From 7724430e3293cbb862d0c50c5308a3b3b0417cac Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 25 Jan 2007 16:00:41 +0000
Subject: [PATCH 1/1] Output annotations

---
 src/jalview/appletgui/AlignFrame.java |   28 ++++++++++++++++++----------
 1 file changed, 18 insertions(+), 10 deletions(-)

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 479d771..4115999 100755
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -502,7 +502,7 @@ public void itemStateChanged(ItemEvent evt)
     else if (source == loadAnnotations)
       loadAnnotations();
     else if (source == outputAnnotations)
-      outputAnnotations();
+      outputAnnotations(true);
     else if(source == outputFeatures)
       outputFeatures(true, "Jalview");
     else if(source==closeMenuItem)
@@ -670,16 +670,24 @@ public void itemStateChanged(ItemEvent evt)
 
   }
 
-  public void outputAnnotations()
+  public String outputAnnotations(boolean displayTextbox)
   {
-    CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
-    Frame frame = new Frame();
-    frame.add(cap);
-    jalview.bin.JalviewLite.addFrame(frame,
-                                     "Annotations",
-                                     600, 500);
-    cap.setText( new AnnotationFile().printAnnotations(
-      viewport.alignment.getAlignmentAnnotation() ) );
+    String annotation = new AnnotationFile().printAnnotations(
+      viewport.alignment.getAlignmentAnnotation() );
+
+    if(displayTextbox)
+    {
+
+      CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
+      Frame frame = new Frame();
+      frame.add(cap);
+      jalview.bin.JalviewLite.addFrame(frame,
+                                       "Annotations",
+                                       600, 500);
+      cap.setText(annotation);
+    }
+
+    return annotation;
   }
 
   public String outputFeatures(boolean displayTextbox, String format)
-- 
1.7.10.2