From eb7824b3ecfdef2aa8c83e4a8520cb866f364d88 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 7 Aug 2006 14:37:33 +0000
Subject: [PATCH] catch out of memory error for consensus when loading groups

---
 src/jalview/datamodel/SequenceGroup.java |   30 ++++++++++++++++++------------
 1 file changed, 18 insertions(+), 12 deletions(-)

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index 161c010..272d81d 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -319,31 +319,37 @@ public class SequenceGroup
         if(cs == null)
           return;
 
-        cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));
-
-
-        if (cs instanceof ClustalxColourScheme)
+        try
         {
-            ((ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
-        }
+          cs.setConsensus(AAFrequency.calculate(sequences, 0, getWidth()));
 
+          if (cs instanceof ClustalxColourScheme)
+          {
+            ( (ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
+          }
 
-        if (cs.conservationApplied())
-        {
+          if (cs.conservationApplied())
+          {
             Conservation c = new Conservation(groupName,
-                    ResidueProperties.propHash, 3, sequences, 0, getWidth());
+                                              ResidueProperties.propHash, 3, sequences,
+                                              0, getWidth());
             c.calculate();
             c.verdict(false, 25);
 
-
             cs.setConservation(c);
 
             if (cs instanceof ClustalxColourScheme)
             {
-                ((ClustalxColourScheme) cs).resetClustalX(sequences,
-                    getWidth());
+              ( (ClustalxColourScheme) cs).resetClustalX(sequences,
+                                                         getWidth());
             }
+          }
         }
+        catch (java.lang.OutOfMemoryError err)
+        {
+          System.out.println("Out of memory loading groups: " + err);
+        }
+
     }
 
     /**
-- 
1.7.10.2