From ee5064ad5cba56f7b2423e8023e5c60204ba0878 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Thu, 3 Jun 2010 15:13:49 +0000
Subject: [PATCH] patch ensuring annotation is output correctly re * JAL-554

---
 src/jalview/gui/PopupMenu.java    |   10 ++++++----
 src/jalview/io/FormatAdapter.java |   23 +++++++++++++----------
 2 files changed, 19 insertions(+), 14 deletions(-)

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 96e61e9..a98c1da 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -1698,10 +1698,12 @@ public class PopupMenu extends JPopupMenu
     omitHidden = ap.av.getViewAsString(true);
     Alignment oal = new Alignment(ap.av.getSequenceSelection());
     AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation();
-    for (int i = 0; i < nala.length; i++)
-    {
-      AlignmentAnnotation na = nala[i];
-      oal.addAnnotation(na);
+    if (nala!=null) {
+      for (int i = 0; i < nala.length; i++)
+      {
+        AlignmentAnnotation na = nala[i];
+        oal.addAnnotation(na);
+      }
     }
     cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
             oal, omitHidden, csel, sg));
diff --git a/src/jalview/io/FormatAdapter.java b/src/jalview/io/FormatAdapter.java
index dc0526d..3c741f4 100755
--- 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);
     }
-- 
1.7.10.2