Jalview 2.6 source licence

[jalview.git] / src / jalview / gui / Jalview2XML.java

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index f0edf7a..b28ed0e 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
@@ -2696,15 +2696,28 @@ public class Jalview2XML
                 {
                   public void run()
                   {
-                    new AppJmol(pdbf, id, sq, alf.alignPanel, fileloc,
+                    AppJmol sview=null;
+                    try {
+                      sview=new AppJmol(pdbf, id, sq, alf.alignPanel, fileloc,
+                    
                             rect, vid);
+                    }
+                    catch (OutOfMemoryError ex)
+                    {
+                      new OOMWarning("restoring structure view for PDB id "+id,(OutOfMemoryError) ex.getCause());
+                      if (sview!=null && sview.isVisible())
+                      {
+                        sview.closeViewer();
+                        sview.setVisible(false);
+                        sview.dispose();
+                      }
+                    }
                   }
                 });
               } catch (InvocationTargetException ex)
               {
-                System.err
-                        .println("Unexpected error when opening Jmol view.");
-                ex.printStackTrace();
+                warn("Unexpected error when opening Jmol view.",ex);
+                
               } catch (InterruptedException e)
               {
                 // e.printStackTrace();