X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;fp=src%2Fjalview%2Fgui%2FJalview2XML.java;h=945651b9dcefd8ec123d90d1a3acb23a1293bb57;hb=8f5031f8cc3b6da5ce8d639a5b6e0365c1904623;hp=01e60d438081efc19751bb2014491d7e8bf4510e;hpb=69f930f786254940db0a7c247cc350098e940bbf;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 01e60d4..945651b 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -4144,25 +4144,25 @@ public class Jalview2XML
     {
       for (int s = 0; s < JSEQ.length; s++)
       {
-        jalview.datamodel.SequenceGroup hidden = new jalview.datamodel.SequenceGroup();
-
+        SequenceGroup hidden = new SequenceGroup();
+        boolean isRepresentative = false;
         for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
         {
-          hidden.addSequence(
-                  al.getSequenceAt(JSEQ[s].getHiddenSequences(r)), false);
+          isRepresentative = true;
+          SequenceI sequenceToHide = al.getSequenceAt(JSEQ[s]
+                  .getHiddenSequences(r));
+          hidden.addSequence(sequenceToHide, false);
+          // remove from hiddenSeqs list so we don't try to hide it twice
+          hiddenSeqs.remove(sequenceToHide);
+        }
+        if (isRepresentative)
+        {
+          SequenceI representativeSequence = al.getSequenceAt(s);
+          hidden.addSequence(representativeSequence, false);
+          af.viewport.hideRepSequences(representativeSequence, hidden);
         }
-        af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
       }
 
-      // jalview.datamodel.SequenceI[] hseqs = new
-      // jalview.datamodel.SequenceI[hiddenSeqs
-      // .size()];
-      //
-      // for (int s = 0; s < hiddenSeqs.size(); s++)
-      // {
-      // hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s);
-      // }
-
       SequenceI[] hseqs = hiddenSeqs.toArray(new SequenceI[hiddenSeqs
               .size()]);
       af.viewport.hideSequence(hseqs);