From 1ae0a3902856d19d5ccc3635ff8b630bdd62faf0 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 24 Feb 2009 17:53:27 +0000
Subject: [PATCH] bugfix for occasional nullpointer exceptions when selecting
 menu items that operate on the current selection

---
 src/jalview/datamodel/SequenceGroup.java |   22 ++++++++++++++++++----
 src/jalview/gui/AlignViewport.java       |   10 +++++-----
 2 files changed, 23 insertions(+), 9 deletions(-)

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index d12f81b..49f270d 100755
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -691,11 +691,12 @@ public class SequenceGroup
 
   /**
    * 
-   * returns the sequences in the group ordered by the ordering given by al
-   * 
+   * returns the sequences in the group ordered by the ordering given by al.
+   * this used to return an array with null entries regardless, new behaviour is below.
+   * TODO: verify that this does not affect use in applet or application
    * @param al
    *                Alignment
-   * @return SequenceI[]
+   * @return SequenceI[] intersection of sequences in group with al, ordered by al, or null if group does not intersect with al
    */
   public SequenceI[] getSequencesInOrder(AlignmentI al)
   {
@@ -712,7 +713,20 @@ public class SequenceGroup
         seqs[index++] = al.getSequenceAt(i);
       }
     }
-
+    if (index==0)
+    {
+      return null;
+    }
+    if (index<seqs.length)
+    {
+      SequenceI[] dummy = seqs;
+      seqs = new SequenceI[index];
+      while (--index>=0)
+      {
+        seqs[index] = dummy[index];
+        dummy[index] = null;
+      }
+    }
     return seqs;
   }
 
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index d07b010..b90d89b 100755
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -1625,14 +1625,14 @@ public class AlignViewport implements SelectionSource
    */
   public SequenceI[] getSequenceSelection()
   {
-    SequenceI[] sequences;
-    if (selectionGroup == null)
+    SequenceI[] sequences=null;
+    if (selectionGroup!=null)
     {
-      sequences = alignment.getSequencesArray();
+      sequences = selectionGroup.getSequencesInOrder(alignment);
     }
-    else
+    if (sequences == null)
     {
-      sequences = selectionGroup.getSequencesInOrder(alignment);
+      sequences = alignment.getSequencesArray();
     }
     return sequences;
   }
-- 
1.7.10.2