From ac46ce1098d76c92285198a083f60eef2672d211 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Wed, 22 Sep 2010 00:58:32 +0000
Subject: [PATCH] trap out of memory errors specifically associated with Jmol
 view creation (needs refinement)

---
 src/jalview/gui/Jalview2XML.java |   21 +++++++++++++++++----
 1 file changed, 17 insertions(+), 4 deletions(-)

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index f0edf7a..e1510de 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -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();
-- 
1.7.10.2