clarified help documentation for annotation file format and tweaked reader code to...

[jalview.git] / src / jalview / io / FormatAdapter.java

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index 84940a8..a23bbba 100755 (executable)
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -1,6 +1,6 @@
 /*\r
 * Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
 *\r
 * This program is free software; you can redistribute it and/or\r
 * modify it under the terms of the GNU General Public License\r
@@ -36,10 +36,13 @@ public class FormatAdapter extends AppletFormatAdapter
     {\r
       if(omitHiddenColumns!=null)\r
       {\r
+        SequenceI [] tmp = new SequenceI[seqs.length];\r
         for(int i=0; i<seqs.length; i++)\r
-          seqs [i] = new Sequence(\r
+          tmp [i] = new Sequence(\r
               seqs[i].getName(), omitHiddenColumns[i],\r
               seqs[i].getStart(), seqs[i].getEnd());\r
+\r
+        seqs = tmp;\r
       }\r
 \r
       return formatSequences(format, seqs);\r