From 03096bd6cafc7d5b10396c5e7cf7086e8d6358a5 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 14 Dec 2016 15:36:13 +0000
Subject: [PATCH] JAL-2360 added check for null annotations array

---
 src/jalview/datamodel/Alignment.java |   17 ++++++++++-------
 1 file changed, 10 insertions(+), 7 deletions(-)

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 290707d..49f6268 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -1561,7 +1561,6 @@ public class Alignment implements AlignmentI
           String calcId, boolean autoCalc, SequenceI seqRef,
           SequenceGroup groupRef)
   {
-    assert (name != null);
     if (annotations != null)
     {
       for (AlignmentAnnotation annot : getAlignmentAnnotation())
@@ -1593,14 +1592,18 @@ public class Alignment implements AlignmentI
   @Override
   public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
   {
-    ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
-    for (AlignmentAnnotation a : getAlignmentAnnotation())
+    List<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+    AlignmentAnnotation[] alignmentAnnotation = getAlignmentAnnotation();
+    if (alignmentAnnotation != null)
     {
-      if (a.getCalcId() == calcId
-              || (a.getCalcId() != null && calcId != null && a.getCalcId()
-                      .equals(calcId)))
+      for (AlignmentAnnotation a : alignmentAnnotation)
       {
-        aa.add(a);
+        if (a.getCalcId() == calcId
+                || (a.getCalcId() != null && calcId != null && a
+                        .getCalcId().equals(calcId)))
+        {
+          aa.add(a);
+        }
       }
     }
     return aa;
-- 
1.7.10.2