   AlignmentPanel ap;
 
   public ConservationThread(AlignViewport alignViewport, AlignmentPanel ap)
@@ -45,15 +60,18 @@ 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;
       }
 
       Conservation cons = new jalview.analysis.Conservation("All",
-              jalview.schemes.ResidueProperties.propHash, 3, this.alignViewport.alignment
-                      .getSequences(), 0, alWidth - 1);
+              jalview.schemes.ResidueProperties.propHash, 3,
+              this.alignViewport.alignment.getSequences(), 0, alWidth - 1);
 
       cons.calculate();
       cons.verdict(false, this.alignViewport.ConsPercGaps);
@@ -62,7 +80,8 @@ class ConservationThread extends Thread
       {
         cons.findQuality();
       }
-      cons.completeAnnotations(alignViewport.conservation,alignViewport.quality, 0, alWidth);
+      cons.completeAnnotations(alignViewport.conservation,
+              alignViewport.quality, 0, alWidth);
     } catch (OutOfMemoryError error)
     {
       new OOMWarning("calculating conservation", error);
@@ -81,4 +100,4 @@ class ConservationThread extends Thread
     }
 
   }
-}
\ No newline at end of file
+}