X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=2901969d0f9a0a85d4e2263d843dcd84d87d08d5;hb=c9c74c082bdd9323850a864144dc8a9b36399157;hp=84940a8b88c936537c29c13875f15e33d062e7d3;hpb=99792d48de35bb2d0e2017871fa44da1c3be38a2;p=jalview.git

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 84940a8..2901969 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -36,10 +36,13 @@ public class FormatAdapter extends AppletFormatAdapter
     {
       if(omitHiddenColumns!=null)
       {
+        SequenceI [] tmp = new SequenceI[seqs.length];
         for(int i=0; i<seqs.length; i++)
-          seqs [i] = new Sequence(
+          tmp [i] = new Sequence(
               seqs[i].getName(), omitHiddenColumns[i],
               seqs[i].getStart(), seqs[i].getEnd());
+
+        seqs = tmp;
       }
 
       return formatSequences(format, seqs);