From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Fri, 31 May 2013 16:09:33 +0000 (+0100)
Subject: JAL-1259 patch to avoid NPE
X-Git-Tag: Release_2_8_0b1~1^2~63^2
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=5ef242d44b8db9edeae9523ad76a5065cb6ef999

JAL-1259 patch to avoid NPE
---

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 83aab4e..1553710 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1385,13 +1385,17 @@ public class Alignment implements AlignmentI
           SequenceGroup groupRef)
   {
     assert (name != null);
-    for (AlignmentAnnotation annot : getAlignmentAnnotation())
+    if (annotations != null)
     {
-      if (annot.autoCalculated == autoCalc && (name.equals(annot.label))
-              && (calcId == null || annot.getCalcId().equals(calcId))
-              && annot.sequenceRef == seqRef && annot.groupRef == groupRef)
+      for (AlignmentAnnotation annot : getAlignmentAnnotation())
       {
-        return annot;
+        if (annot.autoCalculated == autoCalc && (name.equals(annot.label))
+                && (calcId == null || annot.getCalcId().equals(calcId))
+                && annot.sequenceRef == seqRef
+                && annot.groupRef == groupRef)
+        {
+          return annot;
+        }
       }
     }
     AlignmentAnnotation annot = new AlignmentAnnotation(name, name,