From f8ce78dc02ce9d96129fcc4882749f43869928ff Mon Sep 17 00:00:00 2001
From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Tue, 7 Jul 2015 16:18:41 +0100
Subject: [PATCH] JAL-1769 fixed output to jalview (.jpv) file in headless
 mode. Initial cause of failure: NPE while trying to save
 varna viewers (Desktop.destop is null in headless mode)

---
 src/jalview/gui/Jalview2XML.java |    4 ++++
 1 file changed, 4 insertions(+)

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index be56292..e4ec30b 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -1372,6 +1372,10 @@ public class Jalview2XML
           final SequenceI jds, List<String> viewIds, AlignmentPanel ap,
           boolean storeDataset)
   {
+    if (Desktop.desktop == null)
+    {
+      return;
+    }
     JInternalFrame[] frames = Desktop.desktop.getAllFrames();
     for (int f = frames.length - 1; f > -1; f--)
     {
-- 
1.7.10.2