From 5a15b7773aaad3bba1bb342198e2bcf4cc2cdffe Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Fri, 18 Feb 2011 17:12:22 +0000
Subject: [PATCH] fix for occasional race conditions

---
 src/jalview/analysis/Conservation.java |   12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index b557c5a..2ffb4de 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -100,7 +100,7 @@ public class Conservation
     int s, sSize = sequences.size();
     SequenceI[] sarray = new SequenceI[sSize];
     this.sequences = sarray;
-
+    try {
     for (s = 0; s < sSize; s++)
     {
       sarray[s] = (SequenceI) sequences.elementAt(s);
@@ -109,6 +109,12 @@ public class Conservation
         maxLength = sarray[s].getLength();
       }
     }
+    } catch (ArrayIndexOutOfBoundsException ex)
+    {
+      // bail - another thread has modified the sequence array, so the current calculation is probably invalid. 
+      this.sequences=new SequenceI[0];
+      maxLength=0;
+    }
   }
 
   /**
@@ -271,7 +277,9 @@ public class Conservation
         }
       }
 
-      total[i - start] = resultHash;
+      if (total.length>0) {
+        total[i - start] = resultHash;
+      }
     }
   }
 
-- 
1.7.10.2