X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFormatAdapter.java;h=79a9190a4b997365c522ee8e81e535fbeff2086a;hb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;hp=dc0526d8ae2169f74135528450fff135e99c78e7;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index dc0526d..79a9190 100755
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
  * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
@@ -194,23 +194,26 @@ public class FormatAdapter extends AppletFormatAdapter
   {
     if (omitHidden != null)
     {
-      // 
-      Alignment alv = new Alignment(replaceStrings(alignment
-              .getSequencesArray(), omitHidden));
+      //
+      Alignment alv = new Alignment(replaceStrings(
+              alignment.getSequencesArray(), omitHidden));
       AlignmentAnnotation[] ala = alignment.getAlignmentAnnotation();
-      for (int i = 0; i < ala.length; i++)
+      if (ala != null)
       {
-        AlignmentAnnotation na = new AlignmentAnnotation(ala[i]);
-        if (selgp != null)
+        for (int i = 0; i < ala.length; i++)
         {
-          colSel.makeVisibleAnnotation(selgp.getStartRes(), selgp
-                  .getEndRes(), na);
+          AlignmentAnnotation na = new AlignmentAnnotation(ala[i]);
+          if (selgp != null)
+          {
+            colSel.makeVisibleAnnotation(selgp.getStartRes(),
+                    selgp.getEndRes(), na);
+          }
+          else
+          {
+            colSel.makeVisibleAnnotation(na);
+          }
+          alv.addAnnotation(na);
         }
-        else
-        {
-          colSel.makeVisibleAnnotation(na);
-        }
-        alv.addAnnotation(na);
       }
       return this.formatSequences(format, alv, suffix);
     }