X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=51bf82462c37e1b0ddc130c1a000f16317d9df71;hb=92a3a0f396a86b2bc0a8d1a311680ceda4abec7b;hp=b8977c51fd5e2fc46c8844e6e4a012d2b42078ff;hpb=baf23db52aa82cca72d088c0c850b01562599c67;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index b8977c5..51bf824 100755
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -580,21 +580,24 @@ public class Jalview2XML
           }
         }
 
+        Vector seqs = new Vector();
+        int[] ids = groups[i].getSeq();
+
+        for (int s = 0; s < ids.length; s++)
+        {
+          seqs.addElement( (jalview.datamodel.SequenceI) seqids.elementAt(
+              ids[s]));
+        }
+
         jalview.datamodel.SequenceGroup sg = new jalview.datamodel.
-            SequenceGroup(groups[i].getName(),
+            SequenceGroup(seqs, groups[i].getName(),
                           cs, groups[i].getDisplayBoxes(),
                           groups[i].getDisplayText(), groups[i].getColourText(),
                           groups[i].getStart(), groups[i].getEnd());
+
         sg.setOutlineColour(new java.awt.Color(
             groups[i].getOutlineColour()));
 
-        int[] ids = groups[i].getSeq();
-
-        for (int s = 0; s < ids.length; s++)
-        {
-          sg.addSequence( (jalview.datamodel.SequenceI) seqids.elementAt(
-              ids[s]));
-        }
 
         if (groups[i].getConsThreshold() != 0)
         {