X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=96b79604fd2617b088a3996bec41a6264fdf973e;hb=cfe67193109d8d88029c659c8aad4d394677342c;hp=9de9e3b7f7bfb85247d1d26e5248500db2950c48;hpb=252ddd218b716396b003b3fcbe0f8da499bde8c8;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 9de9e3b..96b7960 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -1188,9 +1188,26 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       {
         try
         {
-          PrintWriter out = new PrintWriter(new FileWriter(file));
+          // PrintWriter out = new PrintWriter(new FileWriter(file));
+          PrintWriter out = new PrintWriter(new FileWriter(file), true);
 
+          // TESTING code here
+          boolean TESTING = true;
+          if (TESTING)
+          {
+            out.print("; TESTSTART\n");
+            int count = 20;
+            for (int i = 0; i < count; i++)
+            {
+              Thread.sleep(1000);
+              out.println("; TEST: " + (count - 1 - i));
+            }
+          }
           out.print(output);
+          if (TESTING)
+          {
+            out.print("; TESTEND\n");
+          }
           out.close();
           this.setTitle(file);
           statusBar.setText(MessageManager.formatMessage(
@@ -5305,6 +5322,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   {
     if (avc.createGroup())
     {
+      if (applyAutoAnnotationSettings.isSelected())
+      {
+        alignPanel.updateAnnotation(true, false);
+      }
       alignPanel.alignmentChanged();
     }
   }