patch ensuring annotation is output correctly re * JAL-554

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

diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index dc0526d..3c741f4 100755 (executable)
--- a/src/jalview/io/FormatAdapter.java
+++ b/src/jalview/io/FormatAdapter.java
@@ -198,19 +198,22 @@ public class FormatAdapter extends AppletFormatAdapter
       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);
     }